diff options
| author | Lei Yan | 2017-02-02 19:08:31 +0000 |
|---|---|---|
| committer | Lei Yan | 2017-02-02 19:08:31 +0000 |
| commit | 568adbb1bfe72c22fae9bec7da7a421945674743 (patch) | |
| tree | 1e0c445912af7ccb273a25b858889048eb96f756 | |
| parent | 1cae8e42f0f73718549b369cf0cd4d9f320e230e (diff) | |
| parent | e63c4014e7bc34b440707be19af3779b72102fdb (diff) | |
| download | genenetwork2-568adbb1bfe72c22fae9bec7da7a421945674743.tar.gz | |
Merge /home/zas1024/gene
43 files changed, 1668 insertions, 1473 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index ae7fdcb5..41c5d8ba 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() @@ -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) @@ -280,15 +281,39 @@ class DatasetGroup(object): self._datasets = None self.genofile = 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) 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 276c624a..bf87e879 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -23,6 +23,8 @@ from flask import Flask, g, request from utility.logger import getLogger logger = getLogger(__name__ ) +from wqflask import user_manager + def print_mem(stage=""): mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss print("{}: {}".format(stage, mem/1024)) @@ -55,6 +57,7 @@ class GeneralTrait(object): self.lrs = None self.pvalue = None self.mean = None + self.additive = None self.num_overlap = None self.strand_probe = None self.symbol = None @@ -69,45 +72,9 @@ class GeneralTrait(object): # Todo: These two lines are necessary most of the time, but perhaps not all of the time # So we could add a simple if statement to short-circuit this if necessary - self.retrieve_info(get_qtl_info=get_qtl_info) + self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info) if get_sample_info != False: - self.retrieve_sample_data() - - - def jsonable(self): - """Return a dict suitable for using as json - - Actual turning into json doesn't happen here though""" - - if self.dataset.type == "ProbeSet": - return dict(name=self.name, - symbol=self.symbol, - dataset=self.dataset.name, - description=self.description_display, - mean=self.mean, - location=self.location_repr, - lrs_score=self.LRS_score_repr, - lrs_location=self.LRS_location_repr, - additive=self.additive - ) - elif self.dataset.type == "Publish": - return dict(name=self.name, - dataset=self.dataset.name, - description=self.description_display, - authors=self.authors, - pubmed_text=self.pubmed_text, - pubmed_link=self.pubmed_link, - lrs_score=self.LRS_score_repr, - lrs_location=self.LRS_location_repr, - additive=self.additive - ) - elif self.dataset.type == "Geno": - return dict(name=self.name, - dataset=self.dataset.name, - location=self.location_repr - ) - else: - return dict() + self = retrieve_sample_data(self, self.dataset) def get_name(self): @@ -213,410 +180,6 @@ class GeneralTrait(object): return samples, vals, the_vars, sample_aliases - # - # In ProbeSet, there are maybe several annotations match one sequence - # so we need use sequence(BlatSeq) as the identification, when we update - # one annotation, we update the others who match the sequence also. - # - # Hongqiang Li, 3/3/2008 - # - #def getSequence(self): - # assert self.cursor - # if self.dataset.type == 'ProbeSet': - # self.cursor.execute(''' - # SELECT - # ProbeSet.BlatSeq - # FROM - # ProbeSet, ProbeSetFreeze, ProbeSetXRef - # WHERE - # ProbeSet.Id=ProbeSetXRef.ProbeSetId and - # ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and - # ProbeSet.Name = %s - # ProbeSetFreeze.Name = %s - # ''', self.name, self.dataset.name) - # #self.cursor.execute(query) - # results = self.fetchone() - # - # return results[0] - - - - def retrieve_sample_data(self, samplelist=None): - if samplelist == None: - samplelist = [] - - results = self.dataset.retrieve_sample_data(self.name) - - # Todo: is this necessary? If not remove - self.data.clear() - - all_samples_ordered = self.dataset.group.all_samples_ordered() - - if results: - for item in results: - name, value, variance, num_cases, name2 = item - if not samplelist or (samplelist and name in samplelist): - self.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) - - def retrieve_info(self, get_qtl_info=False): - assert self.dataset, "Dataset doesn't exist" - if self.dataset.type == 'Publish': - query = """ - SELECT - PublishXRef.Id, Publication.PubMed_ID, - Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description, - Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, - Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users, - Publication.Authors, Publication.Title, Publication.Abstract, - Publication.Journal, Publication.Volume, Publication.Pages, - Publication.Month, Publication.Year, PublishXRef.Sequence, - Phenotype.Units, PublishXRef.comments - FROM - PublishXRef, Publication, Phenotype, PublishFreeze - WHERE - PublishXRef.Id = %s AND - Phenotype.Id = PublishXRef.PhenotypeId AND - Publication.Id = PublishXRef.PublicationId AND - PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND - PublishFreeze.Id = %s - """ % (self.name, self.dataset.id) - - logger.sql(query) - trait_info = g.db.execute(query).fetchone() - - - #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name - #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. - elif self.dataset.type == 'ProbeSet': - display_fields_string = ', ProbeSet.'.join(self.dataset.display_fields) - display_fields_string = 'ProbeSet.' + display_fields_string - query = """ - SELECT %s - FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE - ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSetFreeze.Name = '%s' AND - ProbeSet.Name = '%s' - """ % (escape(display_fields_string), - escape(self.dataset.name), - escape(str(self.name))) - logger.sql(query) - trait_info = g.db.execute(query).fetchone() - #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name - # to avoid the problem of same marker name from different species. - elif self.dataset.type == 'Geno': - display_fields_string = string.join(self.dataset.display_fields,',Geno.') - display_fields_string = 'Geno.' + display_fields_string - query = """ - SELECT %s - FROM Geno, GenoFreeze, GenoXRef - WHERE - GenoXRef.GenoFreezeId = GenoFreeze.Id AND - GenoXRef.GenoId = Geno.Id AND - GenoFreeze.Name = '%s' AND - Geno.Name = '%s' - """ % (escape(display_fields_string), - escape(self.dataset.name), - escape(self.name)) - logger.sql(query) - trait_info = g.db.execute(query).fetchone() - else: #Temp type - query = """SELECT %s FROM %s WHERE Name = %s""" - logger.sql(query) - trait_info = g.db.execute(query, - (string.join(self.dataset.display_fields,','), - self.dataset.type, self.name)).fetchone() - if trait_info: - self.haveinfo = True - - #XZ: assign SQL query result to trait attributes. - for i, field in enumerate(self.dataset.display_fields): - holder = trait_info[i] - if isinstance(trait_info[i], basestring): - holder = unicode(trait_info[i], "utf8", "ignore") - setattr(self, field, holder) - - if self.dataset.type == 'Publish': - self.confidential = 0 - if self.pre_publication_description and not self.pubmed_id: - self.confidential = 1 - - description = self.post_publication_description - - #If the dataset is confidential and the user has access to confidential - #phenotype traits, then display the pre-publication description instead - #of the post-publication description - if self.confidential: - self.description_display = self.pre_publication_description - - #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( - # privilege=self.dataset.privilege, - # userName=self.dataset.userName, - # authorized_users=self.authorized_users): - # - # description = self.pre_publication_description - else: - if description: - self.description_display = description.strip() - else: - self.description_display = "" - - if not self.year.isdigit(): - self.pubmed_text = "N/A" - else: - self.pubmed_text = self.year - - if self.pubmed_id: - self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id - - - self.homologeneid = None - if self.dataset.type == 'ProbeSet' and self.dataset.group: - if self.geneid: - #XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number. - #XZ: So I have to test if geneid is number before execute the query. - #XZ: The geneid values in database should be cleaned up. - #try: - # float(self.geneid) - # geneidIsNumber = True - #except ValueError: - # geneidIsNumber = False - #if geneidIsNumber: - query = """ - SELECT - HomologeneId - FROM - Homologene, Species, InbredSet - WHERE - Homologene.GeneId ='%s' AND - InbredSet.Name = '%s' AND - InbredSet.SpeciesId = Species.Id AND - Species.TaxonomyId = Homologene.TaxonomyId - """ % (escape(str(self.geneid)), escape(self.dataset.group.name)) - logger.sql(query) - result = g.db.execute(query).fetchone() - #else: - # result = None - - if result: - self.homologeneid = result[0] - - description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8') - target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') - - if len(description_string) > 1 and description_string != 'None': - description_display = description_string - else: - description_display = self.symbol - - if (len(description_display) > 1 and description_display != 'N/A' and - len(target_string) > 1 and target_string != 'None'): - description_display = description_display + '; ' + target_string.strip() - - # Save it for the jinja2 template - self.description_display = description_display - - #XZ: trait_location_value is used for sorting - trait_location_repr = 'N/A' - trait_location_value = 1000000 - - if self.chr and self.mb: - #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y") - #This is so we can convert the location to a number used for sorting - trait_location_value = convert_location_to_value(self.chr, self.mb) - #try: - # trait_location_value = int(self.chr)*1000 + self.mb - #except ValueError: - # if self.chr.upper() == 'X': - # trait_location_value = 20*1000 + self.mb - # else: - # trait_location_value = (ord(str(self.chr).upper()[0])*1000 + - # self.mb) - - #ZS: Put this in function currently called "convert_location_to_value" - self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb)) - self.location_value = trait_location_value - - - if get_qtl_info: - #LRS and its location - self.LRS_score_repr = "N/A" - self.LRS_score_value = 0 - self.LRS_location_repr = "N/A" - self.LRS_location_value = 1000000 - if self.dataset.type == 'ProbeSet' and not self.cellid: - query = """ - SELECT - ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive - FROM - ProbeSetXRef, ProbeSet - WHERE - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSet.Name = "{}" AND - ProbeSetXRef.ProbeSetFreezeId ={} - """.format(self.name, self.dataset.id) - logger.sql(query) - trait_qtl = g.db.execute(query).fetchone() - if trait_qtl: - self.locus, self.lrs, self.pvalue, self.mean, self.additive= trait_qtl - if self.locus: - query = """ - select Geno.Chr, Geno.Mb from Geno, Species - where Species.Name = '{}' and - Geno.Name = '{}' and - Geno.SpeciesId = Species.Id - """.format(self.dataset.group.species, self.locus) - logger.sql(query) - result = g.db.execute(query).fetchone() - if result: - self.locus_chr = result[0] - self.locus_mb = result[1] - else: - self.locus = self.locus_chr = self.locus_mb = self.additive = "" - else: - self.locus = self.locus_chr = self.locus_mb = self.additive = "" - else: - self.locus = self.locus_chr = self.locus_mb = self.lrs = self.pvalue = self.mean = self.additive = "" - - - if self.dataset.type == 'Publish': - query = """ - SELECT - PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive - FROM - PublishXRef, PublishFreeze - WHERE - PublishXRef.Id = %s AND - PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND - PublishFreeze.Id =%s - """ % (self.name, self.dataset.id) - logger.sql(query) - trait_qtl = g.db.execute(query).fetchone() - if trait_qtl: - self.locus, self.lrs, self.additive = trait_qtl - if self.locus: - query = """ - select Geno.Chr, Geno.Mb from Geno, Species - where Species.Name = '{}' and - Geno.Name = '{}' and - Geno.SpeciesId = Species.Id - """.format(self.dataset.group.species, self.locus) - logger.sql(query) - result = g.db.execute(query).fetchone() - if result: - self.locus_chr = result[0] - self.locus_mb = result[1] - else: - self.locus = self.locus_chr = self.locus_mb = self.additive = "" - else: - self.locus = self.locus_chr = self.locus_mb = self.additive = "" - else: - self.locus = self.lrs = self.additive = "" - - if (self.dataset.type == 'Publish' or self.dataset.type == "ProbeSet") and self.locus_chr != "" and self.locus_mb != "": - #XZ: LRS_location_value is used for sorting - try: - LRS_location_value = int(self.locus_chr)*1000 + float(self.locus_mb) - except: - if self.locus_chr.upper() == 'X': - LRS_location_value = 20*1000 + float(self.locus_mb) - else: - LRS_location_value = ord(str(self.locus_chr).upper()[0])*1000 + float(self.locus_mb) - - self.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (self.locus_chr, float(self.locus_mb)) - if self.lrs != "": - self.LRS_score_repr = LRS_score_repr = '%3.1f' % self.lrs - self.LRS_score_value = LRS_score_value = self.lrs - else: - raise KeyError, `self.name`+' information is not found in the database.' - - def genHTML(self, formName = "", dispFromDatabase=0, privilege="guest", userName="Guest", authorized_users=""): - if not self.haveinfo: - self.retrieveInfo() - - if self.dataset.type == 'Publish': - PubMedLink = "" - if self.pubmed_id: - PubMedLink = HT.Href(text="PubMed %d : " % self.pubmed_id, - target = "_blank", url = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id) - else: - PubMedLink = HT.Span("Unpublished : ", Class="fs15") - - if formName: - setDescription2 = HT.Href(url="javascript:showDatabase3('%s','%s','%s','')" % - (formName, self.dataset.name, self.name), Class = "fs14") - else: - setDescription2 = HT.Href(url="javascript:showDatabase2('%s','%s','')" % - (self.dataset.name,self.name), Class = "fs14") - - if self.confidential and not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=privilege, userName=userName, authorized_users=authorized_users): - setDescription2.append('RecordID/%s - %s' % (self.name, self.pre_publication_description)) - else: - setDescription2.append('RecordID/%s - %s' % (self.name, self.post_publication_description)) - - #XZ 03/26/2011: Xiaodong comment out the following two lins as Rob asked. Need to check with Rob why in PublishXRef table, there are few row whose Sequence > 1. - #if self.sequence > 1: - # setDescription2.append(' btach %d' % self.sequence) - if self.authors: - a1 = string.split(self.authors,',')[0] - while a1[0] == '"' or a1[0] == "'" : - a1 = a1[1:] - setDescription2.append(' by ') - setDescription2.append(HT.Italic('%s, and colleagues' % a1)) - setDescription = HT.Span(PubMedLink, setDescription2) - - elif self.dataset.type == 'Temp': - setDescription = HT.Href(text="%s" % (self.description),url="javascript:showDatabase2\ - ('%s','%s','')" % (self.dataset.name,self.name), Class = "fs14") - setDescription = HT.Span(setDescription) - - elif self.dataset.type == 'Geno': # Genome DB only available for single search - if formName: - setDescription = HT.Href(text="Locus %s [Chr %s @ %s Mb]" % (self.name,self.chr,\ - '%2.3f' % self.mb),url="javascript:showDatabase3('%s','%s','%s','')" % \ - (formName, self.dataset.name, self.name), Class = "fs14") - else: - setDescription = HT.Href(text="Locus %s [Chr %s @ %s Mb]" % (self.name,self.chr,\ - '%2.3f' % self.mb),url="javascript:showDatabase2('%s','%s','')" % \ - (self.dataset.name,self.name), Class = "fs14") - - setDescription = HT.Span(setDescription) - - else: - if self.cellid: - if formName: - setDescription = HT.Href(text="ProbeSet/%s/%s" % (self.name, self.cellid),url=\ - "javascript:showDatabase3('%s','%s','%s','%s')" % (formName, self.dataset.name,self.name,self.cellid), \ - Class = "fs14") - else: - setDescription = HT.Href(text="ProbeSet/%s/%s" % (self.name,self.cellid),url=\ - "javascript:showDatabase2('%s','%s','%s')" % (self.dataset.name,self.name,self.cellid), \ - Class = "fs14") - else: - if formName: - setDescription = HT.Href(text="ProbeSet/%s" % self.name, url=\ - "javascript:showDatabase3('%s','%s','%s','')" % (formName, self.dataset.name,self.name), \ - Class = "fs14") - else: - setDescription = HT.Href(text="ProbeSet/%s" % self.name, url=\ - "javascript:showDatabase2('%s','%s','')" % (self.dataset.name,self.name), \ - Class = "fs14") - if self.symbol and self.chr and self.mb: - setDescription.append(' [') - setDescription.append(HT.Italic('%s' % self.symbol,Class="cdg fwb")) - setDescription.append(' on Chr %s @ %s Mb]' % (self.chr,self.mb)) - if self.description: - setDescription.append(': %s' % self.description) - if self.probe_target_description: - setDescription.append('; %s' % self.probe_target_description) - setDescription = HT.Span(setDescription) - - if self.dataset.type != 'Temp' and dispFromDatabase: - setDescription.append( ' --- FROM : ') - setDescription.append(self.dataset.genHTML(Class='cori')) - return setDescription - @property def name_header_fmt(self): '''Return a human-readable name for use in page header''' @@ -644,7 +207,7 @@ class GeneralTrait(object): formatted = self.post_publication_description else: formatted = "Not available" - return formatted.capitalize() + return formatted @property def alias_fmt(self): @@ -682,62 +245,48 @@ class GeneralTrait(object): return fmt - - def get_database(self): - """ - Returns the database, and the url referring to the database if it exists - - We're going to to return two values here, and we don't want to have to call this twice from - the template. So it's not a property called from the template, but instead is called from the view - - """ - if self.cellid: - query = """ select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze where - ProbeFreeze.Id = - ProbeSetFreeze.ProbeFreezeId AND - ProbeSetFreeze.Id = %d""" % thisTrait.dataset.id - logger.sql(query) - probeDBName = g.db.execute(query).fetchone()[0] - return dict(name = probeDBName, - url = None) - else: - return dict(name = self.dataset.fullname, - url = webqtlConfig.INFOPAGEHREF % self.dataset.name) - - def calculate_correlation(self, values, method): - """Calculate the correlation value and p value according to the method specified""" - - #ZS: This takes the list of values of the trait our selected trait is being correlated against and removes the values of the samples our trait has no value for - #There's probably a better way of dealing with this, but I'll have to ask Christian - updated_raw_values = [] - updated_values = [] - for i in range(len(values)): - if values[i] != "None": - updated_raw_values.append(self.raw_values[i]) - updated_values.append(values[i]) - - self.raw_values = updated_raw_values - values = updated_values - - if method == METHOD_SAMPLE_PEARSON or method == METHOD_LIT or method == METHOD_TISSUE_PEARSON: - corr, nOverlap = webqtlUtil.calCorrelation(self.raw_values, values, len(values)) - else: - corr, nOverlap = webqtlUtil.calCorrelationRank(self.raw_values, values, len(values)) - - self.correlation = corr - self.overlap = nOverlap - - if self.overlap < 3: - self.p_value = 1.0 - else: - #ZS - This is probably the wrong way to deal with this. Correlation values of 1.0 definitely exist (the trait correlated against itself), so zero division needs to br prevented. - if abs(self.correlation) >= 1.0: - self.p_value = 0.0 - else: - ZValue = 0.5*log((1.0+self.correlation)/(1.0-self.correlation)) - ZValue = ZValue*sqrt(self.overlap-3) - self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue))) - +# In ProbeSet, there are maybe several annotations match one sequence +# so we need use sequence(BlatSeq) as the identification, when we update +# one annotation, we update the others who match the sequence also. +# +# Hongqiang Li, 3/3/2008 +def getSequence(trait, dataset_name): + dataset = create_dataset(dataset_name) + + if dataset.type == 'ProbeSet': + results = g.db.execute(''' + SELECT + ProbeSet.BlatSeq + FROM + ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE + ProbeSet.Id=ProbeSetXRef.ProbeSetId and + ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and + ProbeSet.Name = %s + ProbeSetFreeze.Name = %s + ''', trait.name, dataset.name).fetchone() + + return results[0] + +def retrieve_sample_data(trait, dataset, samplelist=None): + if samplelist == None: + samplelist = [] + + results = dataset.retrieve_sample_data(trait.name) + + # Todo: is this necessary? If not remove + trait.data.clear() + + all_samples_ordered = dataset.group.all_samples_ordered() + + if results: + for item in results: + name, value, variance, num_cases, name2 = item + if not samplelist or (samplelist and name in samplelist): + trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) + + return trait + def convert_location_to_value(chromosome, mb): try: location_value = int(chromosome)*1000 + float(mb) @@ -765,3 +314,398 @@ def get_sample_data(): # jsonable_sample_data[sample] = trait_ob.data[sample].value # #return jsonable_sample_data + +def jsonable(trait, dataset_name): + """Return a dict suitable for using as json + + Actual turning into json doesn't happen here though""" + + dataset = create_dataset(dataset_name) + + if dataset.type == "ProbeSet": + return dict(name=trait.name, + symbol=trait.symbol, + dataset=dataset.name, + description=trait.description_display, + mean=trait.mean, + location=trait.location_repr, + lrs_score=trait.LRS_score_repr, + lrs_location=trait.LRS_location_repr, + additive=trait.additive + ) + elif dataset.type == "Publish": + if trait.pubmed_id: + return dict(name=trait.name, + dataset=dataset.name, + description=trait.description_display, + authors=trait.authors, + pubmed_text=trait.pubmed_text, + pubmed_link=trait.pubmed_link, + lrs_score=trait.LRS_score_repr, + lrs_location=trait.LRS_location_repr, + additive=trait.additive + ) + else: + return dict(name=trait.name, + dataset=dataset.name, + description=trait.description_display, + authors=trait.authors, + pubmed_text=trait.pubmed_text, + lrs_score=trait.LRS_score_repr, + lrs_location=trait.LRS_location_repr, + additive=trait.additive + ) + elif dataset.type == "Geno": + return dict(name=trait.name, + dataset=dataset.name, + location=trait.location_repr + ) + else: + return dict() + +def jsonable_table_row(trait, dataset_name, index): + """Return a list suitable for json and intended to be displayed in a table + + Actual turning into json doesn't happen here though""" + + dataset = create_dataset(dataset_name) + + if dataset.type == "ProbeSet": + if trait.mean == "": + mean = "N/A" + else: + mean = "%.3f" % round(float(trait.mean), 2) + if trait.additive == "": + additive = "N/A" + else: + additive = "%.3f" % round(float(trait.additive), 2) + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + index, + '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', + trait.symbol, + trait.description_display, + trait.location_repr, + mean, + trait.LRS_score_repr, + trait.LRS_location_repr, + additive] + elif dataset.type == "Publish": + if trait.additive == "": + additive = "N/A" + else: + additive = "%.2f" % round(float(trait.additive), 2) + if trait.pubmed_id: + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + index, + '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', + trait.description_display, + trait.authors, + '<a href="' + trait.pubmed_link + '">' + trait.pubmed_text + '</href>', + trait.LRS_score_repr, + trait.LRS_location_repr, + additive] + else: + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + index, + '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', + trait.description_display, + trait.authors, + trait.pubmed_text, + trait.LRS_score_repr, + trait.LRS_location_repr, + additive] + elif dataset.type == "Geno": + return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">', + index, + '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>', + trait.location_repr] + else: + return dict() + +def retrieve_trait_info(trait, dataset, get_qtl_info=False): + assert dataset, "Dataset doesn't exist" + + if dataset.type == 'Publish': + query = """ + SELECT + PublishXRef.Id, Publication.PubMed_ID, + Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description, + Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, + Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users, + Publication.Authors, Publication.Title, Publication.Abstract, + Publication.Journal, Publication.Volume, Publication.Pages, + Publication.Month, Publication.Year, PublishXRef.Sequence, + Phenotype.Units, PublishXRef.comments + FROM + PublishXRef, Publication, Phenotype, PublishFreeze + WHERE + PublishXRef.Id = %s AND + Phenotype.Id = PublishXRef.PhenotypeId AND + Publication.Id = PublishXRef.PublicationId AND + PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND + PublishFreeze.Id = %s + """ % (trait.name, dataset.id) + + logger.sql(query) + trait_info = g.db.execute(query).fetchone() + + + #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name + #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. + elif dataset.type == 'ProbeSet': + display_fields_string = ', ProbeSet.'.join(dataset.display_fields) + display_fields_string = 'ProbeSet.' + display_fields_string + query = """ + SELECT %s + FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE + ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND + ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSetFreeze.Name = '%s' AND + ProbeSet.Name = '%s' + """ % (escape(display_fields_string), + escape(dataset.name), + escape(str(trait.name))) + logger.sql(query) + trait_info = g.db.execute(query).fetchone() + #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name + # to avoid the problem of same marker name from different species. + elif dataset.type == 'Geno': + display_fields_string = string.join(dataset.display_fields,',Geno.') + display_fields_string = 'Geno.' + display_fields_string + query = """ + SELECT %s + FROM Geno, GenoFreeze, GenoXRef + WHERE + GenoXRef.GenoFreezeId = GenoFreeze.Id AND + GenoXRef.GenoId = Geno.Id AND + GenoFreeze.Name = '%s' AND + Geno.Name = '%s' + """ % (escape(display_fields_string), + escape(dataset.name), + escape(trait.name)) + logger.sql(query) + trait_info = g.db.execute(query).fetchone() + else: #Temp type + query = """SELECT %s FROM %s WHERE Name = %s""" + logger.sql(query) + trait_info = g.db.execute(query, + (string.join(dataset.display_fields,','), + dataset.type, trait.name)).fetchone() + if trait_info: + trait.haveinfo = True + + #XZ: assign SQL query result to trait attributes. + for i, field in enumerate(dataset.display_fields): + holder = trait_info[i] + if isinstance(trait_info[i], basestring): + holder = unicode(trait_info[i], "utf-8", "ignore") + setattr(trait, field, holder) + + if dataset.type == 'Publish': + trait.confidential = 0 + if trait.pre_publication_description and not trait.pubmed_id: + trait.confidential = 1 + + description = trait.post_publication_description + + #If the dataset is confidential and the user has access to confidential + #phenotype traits, then display the pre-publication description instead + #of the post-publication description + if trait.confidential: + trait.description_display = trait.pre_publication_description + + #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( + # privilege=self.dataset.privilege, + # userName=self.dataset.userName, + # authorized_users=self.authorized_users): + # + # description = self.pre_publication_description + else: + if description: + trait.description_display = description.strip() + else: + trait.description_display = "" + + if not trait.year.isdigit(): + trait.pubmed_text = "N/A" + else: + trait.pubmed_text = trait.year + + if trait.pubmed_id: + trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id + + + trait.homologeneid = None + if dataset.type == 'ProbeSet' and dataset.group: + if trait.geneid: + #XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number. + #XZ: So I have to test if geneid is number before execute the query. + #XZ: The geneid values in database should be cleaned up. + #try: + # float(self.geneid) + # geneidIsNumber = True + #except ValueError: + # geneidIsNumber = False + #if geneidIsNumber: + query = """ + SELECT + HomologeneId + FROM + Homologene, Species, InbredSet + WHERE + Homologene.GeneId ='%s' AND + InbredSet.Name = '%s' AND + InbredSet.SpeciesId = Species.Id AND + Species.TaxonomyId = Homologene.TaxonomyId + """ % (escape(str(trait.geneid)), escape(dataset.group.name)) + logger.sql(query) + result = g.db.execute(query).fetchone() + #else: + # result = None + + if result: + trait.homologeneid = result[0] + + description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8') + target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') + + if len(description_string) > 1 and description_string != 'None': + description_display = description_string + else: + description_display = trait.symbol + + if (len(description_display) > 1 and description_display != 'N/A' and + len(target_string) > 1 and target_string != 'None'): + description_display = description_display + '; ' + target_string.strip() + + # Save it for the jinja2 template + trait.description_display = description_display + + #XZ: trait_location_value is used for sorting + trait.location_repr = 'N/A' + trait.location_value = 1000000 + + if trait.chr and trait.mb: + #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y") + #This is so we can convert the location to a number used for sorting + trait_location_value = convert_location_to_value(trait.chr, trait.mb) + #try: + # trait_location_value = int(self.chr)*1000 + self.mb + #except ValueError: + # if self.chr.upper() == 'X': + # trait_location_value = 20*1000 + self.mb + # else: + # trait_location_value = (ord(str(self.chr).upper()[0])*1000 + + # self.mb) + + #ZS: Put this in function currently called "convert_location_to_value" + trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb)) + trait.location_value = trait_location_value + + elif dataset.type == "Geno": + trait.location_repr = 'N/A' + trait.location_value = 1000000 + + if trait.chr and trait.mb: + #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y") + #This is so we can convert the location to a number used for sorting + trait_location_value = convert_location_to_value(trait.chr, trait.mb) + + #ZS: Put this in function currently called "convert_location_to_value" + trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb)) + trait.location_value = trait_location_value + + if get_qtl_info: + #LRS and its location + trait.LRS_score_repr = "N/A" + trait.LRS_score_value = 0 + trait.LRS_location_repr = "N/A" + trait.LRS_location_value = 1000000 + if dataset.type == 'ProbeSet' and not trait.cellid: + query = """ + SELECT + ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive + FROM + ProbeSetXRef, ProbeSet + WHERE + ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSet.Name = "{}" AND + ProbeSetXRef.ProbeSetFreezeId ={} + """.format(trait.name, dataset.id) + logger.sql(query) + trait_qtl = g.db.execute(query).fetchone() + if trait_qtl: + trait.locus, trait.lrs, trait.pvalue, trait.mean, trait.additive = trait_qtl + if trait.locus: + query = """ + select Geno.Chr, Geno.Mb from Geno, Species + where Species.Name = '{}' and + Geno.Name = '{}' and + Geno.SpeciesId = Species.Id + """.format(dataset.group.species, trait.locus) + logger.sql(query) + result = g.db.execute(query).fetchone() + if result: + trait.locus_chr = result[0] + trait.locus_mb = result[1] + else: + trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = "" + else: + trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = "" + else: + trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.mean = trait.additive = "" + + + if dataset.type == 'Publish': + query = """ + SELECT + PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive + FROM + PublishXRef, PublishFreeze + WHERE + PublishXRef.Id = %s AND + PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND + PublishFreeze.Id =%s + """ % (trait.name, dataset.id) + logger.sql(query) + trait_qtl = g.db.execute(query).fetchone() + if trait_qtl: + trait.locus, trait.lrs, trait.additive = trait_qtl + if trait.locus: + query = """ + select Geno.Chr, Geno.Mb from Geno, Species + where Species.Name = '{}' and + Geno.Name = '{}' and + Geno.SpeciesId = Species.Id + """.format(dataset.group.species, trait.locus) + logger.sql(query) + result = g.db.execute(query).fetchone() + if result: + trait.locus_chr = result[0] + trait.locus_mb = result[1] + else: + trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = "" + else: + trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = "" + else: + trait.locus = trait.lrs = trait.additive = "" + + if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "": + #XZ: LRS_location_value is used for sorting + try: + LRS_location_value = int(trait.locus_chr)*1000 + float(trait.locus_mb) + except: + if trait.locus_chr.upper() == 'X': + LRS_location_value = 20*1000 + float(trait.locus_mb) + else: + LRS_location_value = ord(str(trait.locus_chr).upper()[0])*1000 + float(trait.locus_mb) + + trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb)) + if trait.lrs != "": + trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs + trait.LRS_score_value = LRS_score_value = trait.lrs + else: + raise KeyError, `trait.name`+' information is not found in the database.' + + return trait
