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Diffstat (limited to 'wqflask/base/trait.py')
| -rwxr-xr-x | wqflask/base/trait.py | 708 |
1 files changed, 708 insertions, 0 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py new file mode 100755 index 00000000..d3753fc1 --- /dev/null +++ b/wqflask/base/trait.py @@ -0,0 +1,708 @@ +from __future__ import division, print_function + +import string + +from htmlgen import HTMLgen2 as HT + +import webqtlConfig +from webqtlCaseData import webqtlCaseData +from data_set import create_dataset +from dbFunction import webqtlDatabaseFunction +from utility import webqtlUtil + +from MySQLdb import escape_string as escape +from pprint import pformat as pf + +from flask import Flask, g + +class GeneralTrait: + """ + Trait class defines a trait in webqtl, can be either Microarray, + Published phenotype, genotype, or user input trait + + """ + + def __init__(self, **kw): + print("in GeneralTrait") + self.dataset = kw.get('dataset', None) # database object + self.name = kw.get('name', None) # Trait ID, ProbeSet ID, Published ID, etc. + self.cellid = kw.get('cellid', None) + self.identification = kw.get('identification', 'un-named trait') + #self.group = kw.get('group', None) + self.haveinfo = kw.get('haveinfo', False) + self.sequence = kw.get('sequence', None) # Blat sequence, available for ProbeSet + self.data = kw.get('data', {}) + + if kw.get('fullname'): + name2 = value.split("::") + if len(name2) == 2: + self.dataset, self.name = name2 + elif len(name2) == 3: + self.dataset, self.name, self.cellid = name2 + + #if self.dataset and isinstance(self.dataset, basestring): + self.dataset = create_dataset(self.dataset) + + print("self.dataset is:", self.dataset, type(self.dataset)) + #if self.dataset: + + #self.dataset.get_group() + + #if self.dataset.type == "Temp": + # self.cursor.execute(''' + # SELECT + # InbredSet.Name + # FROM + # InbredSet, Temp + # WHERE + # Temp.InbredSetId = InbredSet.Id AND + # Temp.Name = "%s" + # ''', self.name) + # self.group = self.cursor.fetchone()[0] + #else: + # self.group = self.dataset.get_group() + + #print("trinity, self.group is:", self.group) + + # + # 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 + # + + #XZ, 05/08/2009: This block is not neccessary. We can add 'BlatSeq' into disfield. + # The variable self.sequence should be changed to self.BlatSeq + # It also should be changed in other places where it are used. + + #if self.dataset: + #if self.dataset.type == 'ProbeSet': + # print("Doing ProbeSet Query") + # query = ''' + # SELECT + # ProbeSet.BlatSeq + # FROM + # ProbeSet, ProbeSetFreeze, ProbeSetXRef + # WHERE + # ProbeSet.Id=ProbeSetXRef.ProbeSetId and + # ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId and + # ProbeSet.Name = %s and + # ProbeSetFreeze.Name = %s + # ''', (self.name, self.dataset.name) + # print("query is:", query) + # self.sequence = g.db.execute(*query).fetchone()[0] + # #self.sequence = self.cursor.fetchone()[0] + # print("self.sequence is:", self.sequence) + + + def get_name(self): + stringy = "" + if self.dataset and self.name: + stringy = "%s::%s" % (self.dataset, self.name) + if self.cellid: + stringy += "::" + self.cellid + else: + stringy = self.description + return stringy + + + def get_given_name(self): + """ + when user enter a trait or GN generate a trait, user want show the name + not the name that generated by GN randomly, the two follow function are + used to give the real name and the database. displayName() will show the + database also, getGivenName() just show the name. + For other trait, displayName() as same as getName(), getGivenName() as + same as self.name + + Hongqiang 11/29/07 + + """ + stringy = self.name + if self.dataset and self.name: + desc = self.dataset.get_desc() + if desc: + #desc = self.handle_pca(desc) + stringy = desc + return stringy + + + + def display_name(self): + stringy = "" + if self.dataset and self.name: + desc = self.dataset.get_desc() + #desc = self.handle_pca(desc) + if desc: + #desc = self.handle_pca(desc) + #stringy = desc + #if desc.