From 717677b0c09f6ba08268db12d4889503cc2606d9 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 2 Nov 2016 20:00:04 +0000 Subject: Added Scroller functionality to regular (but not global) search, which increases table load speed In order to implement Scroller (and make table look nicer), all rows are the same height and excess description/authors text is shown in a tooltip Increased table width for non-Geno DBs Fixed issue where Genotype traits did not fetch their location_repr (text for displaying location), causing that column to be blank in searches Fixed issue causing Correlation Matrix cells to not be colored corresponding with their correlation and also increased cell font a little Fixed issue where dataset link in the Correlation Page did not correctly point to corresponding GN1 page --- wqflask/base/data_set.py | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) (limited to 'wqflask/base/data_set.py') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index fddfce58..04436a2e 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -271,7 +271,8 @@ class DatasetGroup(object): self.f1list = None self.parlist = None self.get_f1_parent_strains() - #logger.debug("parents/f1s: {}:{}".format(self.parlist, self.f1list)) + + self.accession_id = self.get_accession_id() self.species = webqtlDatabaseFunction.retrieve_species(self.name) @@ -279,6 +280,20 @@ class DatasetGroup(object): self.allsamples = None self._datasets = None + def get_accession_id(self): + results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where + InbredSet.Name = %s and + PublishFreeze.InbredSetId = InbredSet.Id and + InfoFiles.InfoPageName = PublishFreeze.Name and + PublishFreeze.public > 0 and + PublishFreeze.confidentiality < 1 order by + PublishFreeze.CreateTime desc""", (self.name)).fetchone() + + if results != None: + return str(results[0]) + else: + return "None" + def get_specified_markers(self, markers = []): self.markers = HumanMarkers(self.name, markers) -- cgit v1.2.3 From e63c4014e7bc34b440707be19af3779b72102fdb Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 26 Jan 2017 16:26:16 +0000 Subject: GEMMA now works with CFW data (had to update where it looks for the input files and how it writes the phenotype file) Y-axis for GEMMA now says -log(p) Updated the style of the trait sample data table in the trait page Updated dataset_select_menu_orig.js to also build just the Species and Group drop-downs for the trait input page (as opposed to all 4 drop-downs) Updated dataset menu json file Added option to show and hide columns to regular search page using colVis Changed regular and global search result table styles/column widths Began work on user trait submission code (not working yet though) Began work on static loading page for mapping results --- wqflask/base/data_set.py | 22 ++- wqflask/base/trait.py | 12 +- wqflask/utility/tools.py | 1 + wqflask/wqflask/marker_regression/gemma_mapping.py | 51 +++-- .../wqflask/marker_regression/marker_regression.py | 37 +--- .../marker_regression/marker_regression_gn1.py | 5 +- wqflask/wqflask/show_trait/show_trait.py | 7 +- wqflask/wqflask/static/new/css/main.css | 7 + .../new/javascript/dataset_menu_structure.json | 207 ++++++++++++++------- .../static/new/javascript/dataset_select_menu.js | 12 +- .../new/javascript/dataset_select_menu_orig.js | 15 +- .../packages/DataTables/css/jquery.dataTables.css | 2 +- .../DataTables/extensions/buttons.colVis.min.js | 5 + .../extensions/dataTables.buttons.min.js | 35 ++++ .../extensions/scroller.dataTables.min.css | 1 + wqflask/wqflask/submit_trait.py | 24 +++ wqflask/wqflask/templates/gsearch_gene.html | 90 +++++---- wqflask/wqflask/templates/loading.html | 14 ++ wqflask/wqflask/templates/search_result_page.html | 75 +++++--- .../wqflask/templates/show_trait_edit_data.html | 2 + .../templates/show_trait_mapping_tools.html | 27 ++- wqflask/wqflask/templates/submit_trait.html | 101 ++++++++++ wqflask/wqflask/views.py | 57 ++++++ 23 files changed, 594 insertions(+), 215 deletions(-) create mode 100644 wqflask/wqflask/static/new/packages/DataTables/extensions/buttons.colVis.min.js create mode 100644 wqflask/wqflask/static/new/packages/DataTables/extensions/dataTables.buttons.min.js create mode 100644 wqflask/wqflask/static/new/packages/DataTables/extensions/scroller.dataTables.min.css create mode 100644 wqflask/wqflask/submit_trait.py create mode 100644 wqflask/wqflask/templates/loading.html create mode 100644 wqflask/wqflask/templates/submit_trait.html (limited to 'wqflask/base/data_set.py') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 06e02b02..94b38e13 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -44,7 +44,7 @@ from db import webqtlDatabaseFunction from utility import webqtlUtil from utility.benchmark import Bench from utility import chunks -from utility.tools import locate, locate_ignore_error +from utility.tools import locate, locate_ignore_error, flat_files from maintenance import get_group_samplelists @@ -53,7 +53,7 @@ from pprint import pformat as pf from db.gn_server import menu_main from db.call import fetchall,fetchone,fetch1 -from utility.tools import USE_GN_SERVER, USE_REDIS +from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists from utility.logger import getLogger logger = getLogger(__name__ ) @@ -226,7 +226,7 @@ class Markers(object): class HumanMarkers(Markers): def __init__(self, name, specified_markers = []): - marker_data_fh = open(locate('genotype') + '/' + name + '.bim') + marker_data_fh = open(flat_files('mapping') + '/' + name + '.bim') self.markers = [] for line in marker_data_fh: splat = line.strip().split() @@ -299,11 +299,21 @@ class DatasetGroup(object): self.markers = HumanMarkers(self.name, markers) def get_markers(self): - #logger.debug("self.species is:", self.species) - if self.species == "human": + logger.debug("self.species is:", self.species) + + def check_plink_gemma(): + if flat_file_exists("mapping"): + MAPPING_PATH = flat_files("mapping")+"/" + if (os.path.isfile(MAPPING_PATH+self.name+".bed") and + (os.path.isfile(MAPPING_PATH+self.name+".map") or + os.path.isfile(MAPPING_PATH+self.name+".bim"))): + return True + return False + + if check_plink_gemma(): marker_class = HumanMarkers else: - marker_class = Markers + marker_class = Markers self.markers = marker_class(self.name) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index eb5b91c3..bf87e879 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -207,7 +207,7 @@ class GeneralTrait(object): formatted = self.post_publication_description else: formatted = "Not available" - return formatted.capitalize() + return formatted @property def alias_fmt(self): @@ -379,7 +379,7 @@ def jsonable_table_row(trait, dataset_name, index): additive = "N/A" else: additive = "%.3f" % round(float(trait.additive), 2) - return ['', + return ['', index, ''+str(trait.name)+'', trait.symbol, @@ -395,7 +395,7 @@ def jsonable_table_row(trait, dataset_name, index): else: additive = "%.2f" % round(float(trait.additive), 2) if trait.pubmed_id: - return ['', + return ['', index, ''+str(trait.name)+'', trait.description_display, @@ -405,7 +405,7 @@ def jsonable_table_row(trait, dataset_name, index): trait.LRS_location_repr, additive] else: - return ['', + return ['', index, ''+str(trait.name)+'', trait.description_display, @@ -415,7 +415,7 @@ def jsonable_table_row(trait, dataset_name, index): trait.LRS_location_repr, additive] elif dataset.type == "Geno": - return ['', + return ['', index, ''+str(trait.name)+'', trait.location_repr] @@ -499,7 +499,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): for i, field in enumerate(dataset.display_fields): holder = trait_info[i] if isinstance(trait_info[i], basestring): - holder = unicode(trait_info[i], "utf8", "ignore") + holder = unicode(trait_info[i], "utf-8", "ignore") setattr(trait, field, holder) if dataset.type == 'Publish': diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index df032e48..8db9ac6e 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -215,6 +215,7 @@ GENENETWORK_FILES = get_setting('GENENETWORK_FILES') PYLMM_COMMAND = pylmm_command() GEMMA_COMMAND = gemma_command() +GEMMA_RESULTS_PATH = get_setting('GEMMA_RESULTS_PATH') PLINK_COMMAND = plink_command() TEMPDIR = tempdir() # defaults to UNIX TMPDIR diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index a56362ec..66bed5a2 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -1,7 +1,7 @@ -import os +import os, math from base import webqtlConfig -from utility.tools import GEMMA_COMMAND +from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_RESULTS_PATH def run_gemma(this_dataset, samples, vals): """Generates p-values for each marker using GEMMA""" @@ -10,41 +10,62 @@ def run_gemma(this_dataset, samples, vals): gen_pheno_txt_file(this_dataset, samples, vals) - # Don't do this! - # os.chdir("{}gemma".format(webqtlConfig.GENODIR)) - # use GEMMA_RUN in the next one, create a unique temp file - gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/output/%s.cXX.txt -lmm 1 -o %s_output' % (GEMMA_PATH, + gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -outdir %s/output -o %s_output' % (flat_files('mapping'), this_dataset.group.name, - GEMMA_PATH, + flat_files('mapping'), this_dataset.group.name, + GEMMA_RESULTS_PATH, this_dataset.group.name) print("gemma_command:" + gemma_command) os.system(gemma_command) - included_markers, p_values = parse_gemma_output(this_dataset) + marker_obs = parse_gemma_output(this_dataset) - return included_markers, p_values + return marker_obs def gen_pheno_txt_file(this_dataset, samples, vals): """Generates phenotype file for GEMMA""" - with open("{}/{}.fam".format(GEMMA_PATH, this_dataset.group.name), "w") as outfile: - for i, sample in enumerate(samples): - outfile.write(str(sample) + " " + str(sample) + " 0 0 0 " + str(vals[i]) + "\n") + current_file_data = [] + with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "r") as outfile: + for i, line in enumerate(outfile): + split_line = line.split() + current_file_data.append(split_line) + + with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "w") as outfile: + for i, line in enumerate(current_file_data): + if vals[i] == "x": + this_val = -9 + else: + this_val = vals[i] + outfile.write(line[0] + " " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n") def parse_gemma_output(this_dataset): included_markers = [] p_values = [] - with open("{}/output/{}_output.assoc.txt".format(GEMMA_PATH, this_dataset.group.name)) as output_file: + marker_obs = [] + with open("{}/output/{}_output.assoc.txt".format(GEMMA_RESULTS_PATH, this_dataset.group.name)) as output_file: for line in output_file: if line.startswith("chr"): continue else: + marker = {} + marker['name'] = line.split("\t")[1] + marker['chr'] = int(line.split("\t")[0]) + marker['Mb'] = float(line.split("\t")[2]) / 1000000 + marker['p_value'] = float(line.split("\t")[10]) + if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): + marker['lod_score'] = 0 + #marker['lrs_value'] = 0 + else: + marker['lod_score'] = -math.log10(marker['p_value']) + #marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 + marker_obs.append(marker) + included_markers.append(line.split("\t")[1]) p_values.append(float(line.split("\t")[10])) - #print("p_values: ", p_values) - return included_markers, p_values + return marker_obs diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index d9dbd0da..b1d2f811 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -37,7 +37,7 @@ from utility import temp_data from utility.benchmark import Bench from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping -from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND, TEMPDIR +from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, GEMMA_RESULTS_PATH, PLINK_COMMAND, TEMPDIR from utility.external import shell from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR @@ -140,7 +140,6 @@ class MarkerRegression(object): except: self.num_perm = 0 - self.LRSCheck = self.score_type if self.num_perm > 0: self.permCheck = "ON" else: @@ -151,12 +150,10 @@ class MarkerRegression(object): self.dataset.group.get_markers() if self.mapping_method == "gemma": - self.score_type = "LOD" + self.score_type = "-log(p)" self.manhattan_plot = True with Bench("Running GEMMA"): - included_markers, p_values = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals) - with Bench("Getting markers from csv"): - marker_obs = get_markers_from_csv(included_markers, p_values, self.dataset.group.name) + marker_obs = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals) results = marker_obs elif self.mapping_method == "rqtl_plink": results = self.run_rqtl_plink() @@ -511,8 +508,7 @@ class MarkerRegression(object): logger.debug("Before creating the command") - command = PYLMM_COMMAND+' --key {} --species {}'.format(key, - "human") + command = PYLMM_COMMAND+' --key {} --species {}'.format(key, "human") logger.debug("command is:", command) @@ -610,30 +606,5 @@ def trim_markers_for_table(markers): return sorted_markers -def get_markers_from_csv(included_markers, p_values, group_name): - marker_data_fh = open(os.path.join(webqtlConfig.PYLMM_PATH + group_name + '_markers.csv')) - markers = [] - for marker_name, p_value in itertools.izip(included_markers, p_values): - if not p_value or len(included_markers) < 1: - continue - for line in marker_data_fh: - splat = line.strip().split() - if splat[0] == marker_name: - marker = {} - marker['name'] = splat[0] - marker['chr'] = int(splat[1]) - marker['Mb'] = float(splat[2]) - marker['p_value'] = p_value - if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): - marker['lod_score'] = 0 - marker['lrs_value'] = 0 - else: - marker['lod_score'] = -math.log10(marker['p_value']) - marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 - markers.append(marker) - break - - return markers - if __name__ == '__main__': import cPickle as pickle diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index bc147f75..9ff431a2 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -292,7 +292,10 @@ class MarkerRegression(object): self.graphHeight = self.GRAPH_DEFAULT_HEIGHT self.dominanceChecked = False - self.LRS_LOD = start_vars['LRSCheck'] + if 'LRSCheck' in start_vars.keys(): + self.LRS_LOD = start_vars['LRSCheck'] + else: + self.LRS_LOD = start_vars['score_type'] self.cutoff = start_vars['cutoff'] self.intervalAnalystChecked = True self.draw2X = False diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 