\ No newline at end of file diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index 2f88f778..845a7224 100644 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -44,15 +44,15 @@ class webqtlCaseData(object): def __repr__(self): str = "<webqtlCaseData> " - if self.value != None: + if self.value: str += "value=%2.3f" % self.value - if self.variance != None: + if self.variance: str += " variance=%2.3f" % self.variance - if self.num_cases != None: + if self.num_cases: str += " ndata=%d" % self.num_cases - if self.name != None: + if self.name: str += " name=%s" % self.name - if self.name2 != None: + if self.name2: str += " name2=%s" % self.name2 return str diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 542c0d83..e5726656 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -95,13 +95,13 @@ def get_groups(species): for species_name, _species_full_name in species: Cursor.execute("""select InbredSet.Name, InbredSet.FullName from InbredSet, Species, - ProbeFreeze, GenoFreeze, PublishFreeze where Species.Name = %s + ProbeFreeze, GenoFreeze, PublishFreeze where Species.Name = '%s' and InbredSet.SpeciesId = Species.Id and InbredSet.Name != 'BXD300' and (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) group by InbredSet.Name - order by InbredSet.Name""", (species_name)) + order by InbredSet.Name""" % species_name) groups[species_name] = list(Cursor.fetchall()) return groups @@ -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) @@ -166,13 +166,14 @@ def build_types(species, group): Cursor.execute("""select distinct Tissue.Name from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species - where Species.Name = %s and Species.Id = InbredSet.SpeciesId and - InbredSet.Name = %s and + where Species.Name = '%s' and Species.Id = InbredSet.SpeciesId and + InbredSet.Name = '%s' and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and - ProbeSetFreeze.public > 0 - order by Tissue.Name""", (species, group)) + ProbeSetFreeze.public > 0 and + ProbeSetFreeze.confidentiality < 1 + order by Tissue.Name""" % (species, group)) results = [] for result in Cursor.fetchall(): @@ -205,12 +206,12 @@ def build_datasets(species, group, type_name): if type_name == "Phenotypes": print("GROUP:", group) Cursor.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where - InbredSet.Name = %s and + 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""", (group)) + PublishFreeze.CreateTime desc""" % group) results = Cursor.fetchone() if results != None: @@ -225,12 +226,12 @@ def build_datasets(species, group, type_name): elif type_name == "Genotypes": Cursor.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where - InbredSet.Name = %s and + InbredSet.Name = '%s' and GenoFreeze.InbredSetId = InbredSet.Id and InfoFiles.InfoPageName = GenoFreeze.ShortName and GenoFreeze.public > 0 and GenoFreeze.confidentiality < 1 order by - GenoFreeze.CreateTime desc""", (group)) + GenoFreeze.CreateTime desc""" % group) results = Cursor.fetchone() if results != None: @@ -245,12 +246,12 @@ def build_datasets(species, group, type_name): else: 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 - InbredSet.Name = %s and - ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = %s and + Species.Name = '%s' and Species.Id = InbredSet.SpeciesId and + InbredSet.Name = '%s' and + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = '%s' and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and ProbeSetFreeze.confidentiality < 1 and ProbeSetFreeze.public > 0 order by - ProbeSetFreeze.CreateTime desc""", (species, group, type_name)) + ProbeSetFreeze.CreateTime desc""" % (species, group, type_name)) dataset_results = Cursor.fetchall() datasets = [] 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/collect.py b/wqflask/wqflask/collect.py index 70ae2a1c..ba555094 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -34,6 +34,7 @@ from utility import Bunch, Struct from utility.formatting import numify from base import trait +from base.data_set import create_dataset def get_collection(): if g.user_session.logged_in: @@ -375,12 +376,13 @@ def view_collection(): for atrait in traits: name, dataset_name = atrait.split(':') - - trait_ob = trait.GeneralTrait(name=name, dataset_name=dataset_name) - trait_ob.retrieve_info(get_qtl_info=True) + dataset = create_dataset(dataset_name) + + trait_ob = trait.GeneralTrait(name=name, dataset=dataset) + trait_ob = trait.retrieve_trait_info(trait_ob, dataset, get_qtl_info=True) trait_obs.append(trait_ob) - json_version.append(trait_ob.jsonable()) + json_version.append(trait.jsonable(trait_ob, dataset_name)) if "uc_id" in params: collection_info = dict(trait_obs=trait_obs, diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 401059fd..cc21d1bf 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -216,7 +216,7 @@ class CorrelationResults(object): for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]): trait_object = GeneralTrait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) - if self.dataset.type == "ProbeSet" or self.dataset.type == "Geno": + if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": #ZS: Convert trait chromosome to an int for the location range option chr_as_int = 0 for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 70e21917..630980c7 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -207,7 +207,11 @@ class CorrelationMatrix(object): print("before loop:", self.loadings[0]) for i in range(len(self.trait_list)): loadings_row = [] - for j in range(3): + if len(self.trait_list) > 2: + the_range = 3 + else: + the_range = 2 + for j in range(the_range): position = i + len(self.trait_list)*j loadings_row.append(self.loadings[0][position]) loadings_array.append(loadings_row) diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 3d2d7a37..9515d23a 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -144,7 +144,7 @@ class CTL(object): if trait != "": ts = trait.split(':') gt = TRAIT.GeneralTrait(name = ts[0], dataset_name = ts[1]) - gt.retrieve_sample_data(individuals) + gt = TRAIT.retrieve_sample_data(gt, dataset, individuals) for ind in individuals: if ind in gt.data.keys(): traits.append(gt.data[ind].value) diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 64d638b2..e33e04e1 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -40,6 +40,7 @@ class GSearch(object): AND ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) ) AND ProbeSet.Id = ProbeSetXRef.ProbeSetId AND ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id + AND ProbeSetFreeze.confidentiality < 1 AND ProbeSetFreeze.public > 0 ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name LIMIT 6000 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/search_results.py b/wqflask/wqflask/search_results.py index a924c7c9..59e100d8 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -16,7 +16,7 @@ from pprint import pformat as pf import json from base.data_set import create_dataset -from base.trait import GeneralTrait +from base import trait from wqflask import parser from wqflask import do_search from utility import webqtlUtil,tools @@ -86,12 +86,13 @@ views.py). """ self.trait_list = [] + json_trait_list = [] 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)) - for result in self.results: + for index, result in enumerate(self.results): if not result: continue @@ -99,8 +100,11 @@ views.py). #logger.debug("foo locals are:", locals()) trait_id = result[0] - this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) + this_trait = trait.GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) self.trait_list.append(this_trait) + json_trait_list.append(trait.jsonable_table_row(this_trait, self.dataset.name, index + 1)) + + self.json_trait_list = json.dumps(json_trait_list) #def get_group_species_tree(self): # self.species_groups = collections.default_dict(list) diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 8aff5482..13ae933f 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -95,7 +95,7 @@ class ShowTrait(object): # this_trait.mysqlid) # heritability = self.cursor.fetchone() - self.dispTraitInformation(kw, "", hddn, self.this_trait) #Display trait information + function buttons + #self.dispTraitInformation(kw, "", hddn, self.this_trait) #Display trait information + function buttons self.build_correlation_tools(self.this_trait) @@ -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 @@ -262,467 +263,6 @@ class ShowTrait(object): logger.debug("allTraitData is:", pf(self.allTraitData)) - def dispTraitInformation(self, args, title1Body, hddn, this_trait): - - self.species_name = webqtlDatabaseFunction.retrieve_species(group=self.dataset.group.name) - - #tbl = HT.TableLite(cellpadding=2, Class="collap", style="margin-left:20px;", width="840", valign="top", id="target1") - - #reset=HT.Input(type='Reset',name='',value=' Reset ',Class="button") - - #XZ, August 02, 2011: The display of icons is decided by the trait type (if trait exists), along with user log-in status. Note that the new submitted trait might not be trait object. - addSelectionButton = "" - verifyButton = "" - rnaseqButton = "" - geneWikiButton = "" - probeButton = "" - similarButton = "" - snpBrowserButton = "" - updateButton = "" - - addSelectionText = "" - verifyText = "" - rnaseqText = "" - geneWikiText = "" - probeText = "" - similarText = "" - snpBrowserText = "" - updateText = "" - - #if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']: - # - # if this_trait==None or this_trait.dataset.type=='Temp': - # updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'addPublish');") - # updateButton_img = HT.Image("/images/edit_icon.jpg", name="addnew", alt="Add To Publish", title="Add To Publish", style="border:none;") - # updateButton.append(updateButton_img) - # updateText = "Edit" - # elif this_trait.dataset.type != 'Temp': - # if this_trait.dataset.type == 'Publish' and this_trait.confidential: #XZ: confidential phenotype trait - # if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users): - # updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');") - # updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;") - # updateButton.append(updateButton_img) - # updateText = "Edit" - # else: - # updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');") - # updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;") - # updateButton.append(updateButton_img) - # updateText = "Edit" - # else: - # pass - - result = g.db.execute("SELECT Name FROM InbredSet WHERE Name=%s", self.dataset.group.name) - if this_trait: - addSelectionButton = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (self.dataset.group.name, 'dataInput')) - addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="addselect", alt="Add To Collection", title="Add To Collection", style="border:none;") - #addSelectionButton.append(addSelectionButton_img) - addSelectionText = "Add" - elif result.fetchall(): - addSelectionButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('%s')[0], 'addRecord');" % ('dataInput')) - addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="", alt="Add To Collection", title="Add To Collection", style="border:none;") - #addSelectionButton.append(addSelectionButton_img) - addSelectionText = "Add" - else: - pass - - - # Microarray database information to display - if this_trait and this_trait.dataset and this_trait.dataset.type == 'ProbeSet': #before, this line was only reached if this_trait != 0, but now we need to check - try: - hddn['GeneId'] = int(string.strip(this_trait.geneid)) - except: - pass - - #Info2Disp = HT.Paragraph() - - #XZ: Gene Symbol - if this_trait.symbol: - #XZ: Show SNP Browser only for mouse - if self.species_name == 'mouse': - geneName = g.db.execute("SELECT geneSymbol FROM GeneList WHERE geneSymbol = %s", this_trait.symbol).fetchone() - if geneName: - snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True") + "&geneName=%s" % geneName[0] - else: - if this_trait.chr and this_trait.mb: - snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True") + \ - "&chr=%s&start=%2.6f&end=%2.6f" % (this_trait.chr, this_trait.mb-0.002, this_trait.mb+0.002) - else: - snpurl = "" - - if snpurl: - snpBrowserButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % snpurl) - snpBrowserButton_img = HT.Image("/images/snp_icon.jpg", name="snpbrowser", alt=" View SNPs and Indels ", title=" View SNPs and Indels ", style="border:none;") - snpBrowserText = "SNPs" - - #XZ: Show GeneWiki for all species - geneWikiButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + "?FormID=geneWiki&symbol=%s" % this_trait.symbol)) - geneWikiButton_img = HT.Image("/images/genewiki_icon.jpg", name="genewiki", alt=" Write or review comments about this gene ", title=" Write or review comments about this gene ", style="border:none;") - geneWikiText = 'GeneWiki' - - #XZ: display similar traits in other selected datasets - if this_trait and this_trait.dataset and this_trait.dataset.type=="ProbeSet" and this_trait.symbol: - if self.species_name in ("mouse", "rat", "human"): - similarUrl = "%s?cmd=sch&gene=%s&alias=1&species=%s" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), this_trait.symbol, self.species_name) - similarButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % similarUrl) - similarButton_img = HT.Image("/images/find_icon.jpg", name="similar", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;") - similarText = "Find" - else: - pass - else: - tbl.append(HT.TR( - HT.TD('Gene Symbol: ', Class="fwb fs13", valign="top", nowrap="on"), - HT.TD(width=10, valign="top"), - HT.TD(HT.Span('Not available', Class="fs13 fsI"), valign="top") - )) - - - - ##display Verify Location button - try: - blatsequence = this_trait.blatseq - if not blatsequence: - #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. - self.cursor.execute("""SELECT Probe.Sequence, Probe.Name - FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSetFreeze.Name = '%s' AND - ProbeSet.Name = '%s' AND - Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (this_trait.dataset.name, this_trait.name) ) - seqs = self.cursor.fetchall() - if not seqs: - raise ValueError - else: - blatsequence = '' - for seqt in seqs: - if int(seqt[1][-1]) % 2 == 1: - blatsequence += string.strip(seqt[0])## NEEDED FOR UCSC GENOME BROWSER LINK - - #--------Hongqiang add this part in order to not only blat ProbeSet, but also blat Probe - blatsequence = '%3E'+this_trait.name+'%0A'+blatsequence+'%0A' - #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. - query = """SELECT Probe.Sequence, Probe.Name - FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND - ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSetFreeze.Name = '{}' AND - ProbeSet.Name = '{}' AND - Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""".format(this_trait.dataset.name, this_trait.name) - - logger.sql(query) - seqs = g.db.execute(query).fetchall() - - for seqt in seqs: - if int(seqt[1][-1]) %2 == 1: - blatsequence += '%3EProbe_'+string.strip(seqt[1])+'%0A'+string.strip(seqt[0])+'%0A' - - #XZ: Pay attention to the parameter of version (rn, mm, hg). They need to be changed if necessary. - if self.species_name == "rat": - self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence) - self.UTHSC_BLAT_URL = "" - elif self.species_name == "mouse": - self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', blatsequence) - self.UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', blatsequence) - elif self.species_name == "human": - self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence) - self.UTHSC_BLAT_URL = "" - else: - self.UCSC_BLAT_URL = "" - self.UTHSC_BLAT_URL = "" - - if self.UCSC_BLAT_URL != "": - verifyButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UCSC_BLAT_URL) - verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", - title=" Check probe locations at UCSC ", style="border:none;") - verifyButton.append(verifyButtonImg) - verifyText = 'Verify' - if self.UTHSC_BLAT_URL != "": - rnaseqButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UTHSC_BLAT_URL) - rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", - title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") - rnaseqButton.append(rnaseqButtonImg) - rnaseqText = 'RNA-seq' - tSpan.append(HT.BR()) - except: - pass - - #Display probe information (if any) - if this_trait.dataset.name.find('Liver') >= 0 and this_trait.dataset.name.find('F2') < 0: - pass - else: - query = """SELECT count(*) - FROM Probe, ProbeSet - WHERE ProbeSet.Name = '%s' AND Probe.ProbeSetId = ProbeSet.Id""" % (this_trait.name) - #query database for number of probes associated with trait; if count > 0, set probe tool button and text - logger.sql(query) - probeResult = g.db.execute(query).fetchone() - if probeResult[0] > 0: - self.show_probes = "True" - probeurl = "%s?FormID=showProbeInfo&database=%s&ProbeSetID=%s&CellID=%s&group=%s&incparentsf1=ON" \ - % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), this_trait.dataset, this_trait.name, this_trait.cellid, self.dataset.group.name) - probeButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % probeurl) - probeButton_img = HT.Image("/images/probe_icon.jpg", name="probe", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;") - #probeButton.append(probeButton_img) - probeText = "Probes" - - this_trait.species = self.species_name # We need this in the template, so we tuck it into this_trait - this_trait.database = this_trait.get_database() - - #XZ: ID links - if this_trait.genbankid or this_trait.geneid or this_trait.unigeneid or this_trait.omim or this_trait.homologeneid: - idStyle = "background:#dddddd;padding:2" - tSpan = HT.Span(Class="fs13") - if this_trait.geneid: - gurl = HT.Href(text= 'Gene', target='_blank',\ - url=webqtlConfig.NCBI_LOCUSID % this_trait.geneid, Class="fs14 fwn", title="Info from NCBI Entrez Gene") - #tSpan.append(HT.Span(gurl, style=idStyle), " "*2) - if this_trait.omim: - gurl = HT.Href(text= 'OMIM', target='_blank', \ - url= webqtlConfig.OMIM_ID % this_trait.omim,Class="fs14 fwn", title="Summary from On Mendelian Inheritance in Man") - #tSpan.append(HT.Span(gurl, style=idStyle), " "*2) - if this_trait.unigeneid: - try: - gurl = HT.Href(text= 'UniGene',target='_blank',\ - url= webqtlConfig.UNIGEN_ID % tuple(string.split(this_trait.unigeneid,'.')[:2]),Class="fs14 fwn", title="UniGene ID") - #tSpan.append(HT.Span(gurl, style=idStyle), " "*2) - except: - pass - if this_trait.genbankid: - this_trait.genbankid = '|'.join(this_trait.genbankid.split('|')[0:10]) - if this_trait.genbankid[-1]=='|': - this_trait.genbankid=this_trait.genbankid[0:-1] - gurl = HT.Href(text= 'GenBank', target='_blank', \ - url= webqtlConfig.GENBANK_ID % this_trait.genbankid,Class="fs14 fwn", title="Find the original GenBank sequence used to design the probes") - #tSpan.append(HT.Span(gurl, style=idStyle), " "*2) - if this_trait.homologeneid: - hurl = HT.Href(text= 'HomoloGene', target='_blank',\ - url=webqtlConfig.HOMOLOGENE_ID % this_trait.homologeneid, Class="fs14 fwn", title="Find similar genes in other species") - #tSpan.append(HT.Span(hurl, style=idStyle), " "*2) - - #XZ: Resource Links: - if this_trait.symbol: - #XZ,12/26/2008: Gene symbol may contain single quotation mark. - #For example, Affymetrix, mouse430v2, 1440338_at, the symbol is 2'-Pde (geneid 211948) - #I debug this by using double quotation marks. - if self.species_name == "rat": - result = g.db.execute("SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = %s", (this_trait.symbol)).fetchone() - if result != None: - kgId, chr, txst, txen = result[0], result[1], result[2], result[3] - if chr and txst and txen and kgId: - txst = int(txst*1000000) - txen = int(txen*1000000) - if self.species_name == "mouse": - logger.debug("this_trait.symbol:", this_trait.symbol) - result = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone() - if result != None: - this_chr, txst, txen = result[0], result[1], result[2] - if this_chr and txst and txen and this_trait.refseq_transcriptid : - txst = int(txst*1000000) - txen = int(txen*1000000) - ## NEEDED FOR UCSC GENOME BROWSER LINK - - #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more - #tSpan.append(HT.Span(HT.Href(text= 'SymAtlas',target="mainFrame",\ - # url="http://symatlas.gnf.org/SymAtlas/bioentry?querytext=%s&query=14&species=%s&type=Expression" \ - # % (this_trait.symbol,symatlas_species),Class="fs14 fwn", \ - # title="Expression across many tissues and cell types"), style=linkStyle), " "*2) - if this_trait.geneid and (self.species_name == "mouse" or self.species_name == "rat" or self.species_name == "human"): - #tSpan.append(HT.Span(HT.Href(text= 'BioGPS',target="mainFrame",\ - # url="http://biogps.gnf.org/?org=%s#goto=genereport&id=%s" \ - # % (self.species_name, this_trait.geneid),Class="fs14 fwn", \ - # title="Expression across many tissues and cell types"), style=linkStyle), " "*2) - pass - #tSpan.append(HT.Span(HT.Href(text= 'STRING',target="mainFrame",\ - # url="http://string.embl.de/newstring_cgi/show_link_summary.pl?identifier=%s" \ - # % this_trait.symbol,Class="fs14 fwn", \ - # title="Protein interactions: known and inferred"), style=linkStyle), " "*2) - if this_trait.symbol: - #ZS: The "species scientific" converts the plain English species names we're using to their scientific names, which are needed for PANTHER's input - #We should probably use the scientific name along with the English name (if not instead of) elsewhere as well, given potential non-English speaking users - if self.species_name == "mouse": - species_scientific = "Mus%20musculus" - elif self.species_name == "rat": - species_scientific = "Rattus%20norvegicus" - elif self.species_name == "human": - species_scientific = "Homo%20sapiens" - elif self.species_name == "drosophila": - species_scientific = "Drosophila%20melanogaster" - else: - species_scientific = "all" - - species_scientific - #tSpan.append(HT.Span(HT.Href(text= 'PANTHER',target="mainFrame", \ - # url="http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=%s&listType=1&fieldValue=%s" \ - # % (species_scientific, this_trait.symbol),Class="fs14 fwn", \ - # title="Gene and protein data resources from Celera-ABI"), style=linkStyle), " "*2) - else: - pass - #tSpan.append(HT.Span(HT.Href(text= 'BIND',target="mainFrame",\ - # url="http://bind.ca/?textquery=%s" \ - # % this_trait.symbol,Class="fs14 fwn", \ - # title="Protein interactions"), style=linkStyle), " "*2) - #if this_trait.geneid and (self.species_name == "mouse" or self.species_name == "rat" or self.species_name == "human"): - # tSpan.append(HT.Span(HT.Href(text= 'Gemma',target="mainFrame",\ - # url="http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s" \ - # % this_trait.geneid, Class="fs14 fwn", \ - # title="Meta-analysis of gene expression data"), style=linkStyle), " "*2) - #tSpan.append(HT.Span(HT.Href(text= 'SynDB',target="mainFrame",\ - # url="http://lily.uthsc.edu:8080/20091027_GNInterfaces/20091027_redirectSynDB.jsp?query=%s" \ - # % this_trait.symbol, Class="fs14 fwn", \ - # title="Brain synapse database"), style=linkStyle), " "*2) - #if self.species_name == "mouse": - # tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\ - # url="http://mouse.brain-map.org/brain/%s.html" \ - # % this_trait.symbol, Class="fs14 fwn", \ - # title="Allen Brain Atlas"), style=linkStyle), " "*2) - - if this_trait.geneid: - #if self.species_name == "mouse": - # tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\ - # url="http://www.brain-map.org/search.do?queryText=egeneid=%s" \ - # % this_trait.geneid, Class="fs14 fwn", \ - # title="Allen Brain Atlas"), style=linkStyle), " "*2) - if self.species_name == "human": - #tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\ - # url="http://humancortex.alleninstitute.org/has/human/imageseries/search/1.html?searchSym=t&searchAlt=t&searchName=t&gene_term=&entrez_term=%s" \ - # % this_trait.geneid, Class="fs14 fwn", \ - # title="Allen Brain Atlas"), style=linkStyle), " "*2) - pass - - #for zhou mi's cliques, need to be removed - #if self.database[:6] == 'BXDMic' and self.ProbeSetID in cliqueID: - # Info2Disp.append(HT.Strong('Clique Search: '),HT.Href(text='Search',\ - # url ="http://compbio1.utmem.edu/clique_go/results.php?pid=%s&pval_1=0&pval_2=0.001" \ - # % self.ProbeSetID,target='_blank',Class="normalsize"),HT.BR()) - - elif this_trait and this_trait.dataset and this_trait.dataset.type =='Publish': #Check if trait is phenotype - - #if this_trait.confidential: - # pass - # #tbl.append(HT.TR( - # # HT.TD('Pre-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - # # HT.TD(width=10, valign="top"), - # # HT.TD(HT.Span(this_trait.pre_publication_description, Class="fs13"), valign="top", width=740) - # # )) - # if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users): - # #tbl.append(HT.TR( - # # HT.TD('Post-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - # # HT.TD(width=10, valign="top"), - # # HT.TD(HT.Span(this_trait.post_publication_description, Class="fs13"), valign="top", width=740) - # # )) - # #tbl.append(HT.TR( - # # HT.TD('Pre-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - # # HT.TD(width=10, valign="top"), - # # HT.TD(HT.Span(this_trait.pre_publication_abbreviation, Class="fs13"), valign="top", width=740) - # # )) - # #tbl.append(HT.TR( - # # HT.TD('Post-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - # # HT.TD(width=10, valign="top"), - # # HT.TD(HT.Span(this_trait.post_publication_abbreviation, Class="fs13"), valign="top", width=740) - # # )) - # #tbl.append(HT.TR( - # # HT.TD('Lab code: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - # # HT.TD(width=10, valign="top"), - # # HT.TD(HT.Span(this_trait.lab_code, Class="fs13"), valign="top", width=740) - # # )) - # pass - # #tbl.append(HT.TR( - # # HT.TD('Owner: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - # # HT.TD(width=10, valign="top"), - # # HT.TD(HT.Span(this_trait.owner, Class="fs13"), valign="top", width=740) - # # )) - #else: - # pass - # #tbl.append(HT.TR( - # # HT.TD('Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90), - # # HT.TD(width=10, valign="top"), - # # HT.TD(HT.Span(this_trait.post_publication_description, Class="fs13"), valign="top", width=740) - # # )) - ##tbl.append(HT.TR( - ## HT.TD('Authors: ', Class="fs13 fwb", - ## valign="top", nowrap="on", width=90), - ## HT.TD(width=10, valign="top"), - ## HT.TD(HT.Span(this_trait.authors, Class="fs13"), - ## valign="top", width=740) - ## )) - ##tbl.append(HT.TR( - ## HT.TD('Title: ', Class="fs13 fwb", - ## valign="top", nowrap="on", width=90), - ## HT.TD(width=10, valign="top"), - ## HT.TD(HT.Span(this_trait.title, Class="fs13"), - ## valign="top", width=740) - ## )) - if this_trait.journal: - journal = this_trait.journal - if this_trait.year: - journal = this_trait.journal + " (%s)" % this_trait.year - # - #tbl.append(HT.TR( - # HT.TD('Journal: ', Class="fs13 fwb", - # valign="top", nowrap="on", width=90), - # HT.TD(width=10, valign="top"), - # HT.TD(HT.Span(journal, Class="fs13"), - # valign="top", width=740) - # )) - PubMedLink = "" - if this_trait.pubmed_id: - PubMedLink = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id - if PubMedLink: - #tbl.append(HT.TR( - # HT.TD('Link: ', Class="fs13 fwb", - # valign="top", nowrap="on", width=90), - # HT.TD(width=10, valign="top"), - # HT.TD(HT.Span(HT.Href(url=PubMedLink, text="PubMed",target='_blank',Class="fs14 fwn"), - # style = "background:#cddcff;padding:2"), valign="top", width=740) - # )) - pass - - elif this_trait and this_trait.dataset and this_trait.dataset.type == 'Geno': #Check if trait is genotype - - if this_trait.chr and this_trait.mb: - location = ' Chr %s @ %s Mb' % (this_trait.chr,this_trait.mb) - else: - location = "not available" - - #if this_trait.sequence and len(this_trait.sequence) > 100: - # if self.species_name == "rat": - # UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', this_trait.sequence) - # UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('rat', 'rn3', this_trait.sequence) - # elif self.species_name == "mouse": - # UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', this_trait.sequence) - # UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', this_trait.sequence) - # elif self.species_name == "human": - # UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence) - # UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('human', 'hg19', this_trait.sequence) - # else: - # UCSC_BLAT_URL = "" - # UTHSC_BLAT_URL = "" - # if UCSC_BLAT_URL: - # #verifyButton = HT.Href(url="#", onClick="openNewWin('%s')" % UCSC_BLAT_URL) - # verifyButton = HT.Href(url="#") - # verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;") - # verifyButton.append(verifyButtonImg) - # verifyText = "Verify" - # rnaseqButton = HT.Href(url="#", onClick="openNewWin('%s')" % UTHSC_BLAT_URL) - # rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;") - # rnaseqButton.append(rnaseqButtonImg) - # rnaseqText = "RNA-seq" - - #tbl.append(HT.TR( - # HT.TD('Location: ', Class="fs13 fwb", - # valign="top", nowrap="on", width=90), - # HT.TD(width=10, valign="top"), - # HT.TD(HT.Span(location, Class="fs13"), valign="top", width=740) - # ), - # HT.TR( - # HT.TD('SNP Search: ', Class="fs13 fwb", - # valign="top", nowrap="on", width=90), - # HT.TD(width=10, valign="top"), - # HT.TD(HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp&cmd=search&term=%s" % this_trait.name, 'NCBI',Class="fs13"), - # valign="top", width=740) - # )) - - def dispBasicStatistics(self, fd, this_trait): #XZ, June 22, 2011: The definition and usage of primary_samples, other_samples, specialStrains, all_samples are not clear and hard to understand. But since they are only used in this function for draw graph purpose, they will not hurt the business logic outside. As of June 21, 2011, this function seems work fine, so no hurry to clean up. These parameters and code in this function should be cleaned along with fd.f1list, fd.parlist, fd.samplelist later. @@ -1190,7 +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 = [] @@ -1274,7 +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/create_corr_matrix.js b/wqflask/wqflask/static/new/javascript/create_corr_matrix.js index adb91295..44ed3c81 100644 --- a/wqflask/wqflask/static/new/javascript/create_corr_matrix.js +++ b/wqflask/wqflask/static/new/javascript/create_corr_matrix.js @@ -1,48 +1,47 @@ // Generated by CoffeeScript 1.8.0 -var get_data, get_options, root; +// var get_data, get_options, root; -root = typeof exports !== "undefined" && exports !== null ? exports : this; +// root = typeof exports !== "undefined" && exports !== null ? exports : this; -$(function() { - var chartOpts, data, mychart; - console.log("js_data:", js_data); - chartOpts = get_options(); - data = get_data(); - console.log(data); - return mychart = corr_matrix(data, chartOpts); -}); - -get_options = function() { - var chartOpts; - chartOpts = { - cortitle: "Correlation Matrix", - scattitle: "Scatterplot", - h: 450, - w: 450, - margin: { - left: 100, - top: 40, - right: 5, - bottom: 70, - inner: 5 - } - }; - return chartOpts; -}; +// $(function() { + // var chartOpts, data, mychart; + // console.log("js_data:", js_data); + // chartOpts = get_options(); + // data = get_data(); + // console.log(data); + // return mychart = corr_matrix(data, chartOpts); +// }); -get_data = function() { - var data; - data = {}; - data["var"] = js_data.traits; - data.group = js_data.groups; - data.indID = js_data.samples; - data.dat = js_data.sample_data; - data.corr = js_data.corr_results; - data.cols = js_data.cols; - data.rows = js_data.rows; - return data; -}; +// get_options = function() { + // var chartOpts; + // chartOpts = { + // cortitle: "Correlation Matrix", + // scattitle: "Scatterplot", + // h: 450, + // w: 450, + // margin: { + // left: 100, + // top: 40, + // right: 5, + // bottom: 70, + // inner: 5 + // } + // }; + // return chartOpts; +// }; +// get_data = function() { + // var data; + // data = {}; + // data["var"] = js_data.traits; + // data.group = js_data.groups; + // data.indID = js_data.samples; + // data.dat = js_data.sample_data; + // data.corr = js_data.corr_results; + // data.cols = js_data.cols; + // data.rows = js_data.rows; + // return data; +// }; var neg_color_scale = chroma.scale(['#FF0000', 'white']).domain([-1, -0.4]); var pos_color_scale = chroma.scale(['white', 'aqua']).domain([0.4, 1]) @@ -57,4 +56,26 @@ $('.corr_cell').each( function () { else { $(this).css('background-color', 'white') } +}); + +$('#short_labels').click( function (){ + $('.shortName').each( function() { + if ($(this).css("display") == "none"){ + $(this).css("display", "block"); + } + else { + $(this).css("display", "none"); + } + }); +}); + +$('#long_labels').click( function (){ + $('.verboseName').each( function() { + if ($(this).css("display") == "none"){ + $(this).css("display", "block"); + } + else { + $(this).css("display", "none"); + } + }); });
