From 23e8e222e8016ea8335d4850070f884ab9b043fe Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 29 Apr 2021 21:45:51 +0300 Subject: Run `sed -i 's/(object)//g'` See: https://is.gd/pL7IJF Ran: find . \( -type d -name .git -prune \) -o -type f -print0 | xargs -0 sed -i 's/(object)//g' --- wqflask/utility/gen_geno_ob.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'wqflask/utility/gen_geno_ob.py') diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 81085ffe..0a381c9b 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -1,7 +1,7 @@ import utility.logger logger = utility.logger.getLogger(__name__ ) -class genotype(object): +class genotype: """ Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure """ @@ -119,7 +119,7 @@ class genotype(object): self.chromosomes.append(chr_ob) -class Chr(object): +class Chr: def __init__(self, name, geno_ob): self.name = name self.loci = [] @@ -140,7 +140,7 @@ class Chr(object): def add_marker(self, marker_row): self.loci.append(Locus(self.geno_ob, marker_row)) -class Locus(object): +class Locus: def __init__(self, geno_ob, marker_row = None): self.chr = None self.name = None -- cgit v1.2.3 From c7e661b8ff9f70955418fbc4527378904beb0cf4 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 30 Apr 2021 12:16:51 +0300 Subject: autopep8: Fix E20-E27 Run: python -m autopep8 --in-place --recrusive ./ --select\ E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\ E242,E251,E252,E26,E265,E266,E27 -p 3 --- wqflask/base/data_set.py | 18 +- wqflask/base/mrna_assay_tissue_data.py | 16 +- wqflask/base/species.py | 2 +- wqflask/base/webqtlConfig.py | 40 +- wqflask/db/call.py | 6 +- wqflask/db/gn_server.py | 2 +- wqflask/db/webqtlDatabaseFunction.py | 10 +- wqflask/maintenance/convert_dryad_to_bimbam.py | 6 +- wqflask/maintenance/convert_geno_to_bimbam.py | 10 +- wqflask/maintenance/gen_select_dataset.py | 16 +- .../maintenance/generate_kinship_from_bimbam.py | 4 +- wqflask/maintenance/geno_to_json.py | 26 +- wqflask/maintenance/quantile_normalize.py | 30 +- wqflask/maintenance/set_resource_defaults.py | 26 +- wqflask/tests/unit/wqflask/api/test_correlation.py | 4 +- .../marker_regression/test_gemma_mapping.py | 14 +- .../marker_regression/test_qtlreaper_mapping.py | 24 +- .../wqflask/marker_regression/test_rqtl_mapping.py | 28 +- wqflask/tests/wqflask/show_trait/testSampleList.py | 6 +- wqflask/utility/Plot.py | 180 ++-- wqflask/utility/TDCell.py | 6 +- wqflask/utility/THCell.py | 8 +- wqflask/utility/__init__.py | 2 +- wqflask/utility/benchmark.py | 4 +- wqflask/utility/chunks.py | 2 +- wqflask/utility/corestats.py | 6 +- wqflask/utility/elasticsearch_tools.py | 8 +- wqflask/utility/external.py | 2 +- wqflask/utility/gen_geno_ob.py | 18 +- wqflask/utility/helper_functions.py | 2 +- wqflask/utility/logger.py | 34 +- wqflask/utility/pillow_utils.py | 2 +- wqflask/utility/startup_config.py | 10 +- wqflask/utility/svg.py | 624 +++++------ wqflask/utility/temp_data.py | 2 +- wqflask/utility/tools.py | 112 +- wqflask/utility/type_checking.py | 6 +- wqflask/utility/webqtlUtil.py | 60 +- wqflask/wqflask/__init__.py | 8 +- wqflask/wqflask/api/correlation.py | 44 +- wqflask/wqflask/api/gen_menu.py | 4 +- wqflask/wqflask/api/mapping.py | 12 +- wqflask/wqflask/api/router.py | 196 ++-- wqflask/wqflask/collect.py | 20 +- .../comparison_bar_chart/comparison_bar_chart.py | 12 +- wqflask/wqflask/correlation/corr_scatter_plot.py | 76 +- .../wqflask/correlation/correlation_functions.py | 34 +- wqflask/wqflask/correlation/show_corr_results.py | 38 +- .../wqflask/correlation_matrix/show_corr_matrix.py | 52 +- wqflask/wqflask/ctl/ctl_analysis.py | 88 +- wqflask/wqflask/database.py | 2 +- wqflask/wqflask/do_search.py | 80 +- wqflask/wqflask/export_traits.py | 2 +- wqflask/wqflask/external_tools/send_to_bnw.py | 6 +- .../wqflask/external_tools/send_to_geneweaver.py | 6 +- .../wqflask/external_tools/send_to_webgestalt.py | 26 +- wqflask/wqflask/group_manager.py | 22 +- wqflask/wqflask/gsearch.py | 2 +- wqflask/wqflask/heatmap/heatmap.py | 6 +- wqflask/wqflask/interval_analyst/GeneUtil.py | 24 +- .../marker_regression/display_mapping_results.py | 1114 ++++++++++---------- wqflask/wqflask/marker_regression/gemma_mapping.py | 2 +- wqflask/wqflask/marker_regression/plink_mapping.py | 34 +- .../wqflask/marker_regression/qtlreaper_mapping.py | 70 +- wqflask/wqflask/marker_regression/rqtl_mapping.py | 82 +- wqflask/wqflask/marker_regression/run_mapping.py | 134 +-- wqflask/wqflask/model.py | 8 +- wqflask/wqflask/parser.py | 4 +- wqflask/wqflask/resource_manager.py | 10 +- wqflask/wqflask/search_results.py | 16 +- wqflask/wqflask/show_trait/SampleList.py | 14 +- wqflask/wqflask/show_trait/show_trait.py | 18 +- wqflask/wqflask/snp_browser/snp_browser.py | 42 +- wqflask/wqflask/submit_bnw.py | 2 +- wqflask/wqflask/update_search_results.py | 6 +- wqflask/wqflask/user_login.py | 88 +- wqflask/wqflask/user_manager.py | 143 ++- wqflask/wqflask/user_session.py | 38 +- wqflask/wqflask/views.py | 6 +- wqflask/wsgi.py | 2 +- 80 files changed, 1975 insertions(+), 1994 deletions(-) (limited to 'wqflask/utility/gen_geno_ob.py') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 3183363b..55ab45f5 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -150,7 +150,7 @@ class DatasetType: "FROM PublishFreeze, InbredSet " "WHERE InbredSet.Name = '%s' AND " "PublishFreeze.InbredSetId = InbredSet.Id"), - 'geno': ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE " + 'geno': ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE " "GenoFreeze.Name = \"%s\" ") } @@ -215,7 +215,7 @@ def create_datasets_list(): if USE_REDIS: r.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL)) - r.expire(key, 60*60) + r.expire(key, 60 * 60) return datasets @@ -239,7 +239,7 @@ class Markers: for line in bimbam_fh: marker = {} marker['name'] = line.split(delimiter)[0].rstrip() - marker['Mb'] = float(line.split(delimiter)[1].rstrip())/1000000 + marker['Mb'] = float(line.split(delimiter)[1].rstrip()) / 1000000 marker['chr'] = line.split(delimiter)[2].rstrip() markers.append(marker) @@ -369,8 +369,8 @@ class DatasetGroup: def get_markers(self): def check_plink_gemma(): if flat_file_exists("mapping"): - MAPPING_PATH = flat_files("mapping")+"/" - if os.path.isfile(MAPPING_PATH+self.name+".bed"): + MAPPING_PATH = flat_files("mapping") + "/" + if os.path.isfile(MAPPING_PATH + self.name + ".bed"): return True return False @@ -416,7 +416,7 @@ class DatasetGroup: else: logger.debug("Cache not hit") - genotype_fn = locate_ignore_error(self.name+".geno", 'genotype') + genotype_fn = locate_ignore_error(self.name + ".geno", 'genotype') if genotype_fn: self.samplelist = get_group_samplelists.get_samplelist( "geno", genotype_fn) @@ -425,7 +425,7 @@ class DatasetGroup: if USE_REDIS: r.set(key, json.dumps(self.samplelist)) - r.expire(key, 60*5) + r.expire(key, 60 * 5) def all_samples_ordered(self): result = [] @@ -531,7 +531,7 @@ def datasets(group_name, this_group=None): if USE_REDIS: r.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL)) - r.expire(key, 60*5) + r.expire(key, 60 * 5) if this_group != None: this_group._datasets = dataset_menu @@ -622,7 +622,7 @@ class DataSet: WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND ProbeFreeze.TissueId = Tissue.Id AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s') - """ % (query_args), "/dataset/"+self.name+".json", + """ % (query_args), "/dataset/" + self.name + ".json", lambda r: (r["id"], r["name"], r["full_name"], r["short_name"], r["data_scale"], r["tissue"]) ) diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index 1f8224af..f3264b3d 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -9,7 +9,7 @@ from utility.db_tools import escape from utility.logger import getLogger -logger = getLogger(__name__ ) +logger = getLogger(__name__) class MrnaAssayTissueData: @@ -20,7 +20,7 @@ class MrnaAssayTissueData: self.data = collections.defaultdict(Bunch) - query = '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description + query = '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description from ( select Symbol, max(Mean) as maxmean from TissueProbeSetXRef @@ -31,14 +31,14 @@ class MrnaAssayTissueData: # Due to the limit size of TissueProbeSetFreezeId table in DB, # performance of inner join is acceptable.MrnaAssayTissueData(gene_symbols=symbol_list) if len(gene_symbols) == 0: - query += '''Symbol!='' and Symbol Is Not Null group by Symbol) + query += '''Symbol!='' and Symbol Is Not Null group by Symbol) as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol and t.Mean = x.maxmean; ''' else: in_clause = db_tools.create_in_clause(gene_symbols) - #ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower + # ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower query += ''' Symbol in {} group by Symbol) as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol and t.Mean = x.maxmean; @@ -64,11 +64,11 @@ class MrnaAssayTissueData: self.data[symbol].probe_target_description = result.Probe_Target_Description ########################################################################### - #Input: cursor, symbolList (list), dataIdDict(Dict) - #output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair, + # Input: cursor, symbolList (list), dataIdDict(Dict) + # output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair, # key is symbol, value is one list of expression values of one probeSet; - #function: get one dictionary whose key is gene symbol and value is tissue expression data (list type). - #Attention! All keys are lower case! + # function: get one dictionary whose key is gene symbol and value is tissue expression data (list type). + # Attention! All keys are lower case! ########################################################################### def get_symbol_values_pairs(self): diff --git a/wqflask/base/species.py b/wqflask/base/species.py index eae3325a..cf764d72 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -4,7 +4,7 @@ from flask import Flask, g from utility.logger import getLogger -logger = getLogger(__name__ ) +logger = getLogger(__name__) class TheSpecies: def __init__(self, dataset=None, species_name=None): diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index bb8704a5..872b52eb 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -1,4 +1,4 @@ -#########################################' +# ' # Environment Variables - public # # Note: much of this needs to handled by the settings/environment @@ -10,35 +10,35 @@ from utility.tools import valid_path, mk_dir, assert_dir, assert_writable_dir, flat_files, TEMPDIR -#Debug Level -#1 for debug, mod python will reload import each time +# Debug Level +# 1 for debug, mod python will reload import each time DEBUG = 1 -#USER privilege -USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4} +# USER privilege +USERDICT = {'guest': 1, 'user': 2, 'admin': 3, 'root':4} -#Set privileges +# Set privileges SUPER_PRIVILEGES = {'data': 'edit', 'metadata': 'edit', 'admin': 'edit-admins'} DEFAULT_PRIVILEGES = {'data': 'view', 'metadata': 'view', 'admin': 'not-admin'} -#minimum number of informative strains +# minimum number of informative strains KMININFORMATIVE = 5 -#Daily download limit from one IP +# Daily download limit from one IP DAILYMAXIMUM = 1000 -#maximum LRS value +# maximum LRS value MAXLRS = 460.0 -#MINIMUM Database public value +# MINIMUM Database public value PUBLICTHRESH = 0 -#EXTERNAL LINK ADDRESSES +# EXTERNAL LINK ADDRESSES PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract" UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' UTHSC_BLAT2 = 'http://ucscbrowserbeta.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' -GENOMEBROWSER_URL="https://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s" +GENOMEBROWSER_URL = "https://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s" NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=%s" GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s" OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s" @@ -56,7 +56,7 @@ GEMMA_URL = "http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s" ABA_URL = "http://mouse.brain-map.org/search/show?search_type=gene&search_term=%s" EBIGWAS_URL = "https://www.ebi.ac.uk/gwas/search?query=%s" WIKI_PI_URL = "http://severus.dbmi.pitt.edu/wiki-pi/index.php/search?q=%s" -ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s" +ENSEMBLETRANSCRIPT_URL = "http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s" DBSNP = 'http://ensembl.org/Mus_musculus/Variation/Population?v=%s' PROTEIN_ATLAS_URL = "http://www.proteinatlas.org/search/%s" OPEN_TARGETS_URL = "https://genetics.opentargets.org/gene/%s" @@ -71,13 +71,13 @@ RRID_RAT_URL = "https://rgd.mcw.edu/rgdweb/report/strain/main.html?id=%s" # want to reach this base dir assert_writable_dir(TEMPDIR) -TMPDIR = mk_dir(TEMPDIR+'/gn2/') +TMPDIR = mk_dir(TEMPDIR + '/gn2/') assert_writable_dir(TMPDIR) -CACHEDIR = mk_dir(TMPDIR+'/cache/') +CACHEDIR = mk_dir(TMPDIR + '/cache/') # We can no longer write into the git tree: -GENERATED_IMAGE_DIR = mk_dir(TMPDIR+'generated/') -GENERATED_TEXT_DIR = mk_dir(TMPDIR+'generated_text/') +GENERATED_IMAGE_DIR = mk_dir(TMPDIR + 'generated/') +GENERATED_TEXT_DIR = mk_dir(TMPDIR + 'generated_text/') # Make sure we have permissions to access these assert_writable_dir(CACHEDIR) @@ -85,12 +85,12 @@ assert_writable_dir(GENERATED_IMAGE_DIR) assert_writable_dir(GENERATED_TEXT_DIR) # Flat file directories -GENODIR = flat_files('genotype')+'/' +GENODIR = flat_files('genotype') + '/' assert_dir(GENODIR) # assert_dir(GENODIR+'bimbam') # for gemma # JSON genotypes are OBSOLETE -JSON_GENODIR = flat_files('genotype/json')+'/' +JSON_GENODIR = flat_files('genotype/json') + '/' if not valid_path(JSON_GENODIR): # fall back on old location (move the dir, FIXME) JSON_GENODIR = flat_files('json') @@ -98,4 +98,4 @@ if not valid_path(JSON_GENODIR): # Are we using the following...? PORTADDR = "http://50.16.251.170" INFOPAGEHREF = '/dbdoc/%s.html' -CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR' +CGIDIR = '/webqtl/' # XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR' diff --git a/wqflask/db/call.py b/wqflask/db/call.py index 0971d2a2..555878ad 100644 --- a/wqflask/db/call.py +++ b/wqflask/db/call.py @@ -12,7 +12,7 @@ from utility.tools import USE_GN_SERVER, LOG_SQL, GN_SERVER_URL from utility.benchmark import Bench from utility.logger import getLogger -logger = getLogger(__name__ ) +logger = getLogger(__name__) # from inspect import stack @@ -64,9 +64,9 @@ def gn_server(path): with Bench("GN_SERVER", LOG_SQL): res = () try: - res = urllib.request.urlopen(GN_SERVER_URL+path) + res = urllib.request.urlopen(GN_SERVER_URL + path) except: - res = urllib2.urlopen(GN_SERVER_URL+path) + res = urllib2.urlopen(GN_SERVER_URL + path) rest = res.read() res2 = json.loads(rest) logger.debug(res2) diff --git a/wqflask/db/gn_server.py b/wqflask/db/gn_server.py index da224112..6c7383d0 100644 --- a/wqflask/db/gn_server.py +++ b/wqflask/db/gn_server.py @@ -3,7 +3,7 @@ from db.call import gn_server from utility.logger import getLogger -logger = getLogger(__name__ ) +logger = getLogger(__name__) def menu_main(): return gn_server("/int/menu/main.json") diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py index 2805febd..18ade405 100644 --- a/wqflask/db/webqtlDatabaseFunction.py +++ b/wqflask/db/webqtlDatabaseFunction.py @@ -24,24 +24,24 @@ from db.call import fetch1 from utility.tools import USE_GN_SERVER from utility.logger import getLogger -logger = getLogger(__name__ ) +logger = getLogger(__name__) ########################################################################### -#output: cursor instance -#function: connect to database and return cursor instance +# output: cursor instance +# function: connect to database and return cursor instance ########################################################################### def retrieve_species(group): """Get the species of a group (e.g. returns string "mouse" on "BXD" """ - result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group), "/cross/"+group+".json", lambda r: (r["species"],))[0] + result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group), "/cross/" + group + ".json", lambda r: (r["species"],))[0] logger.debug("retrieve_species result:", result) return result def retrieve_species_id(group): - result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group), "/cross/"+group+".json", lambda r: (r["species_id"],))[0] + result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group), "/cross/" + group + ".json", lambda r: (r["species_id"],))[0] logger.debug("retrieve_species_id result:", result) return result diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py index 12ce35e9..8eab66e8 100644 --- a/wqflask/maintenance/convert_dryad_to_bimbam.py +++ b/wqflask/maintenance/convert_dryad_to_bimbam.py @@ -41,7 +41,7 @@ def read_dryad_file(filename): return geno_rows - #for i, marker in enumerate(marker_list): + # for i, marker in enumerate(marker_list): # this_row = [] # this_row.append(marker) # this_row.append("X") @@ -53,7 +53,7 @@ def read_dryad_file(filename): # print("row: " + str(i)) # geno_rows.append(this_row) # - #return geno_rows + # return geno_rows def write_bimbam_files(geno_rows): with open('/home/zas1024/cfw_data/CFW_geno.txt', 'w') as geno_fh: @@ -64,6 +64,6 @@ def convert_dryad_to_bimbam(filename): geno_file_rows = read_dryad_file(filename) write_bimbam_files(geno_file_rows) -if __name__=="__main__": +if __name__ == "__main__": input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt" convert_dryad_to_bimbam(input_filename) diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py index 0853b3ac..dc01cbb3 100644 --- a/wqflask/maintenance/convert_geno_to_bimbam.py +++ b/wqflask/maintenance/convert_geno_to_bimbam.py @@ -103,9 +103,9 @@ class ConvertGenoFile: with open(self.output_files[2], "w") as snp_fh: for marker in self.markers: if self.mb_exists: - snp_fh.write(marker['name'] +", " + str(int(float(marker['Mb'])*1000000)) + ", " + marker['chr'] + "\n") + snp_fh.write(marker['name'] + ", " + str(int(float(marker['Mb']) * 1000000)) + ", " + marker['chr'] + "\n") else: - snp_fh.write(marker['name'] +", " + str(int(float(marker['cM'])*1000000)) + ", " + marker['chr'] + "\n") + snp_fh.write(marker['name'] + ", " + str(int(float(marker['cM']) * 1000000)) + ", " + marker['chr'] + "\n") def get_sample_list(self, row_contents): self.sample_list = [] @@ -178,12 +178,12 @@ class ConvertGenoFile: print(" Row is:", convertob.latest_row_value) break -if __name__=="__main__": +if __name__ == "__main__": Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype""" New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/bimbam""" #Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno""" #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps""" #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json") - #convertob.convert() + # convertob.convert() ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory) - #ConvertGenoFiles(Geno_Directory) + # ConvertGenoFiles(Geno_Directory) diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 544e2fd1..f480d63f 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -61,10 +61,10 @@ def parse_db_uri(): parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( - db = parsed_uri.path[1:], - host = parsed_uri.hostname, - user = parsed_uri.username, - passwd = parsed_uri.password) + db=parsed_uri.path[1:], + host=parsed_uri.hostname, + user=parsed_uri.username, + passwd=parsed_uri.password) print(db_conn_info) return db_conn_info @@ -120,7 +120,7 @@ def get_types(groups): if not phenotypes_exist(group_name) and not genotypes_exist(group_name): types[species].pop(group_name, None) groups[species] = tuple(group for group in groups[species] if group[0] != group_name) - else: #ZS: This whole else statement might be unnecessary, need to check + else: # ZS: This whole else statement might be unnecessary, need to check types_list = build_types(species, group_name) if len(types_list) > 0: types[species][group_name] = types_list @@ -133,7 +133,7 @@ def get_types(groups): def phenotypes_exist(group_name): #print("group_name:", group_name) Cursor.execute("""select Name from PublishFreeze - where PublishFreeze.Name = '%s'""" % (group_name+"Publish")) + where PublishFreeze.Name = '%s'""" % (group_name + "Publish")) results = Cursor.fetchone() #print("RESULTS:", results) @@ -146,7 +146,7 @@ def phenotypes_exist(group_name): def genotypes_exist(group_name): #print("group_name:", group_name) Cursor.execute("""select Name from GenoFreeze - where GenoFreeze.Name = '%s'""" % (group_name+"Geno")) + where GenoFreeze.Name = '%s'""" % (group_name + "Geno")) results = Cursor.fetchone() #print("RESULTS:", results) @@ -246,7 +246,7 @@ def build_datasets(species, group, type_name): dataset_text = "%s Genotypes" % group datasets.append((dataset_id, dataset_value, dataset_text)) - else: # for mRNA expression/ProbeSet + else: # for mRNA expression/ProbeSet Cursor.execute("""select ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where Species.Name = '%s' and Species.Id = InbredSet.SpeciesId and diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py index 3e4d1741..664e9e48 100644 --- a/wqflask/maintenance/generate_kinship_from_bimbam.py +++ b/wqflask/maintenance/generate_kinship_from_bimbam.py @@ -52,9 +52,9 @@ class GenerateKinshipMatrices: break -if __name__=="__main__": +if __name__ == "__main__": Geno_Directory = """/export/local/home/zas1024/genotype_files/genotype/""" Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/""" GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory) - #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD + # ./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py index f5f7e0e7..fa0dcebd 100644 --- a/wqflask/maintenance/geno_to_json.py +++ b/wqflask/maintenance/geno_to_json.py @@ -66,16 +66,16 @@ class ConvertGenoFile: self.configurations = {} #self.skipped_cols = 3 - #if self.input_file.endswith(".geno.gz"): + # if self.input_file.endswith(".geno.gz"): # print("self.input_file: ", self.input_file) # self.input_fh = gzip.open(self.input_file) - #else: + # else: self.input_fh = open(self.input_file) with open(self.output_file, "w") as self.output_fh: - #if self.file_type == "geno": + # if self.file_type == "geno": self.process_csv() - #elif self.file_type == "snps": + # elif self.file_type == "snps": # self.process_snps_file() @@ -105,7 +105,7 @@ class ConvertGenoFile: this_marker.genotypes.append("NA") #print("this_marker is:", pf(this_marker.__dict__)) - #if this_marker.chr == "14": + # if this_marker.chr == "14": self.markers.append(this_marker.__dict__) with open(self.output_file, 'w') as fh: @@ -115,16 +115,16 @@ class ConvertGenoFile: #self.latest_col_pos = item_count + self.skipped_cols #self.latest_col_value = item - #if item_count != 0: + # if item_count != 0: # self.output_fh.write(" ") - #self.output_fh.write(self.configurations[item.upper()]) + # self.output_fh.write(self.configurations[item.upper()]) - #self.output_fh.write("\n") + # self.output_fh.write("\n") def process_rows(self): for self.latest_row_pos, row in enumerate(self.input_fh): - #if self.input_file.endswith(".geno.gz"): + # if self.input_file.endswith(".geno.gz"): # print("row: ", row) self.latest_row_value = row # Take care of headers @@ -176,21 +176,21 @@ class ConvertGenoFile: print(" Row is:", convertob.latest_row_value) break - #def process_snps_file(cls, snps_file, new_directory): + # def process_snps_file(cls, snps_file, new_directory): # output_file = os.path.join(new_directory, "mouse_families.json") # print("%s -> %s" % (snps_file, output_file)) # convertob = ConvertGenoFile(input_file, output_file) -if __name__=="__main__": +if __name__ == "__main__": Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype""" New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/json""" #Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno""" #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps""" #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json") - #convertob.convert() + # convertob.convert() ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory) - #ConvertGenoFiles(Geno_Directory) + # ConvertGenoFiles(Geno_Directory) #process_csv(Input_File, Output_File) diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index 701b2b50..6751a8e5 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -20,10 +20,10 @@ def parse_db_uri(): parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( - db = parsed_uri.path[1:], - host = parsed_uri.hostname, - user = parsed_uri.username, - passwd = parsed_uri.password) + db=parsed_uri.path[1:], + host=parsed_uri.hostname, + user=parsed_uri.username, + passwd=parsed_uri.password) print(db_conn_info) return db_conn_info @@ -35,16 +35,16 @@ def create_dataframe(input_file): input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols))) return pd.DataFrame(input_array) -#This function taken from https://github.com/ShawnLYU/Quantile_Normalize +# This function taken from https://github.com/ShawnLYU/Quantile_Normalize def quantileNormalize(df_input): df = df_input.copy() - #compute rank + # compute rank dic = {} for col in df: - dic.update({col : sorted(df[col])}) + dic.update({col: sorted(df[col])}) sorted_df = pd.DataFrame(dic) - rank = sorted_df.mean(axis = 1).tolist() - #sort + rank = sorted_df.mean(axis=1).tolist() + # sort for col in df: t = np.searchsorted(np.sort(df[col]), df[col]) df[col] = [rank[i] for i in t] @@ -65,8 +65,8 @@ def set_data(dataset_name): for i, sample in enumerate(sample_names): this_sample = { "name": sample, - "value": line1.split('\t')[i+1], - "qnorm": line2.split('\t')[i+1] + "value": line1.split('\t')[i + 1], + "qnorm": line2.split('\t')[i + 1] } sample_list.append(this_sample) query = """SELECT Species.SpeciesName, InbredSet.InbredSetName, ProbeSetFreeze.FullName @@ -99,9 +99,9 @@ if __name__ == '__main__': Conn = MySQLdb.Connect(**parse_db_uri()) Cursor = Conn.cursor() - #es = Elasticsearch([{ + # es = Elasticsearch([{ # "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT - #}], timeout=60) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None + # }], timeout=60) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None es = get_elasticsearch_connection(for_user=False) @@ -116,8 +116,8 @@ if __name__ == '__main__': success, _ = bulk(es, set_data(sys.argv[1])) response = es.search( - index = "traits", doc_type = "trait", body = { - "query": { "match": { "name": "ENSMUSG00000028982" } } + index="traits", doc_type="trait", body = { + "query": {"match": {"name": "ENSMUSG00000028982"}} } ) diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py index 4177c124..286094dd 100644 --- a/wqflask/maintenance/set_resource_defaults.py +++ b/wqflask/maintenance/set_resource_defaults.py @@ -43,10 +43,10 @@ def parse_db_uri(): parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( - db = parsed_uri.path[1:], - host = parsed_uri.hostname, - user = parsed_uri.username, - passwd = parsed_uri.password) + db=parsed_uri.path[1:], + host=parsed_uri.hostname, + user=parsed_uri.username, + passwd=parsed_uri.password) print(db_conn_info) return db_conn_info @@ -63,14 +63,14 @@ def insert_probeset_resources(default_owner_id): resource_ob = {} resource_ob['name'] = resource[1] resource_ob['owner_id'] = default_owner_id - resource_ob['data'] = { "dataset" : str(resource[0])} + resource_ob['data'] = {"dataset": str(resource[0])} resource_ob['type'] = "dataset-probeset" if resource[2] < 1 and resource[3] > 0: - resource_ob['default_mask'] = { "data": "view", + resource_ob['default_mask'] = {"data": "view", "metadata": "view", "admin": "not-admin"} else: - resource_ob['default_mask'] = { "data": "no-access", + resource_ob['default_mask'] = {"data": "no-access", "metadata": "no-access", "admin": "not-admin"} resource_ob['group_masks'] = {} @@ -97,10 +97,10 @@ def insert_publish_resources(default_owner_id): else: resource_ob['name'] = str(resource[0]) resource_ob['owner_id'] = default_owner_id - resource_ob['data'] = { "dataset" : str(resource[1]) , - "trait" : str(resource[0])} + resource_ob['data'] = {"dataset": str(resource[1]), + "trait": str(resource[0])} resource_ob['type'] = "dataset-publish" - resource_ob['default_mask'] = { "data": "view", + resource_ob['default_mask'] = {"data": "view", "metadata": "view", "admin": "not-admin"} @@ -125,14 +125,14 @@ def insert_geno_resources(default_owner_id): resource_ob['owner_id'] = "c5ce8c56-78a6-474f-bcaf-7129d97f56ae" else: resource_ob['owner_id'] = default_owner_id - resource_ob['data'] = { "dataset" : str(resource[0]) } + resource_ob['data'] = {"dataset": str(resource[0])} resource_ob['type'] = "dataset-geno" if resource[2] < 1: - resource_ob['default_mask'] = { "data": "view", + resource_ob['default_mask'] = {"data": "view", "metadata": "view", "admin": "not-admin"} else: - resource_ob['default_mask'] = { "data": "no-access", + resource_ob['default_mask'] = {"data": "no-access", "metadata": "no-access", "admin": "not-admin"} resource_ob['group_masks'] = {} diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py index d0264b87..bd99838d 100644 --- a/wqflask/tests/unit/wqflask/api/test_correlation.py +++ b/wqflask/tests/unit/wqflask/api/test_correlation.py @@ -127,9 +127,9 @@ class TestCorrelations(unittest.TestCase): expected_pearsonr = [-0.21618688834430866, 0.680771605997119, 6] expected_spearmanr = [-0.11595420713048969, 0.826848213385815, 6] for i, val in enumerate(expected_pearsonr): - self.assertAlmostEqual(val, results_pearsonr[i],4) + self.assertAlmostEqual(val, results_pearsonr[i], 4) for i, val in enumerate(expected_spearmanr): - self.assertAlmostEqual(val, results_spearmanr[i],4) + self.assertAlmostEqual(val, results_spearmanr[i], 4) self.assertEqual(results_num_overlap, None) @mock.patch("wqflask.api.correlation.do_literature_correlation_for_all_traits") diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py index fe2569b8..f194c6c9 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -47,11 +47,11 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.run_mapping.random.choice") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") - def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files,mock_parse_loco): + def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_parse_loco): """add tests for run_gemma where first run is set to true""" - this_chromosomes={} + this_chromosomes = {} for i in range(1, 5): - this_chromosomes[f'CH{i}']=(AttributeSetter({"name": f"CH{i}"})) + this_chromosomes[f'CH{i}'] = (AttributeSetter({"name": f"CH{i}"})) chromosomes = AttributeSetter({"chromosomes": this_chromosomes}) dataset_group = MockGroup( @@ -68,9 +68,9 @@ class TestGemmaMapping(unittest.TestCase): mock_parse_loco.return_value = [] results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ ], vals=[], covariates="", use_loco=True) - self.assertEqual(mock_os.system.call_count,2) + self.assertEqual(mock_os.system.call_count, 2) mock_gen_pheno_txt.assert_called_once() - mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR",True) + mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR", True) mock_os.path.isfile.assert_called_once_with( ('/home/user/imgfile_output.assoc.txt')) self.assertEqual(mock_flat_files.call_count, 4) @@ -144,7 +144,7 @@ class TestGemmaMapping(unittest.TestCase): "files": [["file_name", "user", "~/file1"], ["file_name", "user", "~/file2"]] } - return_file="""X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t + return_file = """X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t chr4\tM2\t12\tQ\tE\tMMB\tR\t24\tW\t0.87\t0.5 Y\tM4\t12\tQ\tE\tMMB\tR\t11.6\tW\t0.21\t0.7 X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6""" @@ -159,7 +159,7 @@ X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6""" mock_open.side_effect = handles results = parse_loco_output( this_dataset={}, gwa_output_filename=".xw/") - expected_results= [ + expected_results = [ {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, 'additive': 23.3, 'lod_score': 0.07058107428570727}, {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, 'additive': 24.0, 'lod_score': 0.3010299956639812}, {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, 'additive': 11.6, 'lod_score': 0.1549019599857432}, diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py index b47f877a..bbb79f98 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py @@ -1,20 +1,20 @@ import unittest -from unittest import mock -from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file +from unittest import mock +from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file -#issues some methods in genofile object are not defined -#modify samples should equal to vals +# issues some methods in genofile object are not defined +# modify samples should equal to vals class TestQtlReaperMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") - def test_gen_pheno_txt_file(self): - vals=["V1","x","V4","V3","x"] - samples=["S1","S2","S3","S4","S5"] - trait_filename="trait_file" + def test_gen_pheno_txt_file(self): + vals = ["V1", "x", "V4", "V3","x"] + samples = ["S1", "S2", "S3", "S4","S5"] + trait_filename = "trait_file" with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_pheno_txt_file(samples=samples,vals=vals,trait_filename=trait_filename) - mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt","w") - filehandler=mock_open() - write_calls= [mock.call('Trait\t'),mock.call('S1\tS3\tS4\n'),mock.call('T1\t'),mock.call('V1\tV4\tV3')] + gen_pheno_txt_file(samples=samples, vals=vals, trait_filename=trait_filename) + mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w") + filehandler = mock_open() + write_calls = [mock.call('Trait\t'), mock.call('S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')] filehandler.write.assert_has_calls(write_calls) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py index c585f1df..0e617e93 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -8,7 +8,7 @@ from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names class TestRqtlMapping(unittest.TestCase): def setUp(self): - self.app_context=app.app_context() + self.app_context = app.app_context() self.app_context.push() def tearDown(self): @@ -17,28 +17,28 @@ class TestRqtlMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.rqtl_mapping.g") @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") - def test_get_trait_data(self,mock_logger,mock_db): + def test_get_trait_data(self, mock_logger, mock_db): """test for getting trait data_type return True""" - query_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" - mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] - results=get_trait_data_type("traid_id") + query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" + mock_db.db.execute.return_value.fetchone.return_value = ["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] + results = get_trait_data_type("traid_id") mock_db.db.execute.assert_called_with(query_value) - self.assertEqual(results,"fer434f") + self.assertEqual(results, "fer434f") def test_sanitize_rqtl_phenotype(self): """test for sanitizing rqtl phenotype""" - vals=['f',"x","r","x","x"] - results=sanitize_rqtl_phenotype(vals) - expected_phenotype_string='c(f,NA,r,NA,NA)' + vals = ['f', "x", "r", "x","x"] + results = sanitize_rqtl_phenotype(vals) + expected_phenotype_string = 'c(f,NA,r,NA,NA)' - self.assertEqual(results,expected_phenotype_string) + self.assertEqual(results, expected_phenotype_string) def test_sanitize_rqtl_names(self): """test for sanitzing rqtl names""" - vals=['f',"x","r","x","x"] - expected_sanitized_name="c('f',NA,'r',NA,NA)" - results=sanitize_rqtl_names(vals) - self.assertEqual(expected_sanitized_name,results) + vals = ['f', "x", "r", "x","x"] + expected_sanitized_name = "c('f',NA,'r',NA,NA)" + results = sanitize_rqtl_names(vals) + self.assertEqual(expected_sanitized_name, results) diff --git a/wqflask/tests/wqflask/show_trait/testSampleList.py b/wqflask/tests/wqflask/show_trait/testSampleList.py index 34c51e3e..441a88a7 100644 --- a/wqflask/tests/wqflask/show_trait/testSampleList.py +++ b/wqflask/tests/wqflask/show_trait/testSampleList.py @@ -10,7 +10,7 @@ class TestSampleList(unittest.TestCase): characters_list = ["z", "f", "q", "s", "t", "a", "g"] names_list = ["temp1", "publish", "Sample", "Dataset"] - sorted_list_a=natural_sort(characters_list) - sorted_list_b=natural_sort(names_list) + sorted_list_a = natural_sort(characters_list) + sorted_list_b = natural_sort(names_list) self.assertEqual(sorted_list_a, ["a", "f", "g", "q", "s", "t", "z"]) - self.assertEqual(sorted_list_b,["Dataset", "Sample", "publish", "temp1"]) + self.assertEqual(sorted_list_b, ["Dataset", "Sample", "publish", "temp1"]) diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 61f408d2..68c2cb72 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -34,7 +34,7 @@ import utility.corestats as corestats from base import webqtlConfig from utility.pillow_utils import draw_rotated_text import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) # ---- Define common colours ---- # BLUE = ImageColor.getrgb("blue") @@ -74,7 +74,7 @@ def frange(start, end=None, inc=1.0): end = start + 0.0 start = 0.0 else: - start += 0.0 # force it to be a float + start += 0.0 # force it to be a float count = int((end - start) / inc) if start + count * inc != end: # Need to adjust the count. AFAICT, it always comes up one short. @@ -119,13 +119,13 @@ def find_outliers(vals): # parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py) # or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py) -def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1): +def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLabel=None, YLabel=None, title=None, offset=(60, 20, 40, 40), zoom=1): im_drawer = ImageDraw.Draw(canvas) xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset plotWidth = canvas.size[0] - xLeftOffset - xRightOffset plotHeight = canvas.size[1] - yTopOffset - yBottomOffset - if plotHeight<=0 or plotWidth<=0: + if plotHeight <= 0 or plotWidth <= 0: return if len(data) < 2: @@ -133,15 +133,15 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab max_D = max(data) min_D = min(data) - #add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong - if max_D == float('inf') or max_D>webqtlConfig.MAXLRS: - max_D=webqtlConfig.MAXLRS #maximum LRS value + # add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong + if max_D == float('inf') or max_D > webqtlConfig.MAXLRS: + max_D = webqtlConfig.MAXLRS # maximum LRS value xLow, xTop, stepX = detScale(min_D, max_D) - #reduce data - #ZS: Used to determine number of bins for permutation output - step = ceil((xTop-xLow)/50.0) + # reduce data + # ZS: Used to determine number of bins for permutation output + step = ceil((xTop - xLow) / 50.0) j = xLow dataXY = [] Count = [] @@ -151,122 +151,122 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab j += step for i, item in enumerate(data): - if item == float('inf') or item>webqtlConfig.MAXLRS: - item = webqtlConfig.MAXLRS #maximum LRS value - j = int((item-xLow)/step) + if item == float('inf') or item > webqtlConfig.MAXLRS: + item = webqtlConfig.MAXLRS # maximum LRS value + j = int((item - xLow) / step) Count[j] += 1 - yLow, yTop, stepY=detScale(0, max(Count)) + yLow, yTop, stepY = detScale(0, max(Count)) - #draw data - xScale = plotWidth/(xTop-xLow) - yScale = plotHeight/(yTop-yLow) - barWidth = xScale*step + # draw data + xScale = plotWidth / (xTop - xLow) + yScale = plotHeight / (yTop - yLow) + barWidth = xScale * step for i, count in enumerate(Count): if count: - xc = (dataXY[i]-xLow)*xScale+xLeftOffset - yc =-(count-yLow)*yScale+yTopOffset+plotHeight + xc = (dataXY[i] - xLow) * xScale + xLeftOffset + yc = -(count - yLow) * yScale + yTopOffset + plotHeight im_drawer.rectangle( - xy=((xc+2, yc), (xc+barWidth-2, yTopOffset+plotHeight)), + xy=((xc + 2, yc), (xc + barWidth - 2, yTopOffset + plotHeight)), outline=barColor, fill=barColor) - #draw drawing region + # draw drawing region im_drawer.rectangle( - xy=((xLeftOffset, yTopOffset), (xLeftOffset+plotWidth, yTopOffset+plotHeight)) + xy=((xLeftOffset, yTopOffset), (xLeftOffset + plotWidth, yTopOffset + plotHeight)) ) - #draw scale - scaleFont=ImageFont.truetype(font=COUR_FILE, size=11) - x=xLow - for i in range(int(stepX)+1): - xc=xLeftOffset+(x-xLow)*xScale + # draw scale + scaleFont = ImageFont.truetype(font=COUR_FILE, size=11) + x = xLow + for i in range(int(stepX) + 1): + xc = xLeftOffset + (x - xLow) * xScale im_drawer.line( - xy=((xc, yTopOffset+plotHeight), (xc, yTopOffset+plotHeight+5)), + xy=((xc, yTopOffset + plotHeight), (xc, yTopOffset + plotHeight + 5)), fill=axesColor) strX = cformat(d=x, rank=0) im_drawer.text( text=strX, - xy=(xc-im_drawer.textsize(strX, font=scaleFont)[0]/2, - yTopOffset+plotHeight+14), font=scaleFont) - x+= (xTop - xLow)/stepX - - y=yLow - for i in range(int(stepY)+1): - yc=yTopOffset+plotHeight-(y-yLow)*yScale - im_drawer.line(xy=((xLeftOffset, yc), (xLeftOffset-5, yc)), fill=axesColor) - strY = "%d" %y + xy=(xc - im_drawer.textsize(strX, font=scaleFont)[0] / 2, + yTopOffset + plotHeight + 14), font=scaleFont) + x += (xTop - xLow) / stepX + + y = yLow + for i in range(int(stepY) + 1): + yc = yTopOffset + plotHeight - (y - yLow) * yScale + im_drawer.line(xy=((xLeftOffset, yc), (xLeftOffset - 5, yc)), fill=axesColor) + strY = "%d" % y im_drawer.text( text=strY, - xy=(xLeftOffset-im_drawer.textsize(strY, font=scaleFont)[0]-6, yc+5), + xy=(xLeftOffset - im_drawer.textsize(strY, font=scaleFont)[0] - 6, yc + 5), font=scaleFont) - y+= (yTop - yLow)/stepY + y += (yTop - yLow) / stepY - #draw label - labelFont=ImageFont.truetype(font=TAHOMA_FILE, size=17) + # draw label + labelFont = ImageFont.truetype(font=TAHOMA_FILE, size=17) if XLabel: im_drawer.text( text=XLabel, - xy=(xLeftOffset+( - plotWidth-im_drawer.textsize(XLabel, font=labelFont)[0])/2.0, - yTopOffset+plotHeight+yBottomOffset-10), + xy=(xLeftOffset + ( + plotWidth - im_drawer.textsize(XLabel, font=labelFont)[0]) / 2.0, + yTopOffset + plotHeight + yBottomOffset-10), font=labelFont, fill=labelColor) if YLabel: draw_rotated_text(canvas, text=YLabel, xy=(19, - yTopOffset+plotHeight-( - plotHeight-im_drawer.textsize( - YLabel, font=labelFont)[0])/2.0), + yTopOffset + plotHeight - ( + plotHeight - im_drawer.textsize( + YLabel, font=labelFont)[0]) / 2.0), font=labelFont, fill=labelColor, angle=90) - labelFont=ImageFont.truetype(font=VERDANA_FILE, size=16) + labelFont = ImageFont.truetype(font=VERDANA_FILE, size=16) if title: im_drawer.text( text=title, - xy=(xLeftOffset+(plotWidth-im_drawer.textsize( - title, font=labelFont)[0])/2.0, + xy=(xLeftOffset + (plotWidth - im_drawer.textsize( + title, font=labelFont)[0]) / 2.0, 20), font=labelFont, fill=labelColor) # This function determines the scale of the plot def detScaleOld(min, max): - if min>=max: + if min >= max: return None elif min == -1.0 and max == 1.0: return [-1.2, 1.2, 12] else: - a=max-min - b=floor(log10(a)) - c=pow(10.0, b) - if a < c*5.0: - c/=2.0 - #print a,b,c - low=c*floor(min/c) - high=c*ceil(max/c) - return [low, high, round((high-low)/c)] - -def detScale(min=0,max=0): - - if min>=max: + a = max - min + b = floor(log10(a)) + c = pow(10.0, b) + if a < c * 5.0: + c /= 2.0 + # print a,b,c + low = c * floor(min / c) + high = c * ceil(max / c) + return [low, high, round((high - low) / c)] + +def detScale(min=0, max=0): + + if min >= max: return None elif min == -1.0 and max == 1.0: return [-1.2, 1.2, 12] else: - a=max-min + a = max - min if max != 0: - max += 0.1*a + max += 0.1 * a if min != 0: - if min > 0 and min < 0.1*a: + if min > 0 and min < 0.1 * a: min = 0.0 else: - min -= 0.1*a - a=max-min - b=floor(log10(a)) - c=pow(10.0, b) - low=c*floor(min/c) - high=c*ceil(max/c) - n = round((high-low)/c) + min -= 0.1 * a + a = max - min + b = floor(log10(a)) + c = pow(10.0, b) + low = c * floor(min / c) + high = c * ceil(max / c) + n = round((high - low) / c) div = 2.0 while n < 5 or n > 15: if n < 5: @@ -274,23 +274,23 @@ def detScale(min=0,max=0): else: c *= div if div == 2.0: - div =5.0 + div = 5.0 else: - div =2.0 - low=c*floor(min/c) - high=c*ceil(max/c) - n = round((high-low)/c) + div = 2.0 + low = c * floor(min / c) + high = c * ceil(max / c) + n = round((high - low) / c) return [low, high, n] def bluefunc(x): - return 1.0 / (1.0 + exp(-10*(x-0.6))) + return 1.0 / (1.0 + exp(-10 * (x - 0.6))) def redfunc(x): - return 1.0 / (1.0 + exp(10*(x-0.5))) + return 1.0 / (1.0 + exp(10 * (x - 0.5))) def greenfunc(x): - return 1 - pow(redfunc(x+0.2), 2) - bluefunc(x-0.3) + return 1 - pow(redfunc(x + 0.2), 2) - bluefunc(x - 0.3) def colorSpectrum(n=100): multiple = 10 @@ -303,17 +303,17 @@ def colorSpectrum(n=100): return [ImageColor.getrgb("rgb(100%,0%,0%)"), ImageColor.getrgb("rgb(0%,100%,0%)"), ImageColor.getrgb("rgb(0%,0%,100%)")] - N = n*multiple - out = [None]*N; + N = n * multiple + out = [None] * N; for i in range(N): - x = float(i)/N + x = float(i) / N out[i] = ImageColor.getrgb("rgb({}%,{}%,{}%".format( - *[int(i*100) for i in ( + *[int(i * 100) for i in ( redfunc(x), greenfunc(x), bluefunc(x))])) out2 = [out[0]] - step = N/float(n-1) + step = N / float(n - 1) j = 0 - for i in range(n-2): + for i in range(n - 2): j += step out2.append(out[int(j)]) out2.append(out[-1]) @@ -324,5 +324,5 @@ def _test(): doctest.testmod() -if __name__=="__main__": +if __name__ == "__main__": _test() diff --git a/wqflask/utility/TDCell.py b/wqflask/utility/TDCell.py index 8de8e050..4b0f4b1d 100644 --- a/wqflask/utility/TDCell.py +++ b/wqflask/utility/TDCell.py @@ -33,9 +33,9 @@ class TDCell: def __init__(self, html="", text="", val=0.0): - self.html = html #html, for web page - self.text = text #text value, for output to a text file - self.val = val #sort by value + self.html = html # html, for web page + self.text = text # text value, for output to a text file + self.val = val # sort by value def __str__(self): return self.text diff --git a/wqflask/utility/THCell.py b/wqflask/utility/THCell.py index dde221b5..f533dcb8 100644 --- a/wqflask/utility/THCell.py +++ b/wqflask/utility/THCell.py @@ -33,10 +33,10 @@ class THCell: def __init__(self, html="", text="", sort=1, idx=-1): - self.html = html #html, for web page - self.text = text #Column text value - self.sort = sort #0: not sortable, 1: yes - self.idx = idx #sort by value + self.html = html # html, for web page + self.text = text # Column text value + self.sort = sort # 0: not sortable, 1: yes + self.idx = idx # sort by value def __str__(self): return self.text diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index df926884..ec7e72d0 100644 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py @@ -4,7 +4,7 @@ from pprint import pformat as pf class Bunch: """Like a dictionary but using object notation""" - def __init__(self, **kw): + def __init__(self, **kw): self.__dict__ = kw def __repr__(self): diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py index 91ea91e8..3d40a3b8 100644 --- a/wqflask/utility/benchmark.py +++ b/wqflask/utility/benchmark.py @@ -4,7 +4,7 @@ import time from utility.tools import LOG_BENCH from utility.logger import getLogger -logger = getLogger(__name__ ) +logger = getLogger(__name__) class Bench: entries = collections.OrderedDict() @@ -39,7 +39,7 @@ class Bench: total_time = sum((time_taken for time_taken in list(cls.entries.values()))) print("\nTiming report\n") for name, time_taken in list(cls.entries.items()): - percent = int(round((time_taken/total_time) * 100)) + percent = int(round((time_taken / total_time) * 100)) print("[{}%] {}: {}".format(percent, name, time_taken)) print() diff --git a/wqflask/utility/chunks.py b/wqflask/utility/chunks.py index 9a7db102..484b5de6 100644 --- a/wqflask/utility/chunks.py +++ b/wqflask/utility/chunks.py @@ -26,6 +26,6 @@ def divide_into_chunks(the_list, number_chunks): chunks = [] for counter in range(0, length, chunksize): - chunks.append(the_list[counter:counter+chunksize]) + chunks.append(the_list[counter:counter + chunksize]) return chunks diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py index 67ca3ad3..15d1cb8d 100644 --- a/wqflask/utility/corestats.py +++ b/wqflask/utility/corestats.py @@ -15,7 +15,7 @@ import sys -#ZS: Should switch to using some third party library for this; maybe scipy has an equivalent +# ZS: Should switch to using some third party library for this; maybe scipy has an equivalent class Stats: def __init__(self, sequence): @@ -63,7 +63,7 @@ class Stats: if len(self.sequence) < 1: value = None elif (percentile >= 100): - sys.stderr.write('ERROR: percentile must be < 100. you supplied: %s\n'% percentile) + sys.stderr.write('ERROR: percentile must be < 100. you supplied: %s\n' % percentile) value = None else: element_idx = int(len(self.sequence) * (percentile / 100.0)) @@ -80,4 +80,4 @@ class Stats: # stats = corestats.Stats(sequence) # print stats.avg() # print stats.percentile(90) -# ------------------------------------------- \ No newline at end of file +# ------------------------------------------- diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py index a5580811..ae1181e4 100644 --- a/wqflask/utility/elasticsearch_tools.py +++ b/wqflask/utility/elasticsearch_tools.py @@ -48,7 +48,7 @@ logger = getLogger(__name__) from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT def test_elasticsearch_connection(): - es = Elasticsearch(['http://'+ELASTICSEARCH_HOST+":"+str(ELASTICSEARCH_PORT)+'/'], verify_certs=True) + es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True) if not es.ping(): logger.warning("Elasticsearch is DOWN") @@ -97,8 +97,8 @@ def get_item_by_unique_column(es, column_name, column_value, index, doc_type): item_details = None try: response = es.search( - index = index, doc_type = doc_type, body = { - "query": { "match": { column_name: column_value } } + index=index, doc_type=doc_type, body = { + "query": {"match": {column_name: column_value}} }) if len(response["hits"]["hits"]) > 0: item_details = response["hits"]["hits"][0]["_source"] @@ -109,4 +109,4 @@ def get_item_by_unique_column(es, column_name, column_value, index, doc_type): def es_save_data(es, index, doc_type, data_item, data_id,): from time import sleep es.create(index, doc_type, body=data_item, id=data_id) - sleep(1) # Delay 1 second to allow indexing + sleep(1) # Delay 1 second to allow indexing diff --git a/wqflask/utility/external.py b/wqflask/utility/external.py index 50afea08..c1bf4043 100644 --- a/wqflask/utility/external.py +++ b/wqflask/utility/external.py @@ -6,4 +6,4 @@ import subprocess def shell(command): if subprocess.call(command, shell=True) != 0: - raise Exception("ERROR: failed on "+command) + raise Exception("ERROR: failed on " + command) diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 0a381c9b..9cfa39f9 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -1,5 +1,5 @@ import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) class genotype: """ @@ -18,7 +18,7 @@ class genotype: self.filler = False self.mb_exists = False - #ZS: This is because I'm not sure if some files switch the column that contains Mb/cM positions; might be unnecessary + # ZS: This is because I'm not sure if some files switch the column that contains Mb/cM positions; might be unnecessary self.cm_column = 2 self.mb_column = 3 @@ -36,14 +36,14 @@ class genotype: return len(self.chromosomes) def read_rdata_output(self, qtl_results): - #ZS: This is necessary because R/qtl requires centimorgan marker positions, which it normally gets from the .geno file, but that doesn't exist for HET3-ITP (which only has RData), so it needs to read in the marker cM positions from the results - self.chromosomes = [] #ZS: Overwriting since the .geno file's contents are just placeholders + # ZS: This is necessary because R/qtl requires centimorgan marker positions, which it normally gets from the .geno file, but that doesn't exist for HET3-ITP (which only has RData), so it needs to read in the marker cM positions from the results + self.chromosomes = [] # ZS: Overwriting since the .geno file's contents are just placeholders - this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers + this_chr = "" # ZS: This is so it can track when the chromosome changes as it iterates through markers chr_ob = None for marker in qtl_results: locus = Locus(self) - if (str(marker['chr']) != this_chr) and this_chr != "X": #ZS: This is really awkward but works as a temporary fix + if (str(marker['chr']) != this_chr) and this_chr != "X": # ZS: This is really awkward but works as a temporary fix if this_chr != "": self.chromosomes.append(chr_ob) this_chr = str(marker['chr']) @@ -68,7 +68,7 @@ class genotype: with open(filename, 'r') as geno_file: lines = geno_file.readlines() - this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers + this_chr = "" # ZS: This is so it can track when the chromosome changes as it iterates through markers chr_ob = None for line in lines: if line[0] == "#": @@ -141,7 +141,7 @@ class Chr: self.loci.append(Locus(self.geno_ob, marker_row)) class Locus: - def __init__(self, geno_ob, marker_row = None): + def __init__(self, geno_ob, marker_row=None): self.chr = None self.name = None self.cM = None @@ -175,5 +175,5 @@ class Locus: for allele in marker_row[start_pos:]: if allele in list(geno_table.keys()): self.genotype.append(geno_table[allele]) - else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown + else: # ZS: Some genotype appears that isn't specified in the metadata, make it unknown self.genotype.append("U") diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 12fd6be5..ecc075ae 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -39,7 +39,7 @@ def get_trait_db_obs(self, trait_db_list): for trait in trait_db_list: data, _separator, hmac_string = trait.rpartition(':') data = data.strip() - assert hmac_string==hmac.hmac_creation(data), "Data tampering?" + assert hmac_string == hmac.hmac_creation(data), "Data tampering?" trait_name, dataset_name = data.split(":")[:2] if dataset_name == "Temp": dataset_ob = data_set.create_dataset( diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py index e904eb94..16912e58 100644 --- a/wqflask/utility/logger.py +++ b/wqflask/utility/logger.py @@ -49,14 +49,14 @@ class GNLogger: """Set the undelying log level""" self.logger.setLevel(value) - def debug(self,*args): + def debug(self, *args): """Call logging.debug for multiple args. Use (lazy) debugf and level=num to filter on LOG_LEVEL_DEBUG. """ self.collect(self.logger.debug, *args) - def debug20(self,*args): + def debug20(self, *args): """Call logging.debug for multiple args. Use level=num to filter on LOG_LEVEL_DEBUG (NYI). @@ -65,29 +65,29 @@ LOG_LEVEL_DEBUG (NYI). if self.logger.getEffectiveLevel() < 20: self.collect(self.logger.debug, *args) - def info(self,*args): + def info(self, *args): """Call logging.info for multiple args""" self.collect(self.logger.info, *args) - def warning(self,*args): + def warning(self, *args): """Call logging.warning for multiple args""" self.collect(self.logger.warning, *args) # self.logger.warning(self.collect(*args)) - def error(self,*args): + def error(self, *args): """Call logging.error for multiple args""" now = datetime.datetime.utcnow() time_str = now.strftime('%H:%M:%S UTC %Y%m%d') - l = [time_str]+list(args) + l = [time_str] + list(args) self.collect(self.logger.error, *l) - def infof(self,*args): + def infof(self, *args): """Call logging.info for multiple args lazily""" # only evaluate function when logging if self.logger.getEffectiveLevel() < 30: self.collectf(self.logger.debug, *args) - def debugf(self,level=0,*args): + def debugf(self, level=0, *args): """Call logging.debug for multiple args lazily and handle LOG_LEVEL_DEBUG correctly @@ -97,7 +97,7 @@ LOG_LEVEL_DEBUG (NYI). if self.logger.getEffectiveLevel() < 20: self.collectf(self.logger.debug, *args) - def sql(self, sqlcommand, fun = None): + def sql(self, sqlcommand, fun=None): """Log SQL command, optionally invoking a timed fun""" if LOG_SQL: caller = stack()[1][3] @@ -110,11 +110,11 @@ LOG_LEVEL_DEBUG (NYI). self.info(result) return result - def collect(self,fun,*args): + def collect(self, fun, *args): """Collect arguments and use fun to output""" - out = "."+stack()[2][3] + out = "." + stack()[2][3] for a in args: - if len(out)>1: + if len(out) > 1: out += ": " if isinstance(a, str): out = out + a @@ -122,11 +122,11 @@ LOG_LEVEL_DEBUG (NYI). out = out + pf(a, width=160) fun(out) - def collectf(self,fun,*args): + def collectf(self, fun, *args): """Collect arguments and use fun to output one by one""" - out = "."+stack()[2][3] + out = "." + stack()[2][3] for a in args: - if len(out)>1: + if len(out) > 1: out += ": " if isfunction(a): out += a() @@ -139,7 +139,7 @@ LOG_LEVEL_DEBUG (NYI). # Get the module logger. You can override log levels at the # module level -def getLogger(name, level = None): +def getLogger(name, level=None): gnlogger = GNLogger(name) logger = gnlogger.logger @@ -148,5 +148,5 @@ def getLogger(name, level = None): else: logger.setLevel(LOG_LEVEL) - logger.info("Log level of "+name+" set to "+logging.getLevelName(logger.getEffectiveLevel())) + logger.info("Log level of " + name + " set to " + logging.getLevelName(logger.getEffectiveLevel())) return gnlogger diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py index c486abba..6e95beb0 100644 --- a/wqflask/utility/pillow_utils.py +++ b/wqflask/utility/pillow_utils.py @@ -3,7 +3,7 @@ from PIL import Image, ImageColor, ImageDraw, ImageFont from utility.tools import TEMPDIR import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) BLACK = ImageColor.getrgb("black") WHITE = ImageColor.getrgb("white") diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py index f1aaebb6..f22f4b14 100644 --- a/wqflask/utility/startup_config.py +++ b/wqflask/utility/startup_config.py @@ -3,12 +3,12 @@ from wqflask import app from utility.tools import WEBSERVER_MODE, show_settings, get_setting_int, get_setting, get_setting_bool import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) -BLUE = '\033[94m' +BLUE = '\033[94m' GREEN = '\033[92m' -BOLD = '\033[1m' -ENDC = '\033[0m' +BOLD = '\033[1m' +ENDC = '\033[0m' def app_config(): app.config['SESSION_TYPE'] = 'filesystem' @@ -27,7 +27,7 @@ def app_config(): port = get_setting_int("SERVER_PORT") if get_setting_bool("USE_GN_SERVER"): - print(("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]")) + print(("GN2 API server URL is [" + BLUE + get_setting("GN_SERVER_URL") + ENDC + "]")) import requests page = requests.get(get_setting("GN_SERVER_URL")) if page.status_code != 200: diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index b92cc2d1..4c478c36 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -172,7 +172,7 @@ def _viewboxlist(a): """formats a tuple""" s = '' for e in a: - s += str(e)+' ' + s += str(e) + ' ' return s @@ -189,7 +189,7 @@ class pathdata: def __init__(self, x=None, y=None): self.path = [] if x is not None and y is not None: - self.path.append('M '+str(x)+' '+str(y)) + self.path.append('M ' + str(x) + ' ' + str(y)) def closepath(self): """ends the path""" @@ -197,79 +197,79 @@ class pathdata: def move(self, x, y): """move to absolute""" - self.path.append('M '+str(x)+' '+str(y)) + self.path.append('M ' + str(x) + ' ' + str(y)) def relmove(self, x, y): """move to relative""" - self.path.append('m '+str(x)+' '+str(y)) + self.path.append('m ' + str(x) + ' ' + str(y)) def line(self, x, y): """line to absolute""" - self.path.append('L '+str(x)+' '+str(y)) + self.path.append('L ' + str(x) + ' ' + str(y)) def relline(self, x, y): """line to relative""" - self.path.append('l '+str(x)+' '+str(y)) + self.path.append('l ' + str(x) + ' ' + str(y)) def hline(self, x): """horizontal line to absolute""" - self.path.append('H'+str(x)) + self.path.append('H' + str(x)) def relhline(self, x): """horizontal line to relative""" - self.path.append('h'+str(x)) + self.path.append('h' + str(x)) def vline(self, y): """verical line to absolute""" - self.path.append('V'+str(y)) + self.path.append('V' + str(y)) def relvline(self, y): """vertical line to relative""" - self.path.append('v'+str(y)) + self.path.append('v' + str(y)) def bezier(self, x1, y1, x2, y2, x, y): """bezier with xy1 and xy2 to xy absolut""" - self.path.append('C'+str(x1)+','+str(y1)+' '+str(x2) + - ','+str(y2)+' '+str(x)+','+str(y)) + self.path.append('C' + str(x1) + ','+str(y1)+' '+str(x2) + + ',' + str(y2) + ' '+str(x)+','+str(y)) def relbezier(self, x1, y1, x2, y2, x, y): """bezier with xy1 and xy2 to xy relative""" - self.path.append('c'+str(x1)+','+str(y1)+' '+str(x2) + - ','+str(y2)+' '+str(x)+','+str(y)) + self.path.append('c' + str(x1) + ','+str(y1)+' '+str(x2) + + ',' + str(y2) + ' '+str(x)+','+str(y)) def smbezier(self, x2, y2, x, y): """smooth bezier with xy2 to xy absolut""" - self.path.append('S'+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) + self.path.append('S' + str(x2) + ',' + str(y2) + ' ' + str(x) + ',' + str(y)) def relsmbezier(self, x2, y2, x, y): """smooth bezier with xy2 to xy relative""" - self.path.append('s'+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) + self.path.append('s' + str(x2) + ',' + str(y2) + ' ' + str(x) + ',' + str(y)) def qbezier(self, x1, y1, x, y): """quadratic bezier with xy1 to xy absolut""" - self.path.append('Q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y)) + self.path.append('Q' + str(x1) + ',' + str(y1) + ' ' + str(x) + ',' + str(y)) def relqbezier(self, x1, y1, x, y): """quadratic bezier with xy1 to xy relative""" - self.path.append('q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y)) + self.path.append('q' + str(x1) + ',' + str(y1) + ' ' + str(x) + ',' + str(y)) def smqbezier(self, x, y): """smooth quadratic bezier to xy absolut""" - self.path.append('T'+str(x)+','+str(y)) + self.path.append('T' + str(x) + ',' + str(y)) def relsmqbezier(self, x, y): """smooth quadratic bezier to xy relative""" - self.path.append('t'+str(x)+','+str(y)) + self.path.append('t' + str(x) + ',' + str(y)) def ellarc(self, rx, ry, xrot, laf, sf, x, y): """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy absolut""" - self.path.append('A'+str(rx)+','+str(ry)+' '+str(xrot) + - ' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) + self.path.append('A' + str(rx) + ','+str(ry)+' '+str(xrot) + + ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y)) def relellarc(self, rx, ry, xrot, laf, sf, x, y): """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy relative""" - self.path.append('a'+str(rx)+','+str(ry)+' '+str(xrot) + - ' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) + self.path.append('a' + str(rx) + ','+str(ry)+' '+str(xrot) + + ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y)) def __repr__(self): return ' '.join(self.path) @@ -312,10 +312,10 @@ class SVGelement: self.elements.append(SVGelement) def toXml(self, level, f): - f.write('\t'*level) - f.write('<'+self.type) + f.write('\t' * level) + f.write('<' + self.type) for attkey in list(self.attributes.keys()): - f.write(' '+_escape(str(attkey))+'=' + + f.write(' ' + _escape(str(attkey)) + '=' + _quoteattr(str(self.attributes[attkey]))) if self.namespace: f.write(' xmlns="' + _escape(str(self.namespace)) + @@ -325,23 +325,23 @@ class SVGelement: if self.elements: f.write('\n') for element in self.elements: - element.toXml(level+1, f) + element.toXml(level + 1, f) if self.cdata: - f.write('\n'+'\t'*(level+1)+'\n') + f.write('\n' + '\t' * (level + 2) + line) + f.write('\n' + '\t' * (level + 1) + ']]>\n') if self.text: if isinstance(self.text, type('')): # If the text is only text f.write(_escape(str(self.text))) else: # If the text is a spannedtext class f.write(str(self.text)) if self.elements: - f.write('\t'*level+'\n') + f.write('\t' * level + '\n') elif self.text: - f.write('\n') + f.write('\n') elif self.cdata: - f.write('\t'*level+'\n') + f.write('\t' * level + '\n') else: f.write('/>\n') @@ -447,38 +447,38 @@ class rect(SVGelement): if width == None or height == None: raise ValueError('both height and width are required') - SVGelement.__init__(self, 'rect', {'width':width,'height':height}, **args) - if x!=None: - self.attributes['x']=x - if y!=None: - self.attributes['y']=y - if fill!=None: - self.attributes['fill']=fill - if stroke!=None: - self.attributes['stroke']=stroke - if stroke_width!=None: - self.attributes['stroke-width']=stroke_width + SVGelement.__init__(self, 'rect', {'width': width, 'height': height}, **args) + if x != None: + self.attributes['x'] = x + if y != None: + self.attributes['y'] = y + if fill != None: + self.attributes['fill'] = fill + if stroke != None: + self.attributes['stroke'] = stroke + if stroke_width != None: + self.attributes['stroke-width'] = stroke_width class ellipse(SVGelement): """e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args) an ellipse is defined as a center and a x and y radius. """ - def __init__(self,cx=None,cy=None,rx=None,ry=None,fill=None,stroke=None,stroke_width=None,**args): - if rx==None or ry== None: + def __init__(self, cx=None, cy=None, rx=None, ry=None,fill=None,stroke=None,stroke_width=None,**args): + if rx == None or ry == None: raise ValueError('both rx and ry are required') - SVGelement.__init__(self, 'ellipse', {'rx':rx,'ry':ry}, **args) - if cx!=None: - self.attributes['cx']=cx - if cy!=None: - self.attributes['cy']=cy - if fill!=None: - self.attributes['fill']=fill - if stroke!=None: - self.attributes['stroke']=stroke - if stroke_width!=None: - self.attributes['stroke-width']=stroke_width + SVGelement.__init__(self, 'ellipse', {'rx': rx, 'ry': ry}, **args) + if cx != None: + self.attributes['cx'] = cx + if cy != None: + self.attributes['cy'] = cy + if fill != None: + self.attributes['fill'] = fill + if stroke != None: + self.attributes['stroke'] = stroke + if stroke_width != None: + self.attributes['stroke-width'] = stroke_width class circle(SVGelement): @@ -486,20 +486,20 @@ class circle(SVGelement): The circle creates an element using a x, y and radius values eg """ - def __init__(self,cx=None,cy=None,r=None,fill=None,stroke=None,stroke_width=None,**args): - if r==None: + def __init__(self, cx=None, cy=None, r=None, fill=None,stroke=None,stroke_width=None,**args): + if r == None: raise ValueError('r is required') - SVGelement.__init__(self, 'circle', {'r':r}, **args) - if cx!=None: - self.attributes['cx']=cx - if cy!=None: - self.attributes['cy']=cy - if fill!=None: - self.attributes['fill']=fill - if stroke!=None: - self.attributes['stroke']=stroke - if stroke_width!=None: - self.attributes['stroke-width']=stroke_width + SVGelement.__init__(self, 'circle', {'r': r}, **args) + if cx != None: + self.attributes['cx'] = cx + if cy != None: + self.attributes['cy'] = cy + if fill != None: + self.attributes['fill'] = fill + if stroke != None: + self.attributes['stroke'] = stroke + if stroke_width != None: + self.attributes['stroke-width'] = stroke_width class point(circle): """p=point(x,y,color) @@ -507,7 +507,7 @@ class point(circle): A point is defined as a circle with a size 1 radius. It may be more efficient to use a very small rectangle if you use many points because a circle is difficult to render. """ - def __init__(self,x,y,fill='black',**args): + def __init__(self, x, y, fill='black', **args): circle.__init__(self, x, y, 1, fill, **args) class line(SVGelement): @@ -515,64 +515,64 @@ class line(SVGelement): A line is defined by a begin x,y pair and an end x,y pair """ - def __init__(self,x1=None,y1=None,x2=None,y2=None,stroke=None,stroke_width=None,**args): + def __init__(self, x1=None, y1=None, x2=None, y2=None,stroke=None,stroke_width=None,**args): SVGelement.__init__(self, 'line', **args) - if x1!=None: - self.attributes['x1']=x1 - if y1!=None: - self.attributes['y1']=y1 - if x2!=None: - self.attributes['x2']=x2 - if y2!=None: - self.attributes['y2']=y2 - if stroke_width!=None: - self.attributes['stroke-width']=stroke_width - if stroke!=None: - self.attributes['stroke']=stroke + if x1 != None: + self.attributes['x1'] = x1 + if y1 != None: + self.attributes['y1'] = y1 + if x2 != None: + self.attributes['x2'] = x2 + if y2 != None: + self.attributes['y2'] = y2 + if stroke_width != None: + self.attributes['stroke-width'] = stroke_width + if stroke != None: + self.attributes['stroke'] = stroke class polyline(SVGelement): """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args) a polyline is defined by a list of xy pairs """ - def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args): - SVGelement.__init__(self, 'polyline', {'points':_xypointlist(points)}, **args) - if fill!=None: - self.attributes['fill']=fill - if stroke_width!=None: - self.attributes['stroke-width']=stroke_width - if stroke!=None: - self.attributes['stroke']=stroke + def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args): + SVGelement.__init__(self, 'polyline', {'points': _xypointlist(points)}, **args) + if fill != None: + self.attributes['fill'] = fill + if stroke_width != None: + self.attributes['stroke-width'] = stroke_width + if stroke != None: + self.attributes['stroke'] = stroke class polygon(SVGelement): """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args) a polygon is defined by a list of xy pairs """ - def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args): - SVGelement.__init__(self, 'polygon', {'points':_xypointlist(points)}, **args) - if fill!=None: - self.attributes['fill']=fill - if stroke_width!=None: - self.attributes['stroke-width']=stroke_width - if stroke!=None: - self.attributes['stroke']=stroke + def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args): + SVGelement.__init__(self, 'polygon', {'points': _xypointlist(points)}, **args) + if fill != None: + self.attributes['fill'] = fill + if stroke_width != None: + self.attributes['stroke-width'] = stroke_width + if stroke != None: + self.attributes['stroke'] = stroke class path(SVGelement): """p=path(path,fill,stroke,stroke_width,**args) a path is defined by a path object and optional width, stroke and fillcolor """ - def __init__(self,pathdata,fill=None,stroke=None,stroke_width=None,id=None,**args): - SVGelement.__init__(self, 'path', {'d':str(pathdata)}, **args) - if stroke!=None: - self.attributes['stroke']=stroke - if fill!=None: - self.attributes['fill']=fill - if stroke_width!=None: - self.attributes['stroke-width']=stroke_width - if id!=None: - self.attributes['id']=id + def __init__(self, pathdata, fill=None, stroke=None, stroke_width=None,id=None,**args): + SVGelement.__init__(self, 'path', {'d': str(pathdata)}, **args) + if stroke != None: + self.attributes['stroke'] = stroke + if fill != None: + self.attributes['fill'] = fill + if stroke_width != None: + self.attributes['stroke-width'] = stroke_width + if id != None: + self.attributes['id'] = id class text(SVGelement): @@ -580,20 +580,20 @@ class text(SVGelement): a text element can bge used for displaying text on the screen """ - def __init__(self,x=None,y=None,text=None,font_size=None,font_family=None,text_anchor=None,**args): + def __init__(self, x=None, y=None, text=None, font_size=None,font_family=None,text_anchor=None,**args): SVGelement.__init__(self, 'text', **args) - if x!=None: - self.attributes['x']=x - if y!=None: - self.attributes['y']=y - if font_size!=None: - self.attributes['font-size']=font_size - if font_family!=None: - self.attributes['font-family']=font_family - if text!=None: - self.text=text - if text_anchor!=None: - self.attributes['text-anchor']=text_anchor + if x != None: + self.attributes['x'] = x + if y != None: + self.attributes['y'] = y + if font_size != None: + self.attributes['font-size'] = font_size + if font_family != None: + self.attributes['font-family'] = font_family + if text != None: + self.text = text + if text_anchor != None: + self.attributes['text-anchor'] = text_anchor class textpath(SVGelement): @@ -601,10 +601,10 @@ class textpath(SVGelement): a textpath places a text on a path which is referenced by a link. """ - def __init__(self,link,text=None,**args): - SVGelement.__init__(self, 'textPath', {'xlink:href':link}, **args) - if text!=None: - self.text=text + def __init__(self, link, text=None, **args): + SVGelement.__init__(self, 'textPath', {'xlink:href': link}, **args) + if text != None: + self.text = text class pattern(SVGelement): """p=pattern(x,y,width,height,patternUnits,**args) @@ -613,18 +613,18 @@ class pattern(SVGelement): graphic object which can be replicated ("tiled") at fixed intervals in x and y to cover the areas to be painted. """ - def __init__(self,x=None,y=None,width=None,height=None,patternUnits=None,**args): + def __init__(self, x=None, y=None, width=None, height=None,patternUnits=None,**args): SVGelement.__init__(self, 'pattern', **args) - if x!=None: - self.attributes['x']=x - if y!=None: - self.attributes['y']=y - if width!=None: - self.attributes['width']=width - if height!=None: - self.attributes['height']=height - if patternUnits!=None: - self.attributes['patternUnits']=patternUnits + if x != None: + self.attributes['x'] = x + if y != None: + self.attributes['y'] = y + if width != None: + self.attributes['width'] = width + if height != None: + self.attributes['height'] = height + if patternUnits != None: + self.attributes['patternUnits'] = patternUnits class title(SVGelement): """t=title(text,**args) @@ -632,10 +632,10 @@ class title(SVGelement): a title is a text element. The text is displayed in the title bar add at least one to the root svg element """ - def __init__(self,text=None,**args): + def __init__(self, text=None, **args): SVGelement.__init__(self, 'title', **args) - if text!=None: - self.text=text + if text != None: + self.text = text class description(SVGelement): """d=description(text,**args) @@ -643,10 +643,10 @@ class description(SVGelement): a description can be added to any element and is used for a tooltip Add this element before adding other elements. """ - def __init__(self,text=None,**args): + def __init__(self, text=None, **args): SVGelement.__init__(self, 'desc', **args) - if text!=None: - self.text=text + if text != None: + self.text = text class lineargradient(SVGelement): """lg=lineargradient(x1,y1,x2,y2,id,**args) @@ -654,18 +654,18 @@ class lineargradient(SVGelement): defines a lineargradient using two xy pairs. stop elements van be added to define the gradient colors. """ - def __init__(self,x1=None,y1=None,x2=None,y2=None,id=None,**args): + def __init__(self, x1=None, y1=None, x2=None, y2=None,id=None,**args): SVGelement.__init__(self, 'linearGradient', **args) - if x1!=None: - self.attributes['x1']=x1 - if y1!=None: - self.attributes['y1']=y1 - if x2!=None: - self.attributes['x2']=x2 - if y2!=None: - self.attributes['y2']=y2 - if id!=None: - self.attributes['id']=id + if x1 != None: + self.attributes['x1'] = x1 + if y1 != None: + self.attributes['y1'] = y1 + if x2 != None: + self.attributes['x2'] = x2 + if y2 != None: + self.attributes['y2'] = y2 + if id != None: + self.attributes['id'] = id class radialgradient(SVGelement): """rg=radialgradient(cx,cy,r,fx,fy,id,**args) @@ -673,38 +673,38 @@ class radialgradient(SVGelement): defines a radial gradient using a outer circle which are defined by a cx,cy and r and by using a focalpoint. stop elements van be added to define the gradient colors. """ - def __init__(self,cx=None,cy=None,r=None,fx=None,fy=None,id=None,**args): + def __init__(self, cx=None, cy=None, r=None, fx=None,fy=None,id=None,**args): SVGelement.__init__(self, 'radialGradient', **args) - if cx!=None: - self.attributes['cx']=cx - if cy!=None: - self.attributes['cy']=cy - if r!=None: - self.attributes['r']=r - if fx!=None: - self.attributes['fx']=fx - if fy!=None: - self.attributes['fy']=fy - if id!=None: - self.attributes['id']=id + if cx != None: + self.attributes['cx'] = cx + if cy != None: + self.attributes['cy'] = cy + if r != None: + self.attributes['r'] = r + if fx != None: + self.attributes['fx'] = fx + if fy != None: + self.attributes['fy'] = fy + if id != None: + self.attributes['id'] = id class stop(SVGelement): """st=stop(offset,stop_color,**args) Puts a stop color at the specified radius """ - def __init__(self,offset,stop_color=None,**args): - SVGelement.__init__(self, 'stop', {'offset':offset}, **args) - if stop_color!=None: - self.attributes['stop-color']=stop_color + def __init__(self, offset, stop_color=None, **args): + SVGelement.__init__(self, 'stop', {'offset': offset}, **args) + if stop_color != None: + self.attributes['stop-color'] = stop_color class style(SVGelement): """st=style(type,cdata=None,**args) Add a CDATA element to this element for defing in line stylesheets etc.. """ - def __init__(self,type,cdata=None,**args): - SVGelement.__init__(self, 'style', {'type':type}, cdata=cdata, **args) + def __init__(self, type, cdata=None, **args): + SVGelement.__init__(self, 'style', {'type': type}, cdata=cdata, **args) class image(SVGelement): @@ -712,22 +712,22 @@ class image(SVGelement): adds an image to the drawing. Supported formats are .png, .jpg and .svg. """ - def __init__(self,url,x=None,y=None,width=None,height=None,**args): - if width==None or height==None: + def __init__(self, url, x=None, y=None, width=None,height=None,**args): + if width == None or height == None: raise ValueError('both height and width are required') - SVGelement.__init__(self, 'image', {'xlink:href':url,'width':width,'height':height}, **args) - if x!=None: - self.attributes['x']=x - if y!=None: - self.attributes['y']=y + SVGelement.__init__(self, 'image', {'xlink:href': url, 'width': width, 'height':height}, **args) + if x != None: + self.attributes['x'] = x + if y != None: + self.attributes['y'] = y class cursor(SVGelement): """c=cursor(url,**args) defines a custom cursor for a element or a drawing """ - def __init__(self,url,**args): - SVGelement.__init__(self, 'cursor', {'xlink:href':url}, **args) + def __init__(self, url, **args): + SVGelement.__init__(self, 'cursor', {'xlink:href': url}, **args) class marker(SVGelement): @@ -736,20 +736,20 @@ class marker(SVGelement): defines a marker which can be used as an endpoint for a line or other pathtypes add an element to it which should be used as a marker. """ - def __init__(self,id=None,viewBox=None,refx=None,refy=None,markerWidth=None,markerHeight=None,**args): + def __init__(self, id=None, viewBox=None, refx=None, refy=None,markerWidth=None,markerHeight=None,**args): SVGelement.__init__(self, 'marker', **args) - if id!=None: - self.attributes['id']=id - if viewBox!=None: - self.attributes['viewBox']=_viewboxlist(viewBox) - if refx!=None: - self.attributes['refX']=refx - if refy!=None: - self.attributes['refY']=refy - if markerWidth!=None: - self.attributes['markerWidth']=markerWidth - if markerHeight!=None: - self.attributes['markerHeight']=markerHeight + if id != None: + self.attributes['id'] = id + if viewBox != None: + self.attributes['viewBox'] = _viewboxlist(viewBox) + if refx != None: + self.attributes['refX'] = refx + if refy != None: + self.attributes['refY'] = refy + if markerWidth != None: + self.attributes['markerWidth'] = markerWidth + if markerHeight != None: + self.attributes['markerHeight'] = markerHeight class group(SVGelement): """g=group(id,**args) @@ -757,10 +757,10 @@ class group(SVGelement): a group is defined by an id and is used to contain elements g.addElement(SVGelement) """ - def __init__(self,id=None,**args): + def __init__(self, id=None, **args): SVGelement.__init__(self, 'g', **args) - if id!=None: - self.attributes['id']=id + if id != None: + self.attributes['id'] = id class symbol(SVGelement): """sy=symbol(id,viewbox,**args) @@ -771,19 +771,19 @@ class symbol(SVGelement): sy.addElement(SVGelement) """ - def __init__(self,id=None,viewBox=None,**args): + def __init__(self, id=None, viewBox=None, **args): SVGelement.__init__(self, 'symbol', **args) - if id!=None: - self.attributes['id']=id - if viewBox!=None: - self.attributes['viewBox']=_viewboxlist(viewBox) + if id != None: + self.attributes['id'] = id + if viewBox != None: + self.attributes['viewBox'] = _viewboxlist(viewBox) class defs(SVGelement): """d=defs(**args) container for defining elements """ - def __init__(self,**args): + def __init__(self, **args): SVGelement.__init__(self, 'defs', **args) class switch(SVGelement): @@ -793,7 +793,7 @@ class switch(SVGelement): requiredFeatures, requiredExtensions and systemLanguage. Refer to the SVG specification for details. """ - def __init__(self,**args): + def __init__(self, **args): SVGelement.__init__(self, 'switch', **args) @@ -802,17 +802,17 @@ class use(SVGelement): references a symbol by linking to its id and its position, height and width """ - def __init__(self,link,x=None,y=None,width=None,height=None,**args): - SVGelement.__init__(self, 'use', {'xlink:href':link}, **args) - if x!=None: - self.attributes['x']=x - if y!=None: - self.attributes['y']=y + def __init__(self, link, x=None, y=None, width=None,height=None,**args): + SVGelement.__init__(self, 'use', {'xlink:href': link}, **args) + if x != None: + self.attributes['x'] = x + if y != None: + self.attributes['y'] = y - if width!=None: - self.attributes['width']=width - if height!=None: - self.attributes['height']=height + if width != None: + self.attributes['width'] = width + if height != None: + self.attributes['height'] = height class link(SVGelement): @@ -821,17 +821,17 @@ class link(SVGelement): a link is defined by a hyperlink. add elements which have to be linked a.addElement(SVGelement) """ - def __init__(self,link='',**args): - SVGelement.__init__(self, 'a', {'xlink:href':link}, **args) + def __init__(self, link='', **args): + SVGelement.__init__(self, 'a', {'xlink:href': link}, **args) class view(SVGelement): """v=view(id,**args) a view can be used to create a view with different attributes""" - def __init__(self,id=None,**args): + def __init__(self, id=None, **args): SVGelement.__init__(self, 'view', **args) - if id!=None: - self.attributes['id']=id + if id != None: + self.attributes['id'] = id class script(SVGelement): """sc=script(type,type,cdata,**args) @@ -839,77 +839,77 @@ class script(SVGelement): adds a script element which contains CDATA to the SVG drawing """ - def __init__(self,type,cdata=None,**args): - SVGelement.__init__(self, 'script', {'type':type}, cdata=cdata, **args) + def __init__(self, type, cdata=None, **args): + SVGelement.__init__(self, 'script', {'type': type}, cdata=cdata, **args) class animate(SVGelement): """an=animate(attribute,from,to,during,**args) animates an attribute. """ - def __init__(self,attribute,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self, 'animate', {'attributeName':attribute}, **args) - if fr!=None: - self.attributes['from']=fr - if to!=None: - self.attributes['to']=to - if dur!=None: - self.attributes['dur']=dur + def __init__(self, attribute, fr=None, to=None, dur=None,**args): + SVGelement.__init__(self, 'animate', {'attributeName': attribute}, **args) + if fr != None: + self.attributes['from'] = fr + if to != None: + self.attributes['to'] = to + if dur != None: + self.attributes['dur'] = dur class animateMotion(SVGelement): """an=animateMotion(pathdata,dur,**args) animates a SVGelement over the given path in dur seconds """ - def __init__(self,pathdata,dur,**args): + def __init__(self, pathdata, dur, **args): SVGelement.__init__(self, 'animateMotion', **args) - if pathdata!=None: - self.attributes['path']=str(pathdata) - if dur!=None: - self.attributes['dur']=dur + if pathdata != None: + self.attributes['path'] = str(pathdata) + if dur != None: + self.attributes['dur'] = dur class animateTransform(SVGelement): """antr=animateTransform(type,from,to,dur,**args) transform an element from and to a value. """ - def __init__(self,type=None,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self, 'animateTransform', {'attributeName':'transform'}, **args) + def __init__(self, type=None, fr=None, to=None, dur=None,**args): + SVGelement.__init__(self, 'animateTransform', {'attributeName': 'transform'}, **args) # As far as I know the attributeName is always transform - if type!=None: - self.attributes['type']=type - if fr!=None: - self.attributes['from']=fr - if to!=None: - self.attributes['to']=to - if dur!=None: - self.attributes['dur']=dur + if type != None: + self.attributes['type'] = type + if fr != None: + self.attributes['from'] = fr + if to != None: + self.attributes['to'] = to + if dur != None: + self.attributes['dur'] = dur class animateColor(SVGelement): """ac=animateColor(attribute,type,from,to,dur,**args) Animates the color of a element """ - def __init__(self,attribute,type=None,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self, 'animateColor', {'attributeName':attribute}, **args) - if type!=None: - self.attributes['type']=type - if fr!=None: - self.attributes['from']=fr - if to!=None: - self.attributes['to']=to - if dur!=None: - self.attributes['dur']=dur + def __init__(self, attribute, type=None, fr=None, to=None,dur=None,**args): + SVGelement.__init__(self, 'animateColor', {'attributeName': attribute}, **args) + if type != None: + self.attributes['type'] = type + if fr != None: + self.attributes['from'] = fr + if to != None: + self.attributes['to'] = to + if dur != None: + self.attributes['dur'] = dur class set(SVGelement): """st=set(attribute,to,during,**args) sets an attribute to a value for a """ - def __init__(self,attribute,to=None,dur=None,**args): - SVGelement.__init__(self, 'set', {'attributeName':attribute}, **args) - if to!=None: - self.attributes['to']=to - if dur!=None: - self.attributes['dur']=dur + def __init__(self, attribute, to=None, dur=None, **args): + SVGelement.__init__(self, 'set', {'attributeName': attribute}, **args) + if to != None: + self.attributes['to'] = to + if dur != None: + self.attributes['dur'] = dur @@ -928,15 +928,15 @@ class svg(SVGelement): d.setSVG(s) d.toXml() """ - def __init__(self,viewBox=None, width=None, height=None,**args): + def __init__(self, viewBox=None, width=None, height=None, **args): SVGelement.__init__(self, 'svg', **args) - if viewBox!=None: - self.attributes['viewBox']=_viewboxlist(viewBox) - if width!=None: - self.attributes['width']=width - if height!