091db50f..13ae933f 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -167,7 +167,8 @@ class ShowTrait(object): if flat_file_exists("mapping"): MAPPING_PATH = flat_files("mapping")+"/" if (os.path.isfile(MAPPING_PATH+self.dataset.group.name+".bed") and - os.path.isfile(MAPPING_PATH+self.dataset.group.name+".map")): + (os.path.isfile(MAPPING_PATH+self.dataset.group.name+".map") or + os.path.isfile(MAPPING_PATH+self.dataset.group.name+".bim"))): return True return False @@ -729,7 +730,7 @@ class ShowTrait(object): def make_sample_lists(self, this_trait): all_samples_ordered = self.dataset.group.all_samples_ordered() - + primary_sample_names = list(all_samples_ordered) other_sample_names = [] @@ -813,7 +814,7 @@ def get_genofiles(this_trait): return jsondata['genofile'] def get_trait_table_width(sample_groups): - table_width = 35 + table_width = 30 if sample_groups[0].se_exists(): table_width += 10 if (table_width + len(sample_groups[0].attributes)*10) > 100: diff --git a/wqflask/wqflask/static/new/css/main.css b/wqflask/wqflask/static/new/css/main.css index 017bbdb8..880395a7 100644 --- a/wqflask/wqflask/static/new/css/main.css +++ b/wqflask/wqflask/static/new/css/main.css @@ -2,3 +2,10 @@ padding-left: 30px; padding-right: 30px; } + +ol { + font-family: Arial; + font-weight: bold; + font-size: 16px; + color: #000082 +} \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index 2f332a4a..06586372 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -1339,15 +1339,15 @@ "HLC_0311", "GSE9588 Human Liver Normal (Mar11) Both Sexes" ], - [ - "384", - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" - ], [ "383", "HLCM_0311", "GSE9588 Human Liver Normal (Mar11) Males" + ], + [ + "384", + "HLCF_0311", + "GSE9588 Human Liver Normal (Mar11) Females" ] ], "Phenotypes": [ @@ -1620,11 +1620,6 @@ }, "B6D2F2": { "Brain mRNA": [ - [ - "77", - "BRF2_M_0805_R", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" - ], [ "76", "BRF2_M_0805_M", @@ -1635,6 +1630,11 @@ "BRF2_M_0805_P", "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" ], + [ + "77", + "BRF2_M_0805_R", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" + ], [ "33", "BRF2_M_0304_P", @@ -1726,11 +1726,6 @@ ] ], "Striatum mRNA": [ - [ - "85", - "SA_M2_0905_P", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" - ], [ "84", "SA_M2_0905_R", @@ -1740,21 +1735,26 @@ "83", "SA_M2_0905_M", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" + ], + [ + "85", + "SA_M2_0905_P", + "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" ] ] }, "BHF2": { "Adipose mRNA": [ - [ - "197", - "UCLA_BHF2_ADIPOSE_FEMALE", - "UCLA BHF2 Adipose Female mlratio" - ], [ "196", "UCLA_BHF2_ADIPOSE_MALE", "UCLA BHF2 Adipose Male mlratio" ], + [ + "197", + "UCLA_BHF2_ADIPOSE_FEMALE", + "UCLA BHF2 Adipose Female mlratio" + ], [ "165", "UCLA_BHF2_ADIPOSE_0605", @@ -1762,16 +1762,16 @@ ] ], "Brain mRNA": [ - [ - "199", - "UCLA_BHF2_BRAIN_FEMALE", - "UCLA BHF2 Brain Female mlratio" - ], [ "198", "UCLA_BHF2_BRAIN_MALE", "UCLA BHF2 Brain Male mlratio" ], + [ + "199", + "UCLA_BHF2_BRAIN_FEMALE", + "UCLA BHF2 Brain Female mlratio" + ], [ "166", "UCLA_BHF2_BRAIN_0605", @@ -1786,16 +1786,16 @@ ] ], "Liver mRNA": [ - [ - "201", - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" - ], [ "200", "UCLA_BHF2_LIVER_MALE", "UCLA BHF2 Liver Male mlratio" ], + [ + "201", + "UCLA_BHF2_LIVER_FEMALE", + "UCLA BHF2 Liver Female mlratio" + ], [ "167", "UCLA_BHF2_LIVER_0605", @@ -1999,11 +1999,6 @@ "BR_U_1105_P", "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" ], - [ - "81", - "BR_U_0805_P", - "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" - ], [ "80", "BR_U_0805_M", @@ -2014,6 +2009,11 @@ "BR_U_0805_R", "UTHSC Brain mRNA U74Av2 (Aug05) RMA" ], + [ + "81", + "BR_U_0805_P", + "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" + ], [ "42", "CB_M_0204_P", @@ -2080,11 +2080,6 @@ "Eye_M2_0908_R_ND", "Eye M430v2 WT Gpnmb (Sep08) RMA" ], - [ - "279", - "Eye_M2_0908_R_WT", - "Eye M430v2 WT Tyrp1 (Sep08) RMA" - ], [ "278", "Eye_M2_0908_R_MT", @@ -2095,6 +2090,11 @@ "Eye_M2_0908_WTWT", "Eye M430v2 WT WT (Sep08) RMA" ], + [ + "279", + "Eye_M2_0908_R_WT", + "Eye M430v2 WT Tyrp1 (Sep08) RMA" + ], [ "400", "DBA2J-ONH-1212", @@ -2331,16 +2331,16 @@ ] ], "Kidney mRNA": [ - [ - "239", - "MA_M2F_0706_R", - "Mouse kidney M430v2 Female (Aug06) RMA" - ], [ "240", "MA_M2M_0706_R", "Mouse kidney M430v2 Male (Aug06) RMA" ], + [ + "239", + "MA_M2F_0706_R", + "Mouse kidney M430v2 Female (Aug06) RMA" + ], [ "118", "MA_M2_0806_R", @@ -2545,15 +2545,15 @@ "HQFNeoc_0208_RankInv", "HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv" ], - [ - "275", - "DevNeocortex_ILM6.2P14RInv_1110", - "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv" - ], [ "274", "DevNeocortex_ILM6.2P3RInv_1110", "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" + ], + [ + "275", + "DevNeocortex_ILM6.2P14RInv_1110", + "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv" ] ], "Nucleus Accumbens mRNA": [ @@ -2760,11 +2760,6 @@ ] ], "Ventral Tegmental Area mRNA": [ - [ - "230", - "VCUEtvsSal_0609_R", - "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA" - ], [ "229", "VCUEtOH_0609_R", @@ -2774,6 +2769,11 @@ "228", "VCUSal_0609_R", "VCU BXD VTA Sal M430 2.0 (Jun09) RMA" + ], + [ + "230", + "VCUEtvsSal_0609_R", + "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA" ] ] }, @@ -2849,6 +2849,36 @@ ] ] }, + "CFW": { + "Hippocampus mRNA": [ + [ + "808", + "UCSD_CFW_HIP_RNA-Seq_0117", + "UCSD CFW Hippocampus (Jan17) RNA-Seq" + ] + ], + "Phenotypes": [ + [ + "None", + "CFWPublish", + "CFW Published Phenotypes" + ] + ], + "Prefrontal Cortex mRNA": [ + [ + "810", + "UCSD_CFW_PFC_RNA-Seq_0117", + "UCSD CFW Prefrontal Cortex (Jan17) RNA-Seq" + ] + ], + "Striatum mRNA": [ + [ + "809", + "UCSD_CFW_SPL_RNA-Seq_0117", + "UCSD CFW Striatum (Jan17) RNA-Seq" + ] + ] + }, "CIE-INIA": { "LCM Brain Regions mRNA": [ [ @@ -3051,11 +3081,6 @@ ] ], "Hippocampus mRNA": [ - [ - "213", - "Illum_LXS_Hipp_NOS_1008", - "Hippocampus Illumina NOS (Oct08) RankInv beta" - ], [ "219", "Illum_LXS_Hipp_NON_1008", @@ -3076,6 +3101,11 @@ "Illum_LXS_Hipp_RSS_1008", "Hippocampus Illumina RSS (Oct08) RankInv beta" ], + [ + "213", + "Illum_LXS_Hipp_NOS_1008", + "Hippocampus Illumina NOS (Oct08) RankInv beta" + ], [ "143", "Illum_LXS_Hipp_loess0807", @@ -3246,6 +3276,17 @@ }, "Scripps-2013": {} }, + "poplar": { + "Poplar": { + "Phenotypes": [ + [ + "649", + "PoplarPublish", + "Poplar Published Phenotypes" + ] + ] + } + }, "rat": { "HSNIH-Palmer": { "Phenotypes": [ @@ -3554,6 +3595,10 @@ "C57BL-6JxC57BL-6NJF2", "Reduced Complexity Cross (B6JxB6N F2)" ], + [ + "CFW", + "CFW Outbred GWAS" + ], [ "CIE-INIA", "Chronic Intermittent Ethanol" @@ -3603,6 +3648,12 @@ "SOTNOT-OHSU" ] ], + "poplar": [ + [ + "Poplar", + "Poplar" + ] + ], "rat": [ [ "HSNIH-Palmer", @@ -3641,15 +3692,15 @@ "species": [ [ "human", - "Human" + "Human (hg19)" ], [ "mouse", - "Mouse" + "Mouse (mm10)" ], [ "rat", - "Rat" + "Rat (rn3)" ], [ "drosophila", @@ -3663,6 +3714,10 @@ "barley", "Barley" ], + [ + "poplar", + "Poplar" + ], [ "soybean", "Soybean" @@ -4682,6 +4737,24 @@ "Genotypes" ] ], + "CFW": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Hippocampus