\ 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 d3db1853..06586372 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -117,14 +117,14 @@ "Barley1 Leaf MAS 5.0 SCRI (Dec06)" ], [ - "125", - "B30_K_1206_R", - "Barley1 Leaf gcRMA SCRI (Dec06)" - ], - [ "126", "B30_K_1206_Rn", "Barley1 Leaf gcRMAn SCRI (Dec06)" + ], + [ + "125", + "B30_K_1206_R", + "Barley1 Leaf gcRMA SCRI (Dec06)" ] ], "Phenotypes": [ @@ -1340,14 +1340,14 @@ "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": [ @@ -1526,14 +1526,14 @@ "NCI Mammary LMT miRNA v2 (Apr09) RMA" ], [ - "36", - "MA_M_0704_M", - "NCI Mammary mRNA M430 (July04) MAS5" - ], - [ "37", "MA_M_0704_R", "NCI Mammary mRNA M430 (July04) RMA" + ], + [ + "36", + "MA_M_0704_M", + "NCI Mammary mRNA M430 (July04) MAS5" ] ] }, @@ -1591,14 +1591,14 @@ ], "Liver mRNA": [ [ - "38", - "LVF2_M_0704_M", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" - ], - [ "39", "LVF2_M_0704_R", "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" + ], + [ + "38", + "LVF2_M_0704_M", + "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" ] ], "Phenotypes": [ @@ -1616,18 +1616,16 @@ "B6D2Publish", "B6D2 Published Phenotypes" ] - ], - "Retina mRNA": [ - [ - "803", - "UTHSC_mm9_B6D2_Ret_0916", - "UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Gene Level RMA" - ] ] }, "B6D2F2": { "Brain mRNA": [ [ + "76", + "BRF2_M_0805_M", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" + ], + [ "78", "BRF2_M_0805_P", "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" @@ -1638,24 +1636,19 @@ "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" ], [ - "76", - "BRF2_M_0805_M", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" - ], - [ "33", "BRF2_M_0304_P", "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" ], [ - "31", - "BRF2_M_0304_M", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" - ], - [ "32", "BRF2_M_0304_R", "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" + ], + [ + "31", + "BRF2_M_0304_M", + "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" ] ], "Genotypes": [ @@ -1683,6 +1676,23 @@ ] }, "B6D2RI": { + "Hippocampus mRNA": [ + [ + "712", + "UTHSC_BXDAged_0615", + "UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Jun15) RMA" + ], + [ + "805", + "UTHSC_BXDAgedEx_1116", + "UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Jun15) Exon Level RMA" + ], + [ + "391", + "UTHSC_B6D2RI_H_0912", + "UTHSC B6D2RI Aged Hippocampus Affy Mouse Gene 1.0 ST (Sep12) RMA" + ] + ], "Phenotypes": [ [ "None", @@ -1717,6 +1727,11 @@ ], "Striatum mRNA": [ [ + "84", + "SA_M2_0905_R", + "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" + ], + [ "83", "SA_M2_0905_M", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" @@ -1725,27 +1740,22 @@ "85", "SA_M2_0905_P", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" - ], - [ - "84", - "SA_M2_0905_R", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" ] ] }, "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", "UCLA BHF2 Adipose (June05) mlratio" @@ -1753,16 +1763,16 @@ ], "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", "UCLA BHF2 Brain (June05) mlratio" @@ -1777,16 +1787,16 @@ ], "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", "UCLA BHF2 Liver (June05) mlratio" @@ -1990,11 +2000,6 @@ "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" ], [ - "81", - "BR_U_0805_P", - "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" - ], - [ "80", "BR_U_0805_M", "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" @@ -2005,6 +2010,11 @@ "UTHSC Brain mRNA U74Av2 (Aug05) RMA" ], [ + "81", + "BR_U_0805_P", + "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" + ], + [ "42", "CB_M_0204_P", "INIA Brain mRNA M430 (Feb04) PDNN" @@ -2071,6 +2081,11 @@ "Eye M430v2 WT Gpnmb (Sep08) RMA" ], [ + "278", + "Eye_M2_0908_R_MT", + "Eye M430v2 Mutant Tyrp1 (Sep08) RMA" + ], + [ "382", "Eye_M2_0908_WTWT", "Eye M430v2 WT WT (Sep08) RMA" @@ -2081,11 +2096,6 @@ "Eye M430v2 WT Tyrp1 (Sep08) RMA" ], [ - "278", - "Eye_M2_0908_R_MT", - "Eye M430v2 Mutant Tyrp1 (Sep08) RMA" - ], - [ "400", "DBA2J-ONH-1212", "Howell et al. 2011, DBA/2J Glaucoma Optic Nerve Head M430 2.0 (Dec12) RMA" @@ -2342,14 +2352,14 @@ "Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN" ], [ - "115", - "MA_M2_0706_R", - "Mouse Kidney M430v2 (Jul06) RMA" - ], - [ "116", "MA_M2_0706_P", "Mouse Kidney M430v2 (Jul06) PDNN" + ], + [ + "115", + "MA_M2_0706_R", + "Mouse Kidney M430v2 (Jul06) RMA" ] ], "Liver Metabolome": [ @@ -2418,8 +2428,23 @@ ], "Liver mRNA": [ [ + "430", + "EPFLMouseLiverRMA0413", + "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" + ], + [ + "431", + "EPFLMouseLiverHFDRMA0413", + "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" + ], + [ + "432", + "EPFLMouseLiverCDRMA0413", + "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" + ], + [ "700", - "UT-VGX_HGL1014", + "UTHSC-VGX_MmBXDHepatocytesRMA1014", "UT-VGX Hepatocytes Affy Mouse Gene 1.0 ST Gene Level (Oct14) RMA" ], [ @@ -2441,21 +2466,6 @@ "702", "SUH_Liv_RMAEx_0611", "SUH BXD Liver CCl4-treated Affy Mouse Gene 1.0 ST Exon Level (Jun11) RMA" - ], - [ - "430", - "EPFLMouseLiverRMA0413", - "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" - ], - [ - "431", - "EPFLMouseLiverHFDRMA0413", - "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" - ], - [ - "432", - "EPFLMouseLiverCDRMA0413", - "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" ] ], "Lung mRNA": [ @@ -2479,21 +2489,6 @@ ], "Muscle mRNA": [ [ - "395", - "EPFLMouseMuscleRMA_Ex1112", - "EPFL/LISP BXD CD+HFD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level" - ], - [ - "396", - "EPFLMouseMuscleHFDRMAEx1112", - "EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level" - ], - [ - "397", - "EPFLMouseMuscleCDRMAEx1112", - "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level" - ], - [ "378", "EPFLMouseMuscleRMA1211", "EPFL/LISP BXD CD+HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA" @@ -2507,20 +2502,35 @@ "379", "EPFLMouseMuscleCDRMA1211", "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA" + ], + [ + "395", + "EPFLMouseMuscleRMA_Ex1112", + "EPFL/LISP BXD CD+HFD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level" + ], + [ + "396", + "EPFLMouseMuscleHFDRMAEx1112", + "EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level" + ], + [ + "397", + "EPFLMouseMuscleCDRMAEx1112", + "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level" ] ], "Neocortex mRNA": [ [ - "374", - "DevNeocortex_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv" - ], - [ "375", "DevNeocortex_ILM6.2P14RInv_1111", "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv" ], [ + "374", + "DevNeocortex_ILM6.2P3RInv_1111", + "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv" + ], + [ "284", "HQFNeoc_1210v2_RankInv", "HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv" @@ -2536,14 +2546,14 @@ "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": [ @@ -2751,6 +2761,11 @@ ], "Ventral Tegmental Area mRNA": [ [ + "229", + "VCUEtOH_0609_R", + "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA" + ], + [ "228", "VCUSal_0609_R", "VCU BXD VTA Sal M430 2.0 (Jun09) RMA" @@ -2759,11 +2774,15 @@ "230", "VCUEtvsSal_0609_R", "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA" - ], + ] + ] + }, + "BXD-Bone": { + "Phenotypes": [ [ - "229", - "VCUEtOH_0609_R", - "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA" + "None", + "BXD-BonePublish", + "BXD-Bone Published Phenotypes" ] ] }, @@ -2830,6 +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": [ [ @@ -2959,14 +3008,14 @@ ], "Hippocampus mRNA": [ [ - "99", - "HC_M2CB_1205_P", - "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" - ], - [ "100", "HC_M2CB_1205_R", "Hippocampus Consortium M430v2 CXB (Dec05) RMA" + ], + [ + "99", + "HC_M2CB_1205_P", + "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" ] ], "Phenotypes": [ @@ -3033,6 +3082,16 @@ ], "Hippocampus mRNA": [ [ + "219", + "Illum_LXS_Hipp_NON_1008", + "Hippocampus Illumina NON (Oct08) RankInv beta" + ], + [ + "212", + "Illum_LXS_Hipp_RSE_1008", + "Hippocampus Illumina RSE (Oct08) RankInv beta" + ], + [ "214", "Illum_LXS_Hipp_NOE_1008", "Hippocampus Illumina NOE (Oct08) RankInv beta" @@ -3048,16 +3107,6 @@ "Hippocampus Illumina NOS (Oct08) RankInv beta" ], [ - "219", - "Illum_LXS_Hipp_NON_1008", - "Hippocampus Illumina NON (Oct08) RankInv beta" - ], - [ - "212", - "Illum_LXS_Hipp_RSE_1008", - "Hippocampus Illumina RSE (Oct08) RankInv beta" - ], - [ "143", "Illum_LXS_Hipp_loess0807", "Hippocampus Illumina (Aug07) LOESS" @@ -3148,14 +3197,14 @@ ], "Hippocampus mRNA": [ [ - "272", - "HC_M2_0606_MDP", - "Hippocampus Consortium M430v2 (Jun06) RMA MDP" - ], - [ "273", "UMUTAffyExon_0209_RMA_MDP", "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" + ], + [ + "272", + "HC_M2_0606_MDP", + "Hippocampus Consortium M430v2 (Jun06) RMA MDP" ] ], "Liver mRNA": [ @@ -3227,6 +3276,17 @@ }, "Scripps-2013": {} }, + "poplar": { + "Poplar": { + "Phenotypes": [ + [ + "649", + "PoplarPublish", + "Poplar Published Phenotypes" + ] + ] + } + }, "rat": { "HSNIH-Palmer": { "Phenotypes": [ @@ -3524,6 +3584,10 @@ "BXD" ], [ + "BXD-Bone", + "BXD Bone" + ], + [ "BXH", "BXH" ], @@ -3532,6 +3596,10 @@ "Reduced Complexity Cross (B6JxB6N F2)" ], [ + "CFW", + "CFW Outbred GWAS" + ], + [ "CIE-INIA", "Chronic Intermittent Ethanol" ], @@ -3580,6 +3648,12 @@ "SOTNOT-OHSU" ] ], + "poplar": [ + [ + "Poplar", + "Poplar" + ] + ], "rat": [ [ "HSNIH-Palmer", @@ -3618,15 +3692,15 @@ "species": [ [ "human", - "Human" + "Human (hg19)" ], [ "mouse", - "Mouse" + "Mouse (mm10)" ], [ "rat", - "Rat" + "Rat (rn3)" ], [ "drosophila", @@ -3641,6 +3715,10 @@ "Barley" ], [ + "poplar", + "Poplar" + ], + [ "soybean", "Soybean" ], @@ -4387,10 +4465,6 @@ [ "Phenotypes", "Phenotypes" - ], - [ - "Retina mRNA", - "Retina mRNA" ] ], "B6D2F2": [ @@ -4417,6 +4491,10 @@ [ "Phenotypes", "Phenotypes" + ], + [ + "Hippocampus mRNA", + "Hippocampus mRNA" ] ], "BDF2-1999": [ @@ -4621,6 +4699,12 @@ "Ventral Tegmental Area mRNA" ] ], + "BXD-Bone": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], "BXH": [ [ "Phenotypes", @@ -4653,6 +4737,24 @@ "Genotypes" ] ], + "CFW": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Hippocampus mRNA", + "Hippocampus mRNA" + ], + [ + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA" + ], + [ + "Striatum mRNA", + "Striatum mRNA" + ] + ], "CIE-INIA": [ [ "Phenotypes", @@ -4813,6 +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/javascript/get_traits_from_collection.js b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js index a73eafe4..bcd83889 100644 --- a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js +++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js @@ -226,10 +226,8 @@ back_to_collections = function() { return $('#collections_holder').colorbox.resize(); }; -$(function() { - console.log("inside get_traits_from_collection"); - $(document).on("click", ".collection_line", collection_click); - $(document).on("click", "#submit", submit_click); - $(document).on("click", ".trait", trait_click); - return $(document).on("click", "#back_to_collections", back_to_collections); -}); +console.log("inside get_traits_from_collection"); +$(".collection_line").on("click", collection_click); +$("#submit").on("click", submit_click); +$(".trait").on("click", trait_click); +$("#back_to_collections").on("click", back_to_collections);
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/histogram.js b/wqflask/wqflask/static/new/javascript/histogram.js index d26d0c03..f71080e8 100644 --- a/wqflask/wqflask/static/new/javascript/histogram.js +++ b/wqflask/wqflask/static/new/javascript/histogram.js @@ -103,7 +103,6 @@ Histogram.prototype.add_bars = function() { var bar, rect_width; - console.log("bar_width:", this.x_scale(this.histogram_data[0].dx)); bar = this.svg.selectAll(".bar").data(this.histogram_data).enter().append("g").attr("class", "bar").attr("transform", (function(_this) { return function(d) { return "translate(" + _this.x_scale(d.x) + "," + _this.y_scale(d.y) + ")"; diff --git a/wqflask/wqflask/static/new/javascript/loadings_plot.js b/wqflask/wqflask/static/new/javascript/loadings_plot.js new file mode 100644 index 00000000..c44288c0 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/loadings_plot.js @@ -0,0 +1,109 @@ +var margin = {top: 20, right: 70, bottom: 60, left: 60} + , width = 960 - margin.left - margin.right + , height = 500 - margin.top - margin.bottom; + +var x = d3.scale.linear() + .domain([d3.min(loadings, function(d) { return d[0]; }) + 0.1*d3.min(loadings, function(d) { return d[0]; }), d3.max(loadings, function(d) { return d[0]; })]) + .range([ 0, width ]); + +var y = d3.scale.linear() + .domain([d3.min(loadings, function(d) { return d[1]; }) + 0.1*d3.min(loadings, function(d) { return d[1]; }), d3.max(loadings, function(d) { return d[1]; })]) + .range([ height, 0 ]); + +var chart = d3.select('#loadings_plot') + .append('svg:svg') + .attr('width', width + margin.right + margin.left) + .attr('height', height + margin.top + margin.bottom) + .attr('class', 'chart') + +var main = chart.append('g') + .attr('transform', 'translate(' + margin.left + ',' + margin.top + ')') + .attr('width', width) + .attr('height', height) + .attr('class', 'main') + +// draw the x axis +var xAxis = d3.svg.axis() + .scale(x) + .orient('bottom'); + +main.append('g') + .attr('transform', 'translate(0,' + height + ')') + .attr('class', 'x axis') + .call(xAxis); + +chart.append("text") + .attr("class", "x label") + .attr("text-anchor", "end") + .attr("x", 550) + .attr("y", 480) + .style("font-size", 14) + .style("fill", "blue") + .text("Factor (1)"); + +chart.append("text") + .attr("class", "y label") + .attr("text-anchor", "end") + .attr("x", -200) + .attr("y", 5) + .attr("dy", ".75em") + .attr("transform", "rotate(-90)") + .style("font-size", 14) + .style("fill", "blue") + .text("Factor (2)"); + +// draw the y axis +var yAxis = d3.svg.axis() + .scale(y) + .orient('left'); + +main.append('g') + .attr('transform', 'translate(0,0)') + .attr('class', 'y axis') + .call(yAxis); + +chart.select('.x.axis') + .selectAll("text") + .style("font-size","14px"); + +chart.select('.y.axis') + .selectAll("text") + .style("font-size","14px"); + +var g = main.append("svg:g"); + +g.selectAll("scatter-dots") + .data(loadings) + .enter().append("svg:circle") + .attr("cx", function (d,i) { return x(d[0]); } ) + .attr("cy", function (d) { return y(d[1]); } ) + .attr("r", 4) + .style("fill", "blue"); + +traits_and_loadings = [] +for (i = 0; i < js_data.traits.length; i++) { + this_trait_loadings = [] + this_trait_loadings[0] = js_data.traits[i] + this_trait_loadings[1] = [loadings[i][0], loadings[i][1]] + traits_and_loadings[i] = this_trait_loadings +} + +g.selectAll("scatter-dots") + .data(traits_and_loadings) + .enter().append("text") + .attr("x", function(d, i) { return x(d[1][0]); }) + .attr("y", function(d) { return y(d[1][1]); }) + .text(function(d) { return d[0]; }) + .style("font-size", 12) + .style("fill", "blue"); + +g.selectAll("scatter-lines") + .data(loadings) + .enter().append("svg:line") + .attr("x1", x(0)) + .attr("y1", y(0)) + .attr("x2", function (d,i) {return x(d[0]); } ) + .attr("y2", function (d) { return y(d[1]); } ) + .attr("stroke-width", 1) + .attr("stroke", "red"); +