__contains__('PCA'): + # desc = desc[desc.rindex(':')+1:].strip() + #else: + # desc = desc[:desc.index('entered')].strip() + #desc = self.handle_pca(desc) + stringy = "%s::%s" % (self.dataset, desc) + else: + stringy = "%s::%s" % (self.dataset, self.name) + if self.cellid: + stringy += "::" + self.cellid + else: + stringy = self.description + + return stringy + + + #def __str__(self): + # #return "%s %s" % (self.getName(), self.group) + # return self.getName() + #__str__ = getName + #__repr__ = __str__ + + def export_data(self, samplelist, the_type="val"): + """ + export data according to samplelist + mostly used in calculating correlation + + """ + result = [] + for sample in samplelist: + if self.data.has_key(sample): + if the_type=='val': + result.append(self.data[sample].val) + elif the_type=='var': + result.append(self.data[sample].var) + elif the_type=='N': + result.append(self.data[sample].N) + else: + raise KeyError, `the_type`+' the_type is incorrect.' + else: + result.append(None) + return result + + def export_informative(self, incVar=0): + """ + export informative sample + mostly used in qtl regression + + """ + samples = [] + vals = [] + the_vars = [] + for sample, value in self.data.items(): + if value.val != None: + if not incVar or value.var != None: + samples.append(sample) + vals.append(value.val) + the_vars.append(value.var) + return samples, vals, the_vars + + + # + # 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 = [] + + assert self.dataset + + #if self.cellid: + # #Probe Data + # query = ''' + # SELECT + # Strain.Name, ProbeData.value, ProbeSE.error, ProbeData.Id + # FROM + # (ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, + # Strain, Probe, ProbeSet) + # left join ProbeSE on + # (ProbeSE.DataId = ProbeData.Id AND ProbeSE.StrainId = ProbeData.StrainId) + # WHERE + # Probe.Name = '%s' AND ProbeSet.Name = '%s' AND + # Probe.ProbeSetId = ProbeSet.Id AND + # ProbeXRef.ProbeId = Probe.Id AND + # ProbeXRef.ProbeFreezeId = ProbeFreeze.Id AND + # ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND + # ProbeSetFreeze.Name = '%s' AND + # ProbeXRef.DataId = ProbeData.Id AND + # ProbeData.StrainId = Strain.Id + # Order BY + # Strain.Name + # ''' % (self.cellid, self.name, self.dataset.name) + # + #else: + results = self.dataset.retrieve_sample_data(self) + + #if self.dataset.type == 'Temp': + # query = ''' + # SELECT + # Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id + # FROM + # TempData, Temp, Strain + # WHERE + # TempData.StrainId = Strain.Id AND + # TempData.Id = Temp.DataId AND + # Temp.name = '%s' + # Order BY + # Strain.Name + # ''' % self.name + ##XZ, 03/02/2009: Xiaodong changed Data to PublishData, SE to PublishSE + #elif self.dataset.type == 'Publish': + # query = ''' + # SELECT + # Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id + # FROM + # (PublishData, Strain, PublishXRef, PublishFreeze) + # left join PublishSE on + # (PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId) + # left join NStrain on + # (NStrain.DataId = PublishData.Id AND + # NStrain.StrainId = PublishData.StrainId) + # WHERE + # PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND + # PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND + # PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id + # Order BY + # Strain.Name + # ''' % (self.name, self.dataset.id) + + #XZ, 03/02/2009: Xiaodong changed Data to ProbeData, SE to ProbeSE + #elif self.cellid: + + #XZ, 03/02/2009: Xiaodong added this block for ProbeSetData and ProbeSetSE + #elif self.dataset.type == 'ProbeSet': + # #ProbeSet Data + # query = ''' + # SELECT + # Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id + # FROM + # (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef) + # left join ProbeSetSE on + # (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId) + # WHERE + # ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + # ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND + # ProbeSetFreeze.Name = '%s' AND + # ProbeSetXRef.DataId = ProbeSetData.Id AND + # ProbeSetData.StrainId = Strain.Id + # Order BY + # Strain.Name + # ''' % (self.name, self.dataset.name) + ##XZ, 03/02/2009: Xiaodong changeded Data to GenoData, SE to GenoSE + #else: + # #Geno Data + # #XZ: The SpeciesId is not necessary, but it's nice to keep it to speed up database search. + # query = ''' + # SELECT + # Strain.Name, GenoData.value, GenoSE.error, GenoData.Id + # FROM + # (GenoData, GenoFreeze, Strain, Geno, GenoXRef) + # left join GenoSE on + # (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId) + # WHERE + # Geno.SpeciesId = %s AND Geno.Name = '%s' AND GenoXRef.GenoId = Geno.Id AND + # GenoXRef.GenoFreezeId = GenoFreeze.Id AND + # GenoFreeze.Name = '%s' AND + # GenoXRef.DataId = GenoData.Id AND + # GenoData.StrainId = Strain.Id + # Order BY + # Strain.Name + # ''' % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.dataset.group), self.name, self.dataset.name) + + + #self.cursor.execute(query) + #results = self.cursor.fetchall() + + # Todo: is this necessary? If not remove + self.data.clear() + + if results: + #self.mysqlid = results[0][-1] + #if samplelist: + for item in results: + #name, value, variance, num_cases = item + if not samplelist or (samplelist and name in samplelist): + #if value != None: + # num_cases = None + # if self.dataset.type in ('Publish', 'Temp'): + # ndata = item[3] + name = item[0] + self.