=None: - self.attributes['height']=height - self.namespace="http://www.w3.org/2000/svg" + if viewBox != None: + self.attributes['viewBox'] = _viewboxlist(viewBox) + if width != None: + self.attributes['width'] = width + if height != None: + self.attributes['height'] = height + self.namespace = "http://www.w3.org/2000/svg" class drawing: """d=drawing() @@ -950,15 +950,15 @@ class drawing: """ def __init__(self, entity={}): - self.svg=None + self.svg = None self.entity = entity def setSVG(self, svg): - self.svg=svg + self.svg = svg # Voeg een element toe aan de grafiek toe. - if use_dom_implementation==0: - def toXml(self, filename='',compress=False): + if use_dom_implementation == 0: + def toXml(self, filename='', compress=False): import io - xml=io.StringIO() + xml = io.StringIO() xml.write("\n") xml.write("to the screen drawing.toXml(filename)---->to the file writes a svg drawing to the screen or to a file @@ -1002,35 +1002,35 @@ class drawing: global root # root is defined global so it can be used by the appender. Its also possible to use it as an arugument but # that is a bit messy. - root=implementation.createDocument(None, None, doctype) + root = implementation.createDocument(None, None, doctype) # Create the xml document. global appender def appender(element, elementroot): """This recursive function appends elements to an element and sets the attributes and type. It stops when alle elements have been appended""" if element.namespace: - e=root.createElementNS(element.namespace, element.type) + e = root.createElementNS(element.namespace, element.type) else: - e=root.createElement(element.type) + e = root.createElement(element.type) if element.text: - textnode=root.createTextNode(element.text) + textnode = root.createTextNode(element.text) e.appendChild(textnode) - for attribute in list(element.attributes.keys()): #in element.attributes is supported from python 2.2 + for attribute in list(element.attributes.keys()): # in element.attributes is supported from python 2.2 e.setAttribute(attribute, str(element.attributes[attribute])) if element.elements: for el in element.elements: - e=appender(el, e) + e = appender(el, e) elementroot.appendChild(e) return elementroot - root=appender(self.svg, root) + root = appender(self.svg, root) if not filename: import io - xml=io.StringIO() + xml = io.StringIO() PrettyPrint(root, xml) if compress: import gzip - f=io.StringIO() - zf=gzip.GzipFile(fileobj=f, mode='wb') + f = io.StringIO() + zf = gzip.GzipFile(fileobj=f, mode='wb') zf.write(xml.getvalue()) zf.close() f.seek(0) @@ -1039,16 +1039,16 @@ class drawing: return xml.getvalue() else: try: - if filename[-4:]=='svgz': + if filename[-4:] == 'svgz': import gzip import io - xml=io.StringIO() + xml = io.StringIO() PrettyPrint(root, xml) - f=gzip.GzipFile(filename=filename, mode='wb', compresslevel=9) + f = gzip.GzipFile(filename=filename, mode='wb', compresslevel=9) f.write(xml.getvalue()) f.close() else: - f=open(filename, 'w') + f = open(filename, 'w') PrettyPrint(root, f) f.close() except: @@ -1058,44 +1058,44 @@ class drawing: import xml.parsers.xmlproc.xmlval except: raise exceptions.ImportError('PyXml is required for validating SVG') - svg=self.toXml() - xv=xml.parsers.xmlproc.xmlval.XMLValidator() + svg = self.toXml() + xv = xml.parsers.xmlproc.xmlval.XMLValidator() try: xv.feed(svg) except: raise Exception("SVG is not well formed, see messages above") else: print("SVG well formed") -if __name__=='__main__': +if __name__ == '__main__': - d=drawing() - s=svg((0, 0, 100, 100)) - r=rect(-100, -100, 300, 300, 'cyan') + d = drawing() + s = svg((0, 0, 100, 100)) + r = rect(-100, -100, 300, 300, 'cyan') s.addElement(r) - t=title('SVGdraw Demo') + t = title('SVGdraw Demo') s.addElement(t) - g=group('animations') - e=ellipse(0, 0, 5, 2) + g = group('animations') + e = ellipse(0, 0, 5, 2) g.addElement(e) - c=circle(0, 0, 1, 'red') + c = circle(0, 0, 1, 'red') g.addElement(c) - pd=pathdata(0, -10) + pd = pathdata(0, -10) for i in range(6): pd.relsmbezier(10, 5, 0, 10) pd.relsmbezier(-10, 5, 0, 10) - an=animateMotion(pd, 10) - an.attributes['rotate']='auto-reverse' - an.attributes['repeatCount']="indefinite" + an = animateMotion(pd, 10) + an.attributes['rotate'] = 'auto-reverse' + an.attributes['repeatCount'] = "indefinite" g.addElement(an) s.addElement(g) for i in range(20, 120, 20): - u=use('#animations', i, 0) + u = use('#animations', i, 0) s.addElement(u) for i in range(0, 120, 20): for j in range(5, 105, 10): - c=circle(i, j, 1, 'red', 'black', .5) + c = circle(i, j, 1, 'red', 'black', .5) s.addElement(c) d.setSVG(s) diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py index b2cbd458..2088ba9a 100644 --- a/wqflask/utility/temp_data.py +++ b/wqflask/utility/temp_data.py @@ -11,7 +11,7 @@ class TempData: def store(self, field, value): self.redis.hset(self.key, field, value) - self.redis.expire(self.key, 60*15) # Expire in 15 minutes + self.redis.expire(self.key, 60 * 15) # Expire in 15 minutes def get_all(self): return self.redis.hgetall(self.key) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 65df59c3..9b751344 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -9,7 +9,7 @@ from wqflask import app # Use the standard logger here to avoid a circular dependency import logging -logger = logging.getLogger(__name__ ) +logger = logging.getLogger(__name__) OVERRIDES = {} @@ -18,7 +18,7 @@ def app_set(command_id, value): app.config.setdefault(command_id, value) return value -def get_setting(command_id,guess=None): +def get_setting(command_id, guess=None): """Resolve a setting from the environment or the global settings in app.config, with valid_path is a function checking whether the path points to an expected directory and returns the full path to @@ -54,7 +54,7 @@ def get_setting(command_id,guess=None): # print("Looking for "+command_id+"\n") command = value(os.environ.get(command_id)) if command is None or command == "": - command = OVERRIDES.get(command_id) # currently not in use + command = OVERRIDES.get(command_id) # currently not in use if command is None: # ---- Check whether setting exists in app command = value(app.config.get(command_id)) @@ -62,7 +62,7 @@ def get_setting(command_id,guess=None): command = value(guess) if command is None or command == "": # print command - raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).') + raise Exception(command_id + ' setting unknown or faulty (update default_settings.py?).') # print("Set "+command_id+"="+str(command)) return command @@ -99,13 +99,13 @@ def js_path(module=None): """ Find the JS module in the two paths """ - try_gn = get_setting("JS_GN_PATH")+"/"+module + try_gn = get_setting("JS_GN_PATH") + "/" + module if valid_path(try_gn): return try_gn - try_guix = get_setting("JS_GUIX_PATH")+"/"+module + try_guix = get_setting("JS_GUIX_PATH") + "/" + module if valid_path(try_guix): return try_guix - raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)" + raise "No JS path found for " + module + " (if not in Guix check JS_GN_PATH)" def reaper_command(guess=None): return get_setting("REAPER_COMMAND", guess) @@ -121,28 +121,28 @@ def plink_command(guess=None): def flat_file_exists(subdir): base = get_setting("GENENETWORK_FILES") - return valid_path(base+"/"+subdir) + return valid_path(base + "/" + subdir) def flat_files(subdir=None): base = get_setting("GENENETWORK_FILES") if subdir: - return assert_dir(base+"/"+subdir) + return assert_dir(base + "/" + subdir) return assert_dir(base) def assert_bin(fn): if not valid_bin(fn): - raise Exception("ERROR: can not find binary "+fn) + raise Exception("ERROR: can not find binary " + fn) return fn def assert_dir(dir): if not valid_path(dir): - raise Exception("ERROR: can not find directory "+dir) + raise Exception("ERROR: can not find directory " + dir) return dir def assert_writable_dir(dir): try: fn = dir + "/test.txt" - fh = open( fn, 'w' ) + fh = open(fn, 'w') fh.write("I am writing this text to the file\n") fh.close() os.remove(fn) @@ -152,7 +152,7 @@ def assert_writable_dir(dir): def assert_file(fn): if not valid_file(fn): - raise Exception('Unable to find file '+fn) + raise Exception('Unable to find file ' + fn) return fn def mk_dir(dir): @@ -168,19 +168,19 @@ def locate(name, subdir=None): """ base = get_setting("GENENETWORK_FILES") if subdir: - base = base+"/"+subdir + base = base + "/" + subdir if valid_path(base): lookfor = base + "/" + name if valid_file(lookfor): - logger.info("Found: file "+lookfor+"\n") + logger.info("Found: file " + lookfor + "\n") return lookfor else: - raise Exception("Can not locate "+lookfor) + raise Exception("Can not locate " + lookfor) if subdir: sys.stderr.write(subdir) - raise Exception("Can not locate "+name+" in "+base) + raise Exception("Can not locate " + name + " in " + base) def locate_phewas(name, subdir=None): - return locate(name, '/phewas/'+subdir) + return locate(name, '/phewas/' + subdir) def locate_ignore_error(name, subdir=None): """ @@ -191,13 +191,13 @@ def locate_ignore_error(name, subdir=None): """ base = get_setting("GENENETWORK_FILES") if subdir: - base = base+"/"+subdir + base = base + "/" + subdir if valid_path(base): lookfor = base + "/" + name if valid_file(lookfor): - logger.debug("Found: file "+name+"\n") + logger.debug("Found: file " + name + "\n") return lookfor - logger.info("WARNING: file "+name+" not found\n") + logger.info("WARNING: file " + name + " not found\n") return None def tempdir(): @@ -206,20 +206,20 @@ def tempdir(): """ return valid_path(get_setting("TMPDIR", "/tmp")) -BLUE = '\033[94m' +BLUE = '\033[94m' GREEN = '\033[92m' -BOLD = '\033[1m' -ENDC = '\033[0m' +BOLD = '\033[1m' +ENDC = '\033[0m' def show_settings(): from utility.tools import LOG_LEVEL - print(("Set global log level to "+BLUE+LOG_LEVEL+ENDC)) + print(("Set global log level to " + BLUE + LOG_LEVEL + ENDC)) log_level = getattr(logging, LOG_LEVEL.upper()) logging.basicConfig(level=log_level) logger.info(OVERRIDES) - logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC) + logger.info(BLUE + "Mr. Mojo Risin 2" + ENDC) keylist = list(app.config.keys()) print("runserver.py: ****** Webserver configuration - k,v pairs from app.config ******") keylist.sort() @@ -231,35 +231,35 @@ def show_settings(): # Cached values -GN_VERSION = get_setting('GN_VERSION') -HOME = get_setting('HOME') -SERVER_PORT = get_setting('SERVER_PORT') -WEBSERVER_MODE = get_setting('WEBSERVER_MODE') -GN2_BASE_URL = get_setting('GN2_BASE_URL') -GN2_BRANCH_URL = get_setting('GN2_BRANCH_URL') -GN_SERVER_URL = get_setting('GN_SERVER_URL') -SERVER_PORT = get_setting_int('SERVER_PORT') -SQL_URI = get_setting('SQL_URI') -LOG_LEVEL = get_setting('LOG_LEVEL') -LOG_LEVEL_DEBUG = get_setting_int('LOG_LEVEL_DEBUG') -LOG_SQL = get_setting_bool('LOG_SQL') -LOG_SQL_ALCHEMY = get_setting_bool('LOG_SQL_ALCHEMY') -LOG_BENCH = get_setting_bool('LOG_BENCH') -LOG_FORMAT = "%(message)s" # not yet in use -USE_REDIS = get_setting_bool('USE_REDIS') -USE_GN_SERVER = get_setting_bool('USE_GN_SERVER') - -GENENETWORK_FILES = get_setting('GENENETWORK_FILES') -JS_GUIX_PATH = get_setting('JS_GUIX_PATH') +GN_VERSION = get_setting('GN_VERSION') +HOME = get_setting('HOME') +SERVER_PORT = get_setting('SERVER_PORT') +WEBSERVER_MODE = get_setting('WEBSERVER_MODE') +GN2_BASE_URL = get_setting('GN2_BASE_URL') +GN2_BRANCH_URL = get_setting('GN2_BRANCH_URL') +GN_SERVER_URL = get_setting('GN_SERVER_URL') +SERVER_PORT = get_setting_int('SERVER_PORT') +SQL_URI = get_setting('SQL_URI') +LOG_LEVEL = get_setting('LOG_LEVEL') +LOG_LEVEL_DEBUG = get_setting_int('LOG_LEVEL_DEBUG') +LOG_SQL = get_setting_bool('LOG_SQL') +LOG_SQL_ALCHEMY = get_setting_bool('LOG_SQL_ALCHEMY') +LOG_BENCH = get_setting_bool('LOG_BENCH') +LOG_FORMAT = "%(message)s" # not yet in use +USE_REDIS = get_setting_bool('USE_REDIS') +USE_GN_SERVER = get_setting_bool('USE_GN_SERVER') + +GENENETWORK_FILES = get_setting('GENENETWORK_FILES') +JS_GUIX_PATH = get_setting('JS_GUIX_PATH') assert_dir(JS_GUIX_PATH) -JS_GN_PATH = get_setting('JS_GN_PATH') +JS_GN_PATH = get_setting('JS_GN_PATH') # assert_dir(JS_GN_PATH) GITHUB_CLIENT_ID = get_setting('GITHUB_CLIENT_ID') GITHUB_CLIENT_SECRET = get_setting('GITHUB_CLIENT_SECRET') if GITHUB_CLIENT_ID != 'UNKNOWN' and GITHUB_CLIENT_SECRET: GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize?client_id=" + \ - GITHUB_CLIENT_ID+"&client_secret="+GITHUB_CLIENT_SECRET + GITHUB_CLIENT_ID + "&client_secret=" + GITHUB_CLIENT_SECRET GITHUB_API_URL = get_setting('GITHUB_API_URL') ORCID_CLIENT_ID = get_setting('ORCID_CLIENT_ID') @@ -267,7 +267,7 @@ ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET') ORCID_AUTH_URL = None if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET: ORCID_AUTH_URL = "https://orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \ - ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2" + ORCID_CLIENT_ID + "&client_secret=" + ORCID_CLIENT_SECRET + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2" ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL') ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST') @@ -279,28 +279,28 @@ SMTP_CONNECT = get_setting('SMTP_CONNECT') SMTP_USERNAME = get_setting('SMTP_USERNAME') SMTP_PASSWORD = get_setting('SMTP_PASSWORD') -REAPER_COMMAND = app_set("REAPER_COMMAND", reaper_command()) -GEMMA_COMMAND = app_set("GEMMA_COMMAND", gemma_command()) +REAPER_COMMAND = app_set("REAPER_COMMAND", reaper_command()) +GEMMA_COMMAND = app_set("GEMMA_COMMAND", gemma_command()) assert(GEMMA_COMMAND is not None) -PLINK_COMMAND = app_set("PLINK_COMMAND", plink_command()) +PLINK_COMMAND = app_set("PLINK_COMMAND", plink_command()) GEMMA_WRAPPER_COMMAND = gemma_wrapper_command() -TEMPDIR = tempdir() # defaults to UNIX TMPDIR +TEMPDIR = tempdir() # defaults to UNIX TMPDIR assert_dir(TEMPDIR) # ---- Handle specific JS modules JS_GUIX_PATH = get_setting("JS_GUIX_PATH") assert_dir(JS_GUIX_PATH) -assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom') +assert_dir(JS_GUIX_PATH + '/cytoscape-panzoom') CSS_PATH = JS_GUIX_PATH # The CSS is bundled together with the JS # assert_dir(JS_PATH) JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH", js_path("javascript-twitter-post-fetcher")) assert_dir(JS_TWITTER_POST_FETCHER_PATH) -assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") +assert_file(JS_TWITTER_POST_FETCHER_PATH + "/js/twitterFetcher_min.js") JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH", js_path("cytoscape")) assert_dir(JS_CYTOSCAPE_PATH) -assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js') +assert_file(JS_CYTOSCAPE_PATH + '/cytoscape.min.js') # assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py index 6b029317..662bf794 100644 --- a/wqflask/utility/type_checking.py +++ b/wqflask/utility/type_checking.py @@ -23,19 +23,19 @@ def is_str(value): except: return False -def get_float(vars_obj,name,default=None): +def get_float(vars_obj, name, default=None): if name in vars_obj: if is_float(vars_obj[name]): return float(vars_obj[name]) return default -def get_int(vars_obj,name,default=None): +def get_int(vars_obj, name, default=None): if name in vars_obj: if is_int(vars_obj[name]): return float(vars_obj[name]) return default -def get_string(vars_obj,name,default=None): +def get_string(vars_obj, name, default=None): if name in vars_obj: if not vars_obj[name] is None: return str(vars_obj[name]) diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index 5681fadf..ed59b0eb 100644 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -33,38 +33,38 @@ from math import * from base import webqtlConfig # NL, 07/27/2010. moved from webqtlForm.py -#Dict of Parents and F1 information, In the order of [F1, Mat, Pat] -ParInfo ={ -'BXH':['BHF1', 'HBF1', 'C57BL/6J', 'C3H/HeJ'], -'AKXD':['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'], -'BXD':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], -'C57BL-6JxC57BL-6NJF2':['', '', 'C57BL/6J', 'C57BL/6NJ'], -'BXD300':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], -'B6BTBRF2':['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'], -'BHHBF2':['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'], -'BHF2':['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'], -'B6D2F2':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], -'BDF2-1999':['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'], -'BDF2-2005':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], -'CTB6F2':['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'], -'CXB':['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'], -'AXBXA':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'], -'AXB':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'], -'BXA':['BAF1', 'ABF1', 'C57BL/6J', 'A/J'], -'LXS':['LSF1', 'SLF1', 'ISS', 'ILS'], -'HXBBXH':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'], -'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'], -'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'], -'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'], -'SXM':['SMF1', 'MSF1', 'Steptoe', 'Morex'], -'HRDP':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'] +# Dict of Parents and F1 information, In the order of [F1, Mat, Pat] +ParInfo = { +'BXH': ['BHF1', 'HBF1', 'C57BL/6J', 'C3H/HeJ'], +'AKXD': ['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'], +'BXD': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], +'C57BL-6JxC57BL-6NJF2': ['', '', 'C57BL/6J', 'C57BL/6NJ'], +'BXD300': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], +'B6BTBRF2': ['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'], +'BHHBF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'], +'BHF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'], +'B6D2F2': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], +'BDF2-1999': ['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'], +'BDF2-2005': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], +'CTB6F2': ['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'], +'CXB': ['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'], +'AXBXA': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'], +'AXB': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'], +'BXA': ['BAF1', 'ABF1', 'C57BL/6J', 'A/J'], +'LXS': ['LSF1', 'SLF1', 'ISS', 'ILS'], +'HXBBXH': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'], +'BayXSha': ['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'], +'ColXBur': ['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'], +'ColXCvi': ['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'], +'SXM': ['SMF1', 'MSF1', 'Steptoe', 'Morex'], +'HRDP': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'] } ######################################### # Accessory Functions ######################################### -def genRandStr(prefix = "", length=8, chars=string.ascii_letters+string.digits): +def genRandStr(prefix="", length=8, chars=string.ascii_letters + string.digits): from random import choice _str = prefix[:] for i in range(length): @@ -83,12 +83,12 @@ def ListNotNull(lst): return 1 return None -def readLineCSV(line): ### dcrowell July 2008 +def readLineCSV(line): # dcrowell July 2008 """Parses a CSV string of text and returns a list containing each element as a string. Used by correlationPage""" returnList = line.split('","') - returnList[-1]=returnList[-1][:-2] - returnList[0]=returnList[0][1:] + returnList[-1] = returnList[-1][:-2] + returnList[0] = returnList[0][1:] return returnList def cmpEigenValue(A, B): @@ -107,7 +107,7 @@ def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users) if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']: access_to_confidential_phenotype_trait = 1 else: - AuthorizedUsersList=[x.strip() for x in authorized_users.split(',')] + AuthorizedUsersList = [x.strip() for x in authorized_users.split(',')] if userName in AuthorizedUsersList: access_to_confidential_phenotype_trait = 1 return access_to_confidential_phenotype_trait diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index 0564cfa7..bab87115 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -7,11 +7,11 @@ from flask import g from flask import Flask from utility import formatting from wqflask.markdown_routes import glossary_blueprint -from wqflask.markdown_routes import references_blueprint -from wqflask.markdown_routes import links_blueprint +from wqflask.markdown_routes import references_blueprint +from wqflask.markdown_routes import links_blueprint from wqflask.markdown_routes import policies_blueprint -from wqflask.markdown_routes import environments_blueprint -from wqflask.markdown_routes import facilities_blueprint +from wqflask.markdown_routes import environments_blueprint +from wqflask.markdown_routes import facilities_blueprint app = Flask(__name__) diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py index f5b50dcd..e0b7fea0 100644 --- a/wqflask/wqflask/api/correlation.py +++ b/wqflask/wqflask/api/correlation.py @@ -16,16 +16,16 @@ from utility import webqtlUtil, helper_functions, corr_result_helpers from utility.benchmark import Bench import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) def do_correlation(start_vars): assert('db' in start_vars) assert('target_db' in start_vars) assert('trait_id' in start_vars) - this_dataset = data_set.create_dataset(dataset_name = start_vars['db']) - target_dataset = data_set.create_dataset(dataset_name = start_vars['target_db']) - this_trait = create_trait(dataset = this_dataset, name = start_vars['trait_id']) + this_dataset = data_set.create_dataset(dataset_name=start_vars['db']) + target_dataset = data_set.create_dataset(dataset_name=start_vars['target_db']) + this_trait = create_trait(dataset=this_dataset, name=start_vars['trait_id']) this_trait = retrieve_sample_data(this_trait, this_dataset) corr_params = init_corr_params(start_vars) @@ -38,26 +38,26 @@ def do_correlation(start_vars): if corr_params['type'] == "tissue": [sample_r, num_overlap, sample_p, symbol] = corr_results[trait] result_dict = { - "trait" : trait, - "sample_r" : sample_r, - "#_strains" : num_overlap, - "p_value" : sample_p, - "symbol" : symbol + "trait": trait, + "sample_r": sample_r, + "#_strains": num_overlap, + "p_value": sample_p, + "symbol": symbol } elif corr_params['type'] == "literature" or corr_params['type'] == "lit": [gene_id, sample_r] = corr_results[trait] result_dict = { - "trait" : trait, - "sample_r" : sample_r, - "gene_id" : gene_id + "trait": trait, + "sample_r": sample_r, + "gene_id": gene_id } else: [sample_r, sample_p, num_overlap] = corr_results[trait] result_dict = { - "trait" : trait, - "sample_r" : sample_r, - "#_strains" : num_overlap, - "p_value" : sample_p + "trait": trait, + "sample_r": sample_r, + "#_strains": num_overlap, + "p_value": sample_p } final_results.append(result_dict) @@ -76,7 +76,7 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params): corr_results = do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params) sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][1]))) - elif corr_params['type'] == "literature" or corr_params['type'] == "lit": #ZS: Just so a user can use either "lit" or "literature" + elif corr_params['type'] == "literature" or corr_params['type'] == "lit": # ZS: Just so a user can use either "lit" or "literature" trait_geneid_dict = this_dataset.retrieve_genes("GeneId") corr_results = do_literature_correlation_for_all_traits(this_trait, this_dataset, trait_geneid_dict, corr_params) sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), @@ -92,8 +92,8 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params): return sorted_results def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params, tissue_dataset_id=1): - #Gets tissue expression values for the primary trait - primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list = [this_trait.symbol]) + # Gets tissue expression values for the primary trait + primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=[this_trait.symbol]) if this_trait.symbol.lower() in primary_trait_tissue_vals_dict: primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower()] @@ -227,9 +227,9 @@ def init_corr_params(start_vars): return_count = int(start_vars['return_count']) corr_params = { - 'method' : method, - 'type' : type, - 'return_count' : return_count + 'method': method, + 'type': type, + 'return_count': return_count } return corr_params diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py index eaddecd7..a64524dd 100644 --- a/wqflask/wqflask/api/gen_menu.py +++ b/wqflask/wqflask/api/gen_menu.py @@ -87,14 +87,14 @@ def phenotypes_exist(group_name): results = g.db.execute( ("SELECT Name FROM PublishFreeze " "WHERE PublishFreeze.Name = " - "'{}'").format(group_name+"Publish")).fetchone() + "'{}'").format(group_name + "Publish")).fetchone() return bool(results) def genotypes_exist(group_name): results = g.db.execute( ("SELECT Name FROM GenoFreeze " + - "WHERE GenoFreeze.Name = '{}'").format(group_name+"Geno")).fetchone() + "WHERE GenoFreeze.Name = '{}'").format(group_name + "Geno")).fetchone() return bool(results) diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py index d59a69df..fbfbc879 100644 --- a/wqflask/wqflask/api/mapping.py +++ b/wqflask/wqflask/api/mapping.py @@ -8,15 +8,15 @@ from utility import helper_functions from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) def do_mapping_for_api(start_vars): assert('db' in start_vars) assert('trait_id' in start_vars) - dataset = data_set.create_dataset(dataset_name = start_vars['db']) + dataset = data_set.create_dataset(dataset_name=start_vars['db']) dataset.group.get_markers() - this_trait = create_trait(dataset = dataset, name = start_vars['trait_id']) + this_trait = create_trait(dataset=dataset, name=start_vars['trait_id']) this_trait = retrieve_sample_data(this_trait, dataset) samples = [] @@ -36,11 +36,11 @@ def do_mapping_for_api(start_vars): mapping_params = initialize_parameters(start_vars, dataset, this_trait) - covariates = "" #ZS: It seems to take an empty string as default. This should probably be changed. + covariates = "" # ZS: It seems to take an empty string as default. This should probably be changed. if mapping_params['mapping_method'] == "gemma": header_row = ["name", "chr", "Mb", "lod_score", "p_value"] - if mapping_params['use_loco'] == "True": #ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api + if mapping_params['use_loco'] == "True": # ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0] else: result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf']) @@ -118,7 +118,7 @@ def initialize_parameters(start_vars, dataset, this_trait): mapping_params['maf'] = 0.01 if 'maf' in start_vars: - mapping_params['maf'] = start_vars['maf'] # Minor allele frequency + mapping_params['maf'] = start_vars['maf'] # Minor allele frequency mapping_params['use_loco'] = True if 'use_loco' in start_vars: diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 60e163f2..b0559a07 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -23,13 +23,13 @@ from wqflask.api import correlation, mapping, gen_menu from utility.tools import flat_files import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) version = "pre1" @app.route("/api/v_{}/".format(version)) def hello_world(): - return flask.jsonify({"hello":"world"}) + return flask.jsonify({"hello": "world"}) @app.route("/api/v_{}/species".format(version)) def get_species_list(): @@ -38,10 +38,10 @@ def get_species_list(): species_list = [] for species in the_species: species_dict = { - "Id" : species[0], - "Name" : species[1], - "FullName" : species[2], - "TaxonomyId" : species[3] + "Id": species[0], + "Name": species[1], + "FullName": species[2], + "TaxonomyId": species[3] } species_list.append(species_dict) @@ -49,17 +49,17 @@ def get_species_list(): @app.route("/api/v_{}/species/".format(version)) @app.route("/api/v_{}/species/.".format(version)) -def get_species_info(species_name, file_format = "json"): +def get_species_info(species_name, file_format="json"): results = g.db.execute("""SELECT SpeciesId, Name, FullName, TaxonomyId FROM Species WHERE (Name="{0}" OR FullName="{0}" OR SpeciesName="{0}");""".format(species_name)) the_species = results.fetchone() species_dict = { - "Id" : the_species[0], - "Name" : the_species[1], - "FullName" : the_species[2], - "TaxonomyId" : the_species[3] + "Id": the_species[0], + "Name": the_species[1], + "FullName": the_species[2], + "TaxonomyId": the_species[3] } return flask.jsonify(species_dict) @@ -87,14 +87,14 @@ def get_groups_list(species_name=None): groups_list = [] for group in the_groups: group_dict = { - "Id" : group[0], - "SpeciesId" : group[1], - "DisplayName" : group[2], - "Name" : group[3], - "FullName" : group[4], - "public" : group[5], - "MappingMethodId" : group[6], - "GeneticType" : group[7] + "Id": group[0], + "SpeciesId": group[1], + "DisplayName": group[2], + "Name": group[3], + "FullName": group[4], + "public": group[5], + "MappingMethodId": group[6], + "GeneticType": group[7] } groups_list.append(group_dict) @@ -106,7 +106,7 @@ def get_groups_list(species_name=None): @app.route("/api/v_{}/group/.".format(version)) @app.route("/api/v_{}/group//".format(version)) @app.route("/api/v_{}/group//.".format(version)) -def get_group_info(group_name, species_name = None, file_format = "json"): +def get_group_info(group_name, species_name=None, file_format="json"): if species_name: results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName, InbredSet.Name, InbredSet.FullName, InbredSet.public, @@ -131,14 +131,14 @@ def get_group_info(group_name, species_name = None, file_format = "json"): group = results.fetchone() if group: group_dict = { - "Id" : group[0], - "SpeciesId" : group[1], - "DisplayName" : group[2], - "Name" : group[3], - "FullName" : group[4], - "public" : group[5], - "MappingMethodId" : group[6], - "GeneticType" : group[7] + "Id": group[0], + "SpeciesId": group[1], + "DisplayName": group[2], + "Name": group[3], + "FullName": group[4], + "public": group[5], + "MappingMethodId": group[6], + "GeneticType": group[7] } return flask.jsonify(group_dict) @@ -179,17 +179,17 @@ def get_datasets_for_group(group_name, species_name=None): datasets_list = [] for dataset in the_datasets: dataset_dict = { - "Id" : dataset[0], - "ProbeFreezeId" : dataset[1], - "AvgID" : dataset[2], - "Short_Abbreviation" : dataset[3], - "Long_Abbreviation" : dataset[4], - "FullName" : dataset[5], - "ShortName" : dataset[6], - "CreateTime" : dataset[7], - "public" : dataset[8], - "confidentiality" : dataset[9], - "DataScale" : dataset[10] + "Id": dataset[0], + "ProbeFreezeId": dataset[1], + "AvgID": dataset[2], + "Short_Abbreviation": dataset[3], + "Long_Abbreviation": dataset[4], + "FullName": dataset[5], + "ShortName": dataset[6], + "CreateTime": dataset[7], + "public": dataset[8], + "confidentiality": dataset[9], + "DataScale": dataset[10] } datasets_list.append(dataset_dict) @@ -201,10 +201,10 @@ def get_datasets_for_group(group_name, species_name=None): @app.route("/api/v_{}/dataset/.".format(version)) @app.route("/api/v_{}/dataset//".format(version)) @app.route("/api/v_{}/dataset//.".format(version)) -def get_dataset_info(dataset_name, group_name = None, file_format="json"): - #ZS: First get ProbeSet (mRNA expression) datasets and then get Phenotype datasets +def get_dataset_info(dataset_name, group_name=None, file_format="json"): + # ZS: First get ProbeSet (mRNA expression) datasets and then get Phenotype datasets - datasets_list = [] #ZS: I figure I might as well return a list if there are multiple matches, though I don"t know if this will actually happen in practice + datasets_list = [] # ZS: I figure I might as well return a list if there are multiple matches, though I don"t know if this will actually happen in practice probeset_query = """ SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, @@ -235,16 +235,16 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): if dataset: dataset_dict = { - "dataset_type" : "mRNA expression", - "id" : dataset[0], - "name" : dataset[1], - "full_name" : dataset[2], - "short_name" : dataset[3], - "data_scale" : dataset[4], - "tissue_id" : dataset[5], - "tissue" : dataset[6], - "public" : dataset[7], - "confidential" : dataset[8] + "dataset_type": "mRNA expression", + "id": dataset[0], + "name": dataset[1], + "full_name": dataset[2], + "short_name": dataset[3], + "data_scale": dataset[4], + "tissue_id": dataset[5], + "tissue": dataset[6], + "public": dataset[7], + "confidential": dataset[8] } datasets_list.append(dataset_dict) @@ -272,25 +272,25 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): if dataset: if dataset[5]: dataset_dict = { - "dataset_type" : "phenotype", - "id" : dataset[0], - "name" : dataset[1], - "description" : dataset[2], - "pubmed_id" : dataset[5], - "title" : dataset[6], - "year" : dataset[7] + "dataset_type": "phenotype", + "id": dataset[0], + "name": dataset[1], + "description": dataset[2], + "pubmed_id": dataset[5], + "title": dataset[6], + "year": dataset[7] } elif dataset[4]: dataset_dict = { - "dataset_type" : "phenotype", - "id" : dataset[0], - "name" : dataset[3], - "description" : dataset[4] + "dataset_type": "phenotype", + "id": dataset[0], + "name": dataset[3], + "description": dataset[4] } else: dataset_dict = { - "dataset_type" : "phenotype", - "id" : dataset[0] + "dataset_type": "phenotype", + "id": dataset[0] } datasets_list.append(dataset_dict) @@ -304,7 +304,7 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): @app.route("/api/v_{}/traits/".format(version), methods=("GET",)) @app.route("/api/v_{}/traits/.".format(version), methods=("GET",)) -def fetch_traits(dataset_name, file_format = "json"): +def fetch_traits(dataset_name, file_format="json"): trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name, request.args) if ("ids_only" in request.args) and (len(trait_ids) > 0): if file_format == "json": @@ -432,7 +432,7 @@ def fetch_traits(dataset_name, file_format = "json"): @app.route("/api/v_{}/sample_data/".format(version)) @app.route("/api/v_{}/sample_data/.".format(version)) -def all_sample_data(dataset_name, file_format = "csv"): +def all_sample_data(dataset_name, file_format="csv"): trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name, request.args) if len(trait_ids) > 0: @@ -538,7 +538,7 @@ def all_sample_data(dataset_name, file_format = "csv"): @app.route("/api/v_{}/sample_data//".format(version)) @app.route("/api/v_{}/sample_data//.".format(version)) -def trait_sample_data(dataset_name, trait_name, file_format = "json"): +def trait_sample_data(dataset_name, trait_name, file_format="json"): probeset_query = """ SELECT Strain.Name, Strain.Name2, ProbeSetData.value, ProbeSetData.Id, ProbeSetSE.error @@ -610,10 +610,10 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): sample_list = [] for sample in sample_data: sample_dict = { - "sample_name" : sample[0], - "sample_name_2" : sample[1], - "value" : sample[2], - "data_id" : sample[3] + "sample_name": sample[0], + "sample_name_2": sample[1], + "value": sample[2], + "data_id": sample[3] } if sample[4]: sample_dict["se"] = sample[4] @@ -629,7 +629,7 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): @app.route("/api/v_{}/trait//.".format(version)) @app.route("/api/v_{}/trait_info//".format(version)) @app.route("/api/v_{}/trait_info//.".format(version)) -def get_trait_info(dataset_name, trait_name, file_format = "json"): +def get_trait_info(dataset_name, trait_name, file_format="json"): probeset_query = """ SELECT ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSet.alias, @@ -648,24 +648,24 @@ def get_trait_info(dataset_name, trait_name, file_format = "json"): trait_info = probeset_results.fetchone() if trait_info: trait_dict = { - "id" : trait_info[0], - "name" : trait_info[1], - "symbol" : trait_info[2], - "description" : trait_info[3], - "chr" : trait_info[4], - "mb" : trait_info[5], - "alias" :trait_info[6], - "mean" : trait_info[7], - "se" : trait_info[8], - "locus" : trait_info[9], - "lrs" : trait_info[10], - "p_value" : trait_info[11], - "additive" : trait_info[12] + "id": trait_info[0], + "name": trait_info[1], + "symbol": trait_info[2], + "description": trait_info[3], + "chr": trait_info[4], + "mb": trait_info[5], + "alias": trait_info[6], + "mean": trait_info[7], + "se": trait_info[8], + "locus": trait_info[9], + "lrs": trait_info[10], + "p_value": trait_info[11], + "additive": trait_info[12] } return flask.jsonify(trait_dict) else: - if "Publish" in dataset_name: #ZS: Check if the user input the dataset_name as BXDPublish, etc (which is always going to be the group name + "Publish" + if "Publish" in dataset_name: # ZS: Check if the user input the dataset_name as BXDPublish, etc (which is always going to be the group name + "Publish" dataset_name = dataset_name.replace("Publish", "") group_id = get_group_id(dataset_name) @@ -684,10 +684,10 @@ def get_trait_info(dataset_name, trait_name, file_format = "json"): trait_info = pheno_results.fetchone() if trait_info: trait_dict = { - "id" : trait_info[0], - "locus" : trait_info[1], - "lrs" : trait_info[2], - "additive" : trait_info[3] + "id": trait_info[0], + "locus": trait_info[1], + "lrs": trait_info[2], + "additive": trait_info[3] } return flask.jsonify(trait_dict) @@ -699,7 +699,7 @@ def get_corr_results(): results = correlation.do_correlation(request.args) if len(results) > 0: - return flask.jsonify(results) #ZS: I think flask.jsonify expects a dict/list instead of JSON + return flask.jsonify(results) # ZS: I think flask.jsonify expects a dict/list instead of JSON else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") @@ -754,7 +754,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): output_lines.append(line.split()) i += 1 - csv_writer = csv.writer(si, delimiter = "\t", escapechar = "\\", quoting = csv.QUOTE_NONE) + csv_writer = csv.writer(si, delimiter="\t", escapechar="\\", quoting = csv.QUOTE_NONE) else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") elif file_format == "rqtl2": @@ -802,7 +802,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): output_lines.append([line.strip() for line in line.split(",")]) i += 1 - csv_writer = csv.writer(si, delimiter = ",") + csv_writer = csv.writer(si, delimiter=",") else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") @@ -826,8 +826,8 @@ def return_error(code, source, title, details): json_ob = {"errors": [ { "status": code, - "source": { "pointer": source }, - "title" : title, + "source": {"pointer": source}, + "title": title, "detail": details } ]} @@ -842,8 +842,8 @@ def get_dataset_trait_ids(dataset_name, start_vars): limit_string = "" if "Geno" in dataset_name: - data_type = "Geno" #ZS: Need to pass back the dataset type - query = """ + data_type = "Geno" # ZS: Need to pass back the dataset type + query = """ SELECT GenoXRef.GenoId, Geno.Name, GenoXRef.GenoFreezeId FROM diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 0291f2b8..6a1b88ca 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -68,18 +68,18 @@ def collections_add(): uc_id = g.user_session.add_collection(collection_name, set()) collections = g.user_session.user_collections - #ZS: One of these might be unnecessary + # ZS: One of these might be unnecessary if 'traits' in request.args: - traits=request.args['traits'] + traits = request.args['traits'] return render_template("collections/add.html", - traits = traits, - collections = collections, + traits=traits, + collections=collections, ) else: hash = request.args['hash'] return render_template("collections/add.html", - hash = hash, - collections = collections, + hash=hash, + collections=collections, ) @app.route("/collections/new") @@ -139,8 +139,8 @@ def list_collections(): user_collections = list(g.user_session.user_collections) return render_template("collections/list.html", - params = params, - collections = user_collections, + params=params, + collections=user_collections, ) @app.route("/collections/remove", methods=('POST',)) @@ -196,7 +196,7 @@ def view_collection(): name, dataset_name = atrait.split(':') if dataset_name == "Temp": group = name.split("_")[2] - dataset = create_dataset(dataset_name, dataset_type = "Temp", group_name = group) + dataset = create_dataset(dataset_name, dataset_type="Temp", group_name=group) trait_ob = create_trait(name=name, dataset=dataset) else: dataset = create_dataset(dataset_name) @@ -207,7 +207,7 @@ def view_collection(): json_version.append(jsonable(trait_ob)) collection_info = dict(trait_obs=trait_obs, - uc = uc) + uc=uc) if "json" in params: return json.dumps(json_version) diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py index 5855ccf0..c135faa3 100644 --- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py +++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py @@ -1,4 +1,4 @@ -## Copyright (C) University of Tennessee Health Science Center, Memphis, TN. +# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. # # This program is free software: you can redistribute it and/or modify it # under the terms of the GNU Affero General Public License @@ -23,7 +23,7 @@ from pprint import pformat as pf from base.trait import create_trait from base import data_set from utility import webqtlUtil, helper_functions, corr_result_helpers -import utility.webqtlUtil #this is for parallel computing only. +import utility.webqtlUtil # this is for parallel computing only. from wqflask.correlation import correlation_functions from MySQLdb import escape_string as escape @@ -41,7 +41,7 @@ class ComparisonBarChart: self.all_sample_list = [] self.traits = [] self.insufficient_shared_samples = False - this_group = self.trait_list[0][1].group.name #ZS: Getting initial group name before verifying all traits are in the same group in the following loop + this_group = self.trait_list[0][1].group.name # ZS: Getting initial group name before verifying all traits are in the same group in the following loop for trait_db in self.trait_list: if trait_db[1].group.name != this_group: @@ -74,9 +74,9 @@ class ComparisonBarChart: this_trait_vals.append('') self.sample_data.append(this_trait_vals) - self.js_data = dict(traits = [trait.name for trait in self.traits], - samples = self.all_sample_list, - sample_data = self.sample_data,) + self.js_data = dict(traits=[trait.name for trait in self.traits], + samples=self.all_sample_list, + sample_data=self.sample_data,) def get_trait_db_obs(self, trait_db_list): diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index d5dc26f5..22941ad5 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -9,18 +9,18 @@ from scipy import stats import numpy as np import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) class CorrScatterPlot: """Page that displays a correlation scatterplot with a line fitted to it""" def __init__(self, params): if "Temp" in params['dataset_1']: - self.dataset_1 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_1'].split("_")[1]) + self.dataset_1 = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_1'].split("_")[1]) else: self.dataset_1 = data_set.create_dataset(params['dataset_1']) if "Temp" in params['dataset_2']: - self.dataset_2 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_2'].split("_")[1]) + self.dataset_2 = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_2'].split("_")[1]) else: self.dataset_2 = data_set.create_dataset(params['dataset_2']) @@ -60,8 +60,8 @@ class CorrScatterPlot: else: slope_string = '%.3f' % slope - x_buffer = (max(vals_1) - min(vals_1))*0.1 - y_buffer = (max(vals_2) - min(vals_2))*0.1 + x_buffer = (max(vals_1) - min(vals_1)) * 0.1 + y_buffer = (max(vals_2) - min(vals_2)) * 0.1 x_range = [min(vals_1) - x_buffer, max(vals_1) + x_buffer] y_range = [min(vals_2) - y_buffer, max(vals_2) + y_buffer] @@ -80,8 +80,8 @@ class CorrScatterPlot: else: srslope_string = '%.3f' % srslope - x_buffer = (max(rx) - min(rx))*0.1 - y_buffer = (max(ry) - min(ry))*0.1 + x_buffer = (max(rx) - min(rx)) * 0.1 + y_buffer = (max(ry) - min(ry)) * 0.1 sr_range = [min(rx) - x_buffer, max(rx) + x_buffer] @@ -92,33 +92,33 @@ class CorrScatterPlot: self.collections_exist = "True" self.js_data = dict( - data = self.data, - rdata = self.rdata, - indIDs = self.indIDs, - trait_1 = self.trait_1.dataset.name + ": " + str(self.trait_1.name), - trait_2 = self.trait_2.dataset.name + ": " + str(self.trait_2.name), - samples_1 = samples_1, - samples_2 = samples_2, - num_overlap = num_overlap, - vals_1 = vals_1, - vals_2 = vals_2, - x_range = x_range, - y_range = y_range, - sr_range = sr_range, - intercept_coords = intercept_coords, - sr_intercept_coords = sr_intercept_coords, - - slope = slope, - slope_string = slope_string, - intercept = intercept, - r_value = r_value, - p_value = p_value, - - srslope = srslope, - srslope_string = srslope_string, - srintercept = srintercept, - srr_value = srr_value, - srp_value = srp_value + data=self.data, + rdata=self.rdata, + indIDs=self.indIDs, + trait_1=self.trait_1.dataset.name + ": " + str(self.trait_1.name), + trait_2=self.trait_2.dataset.name + ": " + str(self.trait_2.name), + samples_1=samples_1, + samples_2=samples_2, + num_overlap=num_overlap, + vals_1=vals_1, + vals_2=vals_2, + x_range=x_range, + y_range=y_range, + sr_range=sr_range, + intercept_coords=intercept_coords, + sr_intercept_coords=sr_intercept_coords, + + slope=slope, + slope_string=slope_string, + intercept=intercept, + r_value=r_value, + p_value=p_value, + + srslope=srslope, + srslope_string=srslope_string, + srintercept=srintercept, + srr_value=srr_value, + srp_value=srp_value #trait3 = self.trait_3.data, #vals_3 = vals_3 @@ -129,10 +129,10 @@ class CorrScatterPlot: def get_intercept_coords(slope, intercept, x_range, y_range): intercept_coords = [] - y1 = slope*x_range[0] + intercept - y2 = slope*x_range[1] + intercept - x1 = (y1-intercept)/slope - x2 = (y2-intercept)/slope + y1 = slope * x_range[0] + intercept + y2 = slope * x_range[1] + intercept + x1 = (y1 - intercept) / slope + x2 = (y2 - intercept) / slope intercept_coords.append([x1, y1]) intercept_coords.append([x2, y2]) diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py index fd7691d4..0f24241a 100644 --- a/wqflask/wqflask/correlation/correlation_functions.py +++ b/wqflask/wqflask/correlation/correlation_functions.py @@ -34,19 +34,19 @@ from flask import Flask, g ##################################################################################### -#Input: primaryValue(list): one list of expression values of one probeSet, +# Input: primaryValue(list): one list of expression values of one probeSet, # targetValue(list): one list of expression values of one probeSet, # method(string): indicate correlation method ('pearson' or 'spearman') -#Output: corr_result(list): first item is Correlation Value, second item is tissue number, +# Output: corr_result(list): first item is Correlation Value, second item is tissue number, # third item is PValue -#Function: get correlation value,Tissue quantity ,p value result by using R; -#Note : This function is special case since both primaryValue and targetValue are from -#the same dataset. So the length of these two parameters is the same. They are pairs. -#Also, in the datatable TissueProbeSetData, all Tissue values are loaded based on -#the same tissue order +# Function: get correlation value,Tissue quantity ,p value result by using R; +# Note : This function is special case since both primaryValue and targetValue are from +# the same dataset. So the length of these two parameters is the same. They are pairs. +# Also, in the datatable TissueProbeSetData, all Tissue values are loaded based on +# the same tissue order ##################################################################################### -def cal_zero_order_corr_for_tiss (primaryValue=[], targetValue=[], method='pearson'): +def cal_zero_order_corr_for_tiss(primaryValue=[], targetValue=[], method='pearson'): R_primary = rpy2.robjects.FloatVector(list(range(len(primaryValue)))) N = len(primaryValue) @@ -55,27 +55,27 @@ def cal_zero_order_corr_for_tiss (primaryValue=[], targetValue=[], method='pears R_target = rpy2.robjects.FloatVector(list(range(len(targetValue)))) for i in range(len(targetValue)): - R_target[i]=targetValue[i] + R_target[i] = targetValue[i] R_corr_test = rpy2.robjects.r['cor.test'] - if method =='spearman': + if method == 'spearman': R_result = R_corr_test(R_primary, R_target, method='spearman') else: R_result = R_corr_test(R_primary, R_target) - corr_result =[] - corr_result.append( R_result[3][0]) - corr_result.append( N ) - corr_result.append( R_result[2][0]) + corr_result = [] + corr_result.append(R_result[3][0]) + corr_result.append(N) + corr_result.append(R_result[2][0]) return corr_result ######################################################################################################## -#input: cursor, symbolList (list), dataIdDict(Dict): key is symbol -#output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair. +# input: cursor, symbolList (list), dataIdDict(Dict): key is symbol +# output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair. # key is symbol, value is one list of expression values of one probeSet. -#function: wrapper function for getSymbolValuePairDict function +# function: wrapper function for getSymbolValuePairDict function # build gene symbol list if necessary, cut it into small lists if necessary, # then call getSymbolValuePairDict function and merge the results. ######################################################################################################## diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index cb341e79..051ac1cb 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -1,4 +1,4 @@ -## Copyright (C) University of Tennessee Health Science Center, Memphis, TN. +# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. # # This program is free software: you can redistribute it and/or modify it # under the terms of the GNU Affero General Public License @@ -78,7 +78,7 @@ class CorrelationResults: with Bench("Doing correlations"): if start_vars['dataset'] == "Temp": - self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group']) + self.dataset = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = start_vars['group']) self.trait_id = start_vars['trait_id'] self.this_trait = create_trait(dataset=self.dataset, name=self.trait_id, @@ -109,8 +109,8 @@ class CorrelationResults: self.get_formatted_corr_type() self.return_number = int(start_vars['corr_return_results']) - #The two if statements below append samples to the sample list based upon whether the user - #rselected Primary Samples Only, Other Samples Only, or All Samples + # The two if statements below append samples to the sample list based upon whether the user + # rselected Primary Samples Only, Other Samples Only, or All Samples primary_samples = self.dataset.group.samplelist if self.dataset.group.parlist != None: @@ -118,13 +118,13 @@ class CorrelationResults: if self.dataset.group.f1list != None: primary_samples += self.dataset.group.f1list - #If either BXD/whatever Only or All Samples, append all of that group's samplelist + # If either BXD/whatever Only or All Samples, append all of that group's samplelist if corr_samples_group != 'samples_other': self.process_samples(start_vars, primary_samples) - #If either Non-BXD/whatever or All Samples, get all samples from this_trait.data and - #exclude the primary samples (because they would have been added in the previous - #if statement if the user selected All Samples) + # If either Non-BXD/whatever or All Samples, get all samples from this_trait.data and + # exclude the primary samples (because they would have been added in the previous + # if statement if the user selected All Samples) if corr_samples_group != 'samples_primary': if corr_samples_group == 'samples_other': primary_samples = [x for x in primary_samples if x not in ( @@ -173,7 +173,7 @@ class CorrelationResults: key=lambda t: -abs(t[1][0]))) - #ZS: Convert min/max chromosome to an int for the location range option + # ZS: Convert min/max chromosome to an int for the location range option range_chr_as_int = None for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()): if 'loc_chr' in start_vars: @@ -259,15 +259,15 @@ class CorrelationResults: def do_tissue_correlation_for_trait_list(self, tissue_dataset_id=1): """Given a list of correlation results (self.correlation_results), gets the tissue correlation value for each""" - #Gets tissue expression values for the primary trait + # Gets tissue expression values for the primary trait primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( - symbol_list = [self.this_trait.symbol]) + symbol_list=[self.this_trait.symbol]) if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict: primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()] gene_symbol_list = [trait.symbol for trait in self.correlation_results if trait.symbol] - corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values( + corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( symbol_list=gene_symbol_list) for trait in self.correlation_results: @@ -282,15 +282,15 @@ class CorrelationResults: trait.tissue_pvalue = result[2] def do_tissue_correlation_for_all_traits(self, tissue_dataset_id=1): - #Gets tissue expression values for the primary trait + # Gets tissue expression values for the primary trait primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( - symbol_list = [self.this_trait.symbol]) + symbol_list=[self.this_trait.symbol]) if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict: primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()] #print("trait_gene_symbols: ", pf(trait_gene_symbols.values())) - corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values( + corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( symbol_list=list(self.trait_symbol_dict.values())) #print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict)) @@ -443,7 +443,7 @@ class CorrelationResults: self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(self.this_trait_vals, target_vals) if num_overlap > 5: - #ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/ + # ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/ if self.corr_method == 'bicor': sample_r, sample_p = do_bicor(self.this_trait_vals, target_vals) elif self.corr_method == 'pearson': @@ -475,16 +475,16 @@ def do_bicor(this_trait_vals, target_trait_vals): r_library("WGCNA") r_bicor = ro.r["bicorAndPvalue"] # Map the bicorAndPvalue function - r_options(stringsAsFactors = False) + r_options(stringsAsFactors=False) this_vals = ro.Vector(this_trait_vals) target_vals = ro.Vector(target_trait_vals) - the_r, the_p, _fisher_transform, _the_t, _n_obs = [numpy.asarray(x) for x in r_bicor(x = this_vals, y = target_vals)] + the_r, the_p, _fisher_transform, _the_t, _n_obs = [numpy.asarray(x) for x in r_bicor(x=this_vals, y=target_vals)] return the_r, the_p -def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api = False): +def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api=False): results_list = [] for i, trait in enumerate(corr_results): if trait.view == False: diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index d0b4a156..94c8931f 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -1,4 +1,4 @@ -## Copyright (C) University of Tennessee Health Science Center, Memphis, TN. +# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. # # This program is free software: you can redistribute it and/or modify it # under the terms of the GNU Affero General Public License @@ -52,7 +52,7 @@ class CorrelationMatrix: self.traits = [] self.insufficient_shared_samples = False self.do_PCA = True - this_group = self.trait_list[0][1].group.name #ZS: Getting initial group name before verifying all traits are in the same group in the following loop + this_group = self.trait_list[0][1].group.name # ZS: Getting initial group name before verifying all traits are in the same group in the following loop for trait_db in self.trait_list: this_group = trait_db[1].group.name this_trait = trait_db[0] @@ -76,10 +76,10 @@ class CorrelationMatrix: this_trait_vals.append('') self.sample_data.append(this_trait_vals) - if len(this_trait_vals) < len(self.trait_list): #Shouldn't do PCA if there are more traits than observations/samples + if len(this_trait_vals) < len(self.trait_list): # Shouldn't do PCA if there are more traits than observations/samples self.do_PCA = False - self.lowest_overlap = 8 #ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning) + self.lowest_overlap = 8 # ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning) self.corr_results = [] self.pca_corr_results = [] @@ -93,7 +93,7 @@ class CorrelationMatrix: corr_result_row = [] pca_corr_result_row = [] - is_spearman = False #ZS: To determine if it's above or below the diagonal + is_spearman = False # ZS: To determine if it's above or below the diagonal for target in self.trait_list: target_trait = target[0] target_db = target[1] @@ -168,12 +168,12 @@ class CorrelationMatrix: except: self.pca_works = "False" - self.js_data = dict(traits = [trait.name for trait in self.traits], - groups = groups, - cols = list(range(len(self.traits))), - rows = list(range(len(self.traits))), - samples = self.all_sample_list, - sample_data = self.sample_data,) + self.js_data = dict(traits=[trait.name for trait in self.traits], + groups=groups, + cols=list(range(len(self.traits))), + rows=list(range(len(self.traits))), + samples=self.all_sample_list, + sample_data=self.sample_data,) def calculate_pca(self, cols, corr_eigen_value, corr_eigen_vectors): base = importr('base') @@ -183,7 +183,7 @@ class CorrelationMatrix: m = robjects.r.matrix(corr_results_to_list, nrow=len(cols)) eigen = base.eigen(m) - pca = stats.princomp(m, cor = "TRUE") + pca = stats.princomp(m, cor="TRUE") self.loadings = pca.rx('loadings') self.scores = pca.rx('scores') self.scale = pca.rx('scale') @@ -193,15 +193,15 @@ class CorrelationMatrix: pca_traits = [] for i, vector in enumerate(trait_array_vectors): - #ZS: Check if below check is necessary - #if corr_eigen_value[i-1] > 100.0/len(self.trait_list): - pca_traits.append((vector*-1.0).tolist()) + # ZS: Check if below check is necessary + # if corr_eigen_value[i-1] > 100.0/len(self.trait_list): + pca_traits.append((vector * -1.0).tolist()) this_group_name = self.trait_list[0][1].group.name - temp_dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = this_group_name) + temp_dataset = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = this_group_name) temp_dataset.group.get_samplelist() for i, pca_trait in enumerate(pca_traits): - trait_id = "PCA" + str(i+1) + "_" + temp_dataset.group.species + "_" + this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S") + trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S") this_vals_string = "" position = 0 for sample in temp_dataset.group.all_samples_ordered(): @@ -228,7 +228,7 @@ class CorrelationMatrix: else: the_range = 2 for j in range(the_range): - position = i + len(self.trait_list)*j + position = i + len(self.trait_list) * j loadings_row.append(self.loadings[0][position]) loadings_array.append(loadings_row) return loadings_array @@ -271,14 +271,14 @@ def zScore(trait_data_array): i = 0 for data in trait_data_array: N = len(data) - S = reduce(lambda x, y: x+y, data, 0.) - SS = reduce(lambda x, y: x+y*y, data, 0.) - mean = S/N - var = SS - S*S/N - stdev = math.sqrt(var/(N-1)) + S = reduce(lambda x, y: x + y, data, 0.) + SS = reduce(lambda x, y: x + y * y, data, 0.) + mean = S / N + var = SS - S * S / N + stdev = math.sqrt(var / (N - 1)) if stdev == 0: stdev = 1e-100 - data2 = [(x-mean)/stdev for x in data] + data2 = [(x - mean) / stdev for x in data] trait_data_array[i] = data2 i += 1 return trait_data_array @@ -298,8 +298,8 @@ def sortEigenVectors(vector): for item in combines: A.append(item[0]) B.append(item[1]) - sum = reduce(lambda x, y: x+y, A, 0.0) - A = [x*100.0/sum for x in A] + sum = reduce(lambda x, y: x + y, A, 0.0) + A = [x * 100.0 / sum for x in A] return [A, B] except: return [] diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 1556e370..2fa90a93 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -25,33 +25,33 @@ from utility.tools import locate, GN2_BRANCH_URL from rpy2.robjects.packages import importr import utility.logger -logger = utility.logger.getLogger(__name__ ) - -## Get pointers to some common R functions -r_library = ro.r["library"] # Map the library function -r_options = ro.r["options"] # Map the options function -r_t = ro.r["t"] # Map the t function -r_unlist = ro.r["unlist"] # Map the unlist function -r_list = ro.r.list # Map the list function -r_png = ro.r["png"] # Map the png function for plotting -r_dev_off = ro.r["dev.off"] # Map the dev.off function -r_write_table = ro.r["write.table"] # Map the write.table function -r_data_frame = ro.r["data.frame"] # Map the write.table function -r_as_numeric = ro.r["as.numeric"] # Map the write.table function +logger = utility.logger.getLogger(__name__) + +# Get pointers to some common R functions +r_library = ro.r["library"] # Map the library function +r_options = ro.r["options"] # Map the options function +r_t = ro.r["t"] # Map the t function +r_unlist = ro.r["unlist"] # Map the unlist function +r_list = ro.r.list # Map the list function +r_png = ro.r["png"] # Map the png function for plotting +r_dev_off = ro.r["dev.off"] # Map the dev.off function +r_write_table = ro.r["write.table"] # Map the write.table function +r_data_frame = ro.r["data.frame"] # Map the write.table function +r_as_numeric = ro.r["as.numeric"] # Map the write.table function class CTL: def __init__(self): logger.info("Initialization of CTL") #log = r_file("/tmp/genenetwork_ctl.log", open = "wt") - #r_sink(log) # Uncomment the r_sink() commands to log output from stdout/stderr to a file + # r_sink(log) # Uncomment the r_sink() commands to log output from stdout/stderr to a file #r_sink(log, type = "message") r_library("ctl") # Load CTL - Should only be done once, since it is quite expensive - r_options(stringsAsFactors = False) + r_options(stringsAsFactors=False) logger.info("Initialization of CTL done, package loaded in R session") - self.r_CTLscan = ro.r["CTLscan"] # Map the CTLscan function - self.r_CTLsignificant = ro.r["CTLsignificant"] # Map the CTLsignificant function - self.r_lineplot = ro.r["ctl.lineplot"] # Map the ctl.lineplot function - self.r_plotCTLobject = ro.r["plot.CTLobject"] # Map the CTLsignificant function + self.r_CTLscan = ro.r["CTLscan"] # Map the CTLscan function + self.r_CTLsignificant = ro.r["CTLsignificant"] # Map the CTLsignificant function + self.r_lineplot = ro.r["ctl.lineplot"] # Map the ctl.lineplot function + self.r_plotCTLobject = ro.r["plot.CTLobject"] # Map the CTLsignificant function self.nodes_list = [] self.edges_list = [] logger.info("Obtained pointers to CTL functions") @@ -59,23 +59,23 @@ class CTL: self.gn2_url = GN2_BRANCH_URL def addNode(self, gt): - node_dict = { 'data' : {'id' : str(gt.name) + ":" + str(gt.dataset.name), - 'sid' : str(gt.name), - 'dataset' : str(gt.dataset.name), - 'label' : gt.name, - 'symbol' : gt.symbol, - 'geneid' : gt.geneid, - 'omim' : gt.omim } } + node_dict = {'data': {'id': str(gt.name) + ":" + str(gt.dataset.name), + 'sid': str(gt.name), + 'dataset': str(gt.dataset.name), + 'label': gt.name, + 'symbol': gt.symbol, + 'geneid': gt.geneid, + 'omim': gt.omim}} self.nodes_list.append(node_dict) def addEdge(self, gtS, gtT, significant, x): - edge_data = {'id' : str(gtS.symbol) + '_' + significant[1][x] + '_' + str(gtT.symbol), - 'source' : str(gtS.name) + ":" + str(gtS.dataset.name), - 'target' : str(gtT.name) + ":" + str(gtT.dataset.name), - 'lod' : significant[3][x], - 'color' : "#ff0000", - 'width' : significant[3][x] } - edge_dict = { 'data' : edge_data } + edge_data = {'id': str(gtS.symbol) + '_' + significant[1][x] + '_' + str(gtT.symbol), + 'source': str(gtS.name) + ":" + str(gtS.dataset.name), + 'target': str(gtT.name) + ":" + str(gtT.dataset.name), + 'lod': significant[3][x], + 'color': "#ff0000", + 'width': significant[3][x]} + edge_dict = {'data': edge_data} self.edges_list.append(edge_dict) def run_analysis(self, requestform): @@ -114,7 +114,7 @@ class CTL: genotypes = list(itertools.chain(*markers)) logger.debug(len(genotypes) / len(individuals), "==", len(parser.markers)) - rGeno = r_t(ro.r.matrix(r_unlist(genotypes), nrow=len(markernames), ncol=len(individuals), dimnames = r_list(markernames, individuals), byrow=True)) + rGeno = r_t(ro.r.matrix(r_unlist(genotypes), nrow=len(markernames), ncol=len(individuals), dimnames=r_list(markernames, individuals), byrow=True)) # Create a phenotype matrix traits = [] @@ -122,7 +122,7 @@ class CTL: logger.debug("retrieving data for", trait) if trait != "": ts = trait.split(':') - gt = create_trait(name = ts[0], dataset_name = ts[1]) + gt = create_trait(name=ts[0], dataset_name=ts[1]) gt = retrieve_sample_data(gt, dataset, individuals) for ind in individuals: if ind in list(gt.data.keys()): @@ -130,23 +130,23 @@ class CTL: else: traits.append("-999") - rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len(individuals), dimnames = r_list(self.trait_db_list, individuals), byrow=True)) + rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len(individuals), dimnames=r_list(self.trait_db_list, individuals), byrow=True)) logger.debug(rPheno) # Use a data frame to store the objects - rPheno = r_data_frame(rPheno, check_names = False) - rGeno = r_data_frame(rGeno, check_names = False) + rPheno = r_data_frame(rPheno, check_names=False) + rGeno = r_data_frame(rGeno, check_names=False) # Debug: Print the genotype and phenotype files to disk #r_write_table(rGeno, "~/outputGN/geno.csv") #r_write_table(rPheno, "~/outputGN/pheno.csv") # Perform the CTL scan - res = self.r_CTLscan(rGeno, rPheno, strategy = strategy, nperm = nperm, parametric = parametric, nthreads=6) + res = self.r_CTLscan(rGeno, rPheno, strategy=strategy, nperm=nperm, parametric = parametric, nthreads=6) # Get significant interactions - significant = self.r_CTLsignificant(res, significance = significance) + significant = self.r_CTLsignificant(res, significance=significance) # Create an image for output self.results = {} @@ -158,7 +158,7 @@ class CTL: # Create the lineplot r_png(self.results['imgloc1'], width=1000, height=600, type='cairo-png') - self.r_lineplot(res, significance = significance) + self.r_lineplot(res, significance=significance) r_dev_off() n = 2 # We start from 2, since R starts from 1 :) @@ -167,7 +167,7 @@ class CTL: self.results['imgurl' + str(n)] = webqtlUtil.genRandStr("CTL_") + ".png" self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + self.results['imgurl' + str(n)] r_png(self.results['imgloc' + str(n)], width=1000, height=600, type='cairo-png') - self.r_plotCTLobject(res, (n-1), significance = significance, main='Phenotype ' + trait) + self.r_plotCTLobject(res, (n - 1), significance=significance, main='Phenotype ' + trait) r_dev_off() n = n + 1 @@ -180,8 +180,8 @@ class CTL: logger.debug(significant[0][x], significant[1][x], significant[2][x]) # Debug to console tsS = significant[0][x].split(':') # Source tsT = significant[2][x].split(':') # Target - gtS = create_trait(name = tsS[0], dataset_name = tsS[1]) # Retrieve Source info from the DB - gtT = create_trait(name = tsT[0], dataset_name = tsT[1]) # Retrieve Target info from the DB + gtS = create_trait(name=tsS[0], dataset_name=tsS[1]) # Retrieve Source info from the DB + gtT = create_trait(name=tsT[0], dataset_name=tsT[1]) # Retrieve Target info from the DB self.addNode(gtS) self.addNode(gtT) self.addEdge(gtS, gtT, significant, x) diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py index adeed6ad..b6e85494 100644 --- a/wqflask/wqflask/database.py +++ b/wqflask/wqflask/database.py @@ -6,7 +6,7 @@ from sqlalchemy.ext.declarative import declarative_base from utility.tools import SQL_URI import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) engine = create_engine(SQL_URI, encoding="latin1") diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 364a3eed..115182e4 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -32,7 +32,7 @@ class DoSearch: self.search_type = search_type if self.dataset: - #Get group information for dataset and the species id + # Get group information for dataset and the species id self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name) def execute(self, query): @@ -137,7 +137,7 @@ class MrnaAssaySearch(DoSearch): return where_clause - def compile_final_query(self, from_clause = '', where_clause = ''): + def compile_final_query(self, from_clause='', where_clause=''): """Generates the final query string""" from_clause = self.normalize_spaces(from_clause) @@ -153,7 +153,7 @@ class MrnaAssaySearch(DoSearch): escape(str(self.dataset.id)))) return query - def run_combined(self, from_clause = '', where_clause = ''): + def run_combined(self, from_clause='', where_clause=''): """Generates and runs a combined search of an mRNA expression dataset""" logger.debug("Running ProbeSetSearch") @@ -218,10 +218,10 @@ class PhenotypeSearch(DoSearch): def get_where_clause(self): """Generate clause for WHERE portion of query""" - #Todo: Zach will figure out exactly what both these lines mean - #and comment here + # Todo: Zach will figure out exactly what both these lines mean + # and comment here - #if "'" not in self.search_term[0]: + # if "'" not in self.search_term[0]: search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0]) + "[[:>:]]" if "_" in self.search_term[0]: if len(self.search_term[0].split("_")[0]) == 3: @@ -236,7 +236,7 @@ class PhenotypeSearch(DoSearch): return where_clause - def compile_final_query(self, from_clause = '', where_clause = ''): + def compile_final_query(self, from_clause='', where_clause=''): """Generates the final query string""" from_clause = self.normalize_spaces(from_clause) @@ -292,7 +292,7 @@ class PhenotypeSearch(DoSearch): def run(self): """Generates and runs a simple search of a phenotype dataset""" - query = self.compile_final_query(where_clause = self.get_where_clause()) + query = self.compile_final_query(where_clause=self.get_where_clause()) return self.execute(query) @@ -334,7 +334,7 @@ class GenotypeSearch(DoSearch): return where_clause - def compile_final_query(self, from_clause = '', where_clause = ''): + def compile_final_query(self, from_clause='', where_clause=''): """Generates the final query string""" from_clause = self.normalize_spaces(from_clause) @@ -344,26 +344,26 @@ class GenotypeSearch(DoSearch): query = (self.base_query + """WHERE Geno.Id = GenoXRef.GenoId and GenoXRef.GenoFreezeId = GenoFreeze.Id - and GenoFreeze.Id = %s"""% (escape(str(self.dataset.id)))) + and GenoFreeze.Id = %s""" % (escape(str(self.dataset.id)))) else: query = (self.base_query + """WHERE %s and Geno.Id = GenoXRef.GenoId and GenoXRef.GenoFreezeId = GenoFreeze.Id - and GenoFreeze.Id = %s"""% (where_clause, + and GenoFreeze.Id = %s""" % (where_clause, escape(str(self.dataset.id)))) return query def run(self): """Generates and runs a simple search of a genotype dataset""" - #Todo: Zach will figure out exactly what both these lines mean - #and comment here + # Todo: Zach will figure out exactly what both these lines mean + # and comment here if self.search_term[0] == "*": self.query = self.compile_final_query() else: - self.query = self.compile_final_query(where_clause = self.get_where_clause()) + self.query = self.compile_final_query(where_clause=self.get_where_clause()) return self.execute(self.query) @@ -393,7 +393,7 @@ class RifSearch(MrnaAssaySearch): class WikiSearch(MrnaAssaySearch): """Searches GeneWiki for traits other people have annotated""" - DoSearch.search_types['ProbeSet_WIKI'] = "WikiSearch" + DoSearch.search_types['ProbeSet_WIKI'] = "WikiSearch" def get_from_clause(self): return ", GeneRIF " @@ -403,7 +403,7 @@ class WikiSearch(MrnaAssaySearch): and GeneRIF.versionId=0 and GeneRIF.display>0 and (GeneRIF.comment REGEXP '%s' or GeneRIF.initial = '%s') """ % (self.dataset.type, - "[[:<:]]"+str(self.search_term[0])+"[[:>:]]", + "[[:<:]]" + str(self.search_term[0]) + "[[:>:]]", str(self.search_term[0])) return where_clause @@ -418,7 +418,7 @@ class WikiSearch(MrnaAssaySearch): class GoSearch(MrnaAssaySearch): """Searches for synapse-associated genes listed in the Gene Ontology.""" - DoSearch.search_types['ProbeSet_GO'] = "GoSearch" + DoSearch.search_types['ProbeSet_GO'] = "GoSearch" def get_from_clause(self): from_clause = """, db_GeneOntology.term as GOterm, @@ -429,7 +429,7 @@ class GoSearch(MrnaAssaySearch): def get_where_clause(self): field = 'GOterm.acc' - go_id = 'GO:' + ('0000000'+self.search_term[0])[-7:] + go_id = 'GO:' + ('0000000' + self.search_term[0])[-7:] statements = ("""%s.symbol=GOgene_product.symbol and GOassociation.gene_product_id=GOgene_product.id and @@ -448,7 +448,7 @@ class GoSearch(MrnaAssaySearch): return self.execute(query) -#ZS: Not sure what the best way to deal with LRS searches is +# ZS: Not sure what the best way to deal with LRS searches is class LrsSearch(DoSearch): """Searches for genes with a QTL within the given LRS values @@ -486,8 +486,8 @@ class LrsSearch(DoSearch): assert isinstance(self.search_term, (list, tuple)) lrs_min, lrs_max = self.search_term[:2] if self.search_type == "LOD": - lrs_min = lrs_min*4.61 - lrs_max = lrs_max*4.61 + lrs_min = lrs_min * 4.61 + lrs_max = lrs_max * 4.61 where_clause = """ %sXRef.LRS > %s and %sXRef.LRS < %s """ % self.mescape(self.dataset.type, @@ -496,7 +496,7 @@ class LrsSearch(DoSearch): max(lrs_min, lrs_max)) if len(self.search_term) > 2: - #If the user typed, for example "Chr4", the "Chr" substring needs to be removed so that all search elements can be converted to floats + # If the user typed, for example "Chr4", the "Chr" substring needs to be removed so that all search elements can be converted to floats chr_num = self.search_term[2] if "chr" in self.search_term[2].lower(): chr_num = self.search_term[2].lower().replace("chr", "") @@ -518,7 +518,7 @@ class LrsSearch(DoSearch): logger.debug("self.search_term is:", self.search_term) lrs_val = self.search_term[0] if self.search_type == "LOD": - lrs_val = lrs_val*4.61 + lrs_val = lrs_val * 4.61 where_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type, self.search_operator, @@ -546,7 +546,7 @@ class MrnaLrsSearch(LrsSearch, MrnaAssaySearch): self.from_clause = self.get_from_clause() self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(from_clause = self.from_clause, where_clause = self.where_clause) + self.query = self.compile_final_query(from_clause=self.from_clause, where_clause=self.where_clause) return self.execute(self.query) @@ -560,7 +560,7 @@ class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch): self.from_clause = self.get_from_clause() self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(from_clause = self.from_clause, where_clause = self.where_clause) + self.query = self.compile_final_query(from_clause=self.from_clause, where_clause=self.where_clause) return self.execute(self.query) @@ -599,7 +599,7 @@ class CisTransLrsSearch(DoSearch): lrs_max = lrs_max * 4.61 sub_clause = """ %sXRef.LRS > %s and - %sXRef.LRS < %s and """ % ( + %sXRef.LRS < %s and """ % ( escape(self.dataset.type), escape(str(min(lrs_min, lrs_max))), escape(self.dataset.type), @@ -607,7 +607,7 @@ class CisTransLrsSearch(DoSearch): ) else: # Deal with >, <, >=, and <= - sub_clause = """ %sXRef.LRS %s %s and """ % ( + sub_clause = """ %sXRef.LRS %s %s and """ % ( escape(self.dataset.type), escape(self.search_operator), escape(self.search_term[0]) @@ -667,7 +667,7 @@ class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch): """ for search_key in ('LRS', 'LOD'): - DoSearch.search_types['ProbeSet_CIS'+search_key] = "CisLrsSearch" + DoSearch.search_types['ProbeSet_CIS' + search_key] = "CisLrsSearch" def get_where_clause(self): return CisTransLrsSearch.get_where_clause(self, "cis") @@ -697,7 +697,7 @@ class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch): """ for search_key in ('LRS', 'LOD'): - DoSearch.search_types['ProbeSet_TRANS'+search_key] = "TransLrsSearch" + DoSearch.search_types['ProbeSet_TRANS' + search_key] = "TransLrsSearch" def get_where_clause(self): return CisTransLrsSearch.get_where_clause(self, "trans") @@ -740,7 +740,7 @@ class MeanSearch(MrnaAssaySearch): self.where_clause = self.get_where_clause() logger.debug("where_clause is:", pf(self.where_clause)) - self.query = self.compile_final_query(where_clause = self.where_clause) + self.query = self.compile_final_query(where_clause=self.where_clause) return self.execute(self.query) @@ -775,7 +775,7 @@ class RangeSearch(MrnaAssaySearch): def run(self): self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(where_clause = self.where_clause) + self.query = self.compile_final_query(where_clause=self.where_clause) return self.execute(self.query) @@ -815,7 +815,7 @@ class PositionSearch(DoSearch): def run(self): self.get_where_clause() - self.query = self.compile_final_query(where_clause = self.where_clause) + self.query = self.compile_final_query(where_clause=self.where_clause) return self.execute(self.query) @@ -823,12 +823,12 @@ class MrnaPositionSearch(PositionSearch, MrnaAssaySearch): """Searches for genes located within a specified range on a specified chromosome""" for search_key in ('POSITION', 'POS', 'MB'): - DoSearch.search_types['ProbeSet_'+search_key] = "MrnaPositionSearch" + DoSearch.search_types['ProbeSet_' + search_key] = "MrnaPositionSearch" def run(self): self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(where_clause = self.where_clause) + self.query = self.compile_final_query(where_clause=self.where_clause) return self.execute(self.query) @@ -836,12 +836,12 @@ class GenotypePositionSearch(PositionSearch, GenotypeSearch): """Searches for genes located within a specified range on a specified chromosome""" for search_key in ('POSITION', 'POS', 'MB'): - DoSearch.search_types['Geno_'+search_key] = "GenotypePositionSearch" + DoSearch.search_types['Geno_' + search_key] = "GenotypePositionSearch" def run(self): self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(where_clause = self.where_clause) + self.query = self.compile_final_query(where_clause=self.where_clause) return self.execute(self.query) @@ -873,7 +873,7 @@ class PvalueSearch(MrnaAssaySearch): logger.debug("where_clause is:", pf(self.where_clause)) - self.query = self.compile_final_query(where_clause = self.where_clause) + self.query = self.compile_final_query(where_clause=self.where_clause) logger.sql(self.query) return self.execute(self.query) @@ -888,7 +888,7 @@ class AuthorSearch(PhenotypeSearch): self.where_clause = """ Publication.Authors REGEXP "[[:<:]]%s[[:>:]]" and """ % (self.search_term[0]) - self.query = self.compile_final_query(where_clause = self.where_clause) + self.query = self.compile_final_query(where_clause=self.where_clause) return self.execute(self.query) @@ -924,8 +924,8 @@ def get_aliases(symbol, species): return filtered_aliases if __name__ == "__main__": - ### Usually this will be used as a library, but call it from the command line for testing - ### And it runs the code below + # Usually this will be used as a library, but call it from the command line for testing + # And it runs the code below import MySQLdb import sys diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py index 6fb760e0..95c20673 100644 --- a/wqflask/wqflask/export_traits.py +++ b/wqflask/wqflask/export_traits.py @@ -13,7 +13,7 @@ from base.trait import create_trait, retrieve_trait_info from pprint import pformat as pf from utility.logger import getLogger -logger = getLogger(__name__ ) +logger = getLogger(__name__) def export_search_results_csv(targs): diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py index c5c79e98..9836eb9c 100644 --- a/wqflask/wqflask/external_tools/send_to_bnw.py +++ b/wqflask/wqflask/external_tools/send_to_bnw.py @@ -1,4 +1,4 @@ -## Copyright (C) University of Tennessee Health Science Center, Memphis, TN. +# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. # # This program is free software: you can redistribute it and/or modify it # under the terms of the GNU Affero General Public License @@ -22,7 +22,7 @@ from base.trait import GeneralTrait from utility import helper_functions, corr_result_helpers import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) class SendToBNW: def __init__(self, start_vars): @@ -40,7 +40,7 @@ class SendToBNW: shared_samples = list(set(trait_samples_list[0]).intersection(*trait_samples_list)) - self.form_value = "" #ZS: string that is passed to BNW through form + self.form_value = "" # ZS: string that is passed to BNW through form values_list = [] for trait_db in self.trait_list: this_trait = trait_db[0] diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py index 47e4c53a..36f1b8e5 100644 --- a/wqflask/wqflask/external_tools/send_to_geneweaver.py +++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py @@ -1,4 +1,4 @@ -## Copyright (C) University of Tennessee Health Science Center, Memphis, TN. +# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. # # This program is free software: you can redistribute it and/or modify it # under the terms of the GNU Affero General Public License @@ -27,7 +27,7 @@ from base.species import TheSpecies from utility import helper_functions, corr_result_helpers import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) class SendToGeneWeaver: def __init__(self, start_vars): @@ -74,7 +74,7 @@ def test_chip(trait_list): FROM GeneChip, ProbeFreeze, ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and - ProbeSetFreeze.Name = '%s'""" % dataset.name).fetchone() + ProbeSetFreeze.Name = '%s'""" % dataset.name).fetchone() if result: chip_name = result[0] diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py index e1e5e655..f50eeb8b 100644 --- a/wqflask/wqflask/external_tools/send_to_webgestalt.py +++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py @@ -1,4 +1,4 @@ -## Copyright (C) University of Tennessee Health Science Center, Memphis, TN. +# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. # # This program is free software: you can redistribute it and/or modify it # under the terms of the GNU Affero General Public License @@ -27,7 +27,7 @@ from base.species import TheSpecies from utility import helper_functions, corr_result_helpers import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) class SendToWebGestalt: def __init__(self, start_vars): @@ -47,16 +47,16 @@ class SendToWebGestalt: id_type = "entrezgene" self.hidden_vars = { - 'gene_list' : "\n".join(gene_id_list), - 'id_type' : "entrezgene", - 'ref_set' : "genome", - 'enriched_database_category' : "geneontology", - 'enriched_database_name' : "Biological_Process", - 'sig_method' : "fdr", - 'sig_value' : "0.05", - 'enrich_method' : "ORA", - 'fdr_method' : "BH", - 'min_num' : "2" + 'gene_list': "\n".join(gene_id_list), + 'id_type': "entrezgene", + 'ref_set': "genome", + 'enriched_database_category': "geneontology", + 'enriched_database_name': "Biological_Process", + 'sig_method': "fdr", + 'sig_value': "0.05", + 'enrich_method': "ORA", + 'fdr_method': "BH", + 'min_num': "2" } species = self.trait_list[0][1].group.species @@ -78,7 +78,7 @@ def test_chip(trait_list): FROM GeneChip, ProbeFreeze, ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and - ProbeSetFreeze.Name = '%s'""" % dataset.name).fetchone() + ProbeSetFreeze.Name = '%s'""" % dataset.name).fetchone() if result: chip_name = result[0] diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py index 69ee9623..f29c0e4d 100644 --- a/wqflask/wqflask/group_manager.py +++ b/wqflask/wqflask/group_manager.py @@ -40,8 +40,8 @@ def view_group(): user_info = get_user_by_unique_column("user_id", user_id) members_info.append(user_info) - #ZS: This whole part might not scale well with many resources - resources_info = [] + # ZS: This whole part might not scale well with many resources + resources_info = [] all_resources = get_resources() for resource_id in all_resources: resource_info = get_resource_info(resource_id) @@ -82,10 +82,10 @@ def add_users(user_type='members'): group_id = request.form['group_id'] if user_type == "admins": user_emails = request.form['admin_emails_to_add'].split(",") - add_users_to_group(g.user_session.user_id, group_id, user_emails, admins = True) + add_users_to_group(g.user_session.user_id, group_id, user_emails, admins=True) elif user_type == "members": user_emails = request.form['member_emails_to_add'].split(",") - add_users_to_group(g.user_session.user_id, group_id, user_emails, admins = False) + add_users_to_group(g.user_session.user_id, group_id, user_emails, admins=False) return redirect(url_for('view_group', id=group_id)) @@ -103,7 +103,7 @@ def add_or_edit_group(): if "group_name" in params: member_user_ids = set() admin_user_ids = set() - admin_user_ids.add(g.user_session.user_id) #ZS: Always add the user creating the group as an admin + admin_user_ids.add(g.user_session.user_id) # ZS: Always add the user creating the group as an admin if "admin_emails_to_add" in params: admin_emails = params['admin_emails_to_add'].split(",") for email in admin_emails: @@ -124,22 +124,22 @@ def add_or_edit_group(): else: return render_template("admin/create_group.html") -#ZS: Will integrate this later, for now just letting users be added directly -def send_group_invites(group_id, user_email_list = [], user_type="members"): +# ZS: Will integrate this later, for now just letting users be added directly +def send_group_invites(group_id, user_email_list=[], user_type="members"): for user_email in user_email_list: user_details = get_user_by_unique_column("email_address", user_email) if user_details: group_info = get_group_info(group_id) - #ZS: Probably not necessary since the group should normally always exist if group_id is being passed here, + # ZS: Probably not necessary since the group should normally always exist if group_id is being passed here, # but it's technically possible to hit it if Redis is cleared out before submitting the new users or something if group_info: - #ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user, + # ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user, # but do add them if they're a regular user and are added as an admin if (user_details['user_id'] in group_info['admins']) or \ ((user_type == "members") and (user_details['user_id'] in group_info['members'])): continue else: - send_verification_email(user_details, template_name = "email/group_verification.txt", key_prefix = "verification_code", subject = "You've been invited to join a GeneNetwork user group") + send_verification_email(user_details, template_name="email/group_verification.txt", key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group") else: temp_password = ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) user_details = { @@ -152,4 +152,4 @@ def send_group_invites(group_id, user_email_list = [], user_type="members"): save_user(user_details, user_details['user_id']) send_invitation_email(user_email, temp_password) -#@app.route() +# @app.route() diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 9bf23d57..8cb81dcc 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -102,7 +102,7 @@ class GSearch: this_trait['locus_chr'] = line[16] this_trait['locus_mb'] = line[17] - dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="ProbeSet",species=this_trait["species"]) + dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="ProbeSet", species=this_trait["species"]) if dataset_ob.id not in dataset_to_permissions: permissions = check_resource_availability(dataset_ob) dataset_to_permissions[dataset_ob.id] = permissions diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 20e3559a..f8ef7028 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -12,7 +12,7 @@ from utility.logger import getLogger Redis = Redis() -logger = getLogger(__name__ ) +logger = getLogger(__name__) class Heatmap: @@ -24,7 +24,7 @@ class Heatmap: self.num_permutations = 5000 self.dataset = self.trait_list[0][1] - self.json_data = {} #The dictionary that will be used to create the json object that contains all the data needed to create the figure + self.json_data = {} # The dictionary that will be used to create the json object that contains all the data needed to create the figure self.all_sample_list = [] self.traits = [] @@ -83,7 +83,7 @@ class Heatmap: self.json_data[trait] = self.trait_results[trait] self.js_data = dict( - json_data = self.json_data + json_data=self.json_data ) def gen_reaper_results(self): diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py index d0dd7aea..9779878e 100644 --- a/wqflask/wqflask/interval_analyst/GeneUtil.py +++ b/wqflask/wqflask/interval_analyst/GeneUtil.py @@ -2,14 +2,14 @@ import string from flask import Flask, g -#Just return a list of dictionaries -#each dictionary contains sub-dictionary +# Just return a list of dictionaries +# each dictionary contains sub-dictionary def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd', 'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID', 'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd'] - ##List All Species in the Gene Table + # List All Species in the Gene Table speciesDict = {} results = g.db.execute(""" SELECT Species.Name, GeneList.SpeciesId @@ -20,7 +20,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): for item in results: speciesDict[item[0]] = item[1] - ##List current Species and other Species + # List current Species and other Species speciesId = speciesDict[species] otherSpecies = [[X, speciesDict[X]] for X in list(speciesDict.keys())] otherSpecies.remove([species, speciesId]) @@ -43,8 +43,8 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): newdict = {} for j, item in enumerate(fetchFields): newdict[item] = result[j] - #count SNPs if possible - if diffCol and species=='mouse': + # count SNPs if possible + if diffCol and species == 'mouse': newdict["snpCount"] = g.db.execute(""" SELECT count(*) FROM BXDSnpPosition @@ -52,16 +52,16 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): Mb >= %2.6f AND Mb < %2.6f AND StrainId1 = %d AND StrainId2 = %d """ % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0] - newdict["snpDensity"] = newdict["snpCount"]/(newdict["TxEnd"]-newdict["TxStart"])/1000.0 + newdict["snpDensity"] = newdict["snpCount"] / (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0 else: newdict["snpDensity"] = newdict["snpCount"] = 0 try: - newdict['GeneLength'] = 1000.0*(newdict['TxEnd'] - newdict['TxStart']) + newdict['GeneLength'] = 1000.0 * (newdict['TxEnd'] - newdict['TxStart']) except: pass - #load gene from other Species by the same name + # load gene from other Species by the same name for item in otherSpecies: othSpec, othSpecId = item newdict2 = {} @@ -74,7 +74,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): for j, item in enumerate(fetchFields): newdict2[item] = resultsOther[j] - #count SNPs if possible, could be a separate function + # count SNPs if possible, could be a separate function if diffCol and othSpec == 'mouse': newdict2["snpCount"] = g.db.execute(""" SELECT count(*) @@ -84,12 +84,12 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): StrainId1 = %d AND StrainId2 = %d """ % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0] - newdict2["snpDensity"] = newdict2["snpCount"]/(newdict2["TxEnd"]-newdict2["TxStart"])/1000.0 + newdict2["snpDensity"] = newdict2["snpCount"] / (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0 else: newdict2["snpDensity"] = newdict2["snpCount"] = 0 try: - newdict2['GeneLength'] = 1000.0*(newdict2['TxEnd'] - newdict2['TxStart']) + newdict2['GeneLength'] = 1000.0 * (newdict2['TxEnd'] - newdict2['TxStart']) except: pass diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 4074f098..3753d1ce 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -51,7 +51,7 @@ try: # Only import this for Python3 from functools import reduce except: pass -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) RED = ImageColor.getrgb("red") BLUE = ImageColor.getrgb("blue") @@ -390,24 +390,24 @@ class DisplayMappingResults: else: self.genotype = self.dataset.group.read_genotype_file() - #Darwing Options + # Darwing Options try: if self.selectedChr > -1: - self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) + self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) else: - self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.MULT_GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) + self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.MULT_GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) except: if self.selectedChr > -1: - self.graphWidth = self.GRAPH_DEFAULT_WIDTH + self.graphWidth = self.GRAPH_DEFAULT_WIDTH else: - self.graphWidth = self.MULT_GRAPH_DEFAULT_WIDTH + self.graphWidth = self.MULT_GRAPH_DEFAULT_WIDTH -## BEGIN HaplotypeAnalyst +# BEGIN HaplotypeAnalyst if 'haplotypeAnalystCheck' in list(start_vars.keys()): self.haplotypeAnalystChecked = start_vars['haplotypeAnalystCheck'] else: self.haplotypeAnalystChecked = False -## END HaplotypeAnalyst +# END HaplotypeAnalyst self.graphHeight = self.GRAPH_DEFAULT_HEIGHT self.dominanceChecked = False @@ -446,7 +446,7 @@ class DisplayMappingResults: except: self.lrsMax = 0 - #Trait Infos + # Trait Infos self.identification = "" ################################################################ @@ -471,10 +471,10 @@ class DisplayMappingResults: Chr_Length.OrderId """ % (self.dataset.group.name, ", ".join(["'%s'" % X[0] for X in self.ChrList[1:]]))) - self.ChrLengthMbList = [x[0]/1000000.0 for x in self.ChrLengthMbList] - self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0) + self.ChrLengthMbList = [x[0] / 1000000.0 for x in self.ChrLengthMbList] + self.ChrLengthMbSum = reduce(lambda x, y: x + y, self.ChrLengthMbList, 0.0) if self.ChrLengthMbList: - self.MbGraphInterval = self.ChrLengthMbSum/(len(self.ChrLengthMbList)*12) #Empirical Mb interval + self.MbGraphInterval = self.ChrLengthMbSum / (len(self.ChrLengthMbList) * 12) # Empirical Mb interval else: self.MbGraphInterval = 1 @@ -482,18 +482,18 @@ class DisplayMappingResults: for i, _chr in enumerate(self.genotype): self.ChrLengthCMList.append(_chr[-1].cM - _chr[0].cM) - self.ChrLengthCMSum = reduce(lambda x, y:x+y, self.ChrLengthCMList, 0.0) + self.ChrLengthCMSum = reduce(lambda x, y: x + y, self.ChrLengthCMList, 0.0) if self.plotScale == 'physic': - self.GraphInterval = self.MbGraphInterval #Mb + self.GraphInterval = self.MbGraphInterval # Mb else: - self.GraphInterval = self.cMGraphInterval #cM + self.GraphInterval = self.cMGraphInterval # cM -## BEGIN HaplotypeAnalyst -## count the amount of individuals to be plotted, and increase self.graphHeight +# BEGIN HaplotypeAnalyst +# count the amount of individuals to be plotted, and increase self.graphHeight if self.haplotypeAnalystChecked and self.selectedChr > -1: thisTrait = self.this_trait - smd=[] + smd = [] for sample in self.sample_vals_dict.keys(): if self.sample_vals_dict[sample] != "x": temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample])) @@ -501,19 +501,19 @@ class DisplayMappingResults: else: continue samplelist = list(self.genotype.prgy) - for j, _geno in enumerate (self.genotype[0][1].genotype): + for j, _geno in enumerate(self.genotype[0][1].genotype): for item in smd: if item.name == samplelist[j]: self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1 # default: - self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS+10) * self.EACH_GENE_HEIGHT -## END HaplotypeAnalyst + self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS + 10) * self.EACH_GENE_HEIGHT +# END HaplotypeAnalyst ######################### - ## Get the sorting column + # Get the sorting column ######################### RISet = self.dataset.group.name if RISet in ('AXB', 'BXA', 'AXBXA'): @@ -529,7 +529,7 @@ class DisplayMappingResults: elif RISet in ('LXS'): self.diffCol = ['ILS', 'ISS'] else: - self.diffCol= [] + self.diffCol = [] for i, strain in enumerate(self.diffCol): self.diffCol[i] = g.db.execute("select Id from Strain where Symbol = %s", strain).fetchone()[0] @@ -546,7 +546,7 @@ class DisplayMappingResults: geneTable = "" self.geneCol = None - if self.plotScale == 'physic' and self.selectedChr > -1 and (self.intervalAnalystChecked or self.geneChecked): + if self.plotScale == 'physic' and self.selectedChr > -1 and (self.intervalAnalystChecked or self.geneChecked): # Draw the genes for this chromosome / region of this chromosome webqtldatabase = self.dataset.name @@ -580,11 +580,11 @@ class DisplayMappingResults: showLocusForm = "" intCanvas = Image.new("RGBA", size=(self.graphWidth, self.graphHeight)) with Bench("Drawing Plot"): - gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm) + gifmap = self.plotIntMapping(intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm) self.gifmap = gifmap.