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index e7df9228..c1c25a58 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -168,7 +168,7 @@ //$("#progress_bar_container").modal(); url = "/marker_regression"; $('input[name=method]').val("pylmm"); - $('input[name=genofile').val($('#genofile_pylmm').val()); + $('input[name=genofile]').val($('#genofile_pylmm').val()); $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val()); $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_pylmm]:checked').val()); form_data = $('#trait_data_form').serialize(); @@ -184,7 +184,7 @@ //$("#progress_bar_container").modal(); url = "/marker_regression"; $('input[name=method]').val("rqtl_geno"); - $('input[name=genofile').val($('#genofile_rqtl_geno').val()); + $('input[name=genofile]').val($('#genofile_rqtl_geno').val()); $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val()); $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val()); $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val()); @@ -244,7 +244,7 @@ //$("#progress_bar_container").modal(); url = "/marker_regression"; $('input[name=method]').val("reaper"); - $('input[name=genofile').val($('#genofile_reaper').val()); + $('input[name=genofile]').val($('#genofile_reaper').val()); $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val()); $('input[name=control_marker]').val($('input[name=control_reaper]').val()); $('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val()); 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 6540d01f..87f602dc 100644 --- a/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css +++ b/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css @@ -20,8 +20,14 @@ table.dataTable tfoot th { } table.dataTable thead th, table.dataTable thead td { - padding: 10px 18px 10px 0px; - border-bottom: 1px solid #111; + font: bold 12px/20px Arial, Sans-serif; + color: #000000; + background-color: #ffffff; + border-collapse: collapse; + border-bottom: #cccccc 2px solid; + padding: 0; + //padding: 10px 18px 10px 0px; + //border-bottom: 1px solid #111; } table.dataTable thead th:active, table.dataTable thead td:active { @@ -29,8 +35,13 @@ table.dataTable thead td:active { } table.dataTable tfoot th, table.dataTable tfoot td { - padding: 10px 18px 6px 18px; - border-top: 1px solid #111; + font: bold 12px/20px Arial, Sans-serif; + color: #000000; + background-color: #ffffff; + border-collapse: collapse; + padding: 0; + //padding: 10px 18px 6px 18px; + //border-top: 1px solid #111; } table.dataTable thead .sorting, table.dataTable thead .sorting_asc, @@ -69,7 +80,8 @@ table.dataTable tbody tr.selected { } table.dataTable tbody th, table.dataTable tbody td { - padding: 4px 5px; + font: 12px Arial, Sans-serif; + padding: 4px 5px 4px 0px; } table.dataTable.row-border tbody th, table.dataTable.row-border tbody td, table.dataTable.display tbody th, table.dataTable.display tbody td { border-top: 1px solid #ddd; 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\ No newline at end of file diff --git a/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css b/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css index 2c20f635..91aaa98f 100644 --- a/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css +++ b/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css @@ -2088,7 +2088,7 @@ th { border-top: 1px solid #ddd; } .table > thead > tr > th { - vertical-align: bottom; + vertical-align: middle; border-bottom: 2px solid #ddd; } .table > caption + thead > tr:first-child > th, diff --git a/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css b/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css index 076b6dae..9da73a8f 100644 --- a/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css +++ b/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css @@ -28,7 +28,7 @@ body { /* Reset the container */ .container { - width: 1200px; + width: 1400px; max-width: none !important; } diff --git a/wqflask/wqflask/submit_trait.py b/wqflask/wqflask/submit_trait.py new file mode 100644 index 00000000..4ab9a4be --- /dev/null +++ b/wqflask/wqflask/submit_trait.py @@ -0,0 +1,24 @@ +from __future__ import print_function, division + +from flask import Flask, g + +from pprint import pformat as pf + +def get_species_groups(): + + species_query = "SELECT SpeciesId, MenuName FROM Species" + + species_ids_and_names = g.db.execute(species_query).fetchall() + + + species_and_groups = [] + for species_id, species_name in species_ids_and_names: + this_species_groups = {} + this_species_groups['species'] = species_name + groups_query = "SELECT InbredSetName FROM InbredSet WHERE SpeciesId = %s" % (species_id) + groups = [group[0] for group in g.db.execute(groups_query).fetchall()] + + this_species_groups['groups'] = groups + species_and_groups.append(this_species_groups) + + return species_and_groups
\ No newline at end of file diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html index 23e976e9..6dc52c4d 100644 --- a/wqflask/wqflask/templates/collections/list.html +++ b/wqflask/wqflask/templates/collections/list.html @@ -26,7 +26,7 @@ {% endif %} </div> - <div id="collections_list" style="width:75%;"> + <div id="collections_list" style="width:50%;"> <table class="table table-hover table-striped" id='trait_table'> <thead> <tr> @@ -49,15 +49,11 @@ {% endif %} <td>{{ timeago(uc.created_timestamp.isoformat() + "Z") }}</td> <td>{{ timeago(uc.changed_timestamp.isoformat() + "Z") }}</td> - <td>{{ uc.num_members }}</td> + <td align="right">{{ uc.num_members }}</td> </tr> {% endfor %} </tbody> </table> - - {# if "color_by_trait" in params #} - <script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script> - {# endif #} </div> </div> @@ -78,17 +74,23 @@ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script> + {% if "color_by_trait" in params %} + <script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script> + {% endif %} <script> $('#trait_table').dataTable( { - "buttons": [ - { - extend: 'csvHtml5', - text: 'Download CSV', - title: 'collection_list', - fieldBoundary: '"' - } + "columns": [ + { "type": "natural", + "width": "10%" }, + { "type": "natural" }, + { "type": "natural", + "width": "25%" }, + { "type": "natural", + "width": "25%" }, + { "type": "natural", + "width": "10%" } ], - "sDom": "RZBtir", + "sDom": "RZtr", "iDisplayLength": -1, "autoWidth": true, "bDeferRender": true, diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index 801266d3..9d03e6d7 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -79,20 +79,20 @@ <button class="btn btn-default" id="export_traits">Download CSV</button> </form> <br /> - <div style="background-color: #eeeeee; border: 1px solid black;"> - <table id="trait_table" class="table table-hover table-striped"> + <div> + <table class="table table-hover table-striped nowrap" id='trait_table' style="float: left;"> <thead> <tr> - <th style="background-color: #eeeeee;"></th> - <th data-export="Index" style="background-color: #eeeeee;">Index</th> - <th data-export="Dataset" style="background-color: #eeeeee;">Dataset</th> - <th data-export="Record" style="background-color: #eeeeee;">Record</th> - <th data-export="Description" style="background-color: #eeeeee;">Description</th> - <th data-export="Location" style="background-color: #eeeeee;">Location</th> - <th data-export="Mean" style="background-color: #eeeeee;">Mean</th> - <th data-export="Max LRS" style="background-color: #eeeeee;">Max LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th> - <th data-export="Max LRS Location" style="background-color: #eeeeee;">Max LRS Location</th> - <th data-export="Additive Effect" style="background-color: #eeeeee;">Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th> + <th></th> + <th data-export="Index">Index</th> + <th data-export="Dataset">Dataset</th> + <th data-export="Record">Record</th> + <th data-export="Description">Description</th> + <th data-export="Location">Location</th> + <th data-export="Mean">Mean</th> + <th data-export="Max LRS">Max LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th> + <th data-export="Max LRS Location">Max LRS Location</th> + <th data-export="Additive Effect">Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th> </tr> </thead> @@ -103,7 +103,7 @@ <INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" VALUE="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"> </TD> - <TD data-export="{{ loop.index }}">{{ loop.index }}</TD> + <TD data-export="{{ loop.index }}" align="right">{{ loop.index }}</TD> <TD data-export="{{ this_trait.dataset.name }}">{{ this_trait.dataset.name }}</TD> <TD data-export="{{ this_trait.name }}"> <a href="{{ url_for('show_trait_page', @@ -113,12 +113,12 @@ {{ this_trait.name }} </a> </TD> - <TD data-export="{{ this_trait.description_display }}">{{ this_trait.description_display }}</TD> + <TD title="{{ this_trait.description_display }}" data-export="{{ this_trait.description_display }}">{{ this_trait.description_display }}</TD> <TD data-export="{{ this_trait.location_repr }}">{{ this_trait.location_repr }}</TD> - <TD data-export="{{ this_trait.mean }}">{{ '%0.3f' % this_trait.mean|float }}</TD> - <TD data-export="{{ this_trait.LRS_score_repr }}">{{ '%0.3f' % this_trait.LRS_score_repr|float }}</TD> + <TD data-export="{{ this_trait.mean }}" align="right">{{ '%0.3f' % this_trait.mean|float }}</TD> + <TD data-export="{{ this_trait.LRS_score_repr }}" align="right">{{ '%0.3f' % this_trait.LRS_score_repr|float }}</TD> <TD data-export="{{ this_trait.LRS_location_repr }}">{{ this_trait.LRS_location_repr }}</TD> - <TD data-export="{{ this_trait.additive }}">{{ '%0.3f' % this_trait.additive|float }}</TD> + <TD data-export="{{ this_trait.additive }}" align="right">{{ '%0.3f' % this_trait.additive|float }}</TD> </TR> {% endfor %} @@ -156,23 +156,34 @@ console.time("Creating table"); $('#trait_table').dataTable( { + "createdRow": function ( row, data, index ) { + if ($('td', row).eq(4).text().length > 50) { + $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 50)); + $('td', row).eq(4).text($('td', row).eq(4).text() + '...') + } + }, "columns": [ { "type": "natural" }, - { "type": "natural" }, + { "type": "natural", "width": "5%" }, { "type": "natural" }, { "type": "natural" }, { "type": "natural", - "width": "35%" }, + "width": "30%" }, { "type": "natural", - "width": "15%" }, + "width": "10%" }, { "type": "cust-txt" }, { "type": "natural", - "width": "9%" }, + "width": "6%" }, + { "type": "natural", + "width": "10%" }, { "type": "natural", - "width": "15%" }, - { "type": "natural" } + "width": "8%" } ], - "sDom": "ZRtir", + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], + "sDom": "ZRtr", "iDisplayLength": -1, "autoWidth": true, "bDeferRender": true, diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index 593c7bea..eb675568 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -12,11 +12,12 @@ {{ header("Correlation Matrix") }} +<div class="container"> {% if lowest_overlap < 8 %} <div style="margin: 20px;" >Caution: This matrix of correlations contains some cells with small sample sizes of fewer than 8.</div> {% endif %} -<table class="matrix" border="1" cellpadding="5" cellspacing="1" style="margin: 20px;" width="80%"> +<table class="matrix" border="1" cellpadding="5" cellspacing="1" width="80%"> <tbody> <tr> <td style="background-color: royalblue;" ></td> @@ -26,35 +27,53 @@ <td align="center" rowspan="{{traits|length + 1 }}" width="10" style="font-weight: Bold; border: 1px solid #999999; padding: 3px; color: #fff; background-color: royalblue;">P e a r s o n r</td> <td width="300"></td> {% for trait in traits %} - <td align="center"><a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}" style="font-weight: Bold;">Trait{{ loop.index }}</a></td> + <td align="center"> + <a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}" style="font-weight: Bold;">Trait{{ loop.index }}</a> + </td> {% endfor %} </tr> {% for trait in traits %} <tr> - <td><a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}" style="font-weight: Bold;">Trait {{ loop.index }}: {{ trait.dataset.name }}::{{ trait.name }}</a><div id="shortName_0" style="display:none">Symbol: {{ trait.symbol }} </div><div id="verboseName_0" style="display:none">{{ trait_symbol }} on Chr {{ trait.chr }} @ {{ trait.mb }} Mb</div><div id="verboseName2_0" style="display:none">{{ trait.description }}</div><div id="verboseName3_0" style="display:none">{{ trait.probe_target_description }}</div></td> + <td> + <a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}" style="font-weight: Bold;">Trait {{ loop.index }}: {{ trait.dataset.name }}::{{ trait.name }}</a> + <div class="shortName" style="display:none">{% if trait.dataset.type == "ProbeSet" %}Symbol: {{ trait.symbol }}{% elif trait.dataset.type == "Publish" %}Phenotype: {{ trait.post_publication_abbreviation }}{% else %}Genotype{% endif %} </div> + <div class="verboseName" style="display: none;"> + {% if trait.dataset.type == "ProbeSet" %} + <div>{{ trait.symbol }} on Chr {{ trait.chr }} @ {{ trait.mb }} Mb</div><div>{{ trait.description }}</div><div>{{ trait.probe_target_description }}</div> + {% elif trait.dataset.type == "Publish" %} + <div>PubMed {{ trait.pubmed_id }}: RecordID/{{ trait.name }}</div><div>Phenotype: {{ trait.description_display }}</div> + {% else %} + <div>Locus {{ trait.name }}</div><div>Chr {{ trait.chr }} @ {{ trait.mb }} Mb</div> + {% endif %} + </div> + </td> {% for result in corr_results[loop.index-1] %} {% if result[0].name == trait.name %} - <td nowrap="ON" align="center" bgcolor="#cccccc"><a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 11px; color: #000000;" ><em>n</em><br>{{ result[2] }}</font></a></td> + <td nowrap="ON" align="center" bgcolor="#cccccc" style="line-height: 1.1;"><a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 12px; color: #000000;" ><em>n</em><br>{{ result[2] }}</font></a></td> {% else %} - <td nowrap="ON" align="middle" class="corr_cell"><a href="/corr_scatter_plot?dataset_1={{ trait.dataset.name }}&dataset_2={{ result[0].dataset.name }}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 11px; color: #000000;" ><span class="corr_value">{{ '%0.3f' % result[1] }}</span><br>{{ result[2] }}</font></a></td> + <td nowrap="ON" align="middle" class="corr_cell" style="line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={{ trait.dataset.name }}&dataset_2={{ result[0].dataset.name }}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #000000;" ><span class="corr_value">{{ '%0.3f' % result[1] }}</span><br>{{ result[2] }}</font></a></td> {% endif %} {% endfor %} </tr> {% endfor %} </tbody> </table> - <br> - +<button class="btn btn-default" id="short_labels">Short Labels</button> +<button class="btn btn-default" id="long_labels">Long Labels</button> +<br> +<br> +<h2>Factor Loadings Plot</h2> <div id="loadings_plot"></div> +<h2>Factor Loadings Table</h2> <table class="table table-hover table-striped" border="1" id='trait_table' style="margin: 20px;" width="40%"> <thead> <tr> <th></th> <th align="right" >Factor 1</th> <th align="right" >Factor 2</th> - <th align="right" >Factor 2</th> + {% if trait_list|length > 2 %}<th align="right" >Factor 3</th>{% endif %} <!