mRNA", + "Hippocampus mRNA" + ], + [ + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA" + ], + [ + "Striatum mRNA", + "Striatum mRNA" + ] + ], "CIE-INIA": [ [ "Phenotypes", @@ -4842,6 +4915,14 @@ ], "Scripps-2013": [] }, + "poplar": { + "Poplar": [ + [ + "Phenotypes", + "Phenotypes" + ] + ] + }, "rat": { "HSNIH-Palmer": [ [ diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js index 43b0960c..9ad38102 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js @@ -1,10 +1,10 @@ $(function() { - var gndata; // loaded once for all to use - process_json = function(data) { - populate_species(); - return apply_default(); - }; - $.getJSON(gn_server_url+"/int/menu/main.json", + var gndata; // loaded once for all to use + process_json = function(data) { + populate_species(); + return apply_default(); + }; + $.getJSON(gn_server_url+"int/menu/main.json", function(data) { gndata = data; console.log("***** GOT DATA from GN_SERVER ****"); diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js index 1fe4cf75..fd96eb78 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js @@ -4,7 +4,9 @@ $(function() { process_json = function(data) { window.jdata = data; populate_species(); - return apply_default(); + if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option) + return apply_default(); + } }; $.ajax('/static/new/javascript/dataset_menu_structure.json', { dataType: 'json', @@ -23,7 +25,9 @@ $(function() { species = $('#species').val(); group_list = this.jdata.groups[species]; redo_dropdown($('#group'), group_list); - return populate_type(); + if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option) + return populate_type(); + } }; window.populate_group = populate_group; populate_type = function() { @@ -70,7 +74,12 @@ $(function() { })(this)); $('#group').change((function(_this) { return function() { - return populate_type(); + if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option) + return populate_type(); + } + else { + return false + } }; })(this)); $('#type').change((function(_this) { diff --git a/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css b/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css index 6e0e7348..87f602dc 100644 --- a/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css +++ b/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css @@ -81,7 +81,7 @@ table.dataTable tbody tr.selected { 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You searched for {{ terms }}.

-

To study a record, click on its ID below.
Check records below and click Add button to add to selection.

+

To study a record, click on its Record ID below.
Check records below and click Add button to add to selection.


@@ -27,36 +27,36 @@
-
- +
+
- - - - - - - - - - - - - - + + + + + + + + + + + + + + {% for this_trait in trait_list %} - + + - @@ -69,20 +69,20 @@ - - - - - - - - - - - - - - + + + + + + + + + + + + + +
IndexSpeciesGroupTissueDatasetRecordSymbolDescriptionLocationMeanMax LRS ?Max LRS LocationAdditive Effect ?IndexRecord IDSpeciesGroupTissueDatasetSymbolDescriptionLocationMeanMax LRS ?Max LRS LocationAdditive Effect ?
{{ loop.index }}{{ this_trait.name }} {{ this_trait.dataset.group.species }} {{ this_trait.dataset.group.name }} {{ this_trait.dataset.tissue }} {{ this_trait.dataset.name }}{{ this_trait.name }} {{ this_trait.symbol }} {{ this_trait.description_display }} {{ this_trait.location_repr }}
IndexSpeciesGroupTissueDatasetRecordSymbolDescriptionLocationMeanMax  
LRS ?		Max LRS LocationAdditive
Effect ?		IndexRecord IDSpeciesGroupTissueDatasetSymbolDescriptionLocationMeanMax LRS ?Max LRS LocationAdditive Effect ?