__str__() - self.filename= webqtlUtil.genRandStr("Itvl_") + self.filename = webqtlUtil.genRandStr("Itvl_") intCanvas.save( "{}.png".format( os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename)), @@ -594,20 +594,20 @@ class DisplayMappingResults: border="0", usemap='#WebQTLImageMap' ) - #Scales plot differently for high resolution + # Scales plot differently for high resolution if self.draw2X: - intCanvasX2 = Image.new("RGBA", size=(self.graphWidth*2, self.graphHeight*2)) - gifmapX2 = self.plotIntMapping(intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2) + intCanvasX2 = Image.new("RGBA", size=(self.graphWidth * 2, self.graphHeight * 2)) + gifmapX2 = self.plotIntMapping(intCanvasX2, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm, zoom=2) intCanvasX2.save( "{}.png".format( os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, - self.filename+"X2")), + self.filename + "X2")), format='png') ################################################################ # Outputs goes here ################################################################ - #this form is used for opening Locus page or trait page, only available for genetic mapping + # this form is used for opening Locus page or trait page, only available for genetic mapping if showLocusForm: showLocusForm = HtmlGenWrapper.create_form_tag( cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), @@ -615,7 +615,7 @@ class DisplayMappingResults: name=showLocusForm, submit=HtmlGenWrapper.create_input_tag(type_='hidden')) - hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'} + hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', 'database': fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'} for key in hddn.keys(): showLocusForm.append(HtmlGenWrapper.create_input_tag( name=key, value=hddn[key], type_='hidden')) @@ -636,9 +636,9 @@ class DisplayMappingResults: btminfo.append(HtmlGenWrapper.create_br_tag()) btminfo.append('Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.') - def plotIntMapping(self, canvas, offset= (80, 120, 90, 100), zoom = 1, startMb = None, endMb = None, showLocusForm = ""): + def plotIntMapping(self, canvas, offset=(80, 120, 90, 100), zoom=1, startMb= None, endMb = None, showLocusForm = ""): im_drawer = ImageDraw.Draw(canvas) - #calculating margins + # calculating margins xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset if self.multipleInterval: yTopOffset = max(90, yTopOffset) @@ -659,34 +659,34 @@ class DisplayMappingResults: xLeftOffset += 20 fontZoom = 1.5 - xLeftOffset = int(xLeftOffset*fontZoom) - xRightOffset = int(xRightOffset*fontZoom) - yBottomOffset = int(yBottomOffset*fontZoom) + xLeftOffset = int(xLeftOffset * fontZoom) + xRightOffset = int(xRightOffset * fontZoom) + yBottomOffset = int(yBottomOffset * fontZoom) cWidth = canvas.size[0] cHeight = canvas.size[1] plotWidth = cWidth - xLeftOffset - xRightOffset plotHeight = cHeight - yTopOffset - yBottomOffset - #Drawing Area Height + # Drawing Area Height drawAreaHeight = plotHeight if self.plotScale == 'physic' and self.selectedChr > -1: if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": - drawAreaHeight -= 4*self.BAND_HEIGHT + 4*self.BAND_SPACING+ 10*zoom + drawAreaHeight -= 4 * self.BAND_HEIGHT + 4 * self.BAND_SPACING + 10 * zoom else: - drawAreaHeight -= 3*self.BAND_HEIGHT + 3*self.BAND_SPACING+ 10*zoom + drawAreaHeight -= 3 * self.BAND_HEIGHT + 3 * self.BAND_SPACING + 10 * zoom if self.geneChecked: - drawAreaHeight -= self.NUM_GENE_ROWS*self.EACH_GENE_HEIGHT + 3*self.BAND_SPACING + 10*zoom + drawAreaHeight -= self.NUM_GENE_ROWS * self.EACH_GENE_HEIGHT + 3 * self.BAND_SPACING + 10 * zoom else: if self.selectedChr > -1: drawAreaHeight -= 20 else: drawAreaHeight -= 30 -## BEGIN HaplotypeAnalyst +# BEGIN HaplotypeAnalyst if self.haplotypeAnalystChecked and self.selectedChr > -1: - drawAreaHeight -= self.EACH_GENE_HEIGHT * (self.NR_INDIVIDUALS+10) * 2 * zoom -## END HaplotypeAnalyst + drawAreaHeight -= self.EACH_GENE_HEIGHT * (self.NR_INDIVIDUALS + 10) * 2 * zoom +# END HaplotypeAnalyst if zoom == 2: drawAreaHeight -= 60 @@ -696,42 +696,42 @@ class DisplayMappingResults: newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset) # Draw the alternating-color background first and get plotXScale - plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb) + plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) - #draw bootstap + # draw bootstap if self.bootChecked and not self.multipleInterval: - self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb) + self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) # Draw clickable region and gene band if selected if self.plotScale == 'physic' and self.selectedChr > -1: - self.drawClickBand(canvas, gifmap, plotXScale, offset=newoffset, zoom = zoom, startMb=startMb, endMb = endMb) + self.drawClickBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) if self.geneChecked and self.geneCol: - self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset, zoom = zoom, startMb=startMb, endMb = endMb) + self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) if self.SNPChecked: - self.drawSNPTrackNew(canvas, offset=newoffset, zoom = 2*zoom, startMb=startMb, endMb = endMb) -## BEGIN HaplotypeAnalyst + self.drawSNPTrackNew(canvas, offset=newoffset, zoom=2 * zoom, startMb=startMb, endMb = endMb) +# BEGIN HaplotypeAnalyst if self.haplotypeAnalystChecked: - self.drawHaplotypeBand(canvas, gifmap, plotXScale, offset=newoffset, zoom = zoom, startMb=startMb, endMb = endMb) -## END HaplotypeAnalyst + self.drawHaplotypeBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) +# END HaplotypeAnalyst # Draw X axis - self.drawXAxis(canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=newoffset, zoom = zoom, startMb=startMb, endMb = endMb) + self.drawXAxis(canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) # Draw QTL curve - self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb) + self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) - #draw legend + # draw legend if self.multipleInterval: self.drawMultiTraitName(fd, canvas, gifmap, showLocusForm, offset=newoffset) elif self.legendChecked: - self.drawLegendPanel(canvas, offset=newoffset, zoom = zoom) + self.drawLegendPanel(canvas, offset=newoffset, zoom=zoom) else: pass - #draw position, no need to use a separate function - self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset, zoom = zoom) + # draw position, no need to use a separate function + self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset, zoom=zoom) return gifmap - def drawBootStrapResult(self, canvas, nboot, drawAreaHeight, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): + def drawBootStrapResult(self, canvas, nboot, drawAreaHeight, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None): im_drawer = ImageDraw.Draw(canvas) xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset plotWidth = canvas.size[0] - xLeftOffset - xRightOffset @@ -741,9 +741,9 @@ class DisplayMappingResults: if zoom == 2: fontZoom = 1.5 - bootHeightThresh = drawAreaHeight*3/4 + bootHeightThresh = drawAreaHeight * 3 / 4 - #break bootstrap result into groups + # break bootstrap result into groups BootCoord = [] i = 0 previous_chr = None @@ -751,7 +751,7 @@ class DisplayMappingResults: startX = xLeftOffset BootChrCoord = [] - if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes + if self.selectedChr == -1: # ZS: If viewing full genome/all chromosomes for i, result in enumerate(self.qtlresults): if result['chr'] != previous_chr: previous_chr = result['chr'] @@ -759,28 +759,28 @@ class DisplayMappingResults: if previous_chr_as_int != 1: BootCoord.append(BootChrCoord) BootChrCoord = [] - startX += (self.ChrLengthDistList[previous_chr_as_int - 2] + self.GraphInterval)*plotXScale + startX += (self.ChrLengthDistList[previous_chr_as_int - 2] + self.GraphInterval) * plotXScale if self.plotScale == 'physic': - Xc = startX + (result['Mb']-self.startMb)*plotXScale + Xc = startX + (result['Mb'] - self.startMb) * plotXScale else: - Xc = startX + (result['cM']-self.qtlresults[0]['cM'])*plotXScale + Xc = startX + (result['cM'] - self.qtlresults[0]['cM']) * plotXScale BootChrCoord.append([Xc, self.bootResult[i]]) else: for i, result in enumerate(self.qtlresults): if str(result['chr']) == str(self.ChrList[self.selectedChr][0]): if self.plotScale == 'physic': - Xc = startX + (result['Mb']-self.startMb)*plotXScale + Xc = startX + (result['Mb'] - self.startMb) * plotXScale else: - Xc = startX + (result['cM']-self.qtlresults[0]['cM'])*plotXScale + Xc = startX + (result['cM'] - self.qtlresults[0]['cM']) * plotXScale BootChrCoord.append([Xc, self.bootResult[i]]) BootCoord = [BootChrCoord] - #reduce bootResult + # reduce bootResult if self.selectedChr > -1: maxBootBar = 80.0 else: maxBootBar = 200.0 - stepBootStrap = plotWidth/maxBootBar + stepBootStrap = plotWidth / maxBootBar reducedBootCoord = [] maxBootCount = 0 @@ -801,8 +801,8 @@ class DisplayMappingResults: bootCount = BootChrCoord[i][1] # end else # end for - #add last piece - if BootChrCoord[-1][0] - bootStartPixX > stepBootStrap/2.0: + # add last piece + if BootChrCoord[-1][0] - bootStartPixX > stepBootStrap / 2.0: reducedBootCoord.append([bootStartPixX, BootChrCoord[-1][0], bootCount]) else: reducedBootCoord[-1][2] += bootCount @@ -815,64 +815,64 @@ class DisplayMappingResults: if item[2] > 0: if item[0] < xLeftOffset: item[0] = xLeftOffset - if item[0] > xLeftOffset+plotWidth: - item[0] = xLeftOffset+plotWidth + if item[0] > xLeftOffset + plotWidth: + item[0] = xLeftOffset + plotWidth if item[1] < xLeftOffset: item[1] = xLeftOffset - if item[1] > xLeftOffset+plotWidth: - item[1] = xLeftOffset+plotWidth + if item[1] > xLeftOffset + plotWidth: + item[1] = xLeftOffset + plotWidth if item[0] != item[1]: im_drawer.rectangle( xy=((item[0], yZero), - (item[1], yZero - item[2]*bootHeightThresh/maxBootCount)), + (item[1], yZero - item[2] * bootHeightThresh / maxBootCount)), fill=self.BOOTSTRAP_BOX_COLOR, outline=BLACK) - ###draw boot scale - highestPercent = (maxBootCount*100.0)/nboot + # draw boot scale + highestPercent = (maxBootCount * 100.0) / nboot bootScale = Plot.detScale(0, highestPercent) - bootScale = Plot.frange(bootScale[0], bootScale[1], bootScale[1]/bootScale[2]) + bootScale = Plot.frange(bootScale[0], bootScale[1], bootScale[1] / bootScale[2]) bootScale = bootScale[:-1] + [highestPercent] - bootOffset = 50*fontZoom - bootScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=13*fontZoom) + bootOffset = 50 * fontZoom + bootScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=13 * fontZoom) im_drawer.rectangle( - xy=((canvas.size[0]-bootOffset, yZero-bootHeightThresh), - (canvas.size[0]-bootOffset-15*zoom, yZero)), - fill = YELLOW, outline=BLACK) + xy=((canvas.size[0] - bootOffset, yZero - bootHeightThresh), + (canvas.size[0] - bootOffset - 15*zoom, yZero)), + fill=YELLOW, outline=BLACK) im_drawer.line( - xy=((canvas.size[0]-bootOffset+4, yZero), - (canvas.size[0]-bootOffset, yZero)), + xy=((canvas.size[0] - bootOffset + 4, yZero), + (canvas.size[0] - bootOffset, yZero)), fill=BLACK) TEXT_Y_DISPLACEMENT = -8 - im_drawer.text(xy=(canvas.size[0]-bootOffset+10, yZero+TEXT_Y_DISPLACEMENT), text='0%', + im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, yZero+TEXT_Y_DISPLACEMENT), text='0%', font=bootScaleFont, fill=BLACK) for item in bootScale: if item == 0: continue - bootY = yZero-bootHeightThresh*item/highestPercent + bootY = yZero - bootHeightThresh * item / highestPercent im_drawer.line( - xy=((canvas.size[0]-bootOffset+4, bootY), - (canvas.size[0]-bootOffset, bootY)), + xy=((canvas.size[0] - bootOffset + 4, bootY), + (canvas.size[0] - bootOffset, bootY)), fill=BLACK) - im_drawer.text(xy=(canvas.size[0]-bootOffset+10, bootY+TEXT_Y_DISPLACEMENT), - text='%2.1f'%item, font=bootScaleFont, fill=BLACK) + im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, bootY+TEXT_Y_DISPLACEMENT), + text='%2.1f' % item, font=bootScaleFont, fill=BLACK) if self.legendChecked: if hasattr(self.traitList[0], 'chr') and hasattr(self.traitList[0], 'mb'): startPosY = 30 else: startPosY = 15 - smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom) + smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12 * fontZoom) leftOffset = canvas.size[0] - xRightOffset - 190 im_drawer.rectangle( - xy=((leftOffset, startPosY-6), (leftOffset+12, startPosY+6)), + xy=((leftOffset, startPosY - 6), (leftOffset + 12, startPosY + 6)), fill=YELLOW, outline=BLACK) - im_drawer.text(xy=(canvas.size[0] - xRightOffset - 170, startPosY+TEXT_Y_DISPLACEMENT), + im_drawer.text(xy=(canvas.size[0] - xRightOffset - 170, startPosY + TEXT_Y_DISPLACEMENT), text='Frequency of the Peak LRS', font=smallLabelFont, fill=BLACK) - def drawProbeSetPosition(self, canvas, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): + def drawProbeSetPosition(self, canvas, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None): im_drawer = ImageDraw.Draw(canvas) if len(self.traitList) != 1: return @@ -896,21 +896,21 @@ class DisplayMappingResults: if self.plotScale == "physic": this_chr = str(self.ChrList[self.selectedChr][0]) else: - this_chr = str(self.ChrList[self.selectedChr][1]+1) + this_chr = str(self.ChrList[self.selectedChr][1] + 1) if self.plotScale == 'physic': if self.selectedChr > -1: if this_chr != Chr or Mb < self.startMb or Mb > self.endMb: return else: - locPixel = xLeftOffset + (Mb-self.startMb)*plotXScale + locPixel = xLeftOffset + (Mb - self.startMb) * plotXScale else: locPixel = xLeftOffset for i, _chr in enumerate(self.ChrList[1:]): if _chr[0] != Chr: - locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale + locPixel += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale else: - locPixel += Mb*plotXScale + locPixel += Mb * plotXScale break else: if self.selectedChr > -1: @@ -918,33 +918,33 @@ class DisplayMappingResults: if qtlresult['chr'] != self.selectedChr: continue - if i==0 and qtlresult['Mb'] >= Mb: - locPixel=-1 + if i == 0 and qtlresult['Mb'] >= Mb: + locPixel = -1 break - #the trait's position is between two traits - if i > 0 and self.qtlresults[i-1]['Mb'] < Mb and qtlresult['Mb'] >= Mb: - locPixel = xLeftOffset + plotXScale*(self.qtlresults[i-1]['Mb']+(qtlresult['Mb']-self.qtlresults[i-1]['Mb'])*(Mb - self.qtlresults[i-1]['Mb'])/(qtlresult['Mb']-self.qtlresults[i-1]['Mb'])) + # the trait's position is between two traits + if i > 0 and self.qtlresults[i - 1]['Mb'] < Mb and qtlresult['Mb'] >= Mb: + locPixel = xLeftOffset + plotXScale * (self.qtlresults[i - 1]['Mb'] + (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb']) * (Mb - self.qtlresults[i - 1]['Mb']) / (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb'])) break - #the trait's position is on the right of the last genotype - if i==len(self.qtlresults) and Mb>=qtlresult['Mb']: + # the trait's position is on the right of the last genotype + if i == len(self.qtlresults) and Mb >= qtlresult['Mb']: locPixel = -1 else: locPixel = xLeftOffset for i, _chr in enumerate(self.ChrList): - if i < (len(self.ChrList)-1): + if i < (len(self.ChrList) - 1): if _chr != Chr: - locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale + locPixel += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale else: - locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale + locPixel += (Mb * (_chr[-1].cM - _chr[0].cM) / self.ChrLengthCMList[i]) * plotXScale break if locPixel >= 0 and self.plotScale == 'physic': - traitPixel = ((locPixel, yZero), (locPixel-7, yZero+14), (locPixel+7, yZero+14)) + traitPixel = ((locPixel, yZero), (locPixel - 7, yZero + 14), (locPixel + 7, yZero + 14)) draw_open_polygon(canvas, xy=traitPixel, outline=BLACK, fill=self.TRANSCRIPT_LOCATION_COLOR) - def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): + def drawSNPTrackNew(self, canvas, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None): im_drawer = ImageDraw.Draw(canvas) if self.plotScale != 'physic' or self.selectedChr == -1 or not self.diffCol: return @@ -963,36 +963,36 @@ class DisplayMappingResults: #chrName = self.genotype[0].name chrName = self.ChrList[self.selectedChr][0] - stepMb = (endMb-startMb)/plotWidth + stepMb = (endMb - startMb) / plotWidth strainId1, strainId2 = self.diffCol SNPCounts = [] - while startMb= %2.6f AND Mb < %2.6f AND StrainId1 = %d AND StrainId2 = %d - """ % (chrName, startMb, startMb+stepMb, strainId1, strainId2)).fetchone()[0] + """ % (chrName, startMb, startMb + stepMb, strainId1, strainId2)).fetchone()[0] SNPCounts.append(snp_count) startMb += stepMb if (len(SNPCounts) > 0): maxCount = max(SNPCounts) - if maxCount>0: + if maxCount > 0: for i in range(xLeftOffset, xLeftOffset + plotWidth): - snpDensity = float(SNPCounts[i-xLeftOffset]*SNP_HEIGHT_MODIFIER/maxCount) + snpDensity = float(SNPCounts[i - xLeftOffset] * SNP_HEIGHT_MODIFIER / maxCount) im_drawer.line( - xy=((i, drawSNPLocationY+(snpDensity)*zoom), - (i, drawSNPLocationY-(snpDensity)*zoom)), + xy=((i, drawSNPLocationY + (snpDensity) * zoom), + (i, drawSNPLocationY - (snpDensity) * zoom)), fill=self.SNP_COLOR, width=1) - def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1): + def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset=(40, 120, 80, 10), zoom=1): nameWidths = [] yPaddingTop = 10 - colorFont=ImageFont.truetype(font=TREBUC_FILE, size=12) - if len(self.qtlresults) >20 and self.selectedChr > -1: + colorFont = ImageFont.truetype(font=TREBUC_FILE, size=12) + if len(self.qtlresults) > 20 and self.selectedChr > -1: rightShift = 20 rightShiftStep = 60 rectWidth = 10 @@ -1004,7 +1004,7 @@ class DisplayMappingResults: for k, thisTrait in enumerate(self.traitList): thisLRSColor = self.colorCollection[k] kstep = k % 4 - if k!=0 and kstep==0: + if k != 0 and kstep == 0: if nameWidths: rightShiftStep = max(nameWidths[-4:]) + rectWidth + 20 rightShift += rightShiftStep @@ -1014,19 +1014,19 @@ class DisplayMappingResults: nameWidths.append(nameWidth) im_drawer.rectangle( - xy=((rightShift, yPaddingTop+kstep*15), - (rectWidth+rightShift, yPaddingTop+10+kstep*15)), + xy=((rightShift, yPaddingTop + kstep * 15), + (rectWidth + rightShift, yPaddingTop + 10+kstep*15)), fill=thisLRSColor, outline=BLACK) im_drawer.text( - text=name, xy=(rectWidth+2+rightShift, yPaddingTop+10+kstep*15), + text=name, xy=(rectWidth + 2 + rightShift, yPaddingTop + 10 + kstep * 15), font=colorFont, fill=BLACK) if thisTrait.db: - COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift, yPaddingTop+kstep*15, rectWidth+2+rightShift+nameWidth, yPaddingTop+10+kstep*15,) - HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name) + COORDS = "%d,%d,%d,%d" % (rectWidth + 2 + rightShift, yPaddingTop + kstep * 15, rectWidth + 2 + rightShift + nameWidth, yPaddingTop + 10 + kstep * 15,) + HREF = "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name) Areas = HtmlGenWrapper.create_area_tag(shape='rect', coords=COORDS, href=HREF) - gifmap.append(Areas) ### TODO + gifmap.append(Areas) # TODO - def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1): + def drawLegendPanel(self, canvas, offset=(40, 120, 80, 10), zoom=1): im_drawer = ImageDraw.Draw(canvas) xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset plotWidth = canvas.size[0] - xLeftOffset - xRightOffset @@ -1037,80 +1037,80 @@ class DisplayMappingResults: if zoom == 2: fontZoom = 1.5 - labelFont=ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom) + labelFont = ImageFont.truetype(font=TREBUC_FILE, size=12 * fontZoom) startPosY = 15 - stepPosY = 12*fontZoom + stepPosY = 12 * fontZoom startPosX = canvas.size[0] - xRightOffset - 415 if hasattr(self.traitList[0], 'chr') and hasattr(self.traitList[0], 'mb'): startPosY = 15 nCol = 2 - smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom) + smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12 * fontZoom) leftOffset = canvas.size[0] - xRightOffset - 190 draw_open_polygon( canvas, xy=( - (leftOffset + 6, startPosY-7), - (leftOffset - 1, startPosY+7), - (leftOffset + 13, startPosY+7)), + (leftOffset + 6, startPosY - 7), + (leftOffset - 1, startPosY + 7), + (leftOffset + 13, startPosY + 7)), outline=BLACK, fill=self.TRANSCRIPT_LOCATION_COLOR ) TEXT_Y_DISPLACEMENT = -8 im_drawer.text( text="Sequence Site", - xy=(leftOffset + 20, startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont, + xy=(leftOffset + 20, startPosY + TEXT_Y_DISPLACEMENT), font=smallLabelFont, fill=self.TOP_RIGHT_INFO_COLOR) if self.manhattan_plot != True: im_drawer.line( - xy=((startPosX, startPosY), (startPosX+32, startPosY)), + xy=((startPosX, startPosY), (startPosX + 32, startPosY)), fill=self.LRS_COLOR, width=2) im_drawer.text( - text=self.LRS_LOD, xy=(startPosX+40, startPosY+TEXT_Y_DISPLACEMENT), + text=self.LRS_LOD, xy=(startPosX + 40, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) startPosY += stepPosY if self.additiveChecked: im_drawer.line( - xy=((startPosX, startPosY), (startPosX+17, startPosY)), + xy=((startPosX, startPosY), (startPosX + 17, startPosY)), fill=self.ADDITIVE_COLOR_POSITIVE, width=2) im_drawer.line( - xy=((startPosX+18, startPosY), (startPosX+32, startPosY)), + xy=((startPosX + 18, startPosY), (startPosX + 32, startPosY)), fill=self.ADDITIVE_COLOR_NEGATIVE, width=2) im_drawer.text( - text='Additive Effect', xy=(startPosX+40, startPosY+TEXT_Y_DISPLACEMENT), + text='Additive Effect', xy=(startPosX + 40, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) startPosY += stepPosY if self.genotype.type == 'intercross' and self.dominanceChecked: im_drawer.line( - xy=((startPosX, startPosY), (startPosX+17, startPosY)), + xy=((startPosX, startPosY), (startPosX + 17, startPosY)), fill=self.DOMINANCE_COLOR_POSITIVE, width=4) im_drawer.line( - xy=((startPosX+18, startPosY), (startPosX+35, startPosY)), + xy=((startPosX + 18, startPosY), (startPosX + 35, startPosY)), fill=self.DOMINANCE_COLOR_NEGATIVE, width=4) im_drawer.text( - text='Dominance Effect', xy=(startPosX+42, startPosY+5), + text='Dominance Effect', xy=(startPosX + 42, startPosY + 5), font=labelFont, fill=BLACK) startPosY += stepPosY if self.haplotypeAnalystChecked: im_drawer.line( - xy=((startPosX-34, startPosY), (startPosX-17, startPosY)), + xy=((startPosX - 34, startPosY), (startPosX - 17, startPosY)), fill=self.HAPLOTYPE_POSITIVE, width=4) im_drawer.line( - xy=((startPosX-17, startPosY), (startPosX, startPosY)), + xy=((startPosX - 17, startPosY), (startPosX, startPosY)), fill=self.HAPLOTYPE_NEGATIVE, width=4) im_drawer.line( - xy=((startPosX, startPosY), (startPosX+17, startPosY)), + xy=((startPosX, startPosY), (startPosX + 17, startPosY)), fill=self.HAPLOTYPE_HETEROZYGOUS, width=4) im_drawer.line( - xy=((startPosX+17, startPosY), (startPosX+34, startPosY)), + xy=((startPosX + 17, startPosY), (startPosX + 34, startPosY)), fill=self.HAPLOTYPE_RECOMBINATION, width=4) im_drawer.text( text='Haplotypes (Pat, Mat, Het, Unk)', - xy=(startPosX+41, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) + xy=(startPosX + 41, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) startPosY += stepPosY if self.permChecked and self.nperm > 0: @@ -1118,20 +1118,20 @@ class DisplayMappingResults: if self.multipleInterval and not self.bootChecked: thisStartX = canvas.size[0] - xRightOffset - 205 im_drawer.line( - xy=((thisStartX, startPosY), ( startPosX + 32, startPosY)), + xy=((thisStartX, startPosY), (startPosX + 32, startPosY)), fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH) im_drawer.line( - xy=((thisStartX, startPosY + stepPosY), ( startPosX + 32, startPosY + stepPosY)), + xy=((thisStartX, startPosY + stepPosY), (startPosX + 32, startPosY + stepPosY)), fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH) im_drawer.text( text='Significant %s = %2.2f' % (self.LRS_LOD, self.significant), - xy=(thisStartX+40, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) + xy=(thisStartX + 40, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) im_drawer.text( text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive), - xy=(thisStartX+40, startPosY + TEXT_Y_DISPLACEMENT +stepPosY), font=labelFont, + xy=(thisStartX + 40, startPosY + TEXT_Y_DISPLACEMENT + stepPosY), font=labelFont, fill=BLACK) - labelFont = ImageFont.truetype(font=VERDANA_FILE, size=12*fontZoom) + labelFont = ImageFont.truetype(font=VERDANA_FILE, size=12 * fontZoom) labelColor = BLACK if self.dataset.type == "Publish" or self.dataset.type == "Geno": @@ -1195,17 +1195,17 @@ class DisplayMappingResults: identification += "Trait: %s" % (self.this_trait.name) identification += " with %s samples" % (self.n_samples) - d = 4+ max( + d = 4 + max( im_drawer.textsize(identification, font=labelFont)[0], im_drawer.textsize(string1, font=labelFont)[0], im_drawer.textsize(string2, font=labelFont)[0]) im_drawer.text( text=identification, - xy=(xLeftOffset, y_constant*fontZoom), font=labelFont, + xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 else: - d = 4+ max( + d = 4 + max( im_drawer.textsize(string1, font=labelFont)[0], im_drawer.textsize(string2, font=labelFont)[0]) @@ -1223,28 +1223,28 @@ class DisplayMappingResults: transform_text += "Invert +/-" im_drawer.text( - text=transform_text, xy=(xLeftOffset, y_constant*fontZoom), + text=transform_text, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 im_drawer.text( - text=string1, xy=(xLeftOffset, y_constant*fontZoom), + text=string1, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 im_drawer.text( - text=string2, xy=(xLeftOffset, y_constant*fontZoom), + text=string2, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 if string3 != '': im_drawer.text( - text=string3, xy=(xLeftOffset, y_constant*fontZoom), + text=string3, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 if string4 != '': im_drawer.text( - text=string4, xy=(xLeftOffset, y_constant*fontZoom), + text=string4, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) - def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): + def drawGeneBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None): im_drawer = ImageDraw.Draw(canvas) if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol: return @@ -1264,9 +1264,9 @@ class DisplayMappingResults: if self.dataset.group.species == "mouse": txStart = theGO["TxStart"] txEnd = theGO["TxEnd"] - geneLength = (txEnd - txStart)*1000.0 - tenPercentLength = geneLength*0.0001 - SNPdensity = theGO["snpCount"]/geneLength + geneLength = (txEnd - txStart) * 1000.0 + tenPercentLength = geneLength * 0.0001 + SNPdensity = theGO["snpCount"] / geneLength exonStarts = list(map(float, theGO['exonStarts'].split(",")[:-1])) exonEnds = list(map(float, theGO['exonEnds'].split(",")[:-1])) @@ -1277,23 +1277,23 @@ class DisplayMappingResults: strand = theGO["Strand"] exonCount = theGO["exonCount"] - geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb) - geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) #at least one pixel + geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) + geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) # at least one pixel if (geneEndPix < xLeftOffset): - return; # this gene is not on the screen + return; # this gene is not on the screen elif (geneEndPix > xLeftOffset + plotWidth): - geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene + geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene if (geneStartPix > xLeftOffset + plotWidth): - return; # we are outside the valid on-screen range, so stop drawing genes + return; # we are outside the valid on-screen range, so stop drawing genes elif (geneStartPix < xLeftOffset): - geneStartPix = xLeftOffset; # clip the first in-range gene + geneStartPix = xLeftOffset; # clip the first in-range gene - #color the gene based on SNP density - #found earlier, needs to be recomputed as snps are added - #always apply colors now, even if SNP Track not checked - Zach 11/24/2010 + # color the gene based on SNP density + # found earlier, needs to be recomputed as snps are added + # always apply colors now, even if SNP Track not checked - Zach 11/24/2010 - densities=[1.0000000000000001e-05, 0.094094033555233408, 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0] + densities = [1.0000000000000001e-05, 0.094094033555233408, 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0] if SNPdensity < densities[0]: myColor = BLACK elif SNPdensity < densities[1]: @@ -1310,11 +1310,11 @@ class DisplayMappingResults: myColor = DARKRED outlineColor = myColor - fillColor = myColor + fillColor = myColor TITLE = "Gene: %s (%s)\nFrom %2.3f to %2.3f Mb (%s)\nNum. exons: %d." % (geneSymbol, accession, float(txStart), float(txEnd), strand, exonCount) # NL: 06-02-2011 Rob required to change this link for gene related - HREF=geneNCBILink %geneSymbol + HREF = geneNCBILink % geneSymbol elif self.dataset.group.species == "rat": exonStarts = [] @@ -1327,85 +1327,85 @@ class DisplayMappingResults: strand = theGO["Strand"] exonCount = 0 - geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb) - geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) #at least one pixel + geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) + geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) # at least one pixel if (geneEndPix < xLeftOffset): - return; # this gene is not on the screen + return; # this gene is not on the screen elif (geneEndPix > xLeftOffset + plotWidth): - geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene + geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene if (geneStartPix > xLeftOffset + plotWidth): - return; # we are outside the valid on-screen range, so stop drawing genes + return; # we are outside the valid on-screen range, so stop drawing genes elif (geneStartPix < xLeftOffset): - geneStartPix = xLeftOffset; # clip the first in-range gene + geneStartPix = xLeftOffset; # clip the first in-range gene outlineColor = DARKBLUE fillColor = DARKBLUE TITLE = "Gene: %s\nFrom %2.3f to %2.3f Mb (%s)" % (geneSymbol, float(txStart), float(txEnd), strand) # NL: 06-02-2011 Rob required to change this link for gene related - HREF=geneNCBILink %geneSymbol + HREF = geneNCBILink % geneSymbol else: outlineColor = ORANGE fillColor = ORANGE TITLE = "Gene: %s" % geneSymbol - #Draw Genes - geneYLocation = yPaddingTop + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT*zoom + # Draw Genes + geneYLocation = yPaddingTop + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT * zoom if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": - geneYLocation += 4*self.BAND_HEIGHT + 4*self.BAND_SPACING + geneYLocation += 4 * self.BAND_HEIGHT + 4 * self.BAND_SPACING else: - geneYLocation += 3*self.BAND_HEIGHT + 3*self.BAND_SPACING + geneYLocation += 3 * self.BAND_HEIGHT + 3 * self.BAND_SPACING - #draw the detail view + # draw the detail view if self.endMb - self.startMb <= self.DRAW_DETAIL_MB and geneEndPix - geneStartPix > self.EACH_GENE_ARROW_SPACING * 3: utrColor = ImageColor.getrgb("rgb(66%, 66%, 66%)") arrowColor = ImageColor.getrgb("rgb(70%, 70%, 70%)") - #draw the line that runs the entire length of the gene + # draw the line that runs the entire length of the gene im_drawer.line( xy=( - (geneStartPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom), - ( geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom)), + (geneStartPix, geneYLocation + self.EACH_GENE_HEIGHT / 2 * zoom), + (geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT / 2 *zoom)), fill=outlineColor, width=1) - #draw the arrows + # draw the arrows if geneEndPix - geneStartPix < 1: genePixRange = 1 else: genePixRange = int(geneEndPix - geneStartPix) for xCoord in range(0, genePixRange): - if (xCoord % self.EACH_GENE_ARROW_SPACING == 0 and xCoord + self.EACH_GENE_ARROW_SPACING < geneEndPix-geneStartPix) or xCoord == 0: + if (xCoord % self.EACH_GENE_ARROW_SPACING == 0 and xCoord + self.EACH_GENE_ARROW_SPACING < geneEndPix - geneStartPix) or xCoord == 0: if strand == "+": im_drawer.line( xy=((geneStartPix + xCoord, geneYLocation), (geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, - geneYLocation +(self.EACH_GENE_HEIGHT / 2)*zoom)), + geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)), fill=arrowColor, width=1) im_drawer.line( xy=((geneStartPix + xCoord, - geneYLocation + self.EACH_GENE_HEIGHT*zoom), - (geneStartPix + xCoord+self.EACH_GENE_ARROW_WIDTH, + geneYLocation + self.EACH_GENE_HEIGHT * zoom), + (geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)), fill=arrowColor, width=1) else: im_drawer.line( xy=((geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation), - ( geneStartPix + xCoord, - geneYLocation +(self.EACH_GENE_HEIGHT / 2)*zoom)), + (geneStartPix + xCoord, + geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)), fill=arrowColor, width=1) im_drawer.line( xy=((geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, - geneYLocation + self.EACH_GENE_HEIGHT*zoom), - ( geneStartPix + xCoord, - geneYLocation + (self.EACH_GENE_HEIGHT / 2)*zoom)), + geneYLocation + self.EACH_GENE_HEIGHT * zoom), + (geneStartPix + xCoord, + geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)), fill=arrowColor, width=1) - #draw the blocks for the exon regions + # draw the blocks for the exon regions for i in range(0, len(exonStarts)): - exonStartPix = (exonStarts[i]-startMb)*plotXScale + xLeftOffset - exonEndPix = (exonEnds[i]-startMb)*plotXScale + xLeftOffset + exonStartPix = (exonStarts[i] - startMb) * plotXScale + xLeftOffset + exonEndPix = (exonEnds[i] - startMb) * plotXScale + xLeftOffset if (exonStartPix < xLeftOffset): exonStartPix = xLeftOffset if (exonEndPix < xLeftOffset): @@ -1416,13 +1416,13 @@ class DisplayMappingResults: exonStartPix = xLeftOffset + plotWidth im_drawer.rectangle( xy=((exonStartPix, geneYLocation), - (exonEndPix, (geneYLocation + self.EACH_GENE_HEIGHT*zoom))), - outline = outlineColor, fill = fillColor) + (exonEndPix, (geneYLocation + self.EACH_GENE_HEIGHT * zoom))), + outline=outlineColor, fill=fillColor) - #draw gray blocks for 3' and 5' UTR blocks + # draw gray blocks for 3' and 5' UTR blocks if cdsStart and cdsEnd: - utrStartPix = (txStart-startMb)*plotXScale + xLeftOffset - utrEndPix = (cdsStart-startMb)*plotXScale + xLeftOffset + utrStartPix = (txStart - startMb) * plotXScale + xLeftOffset + utrEndPix = (cdsStart - startMb) * plotXScale + xLeftOffset if (utrStartPix < xLeftOffset): utrStartPix = xLeftOffset if (utrEndPix < xLeftOffset): @@ -1439,13 +1439,13 @@ class DisplayMappingResults: labelText = "5'" im_drawer.text( text=labelText, - xy=(utrStartPix-9, geneYLocation+self.EACH_GENE_HEIGHT), + xy=(utrStartPix - 9, geneYLocation + self.EACH_GENE_HEIGHT), font=ImageFont.truetype(font=ARIAL_FILE, size=2)) - #the second UTR region + # the second UTR region - utrStartPix = (cdsEnd-startMb)*plotXScale + xLeftOffset - utrEndPix = (txEnd-startMb)*plotXScale + xLeftOffset + utrStartPix = (cdsEnd - startMb) * plotXScale + xLeftOffset + utrEndPix = (txEnd - startMb) * plotXScale + xLeftOffset if (utrStartPix < xLeftOffset): utrStartPix = xLeftOffset if (utrEndPix < xLeftOffset): @@ -1462,17 +1462,17 @@ class DisplayMappingResults: labelText = "3'" im_drawer.text( text=labelText, - xy=(utrEndPix+2, geneYLocation+self.EACH_GENE_HEIGHT), + xy=(utrEndPix + 2, geneYLocation + self.EACH_GENE_HEIGHT), font=ImageFont.truetype(font=ARIAL_FILE, size=2)) - #draw the genes as rectangles + # draw the genes as rectangles else: im_drawer.rectangle( xy=((geneStartPix, geneYLocation), - (geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT*zoom))), - outline= outlineColor, fill = fillColor) + (geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT * zoom))), + outline=outlineColor, fill=fillColor) - COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT)) + COORDS = "%d, %d, %d, %d" % (geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT)) # NL: 06-02-2011 Rob required to display NCBI info in a new window gifmap.append( HtmlGenWrapper.create_area_tag( @@ -1482,8 +1482,8 @@ class DisplayMappingResults: title=TITLE, target="_blank")) -## BEGIN HaplotypeAnalyst - def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): +# BEGIN HaplotypeAnalyst + def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None): if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol: return @@ -1496,7 +1496,7 @@ class DisplayMappingResults: samplelist = list(self.genotype.prgy) - smd=[] + smd = [] for sample in self.sample_vals_dict.keys(): if self.sample_vals_dict[sample] != "x" and sample in samplelist: temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample])) @@ -1504,24 +1504,24 @@ class DisplayMappingResults: else: continue - smd.sort(key = lambda A: A.value) + smd.sort(key=lambda A: A.value) smd.reverse() oldgeneEndPix = -1 - #Initializing plotRight, error before + # Initializing plotRight, error before plotRight = xRightOffset im_drawer = ImageDraw.Draw(canvas) -#### find out PlotRight +# find out PlotRight for _chr in self.genotype: if _chr.name == self.ChrList[self.selectedChr][0]: for i, _locus in enumerate(_chr): txStart = _chr[i].Mb - txEnd = _chr[i].Mb + txEnd = _chr[i].Mb - geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb) - 0 - geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) - 0 + geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) - 0 + geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) - 0 drawit = 1 if (geneStartPix < xLeftOffset): @@ -1530,27 +1530,27 @@ class DisplayMappingResults: drawit = 0; if drawit == 1: - if _chr[i].name != " - " : + if _chr[i].name != " - ": plotRight = geneEndPix + 4 -#### end find out PlotRight +# end find out PlotRight firstGene = 1 lastGene = 0 - #Sets the length to the length of the strain list. Beforehand, "oldgeno = self.genotype[0][i].genotype" - #was the only place it was initialized, which worked as long as the very start (startMb = None/0) wasn't being mapped. - #Now there should always be some value set for "oldgeno" - Zach 12/14/2010 - oldgeno = [None]*len(self.strainlist) + # Sets the length to the length of the strain list. Beforehand, "oldgeno = self.genotype[0][i].genotype" + # was the only place it was initialized, which worked as long as the very start (startMb = None/0) wasn't being mapped. + # Now there should always be some value set for "oldgeno" - Zach 12/14/2010 + oldgeno = [None] * len(self.strainlist) for i, _chr in enumerate(self.genotype): if _chr.name == self.ChrList[self.selectedChr][0]: for j, _locus in enumerate(_chr): txStart = _chr[j].Mb - txEnd = _chr[j].Mb + txEnd = _chr[j].Mb - geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb) - 0 - geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) + 0 + geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) - 0 + geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) + 0 if oldgeneEndPix >= xLeftOffset: drawStart = oldgeneEndPix + 4 @@ -1582,36 +1582,36 @@ class DisplayMappingResults: if drawit == 1: myColor = DARKBLUE outlineColor = myColor - fillColor = myColor + fillColor = myColor - maxind=0 + maxind = 0 - #Draw Genes + # Draw Genes - geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT)*zoom + geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT) * zoom if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": - geneYLocation += 4*self.BAND_HEIGHT + 4*self.BAND_SPACING + geneYLocation += 4 * self.BAND_HEIGHT + 4 * self.BAND_SPACING else: - geneYLocation += 3*self.BAND_HEIGHT + 3*self.BAND_SPACING + geneYLocation += 3 * self.BAND_HEIGHT + 3 * self.BAND_SPACING - if _chr[j].name != " - " : + if _chr[j].name != " - ": if (firstGene == 1) and (lastGene != 1): oldgeneEndPix = drawStart = xLeftOffset oldgeno = _chr[j].genotype continue - for k, _geno in enumerate (_chr[j].genotype): - plotbxd=0 + for k, _geno in enumerate(_chr[j].genotype): + plotbxd = 0 if samplelist[k] in [item.name for item in smd]: - plotbxd=1 + plotbxd = 1 if (plotbxd == 1): ind = 0 if samplelist[k] in [item.name for item in smd]: ind = [item.name for item in smd].index(samplelist[k]) - maxind=max(ind, maxind) + maxind = max(ind, maxind) # lines if (oldgeno[k] == -1 and _geno == -1): @@ -1621,27 +1621,27 @@ class DisplayMappingResults: elif (oldgeno[k] == 0 and _geno == 0): mylineColor = self.HAPLOTYPE_HETEROZYGOUS else: - mylineColor = self.HAPLOTYPE_RECOMBINATION # XZ: Unknown + mylineColor = self.HAPLOTYPE_RECOMBINATION # XZ: Unknown im_drawer.line( xy=((drawStart, - geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom), + geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom), (drawEnd, - geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom)), - fill= mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2)) + geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)), + fill= mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2)) - fillColor=BLACK - outlineColor=BLACK + fillColor = BLACK + outlineColor = BLACK if lastGene == 0: im_drawer.rectangle( xy=((geneStartPix, - geneYLocation+2*ind*self.EACH_GENE_HEIGHT*zoom), + geneYLocation + 2 * ind*self.EACH_GENE_HEIGHT*zoom), (geneEndPix, - geneYLocation+2*ind*self.EACH_GENE_HEIGHT+ 2*self.EACH_GENE_HEIGHT*zoom)), + geneYLocation + 2 *ind*self.EACH_GENE_HEIGHT + 2*self.EACH_GENE_HEIGHT*zoom)), outline=outlineColor, fill=fillColor) - COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT)) + COORDS = "%d, %d, %d, %d" % (geneStartPix, geneYLocation + ind * self.EACH_GENE_HEIGHT, geneEndPix + 1, (geneYLocation + ind * self.EACH_GENE_HEIGHT)) TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart)) HREF = '' gifmap.append( @@ -1658,10 +1658,10 @@ class DisplayMappingResults: mylineColor = self.HAPLOTYPE_RECOMBINATION im_drawer.line( xy=((plotRight, - geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom), + geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom), (drawEnd, - geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom)), - fill= mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2)) + geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)), + fill= mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2)) if lastGene == 0: @@ -1670,7 +1670,7 @@ class DisplayMappingResults: font=ImageFont.truetype(font=VERDANA_FILE, size=12), xy=(geneStartPix, - geneYLocation+17+2*maxind*self.EACH_GENE_HEIGHT*zoom), + geneYLocation + 17 + 2*maxind*self.EACH_GENE_HEIGHT*zoom), fill=BLACK, angle=-90) oldgeneEndPix = geneEndPix; @@ -1683,9 +1683,9 @@ class DisplayMappingResults: if _chr.name == self.ChrList[self.selectedChr][0]: for j, _geno in enumerate(_chr[1].genotype): - plotbxd=0 + plotbxd = 0 if samplelist[j] in [item.name for item in smd]: - plotbxd=1 + plotbxd = 1 if (plotbxd == 1): ind = [item.name for item in smd].index(samplelist[j]) - 1 @@ -1695,19 +1695,19 @@ class DisplayMappingResults: im_drawer.text( text="%s" % (samplelist[j]), xy=((xLeftOffset + plotWidth + 10), - geneYLocation+11+2*ind*self.EACH_GENE_HEIGHT*zoom), + geneYLocation + 11 + 2*ind*self.EACH_GENE_HEIGHT*zoom), font=ImageFont.truetype(font=VERDANA_FILE, size=12), fill=BLACK) im_drawer.text( text="%2.2f" % (expr), xy=((xLeftOffset + plotWidth + 60), - geneYLocation+11+2*ind*self.EACH_GENE_HEIGHT*zoom), + geneYLocation + 11 + 2*ind*self.EACH_GENE_HEIGHT*zoom), font=ImageFont.truetype(font=VERDANA_FILE, size=12), fill=BLACK) -## END HaplotypeAnalyst +# END HaplotypeAnalyst - def drawClickBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): + def drawClickBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None): im_drawer = ImageDraw.Draw(canvas) if self.plotScale != 'physic' or self.selectedChr == -1: return @@ -1724,12 +1724,12 @@ class DisplayMappingResults: # but it makes the HTML huge, and takes forever to render the page in the first place) # Draw the bands that you can click on to go to UCSC / Ensembl MAX_CLICKABLE_REGION_DIVISIONS = 100 - clickableRegionLabelFont=ImageFont.truetype(font=VERDANA_FILE, size=9) - pixelStep = max(5, int(float(plotWidth)/MAX_CLICKABLE_REGION_DIVISIONS)) + clickableRegionLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=9) + pixelStep = max(5, int(float(plotWidth) / MAX_CLICKABLE_REGION_DIVISIONS)) # pixelStep: every N pixels, we make a new clickable area for the user to go to that area of the genome. - numBasesCurrentlyOnScreen = self.kONE_MILLION*abs(startMb - endMb) # Number of bases on screen now - flankingWidthInBases = int ( min( (float(numBasesCurrentlyOnScreen) / 2.0), (5*self.kONE_MILLION) ) ) + numBasesCurrentlyOnScreen = self.kONE_MILLION * abs(startMb - endMb) # Number of bases on screen now + flankingWidthInBases = int (min((float(numBasesCurrentlyOnScreen) / 2.0), (5*self.kONE_MILLION))) webqtlZoomWidth = numBasesCurrentlyOnScreen / 16.0 # Flanking width should be such that we either zoom in to a 10 million base region, or we show the clicked region at the same scale as we are currently seeing. @@ -1739,22 +1739,22 @@ class DisplayMappingResults: paddingTop = yTopOffset if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": phenogenPaddingTop = paddingTop + (self.BAND_HEIGHT + self.BAND_SPACING) - ucscPaddingTop = paddingTop + 2*(self.BAND_HEIGHT + self.BAND_SPACING) - ensemblPaddingTop = paddingTop + 3*(self.BAND_HEIGHT + self.BAND_SPACING) + ucscPaddingTop = paddingTop + 2 * (self.BAND_HEIGHT + self.BAND_SPACING) + ensemblPaddingTop = paddingTop + 3 * (self.BAND_HEIGHT + self.BAND_SPACING) else: ucscPaddingTop = paddingTop + (self.BAND_HEIGHT + self.BAND_SPACING) - ensemblPaddingTop = paddingTop + 2*(self.BAND_HEIGHT + self.BAND_SPACING) + ensemblPaddingTop = paddingTop + 2 * (self.BAND_HEIGHT + self.BAND_SPACING) if zoom == 1: for pixel in range(xLeftOffset, xLeftOffset + plotWidth, pixelStep): - calBase = self.kONE_MILLION*(startMb + (endMb-startMb)*(pixel-xLeftOffset-0.0)/plotWidth) + calBase = self.kONE_MILLION * (startMb + (endMb - startMb) * (pixel - xLeftOffset - 0.0) / plotWidth) xBrowse1 = pixel xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1)) - WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop+self.BAND_HEIGHT)) - WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0) + WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop + self.BAND_HEIGHT)) + WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase - webqtlZoomWidth)) / 1000000.0, (calBase + webqtlZoomWidth) / 1000000.0) WEBQTL_TITLE = "Click to view this section of the genome in WebQTL" gifmap.append( @@ -1769,15 +1769,15 @@ class DisplayMappingResults: outline=self.CLICKABLE_WEBQTL_REGION_COLOR, fill=self.CLICKABLE_WEBQTL_REGION_COLOR) im_drawer.line( - xy=((xBrowse1, paddingTop), ( xBrowse1, (paddingTop + self.BAND_HEIGHT))), + xy=((xBrowse1, paddingTop), (xBrowse1, (paddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR) if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": - PHENOGEN_COORDS = "%d, %d, %d, %d" % (xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT)) + PHENOGEN_COORDS = "%d, %d, %d, %d" % (xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop + self.BAND_HEIGHT)) if self.dataset.group.species == "mouse": - PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) + PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) else: - PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) + PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen" gifmap.append( HtmlGenWrapper.create_area_tag( @@ -1787,18 +1787,18 @@ class DisplayMappingResults: title=PHENOGEN_TITLE)) im_drawer.rectangle( xy=((xBrowse1, phenogenPaddingTop), - (xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT))), + (xBrowse2, (phenogenPaddingTop + self.BAND_HEIGHT))), outline=self.CLICKABLE_PHENOGEN_REGION_COLOR, fill=self.CLICKABLE_PHENOGEN_REGION_COLOR) im_drawer.line( - xy=((xBrowse1, phenogenPaddingTop), ( xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT))), + xy=((xBrowse1, phenogenPaddingTop), (xBrowse1, (phenogenPaddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR) - UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT)) + UCSC_COORDS = "%d, %d, %d, %d" % (xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop + self.BAND_HEIGHT)) if self.dataset.group.species == "mouse": - UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr) + UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr) else: - UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) + UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser" gifmap.append( HtmlGenWrapper.create_area_tag( @@ -1808,19 +1808,19 @@ class DisplayMappingResults: title=UCSC_TITLE)) im_drawer.rectangle( xy=((xBrowse1, ucscPaddingTop), - (xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))), + (xBrowse2, (ucscPaddingTop + self.BAND_HEIGHT))), outline=self.CLICKABLE_UCSC_REGION_COLOR, fill=self.CLICKABLE_UCSC_REGION_COLOR) im_drawer.line( xy=((xBrowse1, ucscPaddingTop), - (xBrowse1, (ucscPaddingTop+self.BAND_HEIGHT))), + (xBrowse1, (ucscPaddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR) - ENSEMBL_COORDS = "%d, %d, %d, %d" %(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT)) + ENSEMBL_COORDS = "%d, %d, %d, %d" % (xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop + self.BAND_HEIGHT)) if self.dataset.group.species == "mouse": - ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) + ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) else: - ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) + ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser" gifmap.append(HtmlGenWrapper.create_area_tag( shape='rect', @@ -1829,36 +1829,36 @@ class DisplayMappingResults: title=ENSEMBL_TITLE)) im_drawer.rectangle( xy=((xBrowse1, ensemblPaddingTop), - (xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT))), + (xBrowse2, (ensemblPaddingTop + self.BAND_HEIGHT))), outline=self.CLICKABLE_ENSEMBL_REGION_COLOR, fill=self.CLICKABLE_ENSEMBL_REGION_COLOR) im_drawer.line( xy=((xBrowse1, ensemblPaddingTop), - (xBrowse1, (ensemblPaddingTop+self.BAND_HEIGHT))), + (xBrowse1, (ensemblPaddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR) # end for im_drawer.text( text="Click to view the corresponding section of the genome in an 8x expanded WebQTL map", - xy=((xLeftOffset + 10), paddingTop),# + self.BAND_HEIGHT/2), + xy=((xLeftOffset + 10), paddingTop), # + self.BAND_HEIGHT/2), font=clickableRegionLabelFont, fill=self.CLICKABLE_WEBQTL_TEXT_COLOR) if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": im_drawer.text( text="Click to view the corresponding section of the genome in PhenoGen", - xy=((xLeftOffset + 10), phenogenPaddingTop),# + self.BAND_HEIGHT/2), + xy=((xLeftOffset + 10), phenogenPaddingTop), # + self.BAND_HEIGHT/2), font=clickableRegionLabelFont, fill=self.CLICKABLE_PHENOGEN_TEXT_COLOR) im_drawer.text( text="Click to view the corresponding section of the genome in the UCSC Genome Browser", - xy=((xLeftOffset + 10), ucscPaddingTop),# + self.BAND_HEIGHT/2), + xy=((xLeftOffset + 10), ucscPaddingTop), # + self.BAND_HEIGHT/2), font=clickableRegionLabelFont, fill=self.CLICKABLE_UCSC_TEXT_COLOR) im_drawer.text( text="Click to view the corresponding section of the genome in the Ensembl Genome Browser", - xy=((xLeftOffset+10), ensemblPaddingTop),# + self.BAND_HEIGHT/2), + xy=((xLeftOffset + 10), ensemblPaddingTop), # + self.BAND_HEIGHT/2), font=clickableRegionLabelFont, fill=self.CLICKABLE_ENSEMBL_TEXT_COLOR) - #draw the gray text - chrFont = ImageFont.truetype(font=VERDANA_BOLD_FILE, size=26*zoom) + # draw the gray text + chrFont = ImageFont.truetype(font=VERDANA_BOLD_FILE, size=26 * zoom) chrX = xLeftOffset + plotWidth - 2 - im_drawer.textsize( "Chr %s" % self.ChrList[self.selectedChr][0], font=chrFont)[0] im_drawer.text( @@ -1866,17 +1866,17 @@ class DisplayMappingResults: xy=(chrX, phenogenPaddingTop), font=chrFont, fill=GRAY) # end of drawBrowserClickableRegions else: - #draw the gray text - chrFont = ImageFont.truetype(font=VERDANA_FILE, size=26*zoom) + # draw the gray text + chrFont = ImageFont.truetype(font=VERDANA_FILE, size=26 * zoom) chrX = xLeftOffset + (plotWidth - im_drawer.textsize( - "Chr %s" % currentChromosome, font=chrFont)[0])/2 + "Chr %s" % currentChromosome, font=chrFont)[0]) / 2 im_drawer.text( text="Chr %s" % currentChromosome, xy=(chrX, 32), font=chrFont, fill=GRAY) # end of drawBrowserClickableRegions pass - def drawXAxis(self, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): + def drawXAxis(self, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None): im_drawer = ImageDraw.Draw(canvas) xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset plotWidth = canvas.size[0] - xLeftOffset - xRightOffset @@ -1886,33 +1886,33 @@ class DisplayMappingResults: if zoom == 2: fontZoom = 1.5 - #Parameters - NUM_MINOR_TICKS = 5 # Number of minor ticks between major ticks + # Parameters + NUM_MINOR_TICKS = 5 # Number of minor ticks between major ticks X_MAJOR_TICK_THICKNESS = 3 X_MINOR_TICK_THICKNESS = 1 - X_AXIS_THICKNESS = 1*zoom + X_AXIS_THICKNESS = 1 * zoom # ======= Alex: Draw the X-axis labels (megabase location) - MBLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=15*zoom) - xMajorTickHeight = 10 * zoom # How high the tick extends below the axis - xMinorTickHeight = 5*zoom + MBLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=15 * zoom) + xMajorTickHeight = 10 * zoom # How high the tick extends below the axis + xMinorTickHeight = 5 * zoom xAxisTickMarkColor = BLACK xAxisLabelColor = BLACK - fontHeight = 12*fontZoom # How tall the font that we're using is + fontHeight = 12 * fontZoom # How tall the font that we're using is spacingFromLabelToAxis = 10 if self.plotScale == 'physic': - strYLoc = yZero + MBLabelFont.font.height/2 - ###Physical single chromosome view + strYLoc = yZero + MBLabelFont.font.height / 2 + # Physical single chromosome view if self.selectedChr > -1: XScale = Plot.detScale(startMb, endMb) XStart, XEnd, XStep = XScale if XStep < 8: XStep *= 2 - spacingAmtX = spacingAmt = (XEnd-XStart)/XStep + spacingAmtX = spacingAmt = (XEnd - XStart) / XStep j = 0 - while abs(spacingAmtX -int(spacingAmtX)) >= spacingAmtX/100.0 and j < 6: + while abs(spacingAmtX - int(spacingAmtX)) >= spacingAmtX / 100.0 and j < 6: j += 1 spacingAmtX *= 10 @@ -1921,13 +1921,13 @@ class DisplayMappingResults: for counter, _Mb in enumerate(Plot.frange(XStart, XEnd, spacingAmt / NUM_MINOR_TICKS)): if _Mb < startMb or _Mb > endMb: continue - Xc = xLeftOffset + plotXScale*(_Mb - startMb) - if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark + Xc = xLeftOffset + plotXScale * (_Mb - startMb) + if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark im_drawer.line(xy=((Xc, yZero), - (Xc, yZero+xMajorTickHeight)), + (Xc, yZero + xMajorTickHeight)), fill=xAxisTickMarkColor, - width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark - labelStr = str(formatStr % _Mb) # What Mbase location to put on the label + width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark + labelStr = str(formatStr % _Mb) # What Mbase location to put on the label strWidth, strHeight = im_drawer.textsize(labelStr, font=MBLabelFont) drawStringXc = (Xc - (strWidth / 2.0)) im_drawer.text(xy=(drawStringXc, strYLoc), @@ -1935,16 +1935,16 @@ class DisplayMappingResults: fill=xAxisLabelColor) else: im_drawer.line(xy=((Xc, yZero), - (Xc, yZero+xMinorTickHeight)), + (Xc, yZero + xMinorTickHeight)), fill=xAxisTickMarkColor, - width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark + width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark - ###Physical genome wide view + # Physical genome wide view else: distScale = 0 startPosX = xLeftOffset for i, distLen in enumerate(self.ChrLengthDistList): - if distScale == 0: #universal scale in whole genome mapping + if distScale == 0: # universal scale in whole genome mapping if distLen > 75: distScale = 25 elif distLen > 30: @@ -1953,51 +1953,51 @@ class DisplayMappingResults: distScale = 5 for j, tickdists in enumerate(range(distScale, int(ceil(distLen)), distScale)): im_drawer.line( - xy=((startPosX+tickdists*plotXScale, yZero), - (startPosX+tickdists*plotXScale, yZero + 7)), - fill=BLACK, width=1*zoom) + xy=((startPosX + tickdists * plotXScale, yZero), + (startPosX + tickdists * plotXScale, yZero + 7)), + fill=BLACK, width=1 * zoom) if j % 2 == 0: draw_rotated_text( canvas, text=str(tickdists), font=MBLabelFont, - xy=(startPosX+tickdists*plotXScale, - yZero+10*zoom), fill=BLACK, angle=270) - startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale + xy=(startPosX + tickdists * plotXScale, + yZero + 10 * zoom), fill=BLACK, angle=270) + startPosX += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale - megabaseLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18*zoom*1.5)) + megabaseLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5)) im_drawer.text( text="Megabases", xy=( - xLeftOffset+(plotWidth-im_drawer.textsize( - "Megabases", font=megabaseLabelFont)[0])/2, - strYLoc+MBLabelFont.font.height+10*(zoom%2)), + xLeftOffset + (plotWidth - im_drawer.textsize( + "Megabases", font=megabaseLabelFont)[0]) / 2, + strYLoc + MBLabelFont.font.height + 10*(zoom%2)), font=megabaseLabelFont, fill=BLACK) pass else: - strYLoc = yZero + spacingFromLabelToAxis + MBLabelFont.font.height/2 + strYLoc = yZero + spacingFromLabelToAxis + MBLabelFont.font.height / 2 ChrAInfo = [] preLpos = -1 distinctCount = 0.0 - if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes + if self.selectedChr == -1: # ZS: If viewing full genome/all chromosomes for i, _chr in enumerate(self.genotype): thisChr = [] Locus0CM = _chr[0].cM nLoci = len(_chr) - if nLoci <= 8: + if nLoci <= 8: for _locus in _chr: if _locus.name != ' - ': if _locus.cM != preLpos: distinctCount += 1 preLpos = _locus.cM - thisChr.append([_locus.name, _locus.cM-Locus0CM]) + thisChr.append([_locus.name, _locus.cM - Locus0CM]) else: - for j in (0, nLoci/4, nLoci/2, nLoci*3/4, -1): + for j in (0, nLoci / 4, nLoci / 2, nLoci*3/4, -1): while _chr[j].name == ' - ': j += 1 if _chr[j].cM != preLpos: distinctCount += 1 preLpos = _chr[j].cM - thisChr.append([_chr[j].name, _chr[j].cM-Locus0CM]) + thisChr.append([_chr[j].name, _chr[j].cM - Locus0CM]) ChrAInfo.append(thisChr) else: for i, _chr in enumerate(self.genotype): @@ -2009,10 +2009,10 @@ class DisplayMappingResults: if _locus.cM != preLpos: distinctCount += 1 preLpos = _locus.cM - thisChr.append([_locus.name, _locus.cM-Locus0CM]) + thisChr.append([_locus.name, _locus.cM - Locus0CM]) ChrAInfo.append(thisChr) - stepA = (plotWidth+0.0)/distinctCount + stepA = (plotWidth + 0.0) / distinctCount LRectWidth = 10 LRectHeight = 3 @@ -2037,28 +2037,28 @@ class DisplayMappingResults: Zorder = 0 if differ: im_drawer.line( - xy=((startPosX+Lpos, yZero), (xLeftOffset+offsetA,\ - yZero+25)), + xy=((startPosX + Lpos, yZero), (xLeftOffset + offsetA,\ + yZero + 25)), fill=lineColor) im_drawer.line( - xy=((xLeftOffset+offsetA, yZero+25), (xLeftOffset+offsetA,\ - yZero+40+Zorder*(LRectWidth+3))), + xy=((xLeftOffset + offsetA, yZero + 25), (xLeftOffset+offsetA,\ + yZero + 40 + Zorder*(LRectWidth+3))), fill=lineColor) rectColor = ORANGE else: im_drawer.line( - xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3), (\ - xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3))), + xy=((xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3)-3), (\ + xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3))), fill=lineColor) rectColor = DEEPPINK im_drawer.rectangle( - xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)), - (xLeftOffset+offsetA-LRectHeight, - yZero+40+Zorder*(LRectWidth+3)+LRectWidth)), - outline=rectColor, fill=rectColor, width = 0) - COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\ - xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth) - HREF = "/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno") + xy=((xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3)), + (xLeftOffset + offsetA - LRectHeight, + yZero + 40 + Zorder*(LRectWidth+3)+LRectWidth)), + outline=rectColor, fill=rectColor, width=0) + COORDS = "%d,%d,%d,%d" % (xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\ + xLeftOffset + offsetA, yZero +40+Zorder*(LRectWidth+3)+LRectWidth) + HREF = "/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name + "Geno") #HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname) Areas = HtmlGenWrapper.create_area_tag( shape='rect', @@ -2067,26 +2067,26 @@ class DisplayMappingResults: target="_blank", title="Locus : {}".format(Lname)) gifmap.append(Areas) - ##piddle bug + # piddle bug if j == 0: im_drawer.line( - xy=((startPosX, yZero), (startPosX, yZero+40)), + xy=((startPosX, yZero), (startPosX, yZero + 40)), fill=lineColor) - startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale + startPosX += (self.ChrLengthDistList[j] + self.GraphInterval) * plotXScale - centimorganLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18*zoom*1.5)) + centimorganLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5)) im_drawer.text( text="Centimorgans", - xy=(xLeftOffset+(plotWidth-im_drawer.textsize( - "Centimorgans", font=centimorganLabelFont)[0])/2, - strYLoc + MBLabelFont.font.height+ 10*(zoom%2)), + xy=(xLeftOffset + (plotWidth - im_drawer.textsize( + "Centimorgans", font=centimorganLabelFont)[0]) / 2, + strYLoc + MBLabelFont.font.height + 10 * (zoom %2)), font=centimorganLabelFont, fill=BLACK) - im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset+plotWidth, yZero)), - fill=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself + im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset + plotWidth, yZero)), + fill=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself - def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): + def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None): im_drawer = ImageDraw.Draw(canvas) xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset plotWidth = canvas.size[0] - xLeftOffset - xRightOffset @@ -2095,16 +2095,16 @@ class DisplayMappingResults: if zoom == 2: fontZoom = 1.5 - INTERCROSS = (self.genotype.type=="intercross") + INTERCROSS = (self.genotype.type == "intercross") - #draw the LRS scale - #We first determine whether or not we are using a sliding scale. - #If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRS_LOD_Max. - #LRSTop is then defined to be above the LRS_LOD_Max by enough to add one additional LRSScale increment. - #if we are using a set-scale, then we set LRSTop to be the user's value, and LRS_LOD_Max doesn't matter. + # draw the LRS scale + # We first determine whether or not we are using a sliding scale. + # If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRS_LOD_Max. + # LRSTop is then defined to be above the LRS_LOD_Max by enough to add one additional LRSScale increment. + # if we are using a set-scale, then we set LRSTop to be the user's value, and LRS_LOD_Max doesn't matter. - #ZS: This is a mess, but I don't know a better way to account for different mapping methods returning results in different formats + the option to change between LRS and LOD - if self.lrsMax <= 0: #sliding scale + # ZS: This is a mess, but I don't know a better way to account for different mapping methods returning results in different formats + the option to change between LRS and LOD + if self.lrsMax <= 0: # sliding scale if "lrs_value" in self.qtlresults[0]: LRS_LOD_Max = max([result['lrs_value'] for result in self.qtlresults]) if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP": @@ -2135,34 +2135,34 @@ class DisplayMappingResults: if self.permChecked and self.nperm > 0 and not self.multipleInterval: LRS_LOD_Max = max(self.significant, LRS_LOD_Max) - #genotype trait will give infinite LRS + # genotype trait will give infinite LRS LRS_LOD_Max = min(LRS_LOD_Max, webqtlConfig.MAXLRS) else: LRS_LOD_Max = self.lrsMax - #ZS: Needed to pass to genome browser + # ZS: Needed to pass to genome browser js_data = json.loads(self.js_data) if self.LRS_LOD == "LRS": - js_data['max_score'] = LRS_LOD_Max/4.61 + js_data['max_score'] = LRS_LOD_Max / 4.61 else: js_data['max_score'] = LRS_LOD_Max self.js_data = json.dumps(js_data) - LRSScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=16*zoom) - LRSLODFont=ImageFont.truetype(font=VERDANA_FILE, size=int(18*zoom*1.5)) + LRSScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom) + LRSLODFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5)) yZero = yTopOffset + plotHeight # LRSHeightThresh = drawAreaHeight # AdditiveHeightThresh = drawAreaHeight/2 # DominanceHeightThresh = drawAreaHeight/2 if self.selectedChr == 1: - LRSHeightThresh = drawAreaHeight - yTopOffset + 30*(zoom - 1) - AdditiveHeightThresh = LRSHeightThresh/2 - DominanceHeightThresh = LRSHeightThresh/2 + LRSHeightThresh = drawAreaHeight - yTopOffset + 30 * (zoom - 1) + AdditiveHeightThresh = LRSHeightThresh / 2 + DominanceHeightThresh = LRSHeightThresh / 2 else: LRSHeightThresh = drawAreaHeight - AdditiveHeightThresh = drawAreaHeight/2 - DominanceHeightThresh = drawAreaHeight/2 + AdditiveHeightThresh = drawAreaHeight / 2 + DominanceHeightThresh = drawAreaHeight / 2 # LRSHeightThresh = (yZero - yTopOffset + 30*(zoom - 1)) # AdditiveHeightThresh = LRSHeightThresh/2 # DominanceHeightThresh = LRSHeightThresh/2 @@ -2178,7 +2178,7 @@ class DisplayMappingResults: LRSAxisList = Plot.frange(LRSScale, LRS_LOD_Max, LRSScale) - #ZS: Convert to int if all axis values are whole numbers + # ZS: Convert to int if all axis values are whole numbers all_int = True for item in LRSAxisList: if isinstance(item, int): @@ -2192,9 +2192,9 @@ class DisplayMappingResults: # else: # max_lrs_width = canvas.stringWidth("%2.1f" % LRS_LOD_Max, font=LRSScaleFont) + 30 - #draw the "LRS" or "LOD" string to the left of the axis - LRSScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=16*zoom) - LRSLODFont=ImageFont.truetype(font=VERDANA_FILE, size=int(18*zoom*1.5)) + # draw the "LRS" or "LOD" string to the left of the axis + LRSScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom) + LRSLODFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5)) yZero = yTopOffset + plotHeight # TEXT_X_DISPLACEMENT = -20 @@ -2210,64 +2210,64 @@ class DisplayMappingResults: draw_rotated_text( canvas, text=self.LRS_LOD, font=LRSLODFont, xy=(xLeftOffset - im_drawer.textsize( - "999.99", font=LRSScaleFont)[0] - 15*(zoom-1) + TEXT_X_DISPLACEMENT, - yZero + TEXT_Y_DISPLACEMENT - 300*(zoom - 1)), + "999.99", font=LRSScaleFont)[0] - 15 * (zoom - 1) + TEXT_X_DISPLACEMENT, + yZero + TEXT_Y_DISPLACEMENT - 300 * (zoom - 1)), fill=BLACK, angle=90) for item in LRSAxisList: if LRS_LOD_Max == 0.0: LRS_LOD_Max = 0.000001 - yTopOffset + 30*(zoom - 1) - yLRS = yZero - (item/LRS_LOD_Max) * LRSHeightThresh - im_drawer.line(xy=((xLeftOffset, yLRS), (xLeftOffset-4, yLRS)), - fill=self.LRS_COLOR, width=1*zoom) + yTopOffset + 30 * (zoom - 1) + yLRS = yZero - (item / LRS_LOD_Max) * LRSHeightThresh + im_drawer.line(xy=((xLeftOffset, yLRS), (xLeftOffset - 4, yLRS)), + fill=self.LRS_COLOR, width=1 * zoom) if all_int: scaleStr = "%d" % item else: scaleStr = "%2.1f" % item - #Draw the LRS/LOD Y axis label + # Draw the LRS/LOD Y axis label TEXT_Y_DISPLACEMENT = -10 im_drawer.text( text=scaleStr, - xy=(xLeftOffset-4-im_drawer.textsize(scaleStr, font=LRSScaleFont)[0]-5, - yLRS+TEXT_Y_DISPLACEMENT), + xy=(xLeftOffset - 4 - im_drawer.textsize(scaleStr, font=LRSScaleFont)[0]-5, + yLRS + TEXT_Y_DISPLACEMENT), font=LRSScaleFont, fill=self.LRS_COLOR) if self.permChecked and self.nperm > 0 and not self.multipleInterval: - significantY = yZero - self.significant*LRSHeightThresh/LRS_LOD_Max - suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRS_LOD_Max + significantY = yZero - self.significant * LRSHeightThresh / LRS_LOD_Max + suggestiveY = yZero - self.suggestive * LRSHeightThresh / LRS_LOD_Max # significantY = yZero - self.significant*LRSHeightThresh/LRSAxisList[-1] # suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRSAxisList[-1] startPosX = xLeftOffset - #"Significant" and "Suggestive" Drawing Routine + # "Significant" and "Suggestive" Drawing Routine # ======= Draw the thick lines for "Significant" and "Suggestive" ===== (crowell: I tried to make the SNPs draw over these lines, but piddle wouldn't have it...) - #ZS: I don't know if what I did here with this inner function is clever or overly complicated, but it's the only way I could think of to avoid duplicating the code inside this function + # ZS: I don't know if what I did here with this inner function is clever or overly complicated, but it's the only way I could think of to avoid duplicating the code inside this function def add_suggestive_significant_lines_and_legend(start_pos_x, chr_length_dist): - rightEdge = int(start_pos_x + chr_length_dist*plotXScale - self.SUGGESTIVE_WIDTH/1.5) + rightEdge = int(start_pos_x + chr_length_dist * plotXScale - self.SUGGESTIVE_WIDTH / 1.5) im_drawer.line( - xy=((start_pos_x+self.SUGGESTIVE_WIDTH/1.5, suggestiveY), + xy=((start_pos_x + self.SUGGESTIVE_WIDTH / 1.5, suggestiveY), (rightEdge, suggestiveY)), - fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH*zoom - #,clipX=(xLeftOffset, xLeftOffset + plotWidth-2) + fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH * zoom + # ,clipX=(xLeftOffset, xLeftOffset + plotWidth-2) ) im_drawer.line( - xy=((start_pos_x+self.SUGGESTIVE_WIDTH/1.5, significantY), + xy=((start_pos_x + self.SUGGESTIVE_WIDTH / 1.5, significantY), (rightEdge, significantY)), fill=self.SIGNIFICANT_COLOR, - width=self.SIGNIFICANT_WIDTH*zoom - #, clipX=(xLeftOffset, xLeftOffset + plotWidth-2) + width=self.SIGNIFICANT_WIDTH * zoom + # , clipX=(xLeftOffset, xLeftOffset + plotWidth-2) ) - sugg_coords = "%d, %d, %d, %d" % (start_pos_x, suggestiveY-2, rightEdge + 2*zoom, suggestiveY+2) - sig_coords = "%d, %d, %d, %d" % (start_pos_x, significantY-2, rightEdge + 2*zoom, significantY+2) + sugg_coords = "%d, %d, %d, %d" % (start_pos_x, suggestiveY - 2, rightEdge + 2 * zoom, suggestiveY + 2) + sig_coords = "%d, %d, %d, %d" % (start_pos_x, significantY - 2, rightEdge + 2 * zoom, significantY + 2) if self.LRS_LOD == 'LRS': sugg_title = "Suggestive LRS = %0.2f" % self.suggestive sig_title = "Significant LRS = %0.2f" % self.significant else: - sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61) - sig_title = "Significant LOD = %0.2f" % (self.significant/4.61) + sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive / 4.61) + sig_title = "Significant LOD = %0.2f" % (self.significant / 4.61) Areas1 = HtmlGenWrapper.create_area_tag( shape='rect', coords=sugg_coords, @@ -2279,7 +2279,7 @@ class DisplayMappingResults: gifmap.append(Areas1) gifmap.append(Areas2) - start_pos_x += (chr_length_dist+self.GraphInterval)*plotXScale + start_pos_x += (chr_length_dist + self.GraphInterval) * plotXScale return start_pos_x for i, _chr in enumerate(self.genotype): @@ -2306,7 +2306,7 @@ class DisplayMappingResults: AdditiveCoordXY = [] DominanceCoordXY = [] - symbolFont = ImageFont.truetype(font=FNT_BS_FILE, size=5) #ZS: For Manhattan Plot + symbolFont = ImageFont.truetype(font=FNT_BS_FILE, size=5) # ZS: For Manhattan Plot previous_chr = 1 previous_chr_as_int = 0 @@ -2332,128 +2332,128 @@ class DisplayMappingResults: minusColor = self.ADDITIVE_COLOR_NEGATIVE for k, aPoint in enumerate(AdditiveCoordXY): if k > 0: - Xc0, Yc0 = AdditiveCoordXY[k-1] + Xc0, Yc0 = AdditiveCoordXY[k - 1] Xc, Yc = aPoint - if (Yc0-yZero)*(Yc-yZero) < 0: - if Xc == Xc0: #genotype , locus distance is 0 + if (Yc0 - yZero) * (Yc-yZero) < 0: + if Xc == Xc0: # genotype , locus distance is 0 Xcm = Xc else: - Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0 + Xcm = (yZero - Yc0) / ((Yc - Yc0) / (Xc - Xc0)) + Xc0 if Yc0 < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xcm, yZero)), fill=plusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) im_drawer.line( - xy=((Xcm, yZero), (Xc, yZero-(Yc-yZero))), + xy=((Xcm, yZero), (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: im_drawer.line( - xy=((Xc0, yZero-(Yc0-yZero)), + xy=((Xc0, yZero - (Yc0 - yZero)), (Xcm, yZero)), fill=minusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) im_drawer.line( xy=((Xcm, yZero), (Xc, Yc)), fill=plusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) - elif (Yc0-yZero)*(Yc-yZero) > 0: + elif (Yc0 - yZero) * (Yc-yZero) > 0: if Yc < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: im_drawer.line( - xy=((Xc0, yZero - (Yc0-yZero)), - (Xc, yZero - (Yc-yZero))), + xy=((Xc0, yZero - (Yc0 - yZero)), + (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: - minYc = min(Yc-yZero, Yc0-yZero) + minYc = min(Yc - yZero, Yc0 - yZero) if minYc < 0: im_drawer.line( xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: im_drawer.line( - xy=((Xc0, yZero - (Yc0-yZero)), - (Xc, yZero - (Yc-yZero))), + xy=((Xc0, yZero - (Yc0 - yZero)), + (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) LRSCoordXY = [] AdditiveCoordXY = [] previous_chr = qtlresult['chr'] previous_chr_as_int += 1 - newStartPosX = (self.ChrLengthDistList[previous_chr_as_int - 1]+self.GraphInterval)*plotXScale + newStartPosX = (self.ChrLengthDistList[previous_chr_as_int - 1] + self.GraphInterval) * plotXScale if newStartPosX != oldStartPosX: startPosX += newStartPosX oldStartPosX = newStartPosX - #ZS: This is because the chromosome value stored in qtlresult['chr'] can be (for example) either X or 20 depending upon the mapping method/scale used + # ZS: This is because the chromosome value stored in qtlresult['chr'] can be (for example) either X or 20 depending upon the mapping method/scale used this_chr = str(self.ChrList[self.selectedChr][0]) if self.plotScale != "physic": - this_chr = str(self.ChrList[self.selectedChr][1]+1) + this_chr = str(self.ChrList[self.selectedChr][1] + 1) if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr: if self.plotScale != "physic" and self.mapping_method == "reaper" and not self.manhattan_plot: - Xc = startPosX + (qtlresult['cM']-startMb)*plotXScale + Xc = startPosX + (qtlresult['cM'] - startMb) * plotXScale if hasattr(self.genotype, "filler"): if self.genotype.filler: if self.selectedChr != -1: start_cm = self.genotype[self.selectedChr - 1][0].cM - Xc = startPosX + (qtlresult['Mb'] - start_cm)*plotXScale + Xc = startPosX + (qtlresult['Mb'] - start_cm) * plotXScale else: start_cm = self.genotype[previous_chr_as_int][0].cM - Xc = startPosX + ((qtlresult['Mb']-start_cm-startMb)*plotXScale)*(((qtlresult['Mb']-start_cm-startMb)*plotXScale)/((qtlresult['Mb']-start_cm-startMb+self.GraphInterval)*plotXScale)) + Xc = startPosX + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) * (((qtlresult['Mb'] - start_cm - startMb) * plotXScale) / ((qtlresult['Mb'] - start_cm - startMb + self.GraphInterval) * plotXScale)) else: - Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale + Xc = startPosX + (qtlresult['Mb'] - startMb) * plotXScale # updated by NL 06-18-2011: # fix the over limit LRS graph issue since genotype trait may give infinite LRS; # for any lrs is over than 460(LRS max in this system), it will be reset to 460 - yLRS = yZero - (item/LRS_LOD_Max) * LRSHeightThresh + yLRS = yZero - (item / LRS_LOD_Max) * LRSHeightThresh if 'lrs_value' in qtlresult: if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP": - if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf': + if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf': #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR) - Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR) + Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / (LRS_LOD_Max * self.LODFACTOR) else: #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR) - Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR) + Yc = yZero - qtlresult['lrs_value'] * LRSHeightThresh / (LRS_LOD_Max * self.LODFACTOR) else: - if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf': + if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf': #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1] - Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max + Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / LRS_LOD_Max else: #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSAxisList[-1] - Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max + Yc = yZero - qtlresult['lrs_value'] * LRSHeightThresh / LRS_LOD_Max else: - if qtlresult['lod_score'] > 100 or qtlresult['lod_score']=='inf': + if qtlresult['lod_score'] > 100 or qtlresult['lod_score'] == 'inf': #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1] - Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max + Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / LRS_LOD_Max else: if self.LRS_LOD == "LRS": #Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRSAxisList[-1] - Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRS_LOD_Max + Yc = yZero - qtlresult['lod_score'] * self.LODFACTOR * LRSHeightThresh / LRS_LOD_Max else: #Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRSAxisList[-1] - Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRS_LOD_Max + Yc = yZero - qtlresult['lod_score'] * LRSHeightThresh / LRS_LOD_Max if self.manhattan_plot == True: if self.color_scheme == "single": @@ -2469,8 +2469,8 @@ class DisplayMappingResults: im_drawer.text( text="5", xy=( - Xc-im_drawer.textsize("5", font=symbolFont)[0]/2+1, - Yc-4), + Xc - im_drawer.textsize("5", font=symbolFont)[0] / 2 + 1, + Yc - 4), fill=point_color, font=symbolFont) else: LRSCoordXY.append((Xc, Yc)) @@ -2478,7 +2478,7 @@ class DisplayMappingResults: if not self.multipleInterval and self.additiveChecked: if additiveMax == 0.0: additiveMax = 0.000001 - Yc = yZero - qtlresult['additive']*AdditiveHeightThresh/additiveMax + Yc = yZero - qtlresult['additive'] * AdditiveHeightThresh / additiveMax AdditiveCoordXY.append((Xc, Yc)) m += 1 @@ -2497,64 +2497,64 @@ class DisplayMappingResults: minusColor = self.ADDITIVE_COLOR_NEGATIVE for k, aPoint in enumerate(AdditiveCoordXY): if k > 0: - Xc0, Yc0 = AdditiveCoordXY[k-1] + Xc0, Yc0 = AdditiveCoordXY[k - 1] Xc, Yc = aPoint - if (Yc0-yZero)*(Yc-yZero) < 0: - if Xc == Xc0: #genotype , locus distance is 0 + if (Yc0 - yZero) * (Yc-yZero) < 0: + if Xc == Xc0: # genotype , locus distance is 0 Xcm = Xc else: - Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0 + Xcm = (yZero - Yc0) / ((Yc - Yc0) / (Xc - Xc0)) + Xc0 if Yc0 < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xcm, yZero)), fill=plusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) im_drawer.line( - xy=((Xcm, yZero), (Xc, yZero-(Yc-yZero))), + xy=((Xcm, yZero), (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: im_drawer.line( - xy=((Xc0, yZero - (Yc0-yZero)), + xy=((Xc0, yZero - (Yc0 - yZero)), (Xcm, yZero)), fill=minusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) im_drawer.line( xy=((Xcm, yZero), (Xc, Yc)), fill=plusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) - elif (Yc0-yZero)*(Yc-yZero) > 0: + elif (Yc0 - yZero) * (Yc-yZero) > 0: if Yc < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: im_drawer.line( - xy=((Xc0, yZero-(Yc0-yZero)), - (Xc, yZero-(Yc-yZero))), + xy=((Xc0, yZero - (Yc0 - yZero)), + (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: - minYc = min(Yc-yZero, Yc0-yZero) + minYc = min(Yc - yZero, Yc0 - yZero) if minYc < 0: im_drawer.line( xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: im_drawer.line( - xy=((Xc0, yZero - (Yc0-yZero)), - (Xc, yZero - (Yc-yZero))), + xy=((Xc0, yZero - (Yc0 - yZero)), + (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) if not self.multipleInterval and INTERCROSS and self.dominanceChecked: @@ -2562,114 +2562,114 @@ class DisplayMappingResults: minusColor = self.DOMINANCE_COLOR_NEGATIVE for k, aPoint in enumerate(DominanceCoordXY): if k > 0: - Xc0, Yc0 = DominanceCoordXY[k-1] + Xc0, Yc0 = DominanceCoordXY[k - 1] Xc, Yc = aPoint - if (Yc0-yZero)*(Yc-yZero) < 0: - if Xc == Xc0: #genotype , locus distance is 0 + if (Yc0 - yZero) * (Yc-yZero) < 0: + if Xc == Xc0: # genotype , locus distance is 0 Xcm = Xc else: - Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0 + Xcm = (yZero - Yc0) / ((Yc - Yc0) / (Xc - Xc0)) + Xc0 if Yc0 < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xcm, yZero)), fill=plusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) im_drawer.line( - xy=((Xcm, yZero), (Xc, yZero-(Yc-yZero))), + xy=((Xcm, yZero), (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: im_drawer.line( - xy=((Xc0, yZero - (Yc0-yZero)), (Xcm, yZero)), + xy=((Xc0, yZero - (Yc0 - yZero)), (Xcm, yZero)), fill=minusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) im_drawer.line( xy=((Xcm, yZero), (Xc, Yc)), fill=plusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) - elif (Yc0-yZero)*(Yc-yZero) > 0: + elif (Yc0 - yZero) * (Yc-yZero) > 0: if Yc < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: im_drawer.line( - xy=((Xc0, yZero - (Yc0-yZero)), - (Xc, yZero - (Yc-yZero))), + xy=((Xc0, yZero - (Yc0 - yZero)), + (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: - minYc = min(Yc-yZero, Yc0-yZero) + minYc = min(Yc - yZero, Yc0 - yZero) if minYc < 0: im_drawer.line( xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: im_drawer.line( - xy=((Xc0, yZero - (Yc0-yZero)), - (Xc, yZero - (Yc-yZero))), fill=minusColor, + xy=((Xc0, yZero - (Yc0 - yZero)), + (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth - #, clipX=(xLeftOffset, xLeftOffset + plotWidth) + # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) - ###draw additive scale + # draw additive scale if not self.multipleInterval and self.additiveChecked: - additiveScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=16*zoom) + additiveScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom) additiveScale = Plot.detScaleOld(0, additiveMax) - additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2] + additiveStep = (additiveScale[1] - additiveScale[0]) / additiveScale[2] additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep) - addPlotScale = AdditiveHeightThresh/additiveMax + addPlotScale = AdditiveHeightThresh / additiveMax TEXT_Y_DISPLACEMENT = -8 additiveAxisList.append(additiveScale[1]) for item in additiveAxisList: - additiveY = yZero - item*addPlotScale + additiveY = yZero - item * addPlotScale im_drawer.line( xy=((xLeftOffset + plotWidth, additiveY), - (xLeftOffset+4+ plotWidth, additiveY)), - fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom) + (xLeftOffset + 4 + plotWidth, additiveY)), + fill=self.ADDITIVE_COLOR_POSITIVE, width=1 * zoom) scaleStr = "%2.3f" % item im_drawer.text( text=scaleStr, - xy=(xLeftOffset + plotWidth +6, additiveY+TEXT_Y_DISPLACEMENT), + xy= (xLeftOffset + plotWidth + 6, additiveY + TEXT_Y_DISPLACEMENT), font=additiveScaleFont, fill=self.ADDITIVE_COLOR_POSITIVE) im_drawer.line( - xy=((xLeftOffset+plotWidth, additiveY), - (xLeftOffset+plotWidth, yZero)), - fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom) + xy=((xLeftOffset + plotWidth, additiveY), + (xLeftOffset + plotWidth, yZero)), + fill=self.ADDITIVE_COLOR_POSITIVE, width=1 * zoom) im_drawer.line( - xy=((xLeftOffset, yZero), (xLeftOffset, yTopOffset + 30*(zoom - 1))), - fill=self.LRS_COLOR, width=1*zoom) #the blue line running up the y axis + xy=((xLeftOffset, yZero), (xLeftOffset, yTopOffset + 30 * (zoom - 1))), + fill=self.LRS_COLOR, width=1 * zoom) # the blue line running up the y axis - def drawGraphBackground(self, canvas, gifmap, offset= (80, 120, 80, 50), zoom = 1, startMb = None, endMb = None): - ##conditions - ##multiple Chromosome view - ##single Chromosome Physical - ##single Chromosome Genetic + def drawGraphBackground(self, canvas, gifmap, offset=(80, 120, 80, 50), zoom=1, startMb= None, endMb = None): + # conditions + # multiple Chromosome view + # single Chromosome Physical + # single Chromosome Genetic im_drawer = ImageDraw.Draw(canvas) xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset plotWidth = canvas.size[0] - xLeftOffset - xRightOffset plotHeight = canvas.size[1] - yTopOffset - yBottomOffset - yBottom = yTopOffset+plotHeight + yBottom = yTopOffset + plotHeight fontZoom = zoom if zoom == 2: fontZoom = 1.5 yTopOffset += 30 - #calculate plot scale + # calculate plot scale if self.plotScale != 'physic': self.ChrLengthDistList = self.ChrLengthCMList drawRegionDistance = self.ChrLengthCMSum @@ -2677,10 +2677,10 @@ class DisplayMappingResults: self.ChrLengthDistList = self.ChrLengthMbList drawRegionDistance = self.ChrLengthMbSum - if self.selectedChr > -1: #single chromosome view - spacingAmt = plotWidth/13.5 + if self.selectedChr > -1: # single chromosome view + spacingAmt = plotWidth / 13.5 i = 0 - for startPix in Plot.frange(xLeftOffset, xLeftOffset+plotWidth, spacingAmt): + for startPix in Plot.frange(xLeftOffset, xLeftOffset + plotWidth, spacingAmt): if (i % 2 == 0): theBackColor = self.GRAPH_BACK_DARK_COLOR else: @@ -2688,25 +2688,25 @@ class DisplayMappingResults: i += 1 im_drawer.rectangle( [(startPix, yTopOffset), - (min(startPix+spacingAmt, xLeftOffset+plotWidth), yBottom)], + (min(startPix + spacingAmt, xLeftOffset + plotWidth), yBottom)], outline=theBackColor, fill=theBackColor) drawRegionDistance = self.ChrLengthDistList[self.ChrList[self.selectedChr][1]] self.ChrLengthDistList = [drawRegionDistance] if self.plotScale == 'physic': - plotXScale = plotWidth / (endMb-startMb) + plotXScale = plotWidth / (endMb - startMb) else: plotXScale = plotWidth / drawRegionDistance - else: #multiple chromosome view - plotXScale = plotWidth / ((len(self.genotype)-1)*self.GraphInterval + drawRegionDistance) + else: # multiple chromosome view + plotXScale = plotWidth / ((len(self.genotype) - 1) * self.GraphInterval + drawRegionDistance) startPosX = xLeftOffset if fontZoom == 1.5: chrFontZoom = 2 else: chrFontZoom = 1 - chrLabelFont=ImageFont.truetype(font=VERDANA_FILE, size=24*chrFontZoom) + chrLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=24 * chrFontZoom) for i, _chr in enumerate(self.genotype): if (i % 2 == 0): @@ -2714,23 +2714,23 @@ class DisplayMappingResults: else: theBackColor = self.GRAPH_BACK_LIGHT_COLOR - #draw the shaded boxes and the sig/sug thick lines + # draw the shaded boxes and the sig/sug thick lines im_drawer.rectangle( ((startPosX, yTopOffset), - (startPosX + self.ChrLengthDistList[i]*plotXScale, yBottom)), + (startPosX + self.ChrLengthDistList[i] * plotXScale, yBottom)), outline=GAINSBORO, fill=theBackColor) chrNameWidth, chrNameHeight = im_drawer.textsize(_chr.name, font=chrLabelFont) - chrStartPix = startPosX + (self.ChrLengthDistList[i]*plotXScale -chrNameWidth)/2 - chrEndPix = startPosX + (self.ChrLengthDistList[i]*plotXScale +chrNameWidth)/2 + chrStartPix = startPosX + (self.ChrLengthDistList[i] * plotXScale - chrNameWidth) / 2 + chrEndPix = startPosX + (self.ChrLengthDistList[i] * plotXScale + chrNameWidth) / 2 TEXT_Y_DISPLACEMENT = 0 im_drawer.text(xy=(chrStartPix, yTopOffset + TEXT_Y_DISPLACEMENT), text=_chr.name, font=chrLabelFont, fill=BLACK) - COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix, yTopOffset +20) + COORDS = "%d,%d,%d,%d" % (chrStartPix, yTopOffset, chrEndPix, yTopOffset + 20) - #add by NL 09-03-2010 + # add by NL 09-03-2010 HREF = "javascript:chrView(%d,%s);" % (i, self.ChrLengthMbList) #HREF = "javascript:changeView(%d,%s);" % (i,self.ChrLengthMbList) Areas = HtmlGenWrapper.create_area_tag( @@ -2738,7 +2738,7 @@ class DisplayMappingResults: coords=COORDS, href=HREF) gifmap.append(Areas) - startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale + startPosX += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale return plotXScale @@ -2748,15 +2748,15 @@ class DisplayMappingResults: ######################################### myCanvas = Image.new("RGBA", size=(500, 300)) if 'lod_score' in self.qtlresults[0] and self.LRS_LOD == "LRS": - perm_output = [value*4.61 for value in self.perm_output] + perm_output = [value * 4.61 for value in self.perm_output] elif 'lod_score' not in self.qtlresults[0] and self.LRS_LOD == "LOD": - perm_output = [value/4.61 for value in self.perm_output] + perm_output = [value / 4.61 for value in self.perm_output] else: perm_output = self.perm_output - filename= webqtlUtil.genRandStr("Reg_") + filename = webqtlUtil.genRandStr("Reg_") Plot.plotBar(myCanvas, perm_output, XLabel=self.LRS_LOD, YLabel='Frequency', title=' Histogram of Permutation Test') - myCanvas.save("{}.gif".format(GENERATED_IMAGE_DIR+filename), + myCanvas.save("{}.gif".format(GENERATED_IMAGE_DIR + filename), format='gif') return filename @@ -2821,18 +2821,18 @@ class DisplayMappingResults: tableIterationsCnt = tableIterationsCnt + 1 - this_row = [] #container for the cells of each row + this_row = [] # container for the cells of each row selectCheck = HtmlGenWrapper.create_input_tag( type_="checkbox", name="selectCheck", value=theGO["GeneSymbol"], Class="checkbox trait_checkbox") # checkbox for each row - geneLength = (theGO["TxEnd"] - theGO["TxStart"])*1000.0 - tenPercentLength = geneLength*0.0001 + geneLength = (theGO["TxEnd"] - theGO["TxStart"]) * 1000.0 + tenPercentLength = geneLength * 0.0001 txStart = theGO["TxStart"] txEnd = theGO["TxEnd"] - theGO["snpDensity"] = theGO["snpCount"]/geneLength + theGO["snpDensity"] = theGO["snpCount"] / geneLength if self.ALEX_DEBUG_BOOL_PRINT_GENE_LIST: geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO["GeneID"] @@ -2844,16 +2844,16 @@ class DisplayMappingResults: f"end={theGO['TxEnd']}&" f"geneName={theGO['GeneSymbol']}&" f"s1={self.diffCol[0]}&s2=%d"), - str(theGO["snpCount"]) # The text to display + str(theGO["snpCount"]) # The text to display ) snpString.set_blank_target() snpString.set_attribute("class", "normalsize") else: snpString = 0 - mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str(int(theGO["TxEnd"]*1000000.0)) +"&pix=620&Submit=submit" + mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str(int(theGO["TxEnd"] * 1000000.0)) + "&pix=620&Submit=submit" - #the chromosomes for human 1 are 1qXX.XX + # the chromosomes for human 1 are 1qXX.XX if theGO['humanGene']: if theGO['humanGene']["TxStart"] == '': humanStartDisplay = "" @@ -2863,20 +2863,20 @@ class DisplayMappingResults: humanChr = theGO['humanGene']["Chromosome"] humanTxStart = theGO['humanGene']["TxStart"] - humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" % (humanChr, int(1000000*theGO['humanGene']["TxStart"]), int(1000000*theGO['humanGene']["TxEnd"])) + humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" % (humanChr, int(1000000 * theGO['humanGene']["TxStart"]), int(1000000 * theGO['humanGene']["TxEnd"])) else: humanStartString = humanChr = humanStartDisplay = "--" geneDescription = theGO["GeneDescription"] if len(geneDescription) > 70: - geneDescription = geneDescription[:70]+"..." + geneDescription = geneDescription[:70] + "..." if theGO["snpDensity"] < 0.000001: snpDensityStr = "0" else: snpDensityStr = "%0.6f" % theGO["snpDensity"] - avgExpr = [] #theGO["avgExprVal"] + avgExpr = [] # theGO["avgExprVal"] if avgExpr in ([], None): avgExpr = "--" else: @@ -2905,8 +2905,8 @@ class DisplayMappingResults: str(HtmlGenWrapper.create_link_tag( "javascript:rangeView('{}', {:f}, {:f})".format( str(chr_as_int), - txStart-tenPercentLength, - txEnd+tenPercentLength), + txStart - tenPercentLength, + txEnd + tenPercentLength), "{:.3f}".format(geneLength))), snpString, snpDensityStr, @@ -2931,8 +2931,8 @@ class DisplayMappingResults: str(HtmlGenWrapper.create_link_tag( "javascript:rangeView('{}', {:f}, {:f})".format( str(chr_as_int), - txStart-tenPercentLength, - txEnd+tenPercentLength), + txStart - tenPercentLength, + txEnd + tenPercentLength), "{:.3f}".format(geneLength))), snpString, snpDensityStr, @@ -2969,7 +2969,7 @@ class DisplayMappingResults: chr_as_int = int(theGO["Chromosome"]) - 1 geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"])) - geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1)) + geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(theGO["TxStart"]) - (geneLength * 0.1), float(theGO["TxEnd"]) + (geneLength * 0.1)) avgExprVal = [] if avgExprVal != "" and avgExprVal: @@ -2977,14 +2977,14 @@ class DisplayMappingResults: else: avgExprVal = "" - #Mouse Gene + # Mouse Gene if theGO['mouseGene']: mouseChr = theGO['mouseGene']["Chromosome"] mouseTxStart = "%0.6f" % theGO['mouseGene']["TxStart"] else: mouseChr = mouseTxStart = "" - #the chromosomes for human 1 are 1qXX.XX + # the chromosomes for human 1 are 1qXX.XX if theGO['humanGene']: humanChr = theGO['humanGene']["Chromosome"] humanTxStart = "%0.6f" % theGO['humanGene']["TxStart"] @@ -2996,12 +2996,12 @@ class DisplayMappingResults: geneDesc = "" this_row = [selectCheck.