-- {% for row in loadings_array %} <th>Factor {{ loop.index }}</th> @@ -79,12 +98,14 @@ </tbody> </table> +</div> {% endblock %} {% block js %} <script> + js_data = {{ js_data | safe }} loadings = {{ loadings_array | safe }} </script> @@ -98,5 +119,6 @@ <script type="text/javascript" src="/static/new/javascript/panelutil.js"></script> <script language="javascript" type="text/javascript" src="/static/new/js_external/chroma.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/loadings_plot.js"></script> + <script type="text/javascript" src="/static/new/javascript/create_corr_matrix.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index c5b4477b..cedb65a1 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -14,8 +14,8 @@ <h1>Correlation Table</h1> </div> - <p>Values of record {{ this_trait.name }} in the <a href="/static/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a> - dataset were compared to all records in the <a href="/static/dbdoc/{{target_dataset.fullname}}">{{ target_dataset.fullname }}</a> + <p>Values of record {{ this_trait.name }} in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId={{ dataset.group.accession_id }}">{{ dataset.fullname }}</a> + dataset were compared to all records in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId={{ target_dataset.group.accession_id }}">{{ target_dataset.fullname }}</a> dataset. The top {{ return_number }} correlations ranked by the {{ formatted_corr_type }} are displayed. You can resort this list by clicking the headers. Select the Record ID to open the trait data and analysis page. @@ -220,6 +220,20 @@ }; + jQuery.fn.dataTableExt.oSort['scientific-asc'] = function ( a, b ) { + var x = parseFloat(a); + var y = parseFloat(b); + return ((x < y) ? -1 : ((x > y) ? 1 : 0)); + }; + + jQuery.fn.dataTableExt.oSort['scientific-desc'] = function ( a, b ) { + var x = parseFloat(a); + var y = parseFloat(b); + return ((x < y) ? 1 : ((x > y) ? -1 : 0)); + }; + + + $(document).ready( function () { $('#trait_table tr').click(function(event) { @@ -258,13 +272,13 @@ { "type": "natural" }, { "type": "natural" }, { "type": "natural" }, - { "type": "numeric-html" }, { "type": "natural" }, { "type": "natural" }, + { "type": "scientific" }, { "type": "natural" }, { "type": "natural" } ], - "order": [[10, "desc" ]], + "order": [[12, "asc" ]], "sDom": "Btir", "autoWidth": false, "bDeferRender": true, @@ -304,9 +318,9 @@ { "type": "natural" }, { "type": "numeric-html" }, { "type": "natural" }, - { "type": "natural" } + { "type": "scientific" } ], - "order": [[9, "desc" ]], + "order": [[11, "asc" ]], "sDom": "Btir", "autoWidth": false, "bDeferRender": true, @@ -337,9 +351,9 @@ { "type": "natural" }, { "type": "numeric-html" }, { "type": "natural" }, - { "type": "natural" } + { "type": "scientific" } ], - "order": [[4, "desc" ]], + "order": [[6, "asc" ]], "sDom": "Btir", "autoWidth": false, "bDeferRender": true, diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 8b8a9057..205d5801 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -9,7 +9,7 @@ <div class="container"> <p>You searched for {{ terms }}.</p> - <p>To study a record, click on its ID below.<br />Check records below and click Add button to add to selection.</p> + <p>To study a record, click on its Record ID below.<br />Check records below and click Add button to add to selection.</p> <div> <br /> @@ -27,36 +27,36 @@ <button class="btn btn-default" id="export_traits">Download CSV</button> </form> <br /> - <div style="width: 2000px; background-color: #eeeeee; border: 1px solid black;"> - <table width="2000px" id="trait_table" class="table table-hover table-striped" > + <div style="width: 2000px;"> + <table width="2000px" id="trait_table" class="table table-hover table-striped nowrap" style="float: left;"> <thead> <tr> - <th style="background-color: #eeeeee;"></th> - <th data-export="Index" style="background-color: #eeeeee;">Index</th> - <th data-export="Species" style="background-color: #eeeeee;">Species</th> - <th data-export="Group" style="background-color: #eeeeee;">Group</th> - <th data-export="Tissue" style="background-color: #eeeeee;">Tissue</th> - <th data-export="Dataset" style="background-color: #eeeeee;">Dataset</th> - <th data-export="Record" style="background-color: #eeeeee;">Record</th> - <th data-export="Symbol" style="background-color: #eeeeee;">Symbol</th> - <th data-export="Description" style="background-color: #eeeeee;">Description</th> - <th data-export="Location" style="background-color: #eeeeee;">Location</th> - <th data-export="Mean" style="background-color: #eeeeee;">Mean</th> - <th data-export="Max LRS" style="background-color: #eeeeee;">Max <br>LRS<a href="http://genenetwork.org/glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th> - <th data-export="Max LRS Location" style="background-color: #eeeeee;">Max LRS Location</th> - <th data-export="Additive Effect" style="background-color: #eeeeee;">Additive<br>Effect<a href="http://genenetwork.org/glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th> + <th></th> + <th data-export="Index">Index</th> + <th data-export="Record">Record ID</th> + <th data-export="Species">Species</th> + <th data-export="Group">Group</th> + <th data-export="Tissue">Tissue</th> + <th data-export="Dataset">Dataset</th> + <th data-export="Symbol">Symbol</th> + <th data-export="Description">Description</th> + <th data-export="Location">Location</th> + <th data-export="Mean">Mean</th> + <th data-export="Max LRS">Max LRS<a href="http://genenetwork.org/glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th> + <th data-export="Max LRS Location">Max LRS Location</th> + <th data-export="Additive Effect">Additive Effect<a href="http://genenetwork.org/glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th> </tr> </thead> <tbody> {% for this_trait in trait_list %} <tr id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}"> - <td><input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"></td> + <td style="padding-left: 5px;"><input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"></td> <td data-export="{{ loop.index }}">{{ loop.index }}</td> + <td data-export="{{ this_trait.name }}"><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset.name)}}">{{ this_trait.name }}</a></td> <td data-export="{{ this_trait.dataset.group.species }}">{{ this_trait.dataset.group.species }}</td> <td data-export="{{ this_trait.dataset.group.name }}">{{ this_trait.dataset.group.name }}</td> <td data-export="{{ this_trait.dataset.tissue }}">{{ this_trait.dataset.tissue }}</td> <td data-export="{{ this_trait.dataset.name }}">{{ this_trait.dataset.name }}</td> - <td data-export="{{ this_trait.name }}"><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset.name)}}">{{ this_trait.name }}</a></td> <td data-export="{{ this_trait.symbol }}">{{ this_trait.symbol }}</td> <td data-export="{{ this_trait.description_display }}">{{ this_trait.description_display }}</td> <td data-export="{{ this_trait.location_repr }}" align="right">{{ this_trait.location_repr }}</td> @@ -69,20 +69,20 @@ </tbody> <tfoot> <tr> - <th style="background-color: #eeeeee;"></th> - <th style="background-color: #eeeeee;">Index</th> - <th style="background-color: #eeeeee;">Species</th> - <th style="background-color: #eeeeee;">Group</th> - <th style="background-color: #eeeeee;">Tissue</th> - <th style="background-color: #eeeeee;">Dataset</th> - <th style="background-color: #eeeeee;">Record</th> - <th style="background-color: #eeeeee;">Symbol</th> - <th style="background-color: #eeeeee;">Description</th> - <th style="background-color: #eeeeee;">Location</th> - <th style="background-color: #eeeeee;">Mean</th> - <th style="background-color: #eeeeee;">Max <br>LRS<a href="http://genenetwork.org/glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th> - <th style="background-color: #eeeeee;">Max LRS Location</th> - <th style="background-color: #eeeeee;">Additive<br>Effect<a href="http://genenetwork.org/glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th> + <th></th> + <th>Index</th> + <th>Record ID</th> + <th>Species</th> + <th>Group</th> + <th>Tissue</th> + <th>Dataset</th> + <th>Symbol</th> + <th>Description</th> + <th>Location</th> + <th>Mean</th> + <th>Max LRS<a href="http://genenetwork.org/glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th> + <th>Max LRS Location</th> + <th>Additive Effect<a href="http://genenetwork.org/glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th> </tr> </tfoot> </table> @@ -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 %} +<form method="post" action="/marker_regression" name="loading_form" id="loading_form"> + <div class="progress" style="position: fixed; top: 50%; left: 50%;"> + <div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width:100%"></div> + </div> +</form> +{% endblock %} +{% block js %} +<script type="text/javascript"> +$("#loading_form").submit(); +</script> +{% 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 0f5e68d7..cafa8b93 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -2,16 +2,15 @@ {% block title %}Search Results{% endblock %} {% block css %} <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> - <link rel="stylesheet" type="text/css" href="//cdn.datatables.net/scroller/1.4.1/css/scroller.dataTables.min.css"> - <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/dataTables.fixedHeader.css" > - <link rel="stylesheet" type="text/css" href="//cdn.datatables.net/fixedcolumns/3.0.4/css/dataTables.fixedColumns.css"> + <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/scroller.dataTables.min.css"> + <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css"> {% endblock %} {% block content %} <!-- Start of body --> {{ header("Search Results", 'GeneNetwork found {}.'.format(numify(results|count, "record", "records"))) }} - <div class="container"> + <div> <input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}"> <!-- Need to customize text more for other types of searches --> @@ -44,7 +43,7 @@ {% endfor %} </p> - <p>To study a record, click on its ID below. Check records below and click Add button to add to selection.</p> + <p>To study a record click on its ID below, and to view the whole description {% if dataset.type == "Publish" %}or list of authors {% endif %} hover over the table cell. Check records below and click Add button to add to selection.</p> <div> <br /> @@ -78,73 +77,33 @@ {% endif %} --> - <div id="table_container" style="background-color: #eeeeee; border: 1px solid black;"> - <table class="table table-hover table-striped" id='trait_table' {% if dataset.type == 'Geno' %}width="400px"{% endif %} style="float: left;"> + <div id="table_container" style="width: {% if dataset.type == 'ProbeSet' %}1300{% elif dataset.type == 'Publish' %}1200{% elif dataset.type == 'Geno' %}500{% endif %}px;"> + <table class="table table-hover table-striped nowrap" id='trait_table' style="float: left;"> <thead> <tr> - <th style="background-color: #eeeeee;"></th> + <th></th> {% for header in header_fields %} {% if header == 'Max LRS' %} - <th data-export="Max LRS" style="background-color: #eeeeee; text-align: right;">Max<br>LRS</th> + <th data-export="Max LRS">Max LRS</th> {% elif header == 'Additive Effect' %} - <th data-export="Additive Effect" style="background-color: #eeeeee; text-align: right;">Additive<br>Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th> + <th data-export="Additive Effect">Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th> {% else %} - <th data-export="{{header}}" style="background-color: #eeeeee;">{{header}}</th> + <th data-export="{{header}}">{{header}}</th> {% endif %} {% endfor %} </tr> </thead> - - <tbody> - {% for this_trait in trait_list %} - <TR id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}"> - <TD><INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" VALUE="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"> - </TD> - <TD data-export="{{ loop.index }}" align="right">{{ loop.index }}</TD> - <TD data-export="{{ this_trait.name }}"> - <a href="{{ url_for('show_trait_page', - trait_id = this_trait.name, - dataset = dataset.name - )}}"> - {{ this_trait.name }} - </a> - </TD> - {% if dataset.type == 'ProbeSet' %} - <TD data-export="{{ this_trait.symbol }}">{{ this_trait.symbol }}</TD> - <TD data-export="{{ this_trait.description_display }}">{{ this_trait.description_display }}</TD> - <TD data-export="{{ this_trait.location_repr }}">{{ this_trait.location_repr }}</TD> - <TD data-export="{{ '%0.3f' % this_trait.mean|float }}" align="right">{{ '%0.3f' % this_trait.mean|float }}</TD> - <TD data-export="{{ '%0.3f' % this_trait.LRS_score_repr|float }}" align="right">{{ '%0.3f' % this_trait.LRS_score_repr|float }}</TD> - <TD data-export="{{ this_trait.LRS_location_repr }}">{{ this_trait.LRS_location_repr }}</TD> - <TD data-export="{{ '%0.3f' % this_trait.additive|float }}" align="right">{{ '%0.3f' % this_trait.additive|float }}</TD> - {% elif dataset.type == 'Publish' %} - <TD data-export="{{ this_trait.description_display }}">{{ this_trait.description_display }}</TD> - <TD data-export="{{ this_trait.authors }}">{{ this_trait.authors }}</TD> - <TD data-export="{{ this_trait.pubmed_text }}" data-sort="{{ this_trait.pubmed_text }}"> - <a href="{{ this_trait.pubmed_link }}"> - {{ this_trait.pubmed_text }} - </a> - </TD> - <TD data-export="{{ '%0.3f' % this_trait.LRS_score_repr|float }}">{{ '%0.3f' % this_trait.LRS_score_repr|float }}</TD> - <TD data-export="{{ this_trait.LRS_location_repr }}">{{ this_trait.LRS_location_repr }}</TD> - <TD data-export="{{ '%0.3f' % this_trait.additive|float }}">{{ '%0.3f' % this_trait.additive|float }}</TD> - {% elif dataset.type == 'Geno' %} - <TD data-export="{{ this_trait.location_repr }}">{{ this_trait.location_repr }}</TD> - {% endif %} - </TR> - {% endfor %} - </tbody> {% if trait_list|length > 20 %} <tfoot> <tr> - <th style="width: 30px;"></th> + <th></th> {% for header in header_fields %} {% if header == 'Max LRS' %} - <th style="text-align: right;">Max<br>LRS</th> + <th data-export="Max LRS">Max LRS</th> {% elif header == 'Additive Effect' %} - <th style="text-align: right;">Additive<br>Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th> + <th data-export="Additive Effect">Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th> {% else %} - <th>{{header}}</th> + <th data-export="{{header}}">{{header}}</th> {% endif %} {% endfor %} </tr> @@ -162,15 +121,18 @@ {% endblock %} {% block js %} - <script type="text/javascript" src="/static/new/javascript/search_results.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/js/jquery.dataTables.min.js"></script> <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.fixedHeader.min.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.buttons.min.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/buttons.colVis.min.js"></script> + <script type='text/javascript'> + var json_trait_list = {{ json_trait_list|safe }}; + </script> + <script type="text/javascript" charset="utf-8"> $(document).ready( function () { @@ -180,71 +142,217 @@ } }); + function change_buttons() { + buttons = ["#add", "#remove"]; + num_checked = $('.trait_checkbox:checked').length; + if (num_checked === 0) { + for (_i = 0, _len = buttons.length; _i < _len; _i++) { + button = buttons[_i]; + $(button).prop("disabled", true); + } + } else { + for (_j = 0, _len2 = buttons.length; _j < _len2; _j++) { + button = buttons[_j]; + $(button).prop("disabled", false); + } + } + //}); + if ($(this).is(":checked")) { + if (!