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) + #end for + # else: + # for item in results: + # val = item[1] + # if val != None: + # var = item[2] + # ndata = None + # if self.dataset.type in ('Publish', 'Temp'): + # ndata = item[3] + # self.data[item[0]] = webqtlCaseData(val, var, ndata) + # #end for + # #end if + + #def keys(self): + # return self.__dict__.keys() + # + #def has_key(self, key): + # return self.__dict__.has_key(key) + # + #def items(self): + # return self.__dict__.items() + + def retrieve_info(self, QTL=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) + traitInfo = 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(self.name)) + traitInfo = g.db.execute(query).fetchone() + print("traitInfo is: ", pf(traitInfo)) + #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)) + traitInfo = g.db.execute(query).fetchone() + print("traitInfo is: ", pf(traitInfo)) + else: #Temp type + query = """SELECT %s FROM %s WHERE Name = %s + """ % (string.join(self.dataset.display_fields,','), + self.dataset.type, self.name) + traitInfo = g.db.execute(query).fetchone() + + + #self.cursor.execute(query) + #traitInfo = self.cursor.fetchone() + if traitInfo: + self.haveinfo = True + + #XZ: assign SQL query result to trait attributes. + for i, field in enumerate(self.dataset.display_fields): + setattr(self, field, traitInfo[i]) + + if self.dataset.type == 'Publish': + self.confidential = 0 + if self.pre_publication_description and not self.pubmed_id: + self.confidential = 1 + + self.homologeneid = None + if self.dataset.type == 'ProbeSet' and self.dataset.group and 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: + junk = float(self.geneid) + geneidIsNumber = 1 + except: + geneidIsNumber = 0 + + 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)) + result = g.db.execute(query).fetchone() + else: + result = None + + if result: + self.homologeneid = result[0] + + if QTL: + if self.dataset.type == 'ProbeSet' and not self.cellid: + traitQTL = g.db.execute(""" + SELECT + ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean + FROM + ProbeSetXRef, ProbeSet + WHERE + ProbeSetXRef.ProbeSetId = ProbeSet.Id AND + ProbeSet.Name = "%s" AND + ProbeSetXRef.ProbeSetFreezeId =%s + """, (self.name, self.dataset.id)).fetchone() + #self.cursor.execute(query) + #traitQTL = self.cursor.fetchone() + if traitQTL: + self.locus, self.lrs, self.pvalue, self.mean = traitQTL + else: + self.locus = self.lrs = self.pvalue = self.mean = "" + if self.dataset.type == 'Publish': + traitQTL = g.db.execute(""" + SELECT + PublishXRef.Locus, PublishXRef.LRS + FROM + PublishXRef, PublishFreeze + WHERE + PublishXRef.Id = %s AND + PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND + PublishFreeze.Id =%s + """, (self.name, self.dataset.id)).fetchone() + #self.cursor.execute(query) + #traitQTL = self.cursor.fetchone() + if traitQTL: + self.locus, self.lrs = traitQTL + else: + self.locus = 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 description_fmt(self): + '''Return a text formated description''' + if self.description: + formatted = self.description + if self.probe_target_description: + formatted += "; " + self.probe_target_description + else: + formatted = "Not available" + return formatted.capitalize() + + @property + def alias_fmt(self): + '''Return a text formatted alias''' + if self.alias: + alias = string.replace(self.alias, ";", " ") + alias = string.join(string.split(alias), ", ") + return alias + + + @property + def location_fmt(self): + '''Return a text formatted location + + While we're at it we set self.location in case we need it later (do we?) + + ''' + + if self.chr and self.mb: + self.location = 'Chr %s @ %s Mb' % (self.chr,self.mb) + elif self.chr: + self.location = 'Chr %s @ Unknown position' % (self.chr) + else: + self.location = 'Not available' + + fmt = self.location + ##XZ: deal with direction + if self.strand_probe == '+': + fmt += (' on the plus strand ') + elif self.strand_probe == '-': + fmt += (' on the minus strand ') + + 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: + self.cursor.execute(""" + select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze + where + ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND + ProbeSetFreeze.Id = %d""" % thisTrait.dataset.id) + probeDBName = self.cursor.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))) |