__str__(), - str(gIndex+1), + str(gIndex + 1), geneSymbolNCBI, "%0.6f" % theGO["TxStart"], str(HtmlGenWrapper.create_link_tag( geneLengthURL, - "{:.3f}".format(geneLength*1000.0))), + "{:.3f}".format(geneLength * 1000.0))), avgExprVal, mouseChr, mouseTxStart, @@ -3013,7 +3013,7 @@ class DisplayMappingResults: return gene_table_body - def getLiteratureCorrelation(cursor,geneId1=None,geneId2=None): + def getLiteratureCorrelation(cursor, geneId1=None, geneId2=None): if not geneId1 or not geneId2: return None if geneId1 == geneId2: @@ -3025,9 +3025,9 @@ class DisplayMappingResults: query = 'SELECT Value FROM LCorrRamin3 WHERE GeneId1 = %s and GeneId2 = %s' for x, y in [(geneId1, geneId2), (geneId2, geneId1)]: cursor.execute(query, (x, y)) - lCorr = cursor.fetchone() + lCorr = cursor.fetchone() if lCorr: lCorr = lCorr[0] break - except: raise #lCorr = None + except: raise # lCorr = None return lCorr diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 06c9300a..68689104 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -149,7 +149,7 @@ def gen_covariates_file(this_dataset, covariates, samples): dataset_name = covariate.split(":")[1] if dataset_name == "Temp": temp_group = trait_name.split("_")[2] - dataset_ob = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group) + dataset_ob = create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = temp_group) else: dataset_ob = create_dataset(covariate.split(":")[1]) trait_ob = create_trait(dataset=dataset_ob, diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index 5d675c38..e6c78536 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -6,7 +6,7 @@ from utility import webqtlUtil from utility.tools import flat_files, PLINK_COMMAND import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) def run_plink(this_trait, dataset, species, vals, maf): plink_output_filename = webqtlUtil.genRandStr(f"{dataset.group.name}_{this_trait.name}_") @@ -34,7 +34,7 @@ def gen_pheno_txt_file(this_dataset, vals): split_line = line.split() current_file_data.append(split_line) - with open(f"{flat_files('mapping')}/{this_dataset.group.name}.fam","w") as outfile: + with open(f"{flat_files('mapping')}/{this_dataset.group.name}.fam", "w") as outfile: for i, line in enumerate(current_file_data): if vals[i] == "x": this_val = -9 @@ -42,7 +42,7 @@ def gen_pheno_txt_file(this_dataset, vals): this_val = vals[i] outfile.write("0 " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n") -def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): +def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename=''): ped_sample_list = get_samples_from_ped_file(dataset) output_file = open(f"{TMPDIR}{pheno_filename}.txt", "wb") header = f"FID\tIID\t{this_trait.name}\n" @@ -50,7 +50,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): new_value_list = [] - #if valueDict does not include some strain, value will be set to -9999 as missing value + # if valueDict does not include some strain, value will be set to -9999 as missing value for i, sample in enumerate(ped_sample_list): try: value = vals[i] @@ -63,11 +63,11 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): new_line = '' for i, sample in enumerate(ped_sample_list): - j = i+1 + j = i + 1 value = new_value_list[i] new_line += f"{sample}\t{sample}\t{value}\n" - if j%1000 == 0: + if j % 1000 == 0: output_file.write(newLine) new_line = '' @@ -78,9 +78,9 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): # get strain name from ped file in order def get_samples_from_ped_file(dataset): - ped_file= open(f"{flat_files('mapping')}{dataset.group.name}.ped","r") + ped_file = open(f"{flat_files('mapping')}{dataset.group.name}.ped", "r") line = ped_file.readline() - sample_list=[] + sample_list = [] while line: lineList = line.strip().split('\t') @@ -94,24 +94,24 @@ def get_samples_from_ped_file(dataset): return sample_list def parse_plink_output(output_filename, species): - plink_results={} + plink_results = {} threshold_p_value = 1 - result_fp = open(f"{TMPDIR}{output_filename}.qassoc","rb") + result_fp = open(f"{TMPDIR}{output_filename}.qassoc", "rb") line = result_fp.readline() - value_list = [] # initialize value list, this list will include snp, bp and pvalue info + value_list = [] # initialize value list, this list will include snp, bp and pvalue info p_value_dict = {} count = 0 while line: - #convert line from str to list + # convert line from str to list line_list = build_line_list(line=line) # only keep the records whose chromosome name is in db - if int(line_list[0]) in species.chromosomes.chromosomes and line_list[-1] and line_list[-1].strip()!='NA': + if int(line_list[0]) in species.chromosomes.chromosomes and line_list[-1] and line_list[-1].strip() != 'NA': chr_name = species.chromosomes.chromosomes[int(line_list[0])] snp = line_list[1] @@ -125,7 +125,7 @@ def parse_plink_output(output_filename, species): value_list = plink_results[chr_name] # pvalue range is [0,1] - if threshold_p_value >=0 and threshold_p_value <= 1: + if threshold_p_value >= 0 and threshold_p_value <= 1: if p_value < threshold_p_value: value_list.append((snp, BP, p_value)) count += 1 @@ -141,7 +141,7 @@ def parse_plink_output(output_filename, species): if value_list: plink_results[chr_name] = value_list - value_list=[] + value_list = [] line = result_fp.readline() else: @@ -155,8 +155,8 @@ def parse_plink_output(output_filename, species): # output: lineList list ####################################################### def build_line_list(line=""): - line_list = line.strip().split(' ')# irregular number of whitespaces between columns - line_list = [item for item in line_list if item !=''] + line_list = line.strip().split(' ') # irregular number of whitespaces between columns + line_list = [item for item in line_list if item != ''] line_list = [item.strip() for item in line_list] return line_list diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 8341ee55..dd044cb0 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -6,7 +6,7 @@ from base.data_set import create_dataset from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boot_check, num_bootstrap, do_control, control_marker, manhattan_plot, first_run=True, output_files=None): """Generates p-values for each marker using qtlreaper""" @@ -17,10 +17,10 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo else: genofile_name = this_dataset.group.name - trait_filename =f"{str(this_trait.name)}_{str(this_dataset.name)}_pheno" + trait_filename = f"{str(this_trait.name)}_{str(this_dataset.name)}_pheno" gen_pheno_txt_file(samples, vals, trait_filename) - output_filename = (f"{this_dataset.group.name}_GWA_"+ + output_filename = (f"{this_dataset.group.name}_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) ) bootstrap_filename = None @@ -36,7 +36,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo opt_list.append(f"--n_bootstrap {str(num_bootstrap)}") opt_list.append(f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt") if num_perm > 0: - permu_filename =("{this_dataset.group.name}_PERM_" + + permu_filename = ("{this_dataset.group.name}_PERM_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) ) @@ -67,8 +67,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo suggestive = 0 significant = 0 if len(permu_vals) > 0: - suggestive = permu_vals[int(num_perm*0.37-1)] - significant = permu_vals[int(num_perm*0.95-1)] + suggestive = permu_vals[int(num_perm * 0.37 - 1)] + significant = permu_vals[int(num_perm * 0.95 - 1)] return (marker_obs, permu_vals, suggestive, significant, bootstrap_vals, [output_filename, permu_filename, bootstrap_filename]) @@ -76,7 +76,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo def gen_pheno_txt_file(samples, vals, trait_filename): """Generates phenotype file for GEMMA""" - with open(f"{TEMPDIR}/gn2/{trait_filename}.txt","w") as outfile: + with open(f"{TEMPDIR}/gn2/{trait_filename}.txt", "w") as outfile: outfile.write("Trait\t") filtered_sample_list = [] @@ -121,7 +121,7 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): marker['cM'] = float(line.split("\t")[3]) else: if float(line.split("\t")[3]) > 1000: - marker['Mb'] = float(line.split("\t")[3])/1000000 + marker['Mb'] = float(line.split("\t")[3]) / 1000000 else: marker['Mb'] = float(line.split("\t")[3]) if float(line.split("\t")[6]) != 1: @@ -132,7 +132,7 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): else: marker['cM'] = float(line.split("\t")[3]) if float(line.split("\t")[4]) > 1000: - marker['Mb'] = float(line.split("\t")[4])/1000000 + marker['Mb'] = float(line.split("\t")[4]) / 1000000 else: marker['Mb'] = float(line.split("\t")[4]) if float(line.split("\t")[7]) != 1: @@ -142,7 +142,7 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): marker['additive'] = float(line.split("\t")[6]) marker_obs.append(marker) - #ZS: Results have to be reordered because the new reaper returns results sorted alphabetically by chr for some reason, resulting in chr 1 being followed by 10, etc + # ZS: Results have to be reordered because the new reaper returns results sorted alphabetically by chr for some reason, resulting in chr 1 being followed by 10, etc sorted_indices = natural_sort(marker_obs) permu_vals = [] @@ -185,18 +185,18 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da suggestive = 0 significant = 0 else: - perm_output = genotype.permutation(strains = trimmed_samples, trait = trimmed_values, nperm=num_perm) - suggestive = perm_output[int(num_perm*0.37-1)] - significant = perm_output[int(num_perm*0.95-1)] - #highly_significant = perm_output[int(num_perm*0.99-1)] #ZS: Currently not used, but leaving it here just in case + perm_output = genotype.permutation(strains=trimmed_samples, trait=trimmed_values, nperm=num_perm) + suggestive = perm_output[int(num_perm * 0.37 - 1)] + significant = perm_output[int(num_perm * 0.95 - 1)] + # highly_significant = perm_output[int(num_perm*0.99-1)] #ZS: Currently not used, but leaving it here just in case json_data['suggestive'] = suggestive json_data['significant'] = significant if control_marker != "" and do_control == "true": - reaper_results = genotype.regression(strains = trimmed_samples, - trait = trimmed_values, - control = str(control_marker)) + reaper_results = genotype.regression(strains=trimmed_samples, + trait=trimmed_values, + control=str(control_marker)) if bootCheck: control_geno = [] control_geno2 = [] @@ -215,31 +215,31 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da _idx = _prgy.index(_strain) control_geno.append(control_geno2[_idx]) - bootstrap_results = genotype.bootstrap(strains = trimmed_samples, - trait = trimmed_values, - control = control_geno, - nboot = num_bootstrap) + bootstrap_results = genotype.bootstrap(strains=trimmed_samples, + trait=trimmed_values, + control=control_geno, + nboot=num_bootstrap) else: - reaper_results = genotype.regression(strains = trimmed_samples, - trait = trimmed_values) + reaper_results = genotype.regression(strains=trimmed_samples, + trait=trimmed_values) if bootCheck: - bootstrap_results = genotype.bootstrap(strains = trimmed_samples, - trait = trimmed_values, - nboot = num_bootstrap) + bootstrap_results = genotype.bootstrap(strains=trimmed_samples, + trait=trimmed_values, + nboot=num_bootstrap) json_data['chr'] = [] json_data['pos'] = [] json_data['lod.hk'] = [] json_data['markernames'] = [] - #if self.additive: + # if self.additive: # self.json_data['additive'] = [] - #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary + # Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary qtl_results = [] for qtl in reaper_results: reaper_locus = qtl.locus - #ZS: Convert chr to int + # ZS: Convert chr to int converted_chr = reaper_locus.chr if reaper_locus.chr != "X" and reaper_locus.chr != "X/Y": converted_chr = int(reaper_locus.chr) @@ -247,11 +247,11 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da json_data['pos'].append(reaper_locus.Mb) json_data['lod.hk'].append(qtl.lrs) json_data['markernames'].append(reaper_locus.name) - #if self.additive: + # if self.additive: # self.json_data['additive'].append(qtl.additive) - locus = {"name":reaper_locus.name, "chr":reaper_locus.chr, "cM":reaper_locus.cM, "Mb":reaper_locus.Mb} - qtl = {"lrs_value": qtl.lrs, "chr":converted_chr, "Mb":reaper_locus.Mb, - "cM":reaper_locus.cM, "name":reaper_locus.name, "additive":qtl.additive, "dominance":qtl.dominance} + locus = {"name": reaper_locus.name, "chr": reaper_locus.chr, "cM": reaper_locus.cM, "Mb": reaper_locus.Mb} + qtl = {"lrs_value": qtl.lrs, "chr": converted_chr, "Mb": reaper_locus.Mb, + "cM": reaper_locus.cM, "name": reaper_locus.name, "additive": qtl.additive, "dominance": qtl.dominance} qtl_results.append(qtl) return qtl_results, json_data, perm_output, suggestive, significant, bootstrap_results @@ -261,5 +261,5 @@ def natural_sort(marker_list): Changed to return indices instead of values, though, since the same reordering needs to be applied to bootstrap results """ convert = lambda text: int(text) if text.isdigit() else text.lower() - alphanum_key = lambda key: [ convert(c) for c in re.split('([0-9]+)', str(marker_list[key]['chr'])) ] - return sorted(list(range(len(marker_list))), key = alphanum_key) \ No newline at end of file + alphanum_key = lambda key: [convert(c) for c in re.split('([0-9]+)', str(marker_list[key]['chr']))] + return sorted(list(range(len(marker_list))), key=alphanum_key) diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 4117a0e5..2bd94512 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -13,7 +13,7 @@ from utility.tools import locate, TEMPDIR from flask import g import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) # Get a trait's type (numeric, categorical, etc) from the DB def get_trait_data_type(trait_db_string): @@ -35,29 +35,29 @@ def get_trait_data_type(trait_db_string): # Run qtl mapping using R/qtl def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors): logger.info("Start run_rqtl_geno"); - ## Get pointers to some common R functions - r_library = ro.r["library"] # Map the library function - r_c = ro.r["c"] # Map the c function - plot = ro.r["plot"] # Map the plot function - png = ro.r["png"] # Map the png function - dev_off = ro.r["dev.off"] # Map the device off function + # Get pointers to some common R functions + r_library = ro.r["library"] # Map the library function + r_c = ro.r["c"] # Map the c function + plot = ro.r["plot"] # Map the plot function + png = ro.r["png"] # Map the png function + dev_off = ro.r["dev.off"] # Map the device off function print((r_library("qtl"))) # Load R/qtl logger.info("QTL library loaded"); - ## Get pointers to some R/qtl functions - scanone = ro.r["scanone"] # Map the scanone function - scantwo = ro.r["scantwo"] # Map the scantwo function - calc_genoprob = ro.r["calc.genoprob"] # Map the calc.genoprob function + # Get pointers to some R/qtl functions + scanone = ro.r["scanone"] # Map the scanone function + scantwo = ro.r["scantwo"] # Map the scantwo function + calc_genoprob = ro.r["calc.genoprob"] # Map the calc.genoprob function crossname = dataset.group.name - #try: + # try: # generate_cross_from_rdata(dataset) # read_cross_from_rdata = ro.r["generate_cross_from_rdata"] # Map the local read_cross_from_rdata function # genofilelocation = locate(crossname + ".RData", "genotype/rdata") # cross_object = read_cross_from_rdata(genofilelocation) # Map the local GENOtoCSVR function - #except: + # except: if mapping_scale == "morgan": scale_units = "cM" @@ -65,10 +65,10 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec scale_units = "Mb" generate_cross_from_geno(dataset, scale_units) - GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the local GENOtoCSVR function + GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the local GENOtoCSVR function crossfilelocation = TMPDIR + crossname + ".cross" if dataset.group.genofile: - genofilelocation = locate(dataset.group.genofile, "genotype") + genofilelocation = locate(dataset.group.genofile, "genotype") else: genofilelocation = locate(dataset.group.name + ".geno", "genotype") logger.info("Going to create a cross from geno"); @@ -95,38 +95,38 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec else: ro.r('all_covars <- marker_covars') covars = ro.r['all_covars'] - #DEBUG to save the session object to file + # DEBUG to save the session object to file if pair_scan: if do_control == "true": - logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method, n_cluster = 16) + logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method, n_cluster = 16) else: - logger.info("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=model, method=method, n_cluster = 16) + logger.info("No covariates"); result_data_frame = scantwo(cross_object, pheno="the_pheno", model=model, method=method, n_cluster=16) pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png" - png(file=TEMPDIR+pair_scan_filename) + png(file=TEMPDIR + pair_scan_filename) plot(result_data_frame) dev_off() return process_pair_scan_results(result_data_frame) else: if do_control == "true" or cofactors != "": - logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method) + logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method) ro.r('save.image(file = "/home/zas1024/gn2-zach/itp_cofactor_test.RData")') else: - logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method=method) + logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno="the_pheno", model=model, method=method) if num_perm > 0 and permCheck == "ON": # Do permutation (if requested by user) - if len(perm_strata_list) > 0: #ZS: The strata list would only be populated if "Stratified" was checked on before mapping + if len(perm_strata_list) > 0: # ZS: The strata list would only be populated if "Stratified" was checked on before mapping cross_object, strata_ob = add_perm_strata(cross_object, perm_strata_list) if do_control == "true" or cofactors != "": - perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covars, n_perm = int(num_perm), perm_strata = strata_ob, model=model, method=method) + perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(num_perm), perm_strata = strata_ob, model=model, method=method) else: - perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, perm_strata = strata_ob, model=model, method=method) + perm_data_frame = scanone(cross_object, pheno_col="the_pheno", n_perm=num_perm, perm_strata = strata_ob, model=model, method=method) else: if do_control == "true" or cofactors != "": - perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covars, n_perm = int(num_perm), model=model, method=method) + perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(num_perm), model=model, method=method) else: - perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, model=model, method=method) + perm_data_frame = scanone(cross_object, pheno_col="the_pheno", n_perm=num_perm, model=model, method=method) perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame) # Functions that sets the thresholds for the webinterface return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species) @@ -134,7 +134,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec return process_rqtl_results(result_data_frame, dataset.group.species) def generate_cross_from_rdata(dataset): - rdata_location = locate(dataset.group.name + ".RData", "genotype/rdata") + rdata_location = locate(dataset.group.name + ".RData", "genotype/rdata") ro.r(""" generate_cross_from_rdata <- function(filename = '%s') { load(file=filename) @@ -206,7 +206,7 @@ def sanitize_rqtl_phenotype(vals): for i, val in enumerate(vals): if val == "x": if i < (len(vals) - 1): - pheno_as_string += "NA," + pheno_as_string += "NA," else: pheno_as_string += "NA" else: @@ -223,7 +223,7 @@ def sanitize_rqtl_names(vals): for i, val in enumerate(vals): if val == "x": if i < (len(vals) - 1): - pheno_as_string += "NA," + pheno_as_string += "NA," else: pheno_as_string += "NA" else: @@ -238,7 +238,7 @@ def sanitize_rqtl_names(vals): def add_phenotype(cross, pheno_as_string, col_name): ro.globalenv["the_cross"] = cross ro.r('pheno <- data.frame(pull.pheno(the_cross))') - ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric('+ pheno_as_string +'))') + ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric(' + pheno_as_string + '))') return ro.r["the_cross"] def add_categorical_covar(cross, covar_as_string, i): @@ -256,8 +256,8 @@ def add_categorical_covar(cross, covar_as_string, i): nCol = int(nCol[0]) logger.info("nCol python int:" + str(nCol)); col_names = [] - #logger.info("loop") - for x in range(1, (nCol+1)): + # logger.info("loop") + for x in range(1, (nCol + 1)): #logger.info("loop" + str(x)); col_name = "covar_" + str(i) + "_" + str(x) #logger.info("col_name" + col_name); @@ -272,12 +272,12 @@ def add_categorical_covar(cross, covar_as_string, i): def add_names(cross, names_as_string, col_name): ro.globalenv["the_cross"] = cross ro.r('pheno <- data.frame(pull.pheno(the_cross))') - ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = '+ names_as_string +')') + ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = ' + names_as_string + ')') return ro.r["the_cross"] def pull_var(var_name, cross, var_string): ro.globalenv["the_cross"] = cross - ro.r(var_name +' <- pull.pheno(the_cross, ' + var_string + ')') + ro.r(var_name + ' <- pull.pheno(the_cross, ' + var_string + ')') return ro.r[var_name] @@ -317,15 +317,15 @@ def add_cofactors(cross, this_dataset, covariates, samples): datatype = get_trait_data_type(covariate) logger.info("Covariate: " + covariate + " is of type: " + datatype); - if(datatype == "categorical"): # Cat variable + if(datatype == "categorical"): # Cat variable logger.info("call of add_categorical_covar"); - cross, col_names = add_categorical_covar(cross, covar_as_string, i) # Expand and add it to the cross + cross, col_names = add_categorical_covar(cross, covar_as_string, i) # Expand and add it to the cross logger.info("add_categorical_covar returned"); - for z, col_name in enumerate(col_names): # Go through the additional covar names + for z, col_name in enumerate(col_names): # Go through the additional covar names if i < (len(covariate_list) - 1): covar_name_string += '"' + col_name + '", ' else: - if(z < (len(col_names) -1)): + if(z < (len(col_names) - 1)): covar_name_string += '"' + col_name + '", ' else: covar_name_string += '"' + col_name + '"' @@ -376,7 +376,7 @@ def process_pair_scan_results(result): def process_rqtl_perm_results(num_perm, results): perm_vals = [] - for line in str(results).split("\n")[1:(num_perm+1)]: + for line in str(results).split("\n")[1:(num_perm + 1)]: #print("R/qtl permutation line:", line.split()) perm_vals.append(float(line.split()[1])) @@ -393,7 +393,7 @@ def process_rqtl_results(result, species_name): # TODO: how to make this for i, line in enumerate(result.iter_row()): marker = {} marker['name'] = result.rownames[i] - if species_name == "mouse" and output[i][0] == 20: #ZS: This is awkward, but I'm not sure how to change the 20s to Xs in the RData file + if species_name == "mouse" and output[i][0] == 20: # ZS: This is awkward, but I'm not sure how to change the 20s to Xs in the RData file marker['chr'] = "X" else: marker['chr'] = output[i][0] @@ -402,4 +402,4 @@ def process_rqtl_results(result, species_name): # TODO: how to make this marker['lod_score'] = output[i][2] qtl_results.append(marker) - return qtl_results \ No newline at end of file + return qtl_results diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 7dd0bcb6..f1665570 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -1,5 +1,5 @@ from base.trait import GeneralTrait -from base import data_set #import create_dataset +from base import data_set # import create_dataset from pprint import pformat as pf @@ -43,16 +43,16 @@ from utility.external import shell from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) class RunMapping: def __init__(self, start_vars, temp_uuid): helper_functions.get_species_dataset_trait(self, start_vars) - self.temp_uuid = temp_uuid #needed to pass temp_uuid to gn1 mapping code (marker_regression_gn1.py) + self.temp_uuid = temp_uuid # needed to pass temp_uuid to gn1 mapping code (marker_regression_gn1.py) - #ZS: Needed to zoom in or remap temp traits like PCA traits + # ZS: Needed to zoom in or remap temp traits like PCA traits if "temp_trait" in start_vars and start_vars['temp_trait'] != "False": self.temp_trait = "True" self.group = self.dataset.group.name @@ -60,7 +60,7 @@ class RunMapping: self.json_data = {} self.json_data['lodnames'] = ['lod.hk'] - #ZS: Sometimes a group may have a genofile that only includes a subset of samples + # ZS: Sometimes a group may have a genofile that only includes a subset of samples genofile_samplelist = [] if 'genofile' in start_vars: if start_vars['genofile'] != "": @@ -93,7 +93,7 @@ class RunMapping: else: self.n_samples = len([val for val in self.vals if val != "x"]) - #ZS: Check if genotypes exist in the DB in order to create links for markers + # ZS: Check if genotypes exist in the DB in order to create links for markers self.geno_db_exists = geno_db_exists(self.dataset) @@ -114,19 +114,19 @@ class RunMapping: self.manhattan_single_color = start_vars['manhattan_single_color'] self.manhattan_plot = True - self.maf = start_vars['maf'] # Minor allele frequency + self.maf = start_vars['maf'] # Minor allele frequency if "use_loco" in start_vars: self.use_loco = start_vars['use_loco'] else: self.use_loco = None self.suggestive = "" self.significant = "" - self.pair_scan = False # Initializing this since it is checked in views to determine which template to use + self.pair_scan = False # Initializing this since it is checked in views to determine which template to use if 'transform' in start_vars: self.transform = start_vars['transform'] else: self.transform = "" - self.score_type = "LRS" #ZS: LRS or LOD + self.score_type = "LRS" # ZS: LRS or LOD self.mapping_scale = "physic" if "mapping_scale" in start_vars: self.mapping_scale = start_vars['mapping_scale'] @@ -136,10 +136,10 @@ class RunMapping: self.covariates = start_vars['covariates'] if "covariates" in start_vars else "" self.categorical_vars = [] - #ZS: This is passed to GN1 code for single chr mapping + # ZS: This is passed to GN1 code for single chr mapping self.selected_chr = -1 if "selected_chr" in start_vars: - if int(start_vars['selected_chr']) != -1: #ZS: Needs to be -1 if showing full map; there's probably a better way to fix this + if int(start_vars['selected_chr']) != -1: # ZS: Needs to be -1 if showing full map; there's probably a better way to fix this self.selected_chr = int(start_vars['selected_chr']) + 1 else: self.selected_chr = int(start_vars['selected_chr']) @@ -153,7 +153,7 @@ class RunMapping: self.lrsMax = start_vars['lrsMax'] if "haplotypeAnalystCheck" in start_vars: self.haplotypeAnalystCheck = start_vars['haplotypeAnalystCheck'] - if "startMb" in start_vars: #ZS: This is to ensure showGenes, Legend, etc are checked the first time you open the mapping page, since startMb will only not be set during the first load + if "startMb" in start_vars: # ZS: This is to ensure showGenes, Legend, etc are checked the first time you open the mapping page, since startMb will only not be set during the first load if "permCheck" in start_vars: self.permCheck = "ON" else: @@ -191,13 +191,13 @@ class RunMapping: self.showGenes = "ON" self.viewLegend = "ON" - #self.dataset.group.get_markers() + # self.dataset.group.get_markers() if self.mapping_method == "gemma": self.first_run = True self.output_files = None if 'output_files' in start_vars: self.output_files = start_vars['output_files'] - if 'first_run' in start_vars: #ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) + if 'first_run' in start_vars: # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) self.first_run = False self.score_type = "-logP" self.manhattan_plot = True @@ -214,9 +214,9 @@ class RunMapping: if "perm_strata" in start_vars and "categorical_vars" in start_vars: self.categorical_vars = start_vars["categorical_vars"].split(",") if len(self.categorical_vars) and start_vars["perm_strata"] == "True": - primary_samples = SampleList(dataset = self.dataset, - sample_names = self.samples, - this_trait = self.this_trait) + primary_samples = SampleList(dataset=self.dataset, + sample_names=self.samples, + this_trait=self.this_trait) perm_strata = get_perm_strata(self.this_trait, primary_samples, self.categorical_vars, self.samples) self.score_type = "LOD" @@ -227,14 +227,14 @@ class RunMapping: else: self.method = "em" self.model = start_vars['mapmodel_rqtl_geno'] - #if start_vars['pair_scan'] == "true": + # if start_vars['pair_scan'] == "true": # self.pair_scan = True if self.permCheck and self.num_perm > 0: - self.perm_output, self.suggestive, self.significant, results= rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates) + self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates) else: results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates) elif self.mapping_method == "reaper": - if "startMb" in start_vars: #ZS: Check if first time page loaded, so it can default to ON + if "startMb" in start_vars: # ZS: Check if first time page loaded, so it can default to ON if "additiveCheck" in start_vars: self.additiveCheck = start_vars['additiveCheck'] else: @@ -267,7 +267,7 @@ class RunMapping: if self.reaper_version == "new": self.first_run = True self.output_files = None - if 'first_run' in start_vars: #ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) + if 'first_run' in start_vars: # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) self.first_run = False if 'output_files' in start_vars: self.output_files = start_vars['output_files'].split(",") @@ -311,7 +311,7 @@ class RunMapping: else: if self.pair_scan == True: self.qtl_results = [] - highest_chr = 1 #This is needed in order to convert the highest chr to X/Y + highest_chr = 1 # This is needed in order to convert the highest chr to X/Y for marker in results: if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y": if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y": @@ -328,51 +328,51 @@ class RunMapping: self.json_data['markernames'].append(qtl['name']) self.js_data = dict( - json_data = self.json_data, - this_trait = self.this_trait.name, - data_set = self.dataset.name, - maf = self.maf, - manhattan_plot = self.manhattan_plot, - mapping_scale = self.mapping_scale, - qtl_results = self.qtl_results + json_data=self.json_data, + this_trait=self.this_trait.name, + data_set=self.dataset.name, + maf=self.maf, + manhattan_plot=self.manhattan_plot, + mapping_scale=self.mapping_scale, + qtl_results=self.qtl_results ) else: self.qtl_results = [] self.results_for_browser = [] self.annotations_for_browser = [] - highest_chr = 1 #This is needed in order to convert the highest chr to X/Y + highest_chr = 1 # This is needed in order to convert the highest chr to X/Y for marker in results: if 'Mb' in marker: - this_ps = marker['Mb']*1000000 + this_ps = marker['Mb'] * 1000000 else: - this_ps = marker['cM']*1000000 + this_ps = marker['cM'] * 1000000 browser_marker = dict( - chr = str(marker['chr']), - rs = marker['name'], - ps = this_ps, - url = "/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno" + chr=str(marker['chr']), + rs=marker['name'], + ps=this_ps, + url="/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno" ) if self.geno_db_exists == "True": annot_marker = dict( - name = str(marker['name']), - chr = str(marker['chr']), - rs = marker['name'], - pos = this_ps, - url = "/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno" + name=str(marker['name']), + chr=str(marker['chr']), + rs=marker['name'], + pos=this_ps, + url="/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno" ) else: annot_marker = dict( - name = str(marker['name']), - chr = str(marker['chr']), - rs = marker['name'], - pos = this_ps + name=str(marker['name']), + chr=str(marker['chr']), + rs=marker['name'], + pos=this_ps ) if 'lrs_value' in marker and marker['lrs_value'] > 0: - browser_marker['p_wald'] = 10**-(marker['lrs_value']/4.61) + browser_marker['p_wald'] = 10**-(marker['lrs_value'] / 4.61) elif 'lod_score' in marker and marker['lod_score'] > 0: browser_marker['p_wald'] = 10**-(marker['lod_score']) else: @@ -417,7 +417,7 @@ class RunMapping: chr_lengths = get_chr_lengths(self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results) - #ZS: For zooming into genome browser, need to pass chromosome name instead of number + # ZS: For zooming into genome browser, need to pass chromosome name instead of number if self.dataset.group.species == "mouse": if self.selected_chr == 20: this_chr = "X" @@ -451,29 +451,29 @@ class RunMapping: #mapping_scale = self.mapping_scale, #chromosomes = chromosome_mb_lengths, #qtl_results = self.qtl_results, - categorical_vars = self.categorical_vars, - chr_lengths = chr_lengths, - num_perm = self.num_perm, - perm_results = self.perm_output, - significant = significant_for_browser, - browser_files = browser_files, - selected_chr = this_chr, - total_markers = total_markers + categorical_vars=self.categorical_vars, + chr_lengths=chr_lengths, + num_perm=self.num_perm, + perm_results=self.perm_output, + significant=significant_for_browser, + browser_files=browser_files, + selected_chr=this_chr, + total_markers=total_markers ) else: self.js_data = dict( - chr_lengths = chr_lengths, - browser_files = browser_files, - selected_chr = this_chr, - total_markers = total_markers + chr_lengths=chr_lengths, + browser_files=browser_files, + selected_chr=this_chr, + total_markers=total_markers ) def run_rqtl_plink(self): # os.chdir("") never do this inside a webserver!! - output_filename = webqtlUtil.genRandStr("%s_%s_"%(self.dataset.group.name, self.this_trait.name)) + output_filename = webqtlUtil.genRandStr("%s_%s_" % (self.dataset.group.name, self.this_trait.name)) - plink_mapping.gen_pheno_txt_file_plink(self.this_trait, self.dataset, self.vals, pheno_filename = output_filename) + plink_mapping.gen_pheno_txt_file_plink(self.this_trait, self.dataset, self.vals, pheno_filename=output_filename) rqtl_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (self.dataset.group.name, self.dataset.group.name, TMPDIR, plink_output_filename, self.this_trait.name, self.maf, TMPDIR, plink_output_filename) @@ -612,11 +612,11 @@ def trim_markers_for_figure(markers): if low_counter % 20 == 0: filtered_markers.append(marker) low_counter += 1 - elif 4.61 <= marker[score_type] < (2*4.61): + elif 4.61 <= marker[score_type] < (2 * 4.61): if med_counter % 10 == 0: filtered_markers.append(marker) med_counter += 1 - elif (2*4.61) <= marker[score_type] <= (3*4.61): + elif (2 * 4.61) <= marker[score_type] <= (3 * 4.61): if high_counter % 2 == 0: filtered_markers.append(marker) high_counter += 1 @@ -630,7 +630,7 @@ def trim_markers_for_table(markers): else: sorted_markers = sorted(markers, key=lambda k: k['lrs_value'], reverse=True) - #ZS: So we end up with a list of just 2000 markers + # ZS: So we end up with a list of just 2000 markers if len(sorted_markers) >= 2000: trimmed_sorted_markers = sorted_markers[:2000] return trimmed_sorted_markers @@ -682,9 +682,9 @@ def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results): highest_pos = float(result['cM']) * 1000000 else: highest_pos = float(result['Mb']) * 1000000 - chr_lengths.append({ "chr": str(this_chr), "size": str(highest_pos)}) + chr_lengths.append({"chr": str(this_chr), "size": str(highest_pos)}) else: - chr_lengths.append({ "chr": str(this_chr), "size": str(highest_pos)}) + chr_lengths.append({"chr": str(this_chr), "size": str(highest_pos)}) this_chr = chr_as_num else: if mapping_method == "reaper": @@ -721,7 +721,7 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): perm_strata_strings.append(combined_string) - d = dict([(y, x+1) for x, y in enumerate(sorted(set(perm_strata_strings)))]) + d = dict([(y, x + 1) for x, y in enumerate(sorted(set(perm_strata_strings)))]) list_to_numbers = [d[x] for x in perm_strata_strings] perm_strata = list_to_numbers diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py index 772f74e4..8abd6516 100644 --- a/wqflask/wqflask/model.py +++ b/wqflask/wqflask/model.py @@ -29,14 +29,14 @@ class User(Base): registration_info = Column(Text) # json detailing when they were registered, etc. - confirmed = Column(Text) # json detailing when they confirmed, etc. + confirmed = Column(Text) # json detailing when they confirmed, etc. - superuser = Column(Text) # json detailing when they became a superuser, otherwise empty + superuser = Column(Text) # json detailing when they became a superuser, otherwise empty # if not superuser logins = relationship("Login", order_by="desc(Login.timestamp)", - lazy='dynamic', # Necessary for filter in login_count + lazy='dynamic', # Necessary for filter in login_count foreign_keys="Login.user", ) @@ -67,7 +67,7 @@ class User(Base): def get_collection_by_name(self, collection_name): try: collect = self.user_collections.filter_by(name=collection_name).first() - except sqlalchemy.orm.exc.NoResultFound: + except sqlalchemy.orm.exc.NoResultFound: collect = None return collect diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py index dcd328c9..dfd374e2 100644 --- a/wqflask/wqflask/parser.py +++ b/wqflask/wqflask/parser.py @@ -22,7 +22,7 @@ import re from pprint import pformat as pf from utility.logger import getLogger -logger = getLogger(__name__ ) +logger = getLogger(__name__) def parse(pstring): """ @@ -52,7 +52,7 @@ def parse(pstring): if '(' in value or '[' in value: assert value.startswith(("(", "[")), "Invalid token" assert value.endswith((")", "]")), "Invalid token" - value = value[1:-1] # Get rid of the parenthesis + value = value[1:-1] # Get rid of the parenthesis values = re.split(r"""\s+|,""", value) value = [value.strip() for value in values if value.strip()] else: diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index 7d51a83d..a1fe0f8f 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -26,7 +26,7 @@ def manage_resource(): owner_display_name = None if owner_id != "none": - try: #ZS: User IDs are sometimes stored in Redis as bytes and sometimes as strings, so this is just to avoid any errors for the time being + try: # ZS: User IDs are sometimes stored in Redis as bytes and sometimes as strings, so this is just to avoid any errors for the time being owner_id = str.encode(owner_id) except: pass @@ -38,7 +38,7 @@ def manage_resource(): elif 'email_address' in owner_info: owner_display_name = owner_info['email_address'] - return render_template("admin/manage_resource.html", owner_name = owner_display_name, resource_id = resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status) + return render_template("admin/manage_resource.html", owner_name=owner_display_name, resource_id=resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status) @app.route("/search_for_users", methods=('POST',)) def search_for_user(): @@ -79,7 +79,7 @@ def change_owner(): flash("You lack the permissions to make this change.", "error") return redirect(url_for("manage_resource", resource_id=resource_id)) else: - return render_template("admin/change_resource_owner.html", resource_id = resource_id) + return render_template("admin/change_resource_owner.html", resource_id=resource_id) @app.route("/resources/change_default_privileges", methods=('POST',)) def change_default_privileges(): @@ -108,7 +108,7 @@ def add_group_to_resource(): group_id = request.form['selected_group'] resource_info = get_resource_info(resource_id) default_privileges = resource_info['default_mask'] - return render_template("admin/set_group_privileges.html", resource_id = resource_id, group_id = group_id, default_privileges = default_privileges) + return render_template("admin/set_group_privileges.html", resource_id=resource_id, group_id=group_id, default_privileges = default_privileges) elif all(key in request.form for key in ('data_privilege', 'metadata_privilege', 'admin_privilege')): group_id = request.form['group_id'] group_name = get_group_info(group_id)['name'] @@ -121,7 +121,7 @@ def add_group_to_resource(): flash("Privileges have been added for group {}.".format(group_name), "alert-info") return redirect(url_for("manage_resource", resource_id=resource_id)) else: - return render_template("admin/search_for_groups.html", resource_id = resource_id) + return render_template("admin/search_for_groups.html", resource_id=resource_id) else: return redirect(url_for("no_access_page")) diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index fd7c132b..16eb1864 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -22,7 +22,7 @@ from utility.tools import GN2_BASE_URL from utility.type_checking import is_str from utility.logger import getLogger -logger = getLogger(__name__ ) +logger = getLogger(__name__) class SearchResultPage: #maxReturn = 3000 @@ -39,7 +39,7 @@ class SearchResultPage: self.uc_id = uuid.uuid4() self.go_term = None - logger.debug("uc_id:", self.uc_id) # contains a unique id + logger.debug("uc_id:", self.uc_id) # contains a unique id logger.debug("kw is:", kw) # dict containing search terms if kw['search_terms_or']: @@ -72,7 +72,7 @@ class SearchResultPage: self.dataset = create_dataset(kw['dataset'], dataset_type) logger.debug("search_terms:", self.search_terms) - #ZS: I don't like using try/except, but it seems like the easiest way to account for all possible bad searches here + # ZS: I don't like using try/except, but it seems like the easiest way to account for all possible bad searches here try: self.search() except: @@ -183,7 +183,7 @@ class SearchResultPage: combined_from_clause = "" combined_where_clause = "" - previous_from_clauses = [] #The same table can't be referenced twice in the from clause + previous_from_clauses = [] # The same table can't be referenced twice in the from clause logger.debug("len(search_terms)>1") symbol_list = [] @@ -231,7 +231,7 @@ class SearchResultPage: combined_from_clause += from_clause where_clause = the_search.get_where_clause() combined_where_clause += "(" + where_clause + ")" - if (i+1) < len(self.search_terms): + if (i + 1) < len(self.search_terms): if self.and_or == "and": combined_where_clause += "AND" else: @@ -291,7 +291,7 @@ def insert_newlines(string, every=64): """ This is because it is seemingly impossible to change the width of the description column, so I'm just manually adding line breaks """ lines = [] for i in range(0, len(string), every): - lines.append(string[i:i+every]) + lines.append(string[i:i + every]) return '\n'.join(lines) def get_aliases(symbol_list, species): @@ -322,9 +322,9 @@ def get_aliases(symbol_list, species): search_terms = [] for alias in filtered_aliases: - the_search_term = {'key': None, + the_search_term = {'key': None, 'search_term': [alias], - 'separator' : None} + 'separator': None} search_terms.append(the_search_term) return search_terms diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index f955f632..388f831f 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -36,16 +36,16 @@ class SampleList: if isinstance(self.this_trait, list): sample = webqtlCaseData.webqtlCaseData(name=sample_name) if counter <= len(self.this_trait): - if isinstance(self.this_trait[counter-1], (bytes, bytearray)): - if (self.this_trait[counter-1].decode("utf-8").lower() != 'x'): + if isinstance(self.this_trait[counter - 1], (bytes, bytearray)): + if (self.this_trait[counter - 1].decode("utf-8").lower() != 'x'): sample = webqtlCaseData.webqtlCaseData( name=sample_name, - value=float(self.this_trait[counter-1])) + value=float(self.this_trait[counter - 1])) else: - if (self.this_trait[counter-1].lower() != 'x'): + if (self.this_trait[counter - 1].lower() != 'x'): sample = webqtlCaseData.webqtlCaseData( name=sample_name, - value=float(self.this_trait[counter-1])) + value=float(self.this_trait[counter - 1])) else: # ZS - If there's no value for the sample/strain, # create the sample object (so samples with no value @@ -69,7 +69,7 @@ class SampleList: sample.extra_attributes = self.sample_attribute_values.get( sample_name, {}) - #ZS: Add a url so RRID case attributes can be displayed as links + # ZS: Add a url so RRID case attributes can be displayed as links if 'rrid' in sample.extra_attributes: if self.dataset.group.species == "mouse": if len(sample.extra_attributes['rrid'].split(":")) > 1: @@ -129,7 +129,7 @@ class SampleList: self.attributes[key].name = name self.attributes[key].distinct_values = [ item.Value for item in values] - self.attributes[key].distinct_values=natural_sort(self.attributes[key].distinct_values) + self.attributes[key].distinct_values = natural_sort(self.attributes[key].distinct_values) all_numbers = True for value in self.attributes[key].distinct_values: try: diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index f9c5fbe6..18cadea4 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -46,7 +46,7 @@ class ShowTrait: resource_id=self.resource_id) elif 'group' in kw: self.temp_trait = True - self.trait_id = "Temp_"+kw['species'] + "_" + kw['group'] + \ + self.trait_id = "Temp_" + kw['species'] + "_" + kw['group'] + \ "_" + datetime.datetime.now().strftime("%m%d%H%M%S") self.temp_species = kw['species'] self.temp_group = kw['group'] @@ -368,8 +368,8 @@ class ShowTrait: chr = transcript_start = transcript_end = None if chr and transcript_start and transcript_end and self.this_trait.refseq_transcriptid: - transcript_start = int(transcript_start*1000000) - transcript_end = int(transcript_end*1000000) + transcript_start = int(transcript_start * 1000000) + transcript_end = int(transcript_end * 1000000) self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ( 'mm10', self.this_trait.refseq_transcriptid, chr, transcript_start, transcript_end) @@ -393,8 +393,8 @@ class ShowTrait: if chr and transcript_start and transcript_end and kgId: # Convert to bases from megabases - transcript_start = int(transcript_start*1000000) - transcript_end = int(transcript_end*1000000) + transcript_start = int(transcript_start * 1000000) + transcript_end = int(transcript_end * 1000000) self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ( 'rn6', kgId, chr, transcript_start, transcript_end) @@ -515,13 +515,13 @@ def quantile_normalize_vals(sample_groups): ranked_vals = ss.rankdata(trait_vals) p_list = [] for i, val in enumerate(trait_vals): - p_list.append(((i+1) - 0.5)/len(trait_vals)) + p_list.append(((i + 1) - 0.5) / len(trait_vals)) z = ss.norm.ppf(p_list) normed_vals = [] for rank in ranked_vals: - normed_vals.append("%0.3f" % z[int(rank)-1]) + normed_vals.append("%0.3f" % z[int(rank) - 1]) return normed_vals @@ -585,7 +585,7 @@ def get_nearest_marker(this_trait, this_db): GenoXRef.GenoId = Geno.Id AND GenoFreeze.Id = GenoXRef.GenoFreezeId AND GenoFreeze.Name = '{}' - ORDER BY ABS( Geno.Mb - {}) LIMIT 1""".format(this_chr, this_db.group.name+"Geno", this_mb) + ORDER BY ABS( Geno.Mb - {}) LIMIT 1""".format(this_chr, this_db.group.name + "Geno", this_mb) logger.sql(query) result = g.db.execute(query).fetchall() @@ -605,7 +605,7 @@ def get_table_widths(sample_groups, sample_column_width, has_num_cases=False): trait_table_width += 80 if has_num_cases: trait_table_width += 80 - trait_table_width += len(sample_groups[0].attributes)*88 + trait_table_width += len(sample_groups[0].attributes) * 88 trait_table_width = str(trait_table_width) + "px" diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index 8658abf8..7a0df94b 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -26,9 +26,9 @@ class SnpBrowser: self.table_rows = [] if self.limit_strains == "true": - self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type = self.variant_type, strains = self.chosen_strains, empty_columns = self.empty_columns) + self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type=self.variant_type, strains=self.chosen_strains, empty_columns = self.empty_columns) else: - self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type = self.variant_type, strains = self.strain_lists, species = self.species_name, empty_columns = self.empty_columns) + self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type=self.variant_type, strains=self.strain_lists, species = self.species_name, empty_columns = self.empty_columns) def initialize_parameters(self, start_vars): if 'first_run' in start_vars: @@ -249,7 +249,7 @@ class SnpBrowser: def filter_results(self, results): filtered_results = [] - strain_index_list = [] #ZS: List of positions of selected strains in strain list + strain_index_list = [] # ZS: List of positions of selected strains in strain list last_mb = -1 if self.limit_strains == "true" and len(self.chosen_strains) > 0: @@ -272,9 +272,9 @@ class SnpBrowser: if self.limit_strains == "true" and len(self.chosen_strains) > 0: for index in strain_index_list: if self.species_id == 1: - display_strains.append(result[29+index]) + display_strains.append(result[29 + index]) elif self.species_id == 2: - display_strains.append(result[31+index]) + display_strains.append(result[31 + index]) self.allele_list = display_strains effect_info_dict = get_effect_info(effect_list) @@ -300,7 +300,7 @@ class SnpBrowser: else: gene = check_if_in_gene(species_id, chr, mb) transcript = exon = function = function_details = '' - if self.redundant == "false" or last_mb != mb: # filter redundant + if self.redundant == "false" or last_mb != mb: # filter redundant if self.include_record(domain, function, snp_source, conservation_score): info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id] info_list.extend(self.allele_list) @@ -366,7 +366,7 @@ class SnpBrowser: if len(gene_name_list) > 0: gene_id_name_dict = get_gene_id_name_dict(self.species_id, gene_name_list) - #ZS: list of booleans representing which columns are entirely empty, so they aren't displayed on the page; only including ones that are sometimes empty (since there's always a location, etc) + # ZS: list of booleans representing which columns are entirely empty, so they aren't displayed on the page; only including ones that are sometimes empty (since there's always a location, etc) self.empty_columns = { "snp_source": "false", "conservation_score": "false", @@ -389,8 +389,8 @@ class SnpBrowser: snp_name = rs else: rs = "" - start_bp = int(mb*1000000 - 100) - end_bp = int(mb*1000000 + 100) + start_bp = int(mb * 1000000 - 100) + end_bp = int(mb * 1000000 + 100) position_info = "chr%s:%d-%d" % (chr, start_bp, end_bp) if self.species_id == 2: snp_url = webqtlConfig.GENOMEBROWSER_URL % ("rn6", position_info) @@ -434,7 +434,7 @@ class SnpBrowser: transcript_link = "" if exon: - exon = exon[1] # exon[0] is exon_id, exon[1] is exon_rank + exon = exon[1] # exon[0] is exon_id, exon[1] is exon_rank self.empty_columns['exon'] = "true" else: exon = "" @@ -575,7 +575,7 @@ class SnpBrowser: if conservation_score: score_as_float = float(conservation_score) try: - input_score_float = float(self.score) # the user-input score + input_score_float = float(self.score) # the user-input score except: input_score_float = 0.0 @@ -628,17 +628,17 @@ class SnpBrowser: left_offset, right_offset, top_offset, bottom_offset = (30, 30, 40, 50) plot_width = canvas_width - left_offset - right_offset plot_height = canvas_height - top_offset - bottom_offset - y_zero = top_offset + plot_height/2 + y_zero = top_offset + plot_height / 2 - x_scale = plot_width/(self.end_mb - self.start_mb) + x_scale = plot_width / (self.end_mb - self.start_mb) - #draw clickable image map at some point + # draw clickable image map at some point n_click = 80.0 - click_step = plot_width/n_click - click_mb_step = (self.end_mb - self.start_mb)/n_click + click_step = plot_width / n_click + click_mb_step = (self.end_mb - self.start_mb) / n_click - #for i in range(n_click): + # for i in range(n_click): # href = url_for('snp_browser', first_run="false", chosen_strains_mouse=self.chosen_strains_mouse, chosen_strains_rat=self.chosen_strains_rat, variant=self.variant_type, species=self.species_name, gene_name=self.gene_name, chr=self.chr, start_mb=self.start_mb, end_mb=self.end_mb, limit_strains=self.limit_strains, domain=self.domain, function=self.function, criteria=self.criteria, score=self.score, diff_alleles=self.diff_alleles) def get_browser_sample_lists(species_id=1): @@ -660,7 +660,7 @@ def get_browser_sample_lists(species_id=1): return strain_lists -def get_header_list(variant_type, strains, species = None, empty_columns = None): +def get_header_list(variant_type, strains, species=None, empty_columns=None): if species == "Mouse": strain_list = strains['mouse'] elif species == "Rat": @@ -668,7 +668,7 @@ def get_header_list(variant_type, strains, species = None, empty_columns = None) else: strain_list = strains - empty_field_count = 0 #ZS: This is an awkward way of letting the javascript know the index where the allele value columns start; there's probably a better way of doing this + empty_field_count = 0 # ZS: This is an awkward way of letting the javascript know the index where the allele value columns start; there's probably a better way of doing this header_fields = [] header_data_names = [] @@ -715,7 +715,7 @@ def get_header_list(variant_type, strains, species = None, empty_columns = None) return header_fields, empty_field_count, header_data_names -def get_effect_details_by_category(effect_name = None, effect_value = None): +def get_effect_details_by_category(effect_name=None, effect_value=None): gene_list = [] transcript_list = [] exon_list = [] @@ -878,7 +878,7 @@ def get_gene_id_name_dict(species_id, gene_name_list): return gene_id_name_dict def check_if_in_gene(species_id, chr, mb): - if species_id != 0: #ZS: Check if this is necessary + if species_id != 0: # ZS: Check if this is necessary query = """SELECT geneId, geneSymbol FROM GeneList WHERE SpeciesId = {0} AND chromosome = '{1}' AND diff --git a/wqflask/wqflask/submit_bnw.py b/wqflask/wqflask/submit_bnw.py index a0e84c8c..4ad6f9e3 100644 --- a/wqflask/wqflask/submit_bnw.py +++ b/wqflask/wqflask/submit_bnw.py @@ -3,7 +3,7 @@ from base import data_set from utility import helper_functions import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) def get_bnw_input(start_vars): logger.debug("BNW VARS:", start_vars) diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py index 22a46ef2..08b4f9f5 100644 --- a/wqflask/wqflask/update_search_results.py +++ b/wqflask/wqflask/update_search_results.py @@ -53,7 +53,7 @@ class GSearch: for line in re: dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False) trait_id = line[4] - #with Bench("Building trait object"): + # with Bench("Building trait object"): this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) self.trait_list.append(this_trait) @@ -108,8 +108,8 @@ class GSearch: json_dict['data'] = [] for i, trait in enumerate(self.trait_list): - trait_row = { "checkbox": "".format(trait.name, trait.dataset.name), - "index": i+1, + trait_row = {"checkbox": "".format(trait.name, trait.dataset.name), + "index": i + 1, "species": trait.dataset.group.species, "group": trait.dataset.group.name, "tissue": trait.dataset.tissue, diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py index b6e7973f..3f5b43ee 100644 --- a/wqflask/wqflask/user_login.py +++ b/wqflask/wqflask/user_login.py @@ -33,9 +33,9 @@ def timestamp(): return datetime.datetime.utcnow().isoformat() def basic_info(): - return dict(timestamp = timestamp(), - ip_address = request.remote_addr, - user_agent = request.headers.get('User-Agent')) + return dict(timestamp=timestamp(), + ip_address=request.remote_addr, + user_agent=request.headers.get('User-Agent')) def encode_password(pass_gen_fields, unencrypted_password): @@ -77,31 +77,31 @@ def get_signed_session_id(user): session_id_signature = hmac.hmac_creation(session_id) session_id_signed = session_id + ":" + session_id_signature - #ZS: Need to check if this is ever actually used or exists + # ZS: Need to check if this is ever actually used or exists if 'user_id' not in user: user['user_id'] = str(uuid.uuid4()) save_user(user, user['user_id']) if 'github_id' in user: - session = dict(login_time = time.time(), - user_type = "github", - user_id = user['user_id'], - github_id = user['github_id'], - user_name = user['name'], - user_url = user['user_url']) + session = dict(login_time=time.time(), + user_type="github", + user_id=user['user_id'], + github_id=user['github_id'], + user_name=user['name'], + user_url=user['user_url']) elif 'orcid' in user: - session = dict(login_time = time.time(), - user_type = "orcid", - user_id = user['user_id'], - github_id = user['orcid'], - user_name = user['name'], - user_url = user['user_url']) + session = dict(login_time=time.time(), + user_type="orcid", + user_id=user['user_id'], + github_id=user['orcid'], + user_name=user['name'], + user_url=user['user_url']) else: - session = dict(login_time = time.time(), - user_type = "gn2", - user_id = user['user_id'], - user_name = user['full_name'], - user_email_address = user['email_address']) + session = dict(login_time=time.time(), + user_type="gn2", + user_id=user['user_id'], + user_name=user['full_name'], + user_email_address=user['email_address']) key = UserSession.user_cookie_name + ":" + session_id Redis.hmset(key, session) @@ -123,23 +123,23 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"): server.login(SMTP_USERNAME, SMTP_PASSWORD) server.sendmail(fromaddr, toaddr, msg) server.quit() - logger.info("Successfully sent email to "+toaddr) + logger.info("Successfully sent email to " + toaddr) -def send_verification_email(user_details, template_name = "email/user_verification.txt", key_prefix = "verification_code", subject = "GeneNetwork e-mail verification"): +def send_verification_email(user_details, template_name="email/user_verification.txt", key_prefix="verification_code", subject = "GeneNetwork e-mail verification"): verification_code = str(uuid.uuid4()) key = key_prefix + ":" + verification_code - data = json.dumps(dict(id=user_details['user_id'], timestamp = timestamp())) + data = json.dumps(dict(id=user_details['user_id'], timestamp=timestamp())) Redis.set(key, data) Redis.expire(key, THREE_DAYS) recipient = user_details['email_address'] - body = render_template(template_name, verification_code = verification_code) + body = render_template(template_name, verification_code=verification_code) send_email(recipient, subject, body) return {"recipient": recipient, "subject": subject, "body": body} -def send_invitation_email(user_email, temp_password, template_name = "email/user_invitation.txt", subject = "You've been added to a GeneNetwork user group"): +def send_invitation_email(user_email, temp_password, template_name="email/user_invitation.txt", subject= "You've been added to a GeneNetwork user group"): recipient = user_email body = render_template(template_name, temp_password) send_email(recipient, subject, body) @@ -154,7 +154,7 @@ def verify_email(): # We might as well log them in session_id_signed = get_signed_session_id(user_details) flash("Thank you for logging in {}.".format(user_details['full_name']), "alert-success") - response = make_response(redirect(url_for('index_page', import_collections = import_col, anon_id = anon_id))) + response = make_response(redirect(url_for('index_page', import_collections=import_col, anon_id=anon_id))) response.set_cookie(UserSession.user_cookie_name, session_id_signed, max_age=None) return response else: @@ -165,15 +165,15 @@ def login(): params = request.form if request.form else request.args logger.debug("in login params are:", params) - if not params: #ZS: If coming to page for first time + if not params: # ZS: If coming to page for first time from utility.tools import GITHUB_AUTH_URL, GITHUB_CLIENT_ID, ORCID_AUTH_URL, ORCID_CLIENT_ID external_login = {} if GITHUB_AUTH_URL and GITHUB_CLIENT_ID != 'UNKNOWN': external_login["github"] = GITHUB_AUTH_URL if ORCID_AUTH_URL and ORCID_CLIENT_ID != 'UNKNOWN': external_login["orcid"] = ORCID_AUTH_URL - return render_template("new_security/login_user.html", external_login = external_login, redis_is_available=is_redis_available()) - else: #ZS: After clicking sign-in + return render_template("new_security/login_user.html", external_login=external_login, redis_is_available=is_redis_available()) + else: # ZS: After clicking sign-in if 'type' in params and 'uid' in params: user_details = get_user_by_unique_column("user_id", params['uid']) if user_details: @@ -204,13 +204,13 @@ def login(): encrypted_pass_fields = encode_password(pwfields, submitted_password) password_match = pbkdf2.safe_str_cmp(encrypted_pass_fields['password'], pwfields['password']) - else: # Invalid e-mail + else: # Invalid e-mail flash("Invalid e-mail address. Please try again.", "alert-danger") response = make_response(redirect(url_for('login'))) return response - if password_match: # If password correct - if user_details['confirmed']: # If account confirmed + if password_match: # If password correct + if user_details['confirmed']: # If account confirmed import_col = "false" anon_id = "" if 'import_collections' in params: @@ -219,14 +219,14 @@ def login(): session_id_signed = get_signed_session_id(user_details) flash("Thank you for logging in {}.".format(user_details['full_name']), "alert-success") - response = make_response(redirect(url_for('index_page', import_collections = import_col, anon_id = anon_id))) + response = make_response(redirect(url_for('index_page', import_collections=import_col, anon_id=anon_id))) response.set_cookie(UserSession.user_cookie_name, session_id_signed, max_age=None) return response else: - email_ob = send_verification_email(user_details, template_name = "email/user_verification.txt") + email_ob = send_verification_email(user_details, template_name="email/user_verification.txt") return render_template("newsecurity/verification_still_needed.html", subject=email_ob['subject']) - else: # Incorrect password - #ZS: It previously seemed to store that there was an incorrect log-in attempt here, but it did so in the MySQL DB so this might need to be reproduced with Redis + else: # Incorrect password + # ZS: It previously seemed to store that there was an incorrect log-in attempt here, but it did so in the MySQL DB so this might need to be reproduced with Redis flash("Invalid password. Please try again.", "alert-danger") response = make_response(redirect(url_for('login'))) @@ -243,7 +243,7 @@ def github_oauth2(): } result = requests.post("https://github.com/login/oauth/access_token", json=data) - result_dict = {arr[0]:arr[1] for arr in [tok.split("=") for tok in result.text.split("&")]} + result_dict = {arr[0]: arr[1] for arr in [tok.split("=") for tok in result.text.split("&")]} github_user = get_github_user_details(result_dict["access_token"]) @@ -261,12 +261,12 @@ def github_oauth2(): } save_user(user_details, user_details["user_id"]) - url = "/n/login?type=github&uid="+user_details["user_id"] + url = "/n/login?type=github&uid=" + user_details["user_id"] return redirect(url) def get_github_user_details(access_token): from utility.tools import GITHUB_API_URL - result = requests.get(GITHUB_API_URL, headers = {'Authorization':'token ' + access_token }).content + result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content return json.loads(result) @@ -303,14 +303,14 @@ def orcid_oauth2(): } save_user(user_details, user_details["user_id"]) - url = "/n/login?type=orcid&uid="+user_details["user_id"] + url = "/n/login?type=orcid&uid=" + user_details["user_id"] else: flash("There was an error getting code from ORCID") return redirect(url) def get_github_user_details(access_token): from utility.tools import GITHUB_API_URL - result = requests.get(GITHUB_API_URL, headers = {'Authorization':'token ' + access_token }).content + result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content return json.loads(result) @@ -337,7 +337,7 @@ def send_forgot_password_email(verification_email): from email.mime.multipart import MIMEMultipart from email.mime.text import MIMEText - template_name = "email/forgot_password.txt" + template_name = "email/forgot_password.txt" key_prefix = "forgot_password_code" subject = "GeneNetwork password reset" fromaddr = "no-reply@genenetwork.org" @@ -353,7 +353,7 @@ def send_forgot_password_email(verification_email): save_verification_code(verification_email, verification_code) - body = render_template(template_name, verification_code = verification_code) + body = render_template(template_name, verification_code=verification_code) msg = MIMEMultipart() msg["To"] = verification_email diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index fcec3b67..013920f9 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -74,11 +74,11 @@ class AnonUser: self.key = "anon_collection:v1:{}".format(self.anon_id) def add_collection(self, new_collection): - collection_dict = dict(name = new_collection.name, - created_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), - changed_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), - num_members = new_collection.num_members, - members = new_collection.get_members()) + collection_dict = dict(name=new_collection.name, + created_timestamp=datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), + changed_timestamp=datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), + num_members=new_collection.num_members, + members=new_collection.get_members()) Redis.set(self.key, json.dumps(collection_dict)) Redis.expire(self.key, 60 * 60 * 24 * 365) @@ -111,7 +111,7 @@ class AnonUser: collection['created_timestamp'] = datetime.datetime.strptime(collection['created_timestamp'], '%b %d %Y %I:%M%p') collection['changed_timestamp'] = datetime.datetime.strptime(collection['changed_timestamp'], '%b %d %Y %I:%M%p') - collections = sorted(collections, key = lambda i: i['changed_timestamp'], reverse = True) + collections = sorted(collections, key=lambda i: i['changed_timestamp'], reverse=True) return collections def import_traits_to_user(self): @@ -182,13 +182,13 @@ class UserSession: # weekend and the site hasn't been visited by the user self.logged_in = False - ########### Grrr...this won't work because of the way flask handles cookies + # Grrr...this won't work because of the way flask handles cookies # Delete the cookie #response = make_response(redirect(url_for('login'))) #response.set_cookie(self.cookie_name, '', expires=0) - #flash( + # flash( # "Due to inactivity your session has expired. If you'd like please login again.") - #return response + # return response return if Redis.ttl(self.redis_key) < THREE_DAYS: @@ -213,7 +213,7 @@ class UserSession: user_email = self.record['user_email_address'] - #ZS: Get user's collections if they exist + # ZS: Get user's collections if they exist user_id = None user_id = get_user_id("email_address", user_email) return user_id @@ -230,7 +230,7 @@ class UserSession: def user_collections(self): """List of user's collections""" - #ZS: Get user's collections if they exist + # ZS: Get user's collections if they exist collections = get_user_collections(self.redis_user_id) return collections @@ -248,7 +248,7 @@ class UserSession: 'created_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), 'changed_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), 'num_members': len(traits), - 'members': list(traits) } + 'members': list(traits)} current_collections = self.user_collections current_collections.append(collection_dict) @@ -347,7 +347,7 @@ def get_cookie(): g.user_session = UserSession() g.cookie_session = AnonUser() -#@app.after_request +# @app.after_request def set_cookie(response): if not request.cookies.get(g.cookie_session.cookie_name): response.set_cookie(g.cookie_session.cookie_name, g.cookie_session.cookie) @@ -455,7 +455,7 @@ def set_password(password, user): class VerificationEmail: - template_name = "email/verification.txt" + template_name = "email/verification.txt" key_prefix = "verification_code" subject = "GeneNetwork email verification" @@ -473,7 +473,7 @@ class VerificationEmail: to = user.email_address subject = self.subject body = render_template(self.template_name, - verification_code = verification_code) + verification_code=verification_code) send_email(to, subject, body) class ForgotPasswordEmail(VerificationEmail): @@ -500,7 +500,7 @@ class ForgotPasswordEmail(VerificationEmail): subject = self.subject body = render_template( self.template_name, - verification_code = verification_code) + verification_code=verification_code) msg = MIMEMultipart() msg["To"] = toaddr @@ -525,11 +525,11 @@ class Password: def basic_info(): - return dict(timestamp = timestamp(), - ip_address = request.remote_addr, - user_agent = request.headers.get('User-Agent')) + return dict(timestamp=timestamp(), + ip_address=request.remote_addr, + user_agent=request.headers.get('User-Agent')) -#@app.route("/manage/verify_email") +# @app.route("/manage/verify_email") def verify_email(): user = DecodeUser(VerificationEmail.key_prefix).user user.confirmed = json.dumps(basic_info(), sort_keys=True) @@ -543,7 +543,7 @@ def verify_email(): response.set_cookie(UserSession.cookie_name, session_id_signed) return response -#@app.route("/n/password_reset", methods=['GET']) +# @app.route("/n/password_reset", methods=['GET']) def password_reset(): """Entry point after user clicks link in E-mail""" logger.debug("in password_reset request.url is:", request.url) @@ -567,7 +567,7 @@ def password_reset(): else: return redirect(url_for("login")) -#@app.route("/n/password_reset_step2", methods=('POST',)) +# @app.route("/n/password_reset_step2", methods=('POST',)) def password_reset_step2(): """Handle confirmation E-mail for password reset""" logger.debug("in password_reset request.url is:", request.url) @@ -611,7 +611,7 @@ class DecodeUser: logger.debug("data is:", data) return model.User.query.get(data['id']) -#@app.route("/n/login", methods=('GET', 'POST')) +# @app.route("/n/login", methods=('GET', 'POST')) def login(): lu = LoginUser() login_type = request.args.get("type") @@ -621,7 +621,7 @@ def login(): else: return lu.standard_login() -#@app.route("/n/login/github_oauth2", methods=('GET', 'POST')) +# @app.route("/n/login/github_oauth2", methods=('GET', 'POST')) def github_oauth2(): from utility.tools import GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET code = request.args.get("code") @@ -631,28 +631,21 @@ def github_oauth2(): "code": code } result = requests.post("https://github.com/login/oauth/access_token", json=data) - result_dict = {arr[0]:arr[1] for arr in [tok.split("=") for tok in [token.encode("utf-8") for token in result.text.split("&")]]} + result_dict = {arr[0]: arr[1] for arr in [tok.split("=") for tok in [token.encode("utf-8") for token in result.text.split("&")]]} github_user = get_github_user_details(result_dict["access_token"]) user_details = get_user_by_unique_column("github_id", github_user["id"]) if user_details == None: user_details = { - "user_id": str(uuid.uuid4()) - , "name": github_user["name"].encode("utf-8") - , "github_id": github_user["id"] - , "user_url": github_user["html_url"].encode("utf-8") - , "login_type": "github" - , "organization": "" - , "active": 1 - , "confirmed": 1 + "user_id": str(uuid.uuid4()), "name": github_user["name"].encode("utf-8"), "github_id": github_user["id"], "user_url": github_user["html_url"].encode("utf-8") , "login_type": "github" , "organization": "" , "active": 1 , "confirmed": 1 } save_user(user_details, user_details["user_id"]) - url = "/n/login?type=github&uid="+user_details["user_id"] + url = "/n/login?type=github&uid=" + user_details["user_id"] return redirect(url) -#@app.route("/n/login/orcid_oauth2", methods=('GET', 'POST')) +# @app.route("/n/login/orcid_oauth2", methods=('GET', 'POST')) def orcid_oauth2(): from uuid import uuid4 from utility.tools import ORCID_CLIENT_ID, ORCID_CLIENT_SECRET, ORCID_TOKEN_URL, ORCID_AUTH_URL @@ -661,10 +654,7 @@ def orcid_oauth2(): url = "/n/login" if code: data = { - "client_id": ORCID_CLIENT_ID - , "client_secret": ORCID_CLIENT_SECRET - , "grant_type": "authorization_code" - , "code": code + "client_id": ORCID_CLIENT_ID, "client_secret": ORCID_CLIENT_SECRET, "grant_type": "authorization_code", "code": code } result = requests.post(ORCID_TOKEN_URL, data=data) result_dict = json.loads(result.text.encode("utf-8")) @@ -672,31 +662,24 @@ def orcid_oauth2(): user_details = get_user_by_unique_column("orcid", result_dict["orcid"]) if user_details == None: user_details = { - "user_id": str(uuid4()) - , "name": result_dict["name"] - , "orcid": result_dict["orcid"] - , "user_url": "%s/%s" % ( + "user_id": str(uuid4()), "name": result_dict["name"], "orcid": result_dict["orcid"], "user_url": "%s/%s" % ( "/".join(ORCID_AUTH_URL.split("/")[:-2]), - result_dict["orcid"]) - , "login_type": "orcid" - , "organization": "" - , "active": 1 - , "confirmed": 1 + result_dict["orcid"]), "login_type": "orcid", "organization": "", "active": 1 , "confirmed": 1 } save_user(user_details, user_details["user_id"]) - url = "/n/login?type=orcid&uid="+user_details["user_id"] + url = "/n/login?type=orcid&uid=" + user_details["user_id"] else: flash("There was an error getting code from ORCID") return redirect(url) def get_github_user_details(access_token): from utility.tools import GITHUB_API_URL - result = requests.get(GITHUB_API_URL, params={"access_token":access_token}) + result = requests.get(GITHUB_API_URL, params={"access_token": access_token}) return result.json() class LoginUser: - remember_time = 60 * 60 * 24 * 30 # One month in seconds + remember_time = 60 * 60 * 24 * 30 # One month in seconds def __init__(self): self.remember_me = False @@ -730,9 +713,7 @@ class LoginUser: external_login["orcid"] = ORCID_AUTH_URL return render_template( - "new_security/login_user.html" - , external_login=external_login - , redis_is_available = is_redis_available()) + "new_security/login_user.html", external_login=external_login, redis_is_available=is_redis_available()) else: user_details = get_user_by_unique_column("email_address", params["email_address"]) #user_details = get_user_by_unique_column(es, "email_address", params["email_address"]) @@ -770,7 +751,7 @@ class LoginUser: else: import_col = "false" - #g.cookie_session.import_traits_to_user() + # g.cookie_session.import_traits_to_user() self.logged_in = True @@ -810,10 +791,10 @@ class LoginUser: if not user.id: user.id = '' - session = dict(login_time = time.time(), - user_id = user.id, - user_name = user.full_name, - user_email_address = user.email_address) + session = dict(login_time=time.time(), + user_id=user.id, + user_name=user.full_name, + user_email_address=user.email_address) key = UserSession.cookie_name + ":" + login_rec.session_id logger.debug("Key when signing:", key) @@ -832,7 +813,7 @@ class LoginUser: db_session.add(login_rec) db_session.commit() -#@app.route("/n/logout") +# @app.route("/n/logout") def logout(): logger.debug("Logging out...") UserSession().delete_session() @@ -843,7 +824,7 @@ def logout(): return response -#@app.route("/n/forgot_password", methods=['GET']) +# @app.route("/n/forgot_password", methods=['GET']) def forgot_password(): """Entry point for forgotten password""" print("ARGS: ", request.args) @@ -851,7 +832,7 @@ def forgot_password(): print("ERRORS: ", errors) return render_template("new_security/forgot_password.html", errors=errors) -#@app.route("/n/forgot_password_submit", methods=('POST',)) +# @app.route("/n/forgot_password_submit", methods=('POST',)) def forgot_password_submit(): """When a forgotten password form is submitted we get here""" params = request.form @@ -886,7 +867,7 @@ def is_redis_available(): ### # ZS: The following 6 functions require the old MySQL User accounts; I'm leaving them commented out just in case we decide to reimplement them using ElasticSearch ### -#def super_only(): +# def super_only(): # try: # superuser = g.user_session.user_ob.superuser # except AttributeError: @@ -895,26 +876,26 @@ def is_redis_available(): # flash("You must be a superuser to access that page.", "alert-error") # abort(401) -#@app.route("/manage/users") -#def manage_users(): +# @app.route("/manage/users") +# def manage_users(): # super_only() # template_vars = UsersManager() # return render_template("admin/user_manager.html", **template_vars.__dict__) -#@app.route("/manage/user") -#def manage_user(): +# @app.route("/manage/user") +# def manage_user(): # super_only() # template_vars = UserManager(request.args) # return render_template("admin/ind_user_manager.html", **template_vars.__dict__) -#@app.route("/manage/groups") -#def manage_groups(): +# @app.route("/manage/groups") +# def manage_groups(): # super_only() # template_vars = GroupsManager(request.args) # return render_template("admin/group_manager.html", **template_vars.