$(this).closest('tr').hasClass('selected')) { + $(this).closest('tr').addClass('selected') + } + } + else { + if ($(this).closest('tr').hasClass('selected')) { + $(this).closest('tr').removeClass('selected') + } + } + } + console.time("Creating table"); {% if dataset.type == 'ProbeSet' %} //ZS: Need to make sort by symbol, also need to make sure blank symbol fields at the bottom and symbols starting with numbers below letters $('#trait_table').DataTable( { + "drawCallback": function( settings ) { + $('#trait_table tr').click(function(event) { + if (event.target.type !== 'checkbox') { + $(':checkbox', this).trigger('click'); + } + }); + $('.trait_checkbox:checkbox').on("change", change_buttons); + }, + "createdRow": function ( row, data, index ) { + $('td', row).eq(1).attr('align', 'right'); + $('td', row).eq(1).attr('data-export', index+1); + $('td', row).eq(2).attr('data-export', $('td', row).eq(2).text()); + $('td', row).eq(3).attr('title', $('td', row).eq(3).text()); + $('td', row).eq(3).attr('data-export', $('td', row).eq(3).text()); + $('td', row).eq(4).attr('title', $('td', row).eq(4).text()); + $('td', row).eq(4).attr('data-export', $('td', row).eq(4).text()); + if ($('td', row).eq(4).text().length > 50) { + $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 50)); + $('td', row).eq(4).text($('td', row).eq(4).text() + '...') + } + $('td', row).eq(5).attr('data-export', $('td', row).eq(5).text()); + $('td', row).eq(6).attr('align', 'right'); + $('td', row).eq(6).attr('data-export', $('td', row).eq(6).text()); + $('td', row).eq(7).attr('align', 'right'); + $('td', row).eq(7).attr('data-export', $('td', row).eq(7).text()); + $('td', row).eq(8).attr('data-export', $('td', row).eq(8).text()); + $('td', row).eq(9).attr('align', 'right'); + $('td', row).eq(9).attr('data-export', $('td', row).eq(9).text()); + }, + "data": json_trait_list, "columns": [ - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural", "width": "40%" }, - { "type": "natural", "width": "15%" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural", "width": "15%" }, - { "type": "natural" } + { "type": "natural", "width": "2%" }, + { "type": "natural", "width": "4%" }, + { "type": "natural", "width": "12%" }, + { "type": "natural", "width": "12%" }, + { "type": "natural", "width": "30%" }, + { "type": "natural", "width": "10%" }, + { "type": "natural", "width": "6%" }, + { "type": "natural", "width": "6%" }, + { "type": "natural", "width": "12%" }, + { "type": "natural", "width": "10%" } ], + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], "order": [[1, "asc" ]], - "sDom": "RZtir", + buttons: [ + { + extend: 'colvis', + text: 'Show or Hide Columns', + columns: ':not(:first-child)', + postfixButtons: [ 'colvisRestore' ] + } + ], + "sDom": "BRZtir", "iDisplayLength": -1, - "bDeferRender": true, + "autoWidth": false, + "deferRender": true, "bSortClasses": false, - "scrollY": true, + "scrollY": "600px", "scrollCollapse": false, + "scroller": true, "paging": false } ); {% elif dataset.type == 'Publish' %} $('#trait_table').DataTable( { + "drawCallback": function( settings ) { + $('#trait_table tr').click(function(event) { + if (event.target.type !== 'checkbox') { + $(':checkbox', this).trigger('click'); + } + }); + $('.trait_checkbox:checkbox').on("change", change_buttons); + }, + "createdRow": function ( row, data, index ) { + $('td', row).eq(1).attr('align', 'right'); + $('td', row).eq(1).attr('data-export', index+1); + $('td', row).eq(2).attr('data-export', $('td', row).eq(2).text()); + $('td', row).eq(3).attr('title', $('td', row).eq(3).text()); + $('td', row).eq(3).attr('data-export', $('td', row).eq(3).text()); + if ($('td', row).eq(3).text().length > 50) { + $('td', row).eq(3).text($('td', row).eq(3).text().substring(0, 50)); + $('td', row).eq(3).text($('td', row).eq(3).text() + '...') + } + $('td', row).eq(4).attr('title', $('td', row).eq(4).text()); + $('td', row).eq(4).attr('data-export', $('td', row).eq(4).text()); + if ($('td', row).eq(4).text().length > 50) { + $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 50)); + $('td', row).eq(4).text($('td', row).eq(4).text() + '...') + } + $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 30)); + $('td', row).eq(5).attr('align', 'right'); + $('td', row).eq(5).attr('data-export', $('td', row).eq(5).text()); + $('td', row).eq(6).attr('align', 'right'); + $('td', row).eq(6).attr('data-export', $('td', row).eq(6).text()); + $('td', row).eq(7).attr('data-export', $('td', row).eq(7).text()); + $('td', row).eq(8).attr('align', 'right'); + $('td', row).eq(8).attr('data-export', $('td', row).eq(8).text()); + }, + "data": json_trait_list, "columns": [ - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural", "width": "15%"}, - { "type": "natural" } + { "type": "natural", "width": "2%" }, + { "type": "natural", "width": "5%" }, + { "type": "natural", "width": "6%" }, + { "type": "natural", "width": "30%" }, + { "type": "natural", "width": "25%" }, + { "type": "natural", "width": "5%" }, + { "type": "natural", "width": "6%" }, + { "type": "natural", "width": "9%" }, + { "type": "natural", "width": "7%" } ], + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], "order": [[1, "asc" ]], - "sDom": "RZtir", + buttons: [ + { + extend: 'colvis', + text: 'Show or Hide Columns', + columns: ':not(:first-child)', + postfixButtons: [ 'colvisRestore' ] + } + ], + "sDom": "BRZtir", "iDisplayLength": -1, "autoWidth": false, - "bDeferRender": true, + "deferRender": true, "bSortClasses": false, - "scrollY": "700px", - "scrollCollapse": false, + "scrollY": "600px", + "scrollCollapse": true, + "scroller": true, "paging": false } ); {% elif dataset.type == 'Geno' %} $('#trait_table').DataTable( { + "drawCallback": function( settings ) { + $('#trait_table tr').click(function(event) { + if (event.target.type !== 'checkbox') { + $(':checkbox', this).trigger('click'); + } + }); + $('.trait_checkbox:checkbox').on("change", change_buttons); + }, + "createdRow": function ( row, data, index ) { + $('td', row).eq(1).attr('align', 'right'); + $('td', row).eq(1).attr('data-export', index+1); + $('td', row).eq(2).attr('data-export', $('td', row).eq(2).text()); + $('td', row).eq(3).attr('data-export', $('td', row).eq(3).text()); + }, + "data": json_trait_list, "columns": [ - { "type": "natural" }, - { "type": "natural" }, - { "type": "natural" }, + { "type": "natural", "width": "8%" }, + { "type": "natural", "width": "12%" }, + { "type": "natural", "width": "40%" }, { "type": "natural", "width": "40%"} ], + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], "order": [[1, "asc" ]], - "sDom": "RZtir", + buttons: [ + { + extend: 'colvis', + text: 'Show or Hide Columns', + columns: ':not(:first-child)', + postfixButtons: [ 'colvisRestore' ] + } + ], + "sDom": "BRZtir", "iDisplayLength": -1, - "autoWidth": true, - "bDeferRender": true, + "autoWidth": false, + "deferRender": true, "bSortClasses": false, - "scrollY": "700px", - "scrollCollapse": false, + "scrollY": "600px", + "scrollCollapse": true, + "scroller": true, "paging": false } ); {% endif %} diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index d76e8af8..d7e60b61 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -213,7 +213,12 @@ {% for attribute in sample_groups[0].attributes %} { "type": "natural" }{% if loop.index < sample_groups[0].attributes|length %},{% endif %} {% endfor %} - ], + ], + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], + "order": [[1, "asc" ]], "sDom": "RZtr", "iDisplayLength": -1, "autoWidth": false, @@ -240,6 +245,11 @@ { "type": "natural" }{% if loop.index < sample_groups[0].attributes|length %},{% endif %} {% endfor %} ], + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], + "order": [[1, "asc" ]], "sDom": "RZtr", "iDisplayLength": -1, "autoWidth": false, diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html index ff5f0c87..8821167b 100644 --- a/wqflask/wqflask/templates/show_trait_edit_data.html +++ b/wqflask/wqflask/templates/show_trait_edit_data.html @@ -77,20 +77,21 @@ {% for sample_type in sample_groups %} <div class="sample_group" style="width:{{ trait_table_width }}%;"> <h3>{{ sample_type.header }}</h3> - <div id="table_container" style="background-color: #eeeeee; border: 1px solid black;"> + <hr> + <div id="table_container"> <table class="table-hover table-striped" id="samples_{{ sample_type.sample_group_type }}" style="float: left;"> <thead> <tr> - <th style="background-color: #eeeeee;"></th> - <th style="background-color: #eeeeee;">Index</th> - <th style="background-color: #eeeeee;">Sample</th> - <th style="background-color: #eeeeee;">Value</th> + <th></th> + <th>Index</th> + <th>Sample</th> + <th>Value</th> {% if sample_type.se_exists() %} - <th style="background-color: #eeeeee;"> </th> - <th style="background-color: #eeeeee;">SE</th> + <th> </th> + <th>SE</th> {% endif %} {% for attribute in sample_type.attributes|sort() %} - <th style="background-color: #eeeeee;"> + <th> {{ sample_type.attributes[attribute].name }} </th> {% endfor %} @@ -146,6 +147,7 @@ </table> </div> </div> + <br> {% endfor %} <!--</div>--> diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 149ad864..283ee7e5 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -16,11 +16,11 @@ </li> {% endif %} {% if use_plink_gemma %} - <li> - <a href="#plink" data-toggle="tab">PLINK</a> + <li class="active"> + <a href="#gemma" data-toggle="tab">GEMMA</a> </li> <li> - <a href="#gemma" data-toggle="tab">GEMMA</a> + <a href="#plink" data-toggle="tab">PLINK</a> </li> {% endif %} <!--<li> @@ -299,40 +299,39 @@ </div> {% endif %} {% if use_plink_gemma %} - <div class="tab-pane" id="plink"> + <div class="tab-pane active" id="gemma"> <div style="padding: 20px" class="form-horizontal"> <div class="mapping_method_fields form-group"> - <label for="maf_plink" class="col-xs-3 control-label">Minor allele threshold</label> + <label for="maf_gemma" class="col-xs-3 control-label">Minor allele threshold</label> <div style="margin-left: 20px;" class="col-xs-3 controls"> - <input name="maf_plink" value="0.01" type="text" class="form-control"> + <input name="maf_gemma" value="0.01" type="text" class="form-control"> </div> </div> </div> <div class="form-group"> - <label for="plink_compute" class="col-xs-1 control-label"></label> + <label for="gemma_compute" class="col-xs-1 control-label"></label> <div style="margin-left:20px;" class="col-xs-4 controls"> - <button id="plink_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression"> + <button id="gemma_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression"> Compute </button> </div> </div> </div> - - <div class="tab-pane" id="gemma"> + <div class="tab-pane" id="plink"> <div style="padding: 20px" class="form-horizontal"> <div class="mapping_method_fields form-group"> - <label for="maf_gemma" class="col-xs-3 control-label">Minor allele threshold</label> + <label for="maf_plink" class="col-xs-3 control-label">Minor allele threshold</label> <div style="margin-left: 20px;" class="col-xs-3 controls"> - <input name="maf_gemma" value="0.01" type="text" class="form-control"> + <input name="maf_plink" value="0.01" type="text" class="form-control"> </div> </div> </div> <div class="form-group"> - <label for="gemma_compute" class="col-xs-1 control-label"></label> + <label for="plink_compute" class="col-xs-1 control-label"></label> <div style="margin-left:20px;" class="col-xs-4 controls"> - <button id="gemma_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression"> + <button id="plink_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression"> Compute </button> </div> diff --git a/wqflask/wqflask/templates/submit_trait.html b/wqflask/wqflask/templates/submit_trait.html new file mode 100644 index 00000000..df6b0bb7 --- /dev/null +++ b/wqflask/wqflask/templates/submit_trait.html @@ -0,0 +1,101 @@ +{% extends "base.html" %} +{% block title %}Trait Submission{% endblock %} +{% block content %} +<!-- Start of body --> + + <div class="container-fluid"> + + {{ flash_me() }} + + <div class="row" style="width: 1400px !important;"> + + <div class="col-xs-5"> + <section id="description"> + <div> + <h2 style="color: #5a5a5a;">Introduction</h2> + <hr> + <p>The trait values that you enter are statistically compared with verified genotypes collected at a set of microsatellite markers in each RI set. The markers are drawn from a set of over 750, but for each set redundant markers have been removed, preferentially retaining those that are most informative.</p> + <p>These error-checked RI mapping data match theoretical expectations for RI strain sets. The cumulative adjusted length of the RI maps are approximately 1400 cM, a value that matches those of both MIT maps and Chromosome Committee Report maps. See our full description of the genetic data collected as part of the WebQTL project.</p> + </div> + </section> + <br> + <section id="description"> + <div> + <h2 style="color: #5a5a5a;">About Your Data</h2> + <hr> + <p>You can open a separate window giving the number of strains for each data set and sample data.</p> + <p>None of your submitted data is copied or stored by this system except during the actual processing of your submission. By the time the reply page displays in your browser, your submission has been cleared from this system.</p> + </div> + </section> + </div> + <div style="padding-left:20px" class="col-xs-6" style="width: 600px !important;"> + <section id="submission_form"> + <div class="form-group"> + <h2 style="color: #5a5a5a;">Trait Submission Form</h2> + <hr> + <div style="padding-bottom: 50px;" class="form-horizontal"> + <h3>1. Choose cross or RI set:</h3> + <br> + <div class="col-xs-2"> + <img src="/static/new/images/step1.gif"> + </div> + <div class="col-xs-10"> + <div class="form-group"> + <label for="species" class="col-xs-2 control-label">Species: </label> + <div class="col-xs-4 controls"> + <select name="species" id="species" class="form-control span3" style="width: 280px !important;"></select> + </div> + </div> + <div class="form-group"> + <label for="group" class="col-xs-2 control-label">Group: </label> + <div class="col-xs-4 controls"> + <select name="group" id="group" class="form-control span3" style="width: 280px !important;"></select> + </div> + </div> + <!-- + <select name="corr_dataset"> + {% for species in species_and_groups %} + <optgroup label="{{ species.species }} ------"> + {% for group in species.groups %} + <option value="{{ group }}"> + {{ group }} + </option> + {% endfor %} + </optgroup> + {% endfor %} + </select> + --> + </div> + </div> + <div style="padding-bottom: 50px;" class="form-horizontal"> + <h3>2. Enter Trait Data:</h3> + <br> + <div class="col-xs-2" style="vertical-align:middle;"> + <img src="/static/new/images/step2.gif"> + </div> + <div class="col-xs-10"> + <div class="form-group"> + <p> + <b>From a File:</b> You can enter data by entering a file name here. The file should contain a series of numbers representing trait values. + The values can be on one line separated by spaces or tabs, or they can be on separate lines. Include one value for each progeny individual + or recombinant inbred line. Represent missing values with a non-numeric character such as "x". If you have chosen a recombinant inbred set, + when you submit your data will be displayed in a form where you can confirm and/or edit them. If you enter a file name here, any data that + you paste into the next section will be ignored. + </p> + <input type="file" name="trait_file" style="border-width: 1px; border-style: solid; border-color: #999999;"> + </div> + </div> + </div> + </section> + </div> + </div> + </div> + +{%endblock%} + +{% block js %} + <script src="/static/new/javascript/dataset_select_menu_orig.js"></script> + <script> + gn_server_url = "{{ gn_server_url }}"; + </script> +{% 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 |