@@ -123,26 +123,34 @@ console.time("Creating table"); $('#trait_table').DataTable( { + "createdRow": function ( row, data, index ) { + $('td', row).eq(8).attr('title', $('td', row).eq(8).text()); + if ($('td', row).eq(8).text().length > 50) { + $('td', row).eq(8).text($('td', row).eq(8).text().substring(0, 50)); + $('td', row).eq(8).text($('td', row).eq(8).text() + '...') + } + }, "paging": false, "columns": [ { "orderDataType": "dom-checkbox" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural", "width": "8%" }, - { "type": "natural" }, + { "type": "natural", "width": "3%" }, + { "type": "natural", "width": "6%" }, + { "type": "natural", "width": "8%" }, { "type": "natural" }, { "type": "natural" }, { "type": "natural" }, { "type": "natural" }, - { "type": "natural", "width": "8%" }, { "type": "natural" }, - { "type": "natural" }, - { "type": "natural", "width": "8%" }, - { "type": "natural" } + { "type": "natural", "width": "7%" }, + { "type": "natural", "width": "4%" }, + { "type": "natural", "width": "5%" }, + { "type": "natural", "width": "7%" }, + { "type": "natural", "width": "7%" } ], "columnDefs": [ { "targets": 0, + "orderable": false, "orderDataType": "dom-checkbox" } ], diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html new file mode 100644 index 00000000..bc2627a0 --- /dev/null +++ b/wqflask/wqflask/templates/loading.html @@ -0,0 +1,14 @@ +{% extends "base.html" %} +{% block title %}Loading Mapping Results{% endblock %} +{% block content %} +
+
+
+
+
+{% endblock %} +{% block js %} + +{% endblock %} \ No newline at end of file diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index f7b450c1..cafa8b93 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -3,6 +3,7 @@ {% block css %} + {% endblock %} {% block content %} @@ -125,9 +126,8 @@ - - - + + + +{% endblock %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 4f6725b3..4f46a904 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -50,6 +50,7 @@ from wqflask.correlation_matrix import show_corr_matrix from wqflask.correlation import corr_scatter_plot from wqflask.wgcna import wgcna_analysis from wqflask.ctl import ctl_analysis +from wqflask.submit_trait import get_species_groups from utility import temp_data from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION @@ -294,6 +295,11 @@ def environments(): doc = docs.Docs("environments") return render_template("docs.html", **doc.__dict__) +@app.route("/submit_trait") +def submit_trait(): + species_and_groups = get_species_groups() + return render_template("submit_trait.html", **{'species_and_groups' : species_and_groups, 'gn_server_url' : GN_SERVER_URL, 'version' : GN_VERSION}) + @app.route('/export_trait_excel', methods=('POST',)) def export_trait_excel(): """Excel file consisting of the sample data from the trait data and analysis page""" @@ -440,6 +446,57 @@ def heatmap_page(): def mapping_results_container_page(): return render_template("mapping_results_container.html") +@app.route("/loading", methods=('POST',)) +def loading_page(): + initial_start_vars = request.form + logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items()) + temp_uuid = initial_start_vars['temp_uuid'] + wanted = ( + 'trait_id', + 'dataset', + 'method', + 'trimmed_markers', + 'selected_chr', + 'chromosomes', + 'mapping_scale', + 'score_type', + 'suggestive', + 'significant', + 'num_perm', + 'permCheck', + 'perm_output', + 'num_bootstrap', + 'bootCheck', + 'bootstrap_results', + 'LRSCheck', + 'maf', + 'manhattan_plot', + 'control_marker', + 'control_marker_db', + 'do_control', + 'genofile', + 'pair_scan', + 'startMb', + 'endMb', + 'graphWidth', + 'lrsMax', + 'additiveCheck', + 'showSNP', + 'showGenes', + 'viewLegend', + 'haplotypeAnalystCheck', + 'mapmethod_rqtl_geno', + 'mapmodel_rqtl_geno' + ) + start_vars = {} + for key, value in initial_start_vars.iteritems(): + if key in wanted or key.startswith(('value:')): + start_vars[key] = value + + rendered_template = render_template("loading.html", **start_vars) + + return rendered_template + @app.route("/marker_regression", methods=('POST',)) def marker_regression_page(): initial_start_vars = request.form -- cgit v1.2.3