__dict__) -#@app.route("/manage/make_superuser") -#def make_superuser(): +# @app.route("/manage/make_superuser") +# def make_superuser(): # super_only() # params = request.args # user_id = params['user_id'] @@ -926,8 +907,8 @@ def is_redis_available(): # flash("We've made {} a superuser!".format(user.name_and_org)) # return redirect(url_for("manage_users")) -#@app.route("/manage/assume_identity") -#def assume_identity(): +# @app.route("/manage/assume_identity") +# def assume_identity(): # super_only() # params = request.args # user_id = params['user_id'] @@ -936,7 +917,7 @@ def is_redis_available(): # return LoginUser().actual_login(user, assumed_by=assumed_by) -#@app.route("/n/register", methods=('GET', 'POST')) +# @app.route("/n/register", methods=('GET', 'POST')) def register(): params = None errors = None @@ -1023,21 +1004,21 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"): """ if SMTP_USERNAME == 'UNKNOWN': - logger.debug("SMTP: connecting with host "+SMTP_CONNECT) + logger.debug("SMTP: connecting with host " + SMTP_CONNECT) server = SMTP(SMTP_CONNECT) server.sendmail(fromaddr, toaddr, msg) else: - logger.debug("SMTP: connecting TLS with host "+SMTP_CONNECT) + logger.debug("SMTP: connecting TLS with host " + SMTP_CONNECT) server = SMTP(SMTP_CONNECT) server.starttls() - logger.debug("SMTP: login with user "+SMTP_USERNAME) + logger.debug("SMTP: login with user " + SMTP_USERNAME) server.login(SMTP_USERNAME, SMTP_PASSWORD) - logger.debug("SMTP: "+fromaddr) - logger.debug("SMTP: "+toaddr) - logger.debug("SMTP: "+msg) + logger.debug("SMTP: " + fromaddr) + logger.debug("SMTP: " + toaddr) + logger.debug("SMTP: " + msg) server.sendmail(fromaddr, toaddr, msg) server.quit() - logger.info("Successfully sent email to "+toaddr) + logger.info("Successfully sent email to " + toaddr) class GroupsManager: def __init__(self, kw): diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py index cc0ac744..78db7bd2 100644 --- a/wqflask/wqflask/user_session.py +++ b/wqflask/wqflask/user_session.py @@ -24,7 +24,7 @@ THIRTY_DAYS = 60 * 60 * 24 * 30 def get_user_session(): logger.info("@app.before_request get_session") g.user_session = UserSession() - #ZS: I think this should solve the issue of deleting the cookie and redirecting to the home page when a user's session has expired + # ZS: I think this should solve the issue of deleting the cookie and redirecting to the home page when a user's session has expired if not g.user_session: response = make_response(redirect(url_for('login'))) response.set_cookie('session_id_v2', '', expires=0) @@ -51,7 +51,7 @@ def create_signed_cookie(): logger.debug("uuid_signed:", uuid_signed) return the_uuid, uuid_signed -@app.route("/user/manage", methods=('GET','POST')) +@app.route("/user/manage", methods=('GET', 'POST')) def manage_user(): params = request.form if request.form else request.args if 'new_full_name' in params: @@ -61,7 +61,7 @@ def manage_user(): user_details = get_user_by_unique_column("user_id", g.user_session.user_id) - return render_template("admin/manage_user.html", user_details = user_details) + return render_template("admin/manage_user.html", user_details=user_details) class UserSession: """Logged in user handling""" @@ -89,25 +89,25 @@ class UserSession: self.session_id = session_id self.record = Redis.hgetall(self.redis_key) - #ZS: If user correctled logged in but their session expired - #ZS: Need to test this by setting the time-out to be really short or something + # ZS: If user correctled logged in but their session expired + # ZS: Need to test this by setting the time-out to be really short or something if not self.record or self.record == []: if user_cookie: self.logged_in = False - self.record = dict(login_time = time.time(), - user_type = "anon", - user_id = str(uuid.uuid4())) + self.record = dict(login_time=time.time(), + user_type="anon", + user_id=str(uuid.uuid4())) Redis.hmset(self.redis_key, self.record) Redis.expire(self.redis_key, THIRTY_DAYS) - ########### Grrr...this won't work because of the way flask handles cookies + # Grrr...this won't work because of the way flask handles cookies # Delete the cookie flash("Due to inactivity your session has expired. If you'd like please login again.") return None else: - self.record = dict(login_time = time.time(), - user_type = "anon", - user_id = str(uuid.uuid4())) + self.record = dict(login_time=time.time(), + user_type="anon", + user_id=str(uuid.uuid4())) Redis.hmset(self.redis_key, self.record) Redis.expire(self.redis_key, THIRTY_DAYS) else: @@ -138,13 +138,13 @@ class UserSession: def redis_user_id(self): """User id from Redis (need to check if this is the same as the id stored in self.records)""" - #ZS: This part is a bit weird. Some accounts used to not have saved user ids, and in the process of testing I think I created some duplicate accounts for myself. - #ZS: Accounts should automatically generate user_ids if they don't already have one now, so this might not be necessary for anything other than my account's collections + # ZS: This part is a bit weird. Some accounts used to not have saved user ids, and in the process of testing I think I created some duplicate accounts for myself. + # ZS: Accounts should automatically generate user_ids if they don't already have one now, so this might not be necessary for anything other than my account's collections if 'user_email_address' in self.record: user_email = self.record['user_email_address'] - #ZS: Get user's collections if they exist + # ZS: Get user's collections if they exist user_id = None user_id = get_user_id("email_address", user_email) elif 'user_id' in self.record: @@ -153,7 +153,7 @@ class UserSession: user_github_id = self.record['github_id'] user_id = None user_id = get_user_id("github_id", user_github_id) - else: #ZS: Anonymous user + else: # ZS: Anonymous user return None return user_id @@ -170,9 +170,9 @@ class UserSession: def user_collections(self): """List of user's collections""" - #ZS: Get user's collections if they exist + # ZS: Get user's collections if they exist collections = get_user_collections(self.user_id) - collections = [item for item in collections if item['name'] != "Your Default Collection"] + [item for item in collections if item['name'] == "Your Default Collection"] #ZS: Ensure Default Collection is last in list + collections = [item for item in collections if item['name'] != "Your Default Collection"] + [item for item in collections if item['name'] == "Your Default Collection"] # ZS: Ensure Default Collection is last in list return collections @property @@ -189,7 +189,7 @@ class UserSession: 'created_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), 'changed_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), 'num_members': len(traits), - 'members': list(traits) } + 'members': list(traits)} current_collections = self.user_collections current_collections.append(collection_dict) diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 37f2094f..2c53012a 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -141,7 +141,7 @@ def handle_bad_request(e): now = datetime.datetime.utcnow() time_str = now.strftime('%l:%M%p UTC %b %d, %Y') formatted_lines = [request.url + - " ("+time_str+")"]+traceback.format_exc().splitlines() + " (" + time_str + ")"]+traceback.format_exc().splitlines() # Handle random animations # Use a cookie to have one animation on refresh @@ -240,7 +240,7 @@ def search_page(): if USE_REDIS and valid_search: Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL)) - Redis.expire(key, 60*60) + Redis.expire(key, 60 * 60) if valid_search: return render_template("search_result_page.html", **result) @@ -601,7 +601,7 @@ def heatmap_page(): pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) logger.info("pickled result length:", len(pickled_result)) Redis.set(key, pickled_result) - Redis.expire(key, 60*60) + Redis.expire(key, 60 * 60) with Bench("Rendering template"): rendered_template = render_template("heatmap.html", **result) diff --git a/wqflask/wsgi.py b/wqflask/wsgi.py index be9c7b37..755da333 100644 --- a/wqflask/wsgi.py +++ b/wqflask/wsgi.py @@ -1,4 +1,4 @@ -from run_gunicorn import app as application # expect application as a name +from run_gunicorn import app as application # expect application as a name if __name__ == "__main__": application.run() -- cgit v1.2.3 From 406eb27859cca232a562c722cbbd37aca2e3be84 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 30 Apr 2021 12:26:19 +0300 Subject: autopep8: Fix E301,E302,E303,E304,E305,E306 --- etc/default_settings.py | 21 +++---- wqflask/base/data_set.py | 1 - wqflask/base/mrna_assay_tissue_data.py | 1 + wqflask/base/species.py | 3 + wqflask/base/webqtlCaseData.py | 3 +- wqflask/db/call.py | 4 ++ wqflask/db/gn_server.py | 1 + wqflask/db/webqtlDatabaseFunction.py | 1 + wqflask/maintenance/convert_dryad_to_bimbam.py | 3 + wqflask/maintenance/convert_geno_to_bimbam.py | 4 ++ wqflask/maintenance/gen_select_dataset.py | 5 ++ .../maintenance/generate_kinship_from_bimbam.py | 1 + .../maintenance/generate_probesetfreeze_file.py | 7 +++ wqflask/maintenance/geno_to_json.py | 6 +- wqflask/maintenance/get_group_samplelists.py | 3 + wqflask/maintenance/print_benchmark.py | 4 ++ wqflask/maintenance/quantile_normalize.py | 6 ++ wqflask/maintenance/set_resource_defaults.py | 7 +++ wqflask/run_gunicorn.py | 2 + wqflask/tests/unit/base/test_webqtl_case_data.py | 1 + .../unit/utility/test_authentication_tools.py | 1 + wqflask/tests/unit/utility/test_chunks.py | 1 + .../test_display_mapping_results.py | 2 + .../marker_regression/test_plink_mapping.py | 3 +- .../marker_regression/test_qtlreaper_mapping.py | 2 + .../wqflask/marker_regression/test_rqtl_mapping.py | 2 +- wqflask/tests/unit/wqflask/test_collect.py | 2 + .../tests/wqflask/show_trait/test_show_trait.py | 1 - wqflask/utility/Plot.py | 13 +++++ wqflask/utility/__init__.py | 2 + wqflask/utility/after.py | 1 + wqflask/utility/authentication_tools.py | 1 + wqflask/utility/benchmark.py | 1 + wqflask/utility/corestats.py | 2 + wqflask/utility/elasticsearch_tools.py | 7 +++ wqflask/utility/external.py | 1 + wqflask/utility/gen_geno_ob.py | 3 + wqflask/utility/genofile_parser.py | 1 + wqflask/utility/logger.py | 3 + wqflask/utility/pillow_utils.py | 4 ++ wqflask/utility/startup_config.py | 1 + wqflask/utility/svg.py | 67 +++++++++++++++++++++- wqflask/utility/temp_data.py | 1 + wqflask/utility/tools.py | 25 ++++++++ wqflask/utility/type_checking.py | 5 ++ wqflask/utility/webqtlUtil.py | 5 ++ wqflask/wqflask/__init__.py | 1 + wqflask/wqflask/api/correlation.py | 7 +++ wqflask/wqflask/api/mapping.py | 2 +- wqflask/wqflask/api/router.py | 20 +++++++ wqflask/wqflask/collect.py | 8 +++ wqflask/wqflask/correlation/corr_scatter_plot.py | 1 + wqflask/wqflask/correlation/show_corr_results.py | 4 +- .../wqflask/correlation_matrix/show_corr_matrix.py | 3 + wqflask/wqflask/ctl/ctl_analysis.py | 1 + wqflask/wqflask/database.py | 2 + wqflask/wqflask/db_info.py | 1 + wqflask/wqflask/do_search.py | 21 ++++++- wqflask/wqflask/docs.py | 2 +- wqflask/wqflask/export_traits.py | 2 + wqflask/wqflask/external_tools/send_to_bnw.py | 1 + .../wqflask/external_tools/send_to_geneweaver.py | 3 + .../wqflask/external_tools/send_to_webgestalt.py | 3 + wqflask/wqflask/group_manager.py | 9 +++ wqflask/wqflask/gsearch.py | 1 + wqflask/wqflask/heatmap/heatmap.py | 3 + wqflask/wqflask/interval_analyst/GeneUtil.py | 2 + .../marker_regression/display_mapping_results.py | 9 --- wqflask/wqflask/marker_regression/plink_mapping.py | 9 ++- .../wqflask/marker_regression/qtlreaper_mapping.py | 5 ++ wqflask/wqflask/marker_regression/rqtl_mapping.py | 15 +++++ wqflask/wqflask/marker_regression/run_mapping.py | 9 +++ wqflask/wqflask/model.py | 7 ++- wqflask/wqflask/network_graph/network_graph.py | 1 + wqflask/wqflask/news.py | 1 + wqflask/wqflask/parser.py | 1 + wqflask/wqflask/pbkdf2.py | 2 + wqflask/wqflask/resource_manager.py | 7 +++ wqflask/wqflask/search_results.py | 4 ++ wqflask/wqflask/send_mail.py | 3 +- wqflask/wqflask/server_side.py | 1 - wqflask/wqflask/show_trait/SampleList.py | 1 + wqflask/wqflask/show_trait/export_trait_data.py | 3 + wqflask/wqflask/snp_browser/snp_browser.py | 9 ++- wqflask/wqflask/submit_bnw.py | 1 + wqflask/wqflask/update_search_results.py | 1 + wqflask/wqflask/user_login.py | 21 +++++++ wqflask/wqflask/user_manager.py | 38 +++++++++++- wqflask/wqflask/user_session.py | 6 ++ 89 files changed, 446 insertions(+), 46 deletions(-) (limited to 'wqflask/utility/gen_geno_ob.py') diff --git a/etc/default_settings.py b/etc/default_settings.py index 27522187..a194b10e 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -73,23 +73,24 @@ SMTP_PASSWORD = "UNKNOWN" # ---- Behavioural settings (defaults) note that logger and log levels can # be overridden at the module level and with enviroment settings -WEBSERVER_MODE = 'DEV' # Python webserver mode (DEBUG|DEV|PROD) +WEBSERVER_MODE = 'DEV' # Python webserver mode (DEBUG|DEV|PROD) WEBSERVER_BRANDING = None # Set the branding (nyi) WEBSERVER_DEPLOY = None # Deployment specifics (nyi) -WEBSERVER_URL = "http://localhost:"+str(SERVER_PORT)+"/" # external URL +WEBSERVER_URL = "http://localhost:" + str(SERVER_PORT) + "/" # external URL -LOG_LEVEL = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL) +LOG_LEVEL = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL) LOG_LEVEL_DEBUG = '0' # logger.debugf log level (0-5, 5 = show all) -LOG_SQL = 'False' # Log SQL/backend and GN_SERVER calls +LOG_SQL = 'False' # Log SQL/backend and GN_SERVER calls LOG_SQL_ALCHEMY = 'False' -LOG_BENCH = True # Log bench marks +LOG_BENCH = True # Log bench marks -USE_REDIS = True # REDIS caching (note that redis will be phased out) -USE_GN_SERVER = 'False' # Use GN_SERVER SQL calls -HOME = os.environ['HOME'] +USE_REDIS = True # REDIS caching (note that redis will be phased out) +USE_GN_SERVER = 'False' # Use GN_SERVER SQL calls +HOME = os.environ['HOME'] # ---- Default locations -GENENETWORK_FILES = HOME+"/genotype_files" # base dir for all static data files +# base dir for all static data files +GENENETWORK_FILES = HOME + "/genotype_files" # ---- Path overrides for Genenetwork - the defaults are normally # picked up from Guix or in the HOME directory @@ -98,7 +99,7 @@ GENENETWORK_FILES = HOME+"/genotype_files" # base dir for all static data fil # PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files (unused) # ---- Local path to JS libraries - for development modules (only) -JS_GN_PATH = os.environ['HOME']+"/genenetwork/javascript" +JS_GN_PATH = os.environ['HOME'] + "/genenetwork/javascript" # ---- GN2 Executables (overwrite for testing only) # PLINK_COMMAND = str.strip(os.popen("which plink2").read()) diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 55ab45f5..c14808d6 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -311,7 +311,6 @@ class HumanMarkers(Markers): marker['Mb'] = float(splat[3]) / 1000000 self.markers.append(marker) - def add_pvalues(self, p_values): super(HumanMarkers, self).add_pvalues(p_values) diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index f3264b3d..cbc05738 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -11,6 +11,7 @@ from utility.db_tools import escape from utility.logger import getLogger logger = getLogger(__name__) + class MrnaAssayTissueData: def __init__(self, gene_symbols=None): diff --git a/wqflask/base/species.py b/wqflask/base/species.py index cf764d72..44f133b5 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -6,6 +6,7 @@ from flask import Flask, g from utility.logger import getLogger logger = getLogger(__name__) + class TheSpecies: def __init__(self, dataset=None, species_name=None): if species_name != None: @@ -15,6 +16,7 @@ class TheSpecies: self.dataset = dataset self.chromosomes = Chromosomes(dataset=self.dataset) + class IndChromosome: def __init__(self, name, length): self.name = name @@ -25,6 +27,7 @@ class IndChromosome: """Chromosome length in megabases""" return self.length / 1000000 + class Chromosomes: def __init__(self, dataset=None, species=None): self.chromosomes = collections.OrderedDict() diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index aa55470f..2d07ab9d 100644 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -28,6 +28,7 @@ import utility.tools utility.tools.show_settings() + class webqtlCaseData: """one case data in one trait""" @@ -78,4 +79,4 @@ class webqtlCaseData: def display_num_cases(self): if self.num_cases is not None: return "%s" % self.num_cases - return "x" \ No newline at end of file + return "x" diff --git a/wqflask/db/call.py b/wqflask/db/call.py index 555878ad..9412b376 100644 --- a/wqflask/db/call.py +++ b/wqflask/db/call.py @@ -16,6 +16,7 @@ logger = getLogger(__name__) # from inspect import stack + def fetch1(query, path=None, func=None): """Fetch one result as a Tuple using either a SQL query or the URI path to GN_SERVER (when USE_GN_SERVER is True). Apply func to @@ -35,6 +36,7 @@ GN_SERVER result when set (which should return a Tuple) else: return fetchone(query) + def fetchone(query): """Return tuple containing one row by calling SQL directly (the original fetchone, but with logging) @@ -46,6 +48,7 @@ original fetchone, but with logging) return res.fetchone() return logger.sql(query, helper) + def fetchall(query): """Return row iterator by calling SQL directly (the original fetchall, but with logging) @@ -57,6 +60,7 @@ original fetchall, but with logging) return res.fetchall() return logger.sql(query, helper) + def gn_server(path): """Return JSON record by calling GN_SERVER diff --git a/wqflask/db/gn_server.py b/wqflask/db/gn_server.py index 6c7383d0..f9b01658 100644 --- a/wqflask/db/gn_server.py +++ b/wqflask/db/gn_server.py @@ -5,5 +5,6 @@ from db.call import gn_server from utility.logger import getLogger logger = getLogger(__name__) + def menu_main(): return gn_server("/int/menu/main.json") diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py index 18ade405..50ac06fd 100644 --- a/wqflask/db/webqtlDatabaseFunction.py +++ b/wqflask/db/webqtlDatabaseFunction.py @@ -31,6 +31,7 @@ logger = getLogger(__name__) # function: connect to database and return cursor instance ########################################################################### + def retrieve_species(group): """Get the species of a group (e.g. returns string "mouse" on "BXD" diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py index 8eab66e8..e417c280 100644 --- a/wqflask/maintenance/convert_dryad_to_bimbam.py +++ b/wqflask/maintenance/convert_dryad_to_bimbam.py @@ -55,15 +55,18 @@ def read_dryad_file(filename): # # return geno_rows + def write_bimbam_files(geno_rows): with open('/home/zas1024/cfw_data/CFW_geno.txt', 'w') as geno_fh: for row in geno_rows: geno_fh.write(", ".join(row) + "\n") + def convert_dryad_to_bimbam(filename): geno_file_rows = read_dryad_file(filename) write_bimbam_files(geno_file_rows) + if __name__ == "__main__": input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt" convert_dryad_to_bimbam(input_filename) diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py index dc01cbb3..5b2369c9 100644 --- a/wqflask/maintenance/convert_geno_to_bimbam.py +++ b/wqflask/maintenance/convert_geno_to_bimbam.py @@ -20,8 +20,10 @@ import simplejson as json from pprint import pformat as pf + class EmptyConfigurations(Exception): pass + class Marker: def __init__(self): self.name = None @@ -30,6 +32,7 @@ class Marker: self.Mb = None self.genotypes = [] + class ConvertGenoFile: def __init__(self, input_file, output_files): @@ -178,6 +181,7 @@ class ConvertGenoFile: print(" Row is:", convertob.latest_row_value) break + if __name__ == "__main__": Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype""" New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/bimbam""" diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index f480d63f..583a06e1 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -55,6 +55,7 @@ from pprint import pformat as pf #conn = Engine.connect() + def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" @@ -143,6 +144,7 @@ def phenotypes_exist(group_name): else: return False + def genotypes_exist(group_name): #print("group_name:", group_name) Cursor.execute("""select Name from GenoFreeze @@ -156,6 +158,7 @@ def genotypes_exist(group_name): else: return False + def build_types(species, group): """Fetches tissues @@ -184,6 +187,7 @@ def build_types(species, group): return results + def get_datasets(types): """Build datasets list""" datasets = {} @@ -308,6 +312,7 @@ def _test_it(): datasets = build_datasets("Mouse", "BXD", "Hippocampus") #print("build_datasets:", pf(datasets)) + if __name__ == '__main__': Conn = MySQLdb.Connect(**parse_db_uri()) Cursor = Conn.cursor() diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py index 664e9e48..7cc60c9e 100644 --- a/wqflask/maintenance/generate_kinship_from_bimbam.py +++ b/wqflask/maintenance/generate_kinship_from_bimbam.py @@ -13,6 +13,7 @@ sys.path.append("..") import os import glob + class GenerateKinshipMatrices: def __init__(self, group_name, geno_file, pheno_file): self.group_name = group_name diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py index b1e41e9a..bd9c2ab4 100644 --- a/wqflask/maintenance/generate_probesetfreeze_file.py +++ b/wqflask/maintenance/generate_probesetfreeze_file.py @@ -23,10 +23,12 @@ def get_cursor(): cursor = con.cursor() return cursor + def show_progress(process, counter): if counter % 1000 == 0: print("{}: {}".format(process, counter)) + def get_strains(cursor): cursor.execute("""select Strain.Name from Strain, StrainXRef, InbredSet @@ -42,6 +44,7 @@ def get_strains(cursor): return strains + def get_probeset_vals(cursor, dataset_name): cursor.execute(""" select ProbeSet.Id, ProbeSet.Name from ProbeSetXRef, @@ -77,6 +80,7 @@ def get_probeset_vals(cursor, dataset_name): return probeset_vals + def trim_strains(strains, probeset_vals): trimmed_strains = [] #print("probeset_vals is:", pf(probeset_vals)) @@ -89,6 +93,7 @@ def trim_strains(strains, probeset_vals): print("trimmed_strains:", pf(trimmed_strains)) return trimmed_strains + def write_data_matrix_file(strains, probeset_vals, filename): with open(filename, "wb") as fh: csv_writer = csv.writer(fh, delimiter=",", quoting=csv.QUOTE_ALL) @@ -103,6 +108,7 @@ def write_data_matrix_file(strains, probeset_vals, filename): csv_writer.writerow(row_data) show_progress("Writing", counter) + def main(): filename = os.path.expanduser("~/gene/wqflask/maintenance/" + "ProbeSetFreezeId_210_FullName_Eye_AXBXA_Illumina_V6.2" + @@ -117,5 +123,6 @@ def main(): trimmed_strains = trim_strains(strains, probeset_vals) write_data_matrix_file(trimmed_strains, probeset_vals, filename) + if __name__ == '__main__': main() diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py index fa0dcebd..ad3f2b72 100644 --- a/wqflask/maintenance/geno_to_json.py +++ b/wqflask/maintenance/geno_to_json.py @@ -25,10 +25,10 @@ from pprint import pformat as pf #from utility.tools import flat_files + class EmptyConfigurations(Exception): pass - class Marker: def __init__(self): self.name = None @@ -37,6 +37,7 @@ class Marker: self.Mb = None self.genotypes = [] + class ConvertGenoFile: def __init__(self, input_file, output_file): @@ -78,7 +79,6 @@ class ConvertGenoFile: # elif self.file_type == "snps": # self.process_snps_file() - def process_csv(self): for row_count, row in enumerate(self.process_rows()): row_items = row.split("\t") @@ -121,7 +121,6 @@ class ConvertGenoFile: # self.output_fh.write("\n") - def process_rows(self): for self.latest_row_pos, row in enumerate(self.input_fh): # if self.input_file.endswith(".geno.gz"): @@ -182,7 +181,6 @@ class ConvertGenoFile: # convertob = ConvertGenoFile(input_file, output_file) - if __name__ == "__main__": Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype""" New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/json""" diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py index 3f9d0278..0a450d3f 100644 --- a/wqflask/maintenance/get_group_samplelists.py +++ b/wqflask/maintenance/get_group_samplelists.py @@ -4,12 +4,14 @@ import gzip from base import webqtlConfig + def get_samplelist(file_type, geno_file): if file_type == "geno": return get_samplelist_from_geno(geno_file) elif file_type == "plink": return get_samplelist_from_plink(geno_file) + def get_samplelist_from_geno(genofilename): if os.path.isfile(genofilename + '.gz'): genofilename += '.gz' @@ -33,6 +35,7 @@ def get_samplelist_from_geno(genofilename): samplelist = headers[3:] return samplelist + def get_samplelist_from_plink(genofilename): genofile = open(genofilename) diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py index a1046c86..9d12da8a 100644 --- a/wqflask/maintenance/print_benchmark.py +++ b/wqflask/maintenance/print_benchmark.py @@ -15,15 +15,18 @@ class TheCounter: self.time_took = time.time() - start_time TheCounter.Counters[self.__class__.__name__] = self.time_took + class PrintAll(TheCounter): def print_it(self, counter): print(counter) + class PrintSome(TheCounter): def print_it(self, counter): if counter % 1000 == 0: print(counter) + class PrintNone(TheCounter): def print_it(self, counter): pass @@ -37,5 +40,6 @@ def new_main(): print(pf(TheCounter.Counters)) + if __name__ == '__main__': new_main() diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index 6751a8e5..1896bc52 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -14,6 +14,7 @@ from wqflask import app from utility.elasticsearch_tools import get_elasticsearch_connection from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT, SQL_URI + def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" @@ -28,6 +29,7 @@ def parse_db_uri(): print(db_conn_info) return db_conn_info + def create_dataframe(input_file): with open(input_file) as f: ncols = len(f.readline().split("\t")) @@ -36,6 +38,8 @@ def create_dataframe(input_file): return pd.DataFrame(input_array) # This function taken from https://github.com/ShawnLYU/Quantile_Normalize + + def quantileNormalize(df_input): df = df_input.copy() # compute rank @@ -50,6 +54,7 @@ def quantileNormalize(df_input): df[col] = [rank[i] for i in t] return df + def set_data(dataset_name): orig_file = "/home/zas1024/cfw_data/" + dataset_name + ".txt" @@ -95,6 +100,7 @@ def set_data(dataset_name): } } + if __name__ == '__main__': Conn = MySQLdb.Connect(**parse_db_uri()) Cursor = Conn.cursor() diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py index 286094dd..c6c4f44c 100644 --- a/wqflask/maintenance/set_resource_defaults.py +++ b/wqflask/maintenance/set_resource_defaults.py @@ -37,6 +37,7 @@ import urllib.parse from utility.logger import getLogger logger = getLogger(__name__) + def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" @@ -51,6 +52,7 @@ def parse_db_uri(): print(db_conn_info) return db_conn_info + def insert_probeset_resources(default_owner_id): current_resources = Redis.hgetall("resources") Cursor.execute(""" SELECT @@ -77,6 +79,7 @@ def insert_probeset_resources(default_owner_id): add_resource(resource_ob, update=False) + def insert_publish_resources(default_owner_id): current_resources = Redis.hgetall("resources") Cursor.execute(""" SELECT @@ -110,6 +113,7 @@ def insert_publish_resources(default_owner_id): else: continue + def insert_geno_resources(default_owner_id): current_resources = Redis.hgetall("resources") Cursor.execute(""" SELECT @@ -139,6 +143,7 @@ def insert_geno_resources(default_owner_id): add_resource(resource_ob, update=False) + def insert_resources(default_owner_id): current_resources = get_resources() print("START") @@ -149,6 +154,7 @@ def insert_resources(default_owner_id): insert_probeset_resources(default_owner_id) print("AFTER PROBESET") + def main(): """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" @@ -158,6 +164,7 @@ def main(): insert_resources(owner_id) + if __name__ == '__main__': Conn = MySQLdb.Connect(**parse_db_uri()) Cursor = Conn.cursor() diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py index 58108e03..03f310eb 100644 --- a/wqflask/run_gunicorn.py +++ b/wqflask/run_gunicorn.py @@ -14,9 +14,11 @@ from utility.startup_config import app_config app_config() + @app.route("/gunicorn") def hello(): return "

Hello There!

" + if __name__ == "__main__": app.run(host='0.0.0.0') diff --git a/wqflask/tests/unit/base/test_webqtl_case_data.py b/wqflask/tests/unit/base/test_webqtl_case_data.py index 8e8ba482..cebd41ce 100644 --- a/wqflask/tests/unit/base/test_webqtl_case_data.py +++ b/wqflask/tests/unit/base/test_webqtl_case_data.py @@ -4,6 +4,7 @@ import unittest from wqflask import app # Required because of utility.tools in webqtlCaseData.py from base.webqtlCaseData import webqtlCaseData + class TestWebqtlCaseData(unittest.TestCase): """Tests for WebqtlCaseData class""" diff --git a/wqflask/tests/unit/utility/test_authentication_tools.py b/wqflask/tests/unit/utility/test_authentication_tools.py index 42dcae88..024ab43f 100644 --- a/wqflask/tests/unit/utility/test_authentication_tools.py +++ b/wqflask/tests/unit/utility/test_authentication_tools.py @@ -5,6 +5,7 @@ from unittest import mock from utility.authentication_tools import check_resource_availability from utility.authentication_tools import add_new_resource + class TestResponse: """Mock Test Response after a request""" @property diff --git a/wqflask/tests/unit/utility/test_chunks.py b/wqflask/tests/unit/utility/test_chunks.py index 8d90a1ec..1d349193 100644 --- a/wqflask/tests/unit/utility/test_chunks.py +++ b/wqflask/tests/unit/utility/test_chunks.py @@ -7,6 +7,7 @@ from utility.chunks import divide_into_chunks class TestChunks(unittest.TestCase): "Test Utility method for chunking" + def test_divide_into_chunks(self): "Check that a list is chunked correctly" self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3), diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py index 8ae0f09f..219a6a29 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py @@ -9,6 +9,7 @@ from wqflask.marker_regression.display_mapping_results import ( class TestDisplayMappingResults(unittest.TestCase): """Basic Methods to test Mapping Results""" + def test_pil_colors(self): """Test that colors use PILLOW color format""" self.assertEqual(DisplayMappingResults.CLICKABLE_WEBQTL_REGION_COLOR, @@ -17,6 +18,7 @@ class TestDisplayMappingResults(unittest.TestCase): class TestHtmlGenWrapper(unittest.TestCase): """Test Wrapper around HTMLGen""" + def test_create_image(self): """Test HT.Image method""" self.assertEqual( diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py index 5eec93f1..fd21a825 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py @@ -12,9 +12,10 @@ class AttributeSetter: def __init__(self, obj): for key, val in obj.items(): setattr(self, key, val) -class TestPlinkMapping(unittest.TestCase): +class TestPlinkMapping(unittest.TestCase): + def test_build_line_list(self): """test for building line list""" line_1 = "this is line one test" diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py index bbb79f98..5cc8fd0f 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py @@ -4,6 +4,8 @@ from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file # issues some methods in genofile object are not defined # modify samples should equal to vals + + class TestQtlReaperMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") def test_gen_pheno_txt_file(self): diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py index 0e617e93..6267ce9a 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -5,6 +5,7 @@ from wqflask.marker_regression.rqtl_mapping import get_trait_data_type from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_phenotype from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names + class TestRqtlMapping(unittest.TestCase): def setUp(self): @@ -14,7 +15,6 @@ class TestRqtlMapping(unittest.TestCase): def tearDown(self): self.app_context.pop() - @mock.patch("wqflask.marker_regression.rqtl_mapping.g") @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") def test_get_trait_data(self, mock_logger, mock_db): diff --git a/wqflask/tests/unit/wqflask/test_collect.py b/wqflask/tests/unit/wqflask/test_collect.py index 9a36132d..2a914fb2 100644 --- a/wqflask/tests/unit/wqflask/test_collect.py +++ b/wqflask/tests/unit/wqflask/test_collect.py @@ -11,6 +11,7 @@ app = Flask(__name__) class MockSession: """Helper class for mocking wqflask.collect.g.user_session.logged_in""" + def __init__(self, is_logged_in=False): self.is_logged_in = is_logged_in @@ -21,6 +22,7 @@ class MockSession: class MockFlaskG: """Helper class for mocking wqflask.collect.g.user_session""" + def __init__(self, is_logged_in=False): self.is_logged_in = is_logged_in diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py index 8c866874..24c3923e 100644 --- a/wqflask/tests/wqflask/show_trait/test_show_trait.py +++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py @@ -242,7 +242,6 @@ class TestTraits(unittest.TestCase): self.assertEqual(get_genotype_scales(file_location), expected_results) mock_get_scales.assert_called_once_with(file_location) - @mock.patch("wqflask.show_trait.show_trait.locate_ignore_error") def test_get_scales_from_genofile_found(self, mock_ignore_location): """"add test for get scales from genofile where file is found""" diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 68c2cb72..d35b2089 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -47,6 +47,7 @@ COUR_FILE = "./wqflask/static/fonts/courbd.ttf" TAHOMA_FILE = "./wqflask/static/fonts/tahoma.ttf" # ---- END: FONT FILES ---- # + def cformat(d, rank=0): 'custom string format' strD = "%2.6f" % d @@ -68,6 +69,7 @@ def cformat(d, rank=0): strD = '0.0' return strD + def frange(start, end=None, inc=1.0): "A faster range-like function that does accept float increments..." if end == None: @@ -84,6 +86,7 @@ def frange(start, end=None, inc=1.0): L[i] = start + i * inc return L + def find_outliers(vals): """Calculates the upper and lower bounds of a set of sample/case values @@ -119,6 +122,8 @@ def find_outliers(vals): # parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py) # or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py) + + def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLabel=None, YLabel=None, title=None, offset=(60, 20, 40, 40), zoom=1): im_drawer = ImageDraw.Draw(canvas) xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset @@ -230,6 +235,8 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab font=labelFont, fill=labelColor) # This function determines the scale of the plot + + def detScaleOld(min, max): if min >= max: return None @@ -246,6 +253,7 @@ def detScaleOld(min, max): high = c * ceil(max / c) return [low, high, round((high - low) / c)] + def detScale(min=0, max=0): if min >= max: @@ -283,15 +291,19 @@ def detScale(min=0, max=0): return [low, high, n] + def bluefunc(x): return 1.0 / (1.0 + exp(-10 * (x - 0.6))) + def redfunc(x): return 1.0 / (1.0 + exp(10 * (x - 0.5))) + def greenfunc(x): return 1 - pow(redfunc(x + 0.2), 2) - bluefunc(x - 0.3) + def colorSpectrum(n=100): multiple = 10 if n == 1: @@ -319,6 +331,7 @@ def colorSpectrum(n=100): out2.append(out[-1]) return out2 + def _test(): import doctest doctest.testmod() diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index ec7e72d0..d540c96e 100644 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py @@ -2,8 +2,10 @@ from pprint import pformat as pf # Todo: Move these out of __init__ + class Bunch: """Like a dictionary but using object notation""" + def __init__(self, **kw): self.__dict__ = kw diff --git a/wqflask/utility/after.py b/wqflask/utility/after.py index 06091ecb..2b560e48 100644 --- a/wqflask/utility/after.py +++ b/wqflask/utility/after.py @@ -7,6 +7,7 @@ from flask import g from wqflask import app + def after_this_request(f): if not hasattr(g, 'after_request_callbacks'): g.after_request_callbacks = [] diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index 672b36d5..57dbf8ba 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -11,6 +11,7 @@ from utility.redis_tools import (get_redis_conn, add_resource) Redis = get_redis_conn() + def check_resource_availability(dataset, trait_id=None): # At least for now assume temporary entered traits are accessible if type(dataset) == str or dataset.type == "Temp": diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py index 3d40a3b8..48ab1dc0 100644 --- a/wqflask/utility/benchmark.py +++ b/wqflask/utility/benchmark.py @@ -6,6 +6,7 @@ from utility.tools import LOG_BENCH from utility.logger import getLogger logger = getLogger(__name__) + class Bench: entries = collections.OrderedDict() diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py index 15d1cb8d..523280a1 100644 --- a/wqflask/utility/corestats.py +++ b/wqflask/utility/corestats.py @@ -16,6 +16,8 @@ import sys # ZS: Should switch to using some third party library for this; maybe scipy has an equivalent + + class Stats: def __init__(self, sequence): diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py index ae1181e4..9415cef0 100644 --- a/wqflask/utility/elasticsearch_tools.py +++ b/wqflask/utility/elasticsearch_tools.py @@ -47,11 +47,13 @@ logger = getLogger(__name__) from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT + def test_elasticsearch_connection(): es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True) if not es.ping(): logger.warning("Elasticsearch is DOWN") + def get_elasticsearch_connection(for_user=True): """Return a connection to ES. Returns None on failure""" logger.info("get_elasticsearch_connection") @@ -77,6 +79,7 @@ def get_elasticsearch_connection(for_user=True): return es + def setup_users_index(es_connection): if es_connection: index_settings = { @@ -87,12 +90,15 @@ def setup_users_index(es_connection): es_connection.indices.create(index='users', ignore=400) es_connection.indices.put_mapping(body=index_settings, index="users", doc_type="local") + def get_user_by_unique_column(es, column_name, column_value, index="users", doc_type="local"): return get_item_by_unique_column(es, column_name, column_value, index=index, doc_type=doc_type) + def save_user(es, user, user_id): es_save_data(es, "users", "local", user, user_id) + def get_item_by_unique_column(es, column_name, column_value, index, doc_type): item_details = None try: @@ -106,6 +112,7 @@ def get_item_by_unique_column(es, column_name, column_value, index, doc_type): pass return item_details + def es_save_data(es, index, doc_type, data_item, data_id,): from time import sleep es.create(index, doc_type, body=data_item, id=data_id) diff --git a/wqflask/utility/external.py b/wqflask/utility/external.py index c1bf4043..805d2ffe 100644 --- a/wqflask/utility/external.py +++ b/wqflask/utility/external.py @@ -4,6 +4,7 @@ import os import sys import subprocess + def shell(command): if subprocess.call(command, shell=True) != 0: raise Exception("ERROR: failed on " + command) diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 9cfa39f9..24604e58 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -1,6 +1,7 @@ import utility.logger logger = utility.logger.getLogger(__name__) + class genotype: """ Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure @@ -119,6 +120,7 @@ class genotype: self.chromosomes.append(chr_ob) + class Chr: def __init__(self, name, geno_ob): self.name = name @@ -140,6 +142,7 @@ class Chr: def add_marker(self, marker_row): self.loci.append(Locus(self.geno_ob, marker_row)) + class Locus: def __init__(self, geno_ob, marker_row=None): self.chr = None diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py index f8e96d19..94a08c17 100644 --- a/wqflask/utility/genofile_parser.py +++ b/wqflask/utility/genofile_parser.py @@ -12,6 +12,7 @@ import simplejson as json from pprint import pformat as pf + class Marker: def __init__(self): self.name = None diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py index 16912e58..47079818 100644 --- a/wqflask/utility/logger.py +++ b/wqflask/utility/logger.py @@ -35,6 +35,7 @@ import datetime from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL + class GNLogger: """A logger class with some additional functionality, such as multiple parameter logging, SQL logging, timing, colors, and lazy @@ -139,6 +140,8 @@ LOG_LEVEL_DEBUG (NYI). # Get the module logger. You can override log levels at the # module level + + def getLogger(name, level=None): gnlogger = GNLogger(name) logger = gnlogger.logger diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py index 6e95beb0..5713e155 100644 --- a/wqflask/utility/pillow_utils.py +++ b/wqflask/utility/pillow_utils.py @@ -9,6 +9,8 @@ BLACK = ImageColor.getrgb("black") WHITE = ImageColor.getrgb("white") # def draw_rotated_text(canvas: Image, text: str, font: ImageFont, xy: tuple, fill: ImageColor=BLACK, angle: int=-90): + + def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90): # type: (Image, str, ImageFont, tuple, ImageColor, int) """Utility function draw rotated text""" @@ -20,6 +22,8 @@ def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90): canvas.paste(im=tmp_img2, box=tuple([int(i) for i in xy])) # def draw_open_polygon(canvas: Image, xy: tuple, fill: ImageColor=WHITE, outline: ImageColor=BLACK): + + def draw_open_polygon(canvas, xy, fill=None, outline=BLACK, width=0): # type: (Image, tuple, ImageColor, ImageColor) draw_ctx = ImageDraw.Draw(canvas) diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py index f22f4b14..92f944bc 100644 --- a/wqflask/utility/startup_config.py +++ b/wqflask/utility/startup_config.py @@ -10,6 +10,7 @@ GREEN = '\033[92m' BOLD = '\033[1m' ENDC = '\033[0m' + def app_config(): app.config['SESSION_TYPE'] = 'filesystem' if not app.config.get('SECRET_KEY'): diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index 4c478c36..f5ef81e1 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -459,11 +459,13 @@ class rect(SVGelement): if stroke_width != None: self.attributes['stroke-width'] = stroke_width + class ellipse(SVGelement): """e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args) an ellipse is defined as a center and a x and y radius. """ + def __init__(self, cx=None, cy=None, rx=None, ry=None,fill=None,stroke=None,stroke_width=None,**args): if rx == None or ry == None: raise ValueError('both rx and ry are required') @@ -486,6 +488,7 @@ class circle(SVGelement): The circle creates an element using a x, y and radius values eg """ + def __init__(self, cx=None, cy=None, r=None, fill=None,stroke=None,stroke_width=None,**args): if r == None: raise ValueError('r is required') @@ -501,20 +504,24 @@ class circle(SVGelement): if stroke_width != None: self.attributes['stroke-width'] = stroke_width + class point(circle): """p=point(x,y,color) A point is defined as a circle with a size 1 radius. It may be more efficient to use a very small rectangle if you use many points because a circle is difficult to render. """ + def __init__(self, x, y, fill='black', **args): circle.__init__(self, x, y, 1, fill, **args) + class line(SVGelement): """l=line(x1,y1,x2,y2,stroke,stroke_width,**args) A line is defined by a begin x,y pair and an end x,y pair """ + def __init__(self, x1=None, y1=None, x2=None, y2=None,stroke=None,stroke_width=None,**args): SVGelement.__init__(self, 'line', **args) if x1 != None: @@ -530,11 +537,13 @@ class line(SVGelement): if stroke != None: self.attributes['stroke'] = stroke + class polyline(SVGelement): """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args) a polyline is defined by a list of xy pairs """ + def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args): SVGelement.__init__(self, 'polyline', {'points': _xypointlist(points)}, **args) if fill != None: @@ -544,11 +553,13 @@ class polyline(SVGelement): if stroke != None: self.attributes['stroke'] = stroke + class polygon(SVGelement): """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args) a polygon is defined by a list of xy pairs """ + def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args): SVGelement.__init__(self, 'polygon', {'points': _xypointlist(points)}, **args) if fill != None: @@ -558,11 +569,13 @@ class polygon(SVGelement): if stroke != None: self.attributes['stroke'] = stroke + class path(SVGelement): """p=path(path,fill,stroke,stroke_width,**args) a path is defined by a path object and optional width, stroke and fillcolor """ + def __init__(self, pathdata, fill=None, stroke=None, stroke_width=None,id=None,**args): SVGelement.__init__(self, 'path', {'d': str(pathdata)}, **args) if stroke != None: @@ -580,6 +593,7 @@ class text(SVGelement): a text element can bge used for displaying text on the screen """ + def __init__(self, x=None, y=None, text=None, font_size=None,font_family=None,text_anchor=None,**args): SVGelement.__init__(self, 'text', **args) if x != None: @@ -601,11 +615,13 @@ class textpath(SVGelement): a textpath places a text on a path which is referenced by a link. """ + def __init__(self, link, text=None, **args): SVGelement.__init__(self, 'textPath', {'xlink:href': link}, **args) if text != None: self.text = text + class pattern(SVGelement): """p=pattern(x,y,width,height,patternUnits,**args) @@ -613,6 +629,7 @@ class pattern(SVGelement): graphic object which can be replicated ("tiled") at fixed intervals in x and y to cover the areas to be painted. """ + def __init__(self, x=None, y=None, width=None, height=None,patternUnits=None,**args): SVGelement.__init__(self, 'pattern', **args) if x != None: @@ -626,34 +643,40 @@ class pattern(SVGelement): if patternUnits != None: self.attributes['patternUnits'] = patternUnits + class title(SVGelement): """t=title(text,**args) a title is a text element. The text is displayed in the title bar add at least one to the root svg element """ + def __init__(self, text=None, **args): SVGelement.__init__(self, 'title', **args) if text != None: self.text = text + class description(SVGelement): """d=description(text,**args) a description can be added to any element and is used for a tooltip Add this element before adding other elements. """ + def __init__(self, text=None, **args): SVGelement.__init__(self, 'desc', **args) if text != None: self.text = text + class lineargradient(SVGelement): """lg=lineargradient(x1,y1,x2,y2,id,**args) defines a lineargradient using two xy pairs. stop elements van be added to define the gradient colors. """ + def __init__(self, x1=None, y1=None, x2=None, y2=None,id=None,**args): SVGelement.__init__(self, 'linearGradient', **args) if x1 != None: @@ -667,12 +690,14 @@ class lineargradient(SVGelement): if id != None: self.attributes['id'] = id + class radialgradient(SVGelement): """rg=radialgradient(cx,cy,r,fx,fy,id,**args) defines a radial gradient using a outer circle which are defined by a cx,cy and r and by using a focalpoint. stop elements van be added to define the gradient colors. """ + def __init__(self, cx=None, cy=None, r=None, fx=None,fy=None,id=None,**args): SVGelement.__init__(self, 'radialGradient', **args) if cx != None: @@ -688,21 +713,25 @@ class radialgradient(SVGelement): if id != None: self.attributes['id'] = id + class stop(SVGelement): """st=stop(offset,stop_color,**args) Puts a stop color at the specified radius """ + def __init__(self, offset, stop_color=None, **args): SVGelement.__init__(self, 'stop', {'offset': offset}, **args) if stop_color != None: self.attributes['stop-color'] = stop_color + class style(SVGelement): """st=style(type,cdata=None,**args) Add a CDATA element to this element for defing in line stylesheets etc.. """ + def __init__(self, type, cdata=None, **args): SVGelement.__init__(self, 'style', {'type': type}, cdata=cdata, **args) @@ -712,6 +741,7 @@ class image(SVGelement): adds an image to the drawing. Supported formats are .png, .jpg and .svg. """ + def __init__(self, url, x=None, y=None, width=None,height=None,**args): if width == None or height == None: raise ValueError('both height and width are required') @@ -721,11 +751,13 @@ class image(SVGelement): if y != None: self.attributes['y'] = y + class cursor(SVGelement): """c=cursor(url,**args) defines a custom cursor for a element or a drawing """ + def __init__(self, url, **args): SVGelement.__init__(self, 'cursor', {'xlink:href': url}, **args) @@ -736,6 +768,7 @@ class marker(SVGelement): defines a marker which can be used as an endpoint for a line or other pathtypes add an element to it which should be used as a marker. """ + def __init__(self, id=None, viewBox=None, refx=None, refy=None,markerWidth=None,markerHeight=None,**args): SVGelement.__init__(self, 'marker', **args) if id != None: @@ -751,17 +784,20 @@ class marker(SVGelement): if markerHeight != None: self.attributes['markerHeight'] = markerHeight + class group(SVGelement): """g=group(id,**args) a group is defined by an id and is used to contain elements g.addElement(SVGelement) """ + def __init__(self, id=None, **args): SVGelement.__init__(self, 'g', **args) if id != None: self.attributes['id'] = id + class symbol(SVGelement): """sy=symbol(id,viewbox,**args) @@ -778,14 +814,17 @@ class symbol(SVGelement): if viewBox != None: self.attributes['viewBox'] = _viewboxlist(viewBox) + class defs(SVGelement): """d=defs(**args) container for defining elements """ + def __init__(self, **args): SVGelement.__init__(self, 'defs', **args) + class switch(SVGelement): """sw=switch(**args) @@ -793,6 +832,7 @@ class switch(SVGelement): requiredFeatures, requiredExtensions and systemLanguage. Refer to the SVG specification for details. """ + def __init__(self, **args): SVGelement.__init__(self, 'switch', **args) @@ -802,6 +842,7 @@ class use(SVGelement): references a symbol by linking to its id and its position, height and width """ + def __init__(self, link, x=None, y=None, width=None,height=None,**args): SVGelement.__init__(self, 'use', {'xlink:href': link}, **args) if x != None: @@ -821,32 +862,39 @@ class link(SVGelement): a link is defined by a hyperlink. add elements which have to be linked a.addElement(SVGelement) """ + def __init__(self, link='', **args): SVGelement.__init__(self, 'a', {'xlink:href': link}, **args) + class view(SVGelement): """v=view(id,**args) a view can be used to create a view with different attributes""" + def __init__(self, id=None, **args): SVGelement.__init__(self, 'view', **args) if id != None: self.attributes['id'] = id + class script(SVGelement): """sc=script(type,type,cdata,**args) adds a script element which contains CDATA to the SVG drawing """ + def __init__(self, type, cdata=None, **args): SVGelement.__init__(self, 'script', {'type': type}, cdata=cdata, **args) + class animate(SVGelement): """an=animate(attribute,from,to,during,**args) animates an attribute. """ + def __init__(self, attribute, fr=None, to=None, dur=None,**args): SVGelement.__init__(self, 'animate', {'attributeName': attribute}, **args) if fr != None: @@ -856,11 +904,13 @@ class animate(SVGelement): if dur != None: self.attributes['dur'] = dur + class animateMotion(SVGelement): """an=animateMotion(pathdata,dur,**args) animates a SVGelement over the given path in dur seconds """ + def __init__(self, pathdata, dur, **args): SVGelement.__init__(self, 'animateMotion', **args) if pathdata != None: @@ -868,11 +918,13 @@ class animateMotion(SVGelement): if dur != None: self.attributes['dur'] = dur + class animateTransform(SVGelement): """antr=animateTransform(type,from,to,dur,**args) transform an element from and to a value. """ + def __init__(self, type=None, fr=None, to=None, dur=None,**args): SVGelement.__init__(self, 'animateTransform', {'attributeName': 'transform'}, **args) # As far as I know the attributeName is always transform @@ -884,11 +936,14 @@ class animateTransform(SVGelement): self.attributes['to'] = to if dur != None: self.attributes['dur'] = dur + + class animateColor(SVGelement): """ac=animateColor(attribute,type,from,to,dur,**args) Animates the color of a element """ + def __init__(self, attribute, type=None, fr=None, to=None,dur=None,**args): SVGelement.__init__(self, 'animateColor', {'attributeName': attribute}, **args) if type != None: @@ -899,11 +954,14 @@ class animateColor(SVGelement): self.attributes['to'] = to if dur != None: self.attributes['dur'] = dur + + class set(SVGelement): """st=set(attribute,to,during,**args) sets an attribute to a value for a """ + def __init__(self, attribute, to=None, dur=None, **args): SVGelement.__init__(self, 'set', {'attributeName': attribute}, **args) if to != None: @@ -912,7 +970,6 @@ class set(SVGelement): self.attributes['dur'] = dur - class svg(SVGelement): """s=svg(viewbox,width,height,**args) @@ -928,6 +985,7 @@ class svg(SVGelement): d.setSVG(s) d.toXml() """ + def __init__(self, viewBox=None, width=None, height=None, **args): SVGelement.__init__(self, 'svg', **args) if viewBox != None: @@ -938,6 +996,7 @@ class svg(SVGelement): self.attributes['height'] = height self.namespace = "http://www.w3.org/2000/svg" + class drawing: """d=drawing() @@ -952,6 +1011,7 @@ class drawing: def __init__(self, entity={}): self.svg = None self.entity = entity + def setSVG(self, svg): self.svg = svg # Voeg een element toe aan de grafiek toe. @@ -1005,6 +1065,7 @@ class drawing: root = implementation.createDocument(None, None, doctype) # Create the xml document. global appender + def appender(element, elementroot): """This recursive function appends elements to an element and sets the attributes and type. It stops when alle elements have been appended""" @@ -1053,6 +1114,7 @@ class drawing: f.close() except: print(("Cannot write SVG file: " + filename)) + def validate(self): try: import xml.parsers.xmlproc.xmlval @@ -1066,9 +1128,10 @@ class drawing: raise Exception("SVG is not well formed, see messages above") else: print("SVG well formed") -if __name__ == '__main__': +if __name__ == '__main__': + d = drawing() s = svg((0, 0, 100, 100)) r = rect(-100, -100, 300, 300, 'cyan') diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py index 2088ba9a..07c5a318 100644 --- a/wqflask/utility/temp_data.py +++ b/wqflask/utility/temp_data.py @@ -2,6 +2,7 @@ from redis import Redis import simplejson as json + class TempData: def __init__(self, temp_uuid): diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 9b751344..4fe4db08 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -13,11 +13,13 @@ logger = logging.getLogger(__name__) OVERRIDES = {} + def app_set(command_id, value): """Set application wide value""" app.config.setdefault(command_id, value) return value + def get_setting(command_id, guess=None): """Resolve a setting from the environment or the global settings in app.config, with valid_path is a function checking whether the @@ -66,12 +68,14 @@ def get_setting(command_id, guess=None): # print("Set "+command_id+"="+str(command)) return command + def get_setting_bool(id): v = get_setting(id) if v not in [0, False, 'False', 'FALSE', None]: return True return False + def get_setting_int(id): v = get_setting(id) if isinstance(v, str): @@ -80,21 +84,25 @@ def get_setting_int(id): return 0 return v + def valid_bin(bin): if os.path.islink(bin) or valid_file(bin): return bin return None + def valid_file(fn): if os.path.isfile(fn): return fn return None + def valid_path(dir): if os.path.isdir(dir): return dir return None + def js_path(module=None): """ Find the JS module in the two paths @@ -107,38 +115,47 @@ def js_path(module=None): return try_guix raise "No JS path found for " + module + " (if not in Guix check JS_GN_PATH)" + def reaper_command(guess=None): return get_setting("REAPER_COMMAND", guess) + def gemma_command(guess=None): return assert_bin(get_setting("GEMMA_COMMAND", guess)) + def gemma_wrapper_command(guess=None): return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND", guess)) + def plink_command(guess=None): return assert_bin(get_setting("PLINK_COMMAND", guess)) + def flat_file_exists(subdir): base = get_setting("GENENETWORK_FILES") return valid_path(base + "/" + subdir) + def flat_files(subdir=None): base = get_setting("GENENETWORK_FILES") if subdir: return assert_dir(base + "/" + subdir) return assert_dir(base) + def assert_bin(fn): if not valid_bin(fn): raise Exception("ERROR: can not find binary " + fn) return fn + def assert_dir(dir): if not valid_path(dir): raise Exception("ERROR: can not find directory " + dir) return dir + def assert_writable_dir(dir): try: fn = dir + "/test.txt" @@ -150,16 +167,19 @@ def assert_writable_dir(dir): raise Exception('Unable to write test.txt to directory ' + dir) return dir + def assert_file(fn): if not valid_file(fn): raise Exception('Unable to find file ' + fn) return fn + def mk_dir(dir): if not valid_path(dir): os.makedirs(dir) return assert_dir(dir) + def locate(name, subdir=None): """ Locate a static flat file in the GENENETWORK_FILES environment. @@ -179,9 +199,11 @@ def locate(name, subdir=None): if subdir: sys.stderr.write(subdir) raise Exception("Can not locate " + name + " in " + base) + def locate_phewas(name, subdir=None): return locate(name, '/phewas/' + subdir) + def locate_ignore_error(name, subdir=None): """ Locate a static flat file in the GENENETWORK_FILES environment. @@ -200,17 +222,20 @@ def locate_ignore_error(name, subdir=None): logger.info("WARNING: file " + name + " not found\n") return None + def tempdir(): """ Get UNIX TMPDIR by default """ return valid_path(get_setting("TMPDIR", "/tmp")) + BLUE = '\033[94m' GREEN = '\033[92m' BOLD = '\033[1m' ENDC = '\033[0m' + def show_settings(): from utility.tools import LOG_LEVEL diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py index 662bf794..00f14ba9 100644 --- a/wqflask/utility/type_checking.py +++ b/wqflask/utility/type_checking.py @@ -7,6 +7,7 @@ def is_float(value): except: return False + def is_int(value): try: int(value) @@ -14,6 +15,7 @@ def is_int(value): except: return False + def is_str(value): if value is None: return False @@ -23,18 +25,21 @@ def is_str(value): except: return False + def get_float(vars_obj, name, default=None): if name in vars_obj: if is_float(vars_obj[name]): return float(vars_obj[name]) return default + def get_int(vars_obj, name, default=None): if name in vars_obj: if is_int(vars_obj[name]): return float(vars_obj[name]) return default + def get_string(vars_obj, name, default=None): if name in vars_obj: if not vars_obj[name] is None: diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index ed59b0eb..f355a865 100644 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -64,6 +64,7 @@ ParInfo = { # Accessory Functions ######################################### + def genRandStr(prefix="", length=8, chars=string.ascii_letters + string.digits): from random import choice _str = prefix[:] @@ -71,6 +72,7 @@ def genRandStr(prefix="", length=8, chars=string.ascii_letters + string.digits): _str += choice(chars) return _str + def ListNotNull(lst): '''Obsolete - Use built in function any (or all or whatever) @@ -83,6 +85,7 @@ def ListNotNull(lst): return 1 return None + def readLineCSV(line): # dcrowell July 2008 """Parses a CSV string of text and returns a list containing each element as a string. Used by correlationPage""" @@ -91,6 +94,7 @@ def readLineCSV(line): # dcrowell July 2008 returnList[0] = returnList[0][1:] return returnList + def cmpEigenValue(A, B): try: if A[0] > B[0]: @@ -102,6 +106,7 @@ def cmpEigenValue(A, B): except: return 0 + def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users): access_to_confidential_phenotype_trait = 0 if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']: diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index bab87115..712517a3 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -30,6 +30,7 @@ app.register_blueprint(policies_blueprint, url_prefix="/policies") app.register_blueprint(environments_blueprint, url_prefix="/environments") app.register_blueprint(facilities_blueprint, url_prefix="/facilities") + @app.before_request def before_request(): g.request_start_time = time.time() diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py index e0b7fea0..f1dd148f 100644 --- a/wqflask/wqflask/api/correlation.py +++ b/wqflask/wqflask/api/correlation.py @@ -18,6 +18,7 @@ from utility.benchmark import Bench import utility.logger logger = utility.logger.getLogger(__name__) + def do_correlation(start_vars): assert('db' in start_vars) assert('target_db' in start_vars) @@ -66,6 +67,7 @@ def do_correlation(start_vars): return final_results + def calculate_results(this_trait, this_dataset, target_dataset, corr_params): corr_results = {} @@ -91,6 +93,7 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params): return sorted_results + def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params, tissue_dataset_id=1): # Gets tissue expression values for the primary trait primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=[this_trait.symbol]) @@ -113,6 +116,7 @@ def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_par return tissue_corr_data + def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_geneid_dict, corr_params): input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid) @@ -145,6 +149,7 @@ def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_g return lit_corr_data + def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, type): """ Calculates the sample r (or rho) and p-value @@ -176,6 +181,7 @@ def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_data else: return [sample_r, sample_p, num_overlap] + def convert_to_mouse_gene_id(species=None, gene_id=None): """If the species is rat or human, translate the gene_id to the mouse geneid @@ -212,6 +218,7 @@ def convert_to_mouse_gene_id(species=None, gene_id=None): return mouse_gene_id + def init_corr_params(start_vars): method = "pearson" if 'method' in start_vars: diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py index fbfbc879..662090d5 100644 --- a/wqflask/wqflask/api/mapping.py +++ b/wqflask/wqflask/api/mapping.py @@ -10,6 +10,7 @@ from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_map import utility.logger logger = utility.logger.getLogger(__name__) + def do_mapping_for_api(start_vars): assert('db' in start_vars) assert('trait_id' in start_vars) @@ -74,7 +75,6 @@ def do_mapping_for_api(start_vars): return result_markers, None - def initialize_parameters(start_vars, dataset, this_trait): mapping_params = {} diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index b0559a07..4f9cc6e5 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -27,10 +27,12 @@ logger = utility.logger.getLogger(__name__) version = "pre1" + @app.route("/api/v_{}/".format(version)) def hello_world(): return flask.jsonify({"hello": "world"}) + @app.route("/api/v_{}/species".format(version)) def get_species_list(): results = g.db.execute("SELECT SpeciesId, Name, FullName, TaxonomyId FROM Species;") @@ -47,6 +49,7 @@ def get_species_list(): return flask.jsonify(species_list) + @app.route("/api/v_{}/species/".format(version)) @app.route("/api/v_{}/species/.".format(version)) def get_species_info(species_name, file_format="json"): @@ -64,6 +67,7 @@ def get_species_info(species_name, file_format="json"): return flask.jsonify(species_dict) + @app.route("/api/v_{}/groups".format(version)) @app.route("/api/v_{}/groups/".format(version)) def get_groups_list(species_name=None): @@ -102,6 +106,7 @@ def get_groups_list(species_name=None): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") + @app.route("/api/v_{}/group/".format(version)) @app.route("/api/v_{}/group/.".format(version)) @app.route("/api/v_{}/group//".format(version)) @@ -145,6 +150,7 @@ def get_group_info(group_name, species_name=None, file_format="json"): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") + @app.route("/api/v_{}/datasets/".format(version)) @app.route("/api/v_{}/datasets//".format(version)) def get_datasets_for_group(group_name, species_name=None): @@ -197,6 +203,7 @@ def get_datasets_for_group(group_name, species_name=None): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") + @app.route("/api/v_{}/dataset/".format(version)) @app.route("/api/v_{}/dataset/.".format(version)) @app.route("/api/v_{}/dataset//".format(version)) @@ -302,6 +309,7 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") + @app.route("/api/v_{}/traits/".format(version), methods=("GET",)) @app.route("/api/v_{}/traits/.".format(version), methods=("GET",)) def fetch_traits(dataset_name, file_format="json"): @@ -430,6 +438,7 @@ def fetch_traits(dataset_name, file_format="json"): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") + @app.route("/api/v_{}/sample_data/".format(version)) @app.route("/api/v_{}/sample_data/.".format(version)) def all_sample_data(dataset_name, file_format="csv"): @@ -536,6 +545,7 @@ def all_sample_data(dataset_name, file_format="csv"): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") + @app.route("/api/v_{}/sample_data//".format(version)) @app.route("/api/v_{}/sample_data//.".format(version)) def trait_sample_data(dataset_name, trait_name, file_format="json"): @@ -625,6 +635,7 @@ def trait_sample_data(dataset_name, trait_name, file_format="json"): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") + @app.route("/api/v_{}/trait//".format(version)) @app.route("/api/v_{}/trait//.".format(version)) @app.route("/api/v_{}/trait_info//".format(version)) @@ -694,6 +705,7 @@ def get_trait_info(dataset_name, trait_name, file_format="json"): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") + @app.route("/api/v_{}/correlation".format(version), methods=("GET",)) def get_corr_results(): results = correlation.do_correlation(request.args) @@ -703,6 +715,7 @@ def get_corr_results(): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") + @app.route("/api/v_{}/mapping".format(version), methods=("GET",)) def get_mapping_results(): results, format = mapping.do_mapping_for_api(request.args) @@ -726,6 +739,7 @@ def get_mapping_results(): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") + @app.route("/api/v_{}/genotypes///.zip".format(version)) @app.route("/api/v_{}/genotypes///".format(version)) @app.route("/api/v_{}/genotypes//.zip".format(version)) @@ -813,6 +827,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): return output + @app.route("/api/v_{}/gen_dropdown".format(version), methods=("GET",)) def gen_dropdown_menu(): results = gen_menu.gen_dropdown_json() @@ -822,6 +837,7 @@ def gen_dropdown_menu(): else: return return_error(code=500, source=request.url_rule.rule, title="Some error occurred", details="") + def return_error(code, source, title, details): json_ob = {"errors": [ { @@ -834,6 +850,7 @@ def return_error(code, source, title, details): return flask.jsonify(json_ob) + def get_dataset_trait_ids(dataset_name, start_vars): if 'limit_to' in start_vars: @@ -906,6 +923,7 @@ def get_dataset_trait_ids(dataset_name, start_vars): dataset_id = results[0][2] return trait_ids, trait_names, data_type, dataset_id + def get_samplelist(dataset_name): group_id = get_group_id_from_dataset(dataset_name) @@ -922,6 +940,7 @@ def get_samplelist(dataset_name): return samplelist + def get_group_id_from_dataset(dataset_name): if "Publish" in dataset_name: query = """ @@ -962,6 +981,7 @@ def get_group_id_from_dataset(dataset_name): else: return None + def get_group_id(group_name): query = """ SELECT InbredSet.Id diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 6a1b88ca..61f73106 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -40,6 +40,7 @@ def process_traits(unprocessed_traits): return traits + def report_change(len_before, len_now): new_length = len_now - len_before if new_length: @@ -48,6 +49,7 @@ def report_change(len_before, len_now): else: logger.debug("No new traits were added.") + @app.route("/collections/store_trait_list", methods=('POST',)) def store_traits_list(): params = request.form @@ -59,6 +61,7 @@ def store_traits_list(): return hash + @app.route("/collections/add") def collections_add(): @@ -82,6 +85,7 @@ def collections_add(): collections=collections, ) + @app.route("/collections/new") def collections_new(): params = request.args @@ -118,6 +122,7 @@ def collections_new(): # CauseAnError pass + def create_new(collection_name): params = request.args @@ -133,6 +138,7 @@ def create_new(collection_name): return redirect(url_for('view_collection', uc_id=uc_id)) + @app.route("/collections/list") def list_collections(): params = request.args @@ -143,6 +149,7 @@ def list_collections(): collections=user_collections, ) + @app.route("/collections/remove", methods=('POST',)) def remove_traits(): params = request.form @@ -216,6 +223,7 @@ def view_collection(): **collection_info ) + @app.route("/collections/change_name", methods=('POST',)) def change_collection_name(): params = request.form diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 22941ad5..6afea715 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -11,6 +11,7 @@ import numpy as np import utility.logger logger = utility.logger.getLogger(__name__) + class CorrScatterPlot: """Page that displays a correlation scatterplot with a line fitted to it""" diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 051ac1cb..e2fe1ff4 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -172,7 +172,6 @@ class CorrelationResults: self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()), key=lambda t: -abs(t[1][0]))) - # ZS: Convert min/max chromosome to an int for the location range option range_chr_as_int = None for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()): @@ -348,7 +347,6 @@ class CorrelationResults: else: trait.lit_corr = 0 - def do_lit_correlation_for_all_traits(self): input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid) @@ -484,6 +482,7 @@ def do_bicor(this_trait_vals, target_trait_vals): return the_r, the_p + def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api=False): results_list = [] for i, trait in enumerate(corr_results): @@ -574,6 +573,7 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap return json.dumps(results_list) + def get_header_fields(data_type, corr_method): if data_type == "ProbeSet": if corr_method == "spearman": diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 94c8931f..331cb1dc 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -233,6 +233,7 @@ class CorrelationMatrix: loadings_array.append(loadings_row) return loadings_array + def export_corr_matrix(corr_results): corr_matrix_filename = "corr_matrix_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) matrix_export_path = "{}{}.csv".format(GENERATED_TEXT_DIR, corr_matrix_filename) @@ -263,6 +264,7 @@ def export_corr_matrix(corr_results): return corr_matrix_filename, matrix_export_path + def zScore(trait_data_array): NN = len(trait_data_array[0]) if NN < 10: @@ -283,6 +285,7 @@ def zScore(trait_data_array): i += 1 return trait_data_array + def sortEigenVectors(vector): try: eigenValues = vector[0].tolist() diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 2fa90a93..ec66e59f 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -39,6 +39,7 @@ r_write_table = ro.r["write.table"] # Map the write.table function r_data_frame = ro.r["data.frame"] # Map the write.table function r_as_numeric = ro.r["as.numeric"] # Map the write.table function + class CTL: def __init__(self): logger.info("Initialization of CTL") diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py index b6e85494..e743c4b3 100644 --- a/wqflask/wqflask/database.py +++ b/wqflask/wqflask/database.py @@ -17,6 +17,7 @@ db_session = scoped_session(sessionmaker(autocommit=False, Base = declarative_base() Base.query = db_session.query_property() + def init_db(): # import all modules here that might define models so that # they will be registered properly on the metadata. Otherwise @@ -27,4 +28,5 @@ def init_db(): Base.metadata.create_all(bind=engine) logger.info("Done creating all model metadata") + init_db() diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py index 25e624ef..c7558ed8 100644 --- a/wqflask/wqflask/db_info.py +++ b/wqflask/wqflask/db_info.py @@ -90,6 +90,7 @@ class InfoPage: except Exception as e: pass + def process_query_results(results): info_ob = { 'info_page_name': results[0], diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 115182e4..7442dc72 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -73,6 +73,7 @@ class DoSearch: else: return None + class MrnaAssaySearch(DoSearch): """A search within an expression dataset, including mRNA, protein, SNP, but not phenotype or metabolites""" @@ -296,6 +297,7 @@ class PhenotypeSearch(DoSearch): return self.execute(query) + class GenotypeSearch(DoSearch): """A search within a genotype dataset""" @@ -339,7 +341,6 @@ class GenotypeSearch(DoSearch): from_clause = self.normalize_spaces(from_clause) - if self.search_term[0] == "*": query = (self.base_query + """WHERE Geno.Id = GenoXRef.GenoId @@ -367,6 +368,7 @@ class GenotypeSearch(DoSearch): return self.execute(self.query) + class RifSearch(MrnaAssaySearch): """Searches for traits with a Gene RIF entry including the search term.""" @@ -390,6 +392,7 @@ class RifSearch(MrnaAssaySearch): return self.execute(query) + class WikiSearch(MrnaAssaySearch): """Searches GeneWiki for traits other people have annotated""" @@ -415,6 +418,7 @@ class WikiSearch(MrnaAssaySearch): return self.execute(query) + class GoSearch(MrnaAssaySearch): """Searches for synapse-associated genes listed in the Gene Ontology.""" @@ -449,6 +453,8 @@ class GoSearch(MrnaAssaySearch): return self.execute(query) # ZS: Not sure what the best way to deal with LRS searches is + + class LrsSearch(DoSearch): """Searches for genes with a QTL within the given LRS values @@ -526,7 +532,6 @@ class LrsSearch(DoSearch): return where_clause - def run(self): self.from_clause = self.get_from_clause() @@ -550,6 +555,7 @@ class MrnaLrsSearch(LrsSearch, MrnaAssaySearch): return self.execute(self.query) + class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch): for search_key in ('LRS', 'LOD'): @@ -649,6 +655,7 @@ class CisTransLrsSearch(DoSearch): return where_clause + class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch): """ Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values @@ -680,6 +687,7 @@ class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch): return self.execute(self.query) + class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch): """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values @@ -744,6 +752,7 @@ class MeanSearch(MrnaAssaySearch): return self.execute(self.query) + class RangeSearch(MrnaAssaySearch): """Searches for genes with a range of expression varying between two values""" @@ -779,6 +788,7 @@ class RangeSearch(MrnaAssaySearch): return self.execute(self.query) + class PositionSearch(DoSearch): """Searches for genes/markers located within a specified range on a specified chromosome""" @@ -800,7 +810,6 @@ class PositionSearch(DoSearch): self.dataset.type, max(self.mb_min, self.mb_max)) - return where_clause def get_chr(self): @@ -819,6 +828,7 @@ class PositionSearch(DoSearch): return self.execute(self.query) + class MrnaPositionSearch(PositionSearch, MrnaAssaySearch): """Searches for genes located within a specified range on a specified chromosome""" @@ -832,6 +842,7 @@ class MrnaPositionSearch(PositionSearch, MrnaAssaySearch): return self.execute(self.query) + class GenotypePositionSearch(PositionSearch, GenotypeSearch): """Searches for genes located within a specified range on a specified chromosome""" @@ -845,6 +856,7 @@ class GenotypePositionSearch(PositionSearch, GenotypeSearch): return self.execute(self.query) + class PvalueSearch(MrnaAssaySearch): """Searches for traits with a permutationed p-value between low and high""" @@ -878,6 +890,7 @@ class PvalueSearch(MrnaAssaySearch): logger.sql(self.query) return self.execute(self.query) + class AuthorSearch(PhenotypeSearch): """Searches for phenotype traits with specified author(s)""" @@ -900,6 +913,7 @@ def is_number(s): except ValueError: return False + def get_aliases(symbol, species): if species == "mouse": symbol_string = symbol.capitalize() @@ -923,6 +937,7 @@ def get_aliases(symbol, species): return filtered_aliases + if __name__ == "__main__": # Usually this will be used as a library, but call it from the command line for testing # And it runs the code below diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py index 207767c4..81424b9c 100644 --- a/wqflask/wqflask/docs.py +++ b/wqflask/wqflask/docs.py @@ -5,6 +5,7 @@ from flask import g from utility.logger import getLogger logger = getLogger(__name__) + class Docs: def __init__(self, entry, start_vars={}): @@ -23,7 +24,6 @@ class Docs: self.title = result[0] self.content = result[1].decode("utf-8") - self.editable = "false" # ZS: Removing option to edit to see if text still gets vandalized try: diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py index 95c20673..d0745ef7 100644 --- a/wqflask/wqflask/export_traits.py +++ b/wqflask/wqflask/export_traits.py @@ -15,6 +15,7 @@ from pprint import pformat as pf from utility.logger import getLogger logger = getLogger(__name__) + def export_search_results_csv(targs): table_data = json.loads(targs['export_data']) @@ -132,6 +133,7 @@ def export_search_results_csv(targs): return file_list + def sort_traits_by_group(trait_list=[]): traits_by_group = {} for trait in trait_list: diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py index 9836eb9c..1556c6a0 100644 --- a/wqflask/wqflask/external_tools/send_to_bnw.py +++ b/wqflask/wqflask/external_tools/send_to_bnw.py @@ -24,6 +24,7 @@ from utility import helper_functions, corr_result_helpers import utility.logger logger = utility.logger.getLogger(__name__) + class SendToBNW: def __init__(self, start_vars): trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py index 36f1b8e5..c55c43e6 100644 --- a/wqflask/wqflask/external_tools/send_to_geneweaver.py +++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py @@ -29,6 +29,7 @@ from utility import helper_functions, corr_result_helpers import utility.logger logger = utility.logger.getLogger(__name__) + class SendToGeneWeaver: def __init__(self, start_vars): trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] @@ -58,6 +59,7 @@ class SendToGeneWeaver: 'list': ",".join(trait_name_list), } + def get_trait_name_list(trait_list): name_list = [] for trait_db in trait_list: @@ -65,6 +67,7 @@ def get_trait_name_list(trait_list): return name_list + def test_chip(trait_list): final_chip_name = "" diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py index f50eeb8b..6b78725c 100644 --- a/wqflask/wqflask/external_tools/send_to_webgestalt.py +++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py @@ -29,6 +29,7 @@ from utility import helper_functions, corr_result_helpers import utility.logger logger = utility.logger.getLogger(__name__) + class SendToWebGestalt: def __init__(self, start_vars): trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] @@ -69,6 +70,7 @@ class SendToWebGestalt: else: self.hidden_vars['organism'] = "others" + def test_chip(trait_list): final_chip_name = "" @@ -113,6 +115,7 @@ def test_chip(trait_list): return chip_name + def gen_gene_id_list(trait_list): trait_name_list = [] gene_id_list = [] diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py index f29c0e4d..92a65112 100644 --- a/wqflask/wqflask/group_manager.py +++ b/wqflask/wqflask/group_manager.py @@ -12,6 +12,7 @@ from utility.redis_tools import get_user_groups, get_group_info, save_user, crea from utility.logger import getLogger logger = getLogger(__name__) + @app.route("/groups/manage", methods=('GET', 'POST')) def manage_groups(): params = request.form if request.form else request.args @@ -21,6 +22,7 @@ def manage_groups(): admin_groups, member_groups = get_user_groups(g.user_session.user_id) return render_template("admin/group_manager.html", admin_groups=admin_groups, member_groups=member_groups) + @app.route("/groups/view", methods=('GET', 'POST')) def view_group(): params = request.form if request.form else request.args @@ -58,6 +60,7 @@ def view_group(): return render_template("admin/view_group.html", group_info=group_info, admins=admins_info, members=members_info, user_is_admin=user_is_admin, resources=resources_info) + @app.route("/groups/remove", methods=('POST',)) def remove_groups(): group_ids_to_remove = request.form['selected_group_ids'] @@ -66,6 +69,7 @@ def remove_groups(): return redirect(url_for('manage_groups')) + @app.route("/groups/remove_users", methods=('POST',)) def remove_users(): group_id = request.form['group_id'] @@ -77,6 +81,7 @@ def remove_users(): return redirect(url_for('view_group', id=group_id)) + @app.route("/groups/add_", methods=('POST',)) def add_users(user_type='members'): group_id = request.form['group_id'] @@ -89,6 +94,7 @@ def add_users(user_type='members'): return redirect(url_for('view_group', id=group_id)) + @app.route("/groups/change_name", methods=('POST',)) def change_name(): group_id = request.form['group_id'] @@ -97,6 +103,7 @@ def change_name(): return new_name + @app.route("/groups/create", methods=('GET', 'POST')) def add_or_edit_group(): params = request.form if request.form else request.args @@ -125,6 +132,8 @@ def add_or_edit_group(): return render_template("admin/create_group.html") # ZS: Will integrate this later, for now just letting users be added directly + + def send_group_invites(group_id, user_email_list=[], user_type="members"): for user_email in user_email_list: user_details = get_user_by_unique_column("email_address", user_email) diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 8cb81dcc..a21dae84 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -18,6 +18,7 @@ from utility.type_checking import is_float, is_int, is_str, get_float, get_int, from utility.logger import getLogger logger = getLogger(__name__) + class GSearch: def __init__(self, kw): diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index f8ef7028..0b477446 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -14,6 +14,7 @@ Redis = Redis() logger = getLogger(__name__) + class Heatmap: def __init__(self, start_vars, temp_uuid): @@ -132,6 +133,7 @@ class Heatmap: else: self.trait_results[this_trait.name].append(float(qtl['lrs_value'])) + def gen_pheno_txt_file(samples, vals, filename): """Generates phenotype file for GEMMA""" @@ -151,6 +153,7 @@ def gen_pheno_txt_file(samples, vals, filename): values_string = "\t".join(filtered_vals_list) outfile.write(values_string) + def parse_reaper_output(gwa_filename): included_markers = [] p_values = [] diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py index 9779878e..8dd1c7c0 100644 --- a/wqflask/wqflask/interval_analyst/GeneUtil.py +++ b/wqflask/wqflask/interval_analyst/GeneUtil.py @@ -4,6 +4,8 @@ from flask import Flask, g # Just return a list of dictionaries # each dictionary contains sub-dictionary + + def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd', 'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID', diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 3753d1ce..5c7b81dd 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -509,9 +509,6 @@ class DisplayMappingResults: self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS + 10) * self.EACH_GENE_HEIGHT # END HaplotypeAnalyst - - - ######################### # Get the sorting column ######################### @@ -1640,7 +1637,6 @@ class DisplayMappingResults: geneYLocation + 2 *ind*self.EACH_GENE_HEIGHT + 2*self.EACH_GENE_HEIGHT*zoom)), outline=outlineColor, fill=fillColor) - COORDS = "%d, %d, %d, %d" % (geneStartPix, geneYLocation + ind * self.EACH_GENE_HEIGHT, geneEndPix + 1, (geneYLocation + ind * self.EACH_GENE_HEIGHT)) TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart)) HREF = '' @@ -1663,7 +1659,6 @@ class DisplayMappingResults: geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)), fill= mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2)) - if lastGene == 0: draw_rotated_text( canvas, text="%s" % (_chr[j].name), @@ -2085,7 +2080,6 @@ class DisplayMappingResults: im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset + plotWidth, yZero)), fill=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself - def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None): im_drawer = ImageDraw.Draw(canvas) xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset @@ -2427,7 +2421,6 @@ class DisplayMappingResults: yLRS = yZero - (item / LRS_LOD_Max) * LRSHeightThresh - if 'lrs_value' in qtlresult: if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP": if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf': @@ -2621,7 +2614,6 @@ class DisplayMappingResults: # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) - # draw additive scale if not self.multipleInterval and self.additiveChecked: additiveScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom) @@ -2653,7 +2645,6 @@ class DisplayMappingResults: xy=((xLeftOffset, yZero), (xLeftOffset, yTopOffset + 30 * (zoom - 1))), fill=self.LRS_COLOR, width=1 * zoom) # the blue line running up the y axis - def drawGraphBackground(self, canvas, gifmap, offset=(80, 120, 80, 50), zoom=1, startMb= None, endMb = None): # conditions # multiple Chromosome view diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index e6c78536..22a50bb8 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -8,11 +8,11 @@ from utility.tools import flat_files, PLINK_COMMAND import utility.logger logger = utility.logger.getLogger(__name__) + def run_plink(this_trait, dataset, species, vals, maf): plink_output_filename = webqtlUtil.genRandStr(f"{dataset.group.name}_{this_trait.name}_") gen_pheno_txt_file(dataset, vals) - plink_command = f"{PLINK_COMMAND} --noweb --bfile {flat_files('mapping')}/{dataset.group.name} --no-pheno --no-fid --no-parents --no-sex --maf {maf} --out { TMPDIR}{plink_output_filename} --assoc " logger.debug("plink_command:", plink_command) @@ -25,6 +25,7 @@ def run_plink(this_trait, dataset, species, vals, maf): return dataset.group.markers.markers + def gen_pheno_txt_file(this_dataset, vals): """Generates phenotype file for GEMMA/PLINK""" @@ -42,6 +43,7 @@ def gen_pheno_txt_file(this_dataset, vals): this_val = vals[i] outfile.write("0 " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n") + def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename=''): ped_sample_list = get_samples_from_ped_file(dataset) output_file = open(f"{TMPDIR}{pheno_filename}.txt", "wb") @@ -77,6 +79,8 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename=''): output_file.close() # get strain name from ped file in order + + def get_samples_from_ped_file(dataset): ped_file = open(f"{flat_files('mapping')}{dataset.group.name}.ped", "r") line = ped_file.readline() @@ -93,6 +97,7 @@ def get_samples_from_ped_file(dataset): return sample_list + def parse_plink_output(output_filename, species): plink_results = {} @@ -154,6 +159,8 @@ def parse_plink_output(output_filename, species): # function: convert line from str to list; # output: lineList list ####################################################### + + def build_line_list(line=""): line_list = line.strip().split(' ') # irregular number of whitespaces between columns line_list = [item for item in line_list if item != ''] diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index dd044cb0..313c40ca 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -8,6 +8,7 @@ from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR import utility.logger logger = utility.logger.getLogger(__name__) + def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boot_check, num_bootstrap, do_control, control_marker, manhattan_plot, first_run=True, output_files=None): """Generates p-values for each marker using qtlreaper""" @@ -73,6 +74,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo return (marker_obs, permu_vals, suggestive, significant, bootstrap_vals, [output_filename, permu_filename, bootstrap_filename]) + def gen_pheno_txt_file(samples, vals, trait_filename): """Generates phenotype file for GEMMA""" @@ -92,6 +94,7 @@ def gen_pheno_txt_file(samples, vals, trait_filename): values_string = "\t".join(filtered_vals_list) outfile.write(values_string) + def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): included_markers = [] p_values = [] @@ -163,6 +166,7 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): return marker_obs, permu_vals, bootstrap_vals + def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot): genotype = dataset.group.read_genotype_file(use_reaper=True) @@ -255,6 +259,7 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da qtl_results.append(qtl) return qtl_results, json_data, perm_output, suggestive, significant, bootstrap_results + def natural_sort(marker_list): """ Function to naturally sort numbers + strings, adopted from user Mark Byers here: https://stackoverflow.com/questions/4836710/does-python-have-a-built-in-function-for-string-natural-sort diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 2bd94512..588600f5 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -16,6 +16,8 @@ import utility.logger logger = utility.logger.getLogger(__name__) # Get a trait's type (numeric, categorical, etc) from the DB + + def get_trait_data_type(trait_db_string): logger.info("get_trait_data_type"); the_query = "SELECT value FROM TraitMetadata WHERE type='trait_data_type'" @@ -133,6 +135,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec else: return process_rqtl_results(result_data_frame, dataset.group.species) + def generate_cross_from_rdata(dataset): rdata_location = locate(dataset.group.name + ".RData", "genotype/rdata") ro.r(""" @@ -143,6 +146,7 @@ def generate_cross_from_rdata(dataset): } """ % (rdata_location)) + def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly ro.r(""" @@ -187,6 +191,7 @@ def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figur } """ % (dataset.group.genofile, scale_units)) + def add_perm_strata(cross, perm_strata): col_string = 'c("the_strata")' perm_strata_string = "c(" @@ -201,6 +206,7 @@ def add_perm_strata(cross, perm_strata): return cross, strata_ob + def sanitize_rqtl_phenotype(vals): pheno_as_string = "c(" for i, val in enumerate(vals): @@ -218,6 +224,7 @@ def sanitize_rqtl_phenotype(vals): return pheno_as_string + def sanitize_rqtl_names(vals): pheno_as_string = "c(" for i, val in enumerate(vals): @@ -235,12 +242,14 @@ def sanitize_rqtl_names(vals): return pheno_as_string + def add_phenotype(cross, pheno_as_string, col_name): ro.globalenv["the_cross"] = cross ro.r('pheno <- data.frame(pull.pheno(the_cross))') ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric(' + pheno_as_string + '))') return ro.r["the_cross"] + def add_categorical_covar(cross, covar_as_string, i): ro.globalenv["the_cross"] = cross logger.info("cross set"); @@ -275,12 +284,14 @@ def add_names(cross, names_as_string, col_name): ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = ' + names_as_string + ')') return ro.r["the_cross"] + def pull_var(var_name, cross, var_string): ro.globalenv["the_cross"] = cross ro.r(var_name + ' <- pull.pheno(the_cross, ' + var_string + ')') return ro.r[var_name] + def add_cofactors(cross, this_dataset, covariates, samples): ro.numpy2ri.activate() @@ -341,6 +352,7 @@ def add_cofactors(cross, this_dataset, covariates, samples): covars_ob = pull_var("trait_covars", cross, covar_name_string) return cross, covars_ob + def create_marker_covariates(control_marker, cross): ro.globalenv["the_cross"] = cross ro.r('genotypes <- pull.geno(the_cross)') # Get the genotype matrix @@ -358,6 +370,7 @@ def create_marker_covariates(control_marker, cross): # TODO: Create a design matrix from the marker covars for the markers in case of an F2, 4way, etc return ro.r["marker_covars"] + def process_pair_scan_results(result): pair_scan_results = [] @@ -374,6 +387,7 @@ def process_pair_scan_results(result): return pair_scan_results + def process_rqtl_perm_results(num_perm, results): perm_vals = [] for line in str(results).split("\n")[1:(num_perm + 1)]: @@ -386,6 +400,7 @@ def process_rqtl_perm_results(num_perm, results): return perm_output, suggestive, significant + def process_rqtl_results(result, species_name): # TODO: how to make this a one liner and not copy the stuff in a loop qtl_results = [] output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)] diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index f1665570..31c58083 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -45,6 +45,7 @@ from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR import utility.logger logger = utility.logger.getLogger(__name__) + class RunMapping: def __init__(self, start_vars, temp_uuid): @@ -504,6 +505,7 @@ class RunMapping: trimmed_genotype_data.append(new_genotypes) return trimmed_genotype_data + def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples): with open(results_path, "w+") as output_file: output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") @@ -564,6 +566,7 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, if i < (len(markers) - 1): output_file.write("\n") + def trim_markers_for_figure(markers): if 'p_wald' in list(markers[0].keys()): score_type = 'p_wald' @@ -624,6 +627,7 @@ def trim_markers_for_figure(markers): filtered_markers.append(marker) return filtered_markers + def trim_markers_for_table(markers): if 'lod_score' in list(markers[0].keys()): sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True) @@ -637,6 +641,7 @@ def trim_markers_for_table(markers): else: return sorted_markers + def write_input_for_browser(this_dataset, gwas_results, annotations): file_base = this_dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) gwas_filename = file_base + "_GWAS" @@ -650,6 +655,7 @@ def write_input_for_browser(this_dataset, gwas_results, annotations): return [gwas_filename, annot_filename] + def geno_db_exists(this_dataset): geno_db_name = this_dataset.group.name + "Geno" try: @@ -658,6 +664,7 @@ def geno_db_exists(this_dataset): except: return "False" + def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results): chr_lengths = [] if mapping_scale == "physic": @@ -696,6 +703,7 @@ def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results): return chr_lengths + def get_genofile_samplelist(dataset): genofile_samplelist = [] @@ -706,6 +714,7 @@ def get_genofile_samplelist(dataset): return genofile_samplelist + def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): perm_strata_strings = [] for sample in used_samples: diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py index 8abd6516..d7c9ef95 100644 --- a/wqflask/wqflask/model.py +++ b/wqflask/wqflask/model.py @@ -14,6 +14,7 @@ from sqlalchemy.orm import relationship from wqflask.database import Base, init_db + class User(Base): __tablename__ = "user" id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4())) @@ -63,7 +64,6 @@ class User(Base): print("Couldn't display_num_collections:", why) return "" - def get_collection_by_name(self, collection_name): try: collect = self.user_collections.filter_by(name=collection_name).first() @@ -83,7 +83,6 @@ class User(Base): def login_count(self): return self.logins.filter_by(successful=True).count() - @property def confirmed_at(self): if self.confirmed: @@ -116,6 +115,7 @@ class User(Base): except IndexError: return None + class Login(Base): __tablename__ = "login" id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4())) @@ -134,6 +134,7 @@ class Login(Base): ################################################################################################## + class UserCollection(Base): __tablename__ = "user_collection" id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4())) @@ -158,12 +159,14 @@ class UserCollection(Base): def members_as_set(self): return set(json.loads(self.members)) + def display_collapsible(number): if number: return number else: return "" + def user_uuid(): """Unique cookie for a user""" user_uuid = request.cookies.get('user_uuid') diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py index 93785a3a..e089643e 100644 --- a/wqflask/wqflask/network_graph/network_graph.py +++ b/wqflask/wqflask/network_graph/network_graph.py @@ -27,6 +27,7 @@ from utility import helper_functions from utility import corr_result_helpers from utility.tools import GN2_BRANCH_URL + class NetworkGraph: def __init__(self, start_vars): diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py index 861a93f2..e262dd51 100644 --- a/wqflask/wqflask/news.py +++ b/wqflask/wqflask/news.py @@ -1,5 +1,6 @@ from flask import g + class News: def __init__(self): diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py index dfd374e2..6b836e20 100644 --- a/wqflask/wqflask/parser.py +++ b/wqflask/wqflask/parser.py @@ -24,6 +24,7 @@ from pprint import pformat as pf from utility.logger import getLogger logger = getLogger(__name__) + def parse(pstring): """ diff --git a/wqflask/wqflask/pbkdf2.py b/wqflask/wqflask/pbkdf2.py index 6346df03..1a965fc5 100644 --- a/wqflask/wqflask/pbkdf2.py +++ b/wqflask/wqflask/pbkdf2.py @@ -4,6 +4,8 @@ from werkzeug.security import safe_str_cmp as ssc # Replace this because it just wraps around Python3's internal # functions. Added this during migration. + + def pbkdf2_hex(data, salt, iterations=1000, keylen=24, hashfunc="sha1"): """Wrapper function of python's hashlib.pbkdf2_hmac. """ diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index a1fe0f8f..4591710c 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -11,6 +11,7 @@ from utility.redis_tools import get_resource_info, get_group_info, get_groups_li from utility.logger import getLogger logger = getLogger(__name__) + @app.route("/resources/manage", methods=('GET', 'POST')) def manage_resource(): params = request.form if request.form else request.args @@ -40,6 +41,7 @@ def manage_resource(): return render_template("admin/manage_resource.html", owner_name=owner_display_name, resource_id=resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status) + @app.route("/search_for_users", methods=('POST',)) def search_for_user(): params = request.form @@ -49,6 +51,7 @@ def search_for_user(): return json.dumps(user_list) + @app.route("/search_for_groups", methods=('POST',)) def search_for_groups(): params = request.form @@ -65,6 +68,7 @@ def search_for_groups(): return json.dumps(group_list) + @app.route("/resources/change_owner", methods=('POST',)) def change_owner(): resource_id = request.form['resource_id'] @@ -81,6 +85,7 @@ def change_owner(): else: return render_template("admin/change_resource_owner.html", resource_id=resource_id) + @app.route("/resources/change_default_privileges", methods=('POST',)) def change_default_privileges(): resource_id = request.form['resource_id'] @@ -99,6 +104,7 @@ def change_default_privileges(): else: return redirect(url_for("no_access_page")) + @app.route("/resources/add_group", methods=('POST',)) def add_group_to_resource(): resource_id = request.form['resource_id'] @@ -125,6 +131,7 @@ def add_group_to_resource(): else: return redirect(url_for("no_access_page")) + def get_group_names(group_masks): group_masks_with_names = {} for group_id, group_mask in list(group_masks.items()): diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 16eb1864..ed5f9bad 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -24,6 +24,7 @@ from utility.type_checking import is_str from utility.logger import getLogger logger = getLogger(__name__) + class SearchResultPage: #maxReturn = 3000 @@ -270,6 +271,7 @@ class SearchResultPage: else: return None + def get_GO_symbols(a_search): query = """SELECT genes FROM GORef @@ -287,6 +289,7 @@ def get_GO_symbols(a_search): return new_terms + def insert_newlines(string, every=64): """ This is because it is seemingly impossible to change the width of the description column, so I'm just manually adding line breaks """ lines = [] @@ -294,6 +297,7 @@ def insert_newlines(string, every=64): lines.append(string[i:i + every]) return '\n'.join(lines) + def get_aliases(symbol_list, species): updated_symbols = [] diff --git a/wqflask/wqflask/send_mail.py b/wqflask/wqflask/send_mail.py index 86e8a558..299c866a 100644 --- a/wqflask/wqflask/send_mail.py +++ b/wqflask/wqflask/send_mail.py @@ -8,10 +8,12 @@ Redis = StrictRedis() import mailer + def timestamp(): ts = datetime.datetime.utcnow() return ts.isoformat() + def main(): while True: print("I'm alive!") @@ -31,7 +33,6 @@ def main(): process_message(msg) - def process_message(msg): msg = json.loads(msg) diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py index 48761fa0..8b3a4faa 100644 --- a/wqflask/wqflask/server_side.py +++ b/wqflask/wqflask/server_side.py @@ -1,7 +1,6 @@ # handles server side table processing - class ServerSideTable: """ This class is used to do server-side processing diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 388f831f..496dee57 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -8,6 +8,7 @@ from pprint import pformat as pf from utility import Plot from utility import Bunch + class SampleList: def __init__(self, dataset, diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py index 379b746c..f0fcd27d 100644 --- a/wqflask/wqflask/show_trait/export_trait_data.py +++ b/wqflask/wqflask/show_trait/export_trait_data.py @@ -5,6 +5,7 @@ from functools import cmp_to_key from base.trait import create_trait from base import data_set + def export_sample_table(targs): sample_data = json.loads(targs['export_data']) @@ -28,6 +29,7 @@ def export_sample_table(targs): return trait_name, final_sample_data + def get_export_metadata(trait_id, dataset_name): dataset = data_set.create_dataset(dataset_name) this_trait = create_trait(dataset=dataset, @@ -64,6 +66,7 @@ def dict_to_sorted_list(dictionary): sorted_values = [item[1] for item in sorted_list] return sorted_values + def cmp_samples(a, b): if b[0] == 'name': return 1 diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index 7a0df94b..e5c67165 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -9,6 +9,7 @@ logger = getLogger(__name__) from base import species from base import webqtlConfig + class SnpBrowser: def __init__(self, start_vars): @@ -472,7 +473,6 @@ class SnpBrowser: base_color_dict = {"A": "#C33232", "C": "#1569C7", "T": "#CFCF32", "G": "#32C332", "t": "#FF6", "c": "#5CB3FF", "a": "#F66", "g": "#CF9", ":": "#FFFFFF", "-": "#FFFFFF", "?": "#FFFFFF"} - the_bases = [] for j, item in enumerate(allele_value_list): if item and isinstance(item, str): @@ -641,6 +641,7 @@ class SnpBrowser: # for i in range(n_click): # href = url_for('snp_browser', first_run="false", chosen_strains_mouse=self.chosen_strains_mouse, chosen_strains_rat=self.chosen_strains_rat, variant=self.variant_type, species=self.species_name, gene_name=self.gene_name, chr=self.chr, start_mb=self.start_mb, end_mb=self.end_mb, limit_strains=self.limit_strains, domain=self.domain, function=self.function, criteria=self.criteria, score=self.score, diff_alleles=self.diff_alleles) + def get_browser_sample_lists(species_id=1): strain_lists = {} mouse_strain_list = [] @@ -660,6 +661,7 @@ def get_browser_sample_lists(species_id=1): return strain_lists + def get_header_list(variant_type, strains, species=None, empty_columns=None): if species == "Mouse": strain_list = strains['mouse'] @@ -715,6 +717,7 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None): return header_fields, empty_field_count, header_data_names + def get_effect_details_by_category(effect_name=None, effect_value=None): gene_list = [] transcript_list = [] @@ -764,6 +767,7 @@ def get_effect_details_by_category(effect_name=None, effect_value=None): return [gene_list, transcript_list, exon_list, function_list, function_detail_list] + def get_effect_info(effect_list): domain = "" effect_detail_list = [] @@ -836,6 +840,7 @@ def get_effect_info(effect_list): return effect_info_dict + def get_gene_id(species_id, gene_name): query = """ SELECT @@ -853,6 +858,7 @@ def get_gene_id(species_id, gene_name): else: return "" + def get_gene_id_name_dict(species_id, gene_name_list): gene_id_name_dict = {} if len(gene_name_list) == 0: @@ -877,6 +883,7 @@ def get_gene_id_name_dict(species_id, gene_name_list): return gene_id_name_dict + def check_if_in_gene(species_id, chr, mb): if species_id != 0: # ZS: Check if this is necessary query = """SELECT geneId, geneSymbol diff --git a/wqflask/wqflask/submit_bnw.py b/wqflask/wqflask/submit_bnw.py index 4ad6f9e3..b21a88cc 100644 --- a/wqflask/wqflask/submit_bnw.py +++ b/wqflask/wqflask/submit_bnw.py @@ -5,5 +5,6 @@ from utility import helper_functions import utility.logger logger = utility.logger.getLogger(__name__) + def get_bnw_input(start_vars): logger.debug("BNW VARS:", start_vars) diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py index 08b4f9f5..07073d6a 100644 --- a/wqflask/wqflask/update_search_results.py +++ b/wqflask/wqflask/update_search_results.py @@ -10,6 +10,7 @@ from utility.benchmark import Bench from utility.logger import getLogger logger = getLogger(__name__) + class GSearch: def __init__(self, kw): diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py index 3f5b43ee..2a2f8484 100644 --- a/wqflask/wqflask/user_login.py +++ b/wqflask/wqflask/user_login.py @@ -29,9 +29,11 @@ from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_AL THREE_DAYS = 60 * 60 * 24 * 3 + def timestamp(): return datetime.datetime.utcnow().isoformat() + def basic_info(): return dict(timestamp=timestamp(), ip_address=request.remote_addr, @@ -54,6 +56,7 @@ def encode_password(pass_gen_fields, unencrypted_password): return pass_gen_fields + def set_password(password): pass_gen_fields = { "unencrypted_password": password, @@ -71,6 +74,7 @@ def set_password(password): return encoded_password + def get_signed_session_id(user): session_id = str(uuid.uuid4()) @@ -109,6 +113,7 @@ def get_signed_session_id(user): return session_id_signed + def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"): """Send an E-mail through SMTP_CONNECT host. If SMTP_USERNAME is not 'UNKNOWN' TLS is used @@ -125,6 +130,7 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"): server.quit() logger.info("Successfully sent email to " + toaddr) + def send_verification_email(user_details, template_name="email/user_verification.txt", key_prefix="verification_code", subject = "GeneNetwork e-mail verification"): verification_code = str(uuid.uuid4()) key = key_prefix + ":" + verification_code @@ -139,12 +145,14 @@ def send_verification_email(user_details, template_name="email/user_verification send_email(recipient, subject, body) return {"recipient": recipient, "subject": subject, "body": body} + def send_invitation_email(user_email, temp_password, template_name="email/user_invitation.txt", subject= "You've been added to a GeneNetwork user group"): recipient = user_email body = render_template(template_name, temp_password) send_email(recipient, subject, body) return {"recipient": recipient, "subject": subject, "body": body} + @app.route("/manage/verify_email") def verify_email(): if 'code' in request.args: @@ -160,6 +168,7 @@ def verify_email(): else: flash("Invalid code: Password reset code does not exist or might have expired!", "error") + @app.route("/n/login", methods=('GET', 'POST')) def login(): params = request.form if request.form else request.args @@ -232,6 +241,7 @@ def login(): return response + @app.route("/n/login/github_oauth2", methods=('GET', 'POST')) def github_oauth2(): from utility.tools import GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET, GITHUB_AUTH_URL @@ -264,12 +274,14 @@ def github_oauth2(): url = "/n/login?type=github&uid=" + user_details["user_id"] return redirect(url) + def get_github_user_details(access_token): from utility.tools import GITHUB_API_URL result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content return json.loads(result) + @app.route("/n/login/orcid_oauth2", methods=('GET', 'POST')) def orcid_oauth2(): from uuid import uuid4 @@ -308,6 +320,7 @@ def orcid_oauth2(): flash("There was an error getting code from ORCID") return redirect(url) + def get_github_user_details(access_token): from utility.tools import GITHUB_API_URL result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content @@ -325,6 +338,7 @@ def logout(): response.set_cookie(UserSession.user_cookie_name, '', expires=0) return response + @app.route("/n/forgot_password", methods=['GET']) def forgot_password(): """Entry point for forgotten password""" @@ -333,6 +347,7 @@ def forgot_password(): print("ERRORS: ", errors) return render_template("new_security/forgot_password.html", errors=errors) + def send_forgot_password_email(verification_email): from email.mime.multipart import MIMEMultipart from email.mime.text import MIMEText @@ -365,6 +380,7 @@ def send_forgot_password_email(verification_email): return subject + @app.route("/n/forgot_password_submit", methods=('POST',)) def forgot_password_submit(): """When a forgotten password form is submitted we get here""" @@ -386,6 +402,7 @@ def forgot_password_submit(): flash("You MUST provide an email", "alert-danger") return redirect(url_for("forgot_password")) + @app.route("/n/password_reset", methods=['GET']) def password_reset(): """Entry point after user clicks link in E-mail""" @@ -405,6 +422,7 @@ def password_reset(): else: return redirect(url_for("login")) + @app.route("/n/password_reset_step2", methods=('POST',)) def password_reset_step2(): """Handle confirmation E-mail for password reset""" @@ -422,6 +440,7 @@ def password_reset_step2(): flash("Password changed successfully. You can now sign in.", "alert-info") return redirect(url_for('login')) + def register_user(params): thank_you_mode = False errors = [] @@ -461,6 +480,7 @@ def register_user(params): return errors + @app.route("/n/register", methods=('GET', 'POST')) def register(): errors = [] @@ -478,6 +498,7 @@ def register(): return render_template("new_security/register_user.html", values=params, errors=errors) + @app.errorhandler(401) def unauthorized(error): return redirect(url_for('login')) diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index 013920f9..a9bd65e6 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -151,6 +151,7 @@ def verify_cookie(cookie): assert the_signature == actual_hmac_creation(the_uuid), "Uh-oh, someone tampering with the cookie?" return the_uuid + def create_signed_cookie(): the_uuid = str(uuid.uuid4()) signature = actual_hmac_creation(the_uuid) @@ -158,6 +159,7 @@ def create_signed_cookie(): logger.debug("uuid_signed:", uuid_signed) return the_uuid, uuid_signed + class UserSession: """Logged in user handling""" @@ -341,6 +343,7 @@ class UserSession: Redis.delete(self.cookie_name) logger.debug("At end of delete_session") + @app.before_request def get_cookie(): logger.info("@app.before_request get cookie") @@ -348,16 +351,20 @@ def get_cookie(): g.cookie_session = AnonUser() # @app.after_request + + def set_cookie(response): if not request.cookies.get(g.cookie_session.cookie_name): response.set_cookie(g.cookie_session.cookie_name, g.cookie_session.cookie) return response + class UsersManager: def __init__(self): self.users = model.User.query.all() logger.debug("Users are:", self.users) + class UserManager: def __init__(self, kw): self.user_id = kw['user_id'] @@ -419,6 +426,7 @@ class RegisterUser: self.user.registration_info = json.dumps(basic_info(), sort_keys=True) save_user(self.user.__dict__, self.user.user_id) + def set_password(password, user): pwfields = Bunch() @@ -476,6 +484,7 @@ class VerificationEmail: verification_code=verification_code) send_email(to, subject, body) + class ForgotPasswordEmail(VerificationEmail): template_name = "email/forgot_password.txt" key_prefix = "forgot_password_code" @@ -496,7 +505,6 @@ class ForgotPasswordEmail(VerificationEmail): save_verification_code(toaddr, verification_code) - subject = self.subject body = render_template( self.template_name, @@ -530,6 +538,8 @@ def basic_info(): user_agent=request.headers.get('User-Agent')) # @app.route("/manage/verify_email") + + def verify_email(): user = DecodeUser(VerificationEmail.key_prefix).user user.confirmed = json.dumps(basic_info(), sort_keys=True) @@ -544,6 +554,8 @@ def verify_email(): return response # @app.route("/n/password_reset", methods=['GET']) + + def password_reset(): """Entry point after user clicks link in E-mail""" logger.debug("in password_reset request.url is:", request.url) @@ -568,6 +580,8 @@ def password_reset(): return redirect(url_for("login")) # @app.route("/n/password_reset_step2", methods=('POST',)) + + def password_reset_step2(): """Handle confirmation E-mail for password reset""" logger.debug("in password_reset request.url is:", request.url) @@ -577,7 +591,6 @@ def password_reset_step2(): logger.debug("locals are:", locals()) - user = Bunch() password = request.form['password'] set_password(password, user) @@ -589,6 +602,7 @@ def password_reset_step2(): return response + class DecodeUser: def __init__(self, code_prefix): @@ -612,6 +626,8 @@ class DecodeUser: return model.User.query.get(data['id']) # @app.route("/n/login", methods=('GET', 'POST')) + + def login(): lu = LoginUser() login_type = request.args.get("type") @@ -622,6 +638,8 @@ def login(): return lu.standard_login() # @app.route("/n/login/github_oauth2", methods=('GET', 'POST')) + + def github_oauth2(): from utility.tools import GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET code = request.args.get("code") @@ -646,6 +664,8 @@ def github_oauth2(): return redirect(url) # @app.route("/n/login/orcid_oauth2", methods=('GET', 'POST')) + + def orcid_oauth2(): from uuid import uuid4 from utility.tools import ORCID_CLIENT_ID, ORCID_CLIENT_SECRET, ORCID_TOKEN_URL, ORCID_AUTH_URL @@ -673,11 +693,13 @@ def orcid_oauth2(): flash("There was an error getting code from ORCID") return redirect(url) + def get_github_user_details(access_token): from utility.tools import GITHUB_API_URL result = requests.get(GITHUB_API_URL, params={"access_token": access_token}) return result.json() + class LoginUser: remember_time = 60 * 60 * 24 * 30 # One month in seconds @@ -814,6 +836,8 @@ class LoginUser: db_session.commit() # @app.route("/n/logout") + + def logout(): logger.debug("Logging out...") UserSession().delete_session() @@ -833,6 +857,8 @@ def forgot_password(): return render_template("new_security/forgot_password.html", errors=errors) # @app.route("/n/forgot_password_submit", methods=('POST',)) + + def forgot_password_submit(): """When a forgotten password form is submitted we get here""" params = request.form @@ -853,10 +879,12 @@ def forgot_password_submit(): flash("You MUST provide an email", "alert-danger") return redirect(url_for("forgot_password")) + @app.errorhandler(401) def unauthorized(error): return redirect(url_for('login')) + def is_redis_available(): try: Redis.ping() @@ -922,7 +950,6 @@ def register(): params = None errors = None - params = request.form if request.form else request.args params = params.to_dict(flat=True) @@ -952,6 +979,7 @@ def url_for_hmac(endpoint, **values): combiner = "?" return url + combiner + "hm=" + hm + def data_hmac(stringy): """Takes arbitray data string and appends :hmac so we know data hasn't been tampered with""" return stringy + ":" + actual_hmac_creation(stringy) @@ -974,6 +1002,7 @@ def verify_url_hmac(url): assert hm == hmac, "Unexpected url (stage 3)" + def actual_hmac_creation(stringy): """Helper function to create the actual hmac""" @@ -986,6 +1015,7 @@ def actual_hmac_creation(stringy): hm = hm[:20] return hm + app.jinja_env.globals.update(url_for_hmac=url_for_hmac, data_hmac=data_hmac) @@ -998,6 +1028,7 @@ app.jinja_env.globals.update(url_for_hmac=url_for_hmac, # Body=body)) # Redis.rpush("mail_queue", msg) + def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"): """Send an E-mail through SMTP_CONNECT host. If SMTP_USERNAME is not 'UNKNOWN' TLS is used @@ -1020,6 +1051,7 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"): server.quit() logger.info("Successfully sent email to " + toaddr) + class GroupsManager: def __init__(self, kw): self.datasets = create_datasets_list() diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py index 78db7bd2..f0f0d60c 100644 --- a/wqflask/wqflask/user_session.py +++ b/wqflask/wqflask/user_session.py @@ -20,6 +20,7 @@ logger = getLogger(__name__) THREE_DAYS = 60 * 60 * 24 * 3 THIRTY_DAYS = 60 * 60 * 24 * 30 + @app.before_request def get_user_session(): logger.info("@app.before_request get_session") @@ -30,6 +31,7 @@ def get_user_session(): response.set_cookie('session_id_v2', '', expires=0) return response + @app.after_request def set_user_session(response): if hasattr(g, 'user_session'): @@ -37,6 +39,7 @@ def set_user_session(response): response.set_cookie(g.user_session.cookie_name, g.user_session.cookie) return response + def verify_cookie(cookie): the_uuid, separator, the_signature = cookie.partition(':') assert len(the_uuid) == 36, "Is session_id a uuid?" @@ -44,6 +47,7 @@ def verify_cookie(cookie): assert the_signature == hmac.hmac_creation(the_uuid), "Uh-oh, someone tampering with the cookie?" return the_uuid + def create_signed_cookie(): the_uuid = str(uuid.uuid4()) signature = hmac.hmac_creation(the_uuid) @@ -51,6 +55,7 @@ def create_signed_cookie(): logger.debug("uuid_signed:", uuid_signed) return the_uuid, uuid_signed + @app.route("/user/manage", methods=('GET', 'POST')) def manage_user(): params = request.form if request.form else request.args @@ -63,6 +68,7 @@ def manage_user(): return render_template("admin/manage_user.html", user_details=user_details) + class UserSession: """Logged in user handling""" -- cgit v1.2.3 From 03b6bcee689c1910bd850c6109cc37adc509cf5a Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 30 Apr 2021 12:45:59 +0300 Subject: autopep8: Fix E501 --- wqflask/base/data_set.py | 6 +- wqflask/base/mrna_assay_tissue_data.py | 3 +- wqflask/base/species.py | 3 +- wqflask/base/webqtlCaseData.py | 6 +- wqflask/db/webqtlDatabaseFunction.py | 6 +- wqflask/maintenance/convert_geno_to_bimbam.py | 21 +- wqflask/maintenance/gen_select_dataset.py | 6 +- .../maintenance/generate_kinship_from_bimbam.py | 13 +- wqflask/maintenance/geno_to_json.py | 3 +- wqflask/maintenance/quantile_normalize.py | 3 +- .../test_display_mapping_results.py | 3 +- .../marker_regression/test_gemma_mapping.py | 15 +- .../marker_regression/test_qtlreaper_mapping.py | 6 +- .../wqflask/marker_regression/test_rqtl_mapping.py | 3 +- .../wqflask/marker_regression/test_run_mapping.py | 3 +- wqflask/tests/unit/wqflask/test_server_side.py | 9 +- wqflask/tests/wqflask/show_trait/testSampleList.py | 3 +- .../tests/wqflask/show_trait/test_show_trait.py | 3 +- wqflask/utility/Plot.py | 9 +- wqflask/utility/benchmark.py | 9 +- wqflask/utility/corestats.py | 3 +- wqflask/utility/elasticsearch_tools.py | 6 +- wqflask/utility/gen_geno_ob.py | 12 +- wqflask/utility/genofile_parser.py | 3 +- wqflask/utility/logger.py | 3 +- wqflask/utility/redis_tools.py | 9 +- wqflask/utility/startup_config.py | 6 +- wqflask/utility/svg.py | 60 ++- wqflask/utility/tools.py | 12 +- wqflask/wqflask/api/correlation.py | 54 +- wqflask/wqflask/api/mapping.py | 15 +- wqflask/wqflask/api/router.py | 48 +- wqflask/wqflask/collect.py | 15 +- .../comparison_bar_chart/comparison_bar_chart.py | 6 +- wqflask/wqflask/correlation/corr_scatter_plot.py | 33 +- wqflask/wqflask/correlation/show_corr_results.py | 75 ++- .../wqflask/correlation_matrix/show_corr_matrix.py | 64 ++- wqflask/wqflask/ctl/ctl_analysis.py | 72 ++- wqflask/wqflask/do_search.py | 69 ++- wqflask/wqflask/docs.py | 6 +- wqflask/wqflask/export_traits.py | 24 +- wqflask/wqflask/external_tools/send_to_bnw.py | 6 +- .../wqflask/external_tools/send_to_geneweaver.py | 3 +- .../wqflask/external_tools/send_to_webgestalt.py | 3 +- wqflask/wqflask/group_manager.py | 24 +- wqflask/wqflask/gsearch.py | 41 +- wqflask/wqflask/heatmap/heatmap.py | 19 +- wqflask/wqflask/interval_analyst/GeneUtil.py | 9 +- .../marker_regression/display_mapping_results.py | 548 ++++++++++++++------- wqflask/wqflask/marker_regression/gemma_mapping.py | 3 +- wqflask/wqflask/marker_regression/plink_mapping.py | 9 +- .../wqflask/marker_regression/qtlreaper_mapping.py | 27 +- wqflask/wqflask/marker_regression/rqtl_mapping.py | 103 ++-- wqflask/wqflask/marker_regression/run_mapping.py | 126 +++-- wqflask/wqflask/model.py | 30 +- wqflask/wqflask/resource_manager.py | 9 +- wqflask/wqflask/search_results.py | 33 +- wqflask/wqflask/show_trait/SampleList.py | 24 +- wqflask/wqflask/show_trait/export_trait_data.py | 21 +- wqflask/wqflask/snp_browser/snp_browser.py | 150 ++++-- wqflask/wqflask/update_search_results.py | 9 +- wqflask/wqflask/user_login.py | 87 ++-- wqflask/wqflask/user_manager.py | 96 ++-- wqflask/wqflask/user_session.py | 28 +- 64 files changed, 1431 insertions(+), 705 deletions(-) (limited to 'wqflask/utility/gen_geno_ob.py') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index c14808d6..8ec0aaad 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -168,7 +168,8 @@ class DatasetType: results = g.db.execute(sql_query_mapping[t] % group_name).fetchone() if results: self.datasets[name] = dataset_name_mapping[t] - self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) + self.redis_instance.set( + "dataset_structure", json.dumps(self.datasets)) return True return None @@ -239,7 +240,8 @@ class Markers: for line in bimbam_fh: marker = {} marker['name'] = line.split(delimiter)[0].rstrip() - marker['Mb'] = float(line.split(delimiter)[1].rstrip()) / 1000000 + marker['Mb'] = float(line.split(delimiter)[ + 1].rstrip()) / 1000000 marker['chr'] = line.split(delimiter)[2].rstrip() markers.append(marker) diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index cbc05738..9bb29664 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -88,6 +88,7 @@ class MrnaAssayTissueData: if result.Symbol.lower() not in symbol_values_dict: symbol_values_dict[result.Symbol.lower()] = [result.value] else: - symbol_values_dict[result.Symbol.lower()].append(result.value) + symbol_values_dict[result.Symbol.lower()].append( + result.value) return symbol_values_dict diff --git a/wqflask/base/species.py b/wqflask/base/species.py index 44f133b5..e3c29916 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -55,4 +55,5 @@ class Chromosomes: results = g.db.execute(query).fetchall() for item in results: - self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length) + self.chromosomes[item.OrderId] = IndChromosome( + item.Name, item.Length) diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index 2d07ab9d..25b6cb8a 100644 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -34,12 +34,14 @@ class webqtlCaseData: def __init__(self, name, value=None, variance=None, num_cases=None, name2=None): self.name = name - self.name2 = name2 # Other name (for traits like BXD65a) + # Other name (for traits like BXD65a) + self.name2 = name2 self.value = value # Trait Value self.variance = variance # Trait Variance self.num_cases = num_cases # Number of individuals/cases self.extra_attributes = None - self.this_id = None # Set a sane default (can't be just "id" cause that's a reserved word) + # Set a sane default (can't be just "id" cause that's a reserved word) + self.this_id = None self.outlier = None # Not set to True/False until later def __repr__(self): diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py index 50ac06fd..29112949 100644 --- a/wqflask/db/webqtlDatabaseFunction.py +++ b/wqflask/db/webqtlDatabaseFunction.py @@ -36,13 +36,15 @@ def retrieve_species(group): """Get the species of a group (e.g. returns string "mouse" on "BXD" """ - result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group), "/cross/" + group + ".json", lambda r: (r["species"],))[0] + result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % ( + group), "/cross/" + group + ".json", lambda r: (r["species"],))[0] logger.debug("retrieve_species result:", result) return result def retrieve_species_id(group): - result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group), "/cross/" + group + ".json", lambda r: (r["species_id"],))[0] + result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % ( + group), "/cross/" + group + ".json", lambda r: (r["species_id"],))[0] logger.debug("retrieve_species_id result:", result) return result diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py index 5b2369c9..a1712500 100644 --- a/wqflask/maintenance/convert_geno_to_bimbam.py +++ b/wqflask/maintenance/convert_geno_to_bimbam.py @@ -83,7 +83,8 @@ class ConvertGenoFile: genotypes = row_items[2:] for item_count, genotype in enumerate(genotypes): if genotype.upper().strip() in self.configurations: - this_marker.genotypes.append(self.configurations[genotype.upper().strip()]) + this_marker.genotypes.append( + self.configurations[genotype.upper().strip()]) else: this_marker.genotypes.append("NA") @@ -106,9 +107,11 @@ class ConvertGenoFile: with open(self.output_files[2], "w") as snp_fh: for marker in self.markers: if self.mb_exists: - snp_fh.write(marker['name'] + ", " + str(int(float(marker['Mb']) * 1000000)) + ", " + marker['chr'] + "\n") + snp_fh.write( + marker['name'] + ", " + str(int(float(marker['Mb']) * 1000000)) + ", " + marker['chr'] + "\n") else: - snp_fh.write(marker['name'] + ", " + str(int(float(marker['cM']) * 1000000)) + ", " + marker['chr'] + "\n") + snp_fh.write( + marker['name'] + ", " + str(int(float(marker['cM']) * 1000000)) + ", " + marker['chr'] + "\n") def get_sample_list(self, row_contents): self.sample_list = [] @@ -160,10 +163,14 @@ class ConvertGenoFile: group_name = ".".join(input_file.split('.')[:-1]) if group_name == "HSNIH-Palmer": continue - geno_output_file = os.path.join(new_directory, group_name + "_geno.txt") - pheno_output_file = os.path.join(new_directory, group_name + "_pheno.txt") - snp_output_file = os.path.join(new_directory, group_name + "_snps.txt") - output_files = [geno_output_file, pheno_output_file, snp_output_file] + geno_output_file = os.path.join( + new_directory, group_name + "_geno.txt") + pheno_output_file = os.path.join( + new_directory, group_name + "_pheno.txt") + snp_output_file = os.path.join( + new_directory, group_name + "_snps.txt") + output_files = [geno_output_file, + pheno_output_file, snp_output_file] print("%s -> %s" % ( os.path.join(old_directory, input_file), geno_output_file)) convertob = ConvertGenoFile(input_file, output_files) diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 583a06e1..484336a6 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -120,14 +120,16 @@ def get_types(groups): else: if not phenotypes_exist(group_name) and not genotypes_exist(group_name): types[species].pop(group_name, None) - groups[species] = tuple(group for group in groups[species] if group[0] != group_name) + groups[species] = tuple( + group for group in groups[species] if group[0] != group_name) else: # ZS: This whole else statement might be unnecessary, need to check types_list = build_types(species, group_name) if len(types_list) > 0: types[species][group_name] = types_list else: types[species].pop(group_name, None) - groups[species] = tuple(group for group in groups[species] if group[0] != group_name) + groups[species] = tuple( + group for group in groups[species] if group[0] != group_name) return types diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py index 7cc60c9e..bed634fa 100644 --- a/wqflask/maintenance/generate_kinship_from_bimbam.py +++ b/wqflask/maintenance/generate_kinship_from_bimbam.py @@ -21,7 +21,9 @@ class GenerateKinshipMatrices: self.pheno_file = pheno_file def generate_kinship(self): - gemma_command = "/gnu/store/xhzgjr0jvakxv6h3blj8z496xjig69b0-profile/bin/gemma -g " + self.geno_file + " -p " + self.pheno_file + " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name + gemma_command = "/gnu/store/xhzgjr0jvakxv6h3blj8z496xjig69b0-profile/bin/gemma -g " + self.geno_file + \ + " -p " + self.pheno_file + \ + " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name print("command:", gemma_command) os.system(gemma_command) @@ -34,9 +36,12 @@ class GenerateKinshipMatrices: group_name = ".".join(input_file.split('.')[:-1]) if group_name == "HSNIH-Palmer": continue - geno_input_file = os.path.join(bimbam_dir, group_name + "_geno.txt") - pheno_input_file = os.path.join(bimbam_dir, group_name + "_pheno.txt") - convertob = GenerateKinshipMatrices(group_name, geno_input_file, pheno_input_file) + geno_input_file = os.path.join( + bimbam_dir, group_name + "_geno.txt") + pheno_input_file = os.path.join( + bimbam_dir, group_name + "_pheno.txt") + convertob = GenerateKinshipMatrices( + group_name, geno_input_file, pheno_input_file) try: convertob.generate_kinship() except EmptyConfigurations as why: diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py index ad3f2b72..7bdf2b53 100644 --- a/wqflask/maintenance/geno_to_json.py +++ b/wqflask/maintenance/geno_to_json.py @@ -100,7 +100,8 @@ class ConvertGenoFile: genotypes = row_items[2:] for item_count, genotype in enumerate(genotypes): if genotype.upper() in self.configurations: - this_marker.genotypes.append(self.configurations[genotype.upper()]) + this_marker.genotypes.append( + self.configurations[genotype.upper()]) else: this_marker.genotypes.append("NA") diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index 1896bc52..ac7689f5 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -34,7 +34,8 @@ def create_dataframe(input_file): with open(input_file) as f: ncols = len(f.readline().split("\t")) - input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols))) + input_array = np.loadtxt(open( + input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols))) return pd.DataFrame(input_array) # This function taken from https://github.com/ShawnLYU/Quantile_Normalize diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py index 219a6a29..f4869c45 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py @@ -39,7 +39,8 @@ class TestHtmlGenWrapper(unittest.TestCase): cgi="/testing/", enctype='multipart/form-data', name="formName", - submit=HtmlGenWrapper.create_input_tag(type_='hidden', name='Default_Name') + submit=HtmlGenWrapper.create_input_tag( + type_='hidden', name='Default_Name') ) test_image = HtmlGenWrapper.create_image_tag( src="test.png", diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py index f194c6c9..5cbaf0e0 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -70,7 +70,8 @@ class TestGemmaMapping(unittest.TestCase): ], vals=[], covariates="", use_loco=True) self.assertEqual(mock_os.system.call_count, 2) mock_gen_pheno_txt.assert_called_once() - mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR", True) + mock_parse_loco.assert_called_once_with( + dataset, "GP1_GWA_RRRRRR", True) mock_os.path.isfile.assert_called_once_with( ('/home/user/imgfile_output.assoc.txt')) self.assertEqual(mock_flat_files.call_count, 4) @@ -102,7 +103,8 @@ class TestGemmaMapping(unittest.TestCase): create_trait_side_effect = [] for i in range(4): - create_dataset_side_effect.append(AttributeSetter({"name": f'name_{i}'})) + create_dataset_side_effect.append( + AttributeSetter({"name": f'name_{i}'})) create_trait_side_effect.append( AttributeSetter({"data": [f'data_{i}']})) @@ -160,9 +162,12 @@ X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6""" results = parse_loco_output( this_dataset={}, gwa_output_filename=".xw/") expected_results = [ - {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, 'additive': 23.3, 'lod_score': 0.07058107428570727}, - {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, 'additive': 24.0, 'lod_score': 0.3010299956639812}, - {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, 'additive': 11.6, 'lod_score': 0.1549019599857432}, + {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, + 'additive': 23.3, 'lod_score': 0.07058107428570727}, + {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, + 'additive': 24.0, 'lod_score': 0.3010299956639812}, + {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, + 'additive': 11.6, 'lod_score': 0.1549019599857432}, {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}] self.assertEqual(expected_results, results) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py index 5cc8fd0f..c762982b 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py @@ -13,10 +13,12 @@ class TestQtlReaperMapping(unittest.TestCase): samples = ["S1", "S2", "S3", "S4","S5"] trait_filename = "trait_file" with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_pheno_txt_file(samples=samples, vals=vals, trait_filename=trait_filename) + gen_pheno_txt_file(samples=samples, vals=vals, + trait_filename=trait_filename) mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w") filehandler = mock_open() - write_calls = [mock.call('Trait\t'), mock.call('S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')] + write_calls = [mock.call('Trait\t'), mock.call( + 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')] filehandler.write.assert_has_calls(write_calls) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py index 6267ce9a..6996c275 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -20,7 +20,8 @@ class TestRqtlMapping(unittest.TestCase): def test_get_trait_data(self, mock_logger, mock_db): """test for getting trait data_type return True""" query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" - mock_db.db.execute.return_value.fetchone.return_value = ["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] + mock_db.db.execute.return_value.fetchone.return_value = [ + """{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] results = get_trait_data_type("traid_id") mock_db.db.execute.assert_called_with(query_value) self.assertEqual(results, "fer434f") diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py index a29d8cfb..78cd3be9 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py @@ -187,7 +187,8 @@ class TestRunMapping(unittest.TestCase): mock.call('Time/Date: 09/01/19 / 10:12:12\n'), mock.call('Population: Human GP1_\n'), mock.call( 'Data Set: dataser_1\n'), - mock.call('N Samples: 100\n'), mock.call('Transform - Quantile Normalized\n'), + mock.call('N Samples: 100\n'), mock.call( + 'Transform - Quantile Normalized\n'), mock.call('Gene Symbol: IGFI\n'), mock.call( 'Location: X1 @ 123313 Mb\n'), mock.call('Cofactors (dataset - trait):\n'), diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/wqflask/tests/unit/wqflask/test_server_side.py index 4f91d8ca..69977146 100644 --- a/wqflask/tests/unit/wqflask/test_server_side.py +++ b/wqflask/tests/unit/wqflask/test_server_side.py @@ -22,10 +22,13 @@ class TestServerSideTableTests(unittest.TestCase): {'first': 'c', 'second': 1, 'third': 'ss'}, ] headers = ['first', 'second', 'third'] - request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1', 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'} + request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1', + 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'} - test_page = ServerSideTable(rows_count, table_rows, headers, request_args).get_page() + test_page = ServerSideTable( + rows_count, table_rows, headers, request_args).get_page() self.assertEqual(test_page['sEcho'], '1') self.assertEqual(test_page['iTotalRecords'], 'nan') self.assertEqual(test_page['iTotalDisplayRecords'], '3') - self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, {'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}]) + self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, { + 'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}]) diff --git a/wqflask/tests/wqflask/show_trait/testSampleList.py b/wqflask/tests/wqflask/show_trait/testSampleList.py index 441a88a7..305586ce 100644 --- a/wqflask/tests/wqflask/show_trait/testSampleList.py +++ b/wqflask/tests/wqflask/show_trait/testSampleList.py @@ -13,4 +13,5 @@ class TestSampleList(unittest.TestCase): sorted_list_a = natural_sort(characters_list) sorted_list_b = natural_sort(names_list) self.assertEqual(sorted_list_a, ["a", "f", "g", "q", "s", "t", "z"]) - self.assertEqual(sorted_list_b, ["Dataset", "Sample", "publish", "temp1"]) + self.assertEqual( + sorted_list_b, ["Dataset", "Sample", "publish", "temp1"]) diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py index 24c3923e..63df2ba5 100644 --- a/wqflask/tests/wqflask/show_trait/test_show_trait.py +++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py @@ -72,7 +72,8 @@ class TestTraits(unittest.TestCase): mock_get.return_value = get_return_obj results = get_ncbi_summary(trait) mock_exists.assert_called_once() - mock_get.assert_called_once_with(f"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={trait.geneid}&retmode=json") + mock_get.assert_called_once_with( + f"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={trait.geneid}&retmode=json") self.assertEqual(results, "this is a summary of the geneid") diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index d35b2089..4f5691c1 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -178,7 +178,8 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab # draw drawing region im_drawer.rectangle( - xy=((xLeftOffset, yTopOffset), (xLeftOffset + plotWidth, yTopOffset + plotHeight)) + xy=((xLeftOffset, yTopOffset), + (xLeftOffset + plotWidth, yTopOffset + plotHeight)) ) # draw scale @@ -199,11 +200,13 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab y = yLow for i in range(int(stepY) + 1): yc = yTopOffset + plotHeight - (y - yLow) * yScale - im_drawer.line(xy=((xLeftOffset, yc), (xLeftOffset - 5, yc)), fill=axesColor) + im_drawer.line( + xy=((xLeftOffset, yc), (xLeftOffset - 5, yc)), fill=axesColor) strY = "%d" % y im_drawer.text( text=strY, - xy=(xLeftOffset - im_drawer.textsize(strY, font=scaleFont)[0] - 6, yc + 5), + xy=(xLeftOffset - im_drawer.textsize(strY, + font=scaleFont)[0] - 6, yc + 5), font=scaleFont) y += (yTop - yLow) / stepY diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py index 48ab1dc0..6ece2f21 100644 --- a/wqflask/utility/benchmark.py +++ b/wqflask/utility/benchmark.py @@ -19,7 +19,8 @@ class Bench: if self.name: logger.debug("Starting benchmark: %s" % (self.name)) else: - logger.debug("Starting benchmark at: %s [%i]" % (inspect.stack()[1][3], inspect.stack()[1][2])) + logger.debug("Starting benchmark at: %s [%i]" % ( + inspect.stack()[1][3], inspect.stack()[1][2])) self.start_time = time.time() def __exit__(self, type, value, traceback): @@ -33,11 +34,13 @@ class Bench: logger.info(" %s took: %f seconds" % (name, (time_taken))) if self.name: - Bench.entries[self.name] = Bench.entries.get(self.name, 0) + time_taken + Bench.entries[self.name] = Bench.entries.get( + self.name, 0) + time_taken @classmethod def report(cls): - total_time = sum((time_taken for time_taken in list(cls.entries.values()))) + total_time = sum( + (time_taken for time_taken in list(cls.entries.values()))) print("\nTiming report\n") for name, time_taken in list(cls.entries.items()): percent = int(round((time_taken / total_time) * 100)) diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py index 523280a1..da0a21db 100644 --- a/wqflask/utility/corestats.py +++ b/wqflask/utility/corestats.py @@ -65,7 +65,8 @@ class Stats: if len(self.sequence) < 1: value = None elif (percentile >= 100): - sys.stderr.write('ERROR: percentile must be < 100. you supplied: %s\n' % percentile) + sys.stderr.write( + 'ERROR: percentile must be < 100. you supplied: %s\n' % percentile) value = None else: element_idx = int(len(self.sequence) * (percentile / 100.0)) diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py index 9415cef0..55907dd5 100644 --- a/wqflask/utility/elasticsearch_tools.py +++ b/wqflask/utility/elasticsearch_tools.py @@ -49,7 +49,8 @@ from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT def test_elasticsearch_connection(): - es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True) + es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + \ + ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True) if not es.ping(): logger.warning("Elasticsearch is DOWN") @@ -88,7 +89,8 @@ def setup_users_index(es_connection): "type": "keyword"}}} es_connection.indices.create(index='users', ignore=400) - es_connection.indices.put_mapping(body=index_settings, index="users", doc_type="local") + es_connection.indices.put_mapping( + body=index_settings, index="users", doc_type="local") def get_user_by_unique_column(es, column_name, column_value, index="users", doc_type="local"): diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 24604e58..e619b7b6 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -38,13 +38,15 @@ class genotype: def read_rdata_output(self, qtl_results): # ZS: This is necessary because R/qtl requires centimorgan marker positions, which it normally gets from the .geno file, but that doesn't exist for HET3-ITP (which only has RData), so it needs to read in the marker cM positions from the results - self.chromosomes = [] # ZS: Overwriting since the .geno file's contents are just placeholders + # ZS: Overwriting since the .geno file's contents are just placeholders + self.chromosomes = [] this_chr = "" # ZS: This is so it can track when the chromosome changes as it iterates through markers chr_ob = None for marker in qtl_results: locus = Locus(self) - if (str(marker['chr']) != this_chr) and this_chr != "X": # ZS: This is really awkward but works as a temporary fix + # ZS: This is really awkward but works as a temporary fix + if (str(marker['chr']) != this_chr) and this_chr != "X": if this_chr != "": self.chromosomes.append(chr_ob) this_chr = str(marker['chr']) @@ -156,9 +158,11 @@ class Locus: try: self.cM = float(marker_row[geno_ob.cm_column]) except: - self.cM = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else 0 + self.cM = float( + marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else 0 try: - self.Mb = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None + self.Mb = float( + marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None except: self.Mb = self.cM diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py index 94a08c17..09100bd9 100644 --- a/wqflask/utility/genofile_parser.py +++ b/wqflask/utility/genofile_parser.py @@ -92,7 +92,8 @@ class ConvertGenoFile: genotypes = row_items[2:] for item_count, genotype in enumerate(genotypes): if genotype.upper().strip() in self.configurations: - this_marker.genotypes.append(self.configurations[genotype.upper().strip()]) + this_marker.genotypes.append( + self.configurations[genotype.upper().strip()]) else: print("WARNING:", genotype.upper()) this_marker.genotypes.append("NA") diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py index 47079818..d706e32a 100644 --- a/wqflask/utility/logger.py +++ b/wqflask/utility/logger.py @@ -151,5 +151,6 @@ def getLogger(name, level=None): else: logger.setLevel(LOG_LEVEL) - logger.info("Log level of " + name + " set to " + logging.getLevelName(logger.getEffectiveLevel())) + logger.info("Log level of " + name + " set to " + \ + logging.getLevelName(logger.getEffectiveLevel())) return gnlogger diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 8052035f..96a4be12 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -133,8 +133,10 @@ def get_user_groups(user_id): for key in groups_list: try: group_ob = json.loads(groups_list[key]) - group_admins = set([this_admin.encode('utf-8') if this_admin else None for this_admin in group_ob['admins']]) - group_members = set([this_member.encode('utf-8') if this_member else None for this_member in group_ob['members']]) + group_admins = set([this_admin.encode( + 'utf-8') if this_admin else None for this_admin in group_ob['admins']]) + group_members = set([this_member.encode( + 'utf-8') if this_member else None for this_member in group_ob['members']]) if user_id in group_admins: admin_group_ids.append(group_ob['id']) elif user_id in group_members: @@ -203,7 +205,8 @@ def get_groups_like_unique_column(column_name, column_value): if column_value in group_info[column_name]: matched_groups.append(group_info) else: - matched_groups.append(load_json_from_redis(group_list, column_value)) + matched_groups.append( + load_json_from_redis(group_list, column_value)) return matched_groups diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py index 92f944bc..05f8a2b0 100644 --- a/wqflask/utility/startup_config.py +++ b/wqflask/utility/startup_config.py @@ -28,7 +28,8 @@ def app_config(): port = get_setting_int("SERVER_PORT") if get_setting_bool("USE_GN_SERVER"): - print(("GN2 API server URL is [" + BLUE + get_setting("GN_SERVER_URL") + ENDC + "]")) + print( + ("GN2 API server URL is [" + BLUE + get_setting("GN_SERVER_URL") + ENDC + "]")) import requests page = requests.get(get_setting("GN_SERVER_URL")) if page.status_code != 200: @@ -37,4 +38,5 @@ def app_config(): # import utility.elasticsearch_tools as es # es.test_elasticsearch_connection() - print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE, str(port), ENDC, get_setting("WEBSERVER_URL")))) + print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % + (BLUE, str(port), ENDC, get_setting("WEBSERVER_URL")))) diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index f5ef81e1..8d2e13ab 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -239,19 +239,23 @@ class pathdata: def smbezier(self, x2, y2, x, y): """smooth bezier with xy2 to xy absolut""" - self.path.append('S' + str(x2) + ',' + str(y2) + ' ' + str(x) + ',' + str(y)) + self.path.append('S' + str(x2) + ',' + str(y2) + \ + ' ' + str(x) + ',' + str(y)) def relsmbezier(self, x2, y2, x, y): """smooth bezier with xy2 to xy relative""" - self.path.append('s' + str(x2) + ',' + str(y2) + ' ' + str(x) + ',' + str(y)) + self.path.append('s' + str(x2) + ',' + str(y2) + \ + ' ' + str(x) + ',' + str(y)) def qbezier(self, x1, y1, x, y): """quadratic bezier with xy1 to xy absolut""" - self.path.append('Q' + str(x1) + ',' + str(y1) + ' ' + str(x) + ',' + str(y)) + self.path.append('Q' + str(x1) + ',' + str(y1) + \ + ' ' + str(x) + ',' + str(y)) def relqbezier(self, x1, y1, x, y): """quadratic bezier with xy1 to xy relative""" - self.path.append('q' + str(x1) + ',' + str(y1) + ' ' + str(x) + ',' + str(y)) + self.path.append('q' + str(x1) + ',' + str(y1) + \ + ' ' + str(x) + ',' + str(y)) def smqbezier(self, x, y): """smooth quadratic bezier to xy absolut""" @@ -447,7 +451,8 @@ class rect(SVGelement): if width == None or height == None: raise ValueError('both height and width are required') - SVGelement.__init__(self, 'rect', {'width': width, 'height': height}, **args) + SVGelement.__init__( + self, 'rect', {'width': width, 'height': height}, **args) if x != None: self.attributes['x'] = x if y != None: @@ -545,7 +550,8 @@ class polyline(SVGelement): """ def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args): - SVGelement.__init__(self, 'polyline', {'points': _xypointlist(points)}, **args) + SVGelement.__init__(self, 'polyline', { + 'points': _xypointlist(points)}, **args) if fill != None: self.attributes['fill'] = fill if stroke_width != None: @@ -561,7 +567,8 @@ class polygon(SVGelement): """ def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args): - SVGelement.__init__(self, 'polygon', {'points': _xypointlist(points)}, **args) + SVGelement.__init__( + self, 'polygon', {'points': _xypointlist(points)}, **args) if fill != None: self.attributes['fill'] = fill if stroke_width != None: @@ -745,7 +752,8 @@ class image(SVGelement): def __init__(self, url, x=None, y=None, width=None,height=None,**args): if width == None or height == None: raise ValueError('both height and width are required') - SVGelement.__init__(self, 'image', {'xlink:href': url, 'width': width, 'height':height}, **args) + SVGelement.__init__( + self, 'image', {'xlink:href': url, 'width': width, 'height':height}, **args) if x != None: self.attributes['x'] = x if y != None: @@ -886,7 +894,8 @@ class script(SVGelement): """ def __init__(self, type, cdata=None, **args): - SVGelement.__init__(self, 'script', {'type': type}, cdata=cdata, **args) + SVGelement.__init__( + self, 'script', {'type': type}, cdata=cdata, **args) class animate(SVGelement): @@ -896,7 +905,8 @@ class animate(SVGelement): """ def __init__(self, attribute, fr=None, to=None, dur=None,**args): - SVGelement.__init__(self, 'animate', {'attributeName': attribute}, **args) + SVGelement.__init__( + self, 'animate', {'attributeName': attribute}, **args) if fr != None: self.attributes['from'] = fr if to != None: @@ -926,7 +936,8 @@ class animateTransform(SVGelement): """ def __init__(self, type=None, fr=None, to=None, dur=None,**args): - SVGelement.__init__(self, 'animateTransform', {'attributeName': 'transform'}, **args) + SVGelement.__init__(self, 'animateTransform', { + 'attributeName': 'transform'}, **args) # As far as I know the attributeName is always transform if type != None: self.attributes['type'] = type @@ -945,7 +956,8 @@ class animateColor(SVGelement): """ def __init__(self, attribute, type=None, fr=None, to=None,dur=None,**args): - SVGelement.__init__(self, 'animateColor', {'attributeName': attribute}, **args) + SVGelement.__init__(self, 'animateColor', { + 'attributeName': attribute}, **args) if type != None: self.attributes['type'] = type if fr != None: @@ -1020,11 +1032,13 @@ class drawing: import io xml = io.StringIO() xml.write("\n") - xml.write("\n" % (item, self.entity[item])) + xml.write("\n" % + (item, self.entity[item])) xml.write("]") xml.write(">\n") self.svg.toXml(0, xml) @@ -1042,7 +1056,8 @@ class drawing: else: if filename[-4:] == 'svgz': import gzip - f = gzip.GzipFile(filename=filename, mode="wb", compresslevel=9) + f = gzip.GzipFile(filename=filename, + mode="wb", compresslevel=9) f.write(xml.getvalue()) f.close() else: @@ -1057,7 +1072,8 @@ class drawing: writes a svg drawing to the screen or to a file compresses if filename ends with svgz or if compress is true """ - doctype = implementation.createDocumentType('svg', "-//W3C//DTD SVG 1.0//EN""", 'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ') + doctype = implementation.createDocumentType( + 'svg', "-//W3C//DTD SVG 1.0//EN""", 'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ') global root # root is defined global so it can be used by the appender. Its also possible to use it as an arugument but @@ -1076,8 +1092,10 @@ class drawing: if element.text: textnode = root.createTextNode(element.text) e.appendChild(textnode) - for attribute in list(element.attributes.keys()): # in element.attributes is supported from python 2.2 - e.setAttribute(attribute, str(element.attributes[attribute])) + # in element.attributes is supported from python 2.2 + for attribute in list(element.attributes.keys()): + e.setAttribute(attribute, str( + element.attributes[attribute])) if element.elements: for el in element.elements: e = appender(el, e) @@ -1105,7 +1123,8 @@ class drawing: import io xml = io.StringIO() PrettyPrint(root, xml) - f = gzip.GzipFile(filename=filename, mode='wb', compresslevel=9) + f = gzip.GzipFile(filename=filename, + mode='wb', compresslevel=9) f.write(xml.getvalue()) f.close() else: @@ -1119,7 +1138,8 @@ class drawing: try: import xml.parsers.xmlproc.xmlval except: - raise exceptions.ImportError('PyXml is required for validating SVG') + raise exceptions.ImportError( + 'PyXml is required for validating SVG') svg = self.toXml() xv = xml.parsers.xmlproc.xmlval.XMLValidator() try: diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 4fe4db08..263c3948 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -64,7 +64,8 @@ def get_setting(command_id, guess=None): command = value(guess) if command is None or command == "": # print command - raise Exception(command_id + ' setting unknown or faulty (update default_settings.py?).') + raise Exception( + command_id + ' setting unknown or faulty (update default_settings.py?).') # print("Set "+command_id+"="+str(command)) return command @@ -113,7 +114,8 @@ def js_path(module=None): try_guix = get_setting("JS_GUIX_PATH") + "/" + module if valid_path(try_guix): return try_guix - raise "No JS path found for " + module + " (if not in Guix check JS_GN_PATH)" + raise "No JS path found for " + module + \ + " (if not in Guix check JS_GN_PATH)" def reaper_command(guess=None): @@ -292,7 +294,8 @@ ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET') ORCID_AUTH_URL = None if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET: ORCID_AUTH_URL = "https://orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \ - ORCID_CLIENT_ID + "&client_secret=" + ORCID_CLIENT_SECRET + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2" + ORCID_CLIENT_ID + "&client_secret=" + ORCID_CLIENT_SECRET + \ + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2" ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL') ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST') @@ -320,7 +323,8 @@ assert_dir(JS_GUIX_PATH + '/cytoscape-panzoom') CSS_PATH = JS_GUIX_PATH # The CSS is bundled together with the JS # assert_dir(JS_PATH) -JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH", js_path("javascript-twitter-post-fetcher")) +JS_TWITTER_POST_FETCHER_PATH = get_setting( + "JS_TWITTER_POST_FETCHER_PATH", js_path("javascript-twitter-post-fetcher")) assert_dir(JS_TWITTER_POST_FETCHER_PATH) assert_file(JS_TWITTER_POST_FETCHER_PATH + "/js/twitterFetcher_min.js") diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py index f1dd148f..52026a82 100644 --- a/wqflask/wqflask/api/correlation.py +++ b/wqflask/wqflask/api/correlation.py @@ -25,13 +25,16 @@ def do_correlation(start_vars): assert('trait_id' in start_vars) this_dataset = data_set.create_dataset(dataset_name=start_vars['db']) - target_dataset = data_set.create_dataset(dataset_name=start_vars['target_db']) - this_trait = create_trait(dataset=this_dataset, name=start_vars['trait_id']) + target_dataset = data_set.create_dataset( + dataset_name=start_vars['target_db']) + this_trait = create_trait(dataset=this_dataset, + name=start_vars['trait_id']) this_trait = retrieve_sample_data(this_trait, this_dataset) corr_params = init_corr_params(start_vars) - corr_results = calculate_results(this_trait, this_dataset, target_dataset, corr_params) + corr_results = calculate_results( + this_trait, this_dataset, target_dataset, corr_params) #corr_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0]))) final_results = [] @@ -75,54 +78,66 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params): if corr_params['type'] == "tissue": trait_symbol_dict = this_dataset.retrieve_genes("Symbol") - corr_results = do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params) + corr_results = do_tissue_correlation_for_all_traits( + this_trait, trait_symbol_dict, corr_params) sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][1]))) - elif corr_params['type'] == "literature" or corr_params['type'] == "lit": # ZS: Just so a user can use either "lit" or "literature" + # ZS: Just so a user can use either "lit" or "literature" + elif corr_params['type'] == "literature" or corr_params['type'] == "lit": trait_geneid_dict = this_dataset.retrieve_genes("GeneId") - corr_results = do_literature_correlation_for_all_traits(this_trait, this_dataset, trait_geneid_dict, corr_params) + corr_results = do_literature_correlation_for_all_traits( + this_trait, this_dataset, trait_geneid_dict, corr_params) sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][1]))) else: for target_trait, target_vals in list(target_dataset.trait_data.items()): - result = get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, corr_params['type']) + result = get_sample_r_and_p_values( + this_trait, this_dataset, target_vals, target_dataset, corr_params['type']) if result is not None: corr_results[target_trait] = result - sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][0]))) + sorted_results = collections.OrderedDict( + sorted(list(corr_results.items()), key=lambda t: -abs(t[1][0]))) return sorted_results def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params, tissue_dataset_id=1): # Gets tissue expression values for the primary trait - primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=[this_trait.symbol]) + primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( + symbol_list=[this_trait.symbol]) if this_trait.symbol.lower() in primary_trait_tissue_vals_dict: - primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower()] + primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower( + )] - corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=list(trait_symbol_dict.values())) + corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( + symbol_list=list(trait_symbol_dict.values())) tissue_corr_data = {} for trait, symbol in list(trait_symbol_dict.items()): if symbol and symbol.lower() in corr_result_tissue_vals_dict: - this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()] + this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower( + )] result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values, this_trait_tissue_values, corr_params['method']) - tissue_corr_data[trait] = [result[0], result[1], result[2], symbol] + tissue_corr_data[trait] = [ + result[0], result[1], result[2], symbol] return tissue_corr_data def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_geneid_dict, corr_params): - input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid) + input_trait_mouse_gene_id = convert_to_mouse_gene_id( + target_dataset.group.species.lower(), this_trait.geneid) lit_corr_data = {} for trait, gene_id in list(trait_geneid_dict.items()): - mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), gene_id) + mouse_gene_id = convert_to_mouse_gene_id( + target_dataset.group.species.lower(), gene_id) if mouse_gene_id and str(mouse_gene_id).find(";") == -1: result = g.db.execute( @@ -168,12 +183,15 @@ def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_data this_trait_vals.append(this_sample_value) shared_target_vals.append(target_sample_value) - this_trait_vals, shared_target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, shared_target_vals) + this_trait_vals, shared_target_vals, num_overlap = corr_result_helpers.normalize_values( + this_trait_vals, shared_target_vals) if type == 'pearson': - sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, shared_target_vals) + sample_r, sample_p = scipy.stats.pearsonr( + this_trait_vals, shared_target_vals) else: - sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, shared_target_vals) + sample_r, sample_p = scipy.stats.spearmanr( + this_trait_vals, shared_target_vals) if num_overlap > 5: if scipy.isnan(sample_r): diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py index 662090d5..c22b44a9 100644 --- a/wqflask/wqflask/api/mapping.py +++ b/wqflask/wqflask/api/mapping.py @@ -37,20 +37,25 @@ def do_mapping_for_api(start_vars): mapping_params = initialize_parameters(start_vars, dataset, this_trait) - covariates = "" # ZS: It seems to take an empty string as default. This should probably be changed. + # ZS: It seems to take an empty string as default. This should probably be changed. + covariates = "" if mapping_params['mapping_method'] == "gemma": header_row = ["name", "chr", "Mb", "lod_score", "p_value"] - if mapping_params['use_loco'] == "True": # ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api - result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0] + # ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api + if mapping_params['use_loco'] == "True": + result_markers = gemma_mapping.run_gemma( + this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0] else: - result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf']) + result_markers = gemma_mapping.run_gemma( + this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf']) elif mapping_params['mapping_method'] == "rqtl": header_row = ["name", "chr", "cM", "lod_score"] if mapping_params['num_perm'] > 0: _sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], mapping_params['perm_check'], mapping_params['num_perm'], - mapping_params['do_control'], mapping_params['control_marker'], + mapping_params['do_control'], mapping_params[ + 'control_marker'], mapping_params['manhattan_plot'], mapping_params['pair_scan']) else: result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 4f9cc6e5..e7dfa4e0 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -35,7 +35,8 @@ def hello_world(): @app.route("/api/v_{}/species".format(version)) def get_species_list(): - results = g.db.execute("SELECT SpeciesId, Name, FullName, TaxonomyId FROM Species;") + results = g.db.execute( + "SELECT SpeciesId, Name, FullName, TaxonomyId FROM Species;") the_species = results.fetchall() species_list = [] for species in the_species: @@ -313,7 +314,8 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"): @app.route("/api/v_{}/traits/".format(version), methods=("GET",)) @app.route("/api/v_{}/traits/.".format(version), methods=("GET",)) def fetch_traits(dataset_name, file_format="json"): - trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name, request.args) + trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids( + dataset_name, request.args) if ("ids_only" in request.args) and (len(trait_ids) > 0): if file_format == "json": filename = dataset_name + "_trait_ids.json" @@ -361,7 +363,8 @@ def fetch_traits(dataset_name, file_format="json"): ProbeSet.Id """ - field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb", "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"] + field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb", + "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"] elif data_type == "Geno": query = """ SELECT @@ -378,7 +381,8 @@ def fetch_traits(dataset_name, file_format="json"): Geno.Id """ - field_list = ["Id", "Name", "Marker_Name", "Chr", "Mb", "Sequence", "Source"] + field_list = ["Id", "Name", "Marker_Name", + "Chr", "Mb", "Sequence", "Source"] else: query = """ SELECT @@ -394,7 +398,8 @@ def fetch_traits(dataset_name, file_format="json"): PublishXRef.Id """ - field_list = ["Id", "PhenotypeId", "PublicationId", "Locus", "LRS", "Additive", "Sequence"] + field_list = ["Id", "PhenotypeId", "PublicationId", + "Locus", "LRS", "Additive", "Sequence"] if 'limit_to' in request.args: limit_number = request.args['limit_to'] @@ -442,7 +447,8 @@ def fetch_traits(dataset_name, file_format="json"): @app.route("/api/v_{}/sample_data/".format(version)) @app.route("/api/v_{}/sample_data/.".format(version)) def all_sample_data(dataset_name, file_format="csv"): - trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name, request.args) + trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids( + dataset_name, request.args) if len(trait_ids) > 0: sample_list = get_samplelist(dataset_name) @@ -676,7 +682,8 @@ def get_trait_info(dataset_name, trait_name, file_format="json"): return flask.jsonify(trait_dict) else: - if "Publish" in dataset_name: # ZS: Check if the user input the dataset_name as BXDPublish, etc (which is always going to be the group name + "Publish" + # ZS: Check if the user input the dataset_name as BXDPublish, etc (which is always going to be the group name + "Publish" + if "Publish" in dataset_name: dataset_name = dataset_name.replace("Publish", "") group_id = get_group_id(dataset_name) @@ -711,7 +718,8 @@ def get_corr_results(): results = correlation.do_correlation(request.args) if len(results) > 0: - return flask.jsonify(results) # ZS: I think flask.jsonify expects a dict/list instead of JSON + # ZS: I think flask.jsonify expects a dict/list instead of JSON + return flask.jsonify(results) else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") @@ -768,7 +776,8 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): output_lines.append(line.split()) i += 1 - csv_writer = csv.writer(si, delimiter="\t", escapechar="\\", quoting = csv.QUOTE_NONE) + csv_writer = csv.writer( + si, delimiter="\t", escapechar="\\", quoting = csv.QUOTE_NONE) else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") elif file_format == "rqtl2": @@ -779,18 +788,23 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): filename = group_name if os.path.isfile("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name)): - yaml_file = json.load(open("{0}/{1}.json".format(flat_files("genotype/rqtl2"), group_name))) + yaml_file = json.load( + open("{0}/{1}.json".format(flat_files("genotype/rqtl2"), group_name))) yaml_file["geno"] = filename + "_geno.csv" yaml_file["gmap"] = filename + "_gmap.csv" yaml_file["pheno"] = filename + "_pheno.csv" config_file = [filename + ".json", json.dumps(yaml_file)] #config_file = [filename + ".yaml", open("{0}/{1}.yaml".format(flat_files("genotype/rqtl2"), group_name))] - geno_file = [filename + "_geno.csv", open("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name))] - gmap_file = [filename + "_gmap.csv", open("{0}/{1}_gmap.csv".format(flat_files("genotype/rqtl2"), group_name))] + geno_file = [filename + "_geno.csv", + open("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name))] + gmap_file = [filename + "_gmap.csv", + open("{0}/{1}_gmap.csv".format(flat_files("genotype/rqtl2"), group_name))] if dataset_name: - phenotypes = requests.get("http://gn2.genenetwork.org/api/v_pre1/sample_data/" + dataset_name) + phenotypes = requests.get( + "http://gn2.genenetwork.org/api/v_pre1/sample_data/" + dataset_name) else: - phenotypes = requests.get("http://gn2.genenetwork.org/api/v_pre1/sample_data/" + group_name + "Publish") + phenotypes = requests.get( + "http://gn2.genenetwork.org/api/v_pre1/sample_data/" + group_name + "Publish") with ZipFile(memory_file, 'w', compression=ZIP_DEFLATED) as zf: zf.writestr(config_file[0], config_file[1]) @@ -813,7 +827,8 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): for line in genofile: if limit_num and i >= limit_num: break - output_lines.append([line.strip() for line in line.split(",")]) + output_lines.append([line.strip() + for line in line.split(",")]) i += 1 csv_writer = csv.writer(si, delimiter=",") @@ -898,7 +913,8 @@ def get_dataset_trait_ids(dataset_name, start_vars): results = g.db.execute(query).fetchall() trait_ids = [result[0] for result in results] - trait_names = [str(result[2]) + "_" + str(result[1]) for result in results] + trait_names = [str(result[2]) + "_" + str(result[1]) + for result in results] return trait_ids, trait_names, data_type, dataset_id diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 61f73106..1fcf15f0 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -158,7 +158,8 @@ def remove_traits(): traits_to_remove = params['trait_list'] traits_to_remove = process_traits(traits_to_remove) - members_now = g.user_session.remove_traits_from_collection(uc_id, traits_to_remove) + members_now = g.user_session.remove_traits_from_collection( + uc_id, traits_to_remove) return redirect(url_for("view_collection", uc_id=uc_id)) @@ -181,7 +182,8 @@ def delete_collection(): else: flash("We've deleted the selected collection.", "alert-info") else: - flash("We've deleted the collection: {}.".format(collection_name), "alert-info") + flash("We've deleted the collection: {}.".format( + collection_name), "alert-info") return redirect(url_for('list_collections')) @@ -191,7 +193,8 @@ def view_collection(): params = request.args uc_id = params['uc_id'] - uc = next((collection for collection in g.user_session.user_collections if collection["id"] == uc_id)) + uc = next( + (collection for collection in g.user_session.user_collections if collection["id"] == uc_id)) traits = uc["members"] trait_obs = [] @@ -203,12 +206,14 @@ def view_collection(): name, dataset_name = atrait.split(':') if dataset_name == "Temp": group = name.split("_")[2] - dataset = create_dataset(dataset_name, dataset_type="Temp", group_name=group) + dataset = create_dataset( + dataset_name, dataset_type="Temp", group_name=group) trait_ob = create_trait(name=name, dataset=dataset) else: dataset = create_dataset(dataset_name) trait_ob = create_trait(name=name, dataset=dataset) - trait_ob = retrieve_trait_info(trait_ob, dataset, get_qtl_info=True) + trait_ob = retrieve_trait_info( + trait_ob, dataset, get_qtl_info=True) trait_obs.append(trait_ob) json_version.append(jsonable(trait_ob)) diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py index c135faa3..0fabb833 100644 --- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py +++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py @@ -34,14 +34,16 @@ from flask import Flask, g class ComparisonBarChart: def __init__(self, start_vars): - trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] + trait_db_list = [trait.strip() + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) self.all_sample_list = [] self.traits = [] self.insufficient_shared_samples = False - this_group = self.trait_list[0][1].group.name # ZS: Getting initial group name before verifying all traits are in the same group in the following loop + # ZS: Getting initial group name before verifying all traits are in the same group in the following loop + this_group = self.trait_list[0][1].group.name for trait_db in self.trait_list: if trait_db[1].group.name != this_group: diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 6afea715..f9a0ea11 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -17,17 +17,21 @@ class CorrScatterPlot: def __init__(self, params): if "Temp" in params['dataset_1']: - self.dataset_1 = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_1'].split("_")[1]) + self.dataset_1 = data_set.create_dataset( + dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_1'].split("_")[1]) else: self.dataset_1 = data_set.create_dataset(params['dataset_1']) if "Temp" in params['dataset_2']: - self.dataset_2 = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_2'].split("_")[1]) + self.dataset_2 = data_set.create_dataset( + dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_2'].split("_")[1]) else: self.dataset_2 = data_set.create_dataset(params['dataset_2']) #self.dataset_3 = data_set.create_dataset(params['dataset_3']) - self.trait_1 = create_trait(name=params['trait_1'], dataset=self.dataset_1) - self.trait_2 = create_trait(name=params['trait_2'], dataset=self.dataset_2) + self.trait_1 = create_trait( + name=params['trait_1'], dataset=self.dataset_1) + self.trait_2 = create_trait( + name=params['trait_2'], dataset=self.dataset_2) #self.trait_3 = create_trait(name=params['trait_3'], dataset=self.dataset_3) self.method = params['method'] @@ -38,10 +42,13 @@ class CorrScatterPlot: if self.dataset_1.group.f1list != None: primary_samples += self.dataset_1.group.f1list - self.trait_1 = retrieve_sample_data(self.trait_1, self.dataset_1, primary_samples) - self.trait_2 = retrieve_sample_data(self.trait_2, self.dataset_2, primary_samples) + self.trait_1 = retrieve_sample_data( + self.trait_1, self.dataset_1, primary_samples) + self.trait_2 = retrieve_sample_data( + self.trait_2, self.dataset_2, primary_samples) - samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(self.trait_1.data, self.trait_2.data) + samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples( + self.trait_1.data, self.trait_2.data) self.data = [] self.indIDs = list(samples_1.keys()) @@ -54,7 +61,8 @@ class CorrScatterPlot: vals_2.append(samples_2[sample].value) self.data.append(vals_2) - slope, intercept, r_value, p_value, std_err = stats.linregress(vals_1, vals_2) + slope, intercept, r_value, p_value, std_err = stats.linregress( + vals_1, vals_2) if slope < 0.001: slope_string = '%.3E' % slope @@ -67,14 +75,16 @@ class CorrScatterPlot: x_range = [min(vals_1) - x_buffer, max(vals_1) + x_buffer] y_range = [min(vals_2) - y_buffer, max(vals_2) + y_buffer] - intercept_coords = get_intercept_coords(slope, intercept, x_range, y_range) + intercept_coords = get_intercept_coords( + slope, intercept, x_range, y_range) rx = stats.rankdata(vals_1) ry = stats.rankdata(vals_2) self.rdata = [] self.rdata.append(rx.tolist()) self.rdata.append(ry.tolist()) - srslope, srintercept, srr_value, srp_value, srstd_err = stats.linregress(rx, ry) + srslope, srintercept, srr_value, srp_value, srstd_err = stats.linregress( + rx, ry) if srslope < 0.001: srslope_string = '%.3E' % srslope @@ -86,7 +96,8 @@ class CorrScatterPlot: sr_range = [min(rx) - x_buffer, max(rx) + x_buffer] - sr_intercept_coords = get_intercept_coords(srslope, srintercept, sr_range, sr_range) + sr_intercept_coords = get_intercept_coords( + srslope, srintercept, sr_range, sr_range) self.collections_exist = "False" if g.user_session.num_collections > 0: diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index e2fe1ff4..e75c4a85 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -78,7 +78,8 @@ class CorrelationResults: with Bench("Doing correlations"): if start_vars['dataset'] == "Temp": - self.dataset = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = start_vars['group']) + self.dataset = data_set.create_dataset( + dataset_name="Temp", dataset_type="Temp", group_name = start_vars['group']) self.trait_id = start_vars['trait_id'] self.this_trait = create_trait(dataset=self.dataset, name=self.trait_id, @@ -129,12 +130,15 @@ class CorrelationResults: if corr_samples_group == 'samples_other': primary_samples = [x for x in primary_samples if x not in ( self.dataset.group.parlist + self.dataset.group.f1list)] - self.process_samples(start_vars, list(self.this_trait.data.keys()), primary_samples) + self.process_samples(start_vars, list( + self.this_trait.data.keys()), primary_samples) - self.target_dataset = data_set.create_dataset(start_vars['corr_dataset']) + self.target_dataset = data_set.create_dataset( + start_vars['corr_dataset']) self.target_dataset.get_trait_data(list(self.sample_data.keys())) - self.header_fields = get_header_fields(self.target_dataset.type, self.corr_method) + self.header_fields = get_header_fields( + self.target_dataset.type, self.corr_method) if self.target_dataset.type == "ProbeSet": self.filter_cols = [7, 6] @@ -153,7 +157,8 @@ class CorrelationResults: tissue_corr_data = self.do_tissue_correlation_for_all_traits() if tissue_corr_data != None: for trait in list(tissue_corr_data.keys())[:self.return_number]: - self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait]) + self.get_sample_r_and_p_values( + trait, self.target_dataset.trait_data[trait]) else: for trait, values in list(self.target_dataset.trait_data.items()): self.get_sample_r_and_p_values(trait, values) @@ -163,7 +168,8 @@ class CorrelationResults: lit_corr_data = self.do_lit_correlation_for_all_traits() for trait in list(lit_corr_data.keys())[:self.return_number]: - self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait]) + self.get_sample_r_and_p_values( + trait, self.target_dataset.trait_data[trait]) elif self.corr_type == "sample": for trait, values in list(self.target_dataset.trait_data.items()): @@ -180,7 +186,8 @@ class CorrelationResults: range_chr_as_int = order_id for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]): - trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) + trait_object = create_trait( + dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) if not trait_object: continue @@ -235,7 +242,8 @@ class CorrelationResults: if self.corr_type != "tissue" and self.dataset.type == "ProbeSet" and self.target_dataset.type == "ProbeSet": self.do_tissue_correlation_for_trait_list() - self.json_results = generate_corr_json(self.correlation_results, self.this_trait, self.dataset, self.target_dataset) + self.json_results = generate_corr_json( + self.correlation_results, self.this_trait, self.dataset, self.target_dataset) ############################################################################################################################################ @@ -263,15 +271,18 @@ class CorrelationResults: symbol_list=[self.this_trait.symbol]) if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict: - primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()] - gene_symbol_list = [trait.symbol for trait in self.correlation_results if trait.symbol] + primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower( + )] + gene_symbol_list = [ + trait.symbol for trait in self.correlation_results if trait.symbol] corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( symbol_list=gene_symbol_list) for trait in self.correlation_results: if trait.symbol and trait.symbol.lower() in corr_result_tissue_vals_dict: - this_trait_tissue_values = corr_result_tissue_vals_dict[trait.symbol.lower()] + this_trait_tissue_values = corr_result_tissue_vals_dict[trait.symbol.lower( + )] result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values, this_trait_tissue_values, @@ -286,7 +297,8 @@ class CorrelationResults: symbol_list=[self.this_trait.symbol]) if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict: - primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()] + primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower( + )] #print("trait_gene_symbols: ", pf(trait_gene_symbols.values())) corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( @@ -299,7 +311,8 @@ class CorrelationResults: tissue_corr_data = {} for trait, symbol in list(self.trait_symbol_dict.items()): if symbol and symbol.lower() in corr_result_tissue_vals_dict: - this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()] + this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower( + )] result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values, this_trait_tissue_values, @@ -314,12 +327,14 @@ class CorrelationResults: def do_lit_correlation_for_trait_list(self): - input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid) + input_trait_mouse_gene_id = self.convert_to_mouse_gene_id( + self.dataset.group.species.lower(), self.this_trait.geneid) for trait in self.correlation_results: if trait.geneid: - trait.mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), trait.geneid) + trait.mouse_gene_id = self.convert_to_mouse_gene_id( + self.dataset.group.species.lower(), trait.geneid) else: trait.mouse_gene_id = None @@ -348,11 +363,13 @@ class CorrelationResults: trait.lit_corr = 0 def do_lit_correlation_for_all_traits(self): - input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid) + input_trait_mouse_gene_id = self.convert_to_mouse_gene_id( + self.dataset.group.species.lower(), self.this_trait.geneid) lit_corr_data = {} for trait, gene_id in list(self.trait_geneid_dict.items()): - mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), gene_id) + mouse_gene_id = self.convert_to_mouse_gene_id( + self.dataset.group.species.lower(), gene_id) if mouse_gene_id and str(mouse_gene_id).find(";") == -1: #print("gene_symbols:", input_trait_mouse_gene_id + " / " + mouse_gene_id) @@ -438,21 +455,26 @@ class CorrelationResults: self.this_trait_vals.append(sample_value) target_vals.append(target_sample_value) - self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(self.this_trait_vals, target_vals) + self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values( + self.this_trait_vals, target_vals) if num_overlap > 5: # ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/ if self.corr_method == 'bicor': - sample_r, sample_p = do_bicor(self.this_trait_vals, target_vals) + sample_r, sample_p = do_bicor( + self.this_trait_vals, target_vals) elif self.corr_method == 'pearson': - sample_r, sample_p = scipy.stats.pearsonr(self.this_trait_vals, target_vals) + sample_r, sample_p = scipy.stats.pearsonr( + self.this_trait_vals, target_vals) else: - sample_r, sample_p = scipy.stats.spearmanr(self.this_trait_vals, target_vals) + sample_r, sample_p = scipy.stats.spearmanr( + self.this_trait_vals, target_vals) if numpy.isnan(sample_r): pass else: - self.correlation_data[trait] = [sample_r, sample_p, num_overlap] + self.correlation_data[trait] = [ + sample_r, sample_p, num_overlap] def process_samples(self, start_vars, sample_names, excluded_samples=None): if not excluded_samples: @@ -478,7 +500,8 @@ def do_bicor(this_trait_vals, target_trait_vals): this_vals = ro.Vector(this_trait_vals) target_vals = ro.Vector(target_trait_vals) - the_r, the_p, _fisher_transform, _the_t, _n_obs = [numpy.asarray(x) for x in r_bicor(x=this_vals, y=target_vals)] + the_r, the_p, _fisher_transform, _the_t, _n_obs = [ + numpy.asarray(x) for x in r_bicor(x=this_vals, y=target_vals)] return the_r, the_p @@ -492,7 +515,8 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap results_dict['index'] = i + 1 results_dict['trait_id'] = trait.name results_dict['dataset'] = trait.dataset.name - results_dict['hmac'] = hmac.data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) + results_dict['hmac'] = hmac.data_hmac( + '{}:{}'.format(trait.name, trait.dataset.name)) if target_dataset.type == "ProbeSet": results_dict['symbol'] = trait.symbol results_dict['description'] = "N/A" @@ -543,7 +567,8 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap if bool(trait.authors): authors_list = trait.authors.split(',') if len(authors_list) > 6: - results_dict['authors_display'] = ", ".join(authors_list[:6]) + ", et al." + results_dict['authors_display'] = ", ".join( + authors_list[:6]) + ", et al." else: results_dict['authors_display'] = trait.authors if bool(trait.pubmed_id): diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 331cb1dc..aefb4453 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -44,7 +44,8 @@ THIRTY_DAYS = 60 * 60 * 24 * 30 class CorrelationMatrix: def __init__(self, start_vars): - trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] + trait_db_list = [trait.strip() + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) @@ -52,7 +53,8 @@ class CorrelationMatrix: self.traits = [] self.insufficient_shared_samples = False self.do_PCA = True - this_group = self.trait_list[0][1].group.name # ZS: Getting initial group name before verifying all traits are in the same group in the following loop + # ZS: Getting initial group name before verifying all traits are in the same group in the following loop + this_group = self.trait_list[0][1].group.name for trait_db in self.trait_list: this_group = trait_db[1].group.name this_trait = trait_db[0] @@ -76,10 +78,12 @@ class CorrelationMatrix: this_trait_vals.append('') self.sample_data.append(this_trait_vals) - if len(this_trait_vals) < len(self.trait_list): # Shouldn't do PCA if there are more traits than observations/samples + # Shouldn't do PCA if there are more traits than observations/samples + if len(this_trait_vals) < len(self.trait_list): self.do_PCA = False - self.lowest_overlap = 8 # ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning) + # ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning) + self.lowest_overlap = 8 self.corr_results = [] self.pca_corr_results = [] @@ -112,7 +116,8 @@ class CorrelationMatrix: if sample in self.shared_samples_list: self.shared_samples_list.remove(sample) - this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, target_vals) + this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values( + this_trait_vals, target_vals) if num_overlap < self.lowest_overlap: self.lowest_overlap = num_overlap @@ -120,21 +125,25 @@ class CorrelationMatrix: corr_result_row.append([target_trait, 0, num_overlap]) pca_corr_result_row.append(0) else: - pearson_r, pearson_p = scipy.stats.pearsonr(this_trait_vals, target_vals) + pearson_r, pearson_p = scipy.stats.pearsonr( + this_trait_vals, target_vals) if is_spearman == False: sample_r, sample_p = pearson_r, pearson_p if sample_r == 1: is_spearman = True else: - sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, target_vals) + sample_r, sample_p = scipy.stats.spearmanr( + this_trait_vals, target_vals) - corr_result_row.append([target_trait, sample_r, num_overlap]) + corr_result_row.append( + [target_trait, sample_r, num_overlap]) pca_corr_result_row.append(pearson_r) self.corr_results.append(corr_result_row) self.pca_corr_results.append(pca_corr_result_row) - self.export_filename, self.export_filepath = export_corr_matrix(self.corr_results) + self.export_filename, self.export_filepath = export_corr_matrix( + self.corr_results) self.trait_data_array = [] for trait_db in self.trait_list: @@ -156,12 +165,14 @@ class CorrelationMatrix: try: corr_result_eigen = np.linalg.eig(np.array(self.pca_corr_results)) - corr_eigen_value, corr_eigen_vectors = sortEigenVectors(corr_result_eigen) + corr_eigen_value, corr_eigen_vectors = sortEigenVectors( + corr_result_eigen) if self.do_PCA == True: self.pca_works = "True" self.pca_trait_ids = [] - pca = self.calculate_pca(list(range(len(self.traits))), corr_eigen_value, corr_eigen_vectors) + pca = self.calculate_pca( + list(range(len(self.traits))), corr_eigen_value, corr_eigen_vectors) self.loadings_array = self.process_loadings() else: self.pca_works = "False" @@ -179,7 +190,8 @@ class CorrelationMatrix: base = importr('base') stats = importr('stats') - corr_results_to_list = robjects.FloatVector([item for sublist in self.pca_corr_results for item in sublist]) + corr_results_to_list = robjects.FloatVector( + [item for sublist in self.pca_corr_results for item in sublist]) m = robjects.r.matrix(corr_results_to_list, nrow=len(cols)) eigen = base.eigen(m) @@ -198,10 +210,12 @@ class CorrelationMatrix: pca_traits.append((vector * -1.0).tolist()) this_group_name = self.trait_list[0][1].group.name - temp_dataset = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = this_group_name) + temp_dataset = data_set.create_dataset( + dataset_name="Temp", dataset_type="Temp", group_name = this_group_name) temp_dataset.group.get_samplelist() for i, pca_trait in enumerate(pca_traits): - trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S") + trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + \ + this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S") this_vals_string = "" position = 0 for sample in temp_dataset.group.all_samples_ordered(): @@ -235,17 +249,23 @@ class CorrelationMatrix: def export_corr_matrix(corr_results): - corr_matrix_filename = "corr_matrix_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) - matrix_export_path = "{}{}.csv".format(GENERATED_TEXT_DIR, corr_matrix_filename) + corr_matrix_filename = "corr_matrix_" + \ + ''.join(random.choice(string.ascii_uppercase + string.digits) + for _ in range(6)) + matrix_export_path = "{}{}.csv".format( + GENERATED_TEXT_DIR, corr_matrix_filename) with open(matrix_export_path, "w+") as output_file: - output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") + output_file.write( + "Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") output_file.write("\n") output_file.write("Correlation ") for i, item in enumerate(corr_results[0]): - output_file.write("Trait" + str(i + 1) + ": " + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t") + output_file.write("Trait" + str(i + 1) + ": " + \ + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t") output_file.write("\n") for i, row in enumerate(corr_results): - output_file.write("Trait" + str(i + 1) + ": " + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t") + output_file.write("Trait" + str(i + 1) + ": " + \ + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t") for item in row: output_file.write(str(item[1]) + "\t") output_file.write("\n") @@ -254,10 +274,12 @@ def export_corr_matrix(corr_results): output_file.write("\n") output_file.write("N ") for i, item in enumerate(corr_results[0]): - output_file.write("Trait" + str(i) + ": " + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t") + output_file.write("Trait" + str(i) + ": " + \ + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t") output_file.write("\n") for i, row in enumerate(corr_results): - output_file.write("Trait" + str(i) + ": " + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t") + output_file.write("Trait" + str(i) + ": " + \ + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t") for item in row: output_file.write(str(item[2]) + "\t") output_file.write("\n") diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index ec66e59f..48a82435 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -46,13 +46,18 @@ class CTL: #log = r_file("/tmp/genenetwork_ctl.log", open = "wt") # r_sink(log) # Uncomment the r_sink() commands to log output from stdout/stderr to a file #r_sink(log, type = "message") - r_library("ctl") # Load CTL - Should only be done once, since it is quite expensive + # Load CTL - Should only be done once, since it is quite expensive + r_library("ctl") r_options(stringsAsFactors=False) logger.info("Initialization of CTL done, package loaded in R session") - self.r_CTLscan = ro.r["CTLscan"] # Map the CTLscan function - self.r_CTLsignificant = ro.r["CTLsignificant"] # Map the CTLsignificant function - self.r_lineplot = ro.r["ctl.lineplot"] # Map the ctl.lineplot function - self.r_plotCTLobject = ro.r["plot.CTLobject"] # Map the CTLsignificant function + # Map the CTLscan function + self.r_CTLscan = ro.r["CTLscan"] + # Map the CTLsignificant function + self.r_CTLsignificant = ro.r["CTLsignificant"] + # Map the ctl.lineplot function + self.r_lineplot = ro.r["ctl.lineplot"] + # Map the CTLsignificant function + self.r_plotCTLobject = ro.r["plot.CTLobject"] self.nodes_list = [] self.edges_list = [] logger.info("Obtained pointers to CTL functions") @@ -81,7 +86,8 @@ class CTL: def run_analysis(self, requestform): logger.info("Starting CTL analysis on dataset") - self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')] + self.trait_db_list = [trait.strip() + for trait in requestform['trait_list'].split(',')] self.trait_db_list = [x for x in self.trait_db_list if x] logger.debug("strategy:", requestform.get("strategy")) @@ -113,9 +119,11 @@ class CTL: markers.append(marker["genotypes"]) genotypes = list(itertools.chain(*markers)) - logger.debug(len(genotypes) / len(individuals), "==", len(parser.markers)) + logger.debug(len(genotypes) / len(individuals), + "==", len(parser.markers)) - rGeno = r_t(ro.r.matrix(r_unlist(genotypes), nrow=len(markernames), ncol=len(individuals), dimnames=r_list(markernames, individuals), byrow=True)) + rGeno = r_t(ro.r.matrix(r_unlist(genotypes), nrow=len(markernames), ncol=len( + individuals), dimnames=r_list(markernames, individuals), byrow=True)) # Create a phenotype matrix traits = [] @@ -131,7 +139,8 @@ class CTL: else: traits.append("-999") - rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len(individuals), dimnames=r_list(self.trait_db_list, individuals), byrow=True)) + rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len( + individuals), dimnames=r_list(self.trait_db_list, individuals), byrow=True)) logger.debug(rPheno) @@ -144,7 +153,8 @@ class CTL: #r_write_table(rPheno, "~/outputGN/pheno.csv") # Perform the CTL scan - res = self.r_CTLscan(rGeno, rPheno, strategy=strategy, nperm=nperm, parametric = parametric, nthreads=6) + res = self.r_CTLscan(rGeno, rPheno, strategy=strategy, + nperm=nperm, parametric = parametric, nthreads=6) # Get significant interactions significant = self.r_CTLsignificant(res, significance=significance) @@ -155,20 +165,27 @@ class CTL: self.results['imgloc1'] = GENERATED_IMAGE_DIR + self.results['imgurl1'] self.results['ctlresult'] = significant - self.results['requestform'] = requestform # Store the user specified parameters for the output page + # Store the user specified parameters for the output page + self.results['requestform'] = requestform # Create the lineplot - r_png(self.results['imgloc1'], width=1000, height=600, type='cairo-png') + r_png(self.results['imgloc1'], width=1000, + height=600, type='cairo-png') self.r_lineplot(res, significance=significance) r_dev_off() - n = 2 # We start from 2, since R starts from 1 :) + # We start from 2, since R starts from 1 :) + n = 2 for trait in self.trait_db_list: # Create the QTL like CTL plots - self.results['imgurl' + str(n)] = webqtlUtil.genRandStr("CTL_") + ".png" - self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + self.results['imgurl' + str(n)] - r_png(self.results['imgloc' + str(n)], width=1000, height=600, type='cairo-png') - self.r_plotCTLobject(res, (n - 1), significance=significance, main='Phenotype ' + trait) + self.results['imgurl' + \ + str(n)] = webqtlUtil.genRandStr("CTL_") + ".png" + self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + \ + self.results['imgurl' + str(n)] + r_png(self.results['imgloc' + str(n)], + width=1000, height=600, type='cairo-png') + self.r_plotCTLobject( + res, (n - 1), significance=significance, main='Phenotype ' + trait) r_dev_off() n = n + 1 @@ -178,17 +195,24 @@ class CTL: # Create the interactive graph for cytoscape visualization (Nodes and Edges) if not isinstance(significant, ri.RNULLType): for x in range(len(significant[0])): - logger.debug(significant[0][x], significant[1][x], significant[2][x]) # Debug to console - tsS = significant[0][x].split(':') # Source - tsT = significant[2][x].split(':') # Target - gtS = create_trait(name=tsS[0], dataset_name=tsS[1]) # Retrieve Source info from the DB - gtT = create_trait(name=tsT[0], dataset_name=tsT[1]) # Retrieve Target info from the DB + logger.debug(significant[0][x], significant[1] + [x], significant[2][x]) # Debug to console + # Source + tsS = significant[0][x].split(':') + # Target + tsT = significant[2][x].split(':') + # Retrieve Source info from the DB + gtS = create_trait(name=tsS[0], dataset_name=tsS[1]) + # Retrieve Target info from the DB + gtT = create_trait(name=tsT[0], dataset_name=tsT[1]) self.addNode(gtS) self.addNode(gtT) self.addEdge(gtS, gtT, significant, x) - significant[0][x] = "{} ({})".format(gtS.symbol, gtS.name) # Update the trait name for the displayed table - significant[2][x] = "{} ({})".format(gtT.symbol, gtT.name) # Update the trait name for the displayed table + # Update the trait name for the displayed table + significant[0][x] = "{} ({})".format(gtS.symbol, gtS.name) + # Update the trait name for the displayed table + significant[2][x] = "{} ({})".format(gtT.symbol, gtT.name) self.elements = json.dumps(self.nodes_list + self.edges_list) diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 7442dc72..e50ff50b 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -26,14 +26,16 @@ class DoSearch: def __init__(self, search_term, search_operator=None, dataset=None, search_type=None): self.search_term = search_term # Make sure search_operator is something we expect - assert search_operator in (None, "=", "<", ">", "<=", ">="), "Bad search operator" + assert search_operator in ( + None, "=", "<", ">", "<=", ">="), "Bad search operator" self.search_operator = search_operator self.dataset = dataset self.search_type = search_type if self.dataset: # Get group information for dataset and the species id - self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name) + self.species_id = webqtlDatabaseFunction.retrieve_species_id( + self.dataset.group.name) def execute(self, query): """Executes query and returns results""" @@ -104,7 +106,8 @@ class MrnaAssaySearch(DoSearch): search_string = escape(self.search_term[0]) if self.search_term[0] != "*": - match_clause = """((MATCH (ProbeSet.symbol) AGAINST ('%s' IN BOOLEAN MODE))) and """ % (search_string) + match_clause = """((MATCH (ProbeSet.symbol) AGAINST ('%s' IN BOOLEAN MODE))) and """ % ( + search_string) else: match_clause = "" @@ -223,16 +226,19 @@ class PhenotypeSearch(DoSearch): # and comment here # if "'" not in self.search_term[0]: - search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0]) + "[[:>:]]" + search_term = "[[:<:]]" + \ + self.handle_wildcard(self.search_term[0]) + "[[:>:]]" if "_" in self.search_term[0]: if len(self.search_term[0].split("_")[0]) == 3: - search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0].split("_")[1]) + "[[:>:]]" + search_term = "[[:<:]]" + self.handle_wildcard( + self.search_term[0].split("_")[1]) + "[[:>:]]" # This adds a clause to the query that matches the search term # against each field in the search_fields tuple where_clause_list = [] for field in self.search_fields: - where_clause_list.append('''%s REGEXP "%s"''' % (field, search_term)) + where_clause_list.append('''%s REGEXP "%s"''' % + (field, search_term)) where_clause = "(%s) " % ' OR '.join(where_clause_list) return where_clause @@ -364,7 +370,8 @@ class GenotypeSearch(DoSearch): if self.search_term[0] == "*": self.query = self.compile_final_query() else: - self.query = self.compile_final_query(where_clause=self.get_where_clause()) + self.query = self.compile_final_query( + where_clause=self.get_where_clause()) return self.execute(self.query) @@ -497,7 +504,8 @@ class LrsSearch(DoSearch): where_clause = """ %sXRef.LRS > %s and %sXRef.LRS < %s """ % self.mescape(self.dataset.type, - min(lrs_min, lrs_max), + min(lrs_min, + lrs_max), self.dataset.type, max(lrs_min, lrs_max)) @@ -537,7 +545,8 @@ class LrsSearch(DoSearch): self.from_clause = self.get_from_clause() self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(self.from_clause, self.where_clause) + self.query = self.compile_final_query( + self.from_clause, self.where_clause) return self.execute(self.query) @@ -551,7 +560,8 @@ class MrnaLrsSearch(LrsSearch, MrnaAssaySearch): self.from_clause = self.get_from_clause() self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(from_clause=self.from_clause, where_clause=self.where_clause) + self.query = self.compile_final_query( + from_clause=self.from_clause, where_clause=self.where_clause) return self.execute(self.query) @@ -566,7 +576,8 @@ class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch): self.from_clause = self.get_from_clause() self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(from_clause=self.from_clause, where_clause=self.where_clause) + self.query = self.compile_final_query( + from_clause=self.from_clause, where_clause=self.where_clause) return self.execute(self.query) @@ -593,7 +604,8 @@ class CisTransLrsSearch(DoSearch): elif len(self.search_term) == 3: lrs_min, lrs_max, self.mb_buffer = self.search_term elif len(self.search_term) == 4: - lrs_min, lrs_max, self.mb_buffer = [float(value) for value in self.search_term[:3]] + lrs_min, lrs_max, self.mb_buffer = [ + float(value) for value in self.search_term[:3]] chromosome = self.search_term[3] if "Chr" in chromosome or "chr" in chromosome: chromosome = int(chromosome[3:]) @@ -636,14 +648,19 @@ class CisTransLrsSearch(DoSearch): if chromosome: location_clause = "(%s.Chr = '%s' and %s.Chr = Geno.Chr and ABS(%s.Mb-Geno.Mb) %s %s) or (%s.Chr != Geno.Chr and Geno.Chr = '%s')" % (escape(self.dataset.type), chromosome, - escape(self.dataset.type), - escape(self.dataset.type), + escape( + self.dataset.type), + escape( + self.dataset.type), the_operator, - escape(str(self.mb_buffer)), - escape(self.dataset.type), + escape( + str(self.mb_buffer)), + escape( + self.dataset.type), chromosome) else: - location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape(self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type), escape(self.dataset.type)) + location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape( + self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type), escape(self.dataset.type)) where_clause = sub_clause + """ %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and @@ -683,7 +700,8 @@ class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch): self.from_clause = self.get_from_clause() self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(self.from_clause, self.where_clause) + self.query = self.compile_final_query( + self.from_clause, self.where_clause) return self.execute(self.query) @@ -714,7 +732,8 @@ class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch): self.from_clause = self.get_from_clause() self.where_clause = self.get_where_clause() - self.query = self.compile_final_query(self.from_clause, self.where_clause) + self.query = self.compile_final_query( + self.from_clause, self.where_clause) return self.execute(self.query) @@ -733,7 +752,8 @@ class MeanSearch(MrnaAssaySearch): where_clause = """ %sXRef.mean > %s and %sXRef.mean < %s """ % self.mescape(self.dataset.type, - min(self.mean_min, self.mean_max), + min(self.mean_min, + self.mean_max), self.dataset.type, max(self.mean_min, self.mean_max)) else: @@ -796,7 +816,8 @@ class PositionSearch(DoSearch): DoSearch.search_types[search_key] = "PositionSearch" def get_where_clause(self): - self.search_term = [float(value) if is_number(value) else value for value in self.search_term] + self.search_term = [float(value) if is_number( + value) else value for value in self.search_term] chr, self.mb_min, self.mb_max = self.search_term[:3] self.chr = str(chr).lower() self.get_chr() @@ -806,7 +827,8 @@ class PositionSearch(DoSearch): %s.Mb < %s """ % self.mescape(self.dataset.type, self.chr, self.dataset.type, - min(self.mb_min, self.mb_max), + min(self.mb_min, + self.mb_max), self.dataset.type, max(self.mb_min, self.mb_max)) @@ -923,7 +945,8 @@ def get_aliases(symbol, species): return [] filtered_aliases = [] - response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases/" + symbol_string) + response = requests.get( + GN2_BASE_URL + "/gn3/gene/aliases/" + symbol_string) if response: alias_list = json.loads(response.content) diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py index 81424b9c..fc93248a 100644 --- a/wqflask/wqflask/docs.py +++ b/wqflask/wqflask/docs.py @@ -35,11 +35,13 @@ class Docs: def update_text(start_vars): content = start_vars['ckcontent'] - content = content.replace('%', '%%').replace('"', '\\"').replace("'", "\\'") + content = content.replace('%', '%%').replace( + '"', '\\"').replace("'", "\\'") try: if g.user_session.record['user_email_address'] == "zachary.a.sloan@gmail.com" or g.user_session.record['user_email_address'] == "labwilliams@gmail.com": - sql = "UPDATE Docs SET content='{0}' WHERE entry='{1}';".format(content, start_vars['entry_type']) + sql = "UPDATE Docs SET content='{0}' WHERE entry='{1}';".format( + content, start_vars['entry_type']) g.db.execute(sql) except: pass diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py index d0745ef7..5bd54f9d 100644 --- a/wqflask/wqflask/export_traits.py +++ b/wqflask/wqflask/export_traits.py @@ -35,9 +35,12 @@ def export_search_results_csv(targs): metadata.append(["Data Set: " + targs['database_name']]) if 'accession_id' in targs: if targs['accession_id'] != "None": - metadata.append(["Metadata Link: http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=" + targs['accession_id']]) - metadata.append(["Export Date: " + datetime.datetime.now().strftime("%B %d, %Y")]) - metadata.append(["Export Time: " + datetime.datetime.now().strftime("%H:%M GMT")]) + metadata.append( + ["Metadata Link: http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=" + targs['accession_id']]) + metadata.append( + ["Export Date: " + datetime.datetime.now().strftime("%B %d, %Y")]) + metadata.append( + ["Export Time: " + datetime.datetime.now().strftime("%H:%M GMT")]) if 'search_string' in targs: if targs['search_string'] != "None": metadata.append(["Search Query: " + targs['search_string']]) @@ -52,10 +55,12 @@ def export_search_results_csv(targs): for trait in table_rows: trait_name, dataset_name, _hash = trait.split(":") trait_ob = create_trait(name=trait_name, dataset_name=dataset_name) - trait_ob = retrieve_trait_info(trait_ob, trait_ob.dataset, get_qtl_info=True) + trait_ob = retrieve_trait_info( + trait_ob, trait_ob.dataset, get_qtl_info=True) trait_list.append(trait_ob) - table_headers = ['Index', 'URL', 'Species', 'Group', 'Dataset', 'Record ID', 'Symbol', 'Description', 'ProbeTarget', 'PubMed_ID', 'Chr', 'Mb', 'Alias', 'Gene_ID', 'Homologene_ID', 'UniGene_ID', 'Strand_Probe', 'Probe_set_specificity', 'Probe_set_BLAT_score', 'Probe_set_BLAT_Mb_start', 'Probe_set_BLAT_Mb_end', 'QTL_Chr', 'QTL_Mb', 'Locus_at_Peak', 'Max_LRS', 'P_value_of_MAX', 'Mean_Expression'] + table_headers = ['Index', 'URL', 'Species', 'Group', 'Dataset', 'Record ID', 'Symbol', 'Description', 'ProbeTarget', 'PubMed_ID', 'Chr', 'Mb', 'Alias', 'Gene_ID', 'Homologene_ID', 'UniGene_ID', + 'Strand_Probe', 'Probe_set_specificity', 'Probe_set_BLAT_score', 'Probe_set_BLAT_Mb_start', 'Probe_set_BLAT_Mb_end', 'QTL_Chr', 'QTL_Mb', 'Locus_at_Peak', 'Max_LRS', 'P_value_of_MAX', 'Mean_Expression'] traits_by_group = sort_traits_by_group(trait_list) @@ -87,7 +92,8 @@ def export_search_results_csv(targs): trait_symbol = "N/A" row_contents = [ i + 1, - "https://genenetwork.org/show_trait?trait_id=" + str(trait.name) + "&dataset=" + str(trait.dataset.name), + "https://genenetwork.org/show_trait?trait_id=" + \ + str(trait.name) + "&dataset=" + str(trait.dataset.name), trait.dataset.group.species, trait.dataset.group.name, trait.dataset.name, @@ -117,13 +123,15 @@ def export_search_results_csv(targs): for sample in trait.dataset.group.samplelist: if sample in trait.data: - row_contents += [trait.data[sample].value, trait.data[sample].variance] + row_contents += [trait.data[sample].value, + trait.data[sample].variance] else: row_contents += ["x", "x"] csv_rows.append(row_contents) - csv_rows = list(map(list, itertools.zip_longest(*[row for row in csv_rows]))) + csv_rows = list( + map(list, itertools.zip_longest(*[row for row in csv_rows]))) writer.writerows(csv_rows) csv_data = buff.getvalue() buff.close() diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py index 1556c6a0..3c0f2ca7 100644 --- a/wqflask/wqflask/external_tools/send_to_bnw.py +++ b/wqflask/wqflask/external_tools/send_to_bnw.py @@ -27,7 +27,8 @@ logger = utility.logger.getLogger(__name__) class SendToBNW: def __init__(self, start_vars): - trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] + trait_db_list = [trait.strip() + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) trait_samples_list = [] @@ -39,7 +40,8 @@ class SendToBNW: trait1_samples = list(this_sample_data.keys()) trait_samples_list.append(trait1_samples) - shared_samples = list(set(trait_samples_list[0]).intersection(*trait_samples_list)) + shared_samples = list( + set(trait_samples_list[0]).intersection(*trait_samples_list)) self.form_value = "" # ZS: string that is passed to BNW through form values_list = [] diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py index c55c43e6..8af9bee9 100644 --- a/wqflask/wqflask/external_tools/send_to_geneweaver.py +++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py @@ -32,7 +32,8 @@ logger = utility.logger.getLogger(__name__) class SendToGeneWeaver: def __init__(self, start_vars): - trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] + trait_db_list = [trait.strip() + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) self.chip_name = test_chip(self.trait_list) diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py index 6b78725c..fd12562f 100644 --- a/wqflask/wqflask/external_tools/send_to_webgestalt.py +++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py @@ -32,7 +32,8 @@ logger = utility.logger.getLogger(__name__) class SendToWebGestalt: def __init__(self, start_vars): - trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] + trait_db_list = [trait.strip() + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) self.chip_name = test_chip(self.trait_list) diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py index 69ce3e7a..55a7da0e 100644 --- a/wqflask/wqflask/group_manager.py +++ b/wqflask/wqflask/group_manager.py @@ -77,8 +77,10 @@ def remove_users(): admin_ids_to_remove = request.form['selected_admin_ids'] member_ids_to_remove = request.form['selected_member_ids'] - remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split(":"), group_id, user_type="admins") - remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split(":"), group_id, user_type="members") + remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split( + ":"), group_id, user_type="admins") + remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split( + ":"), group_id, user_type="members") return redirect(url_for('view_group', id=group_id)) @@ -88,10 +90,12 @@ def add_users(user_type='members'): group_id = request.form['group_id'] if user_type == "admins": user_emails = request.form['admin_emails_to_add'].split(",") - add_users_to_group(g.user_session.user_id, group_id, user_emails, admins=True) + add_users_to_group(g.user_session.user_id, group_id, + user_emails, admins=True) elif user_type == "members": user_emails = request.form['member_emails_to_add'].split(",") - add_users_to_group(g.user_session.user_id, group_id, user_emails, admins=False) + add_users_to_group(g.user_session.user_id, group_id, + user_emails, admins=False) return redirect(url_for('view_group', id=group_id)) @@ -111,7 +115,8 @@ def add_or_edit_group(): if "group_name" in params: member_user_ids = set() admin_user_ids = set() - admin_user_ids.add(g.user_session.user_id) # ZS: Always add the user creating the group as an admin + # ZS: Always add the user creating the group as an admin + admin_user_ids.add(g.user_session.user_id) if "admin_emails_to_add" in params: admin_emails = params['admin_emails_to_add'].split(",") for email in admin_emails: @@ -127,7 +132,8 @@ def add_or_edit_group(): member_user_ids.add(user_details['user_id']) #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members") - create_group(list(admin_user_ids), list(member_user_ids), params['group_name']) + create_group(list(admin_user_ids), list( + member_user_ids), params['group_name']) return redirect(url_for('manage_groups')) else: return render_template("admin/create_group.html") @@ -149,9 +155,11 @@ def send_group_invites(group_id, user_email_list=[], user_type="members"): ((user_type == "members") and (user_details['user_id'] in group_info['members'])): continue else: - send_verification_email(user_details, template_name="email/group_verification.txt", key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group") + send_verification_email(user_details, template_name="email/group_verification.txt", + key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group") else: - temp_password = ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + temp_password = ''.join(random.choice( + string.ascii_uppercase + string.digits) for _ in range(6)) user_details = { 'user_id': str(uuid.uuid4()), 'email_address': user_email, diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index a21dae84..9548d130 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -77,18 +77,21 @@ class GSearch: this_trait['name'] = line[5] this_trait['dataset'] = line[3] this_trait['dataset_fullname'] = line[4] - this_trait['hmac'] = hmac.data_hmac('{}:{}'.format(line[5], line[3])) + this_trait['hmac'] = hmac.data_hmac( + '{}:{}'.format(line[5], line[3])) this_trait['species'] = line[0] this_trait['group'] = line[1] this_trait['tissue'] = line[2] this_trait['symbol'] = line[6] if line[7]: - this_trait['description'] = line[7].decode('utf-8', 'replace') + this_trait['description'] = line[7].decode( + 'utf-8', 'replace') else: this_trait['description'] = "N/A" this_trait['location_repr'] = 'N/A' if (line[8] != "NULL" and line[8] != "") and (line[9] != 0): - this_trait['location_repr'] = 'Chr%s: %.6f' % (line[8], float(line[9])) + this_trait['location_repr'] = 'Chr%s: %.6f' % ( + line[8], float(line[9])) try: this_trait['mean'] = '%.3f' % line[10] except: @@ -103,7 +106,8 @@ class GSearch: this_trait['locus_chr'] = line[16] this_trait['locus_mb'] = line[17] - dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="ProbeSet", species=this_trait["species"]) + dataset_ob = SimpleNamespace( + id=this_trait["dataset_id"], type="ProbeSet", species=this_trait["species"]) if dataset_ob.id not in dataset_to_permissions: permissions = check_resource_availability(dataset_ob) dataset_to_permissions[dataset_ob.id] = permissions @@ -118,7 +122,9 @@ class GSearch: max_lrs_text = "N/A" if this_trait['locus_chr'] != None and this_trait['locus_mb'] != None: - max_lrs_text = "Chr" + str(this_trait['locus_chr']) + ": " + str(this_trait['locus_mb']) + max_lrs_text = "Chr" + \ + str(this_trait['locus_chr']) + \ + ": " + str(this_trait['locus_mb']) this_trait['max_lrs_text'] = max_lrs_text trait_list.append(this_trait) @@ -146,7 +152,8 @@ class GSearch: if "_" in self.terms: if len(self.terms.split("_")[0]) == 3: search_term = self.terms.split("_")[1] - group_clause = "AND InbredSet.`InbredSetCode` = '{}'".format(self.terms.split("_")[0]) + group_clause = "AND InbredSet.`InbredSetCode` = '{}'".format( + self.terms.split("_")[0]) sql = """ SELECT Species.`Name`, @@ -192,18 +199,22 @@ class GSearch: this_trait['index'] = i + 1 this_trait['name'] = str(line[4]) if len(str(line[12])) == 3: - this_trait['display_name'] = str(line[12]) + "_" + this_trait['name'] + this_trait['display_name'] = str( + line[12]) + "_" + this_trait['name'] else: this_trait['display_name'] = this_trait['name'] this_trait['dataset'] = line[2] this_trait['dataset_fullname'] = line[3] - this_trait['hmac'] = hmac.data_hmac('{}:{}'.format(line[4], line[2])) + this_trait['hmac'] = hmac.data_hmac( + '{}:{}'.format(line[4], line[2])) this_trait['species'] = line[0] this_trait['group'] = line[1] if line[9] != None and line[6] != None: - this_trait['description'] = line[6].decode('utf-8', 'replace') + this_trait['description'] = line[6].decode( + 'utf-8', 'replace') elif line[5] != None: - this_trait['description'] = line[5].decode('utf-8', 'replace') + this_trait['description'] = line[5].decode( + 'utf-8', 'replace') else: this_trait['description'] = "N/A" if line[13] != None and line[13] != "": @@ -221,7 +232,8 @@ class GSearch: else: this_trait['pubmed_link'] = "N/A" if line[12]: - this_trait['display_name'] = line[12] + "_" + str(this_trait['name']) + this_trait['display_name'] = line[12] + \ + "_" + str(this_trait['name']) this_trait['LRS_score_repr'] = "N/A" if line[10] != "" and line[10] != None: this_trait['LRS_score_repr'] = '%3.1f' % line[10] @@ -230,13 +242,16 @@ class GSearch: this_trait['additive'] = '%.3f' % line[11] this_trait['max_lrs_text'] = "N/A" - trait_ob = create_trait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False) + trait_ob = create_trait( + dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False) if not trait_ob: continue if this_trait['dataset'] == this_trait['group'] + "Publish": try: if trait_ob.locus_chr != "" and trait_ob.locus_mb != "": - this_trait['max_lrs_text'] = "Chr" + str(trait_ob.locus_chr) + ": " + str(trait_ob.locus_mb) + this_trait['max_lrs_text'] = "Chr" + \ + str(trait_ob.locus_chr) + \ + ": " + str(trait_ob.locus_mb) except: this_trait['max_lrs_text'] = "N/A" diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 0b477446..aa11caa8 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -18,7 +18,8 @@ logger = getLogger(__name__) class Heatmap: def __init__(self, start_vars, temp_uuid): - trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] + trait_db_list = [trait.strip() + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) self.temp_uuid = temp_uuid @@ -33,7 +34,8 @@ class Heatmap: chrnames = [] self.species = species.TheSpecies(dataset=self.trait_list[0][1]) for key in list(self.species.chromosomes.chromosomes.keys()): - chrnames.append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length]) + chrnames.append([self.species.chromosomes.chromosomes[key].name, + self.species.chromosomes.chromosomes[key].mb_length]) for trait_db in self.trait_list: @@ -108,10 +110,13 @@ class Heatmap: trimmed_samples.append(str(samples[i])) trimmed_values.append(values[i]) - trait_filename = str(this_trait.name) + "_" + str(self.dataset.name) + "_pheno" + trait_filename = str(this_trait.name) + "_" + \ + str(self.dataset.name) + "_pheno" gen_pheno_txt_file(trimmed_samples, trimmed_values, trait_filename) - output_filename = self.dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + output_filename = self.dataset.group.name + "_GWA_" + \ + ''.join(random.choice(string.ascii_uppercase + string.digits) + for _ in range(6)) reaper_command = REAPER_COMMAND + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt -n 1000 -o {4}{5}.txt'.format(flat_files('genotype'), genofile_name, @@ -129,9 +134,11 @@ class Heatmap: self.trait_results[this_trait.name] = [] for qtl in reaper_results: if qtl['additive'] > 0: - self.trait_results[this_trait.name].append(-float(qtl['lrs_value'])) + self.trait_results[this_trait.name].append( + -float(qtl['lrs_value'])) else: - self.trait_results[this_trait.name].append(float(qtl['lrs_value'])) + self.trait_results[this_trait.name].append( + float(qtl['lrs_value'])) def gen_pheno_txt_file(samples, vals, filename): diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py index 8dd1c7c0..cadff080 100644 --- a/wqflask/wqflask/interval_analyst/GeneUtil.py +++ b/wqflask/wqflask/interval_analyst/GeneUtil.py @@ -54,7 +54,8 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): Mb >= %2.6f AND Mb < %2.6f AND StrainId1 = %d AND StrainId2 = %d """ % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0] - newdict["snpDensity"] = newdict["snpCount"] / (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0 + newdict["snpDensity"] = newdict["snpCount"] / \ + (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0 else: newdict["snpDensity"] = newdict["snpCount"] = 0 @@ -86,12 +87,14 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): StrainId1 = %d AND StrainId2 = %d """ % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0] - newdict2["snpDensity"] = newdict2["snpCount"] / (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0 + newdict2["snpDensity"] = newdict2["snpCount"] / \ + (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0 else: newdict2["snpDensity"] = newdict2["snpCount"] = 0 try: - newdict2['GeneLength'] = 1000.0 * (newdict2['TxEnd'] - newdict2['TxStart']) + newdict2['GeneLength'] = 1000.0 * \ + (newdict2['TxEnd'] - newdict2['TxStart']) except: pass diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 5c7b81dd..cde822e8 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -307,7 +307,8 @@ class DisplayMappingResults: if 'color_scheme' in start_vars: self.color_scheme = start_vars['color_scheme'] if self.color_scheme == "single": - self.manhattan_single_color = ImageColor.getrgb("#" + start_vars['manhattan_single_color']) + self.manhattan_single_color = ImageColor.getrgb( + "#" + start_vars['manhattan_single_color']) if 'permCheck' in list(start_vars.keys()): self.permChecked = start_vars['permCheck'] @@ -357,7 +358,8 @@ class DisplayMappingResults: if 'reaper_version' in list(start_vars.keys()) and self.mapping_method == "reaper": self.reaper_version = start_vars['reaper_version'] if 'output_files' in start_vars: - self.output_files = ",".join([(the_file if the_file is not None else "") for the_file in start_vars['output_files']]) + self.output_files = ",".join( + [(the_file if the_file is not None else "") for the_file in start_vars['output_files']]) self.categorical_vars = "" self.perm_strata = "" @@ -386,16 +388,19 @@ class DisplayMappingResults: self.dataset.group.genofile = self.genofile_string.split(":")[0] if self.mapping_method == "reaper" and self.manhattan_plot != True: - self.genotype = self.dataset.group.read_genotype_file(use_reaper=True) + self.genotype = self.dataset.group.read_genotype_file( + use_reaper=True) else: self.genotype = self.dataset.group.read_genotype_file() # Darwing Options try: if self.selectedChr > -1: - self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) + self.graphWidth = min(self.GRAPH_MAX_WIDTH, max( + self.GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) else: - self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.MULT_GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) + self.graphWidth = min(self.GRAPH_MAX_WIDTH, max( + self.MULT_GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) except: if self.selectedChr > -1: self.graphWidth = self.GRAPH_DEFAULT_WIDTH @@ -472,9 +477,11 @@ class DisplayMappingResults: """ % (self.dataset.group.name, ", ".join(["'%s'" % X[0] for X in self.ChrList[1:]]))) self.ChrLengthMbList = [x[0] / 1000000.0 for x in self.ChrLengthMbList] - self.ChrLengthMbSum = reduce(lambda x, y: x + y, self.ChrLengthMbList, 0.0) + self.ChrLengthMbSum = reduce( + lambda x, y: x + y, self.ChrLengthMbList, 0.0) if self.ChrLengthMbList: - self.MbGraphInterval = self.ChrLengthMbSum / (len(self.ChrLengthMbList) * 12) # Empirical Mb interval + self.MbGraphInterval = self.ChrLengthMbSum / \ + (len(self.ChrLengthMbList) * 12) # Empirical Mb interval else: self.MbGraphInterval = 1 @@ -482,7 +489,8 @@ class DisplayMappingResults: for i, _chr in enumerate(self.genotype): self.ChrLengthCMList.append(_chr[-1].cM - _chr[0].cM) - self.ChrLengthCMSum = reduce(lambda x, y: x + y, self.ChrLengthCMList, 0.0) + self.ChrLengthCMSum = reduce( + lambda x, y: x + y, self.ChrLengthCMList, 0.0) if self.plotScale == 'physic': self.GraphInterval = self.MbGraphInterval # Mb @@ -496,7 +504,8 @@ class DisplayMappingResults: smd = [] for sample in self.sample_vals_dict.keys(): if self.sample_vals_dict[sample] != "x": - temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample])) + temp = GeneralObject(name=sample, value=float( + self.sample_vals_dict[sample])) smd.append(temp) else: continue @@ -506,7 +515,8 @@ class DisplayMappingResults: if item.name == samplelist[j]: self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1 # default: - self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS + 10) * self.EACH_GENE_HEIGHT + self.graphHeight = self.graphHeight + 2 * \ + (self.NR_INDIVIDUALS + 10) * self.EACH_GENE_HEIGHT # END HaplotypeAnalyst ######################### @@ -529,7 +539,8 @@ class DisplayMappingResults: self.diffCol = [] for i, strain in enumerate(self.diffCol): - self.diffCol[i] = g.db.execute("select Id from Strain where Symbol = %s", strain).fetchone()[0] + self.diffCol[i] = g.db.execute( + "select Id from Strain where Symbol = %s", strain).fetchone()[0] ################################################################ # GeneCollection goes here @@ -552,13 +563,15 @@ class DisplayMappingResults: chrName = "X" else: chrName = self.selectedChr - self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, "mouse") + self.geneCol = GeneUtil.loadGenes( + chrName, self.diffCol, self.startMb, self.endMb, "mouse") elif self.dataset.group.species == "rat": if self.selectedChr == 21: chrName = "X" else: chrName = self.selectedChr - self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, "rat") + self.geneCol = GeneUtil.loadGenes( + chrName, self.diffCol, self.startMb, self.endMb, "rat") if self.geneCol and self.intervalAnalystChecked: ####################################################################### @@ -577,7 +590,8 @@ class DisplayMappingResults: showLocusForm = "" intCanvas = Image.new("RGBA", size=(self.graphWidth, self.graphHeight)) with Bench("Drawing Plot"): - gifmap = self.plotIntMapping(intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm) + gifmap = self.plotIntMapping( + intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm) self.gifmap = gifmap.__str__() @@ -593,8 +607,10 @@ class DisplayMappingResults: # Scales plot differently for high resolution if self.draw2X: - intCanvasX2 = Image.new("RGBA", size=(self.graphWidth * 2, self.graphHeight * 2)) - gifmapX2 = self.plotIntMapping(intCanvasX2, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm, zoom=2) + intCanvasX2 = Image.new("RGBA", size=( + self.graphWidth * 2, self.graphHeight * 2)) + gifmapX2 = self.plotIntMapping( + intCanvasX2, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm, zoom=2) intCanvasX2.save( "{}.png".format( os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, @@ -612,7 +628,8 @@ class DisplayMappingResults: name=showLocusForm, submit=HtmlGenWrapper.create_input_tag(type_='hidden')) - hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', 'database': fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'} + hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', 'database': fd.RISet+ \ + "Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'} for key in hddn.keys(): showLocusForm.append(HtmlGenWrapper.create_input_tag( name=key, value=hddn[key], type_='hidden')) @@ -631,7 +648,8 @@ class DisplayMappingResults: if self.traitList and self.traitList[0].dataset and self.traitList[0].dataset.type == 'Geno': btminfo.append(HtmlGenWrapper.create_br_tag()) - btminfo.append('Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.') + btminfo.append( + 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.') def plotIntMapping(self, canvas, offset=(80, 120, 90, 100), zoom=1, startMb= None, endMb = None, showLocusForm = ""): im_drawer = ImageDraw.Draw(canvas) @@ -673,7 +691,8 @@ class DisplayMappingResults: else: drawAreaHeight -= 3 * self.BAND_HEIGHT + 3 * self.BAND_SPACING + 10 * zoom if self.geneChecked: - drawAreaHeight -= self.NUM_GENE_ROWS * self.EACH_GENE_HEIGHT + 3 * self.BAND_SPACING + 10 * zoom + drawAreaHeight -= self.NUM_GENE_ROWS * \ + self.EACH_GENE_HEIGHT + 3 * self.BAND_SPACING + 10 * zoom else: if self.selectedChr > -1: drawAreaHeight -= 20 @@ -682,7 +701,8 @@ class DisplayMappingResults: # BEGIN HaplotypeAnalyst if self.haplotypeAnalystChecked and self.selectedChr > -1: - drawAreaHeight -= self.EACH_GENE_HEIGHT * (self.NR_INDIVIDUALS + 10) * 2 * zoom + drawAreaHeight -= self.EACH_GENE_HEIGHT * \ + (self.NR_INDIVIDUALS + 10) * 2 * zoom # END HaplotypeAnalyst if zoom == 2: @@ -693,38 +713,48 @@ class DisplayMappingResults: newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset) # Draw the alternating-color background first and get plotXScale - plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + plotXScale = self.drawGraphBackground( + canvas, gifmap, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) # draw bootstap if self.bootChecked and not self.multipleInterval: - self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, + offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) # Draw clickable region and gene band if selected if self.plotScale == 'physic' and self.selectedChr > -1: - self.drawClickBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + self.drawClickBand(canvas, gifmap, plotXScale, offset=newoffset, + zoom=zoom, startMb=startMb, endMb=endMb) if self.geneChecked and self.geneCol: - self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset, + zoom=zoom, startMb=startMb, endMb=endMb) if self.SNPChecked: - self.drawSNPTrackNew(canvas, offset=newoffset, zoom=2 * zoom, startMb=startMb, endMb = endMb) + self.drawSNPTrackNew( + canvas, offset=newoffset, zoom=2 * zoom, startMb=startMb, endMb = endMb) # BEGIN HaplotypeAnalyst if self.haplotypeAnalystChecked: - self.drawHaplotypeBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + self.drawHaplotypeBand( + canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) # END HaplotypeAnalyst # Draw X axis - self.drawXAxis(canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + self.drawXAxis(canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, + offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) # Draw QTL curve - self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale, + offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) # draw legend if self.multipleInterval: - self.drawMultiTraitName(fd, canvas, gifmap, showLocusForm, offset=newoffset) + self.drawMultiTraitName( + fd, canvas, gifmap, showLocusForm, offset=newoffset) elif self.legendChecked: self.drawLegendPanel(canvas, offset=newoffset, zoom=zoom) else: pass # draw position, no need to use a separate function - self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset, zoom=zoom) + self.drawProbeSetPosition( + canvas, plotXScale, offset=newoffset, zoom=zoom) return gifmap @@ -756,19 +786,24 @@ class DisplayMappingResults: if previous_chr_as_int != 1: BootCoord.append(BootChrCoord) BootChrCoord = [] - startX += (self.ChrLengthDistList[previous_chr_as_int - 2] + self.GraphInterval) * plotXScale + startX += ( + self.ChrLengthDistList[previous_chr_as_int - 2] + self.GraphInterval) * plotXScale if self.plotScale == 'physic': Xc = startX + (result['Mb'] - self.startMb) * plotXScale else: - Xc = startX + (result['cM'] - self.qtlresults[0]['cM']) * plotXScale + Xc = startX + \ + (result['cM'] - self.qtlresults[0]['cM']) * plotXScale BootChrCoord.append([Xc, self.bootResult[i]]) else: for i, result in enumerate(self.qtlresults): if str(result['chr']) == str(self.ChrList[self.selectedChr][0]): if self.plotScale == 'physic': - Xc = startX + (result['Mb'] - self.startMb) * plotXScale + Xc = startX + (result['Mb'] - \ + self.startMb) * plotXScale else: - Xc = startX + (result['cM'] - self.qtlresults[0]['cM']) * plotXScale + Xc = startX + \ + (result['cM'] - self.qtlresults[0] + ['cM']) * plotXScale BootChrCoord.append([Xc, self.bootResult[i]]) BootCoord = [BootChrCoord] @@ -793,14 +828,16 @@ class DisplayMappingResults: if maxBootCount < bootCount: maxBootCount = bootCount # end if - reducedBootCoord.append([bootStartPixX, BootChrCoord[i][0], bootCount]) + reducedBootCoord.append( + [bootStartPixX, BootChrCoord[i][0], bootCount]) bootStartPixX = BootChrCoord[i][0] bootCount = BootChrCoord[i][1] # end else # end for # add last piece if BootChrCoord[-1][0] - bootStartPixX > stepBootStrap / 2.0: - reducedBootCoord.append([bootStartPixX, BootChrCoord[-1][0], bootCount]) + reducedBootCoord.append( + [bootStartPixX, BootChrCoord[-1][0], bootCount]) else: reducedBootCoord[-1][2] += bootCount reducedBootCoord[-1][1] = BootChrCoord[-1][0] @@ -827,11 +864,13 @@ class DisplayMappingResults: # draw boot scale highestPercent = (maxBootCount * 100.0) / nboot bootScale = Plot.detScale(0, highestPercent) - bootScale = Plot.frange(bootScale[0], bootScale[1], bootScale[1] / bootScale[2]) + bootScale = Plot.frange( + bootScale[0], bootScale[1], bootScale[1] / bootScale[2]) bootScale = bootScale[:-1] + [highestPercent] bootOffset = 50 * fontZoom - bootScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=13 * fontZoom) + bootScaleFont = ImageFont.truetype( + font=VERDANA_FILE, size=13 * fontZoom) im_drawer.rectangle( xy=((canvas.size[0] - bootOffset, yZero - bootHeightThresh), (canvas.size[0] - bootOffset - 15*zoom, yZero)), @@ -860,10 +899,12 @@ class DisplayMappingResults: startPosY = 30 else: startPosY = 15 - smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12 * fontZoom) + smallLabelFont = ImageFont.truetype( + font=TREBUC_FILE, size=12 * fontZoom) leftOffset = canvas.size[0] - xRightOffset - 190 im_drawer.rectangle( - xy=((leftOffset, startPosY - 6), (leftOffset + 12, startPosY + 6)), + xy=((leftOffset, startPosY - 6), + (leftOffset + 12, startPosY + 6)), fill=YELLOW, outline=BLACK) im_drawer.text(xy=(canvas.size[0] - xRightOffset - 170, startPosY + TEXT_Y_DISPLACEMENT), text='Frequency of the Peak LRS', @@ -905,7 +946,8 @@ class DisplayMappingResults: locPixel = xLeftOffset for i, _chr in enumerate(self.ChrList[1:]): if _chr[0] != Chr: - locPixel += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale + locPixel += (self.ChrLengthDistList[i] + \ + self.GraphInterval) * plotXScale else: locPixel += Mb * plotXScale break @@ -921,7 +963,8 @@ class DisplayMappingResults: # the trait's position is between two traits if i > 0 and self.qtlresults[i - 1]['Mb'] < Mb and qtlresult['Mb'] >= Mb: - locPixel = xLeftOffset + plotXScale * (self.qtlresults[i - 1]['Mb'] + (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb']) * (Mb - self.qtlresults[i - 1]['Mb']) / (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb'])) + locPixel = xLeftOffset + plotXScale * (self.qtlresults[i - 1]['Mb'] + (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb']) * ( + Mb - self.qtlresults[i - 1]['Mb']) / (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb'])) break # the trait's position is on the right of the last genotype @@ -932,12 +975,15 @@ class DisplayMappingResults: for i, _chr in enumerate(self.ChrList): if i < (len(self.ChrList) - 1): if _chr != Chr: - locPixel += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale + locPixel += (self.ChrLengthDistList[i] + \ + self.GraphInterval) * plotXScale else: - locPixel += (Mb * (_chr[-1].cM - _chr[0].cM) / self.ChrLengthCMList[i]) * plotXScale + locPixel += (Mb * (_chr[-1].cM - _chr[0].cM) / \ + self.ChrLengthCMList[i]) * plotXScale break if locPixel >= 0 and self.plotScale == 'physic': - traitPixel = ((locPixel, yZero), (locPixel - 7, yZero + 14), (locPixel + 7, yZero + 14)) + traitPixel = ((locPixel, yZero), (locPixel - 7, + yZero + 14), (locPixel + 7, yZero + 14)) draw_open_polygon(canvas, xy=traitPixel, outline=BLACK, fill=self.TRANSCRIPT_LOCATION_COLOR) @@ -979,7 +1025,8 @@ class DisplayMappingResults: maxCount = max(SNPCounts) if maxCount > 0: for i in range(xLeftOffset, xLeftOffset + plotWidth): - snpDensity = float(SNPCounts[i - xLeftOffset] * SNP_HEIGHT_MODIFIER / maxCount) + snpDensity = float( + SNPCounts[i - xLeftOffset] * SNP_HEIGHT_MODIFIER / maxCount) im_drawer.line( xy=((i, drawSNPLocationY + (snpDensity) * zoom), (i, drawSNPLocationY - (snpDensity) * zoom)), @@ -1015,12 +1062,16 @@ class DisplayMappingResults: (rectWidth + rightShift, yPaddingTop + 10+kstep*15)), fill=thisLRSColor, outline=BLACK) im_drawer.text( - text=name, xy=(rectWidth + 2 + rightShift, yPaddingTop + 10 + kstep * 15), + text=name, xy=(rectWidth + 2 + rightShift, + yPaddingTop + 10 + kstep * 15), font=colorFont, fill=BLACK) if thisTrait.db: - COORDS = "%d,%d,%d,%d" % (rectWidth + 2 + rightShift, yPaddingTop + kstep * 15, rectWidth + 2 + rightShift + nameWidth, yPaddingTop + 10 + kstep * 15,) - HREF = "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name) - Areas = HtmlGenWrapper.create_area_tag(shape='rect', coords=COORDS, href=HREF) + COORDS = "%d,%d,%d,%d" % (rectWidth + 2 + rightShift, yPaddingTop + kstep * \ + 15, rectWidth + 2 + rightShift + nameWidth, yPaddingTop + 10 + kstep * 15,) + HREF = "javascript:showDatabase3('%s','%s','%s','');" % ( + showLocusForm, thisTrait.db.name, thisTrait.name) + Areas = HtmlGenWrapper.create_area_tag( + shape='rect', coords=COORDS, href=HREF) gifmap.append(Areas) # TODO def drawLegendPanel(self, canvas, offset=(40, 120, 80, 10), zoom=1): @@ -1042,7 +1093,8 @@ class DisplayMappingResults: if hasattr(self.traitList[0], 'chr') and hasattr(self.traitList[0], 'mb'): startPosY = 15 nCol = 2 - smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12 * fontZoom) + smallLabelFont = ImageFont.truetype( + font=TREBUC_FILE, size=12 * fontZoom) leftOffset = canvas.size[0] - xRightOffset - 190 draw_open_polygon( @@ -1064,7 +1116,8 @@ class DisplayMappingResults: xy=((startPosX, startPosY), (startPosX + 32, startPosY)), fill=self.LRS_COLOR, width=2) im_drawer.text( - text=self.LRS_LOD, xy=(startPosX + 40, startPosY + TEXT_Y_DISPLACEMENT), + text=self.LRS_LOD, xy=( + startPosX + 40, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) startPosY += stepPosY @@ -1118,10 +1171,12 @@ class DisplayMappingResults: xy=((thisStartX, startPosY), (startPosX + 32, startPosY)), fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH) im_drawer.line( - xy=((thisStartX, startPosY + stepPosY), (startPosX + 32, startPosY + stepPosY)), + xy=((thisStartX, startPosY + stepPosY), + (startPosX + 32, startPosY + stepPosY)), fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH) im_drawer.text( - text='Significant %s = %2.2f' % (self.LRS_LOD, self.significant), + text='Significant %s = %2.2f' % ( + self.LRS_LOD, self.significant), xy=(thisStartX + 40, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) im_drawer.text( text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive), @@ -1134,7 +1189,8 @@ class DisplayMappingResults: if self.dataset.type == "Publish" or self.dataset.type == "Geno": dataset_label = self.dataset.fullname else: - dataset_label = "%s - %s" % (self.dataset.group.name, self.dataset.fullname) + dataset_label = "%s - %s" % (self.dataset.group.name, + self.dataset.fullname) string1 = 'Dataset: %s' % (dataset_label) @@ -1151,7 +1207,8 @@ class DisplayMappingResults: string3 = 'Using GEMMA mapping method with ' if self.covariates != "": string3 += 'the cofactors below:' - cofactor_names = ", ".join([covar.split(":")[0] for covar in self.covariates.split(",")]) + cofactor_names = ", ".join( + [covar.split(":")[0] for covar in self.covariates.split(",")]) string4 = cofactor_names else: string3 += 'no cofactors' @@ -1159,7 +1216,8 @@ class DisplayMappingResults: string3 = 'Using R/qtl mapping method with ' if self.covariates != "": string3 += 'the cofactors below:' - cofactor_names = ", ".join([covar.split(":")[0] for covar in self.covariates.split(",")]) + cofactor_names = ", ".join( + [covar.split(":")[0] for covar in self.covariates.split(",")]) string4 = cofactor_names elif self.controlLocus and self.doControl != "false": string3 += '%s as control' % self.controlLocus @@ -1177,15 +1235,19 @@ class DisplayMappingResults: if self.selectedChr == -1: identification = "Mapping on All Chromosomes for " else: - identification = "Mapping on Chromosome %s for " % (self.ChrList[self.selectedChr][0]) + identification = "Mapping on Chromosome %s for " % ( + self.ChrList[self.selectedChr][0]) if self.this_trait.symbol: - identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.symbol) + identification += "Trait: %s - %s" % ( + self.this_trait.name, self.this_trait.symbol) elif self.dataset.type == "Publish": if self.this_trait.post_publication_abbreviation: - identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.post_publication_abbreviation) + identification += "Trait: %s - %s" % ( + self.this_trait.name, self.this_trait.post_publication_abbreviation) elif self.this_trait.pre_publication_abbreviation: - identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.pre_publication_abbreviation) + identification += "Trait: %s - %s" % ( + self.this_trait.name, self.this_trait.pre_publication_abbreviation) else: identification += "Trait: %s" % (self.this_trait.name) else: @@ -1265,7 +1327,8 @@ class DisplayMappingResults: tenPercentLength = geneLength * 0.0001 SNPdensity = theGO["snpCount"] / geneLength - exonStarts = list(map(float, theGO['exonStarts'].split(",")[:-1])) + exonStarts = list( + map(float, theGO['exonStarts'].split(",")[:-1])) exonEnds = list(map(float, theGO['exonEnds'].split(",")[:-1])) cdsStart = theGO['cdsStart'] cdsEnd = theGO['cdsEnd'] @@ -1274,8 +1337,10 @@ class DisplayMappingResults: strand = theGO["Strand"] exonCount = theGO["exonCount"] - geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) - geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) # at least one pixel + geneStartPix = xLeftOffset + \ + plotXScale * (float(txStart) - startMb) + geneEndPix = xLeftOffset + plotXScale * \ + (float(txEnd) - startMb) # at least one pixel if (geneEndPix < xLeftOffset): return; # this gene is not on the screen @@ -1290,7 +1355,8 @@ class DisplayMappingResults: # found earlier, needs to be recomputed as snps are added # always apply colors now, even if SNP Track not checked - Zach 11/24/2010 - densities = [1.0000000000000001e-05, 0.094094033555233408, 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0] + densities = [1.0000000000000001e-05, 0.094094033555233408, + 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0] if SNPdensity < densities[0]: myColor = BLACK elif SNPdensity < densities[1]: @@ -1309,7 +1375,8 @@ class DisplayMappingResults: outlineColor = myColor fillColor = myColor - TITLE = "Gene: %s (%s)\nFrom %2.3f to %2.3f Mb (%s)\nNum. exons: %d." % (geneSymbol, accession, float(txStart), float(txEnd), strand, exonCount) + TITLE = "Gene: %s (%s)\nFrom %2.3f to %2.3f Mb (%s)\nNum. exons: %d." % ( + geneSymbol, accession, float(txStart), float(txEnd), strand, exonCount) # NL: 06-02-2011 Rob required to change this link for gene related HREF = geneNCBILink % geneSymbol @@ -1324,8 +1391,10 @@ class DisplayMappingResults: strand = theGO["Strand"] exonCount = 0 - geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) - geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) # at least one pixel + geneStartPix = xLeftOffset + \ + plotXScale * (float(txStart) - startMb) + geneEndPix = xLeftOffset + plotXScale * \ + (float(txEnd) - startMb) # at least one pixel if (geneEndPix < xLeftOffset): return; # this gene is not on the screen @@ -1338,7 +1407,8 @@ class DisplayMappingResults: outlineColor = DARKBLUE fillColor = DARKBLUE - TITLE = "Gene: %s\nFrom %2.3f to %2.3f Mb (%s)" % (geneSymbol, float(txStart), float(txEnd), strand) + TITLE = "Gene: %s\nFrom %2.3f to %2.3f Mb (%s)" % ( + geneSymbol, float(txStart), float(txEnd), strand) # NL: 06-02-2011 Rob required to change this link for gene related HREF = geneNCBILink % geneSymbol else: @@ -1347,7 +1417,8 @@ class DisplayMappingResults: TITLE = "Gene: %s" % geneSymbol # Draw Genes - geneYLocation = yPaddingTop + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT * zoom + geneYLocation = yPaddingTop + \ + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT * zoom if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": geneYLocation += 4 * self.BAND_HEIGHT + 4 * self.BAND_SPACING else: @@ -1361,7 +1432,8 @@ class DisplayMappingResults: # draw the line that runs the entire length of the gene im_drawer.line( xy=( - (geneStartPix, geneYLocation + self.EACH_GENE_HEIGHT / 2 * zoom), + (geneStartPix, geneYLocation + \ + self.EACH_GENE_HEIGHT / 2 * zoom), (geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT / 2 *zoom)), fill=outlineColor, width=1) @@ -1401,8 +1473,10 @@ class DisplayMappingResults: # draw the blocks for the exon regions for i in range(0, len(exonStarts)): - exonStartPix = (exonStarts[i] - startMb) * plotXScale + xLeftOffset - exonEndPix = (exonEnds[i] - startMb) * plotXScale + xLeftOffset + exonStartPix = ( + exonStarts[i] - startMb) * plotXScale + xLeftOffset + exonEndPix = (exonEnds[i] - startMb) * \ + plotXScale + xLeftOffset if (exonStartPix < xLeftOffset): exonStartPix = xLeftOffset if (exonEndPix < xLeftOffset): @@ -1418,7 +1492,8 @@ class DisplayMappingResults: # draw gray blocks for 3' and 5' UTR blocks if cdsStart and cdsEnd: - utrStartPix = (txStart - startMb) * plotXScale + xLeftOffset + utrStartPix = (txStart - startMb) * \ + plotXScale + xLeftOffset utrEndPix = (cdsStart - startMb) * plotXScale + xLeftOffset if (utrStartPix < xLeftOffset): utrStartPix = xLeftOffset @@ -1436,7 +1511,8 @@ class DisplayMappingResults: labelText = "5'" im_drawer.text( text=labelText, - xy=(utrStartPix - 9, geneYLocation + self.EACH_GENE_HEIGHT), + xy=(utrStartPix - 9, geneYLocation + \ + self.EACH_GENE_HEIGHT), font=ImageFont.truetype(font=ARIAL_FILE, size=2)) # the second UTR region @@ -1459,7 +1535,8 @@ class DisplayMappingResults: labelText = "3'" im_drawer.text( text=labelText, - xy=(utrEndPix + 2, geneYLocation + self.EACH_GENE_HEIGHT), + xy=(utrEndPix + 2, geneYLocation + \ + self.EACH_GENE_HEIGHT), font=ImageFont.truetype(font=ARIAL_FILE, size=2)) # draw the genes as rectangles @@ -1469,7 +1546,8 @@ class DisplayMappingResults: (geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT * zoom))), outline=outlineColor, fill=fillColor) - COORDS = "%d, %d, %d, %d" % (geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT)) + COORDS = "%d, %d, %d, %d" % ( + geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT)) # NL: 06-02-2011 Rob required to display NCBI info in a new window gifmap.append( HtmlGenWrapper.create_area_tag( @@ -1496,7 +1574,8 @@ class DisplayMappingResults: smd = [] for sample in self.sample_vals_dict.keys(): if self.sample_vals_dict[sample] != "x" and sample in samplelist: - temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample])) + temp = GeneralObject(name=sample, value=float( + self.sample_vals_dict[sample])) smd.append(temp) else: continue @@ -1517,8 +1596,10 @@ class DisplayMappingResults: txStart = _chr[i].Mb txEnd = _chr[i].Mb - geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) - 0 - geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) - 0 + geneStartPix = xLeftOffset + plotXScale * \ + (float(txStart) - startMb) - 0 + geneEndPix = xLeftOffset + plotXScale * \ + (float(txEnd) - startMb) - 0 drawit = 1 if (geneStartPix < xLeftOffset): @@ -1546,8 +1627,10 @@ class DisplayMappingResults: txStart = _chr[j].Mb txEnd = _chr[j].Mb - geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) - 0 - geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) + 0 + geneStartPix = xLeftOffset + plotXScale * \ + (float(txStart) - startMb) - 0 + geneEndPix = xLeftOffset + plotXScale * \ + (float(txEnd) - startMb) + 0 if oldgeneEndPix >= xLeftOffset: drawStart = oldgeneEndPix + 4 @@ -1585,7 +1668,8 @@ class DisplayMappingResults: # Draw Genes - geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT) * zoom + geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * \ + (self.EACH_GENE_HEIGHT) * zoom if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": geneYLocation += 4 * self.BAND_HEIGHT + 4 * self.BAND_SPACING else: @@ -1606,7 +1690,8 @@ class DisplayMappingResults: if (plotbxd == 1): ind = 0 if samplelist[k] in [item.name for item in smd]: - ind = [item.name for item in smd].index(samplelist[k]) + ind = [item.name for item in smd].index( + samplelist[k]) maxind = max(ind, maxind) @@ -1637,8 +1722,10 @@ class DisplayMappingResults: geneYLocation + 2 *ind*self.EACH_GENE_HEIGHT + 2*self.EACH_GENE_HEIGHT*zoom)), outline=outlineColor, fill=fillColor) - COORDS = "%d, %d, %d, %d" % (geneStartPix, geneYLocation + ind * self.EACH_GENE_HEIGHT, geneEndPix + 1, (geneYLocation + ind * self.EACH_GENE_HEIGHT)) - TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart)) + COORDS = "%d, %d, %d, %d" % ( + geneStartPix, geneYLocation + ind * self.EACH_GENE_HEIGHT, geneEndPix + 1, (geneYLocation + ind * self.EACH_GENE_HEIGHT)) + TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % ( + samplelist[k], _chr[j].name, float(txStart)) HREF = '' gifmap.append( HtmlGenWrapper.create_area_tag( @@ -1683,7 +1770,8 @@ class DisplayMappingResults: plotbxd = 1 if (plotbxd == 1): - ind = [item.name for item in smd].index(samplelist[j]) - 1 + ind = [item.name for item in smd].index( + samplelist[j]) - 1 expr = smd[ind].value # Place where font is hardcoded @@ -1691,13 +1779,15 @@ class DisplayMappingResults: text="%s" % (samplelist[j]), xy=((xLeftOffset + plotWidth + 10), geneYLocation + 11 + 2*ind*self.EACH_GENE_HEIGHT*zoom), - font=ImageFont.truetype(font=VERDANA_FILE, size=12), + font=ImageFont.truetype( + font=VERDANA_FILE, size=12), fill=BLACK) im_drawer.text( text="%2.2f" % (expr), xy=((xLeftOffset + plotWidth + 60), geneYLocation + 11 + 2*ind*self.EACH_GENE_HEIGHT*zoom), - font=ImageFont.truetype(font=VERDANA_FILE, size=12), + font=ImageFont.truetype( + font=VERDANA_FILE, size=12), fill=BLACK) # END HaplotypeAnalyst @@ -1719,12 +1809,16 @@ class DisplayMappingResults: # but it makes the HTML huge, and takes forever to render the page in the first place) # Draw the bands that you can click on to go to UCSC / Ensembl MAX_CLICKABLE_REGION_DIVISIONS = 100 - clickableRegionLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=9) - pixelStep = max(5, int(float(plotWidth) / MAX_CLICKABLE_REGION_DIVISIONS)) + clickableRegionLabelFont = ImageFont.truetype( + font=VERDANA_FILE, size=9) + pixelStep = max( + 5, int(float(plotWidth) / MAX_CLICKABLE_REGION_DIVISIONS)) # pixelStep: every N pixels, we make a new clickable area for the user to go to that area of the genome. - numBasesCurrentlyOnScreen = self.kONE_MILLION * abs(startMb - endMb) # Number of bases on screen now - flankingWidthInBases = int (min((float(numBasesCurrentlyOnScreen) / 2.0), (5*self.kONE_MILLION))) + numBasesCurrentlyOnScreen = self.kONE_MILLION * \ + abs(startMb - endMb) # Number of bases on screen now + flankingWidthInBases = int ( + min((float(numBasesCurrentlyOnScreen) / 2.0), (5*self.kONE_MILLION))) webqtlZoomWidth = numBasesCurrentlyOnScreen / 16.0 # Flanking width should be such that we either zoom in to a 10 million base region, or we show the clicked region at the same scale as we are currently seeing. @@ -1733,23 +1827,33 @@ class DisplayMappingResults: paddingTop = yTopOffset if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": - phenogenPaddingTop = paddingTop + (self.BAND_HEIGHT + self.BAND_SPACING) - ucscPaddingTop = paddingTop + 2 * (self.BAND_HEIGHT + self.BAND_SPACING) - ensemblPaddingTop = paddingTop + 3 * (self.BAND_HEIGHT + self.BAND_SPACING) + phenogenPaddingTop = paddingTop + \ + (self.BAND_HEIGHT + self.BAND_SPACING) + ucscPaddingTop = paddingTop + 2 * \ + (self.BAND_HEIGHT + self.BAND_SPACING) + ensemblPaddingTop = paddingTop + 3 * \ + (self.BAND_HEIGHT + self.BAND_SPACING) else: - ucscPaddingTop = paddingTop + (self.BAND_HEIGHT + self.BAND_SPACING) - ensemblPaddingTop = paddingTop + 2 * (self.BAND_HEIGHT + self.BAND_SPACING) + ucscPaddingTop = paddingTop + \ + (self.BAND_HEIGHT + self.BAND_SPACING) + ensemblPaddingTop = paddingTop + 2 * \ + (self.BAND_HEIGHT + self.BAND_SPACING) if zoom == 1: for pixel in range(xLeftOffset, xLeftOffset + plotWidth, pixelStep): - calBase = self.kONE_MILLION * (startMb + (endMb - startMb) * (pixel - xLeftOffset - 0.0) / plotWidth) + calBase = self.kONE_MILLION * \ + (startMb + (endMb - startMb) * \ + (pixel - xLeftOffset - 0.0) / plotWidth) xBrowse1 = pixel - xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1)) + xBrowse2 = min(xLeftOffset + plotWidth, + (pixel + pixelStep - 1)) - WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop + self.BAND_HEIGHT)) - WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase - webqtlZoomWidth)) / 1000000.0, (calBase + webqtlZoomWidth) / 1000000.0) + WEBQTL_COORDS = "%d, %d, %d, %d" % ( + xBrowse1, paddingTop, xBrowse2, (paddingTop + self.BAND_HEIGHT)) + WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max( + 0, (calBase - webqtlZoomWidth)) / 1000000.0, (calBase + webqtlZoomWidth) / 1000000.0) WEBQTL_TITLE = "Click to view this section of the genome in WebQTL" gifmap.append( @@ -1764,15 +1868,19 @@ class DisplayMappingResults: outline=self.CLICKABLE_WEBQTL_REGION_COLOR, fill=self.CLICKABLE_WEBQTL_REGION_COLOR) im_drawer.line( - xy=((xBrowse1, paddingTop), (xBrowse1, (paddingTop + self.BAND_HEIGHT))), + xy=((xBrowse1, paddingTop), (xBrowse1, + (paddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR) if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": - PHENOGEN_COORDS = "%d, %d, %d, %d" % (xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop + self.BAND_HEIGHT)) + PHENOGEN_COORDS = "%d, %d, %d, %d" % ( + xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop + self.BAND_HEIGHT)) if self.dataset.group.species == "mouse": - PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) + PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % ( + self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) else: - PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) + PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % ( + self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen" gifmap.append( HtmlGenWrapper.create_area_tag( @@ -1786,14 +1894,18 @@ class DisplayMappingResults: outline=self.CLICKABLE_PHENOGEN_REGION_COLOR, fill=self.CLICKABLE_PHENOGEN_REGION_COLOR) im_drawer.line( - xy=((xBrowse1, phenogenPaddingTop), (xBrowse1, (phenogenPaddingTop + self.BAND_HEIGHT))), + xy=((xBrowse1, phenogenPaddingTop), (xBrowse1, + (phenogenPaddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR) - UCSC_COORDS = "%d, %d, %d, %d" % (xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop + self.BAND_HEIGHT)) + UCSC_COORDS = "%d, %d, %d, %d" % ( + xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop + self.BAND_HEIGHT)) if self.dataset.group.species == "mouse": - UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr) + UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % ( + self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr) else: - UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) + UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % ( + self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser" gifmap.append( HtmlGenWrapper.create_area_tag( @@ -1811,11 +1923,14 @@ class DisplayMappingResults: (xBrowse1, (ucscPaddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR) - ENSEMBL_COORDS = "%d, %d, %d, %d" % (xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop + self.BAND_HEIGHT)) + ENSEMBL_COORDS = "%d, %d, %d, %d" % ( + xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop + self.BAND_HEIGHT)) if self.dataset.group.species == "mouse": - ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) + ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % ( + self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) else: - ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) + ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % ( + self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser" gifmap.append(HtmlGenWrapper.create_area_tag( shape='rect', @@ -1841,19 +1956,23 @@ class DisplayMappingResults: if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": im_drawer.text( text="Click to view the corresponding section of the genome in PhenoGen", - xy=((xLeftOffset + 10), phenogenPaddingTop), # + self.BAND_HEIGHT/2), + # + self.BAND_HEIGHT/2), + xy=((xLeftOffset + 10), phenogenPaddingTop), font=clickableRegionLabelFont, fill=self.CLICKABLE_PHENOGEN_TEXT_COLOR) im_drawer.text( text="Click to view the corresponding section of the genome in the UCSC Genome Browser", - xy=((xLeftOffset + 10), ucscPaddingTop), # + self.BAND_HEIGHT/2), + # + self.BAND_HEIGHT/2), + xy=((xLeftOffset + 10), ucscPaddingTop), font=clickableRegionLabelFont, fill=self.CLICKABLE_UCSC_TEXT_COLOR) im_drawer.text( text="Click to view the corresponding section of the genome in the Ensembl Genome Browser", - xy=((xLeftOffset + 10), ensemblPaddingTop), # + self.BAND_HEIGHT/2), + # + self.BAND_HEIGHT/2), + xy=((xLeftOffset + 10), ensemblPaddingTop), font=clickableRegionLabelFont, fill=self.CLICKABLE_ENSEMBL_TEXT_COLOR) # draw the gray text - chrFont = ImageFont.truetype(font=VERDANA_BOLD_FILE, size=26 * zoom) + chrFont = ImageFont.truetype( + font=VERDANA_BOLD_FILE, size=26 * zoom) chrX = xLeftOffset + plotWidth - 2 - im_drawer.textsize( "Chr %s" % self.ChrList[self.selectedChr][0], font=chrFont)[0] im_drawer.text( @@ -1922,8 +2041,10 @@ class DisplayMappingResults: (Xc, yZero + xMajorTickHeight)), fill=xAxisTickMarkColor, width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark - labelStr = str(formatStr % _Mb) # What Mbase location to put on the label - strWidth, strHeight = im_drawer.textsize(labelStr, font=MBLabelFont) + # What Mbase location to put on the label + labelStr = str(formatStr % _Mb) + strWidth, strHeight = im_drawer.textsize( + labelStr, font=MBLabelFont) drawStringXc = (Xc - (strWidth / 2.0)) im_drawer.text(xy=(drawStringXc, strYLoc), text=labelStr, font=MBLabelFont, @@ -1956,9 +2077,11 @@ class DisplayMappingResults: canvas, text=str(tickdists), font=MBLabelFont, xy=(startPosX + tickdists * plotXScale, yZero + 10 * zoom), fill=BLACK, angle=270) - startPosX += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale + startPosX += (self.ChrLengthDistList[i] + \ + self.GraphInterval) * plotXScale - megabaseLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5)) + megabaseLabelFont = ImageFont.truetype( + font=VERDANA_FILE, size=int(18 * zoom * 1.5)) im_drawer.text( text="Megabases", xy=( @@ -1984,7 +2107,8 @@ class DisplayMappingResults: if _locus.cM != preLpos: distinctCount += 1 preLpos = _locus.cM - thisChr.append([_locus.name, _locus.cM - Locus0CM]) + thisChr.append( + [_locus.name, _locus.cM - Locus0CM]) else: for j in (0, nLoci / 4, nLoci / 2, nLoci*3/4, -1): while _chr[j].name == ' - ': @@ -1992,7 +2116,8 @@ class DisplayMappingResults: if _chr[j].cM != preLpos: distinctCount += 1 preLpos = _chr[j].cM - thisChr.append([_chr[j].name, _chr[j].cM - Locus0CM]) + thisChr.append( + [_chr[j].name, _chr[j].cM - Locus0CM]) ChrAInfo.append(thisChr) else: for i, _chr in enumerate(self.genotype): @@ -2004,7 +2129,8 @@ class DisplayMappingResults: if _locus.cM != preLpos: distinctCount += 1 preLpos = _locus.cM - thisChr.append([_locus.name, _locus.cM - Locus0CM]) + thisChr.append( + [_locus.name, _locus.cM - Locus0CM]) ChrAInfo.append(thisChr) stepA = (plotWidth + 0.0) / distinctCount @@ -2053,7 +2179,8 @@ class DisplayMappingResults: outline=rectColor, fill=rectColor, width=0) COORDS = "%d,%d,%d,%d" % (xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\ xLeftOffset + offsetA, yZero +40+Zorder*(LRectWidth+3)+LRectWidth) - HREF = "/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name + "Geno") + HREF = "/show_trait?trait_id=%s&dataset=%s" % ( + Lname, self.dataset.group.name + "Geno") #HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname) Areas = HtmlGenWrapper.create_area_tag( shape='rect', @@ -2067,9 +2194,11 @@ class DisplayMappingResults: im_drawer.line( xy=((startPosX, yZero), (startPosX, yZero + 40)), fill=lineColor) - startPosX += (self.ChrLengthDistList[j] + self.GraphInterval) * plotXScale + startPosX += (self.ChrLengthDistList[j] + \ + self.GraphInterval) * plotXScale - centimorganLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5)) + centimorganLabelFont = ImageFont.truetype( + font=VERDANA_FILE, size=int(18 * zoom * 1.5)) im_drawer.text( text="Centimorgans", xy=(xLeftOffset + (plotWidth - im_drawer.textsize( @@ -2100,29 +2229,39 @@ class DisplayMappingResults: # ZS: This is a mess, but I don't know a better way to account for different mapping methods returning results in different formats + the option to change between LRS and LOD if self.lrsMax <= 0: # sliding scale if "lrs_value" in self.qtlresults[0]: - LRS_LOD_Max = max([result['lrs_value'] for result in self.qtlresults]) + LRS_LOD_Max = max([result['lrs_value'] + for result in self.qtlresults]) if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP": LRS_LOD_Max = LRS_LOD_Max / self.LODFACTOR if self.permChecked and self.nperm > 0 and not self.multipleInterval: - self.significant = min(self.significant / self.LODFACTOR, webqtlConfig.MAXLRS) - self.suggestive = min(self.suggestive / self.LODFACTOR, webqtlConfig.MAXLRS) + self.significant = min( + self.significant / self.LODFACTOR, webqtlConfig.MAXLRS) + self.suggestive = min( + self.suggestive / self.LODFACTOR, webqtlConfig.MAXLRS) else: if self.permChecked and self.nperm > 0 and not self.multipleInterval: - self.significant = min(self.significant, webqtlConfig.MAXLRS) - self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS) + self.significant = min( + self.significant, webqtlConfig.MAXLRS) + self.suggestive = min( + self.suggestive, webqtlConfig.MAXLRS) else: pass else: - LRS_LOD_Max = max([result['lod_score'] for result in self.qtlresults]) + LRS_LOD_Max = max([result['lod_score'] + for result in self.qtlresults]) if self.LRS_LOD == "LRS": LRS_LOD_Max = LRS_LOD_Max * self.LODFACTOR if self.permChecked and self.nperm > 0 and not self.multipleInterval: - self.significant = min(self.significant * self.LODFACTOR, webqtlConfig.MAXLRS) - self.suggestive = min(self.suggestive * self.LODFACTOR, webqtlConfig.MAXLRS) + self.significant = min( + self.significant * self.LODFACTOR, webqtlConfig.MAXLRS) + self.suggestive = min( + self.suggestive * self.LODFACTOR, webqtlConfig.MAXLRS) else: if self.permChecked and self.nperm > 0 and not self.multipleInterval: - self.significant = min(self.significant, webqtlConfig.MAXLRS) - self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS) + self.significant = min( + self.significant, webqtlConfig.MAXLRS) + self.suggestive = min( + self.suggestive, webqtlConfig.MAXLRS) else: pass @@ -2143,7 +2282,8 @@ class DisplayMappingResults: self.js_data = json.dumps(js_data) LRSScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom) - LRSLODFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5)) + LRSLODFont = ImageFont.truetype( + font=VERDANA_FILE, size=int(18 * zoom * 1.5)) yZero = yTopOffset + plotHeight # LRSHeightThresh = drawAreaHeight @@ -2188,7 +2328,8 @@ class DisplayMappingResults: # draw the "LRS" or "LOD" string to the left of the axis LRSScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom) - LRSLODFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5)) + LRSLODFont = ImageFont.truetype( + font=VERDANA_FILE, size=int(18 * zoom * 1.5)) yZero = yTopOffset + plotHeight # TEXT_X_DISPLACEMENT = -20 @@ -2239,7 +2380,8 @@ class DisplayMappingResults: # ZS: I don't know if what I did here with this inner function is clever or overly complicated, but it's the only way I could think of to avoid duplicating the code inside this function def add_suggestive_significant_lines_and_legend(start_pos_x, chr_length_dist): - rightEdge = int(start_pos_x + chr_length_dist * plotXScale - self.SUGGESTIVE_WIDTH / 1.5) + rightEdge = int(start_pos_x + chr_length_dist * \ + plotXScale - self.SUGGESTIVE_WIDTH / 1.5) im_drawer.line( xy=((start_pos_x + self.SUGGESTIVE_WIDTH / 1.5, suggestiveY), (rightEdge, suggestiveY)), @@ -2253,15 +2395,19 @@ class DisplayMappingResults: width=self.SIGNIFICANT_WIDTH * zoom # , clipX=(xLeftOffset, xLeftOffset + plotWidth-2) ) - sugg_coords = "%d, %d, %d, %d" % (start_pos_x, suggestiveY - 2, rightEdge + 2 * zoom, suggestiveY + 2) - sig_coords = "%d, %d, %d, %d" % (start_pos_x, significantY - 2, rightEdge + 2 * zoom, significantY + 2) + sugg_coords = "%d, %d, %d, %d" % ( + start_pos_x, suggestiveY - 2, rightEdge + 2 * zoom, suggestiveY + 2) + sig_coords = "%d, %d, %d, %d" % ( + start_pos_x, significantY - 2, rightEdge + 2 * zoom, significantY + 2) if self.LRS_LOD == 'LRS': sugg_title = "Suggestive LRS = %0.2f" % self.suggestive sig_title = "Significant LRS = %0.2f" % self.significant else: - sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive / 4.61) - sig_title = "Significant LOD = %0.2f" % (self.significant / 4.61) + sugg_title = "Suggestive LOD = %0.2f" % ( + self.suggestive / 4.61) + sig_title = "Significant LOD = %0.2f" % ( + self.significant / 4.61) Areas1 = HtmlGenWrapper.create_area_tag( shape='rect', coords=sugg_coords, @@ -2273,24 +2419,28 @@ class DisplayMappingResults: gifmap.append(Areas1) gifmap.append(Areas2) - start_pos_x += (chr_length_dist + self.GraphInterval) * plotXScale + start_pos_x += (chr_length_dist + \ + self.GraphInterval) * plotXScale return start_pos_x for i, _chr in enumerate(self.genotype): if self.selectedChr != -1: if _chr.name == self.ChrList[self.selectedChr][0]: - startPosX = add_suggestive_significant_lines_and_legend(startPosX, self.ChrLengthDistList[0]) + startPosX = add_suggestive_significant_lines_and_legend( + startPosX, self.ChrLengthDistList[0]) break else: continue else: - startPosX = add_suggestive_significant_lines_and_legend(startPosX, self.ChrLengthDistList[i]) + startPosX = add_suggestive_significant_lines_and_legend( + startPosX, self.ChrLengthDistList[i]) if self.multipleInterval: lrsEdgeWidth = 1 else: if self.additiveChecked: - additiveMax = max([abs(X['additive']) for X in self.qtlresults]) + additiveMax = max([abs(X['additive']) + for X in self.qtlresults]) lrsEdgeWidth = 3 if zoom == 2: @@ -2300,7 +2450,8 @@ class DisplayMappingResults: AdditiveCoordXY = [] DominanceCoordXY = [] - symbolFont = ImageFont.truetype(font=FNT_BS_FILE, size=5) # ZS: For Manhattan Plot + symbolFont = ImageFont.truetype( + font=FNT_BS_FILE, size=5) # ZS: For Manhattan Plot previous_chr = 1 previous_chr_as_int = 0 @@ -2332,7 +2483,8 @@ class DisplayMappingResults: if Xc == Xc0: # genotype , locus distance is 0 Xcm = Xc else: - Xcm = (yZero - Yc0) / ((Yc - Yc0) / (Xc - Xc0)) + Xc0 + Xcm = (yZero - Yc0) / \ + ((Yc - Yc0) / (Xc - Xc0)) + Xc0 if Yc0 < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xcm, yZero)), @@ -2340,7 +2492,8 @@ class DisplayMappingResults: # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) im_drawer.line( - xy=((Xcm, yZero), (Xc, yZero - (Yc - yZero))), + xy=((Xcm, yZero), + (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) @@ -2391,7 +2544,8 @@ class DisplayMappingResults: AdditiveCoordXY = [] previous_chr = qtlresult['chr'] previous_chr_as_int += 1 - newStartPosX = (self.ChrLengthDistList[previous_chr_as_int - 1] + self.GraphInterval) * plotXScale + newStartPosX = ( + self.ChrLengthDistList[previous_chr_as_int - 1] + self.GraphInterval) * plotXScale if newStartPosX != oldStartPosX: startPosX += newStartPosX oldStartPosX = newStartPosX @@ -2408,10 +2562,12 @@ class DisplayMappingResults: if self.genotype.filler: if self.selectedChr != -1: start_cm = self.genotype[self.selectedChr - 1][0].cM - Xc = startPosX + (qtlresult['Mb'] - start_cm) * plotXScale + Xc = startPosX + \ + (qtlresult['Mb'] - start_cm) * plotXScale else: start_cm = self.genotype[previous_chr_as_int][0].cM - Xc = startPosX + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) * (((qtlresult['Mb'] - start_cm - startMb) * plotXScale) / ((qtlresult['Mb'] - start_cm - startMb + self.GraphInterval) * plotXScale)) + Xc = startPosX + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) * ( + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) / ((qtlresult['Mb'] - start_cm - startMb + self.GraphInterval) * plotXScale)) else: Xc = startPosX + (qtlresult['Mb'] - startMb) * plotXScale @@ -2425,17 +2581,23 @@ class DisplayMappingResults: if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP": if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf': #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR) - Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / (LRS_LOD_Max * self.LODFACTOR) + Yc = yZero - webqtlConfig.MAXLRS * \ + LRSHeightThresh / \ + (LRS_LOD_Max * self.LODFACTOR) else: #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR) - Yc = yZero - qtlresult['lrs_value'] * LRSHeightThresh / (LRS_LOD_Max * self.LODFACTOR) + Yc = yZero - \ + qtlresult['lrs_value'] * LRSHeightThresh / \ + (LRS_LOD_Max * self.LODFACTOR) else: if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf': #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1] Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / LRS_LOD_Max else: #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSAxisList[-1] - Yc = yZero - qtlresult['lrs_value'] * LRSHeightThresh / LRS_LOD_Max + Yc = yZero - \ + qtlresult['lrs_value'] * \ + LRSHeightThresh / LRS_LOD_Max else: if qtlresult['lod_score'] > 100 or qtlresult['lod_score'] == 'inf': #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1] @@ -2443,10 +2605,14 @@ class DisplayMappingResults: else: if self.LRS_LOD == "LRS": #Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRSAxisList[-1] - Yc = yZero - qtlresult['lod_score'] * self.LODFACTOR * LRSHeightThresh / LRS_LOD_Max + Yc = yZero - \ + qtlresult['lod_score'] * self.LODFACTOR * \ + LRSHeightThresh / LRS_LOD_Max else: #Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRSAxisList[-1] - Yc = yZero - qtlresult['lod_score'] * LRSHeightThresh / LRS_LOD_Max + Yc = yZero - \ + qtlresult['lod_score'] * \ + LRSHeightThresh / LRS_LOD_Max if self.manhattan_plot == True: if self.color_scheme == "single": @@ -2462,7 +2628,8 @@ class DisplayMappingResults: im_drawer.text( text="5", xy=( - Xc - im_drawer.textsize("5", font=symbolFont)[0] / 2 + 1, + Xc - im_drawer.textsize("5", + font=symbolFont)[0] / 2 + 1, Yc - 4), fill=point_color, font=symbolFont) else: @@ -2471,7 +2638,8 @@ class DisplayMappingResults: if not self.multipleInterval and self.additiveChecked: if additiveMax == 0.0: additiveMax = 0.000001 - Yc = yZero - qtlresult['additive'] * AdditiveHeightThresh / additiveMax + Yc = yZero - qtlresult['additive'] * \ + AdditiveHeightThresh / additiveMax AdditiveCoordXY.append((Xc, Yc)) m += 1 @@ -2496,7 +2664,8 @@ class DisplayMappingResults: if Xc == Xc0: # genotype , locus distance is 0 Xcm = Xc else: - Xcm = (yZero - Yc0) / ((Yc - Yc0) / (Xc - Xc0)) + Xc0 + Xcm = (yZero - Yc0) / \ + ((Yc - Yc0) / (Xc - Xc0)) + Xc0 if Yc0 < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xcm, yZero)), @@ -2561,7 +2730,8 @@ class DisplayMappingResults: if Xc == Xc0: # genotype , locus distance is 0 Xcm = Xc else: - Xcm = (yZero - Yc0) / ((Yc - Yc0) / (Xc - Xc0)) + Xc0 + Xcm = (yZero - Yc0) / \ + ((Yc - Yc0) / (Xc - Xc0)) + Xc0 if Yc0 < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xcm, yZero)), @@ -2616,9 +2786,11 @@ class DisplayMappingResults: # draw additive scale if not self.multipleInterval and self.additiveChecked: - additiveScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom) + additiveScaleFont = ImageFont.truetype( + font=VERDANA_FILE, size=16 * zoom) additiveScale = Plot.detScaleOld(0, additiveMax) - additiveStep = (additiveScale[1] - additiveScale[0]) / additiveScale[2] + additiveStep = (additiveScale[1] - \ + additiveScale[0]) / additiveScale[2] additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep) addPlotScale = AdditiveHeightThresh / additiveMax TEXT_Y_DISPLACEMENT = -8 @@ -2633,7 +2805,8 @@ class DisplayMappingResults: scaleStr = "%2.3f" % item im_drawer.text( text=scaleStr, - xy= (xLeftOffset + plotWidth + 6, additiveY + TEXT_Y_DISPLACEMENT), + xy= (xLeftOffset + plotWidth + 6, + additiveY + TEXT_Y_DISPLACEMENT), font=additiveScaleFont, fill=self.ADDITIVE_COLOR_POSITIVE) im_drawer.line( @@ -2690,14 +2863,16 @@ class DisplayMappingResults: plotXScale = plotWidth / drawRegionDistance else: # multiple chromosome view - plotXScale = plotWidth / ((len(self.genotype) - 1) * self.GraphInterval + drawRegionDistance) + plotXScale = plotWidth / \ + ((len(self.genotype) - 1) * self.GraphInterval + drawRegionDistance) startPosX = xLeftOffset if fontZoom == 1.5: chrFontZoom = 2 else: chrFontZoom = 1 - chrLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=24 * chrFontZoom) + chrLabelFont = ImageFont.truetype( + font=VERDANA_FILE, size=24 * chrFontZoom) for i, _chr in enumerate(self.genotype): if (i % 2 == 0): @@ -2712,14 +2887,18 @@ class DisplayMappingResults: outline=GAINSBORO, fill=theBackColor) - chrNameWidth, chrNameHeight = im_drawer.textsize(_chr.name, font=chrLabelFont) - chrStartPix = startPosX + (self.ChrLengthDistList[i] * plotXScale - chrNameWidth) / 2 - chrEndPix = startPosX + (self.ChrLengthDistList[i] * plotXScale + chrNameWidth) / 2 + chrNameWidth, chrNameHeight = im_drawer.textsize( + _chr.name, font=chrLabelFont) + chrStartPix = startPosX + \ + (self.ChrLengthDistList[i] * plotXScale - chrNameWidth) / 2 + chrEndPix = startPosX + \ + (self.ChrLengthDistList[i] * plotXScale + chrNameWidth) / 2 TEXT_Y_DISPLACEMENT = 0 im_drawer.text(xy=(chrStartPix, yTopOffset + TEXT_Y_DISPLACEMENT), text=_chr.name, font=chrLabelFont, fill=BLACK) - COORDS = "%d,%d,%d,%d" % (chrStartPix, yTopOffset, chrEndPix, yTopOffset + 20) + COORDS = "%d,%d,%d,%d" % ( + chrStartPix, yTopOffset, chrEndPix, yTopOffset + 20) # add by NL 09-03-2010 HREF = "javascript:chrView(%d,%s);" % (i, self.ChrLengthMbList) @@ -2729,7 +2908,8 @@ class DisplayMappingResults: coords=COORDS, href=HREF) gifmap.append(Areas) - startPosX += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale + startPosX += (self.ChrLengthDistList[i] + \ + self.GraphInterval) * plotXScale return plotXScale @@ -2746,7 +2926,8 @@ class DisplayMappingResults: perm_output = self.perm_output filename = webqtlUtil.genRandStr("Reg_") - Plot.plotBar(myCanvas, perm_output, XLabel=self.LRS_LOD, YLabel='Frequency', title=' Histogram of Permutation Test') + Plot.plotBar(myCanvas, perm_output, XLabel=self.LRS_LOD, + YLabel='Frequency', title=' Histogram of Permutation Test') myCanvas.save("{}.gif".format(GENERATED_IMAGE_DIR + filename), format='gif') @@ -2825,7 +3006,8 @@ class DisplayMappingResults: txEnd = theGO["TxEnd"] theGO["snpDensity"] = theGO["snpCount"] / geneLength if self.ALEX_DEBUG_BOOL_PRINT_GENE_LIST: - geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO["GeneID"] + geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO[ + "GeneID"] if theGO["snpCount"]: snpString = HT.Link( @@ -2842,7 +3024,9 @@ class DisplayMappingResults: else: snpString = 0 - mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str(int(theGO["TxEnd"] * 1000000.0)) + "&pix=620&Submit=submit" + mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + \ + theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str( + int(theGO["TxEnd"] * 1000000.0)) + "&pix=620&Submit=submit" # the chromosomes for human 1 are 1qXX.XX if theGO['humanGene']: @@ -2854,7 +3038,8 @@ class DisplayMappingResults: humanChr = theGO['humanGene']["Chromosome"] humanTxStart = theGO['humanGene']["TxStart"] - humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" % (humanChr, int(1000000 * theGO['humanGene']["TxStart"]), int(1000000 * theGO['humanGene']["TxEnd"])) + humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" % ( + humanChr, int(1000000 * theGO['humanGene']["TxStart"]), int(1000000 * theGO['humanGene']["TxEnd"])) else: humanStartString = humanChr = humanStartDisplay = "--" @@ -2879,7 +3064,8 @@ class DisplayMappingResults: else: chr_as_int = int(theGO["Chromosome"]) - 1 if refGene: - literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor, refGene, theGO['GeneID']) or "N/A") + literatureCorrelationString = str(self.getLiteratureCorrelation( + self.cursor, refGene, theGO['GeneID']) or "N/A") this_row = [selectCheck.__str__(), str(tableIterationsCnt), @@ -2947,7 +3133,8 @@ class DisplayMappingResults: if theGO["GeneID"] != "": geneSymbolNCBI = str(HtmlGenWrapper.create_link_tag( - "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={}".format(theGO["GeneID"]), + "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={}".format( + theGO["GeneID"]), theGO["GeneSymbol"], Class="normalsize", target="_blank")) @@ -2960,7 +3147,8 @@ class DisplayMappingResults: chr_as_int = int(theGO["Chromosome"]) - 1 geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"])) - geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(theGO["TxStart"]) - (geneLength * 0.1), float(theGO["TxEnd"]) + (geneLength * 0.1)) + geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float( + theGO["TxStart"]) - (geneLength * 0.1), float(theGO["TxEnd"]) + (geneLength * 0.1)) avgExprVal = [] if avgExprVal != "" and avgExprVal: diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 68689104..289f1d5c 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -149,7 +149,8 @@ def gen_covariates_file(this_dataset, covariates, samples): dataset_name = covariate.split(":")[1] if dataset_name == "Temp": temp_group = trait_name.split("_")[2] - dataset_ob = create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = temp_group) + dataset_ob = create_dataset( + dataset_name="Temp", dataset_type="Temp", group_name = temp_group) else: dataset_ob = create_dataset(covariate.split(":")[1]) trait_ob = create_trait(dataset=dataset_ob, diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index 22a50bb8..2fa80841 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -10,7 +10,8 @@ logger = utility.logger.getLogger(__name__) def run_plink(this_trait, dataset, species, vals, maf): - plink_output_filename = webqtlUtil.genRandStr(f"{dataset.group.name}_{this_trait.name}_") + plink_output_filename = webqtlUtil.genRandStr( + f"{dataset.group.name}_{this_trait.name}_") gen_pheno_txt_file(dataset, vals) plink_command = f"{PLINK_COMMAND} --noweb --bfile {flat_files('mapping')}/{dataset.group.name} --no-pheno --no-fid --no-parents --no-sex --maf {maf} --out { TMPDIR}{plink_output_filename} --assoc " @@ -41,7 +42,8 @@ def gen_pheno_txt_file(this_dataset, vals): this_val = -9 else: this_val = vals[i] - outfile.write("0 " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n") + outfile.write("0 " + line[1] + " " + line[2] + " " + \ + line[3] + " " + line[4] + " " + str(this_val) + "\n") def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename=''): @@ -162,7 +164,8 @@ def parse_plink_output(output_filename, species): def build_line_list(line=""): - line_list = line.strip().split(' ') # irregular number of whitespaces between columns + # irregular number of whitespaces between columns + line_list = line.strip().split(' ') line_list = [item for item in line_list if item != ''] line_list = [item.strip() for item in line_list] diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index b8fe2c37..f932498f 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -26,7 +26,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo gen_pheno_txt_file(samples, vals, trait_filename) output_filename = (f"{this_dataset.group.name}_GWA_" + - ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + ''.join(random.choice(string.ascii_uppercase + string.digits) + for _ in range(6)) ) bootstrap_filename = None permu_filename = None @@ -34,19 +35,22 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo opt_list = [] if boot_check and num_bootstrap > 0: bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_" + - ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + ''.join(random.choice(string.ascii_uppercase + string.digits) + for _ in range(6)) ) opt_list.append("-b") opt_list.append(f"--n_bootstrap {str(num_bootstrap)}") - opt_list.append(f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt") + opt_list.append( + f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt") if num_perm > 0: permu_filename = ("{this_dataset.group.name}_PERM_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) ) opt_list.append("-n " + str(num_perm)) - opt_list.append("--permu_output " + webqtlConfig.GENERATED_IMAGE_DIR + permu_filename + ".txt") + opt_list.append( + "--permu_output " + webqtlConfig.GENERATED_IMAGE_DIR + permu_filename + ".txt") if control_marker != "" and do_control == "true": opt_list.append("-c " + control_marker) if manhattan_plot != True: @@ -58,7 +62,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo genofile_name, TEMPDIR, trait_filename, - " ".join(opt_list), + " ".join( + opt_list), webqtlConfig.GENERATED_IMAGE_DIR, output_filename)) @@ -67,7 +72,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo else: output_filename, permu_filename, bootstrap_filename = output_files - marker_obs, permu_vals, bootstrap_vals = parse_reaper_output(output_filename, permu_filename, bootstrap_filename) + marker_obs, permu_vals, bootstrap_vals = parse_reaper_output( + output_filename, permu_filename, bootstrap_filename) suggestive = 0 significant = 0 @@ -193,7 +199,8 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da suggestive = 0 significant = 0 else: - perm_output = genotype.permutation(strains=trimmed_samples, trait=trimmed_values, nperm=num_perm) + perm_output = genotype.permutation( + strains=trimmed_samples, trait=trimmed_values, nperm=num_perm) suggestive = perm_output[int(num_perm * 0.37 - 1)] significant = perm_output[int(num_perm * 0.95 - 1)] # highly_significant = perm_output[int(num_perm*0.99-1)] #ZS: Currently not used, but leaving it here just in case @@ -257,7 +264,8 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da json_data['markernames'].append(reaper_locus.name) # if self.additive: # self.json_data['additive'].append(qtl.additive) - locus = {"name": reaper_locus.name, "chr": reaper_locus.chr, "cM": reaper_locus.cM, "Mb": reaper_locus.Mb} + locus = {"name": reaper_locus.name, "chr": reaper_locus.chr, + "cM": reaper_locus.cM, "Mb": reaper_locus.Mb} qtl = {"lrs_value": qtl.lrs, "chr": converted_chr, "Mb": reaper_locus.Mb, "cM": reaper_locus.cM, "name": reaper_locus.name, "additive": qtl.additive, "dominance": qtl.dominance} qtl_results.append(qtl) @@ -270,5 +278,6 @@ def natural_sort(marker_list): Changed to return indices instead of values, though, since the same reordering needs to be applied to bootstrap results """ convert = lambda text: int(text) if text.isdigit() else text.lower() - alphanum_key = lambda key: [convert(c) for c in re.split('([0-9]+)', str(marker_list[key]['chr']))] + alphanum_key = lambda key: [convert(c) for c in re.split( + '([0-9]+)', str(marker_list[key]['chr']))] return sorted(list(range(len(marker_list))), key=alphanum_key) diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 588600f5..c2b165a4 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -51,7 +51,8 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec # Get pointers to some R/qtl functions scanone = ro.r["scanone"] # Map the scanone function scantwo = ro.r["scantwo"] # Map the scantwo function - calc_genoprob = ro.r["calc.genoprob"] # Map the calc.genoprob function + # Map the calc.genoprob function + calc_genoprob = ro.r["calc.genoprob"] crossname = dataset.group.name # try: @@ -67,14 +68,16 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec scale_units = "Mb" generate_cross_from_geno(dataset, scale_units) - GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the local GENOtoCSVR function + # Map the local GENOtoCSVR function + GENOtoCSVR = ro.r["GENOtoCSVR"] crossfilelocation = TMPDIR + crossname + ".cross" if dataset.group.genofile: genofilelocation = locate(dataset.group.genofile, "genotype") else: genofilelocation = locate(dataset.group.name + ".geno", "genotype") logger.info("Going to create a cross from geno"); - cross_object = GENOtoCSVR(genofilelocation, crossfilelocation) # TODO: Add the SEX if that is available + # TODO: Add the SEX if that is available + cross_object = GENOtoCSVR(genofilelocation, crossfilelocation) logger.info("before calc_genoprob"); if manhattan_plot: cross_object = calc_genoprob(cross_object) @@ -85,14 +88,19 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec logger.info("phenostring done"); names_string = sanitize_rqtl_names(samples) logger.info("sanitized pheno and names"); - cross_object = add_phenotype(cross_object, pheno_string, "the_pheno") # Add the phenotype - cross_object = add_names(cross_object, names_string, "the_names") # Add the phenotype + # Add the phenotype + cross_object = add_phenotype(cross_object, pheno_string, "the_pheno") + # Add the phenotype + cross_object = add_names(cross_object, names_string, "the_names") logger.info("Added pheno and names"); - marker_covars = create_marker_covariates(control_marker, cross_object) # Create the additive covariate markers + # Create the additive covariate markers + marker_covars = create_marker_covariates(control_marker, cross_object) logger.info("Marker covars done"); if cofactors != "": logger.info("Cofactors: " + cofactors); - cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits + # Create the covariates from selected traits + cross_object, trait_covars = add_cofactors( + cross_object, dataset, cofactors, samples) ro.r('all_covars <- cbind(marker_covars, trait_covars)') else: ro.r('all_covars <- marker_covars') @@ -100,9 +108,11 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec # DEBUG to save the session object to file if pair_scan: if do_control == "true": - logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method, n_cluster = 16) + logger.info("Using covariate"); result_data_frame = scantwo( + cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method, n_cluster = 16) else: - logger.info("No covariates"); result_data_frame = scantwo(cross_object, pheno="the_pheno", model=model, method=method, n_cluster=16) + logger.info("No covariates"); result_data_frame = scantwo( + cross_object, pheno="the_pheno", model=model, method=method, n_cluster=16) pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png" png(file=TEMPDIR + pair_scan_filename) @@ -112,25 +122,36 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec return process_pair_scan_results(result_data_frame) else: if do_control == "true" or cofactors != "": - logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method) + logger.info("Using covariate"); result_data_frame = scanone( + cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method) ro.r('save.image(file = "/home/zas1024/gn2-zach/itp_cofactor_test.RData")') else: - logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno="the_pheno", model=model, method=method) - - if num_perm > 0 and permCheck == "ON": # Do permutation (if requested by user) - if len(perm_strata_list) > 0: # ZS: The strata list would only be populated if "Stratified" was checked on before mapping - cross_object, strata_ob = add_perm_strata(cross_object, perm_strata_list) + logger.info("No covariates"); result_data_frame = scanone( + cross_object, pheno="the_pheno", model=model, method=method) + + # Do permutation (if requested by user) + if num_perm > 0 and permCheck == "ON": + # ZS: The strata list would only be populated if "Stratified" was checked on before mapping + if len(perm_strata_list) > 0: + cross_object, strata_ob = add_perm_strata( + cross_object, perm_strata_list) if do_control == "true" or cofactors != "": - perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(num_perm), perm_strata = strata_ob, model=model, method=method) + perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int( + num_perm), perm_strata = strata_ob, model=model, method=method) else: - perm_data_frame = scanone(cross_object, pheno_col="the_pheno", n_perm=num_perm, perm_strata = strata_ob, model=model, method=method) + perm_data_frame = scanone( + cross_object, pheno_col="the_pheno", n_perm=num_perm, perm_strata = strata_ob, model=model, method=method) else: if do_control == "true" or cofactors != "": - perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(num_perm), model=model, method=method) + perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int( + num_perm), model=model, method=method) else: - perm_data_frame = scanone(cross_object, pheno_col="the_pheno", n_perm=num_perm, model=model, method=method) + perm_data_frame = scanone( + cross_object, pheno_col="the_pheno", n_perm=num_perm, model=model, method=method) - perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame) # Functions that sets the thresholds for the webinterface + # Functions that sets the thresholds for the webinterface + perm_output, suggestive, significant = process_rqtl_perm_results( + num_perm, perm_data_frame) return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species) else: return process_rqtl_results(result_data_frame, dataset.group.species) @@ -147,7 +168,8 @@ def generate_cross_from_rdata(dataset): """ % (rdata_location)) -def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly +# TODO: Need to figure out why some genofiles have the wrong format and don't convert properly +def generate_cross_from_geno(dataset, scale_units): ro.r(""" trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) } @@ -246,7 +268,8 @@ def sanitize_rqtl_names(vals): def add_phenotype(cross, pheno_as_string, col_name): ro.globalenv["the_cross"] = cross ro.r('pheno <- data.frame(pull.pheno(the_cross))') - ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric(' + pheno_as_string + '))') + ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + \ + ' = as.numeric(' + pheno_as_string + '))') return ro.r["the_cross"] @@ -270,7 +293,8 @@ def add_categorical_covar(cross, covar_as_string, i): #logger.info("loop" + str(x)); col_name = "covar_" + str(i) + "_" + str(x) #logger.info("col_name" + col_name); - ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = newcovar[,' + str(x) + '])') + ro.r('the_cross$pheno <- cbind(pheno, ' + \ + col_name + ' = newcovar[,' + str(x) + '])') col_names.append(col_name) #logger.info("loop" + str(x) + "done"); @@ -281,7 +305,8 @@ def add_categorical_covar(cross, covar_as_string, i): def add_names(cross, names_as_string, col_name): ro.globalenv["the_cross"] = cross ro.r('pheno <- data.frame(pull.pheno(the_cross))') - ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = ' + names_as_string + ')') + ro.r('the_cross$pheno <- cbind(pheno, ' + \ + col_name + ' = ' + names_as_string + ')') return ro.r["the_cross"] @@ -330,9 +355,11 @@ def add_cofactors(cross, this_dataset, covariates, samples): logger.info("Covariate: " + covariate + " is of type: " + datatype); if(datatype == "categorical"): # Cat variable logger.info("call of add_categorical_covar"); - cross, col_names = add_categorical_covar(cross, covar_as_string, i) # Expand and add it to the cross + cross, col_names = add_categorical_covar( + cross, covar_as_string, i) # Expand and add it to the cross logger.info("add_categorical_covar returned"); - for z, col_name in enumerate(col_names): # Go through the additional covar names + # Go through the additional covar names + for z, col_name in enumerate(col_names): if i < (len(covariate_list) - 1): covar_name_string += '"' + col_name + '", ' else: @@ -355,18 +382,22 @@ def add_cofactors(cross, this_dataset, covariates, samples): def create_marker_covariates(control_marker, cross): ro.globalenv["the_cross"] = cross - ro.r('genotypes <- pull.geno(the_cross)') # Get the genotype matrix - userinput_sanitized = control_marker.replace(" ", "").split(",") # TODO: sanitize user input, Never Ever trust a user + # Get the genotype matrix + ro.r('genotypes <- pull.geno(the_cross)') + # TODO: sanitize user input, Never Ever trust a user + userinput_sanitized = control_marker.replace(" ", "").split(",") logger.debug(userinput_sanitized) if len(userinput_sanitized) > 0: - covariate_names = ', '.join('"{0}"'.format(w) for w in userinput_sanitized) + covariate_names = ', '.join('"{0}"'.format(w) + for w in userinput_sanitized) ro.r('covnames <- c(' + covariate_names + ')') else: ro.r('covnames <- c()') ro.r('covInGeno <- which(covnames %in% colnames(genotypes))') ro.r('covnames <- covnames[covInGeno]') ro.r("cat('covnames (purged): ', covnames,'\n')") - ro.r('marker_covars <- genotypes[,covnames]') # Get the covariate matrix by using the marker name as index to the genotype file + # Get the covariate matrix by using the marker name as index to the genotype file + ro.r('marker_covars <- genotypes[,covnames]') # TODO: Create a design matrix from the marker covars for the markers in case of an F2, 4way, etc return ro.r["marker_covars"] @@ -375,7 +406,8 @@ def process_pair_scan_results(result): pair_scan_results = [] result = result[1] - output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)] + output = [tuple([result[j][i] for j in range(result.ncol)]) + for i in range(result.nrow)] for i, line in enumerate(result.iter_row()): marker = {} @@ -401,14 +433,17 @@ def process_rqtl_perm_results(num_perm, results): return perm_output, suggestive, significant -def process_rqtl_results(result, species_name): # TODO: how to make this a one liner and not copy the stuff in a loop +# TODO: how to make this a one liner and not copy the stuff in a loop +def process_rqtl_results(result, species_name): qtl_results = [] - output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)] + output = [tuple([result[j][i] for j in range(result.ncol)]) + for i in range(result.nrow)] for i, line in enumerate(result.iter_row()): marker = {} marker['name'] = result.rownames[i] - if species_name == "mouse" and output[i][0] == 20: # ZS: This is awkward, but I'm not sure how to change the 20s to Xs in the RData file + # ZS: This is awkward, but I'm not sure how to change the 20s to Xs in the RData file + if species_name == "mouse" and output[i][0] == 20: marker['chr'] = "X" else: marker['chr'] = output[i][0] diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 31c58083..d9b28fba 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -51,7 +51,8 @@ class RunMapping: def __init__(self, start_vars, temp_uuid): helper_functions.get_species_dataset_trait(self, start_vars) - self.temp_uuid = temp_uuid # needed to pass temp_uuid to gn1 mapping code (marker_regression_gn1.py) + # needed to pass temp_uuid to gn1 mapping code (marker_regression_gn1.py) + self.temp_uuid = temp_uuid # ZS: Needed to zoom in or remap temp traits like PCA traits if "temp_trait" in start_vars and start_vars['temp_trait'] != "False": @@ -102,8 +103,11 @@ class RunMapping: if "results_path" in start_vars: self.mapping_results_path = start_vars['results_path'] else: - mapping_results_filename = self.dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) - self.mapping_results_path = "{}{}.csv".format(webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename) + mapping_results_filename = self.dataset.group.name + "_" + \ + ''.join(random.choice(string.ascii_uppercase + string.digits) + for _ in range(6)) + self.mapping_results_path = "{}{}.csv".format( + webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename) self.manhattan_plot = False if 'manhattan_plot' in start_vars: @@ -122,7 +126,8 @@ class RunMapping: self.use_loco = None self.suggestive = "" self.significant = "" - self.pair_scan = False # Initializing this since it is checked in views to determine which template to use + # Initializing this since it is checked in views to determine which template to use + self.pair_scan = False if 'transform' in start_vars: self.transform = start_vars['transform'] else: @@ -140,7 +145,8 @@ class RunMapping: # ZS: This is passed to GN1 code for single chr mapping self.selected_chr = -1 if "selected_chr" in start_vars: - if int(start_vars['selected_chr']) != -1: # ZS: Needs to be -1 if showing full map; there's probably a better way to fix this + # ZS: Needs to be -1 if showing full map; there's probably a better way to fix this + if int(start_vars['selected_chr']) != -1: self.selected_chr = int(start_vars['selected_chr']) + 1 else: self.selected_chr = int(start_vars['selected_chr']) @@ -198,28 +204,33 @@ class RunMapping: self.output_files = None if 'output_files' in start_vars: self.output_files = start_vars['output_files'] - if 'first_run' in start_vars: # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) + # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) + if 'first_run' in start_vars: self.first_run = False self.score_type = "-logP" self.manhattan_plot = True with Bench("Running GEMMA"): if self.use_loco == "True": - marker_obs, self.output_files = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files) + marker_obs, self.output_files = gemma_mapping.run_gemma( + self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files) else: - marker_obs, self.output_files = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files) + marker_obs, self.output_files = gemma_mapping.run_gemma( + self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files) results = marker_obs elif self.mapping_method == "rqtl_plink": results = self.run_rqtl_plink() elif self.mapping_method == "rqtl_geno": perm_strata = [] if "perm_strata" in start_vars and "categorical_vars" in start_vars: - self.categorical_vars = start_vars["categorical_vars"].split(",") + self.categorical_vars = start_vars["categorical_vars"].split( + ",") if len(self.categorical_vars) and start_vars["perm_strata"] == "True": primary_samples = SampleList(dataset=self.dataset, sample_names=self.samples, this_trait=self.this_trait) - perm_strata = get_perm_strata(self.this_trait, primary_samples, self.categorical_vars, self.samples) + perm_strata = get_perm_strata( + self.this_trait, primary_samples, self.categorical_vars, self.samples) self.score_type = "LOD" self.control_marker = start_vars['control_marker'] self.do_control = start_vars['do_control'] @@ -231,9 +242,11 @@ class RunMapping: # if start_vars['pair_scan'] == "true": # self.pair_scan = True if self.permCheck and self.num_perm > 0: - self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates) + self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno( + self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates) else: - results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates) + results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, + self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates) elif self.mapping_method == "reaper": if "startMb" in start_vars: # ZS: Check if first time page loaded, so it can default to ON if "additiveCheck" in start_vars: @@ -268,10 +281,12 @@ class RunMapping: if self.reaper_version == "new": self.first_run = True self.output_files = None - if 'first_run' in start_vars: # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) + # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) + if 'first_run' in start_vars: self.first_run = False if 'output_files' in start_vars: - self.output_files = start_vars['output_files'].split(",") + self.output_files = start_vars['output_files'].split( + ",") results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait, self.dataset, @@ -301,7 +316,8 @@ class RunMapping: elif self.mapping_method == "plink": self.score_type = "-logP" self.manhattan_plot = True - results = plink_mapping.run_plink(self.this_trait, self.dataset, self.species, self.vals, self.maf) + results = plink_mapping.run_plink( + self.this_trait, self.dataset, self.species, self.vals, self.maf) #results = self.run_plink() else: logger.debug("RUNNING NOTHING") @@ -353,7 +369,9 @@ class RunMapping: chr=str(marker['chr']), rs=marker['name'], ps=this_ps, - url="/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno" + url="/show_trait?trait_id=" + \ + marker['name'] + "&dataset=" + \ + self.dataset.group.name + "Geno" ) if self.geno_db_exists == "True": @@ -362,7 +380,9 @@ class RunMapping: chr=str(marker['chr']), rs=marker['name'], pos=this_ps, - url="/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno" + url="/show_trait?trait_id=" + \ + marker['name'] + "&dataset=" + \ + self.dataset.group.name + "Geno" ) else: annot_marker = dict( @@ -373,7 +393,8 @@ class RunMapping: ) if 'lrs_value' in marker and marker['lrs_value'] > 0: - browser_marker['p_wald'] = 10**-(marker['lrs_value'] / 4.61) + browser_marker['p_wald'] = 10**- \ + (marker['lrs_value'] / 4.61) elif 'lod_score' in marker and marker['lod_score'] > 0: browser_marker['p_wald'] = 10**-(marker['lod_score']) else: @@ -386,9 +407,13 @@ class RunMapping: highest_chr = marker['chr'] if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()): if 'Mb' in marker.keys(): - marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.6f}".format(marker['Mb']) + marker['display_pos'] = "Chr" + \ + str(marker['chr']) + ": " + \ + "{:.6f}".format(marker['Mb']) elif 'cM' in marker.keys(): - marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.3f}".format(marker['cM']) + marker['display_pos'] = "Chr" + \ + str(marker['chr']) + ": " + \ + "{:.3f}".format(marker['cM']) else: marker['display_pos'] = "N/A" self.qtl_results.append(marker) @@ -396,12 +421,15 @@ class RunMapping: total_markers = len(self.qtl_results) with Bench("Exporting Results"): - export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples) + export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, + self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples) with Bench("Trimming Markers for Figure"): if len(self.qtl_results) > 30000: - self.qtl_results = trim_markers_for_figure(self.qtl_results) - self.results_for_browser = trim_markers_for_figure(self.results_for_browser) + self.qtl_results = trim_markers_for_figure( + self.qtl_results) + self.results_for_browser = trim_markers_for_figure( + self.results_for_browser) filtered_annotations = [] for marker in self.results_for_browser: for annot_marker in self.annotations_for_browser: @@ -409,14 +437,17 @@ class RunMapping: filtered_annotations.append(annot_marker) break self.annotations_for_browser = filtered_annotations - browser_files = write_input_for_browser(self.dataset, self.results_for_browser, self.annotations_for_browser) + browser_files = write_input_for_browser( + self.dataset, self.results_for_browser, self.annotations_for_browser) else: - browser_files = write_input_for_browser(self.dataset, self.results_for_browser, self.annotations_for_browser) + browser_files = write_input_for_browser( + self.dataset, self.results_for_browser, self.annotations_for_browser) with Bench("Trimming Markers for Table"): self.trimmed_markers = trim_markers_for_table(results) - chr_lengths = get_chr_lengths(self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results) + chr_lengths = get_chr_lengths( + self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results) # ZS: For zooming into genome browser, need to pass chromosome name instead of number if self.dataset.group.species == "mouse": @@ -472,11 +503,14 @@ class RunMapping: def run_rqtl_plink(self): # os.chdir("") never do this inside a webserver!! - output_filename = webqtlUtil.genRandStr("%s_%s_" % (self.dataset.group.name, self.this_trait.name)) + output_filename = webqtlUtil.genRandStr("%s_%s_" % ( + self.dataset.group.name, self.this_trait.name)) - plink_mapping.gen_pheno_txt_file_plink(self.this_trait, self.dataset, self.vals, pheno_filename=output_filename) + plink_mapping.gen_pheno_txt_file_plink( + self.this_trait, self.dataset, self.vals, pheno_filename=output_filename) - rqtl_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (self.dataset.group.name, self.dataset.group.name, TMPDIR, plink_output_filename, self.this_trait.name, self.maf, TMPDIR, plink_output_filename) + rqtl_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % ( + self.dataset.group.name, self.dataset.group.name, TMPDIR, plink_output_filename, self.this_trait.name, self.maf, TMPDIR, plink_output_filename) os.system(rqtl_command) @@ -508,8 +542,10 @@ class RunMapping: def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples): with open(results_path, "w+") as output_file: - output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") - output_file.write("Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n") + output_file.write( + "Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") + output_file.write( + "Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n") output_file.write("Data Set: " + dataset.fullname + "\n") output_file.write("N Samples: " + str(n_samples) + "\n") if len(transform) > 0: @@ -529,7 +565,8 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write(transform_text + "\n") if dataset.type == "ProbeSet": output_file.write("Gene Symbol: " + trait.symbol + "\n") - output_file.write("Location: " + str(trait.chr) + " @ " + str(trait.mb) + " Mb\n") + output_file.write("Location: " + str(trait.chr) + \ + " @ " + str(trait.mb) + " Mb\n") if len(covariates) > 0: output_file.write("Cofactors (dataset - trait):\n") for covariate in covariates.split(","): @@ -630,9 +667,11 @@ def trim_markers_for_figure(markers): def trim_markers_for_table(markers): if 'lod_score' in list(markers[0].keys()): - sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True) + sorted_markers = sorted( + markers, key=lambda k: k['lod_score'], reverse=True) else: - sorted_markers = sorted(markers, key=lambda k: k['lrs_value'], reverse=True) + sorted_markers = sorted( + markers, key=lambda k: k['lrs_value'], reverse=True) # ZS: So we end up with a list of just 2000 markers if len(sorted_markers) >= 2000: @@ -643,7 +682,9 @@ def trim_markers_for_table(markers): def write_input_for_browser(this_dataset, gwas_results, annotations): - file_base = this_dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + file_base = this_dataset.group.name + "_" + \ + ''.join(random.choice(string.ascii_uppercase + string.digits) + for _ in range(6)) gwas_filename = file_base + "_GWAS" annot_filename = file_base + "_ANNOT" gwas_path = "{}/gn2/".format(TEMPDIR) + gwas_filename @@ -659,7 +700,8 @@ def write_input_for_browser(this_dataset, gwas_results, annotations): def geno_db_exists(this_dataset): geno_db_name = this_dataset.group.name + "Geno" try: - geno_db = data_set.create_dataset(dataset_name=geno_db_name, get_samplelist=False) + geno_db = data_set.create_dataset( + dataset_name=geno_db_name, get_samplelist=False) return "True" except: return "False" @@ -689,9 +731,11 @@ def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results): highest_pos = float(result['cM']) * 1000000 else: highest_pos = float(result['Mb']) * 1000000 - chr_lengths.append({"chr": str(this_chr), "size": str(highest_pos)}) + chr_lengths.append( + {"chr": str(this_chr), "size": str(highest_pos)}) else: - chr_lengths.append({"chr": str(this_chr), "size": str(highest_pos)}) + chr_lengths.append( + {"chr": str(this_chr), "size": str(highest_pos)}) this_chr = chr_as_num else: if mapping_method == "reaper": @@ -722,7 +766,8 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): combined_string = "" for var in categorical_vars: if var in list(sample_list.sample_attribute_values[sample].keys()): - combined_string += str(sample_list.sample_attribute_values[sample][var]) + combined_string += str( + sample_list.sample_attribute_values[sample][var]) else: combined_string += "NA" else: @@ -730,7 +775,8 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): perm_strata_strings.append(combined_string) - d = dict([(y, x + 1) for x, y in enumerate(sorted(set(perm_strata_strings)))]) + d = dict([(y, x + 1) + for x, y in enumerate(sorted(set(perm_strata_strings)))]) list_to_numbers = [d[x] for x in perm_strata_strings] perm_strata = list_to_numbers diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py index d7c9ef95..7b9ff8fe 100644 --- a/wqflask/wqflask/model.py +++ b/wqflask/wqflask/model.py @@ -17,7 +17,8 @@ from wqflask.database import Base, init_db class User(Base): __tablename__ = "user" - id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4())) + id = Column(Unicode(36), primary_key=True, + default=lambda: str(uuid.uuid4())) email_address = Column(Unicode(50), unique=True, nullable=False) # Todo: Turn on strict mode for Mysql @@ -28,11 +29,13 @@ class User(Base): active = Column(Boolean(), nullable=False, default=True) - registration_info = Column(Text) # json detailing when they were registered, etc. + # json detailing when they were registered, etc. + registration_info = Column(Text) confirmed = Column(Text) # json detailing when they confirmed, etc. - superuser = Column(Text) # json detailing when they became a superuser, otherwise empty + # json detailing when they became a superuser, otherwise empty + superuser = Column(Text) # if not superuser logins = relationship("Login", @@ -66,7 +69,8 @@ class User(Base): def get_collection_by_name(self, collection_name): try: - collect = self.user_collections.filter_by(name=collection_name).first() + collect = self.user_collections.filter_by( + name=collection_name).first() except sqlalchemy.orm.exc.NoResultFound: collect = None return collect @@ -118,12 +122,15 @@ class User(Base): class Login(Base): __tablename__ = "login" - id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4())) + id = Column(Unicode(36), primary_key=True, + default=lambda: str(uuid.uuid4())) user = Column(Unicode(36), ForeignKey('user.id')) timestamp = Column(DateTime(), default=lambda: datetime.datetime.utcnow()) ip_address = Column(Unicode(39)) - successful = Column(Boolean(), nullable=False) # False if wrong password was entered - session_id = Column(Text) # Set only if successfully logged in, otherwise should be blank + # False if wrong password was entered + successful = Column(Boolean(), nullable=False) + # Set only if successfully logged in, otherwise should be blank + session_id = Column(Text) # Set to user who assumes identity if this was a login for debugging purposes by a superuser assumed_by = Column(Unicode(36), ForeignKey('user.id')) @@ -137,13 +144,16 @@ class Login(Base): class UserCollection(Base): __tablename__ = "user_collection" - id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4())) + id = Column(Unicode(36), primary_key=True, + default=lambda: str(uuid.uuid4())) user = Column(Unicode(36), ForeignKey('user.id')) # I'd prefer this to not have a length, but for the index below it needs one name = Column(Unicode(50)) - created_timestamp = Column(DateTime(), default=lambda: datetime.datetime.utcnow()) - changed_timestamp = Column(DateTime(), default=lambda: datetime.datetime.utcnow()) + created_timestamp = Column( + DateTime(), default=lambda: datetime.datetime.utcnow()) + changed_timestamp = Column( + DateTime(), default=lambda: datetime.datetime.utcnow()) members = Column(Text) # We're going to store them as a json list # This index ensures a user doesn't have more than one collection with the same name diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index 4591710c..36d4cd61 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -47,7 +47,8 @@ def search_for_user(): params = request.form user_list = [] user_list += get_users_like_unique_column("full_name", params['user_name']) - user_list += get_users_like_unique_column("email_address", params['user_email']) + user_list += get_users_like_unique_column( + "email_address", params['user_email']) return json.dumps(user_list) @@ -61,7 +62,8 @@ def search_for_groups(): user_list = [] user_list += get_users_like_unique_column("full_name", params['user_name']) - user_list += get_users_like_unique_column("email_address", params['user_email']) + user_list += get_users_like_unique_column( + "email_address", params['user_email']) for user in user_list: group_list += get_groups_like_unique_column("admins", user['user_id']) group_list += get_groups_like_unique_column("members", user['user_id']) @@ -124,7 +126,8 @@ def add_group_to_resource(): 'admin': request.form['admin_privilege'] } add_access_mask(resource_id, group_id, access_mask) - flash("Privileges have been added for group {}.".format(group_name), "alert-info") + flash("Privileges have been added for group {}.".format( + group_name), "alert-info") return redirect(url_for("manage_resource", resource_id=resource_id)) else: return render_template("admin/search_for_groups.html", resource_id=resource_id) diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index ed5f9bad..273a97a4 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -52,7 +52,8 @@ class SearchResultPage: search = self.search_terms self.original_search_string = self.search_terms # check for dodgy search terms - rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*', re.IGNORECASE) + rx = re.compile( + r'.*\W(href|http|sql|select|update)\W.*', re.IGNORECASE) if rx.match(search): logger.info("Regex failed search") self.search_term_exists = False @@ -96,7 +97,8 @@ class SearchResultPage: trait_list = [] json_trait_list = [] - species = webqtlDatabaseFunction.retrieve_species(self.dataset.group.name) + species = webqtlDatabaseFunction.retrieve_species( + self.dataset.group.name) # result_set represents the results for each search term; a search of # "shh grin2b" would have two sets of results, one for each term logger.debug("self.results is:", pf(self.results)) @@ -109,7 +111,8 @@ class SearchResultPage: trait_dict = {} trait_id = result[0] - this_trait = create_trait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) + this_trait = create_trait( + dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) if this_trait: trait_dict['index'] = index + 1 trait_dict['name'] = this_trait.name @@ -118,7 +121,8 @@ class SearchResultPage: else: trait_dict['display_name'] = this_trait.name trait_dict['dataset'] = this_trait.dataset.name - trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) + trait_dict['hmac'] = hmac.data_hmac( + '{}:{}'.format(this_trait.name, this_trait.dataset.name)) if this_trait.dataset.type == "ProbeSet": trait_dict['symbol'] = this_trait.symbol if this_trait.symbol else "N/A" trait_dict['description'] = "N/A" @@ -168,9 +172,11 @@ class SearchResultPage: self.trait_list = trait_list if self.dataset.type == "ProbeSet": - self.header_data_names = ['index', 'display_name', 'symbol', 'description', 'location', 'mean', 'lrs_score', 'lrs_location', 'additive'] + self.header_data_names = ['index', 'display_name', 'symbol', 'description', + 'location', 'mean', 'lrs_score', 'lrs_location', 'additive'] elif self.dataset.type == "Publish": - self.header_data_names = ['index', 'display_name', 'description', 'mean', 'authors', 'pubmed_text', 'lrs_score', 'lrs_location', 'additive'] + self.header_data_names = ['index', 'display_name', 'description', 'mean', + 'authors', 'pubmed_text', 'lrs_score', 'lrs_location', 'additive'] elif self.dataset.type == "Geno": self.header_data_names = ['index', 'display_name', 'location'] @@ -184,7 +190,8 @@ class SearchResultPage: combined_from_clause = "" combined_where_clause = "" - previous_from_clauses = [] # The same table can't be referenced twice in the from clause + # The same table can't be referenced twice in the from clause + previous_from_clauses = [] logger.debug("len(search_terms)>1") symbol_list = [] @@ -198,7 +205,8 @@ class SearchResultPage: for i, a_search in enumerate(alias_terms): the_search = self.get_search_ob(a_search) if the_search != None: - get_from_clause = getattr(the_search, "get_from_clause", None) + get_from_clause = getattr( + the_search, "get_from_clause", None) if callable(get_from_clause): from_clause = the_search.get_from_clause() if from_clause in previous_from_clauses: @@ -222,7 +230,8 @@ class SearchResultPage: else: the_search = self.get_search_ob(a_search) if the_search != None: - get_from_clause = getattr(the_search, "get_from_clause", None) + get_from_clause = getattr( + the_search, "get_from_clause", None) if callable(get_from_clause): from_clause = the_search.get_from_clause() if from_clause in previous_from_clauses: @@ -241,7 +250,8 @@ class SearchResultPage: self.search_term_exists = False if self.search_term_exists: combined_where_clause = "(" + combined_where_clause + ")" - final_query = the_search.compile_final_query(combined_from_clause, combined_where_clause) + final_query = the_search.compile_final_query( + combined_from_clause, combined_where_clause) results = the_search.execute(final_query) self.results.extend(results) @@ -312,7 +322,8 @@ def get_aliases(symbol_list, species): symbols_string = ",".join(updated_symbols) filtered_aliases = [] - response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases2/" + symbols_string) + response = requests.get( + GN2_BASE_URL + "/gn3/gene/aliases2/" + symbols_string) if response: alias_lists = json.loads(response.content) seen = set() diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 496dee57..6419335e 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -74,14 +74,20 @@ class SampleList: if 'rrid' in sample.extra_attributes: if self.dataset.group.species == "mouse": if len(sample.extra_attributes['rrid'].split(":")) > 1: - the_rrid = sample.extra_attributes['rrid'].split(":")[1] - sample.extra_attributes['rrid'] = [sample.extra_attributes['rrid']] - sample.extra_attributes['rrid'].append(webqtlConfig.RRID_MOUSE_URL % the_rrid) + the_rrid = sample.extra_attributes['rrid'].split(":")[ + 1] + sample.extra_attributes['rrid'] = [ + sample.extra_attributes['rrid']] + sample.extra_attributes['rrid'].append( + webqtlConfig.RRID_MOUSE_URL % the_rrid) elif self.dataset.group.species == "rat": if len(str(sample.extra_attributes['rrid'])): - the_rrid = sample.extra_attributes['rrid'].split("_")[1] - sample.extra_attributes['rrid'] = [sample.extra_attributes['rrid']] - sample.extra_attributes['rrid'].append(webqtlConfig.RRID_RAT_URL % the_rrid) + the_rrid = sample.extra_attributes['rrid'].split("_")[ + 1] + sample.extra_attributes['rrid'] = [ + sample.extra_attributes['rrid']] + sample.extra_attributes['rrid'].append( + webqtlConfig.RRID_RAT_URL % the_rrid) self.sample_list.append(sample) @@ -130,7 +136,8 @@ class SampleList: self.attributes[key].name = name self.attributes[key].distinct_values = [ item.Value for item in values] - self.attributes[key].distinct_values = natural_sort(self.attributes[key].distinct_values) + self.attributes[key].distinct_values = natural_sort( + self.attributes[key].distinct_values) all_numbers = True for value in self.attributes[key].distinct_values: try: @@ -170,7 +177,8 @@ class SampleList: except ValueError: pass - attribute_values[self.attributes[item.Id].name.lower()] = attribute_value + attribute_values[self.attributes[item.Id].name.lower( + )] = attribute_value self.sample_attribute_values[sample_name] = attribute_values def get_first_attr_col(self): diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py index f0fcd27d..81e7903b 100644 --- a/wqflask/wqflask/show_trait/export_trait_data.py +++ b/wqflask/wqflask/show_trait/export_trait_data.py @@ -40,16 +40,23 @@ def get_export_metadata(trait_id, dataset_name): metadata = [] if dataset.type == "Publish": metadata.append(["Phenotype ID: " + trait_id]) - metadata.append(["Phenotype URL: " + "http://genenetwork.org/show_trait?trait_id=" + trait_id + "&dataset=" + dataset_name]) + metadata.append(["Phenotype URL: " + "http://genenetwork.org/show_trait?trait_id=" + \ + trait_id + "&dataset=" + dataset_name]) metadata.append(["Group: " + dataset.group.name]) - metadata.append(["Phenotype: " + this_trait.description_display.replace(",", "\",\"")]) - metadata.append(["Authors: " + (this_trait.authors if this_trait.authors else "N/A")]) - metadata.append(["Title: " + (this_trait.title if this_trait.title else "N/A")]) - metadata.append(["Journal: " + (this_trait.journal if this_trait.journal else "N/A")]) - metadata.append(["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset.name]) + metadata.append( + ["Phenotype: " + this_trait.description_display.replace(",", "\",\"")]) + metadata.append( + ["Authors: " + (this_trait.authors if this_trait.authors else "N/A")]) + metadata.append( + ["Title: " + (this_trait.title if this_trait.title else "N/A")]) + metadata.append( + ["Journal: " + (this_trait.journal if this_trait.journal else "N/A")]) + metadata.append( + ["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset.name]) else: metadata.append(["Record ID: " + trait_id]) - metadata.append(["Trait URL: " + "http://genenetwork.org/show_trait?trait_id=" + trait_id + "&dataset=" + dataset_name]) + metadata.append(["Trait URL: " + "http://genenetwork.org/show_trait?trait_id=" + \ + trait_id + "&dataset=" + dataset_name]) if this_trait.symbol: metadata.append(["Symbol: " + this_trait.symbol]) metadata.append(["Dataset: " + dataset.name]) diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index e5c67165..7fcbe984 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -27,9 +27,11 @@ class SnpBrowser: self.table_rows = [] if self.limit_strains == "true": - self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type=self.variant_type, strains=self.chosen_strains, empty_columns = self.empty_columns) + self.header_fields, self.empty_field_count, self.header_data_names = get_header_list( + variant_type=self.variant_type, strains=self.chosen_strains, empty_columns = self.empty_columns) else: - self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type=self.variant_type, strains=self.strain_lists, species = self.species_name, empty_columns = self.empty_columns) + self.header_fields, self.empty_field_count, self.header_data_names = get_header_list( + variant_type=self.variant_type, strains=self.strain_lists, species = self.species_name, empty_columns = self.empty_columns) def initialize_parameters(self, start_vars): if 'first_run' in start_vars: @@ -53,10 +55,12 @@ class SnpBrowser: self.rat_chr_list = [] mouse_species_ob = species.TheSpecies(species_name="Mouse") for key in mouse_species_ob.chromosomes.chromosomes: - self.mouse_chr_list.append(mouse_species_ob.chromosomes.chromosomes[key].name) + self.mouse_chr_list.append( + mouse_species_ob.chromosomes.chromosomes[key].name) rat_species_ob = species.TheSpecies(species_name="Rat") for key in rat_species_ob.chromosomes.chromosomes: - self.rat_chr_list.append(rat_species_ob.chromosomes.chromosomes[key].name) + self.rat_chr_list.append( + rat_species_ob.chromosomes.chromosomes[key].name) if self.species_id == 1: self.this_chr_list = self.mouse_chr_list @@ -109,9 +113,11 @@ class SnpBrowser: "CAST/EiJ"] self.chosen_strains_rat = ["BN", "F344", "WLI", "WMI"] if 'chosen_strains_mouse' in start_vars: - self.chosen_strains_mouse = start_vars['chosen_strains_mouse'].split(",") + self.chosen_strains_mouse = start_vars['chosen_strains_mouse'].split( + ",") if 'chosen_strains_rat' in start_vars: - self.chosen_strains_rat = start_vars['chosen_strains_rat'].split(",") + self.chosen_strains_rat = start_vars['chosen_strains_rat'].split( + ",") if self.species_id == 1: self.chosen_strains = self.chosen_strains_mouse @@ -150,9 +156,11 @@ class SnpBrowser: if self.gene_name != "": if self.species_id != 0: - query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE SpeciesId = %s AND geneSymbol = '%s'" % (self.species_id, self.gene_name) + query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE SpeciesId = %s AND geneSymbol = '%s'" % ( + self.species_id, self.gene_name) else: - query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE geneSymbol = '%s'" % (self.gene_name) + query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE geneSymbol = '%s'" % ( + self.gene_name) result = g.db.execute(query).fetchone() if result: self.gene_name, self.chr, self.start_mb, self.end_mb = result @@ -163,9 +171,11 @@ class SnpBrowser: query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll WHERE Rs = '%s'" % self.gene_name else: if self.species_id != 0: - query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SpeciesId = %s AND SnpName = '%s'" % (self.species_id, self.gene_name) + query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SpeciesId = %s AND SnpName = '%s'" % ( + self.species_id, self.gene_name) else: - query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SnpName = '%s'" % (self.gene_name) + query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SnpName = '%s'" % ( + self.gene_name) result_snp = g.db.execute(query).fetchall() if result_snp: self.snp_list = [item[0] for item in result_snp] @@ -177,9 +187,11 @@ class SnpBrowser: elif self.variant_type == "InDel": if self.gene_name[0] == "I": if self.species_id != 0: - query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE SpeciesId = %s AND Name = '%s'" % (self.species_id, self.gene_name) + query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE SpeciesId = %s AND Name = '%s'" % ( + self.species_id, self.gene_name) else: - query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE Name = '%s'" % (self.gene_name) + query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE Name = '%s'" % ( + self.gene_name) result_snp = g.db.execute(query).fetchall() if result_snp: self.snp_list = [item[0] for item in result_snp] @@ -255,7 +267,8 @@ class SnpBrowser: if self.limit_strains == "true" and len(self.chosen_strains) > 0: for item in self.chosen_strains: - index = self.strain_lists[self.species_name.lower()].index(item) + index = self.strain_lists[self.species_name.lower()].index( + item) strain_index_list.append(index) for seq, result in enumerate(results): @@ -263,7 +276,8 @@ class SnpBrowser: if self.variant_type == "SNP": display_strains = [] - snp_id, species_id, snp_name, rs, chr, mb, mb_2016, alleles, snp_source, conservation_score = result[:10] + snp_id, species_id, snp_name, rs, chr, mb, mb_2016, alleles, snp_source, conservation_score = result[ + :10] effect_list = result[10:28] if self.species_id == 1: self.allele_list = result[30:] @@ -279,7 +293,8 @@ class SnpBrowser: self.allele_list = display_strains effect_info_dict = get_effect_info(effect_list) - coding_domain_list = ['Start Gained', 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] + coding_domain_list = ['Start Gained', 'Start Lost', + 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] intron_domain_list = ['Splice Site', 'Nonsplice Site'] for key in effect_info_dict: @@ -296,19 +311,22 @@ class SnpBrowser: if 'Intergenic' in domain: if self.gene_name != "": - gene_id = get_gene_id(self.species_id, self.gene_name) + gene_id = get_gene_id( + self.species_id, self.gene_name) gene = [gene_id, self.gene_name] else: gene = check_if_in_gene(species_id, chr, mb) transcript = exon = function = function_details = '' if self.redundant == "false" or last_mb != mb: # filter redundant if self.include_record(domain, function, snp_source, conservation_score): - info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id] + info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, + function, function_details, snp_source, conservation_score, snp_id] info_list.extend(self.allele_list) filtered_results.append(info_list) last_mb = mb else: - gene_list, transcript_list, exon_list, function_list, function_details_list = effect_info_dict[key] + gene_list, transcript_list, exon_list, function_list, function_details_list = effect_info_dict[ + key] for index, item in enumerate(gene_list): gene = item transcript = transcript_list[index] @@ -325,13 +343,15 @@ class SnpBrowser: function = "" if function_details_list: - function_details = "Biotype: " + function_details_list[index] + function_details = "Biotype: " + \ + function_details_list[index] else: function_details = "" if self.redundant == "false" or last_mb != mb: if self.include_record(domain, function, snp_source, conservation_score): - info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id] + info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, + function, function_details, snp_source, conservation_score, snp_id] info_list.extend(self.allele_list) filtered_results.append(info_list) last_mb = mb @@ -345,7 +365,8 @@ class SnpBrowser: gene = "No Gene" domain = conservation_score = snp_id = snp_name = rs = flank_3 = flank_5 = ncbi = function = "" if self.include_record(domain, function, source_name, conservation_score): - filtered_results.append([indel_name, indel_chr, indel_mb_start, indel_mb_end, indel_strand, indel_type, indel_size, indel_sequence, source_name]) + filtered_results.append([indel_name, indel_chr, indel_mb_start, indel_mb_end, + indel_strand, indel_type, indel_size, indel_sequence, source_name]) last_mb = indel_mb_start else: @@ -365,7 +386,8 @@ class SnpBrowser: if gene_name and (gene_name not in gene_name_list): gene_name_list.append(gene_name) if len(gene_name_list) > 0: - gene_id_name_dict = get_gene_id_name_dict(self.species_id, gene_name_list) + gene_id_name_dict = get_gene_id_name_dict( + self.species_id, gene_name_list) # ZS: list of booleans representing which columns are entirely empty, so they aren't displayed on the page; only including ones that are sometimes empty (since there's always a location, etc) self.empty_columns = { @@ -383,7 +405,8 @@ class SnpBrowser: for i, result in enumerate(self.filtered_results): this_row = {} if self.variant_type == "SNP": - snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id = result[:14] + snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id = result[ + :14] allele_value_list = result[14:] if rs: snp_url = webqtlConfig.DBSNP % (rs) @@ -394,9 +417,11 @@ class SnpBrowser: end_bp = int(mb * 1000000 + 100) position_info = "chr%s:%d-%d" % (chr, start_bp, end_bp) if self.species_id == 2: - snp_url = webqtlConfig.GENOMEBROWSER_URL % ("rn6", position_info) + snp_url = webqtlConfig.GENOMEBROWSER_URL % ( + "rn6", position_info) else: - snp_url = webqtlConfig.GENOMEBROWSER_URL % ("mm10", position_info) + snp_url = webqtlConfig.GENOMEBROWSER_URL % ( + "mm10", position_info) mb = float(mb) mb_formatted = "%2.6f" % mb @@ -429,7 +454,8 @@ class SnpBrowser: gene_link = "" if transcript: - transcript_link = webqtlConfig.ENSEMBLETRANSCRIPT_URL % (transcript) + transcript_link = webqtlConfig.ENSEMBLETRANSCRIPT_URL % ( + transcript) self.empty_columns['transcript'] = "true" else: transcript_link = "" @@ -460,7 +486,8 @@ class SnpBrowser: function_list = function_details.strip().split(",") function_list = [item.strip() for item in function_list] function_list[0] = function_list[0].title() - function_details = ", ".join(item for item in function_list) + function_details = ", ".join( + item for item in function_list) function_details = function_details.replace("_", " ") function_details = function_details.replace("/", " -> ") if function_details == "Biotype: Protein Coding": @@ -675,8 +702,10 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None): header_fields = [] header_data_names = [] if variant_type == "SNP": - header_fields.append(['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore', 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details']) - header_data_names = ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', 'snp_source', 'conservation_score', 'gene_name', 'transcript', 'exon', 'domain_1', 'domain_2', 'function', 'function_details'] + header_fields.append(['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore', + 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details']) + header_data_names = ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', 'snp_source', 'conservation_score', + 'gene_name', 'transcript', 'exon', 'domain_1', 'domain_2', 'function', 'function_details'] header_fields.append(strain_list) header_data_names += strain_list @@ -712,8 +741,10 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None): header_data_names.remove(col) elif variant_type == "InDel": - header_fields = ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'] - header_data_names = ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s', 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'] + header_fields = ['Index', 'ID', 'Type', 'InDel Chr', + 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'] + header_data_names = ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s', + 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'] return header_fields, empty_field_count, header_data_names @@ -726,10 +757,13 @@ def get_effect_details_by_category(effect_name=None, effect_value=None): function_detail_list = [] tmp_list = [] - gene_group_list = ['Upstream', 'Downstream', 'Splice Site', 'Nonsplice Site', '3\' UTR'] - biotype_group_list = ['Unknown Effect In Exon', 'Start Gained', 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] + gene_group_list = ['Upstream', 'Downstream', + 'Splice Site', 'Nonsplice Site', '3\' UTR'] + biotype_group_list = ['Unknown Effect In Exon', 'Start Gained', + 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] new_codon_group_list = ['Start Gained'] - codon_effect_group_list = ['Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] + codon_effect_group_list = [ + 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] effect_detail_list = effect_value.strip().split('|') effect_detail_list = [item.strip() for item in effect_detail_list] @@ -773,8 +807,10 @@ def get_effect_info(effect_list): effect_detail_list = [] effect_info_dict = {} - prime3_utr, prime5_utr, upstream, downstream, intron, nonsplice_site, splice_site, intergenic = effect_list[:8] - exon, non_synonymous_coding, synonymous_coding, start_gained, start_lost, stop_gained, stop_lost, unknown_effect_in_exon = effect_list[8:16] + prime3_utr, prime5_utr, upstream, downstream, intron, nonsplice_site, splice_site, intergenic = effect_list[ + :8] + exon, non_synonymous_coding, synonymous_coding, start_gained, start_lost, stop_gained, stop_lost, unknown_effect_in_exon = effect_list[ + 8:16] if intergenic: domain = "Intergenic" @@ -783,59 +819,72 @@ def get_effect_info(effect_list): # if not exon, get gene list/transcript list info if upstream: domain = "Upstream" - effect_detail_list = get_effect_details_by_category(effect_name='Upstream', effect_value=upstream) + effect_detail_list = get_effect_details_by_category( + effect_name='Upstream', effect_value=upstream) effect_info_dict[domain] = effect_detail_list if downstream: domain = "Downstream" - effect_detail_list = get_effect_details_by_category(effect_name='Downstream', effect_value=downstream) + effect_detail_list = get_effect_details_by_category( + effect_name='Downstream', effect_value=downstream) effect_info_dict[domain] = effect_detail_list if intron: if splice_site: domain = "Splice Site" - effect_detail_list = get_effect_details_by_category(effect_name='Splice Site', effect_value=splice_site) + effect_detail_list = get_effect_details_by_category( + effect_name='Splice Site', effect_value=splice_site) effect_info_dict[domain] = effect_detail_list if nonsplice_site: domain = "Nonsplice Site" - effect_detail_list = get_effect_details_by_category(effect_name='Nonsplice Site', effect_value=nonsplice_site) + effect_detail_list = get_effect_details_by_category( + effect_name='Nonsplice Site', effect_value=nonsplice_site) effect_info_dict[domain] = effect_detail_list # get gene, transcript_list, and exon info if prime3_utr: domain = "3\' UTR" - effect_detail_list = get_effect_details_by_category(effect_name='3\' UTR', effect_value=prime3_utr) + effect_detail_list = get_effect_details_by_category( + effect_name='3\' UTR', effect_value=prime3_utr) effect_info_dict[domain] = effect_detail_list if prime5_utr: domain = "5\' UTR" - effect_detail_list = get_effect_details_by_category(effect_name='5\' UTR', effect_value=prime5_utr) + effect_detail_list = get_effect_details_by_category( + effect_name='5\' UTR', effect_value=prime5_utr) effect_info_dict[domain] = effect_detail_list if start_gained: domain = "Start Gained" - effect_detail_list = get_effect_details_by_category(effect_name='Start Gained', effect_value=start_gained) + effect_detail_list = get_effect_details_by_category( + effect_name='Start Gained', effect_value=start_gained) effect_info_dict[domain] = effect_detail_list if unknown_effect_in_exon: domain = "Unknown Effect In Exon" - effect_detail_list = get_effect_details_by_category(effect_name='Unknown Effect In Exon', effect_value=unknown_effect_in_exon) + effect_detail_list = get_effect_details_by_category( + effect_name='Unknown Effect In Exon', effect_value=unknown_effect_in_exon) effect_info_dict[domain] = effect_detail_list if start_lost: domain = "Start Lost" - effect_detail_list = get_effect_details_by_category(effect_name='Start Lost', effect_value=start_lost) + effect_detail_list = get_effect_details_by_category( + effect_name='Start Lost', effect_value=start_lost) effect_info_dict[domain] = effect_detail_list if stop_gained: domain = "Stop Gained" - effect_detail_list = get_effect_details_by_category(effect_name='Stop Gained', effect_value=stop_gained) + effect_detail_list = get_effect_details_by_category( + effect_name='Stop Gained', effect_value=stop_gained) effect_info_dict[domain] = effect_detail_list if stop_lost: domain = "Stop Lost" - effect_detail_list = get_effect_details_by_category(effect_name='Stop Lost', effect_value=stop_lost) + effect_detail_list = get_effect_details_by_category( + effect_name='Stop Lost', effect_value=stop_lost) effect_info_dict[domain] = effect_detail_list if non_synonymous_coding: domain = "Nonsynonymous" - effect_detail_list = get_effect_details_by_category(effect_name='Nonsynonymous', effect_value=non_synonymous_coding) + effect_detail_list = get_effect_details_by_category( + effect_name='Nonsynonymous', effect_value=non_synonymous_coding) effect_info_dict[domain] = effect_detail_list if synonymous_coding: domain = "Synonymous" - effect_detail_list = get_effect_details_by_category(effect_name='Synonymous', effect_value=synonymous_coding) + effect_detail_list = get_effect_details_by_category( + effect_name='Synonymous', effect_value=synonymous_coding) effect_info_dict[domain] = effect_detail_list return effect_info_dict @@ -863,7 +912,8 @@ def get_gene_id_name_dict(species_id, gene_name_list): gene_id_name_dict = {} if len(gene_name_list) == 0: return "" - gene_name_str_list = ["'" + gene_name + "'" for gene_name in gene_name_list] + gene_name_str_list = ["'" + gene_name + \ + "'" for gene_name in gene_name_list] gene_name_str = ",".join(gene_name_str_list) query = """ diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py index 07073d6a..2e467dc8 100644 --- a/wqflask/wqflask/update_search_results.py +++ b/wqflask/wqflask/update_search_results.py @@ -52,10 +52,12 @@ class GSearch: self.trait_list = [] with Bench("Creating trait objects"): for line in re: - dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False) + dataset = create_dataset( + line[3], "ProbeSet", get_samplelist=False) trait_id = line[4] # with Bench("Building trait object"): - this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) + this_trait = GeneralTrait( + dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) self.trait_list.append(this_trait) elif self.type == "phenotype": @@ -97,7 +99,8 @@ class GSearch: for line in re: dataset = create_dataset(line[2], "Publish") trait_id = line[3] - this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) + this_trait = GeneralTrait( + dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) self.trait_list.append(this_trait) self.results = self.convert_to_json() diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py index 2a2f8484..708d43d2 100644 --- a/wqflask/wqflask/user_login.py +++ b/wqflask/wqflask/user_login.py @@ -70,7 +70,8 @@ def set_password(password): assert len(password) >= 6, "Password shouldn't be shorter than 6 characters" - encoded_password = encode_password(pass_gen_fields, pass_gen_fields['unencrypted_password']) + encoded_password = encode_password( + pass_gen_fields, pass_gen_fields['unencrypted_password']) return encoded_password @@ -161,12 +162,16 @@ def verify_email(): # As long as they have access to the email account # We might as well log them in session_id_signed = get_signed_session_id(user_details) - flash("Thank you for logging in {}.".format(user_details['full_name']), "alert-success") - response = make_response(redirect(url_for('index_page', import_collections=import_col, anon_id=anon_id))) - response.set_cookie(UserSession.user_cookie_name, session_id_signed, max_age=None) + flash("Thank you for logging in {}.".format( + user_details['full_name']), "alert-success") + response = make_response(redirect( + url_for('index_page', import_collections=import_col, anon_id=anon_id))) + response.set_cookie(UserSession.user_cookie_name, + session_id_signed, max_age=None) return response else: - flash("Invalid code: Password reset code does not exist or might have expired!", "error") + flash( + "Invalid code: Password reset code does not exist or might have expired!", "error") @app.route("/n/login", methods=('GET', 'POST')) @@ -195,23 +200,28 @@ def login(): display_id = user_details['orcid'] else: display_id = "" - flash("Thank you for logging in {}.".format(display_id), "alert-success") + flash("Thank you for logging in {}.".format( + display_id), "alert-success") response = make_response(redirect(url_for('index_page'))) - response.set_cookie(UserSession.user_cookie_name, session_id_signed, max_age=None) + response.set_cookie( + UserSession.user_cookie_name, session_id_signed, max_age=None) else: flash("Something went unexpectedly wrong.", "alert-danger") response = make_response(redirect(url_for('index_page'))) return response else: - user_details = get_user_by_unique_column("email_address", params['email_address']) + user_details = get_user_by_unique_column( + "email_address", params['email_address']) password_match = False if user_details: submitted_password = params['password'] pwfields = user_details['password'] if isinstance(pwfields, str): pwfields = json.loads(pwfields) - encrypted_pass_fields = encode_password(pwfields, submitted_password) - password_match = pbkdf2.safe_str_cmp(encrypted_pass_fields['password'], pwfields['password']) + encrypted_pass_fields = encode_password( + pwfields, submitted_password) + password_match = pbkdf2.safe_str_cmp( + encrypted_pass_fields['password'], pwfields['password']) else: # Invalid e-mail flash("Invalid e-mail address. Please try again.", "alert-danger") @@ -227,12 +237,16 @@ def login(): anon_id = params['anon_id'] session_id_signed = get_signed_session_id(user_details) - flash("Thank you for logging in {}.".format(user_details['full_name']), "alert-success") - response = make_response(redirect(url_for('index_page', import_collections=import_col, anon_id=anon_id))) - response.set_cookie(UserSession.user_cookie_name, session_id_signed, max_age=None) + flash("Thank you for logging in {}.".format( + user_details['full_name']), "alert-success") + response = make_response(redirect( + url_for('index_page', import_collections=import_col, anon_id=anon_id))) + response.set_cookie( + UserSession.user_cookie_name, session_id_signed, max_age=None) return response else: - email_ob = send_verification_email(user_details, template_name="email/user_verification.txt") + email_ob = send_verification_email( + user_details, template_name="email/user_verification.txt") return render_template("newsecurity/verification_still_needed.html", subject=email_ob['subject']) else: # Incorrect password # ZS: It previously seemed to store that there was an incorrect log-in attempt here, but it did so in the MySQL DB so this might need to be reproduced with Redis @@ -252,8 +266,10 @@ def github_oauth2(): "code": code } - result = requests.post("https://github.com/login/oauth/access_token", json=data) - result_dict = {arr[0]: arr[1] for arr in [tok.split("=") for tok in result.text.split("&")]} + result = requests.post( + "https://github.com/login/oauth/access_token", json=data) + result_dict = {arr[0]: arr[1] + for arr in [tok.split("=") for tok in result.text.split("&")]} github_user = get_github_user_details(result_dict["access_token"]) @@ -277,7 +293,8 @@ def github_oauth2(): def get_github_user_details(access_token): from utility.tools import GITHUB_API_URL - result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content + result = requests.get(GITHUB_API_URL, headers={ + 'Authorization': 'token ' + access_token}).content return json.loads(result) @@ -323,7 +340,8 @@ def orcid_oauth2(): def get_github_user_details(access_token): from utility.tools import GITHUB_API_URL - result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content + result = requests.get(GITHUB_API_URL, headers={ + 'Authorization': 'token ' + access_token}).content return json.loads(result) @@ -389,13 +407,16 @@ def forgot_password_submit(): next_page = None if email_address != "": logger.debug("Wants to send password E-mail to ", email_address) - user_details = get_user_by_unique_column("email_address", email_address) + user_details = get_user_by_unique_column( + "email_address", email_address) if user_details: - email_subject = send_forgot_password_email(user_details["email_address"]) + email_subject = send_forgot_password_email( + user_details["email_address"]) return render_template("new_security/forgot_password_step2.html", subject=email_subject) else: - flash("The e-mail entered is not associated with an account.", "alert-danger") + flash("The e-mail entered is not associated with an account.", + "alert-danger") return redirect(url_for("forgot_password")) else: @@ -417,7 +438,8 @@ def password_reset(): return render_template( "new_security/password_reset.html", user_encode=user_details["email_address"]) else: - flash("Invalid code: Password reset code does not exist or might have expired!", "error") + flash( + "Invalid code: Password reset code does not exist or might have expired!", "error") return redirect(url_for("login")) else: return redirect(url_for("login")) @@ -446,21 +468,27 @@ def register_user(params): errors = [] user_details = {} - user_details['email_address'] = params.get('email_address', '').encode("utf-8").strip() + user_details['email_address'] = params.get( + 'email_address', '').encode("utf-8").strip() if not (5 <= len(user_details['email_address']) <= 50): - errors.append('Email Address needs to be between 5 and 50 characters.') + errors.append( + 'Email Address needs to be between 5 and 50 characters.') else: - email_exists = get_user_by_unique_column("email_address", user_details['email_address']) + email_exists = get_user_by_unique_column( + "email_address", user_details['email_address']) if email_exists: errors.append('User already exists with that email') - user_details['full_name'] = params.get('full_name', '').encode("utf-8").strip() + user_details['full_name'] = params.get( + 'full_name', '').encode("utf-8").strip() if not (5 <= len(user_details['full_name']) <= 50): errors.append('Full Name needs to be between 5 and 50 characters.') - user_details['organization'] = params.get('organization', '').encode("utf-8").strip() + user_details['organization'] = params.get( + 'organization', '').encode("utf-8").strip() if user_details['organization'] and not (5 <= len(user_details['organization']) <= 50): - errors.append('Organization needs to be empty or between 5 and 50 characters.') + errors.append( + 'Organization needs to be empty or between 5 and 50 characters.') password = str(params.get('password', '')) if not (6 <= len(password)): @@ -493,7 +521,8 @@ def register(): errors = register_user(params) if len(errors) == 0: - flash("Registration successful. You may login with your new account", "alert-info") + flash( + "Registration successful. You may login with your new account", "alert-info") return redirect(url_for("login")) return render_template("new_security/register_user.html", values=params, errors=errors) diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index a9bd65e6..5610833b 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -93,8 +93,10 @@ class AnonUser: this_collection = {} this_collection['id'] = collection['id'] this_collection['name'] = collection['name'] - this_collection['created_timestamp'] = collection['created_timestamp'].strftime('%b %d %Y %I:%M%p') - this_collection['changed_timestamp'] = collection['changed_timestamp'].strftime('%b %d %Y %I:%M%p') + this_collection['created_timestamp'] = collection['created_timestamp'].strftime( + '%b %d %Y %I:%M%p') + this_collection['changed_timestamp'] = collection['changed_timestamp'].strftime( + '%b %d %Y %I:%M%p') this_collection['num_members'] = collection['num_members'] this_collection['members'] = collection['members'] updated_collections.append(this_collection) @@ -108,21 +110,26 @@ class AnonUser: else: collections = json.loads(json_collections) for collection in collections: - collection['created_timestamp'] = datetime.datetime.strptime(collection['created_timestamp'], '%b %d %Y %I:%M%p') - collection['changed_timestamp'] = datetime.datetime.strptime(collection['changed_timestamp'], '%b %d %Y %I:%M%p') + collection['created_timestamp'] = datetime.datetime.strptime( + collection['created_timestamp'], '%b %d %Y %I:%M%p') + collection['changed_timestamp'] = datetime.datetime.strptime( + collection['changed_timestamp'], '%b %d %Y %I:%M%p') - collections = sorted(collections, key=lambda i: i['changed_timestamp'], reverse=True) + collections = sorted( + collections, key=lambda i: i['changed_timestamp'], reverse=True) return collections def import_traits_to_user(self): result = Redis.get(self.key) collections_list = json.loads(result if result else "[]") for collection in collections_list: - collection_exists = g.user_session.get_collection_by_name(collection['name']) + collection_exists = g.user_session.get_collection_by_name( + collection['name']) if collection_exists: continue else: - g.user_session.add_collection(collection['name'], collection['members']) + g.user_session.add_collection( + collection['name'], collection['members']) def display_num_collections(self): """ @@ -148,7 +155,8 @@ def verify_cookie(cookie): the_uuid, separator, the_signature = cookie.partition(':') assert len(the_uuid) == 36, "Is session_id a uuid?" assert separator == ":", "Expected a : here" - assert the_signature == actual_hmac_creation(the_uuid), "Uh-oh, someone tampering with the cookie?" + assert the_signature == actual_hmac_creation( + the_uuid), "Uh-oh, someone tampering with the cookie?" return the_uuid @@ -282,7 +290,8 @@ class UserSession: updated_collection['members'] = updated_traits updated_collection['num_members'] = len(updated_traits) - updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime( + '%b %d %Y %I:%M%p') updated_collections = [] for collection in self.user_collections: @@ -308,7 +317,8 @@ class UserSession: updated_collection['members'] = updated_traits updated_collection['num_members'] = len(updated_traits) - updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime( + '%b %d %Y %I:%M%p') updated_collections = [] for collection in self.user_collections: @@ -355,7 +365,8 @@ def get_cookie(): def set_cookie(response): if not request.cookies.get(g.cookie_session.cookie_name): - response.set_cookie(g.cookie_session.cookie_name, g.cookie_session.cookie) + response.set_cookie(g.cookie_session.cookie_name, + g.cookie_session.cookie) return response @@ -390,22 +401,28 @@ class RegisterUser: self.errors = [] self.user = Bunch() - self.user.email_address = kw.get('email_address', '').encode("utf-8").strip() + self.user.email_address = kw.get( + 'email_address', '').encode("utf-8").strip() if not (5 <= len(self.user.email_address) <= 50): - self.errors.append('Email Address needs to be between 5 and 50 characters.') + self.errors.append( + 'Email Address needs to be between 5 and 50 characters.') else: - email_exists = get_user_by_unique_column("email_address", self.user.email_address) + email_exists = get_user_by_unique_column( + "email_address", self.user.email_address) #email_exists = get_user_by_unique_column(es, "email_address", self.user.email_address) if email_exists: self.errors.append('User already exists with that email') self.user.full_name = kw.get('full_name', '').encode("utf-8").strip() if not (5 <= len(self.user.full_name) <= 50): - self.errors.append('Full Name needs to be between 5 and 50 characters.') + self.errors.append( + 'Full Name needs to be between 5 and 50 characters.') - self.user.organization = kw.get('organization', '').encode("utf-8").strip() + self.user.organization = kw.get( + 'organization', '').encode("utf-8").strip() if self.user.organization and not (5 <= len(self.user.organization) <= 50): - self.errors.append('Organization needs to be empty or between 5 and 50 characters.') + self.errors.append( + 'Organization needs to be empty or between 5 and 50 characters.') password = str(kw.get('password', '')) if not (6 <= len(password)): @@ -568,14 +585,16 @@ def password_reset(): if verification_code: user_email = check_verification_code(verification_code) if user_email: - user_details = get_user_by_unique_column('email_address', user_email) + user_details = get_user_by_unique_column( + 'email_address', user_email) if user_details: return render_template( "new_security/password_reset.html", user_encode=user_details["user_id"]) else: flash("Invalid code: User no longer exists!", "error") else: - flash("Invalid code: Password reset code does not exist or might have expired!", "error") + flash( + "Invalid code: Password reset code does not exist or might have expired!", "error") else: return redirect(url_for("login")) @@ -648,8 +667,10 @@ def github_oauth2(): "client_secret": GITHUB_CLIENT_SECRET, "code": code } - result = requests.post("https://github.com/login/oauth/access_token", json=data) - result_dict = {arr[0]: arr[1] for arr in [tok.split("=") for tok in [token.encode("utf-8") for token in result.text.split("&")]]} + result = requests.post( + "https://github.com/login/oauth/access_token", json=data) + result_dict = {arr[0]: arr[1] for arr in [tok.split( + "=") for tok in [token.encode("utf-8") for token in result.text.split("&")]]} github_user = get_github_user_details(result_dict["access_token"]) @@ -696,7 +717,8 @@ def orcid_oauth2(): def get_github_user_details(access_token): from utility.tools import GITHUB_API_URL - result = requests.get(GITHUB_API_URL, params={"access_token": access_token}) + result = requests.get(GITHUB_API_URL, params={ + "access_token": access_token}) return result.json() @@ -737,7 +759,8 @@ class LoginUser: return render_template( "new_security/login_user.html", external_login=external_login, redis_is_available=is_redis_available()) else: - user_details = get_user_by_unique_column("email_address", params["email_address"]) + user_details = get_user_by_unique_column( + "email_address", params["email_address"]) #user_details = get_user_by_unique_column(es, "email_address", params["email_address"]) user = None valid = None @@ -755,8 +778,10 @@ class LoginUser: pwfields.iterations, pwfields.keylength, pwfields.hashfunc) - logger.debug("\n\nComparing:\n{}\n{}\n".format(encrypted.password, pwfields.password)) - valid = pbkdf2.safe_str_cmp(encrypted.password, pwfields.password) + logger.debug("\n\nComparing:\n{}\n{}\n".format( + encrypted.password, pwfields.password)) + valid = pbkdf2.safe_str_cmp( + encrypted.password, pwfields.password) logger.debug("valid is:", valid) if valid and not user.confirmed: @@ -782,7 +807,8 @@ class LoginUser: else: if user: self.unsuccessful_login(user) - flash("Invalid email-address or password. Please try again.", "alert-danger") + flash("Invalid email-address or password. Please try again.", + "alert-danger") response = make_response(redirect(url_for('login'))) return response @@ -790,14 +816,17 @@ class LoginUser: def actual_login(self, user, assumed_by=None, import_collections=None): """The meat of the logging in process""" session_id_signed = self.successful_login(user, assumed_by) - flash("Thank you for logging in {}.".format(user.full_name), "alert-success") - response = make_response(redirect(url_for('index_page', import_collections=import_collections))) + flash("Thank you for logging in {}.".format( + user.full_name), "alert-success") + response = make_response( + redirect(url_for('index_page', import_collections=import_collections))) if self.remember_me: max_age = self.remember_time else: max_age = None - response.set_cookie(UserSession.cookie_name, session_id_signed, max_age=max_age) + response.set_cookie(UserSession.cookie_name, + session_id_signed, max_age=max_age) return response def successful_login(self, user, assumed_by=None): @@ -866,13 +895,15 @@ def forgot_password_submit(): next_page = None if email_address != "": logger.debug("Wants to send password E-mail to ", email_address) - user_details = get_user_by_unique_column("email_address", email_address) + user_details = get_user_by_unique_column( + "email_address", email_address) if user_details: ForgotPasswordEmail(user_details["email_address"]) return render_template("new_security/forgot_password_step2.html", subject=ForgotPasswordEmail.subject) else: - flash("The e-mail entered is not associated with an account.", "alert-danger") + flash("The e-mail entered is not associated with an account.", + "alert-danger") return redirect(url_for("forgot_password")) else: @@ -959,7 +990,8 @@ def register(): errors = result.errors if len(errors) == 0: - flash("Registration successful. You may login with your new account", "alert-info") + flash( + "Registration successful. You may login with your new account", "alert-info") return redirect(url_for("login")) return render_template("new_security/register_user.html", values=params, errors=errors) diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py index f0f0d60c..6ccb2e80 100644 --- a/wqflask/wqflask/user_session.py +++ b/wqflask/wqflask/user_session.py @@ -36,7 +36,8 @@ def get_user_session(): def set_user_session(response): if hasattr(g, 'user_session'): if not request.cookies.get(g.user_session.cookie_name): - response.set_cookie(g.user_session.cookie_name, g.user_session.cookie) + response.set_cookie(g.user_session.cookie_name, + g.user_session.cookie) return response @@ -44,7 +45,8 @@ def verify_cookie(cookie): the_uuid, separator, the_signature = cookie.partition(':') assert len(the_uuid) == 36, "Is session_id a uuid?" assert separator == ":", "Expected a : here" - assert the_signature == hmac.hmac_creation(the_uuid), "Uh-oh, someone tampering with the cookie?" + assert the_signature == hmac.hmac_creation( + the_uuid), "Uh-oh, someone tampering with the cookie?" return the_uuid @@ -60,9 +62,11 @@ def create_signed_cookie(): def manage_user(): params = request.form if request.form else request.args if 'new_full_name' in params: - set_user_attribute(g.user_session.user_id, 'full_name', params['new_full_name']) + set_user_attribute(g.user_session.user_id, + 'full_name', params['new_full_name']) if 'new_organization' in params: - set_user_attribute(g.user_session.user_id, 'organization', params['new_organization']) + set_user_attribute(g.user_session.user_id, + 'organization', params['new_organization']) user_details = get_user_by_unique_column("user_id", g.user_session.user_id) @@ -108,7 +112,8 @@ class UserSession: # Grrr...this won't work because of the way flask handles cookies # Delete the cookie - flash("Due to inactivity your session has expired. If you'd like please login again.") + flash( + "Due to inactivity your session has expired. If you'd like please login again.") return None else: self.record = dict(login_time=time.time(), @@ -178,7 +183,9 @@ class UserSession: # ZS: Get user's collections if they exist collections = get_user_collections(self.user_id) - collections = [item for item in collections if item['name'] != "Your Default Collection"] + [item for item in collections if item['name'] == "Your Default Collection"] # ZS: Ensure Default Collection is last in list + collections = [item for item in collections if item['name'] != "Your Default Collection"] + \ + [item for item in collections if item['name'] == + "Your Default Collection"] # ZS: Ensure Default Collection is last in list return collections @property @@ -234,12 +241,14 @@ class UserSession: this_collection = self.get_collection_by_id(collection_id) updated_collection = this_collection - current_members_minus_new = [member for member in this_collection['members'] if member not in traits_to_add] + current_members_minus_new = [ + member for member in this_collection['members'] if member not in traits_to_add] updated_traits = traits_to_add + current_members_minus_new updated_collection['members'] = updated_traits updated_collection['num_members'] = len(updated_traits) - updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime( + '%b %d %Y %I:%M%p') updated_collections = [] for collection in self.user_collections: @@ -265,7 +274,8 @@ class UserSession: updated_collection['members'] = updated_traits updated_collection['num_members'] = len(updated_traits) - updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') + updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime( + '%b %d %Y %I:%M%p') updated_collections = [] for collection in self.user_collections: -- cgit v1.2.3