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 pprint import pformat as pf from flask import Flask, g class webqtlTrait: """ Trait class defines a trait in webqtl, can be either Microarray, Published phenotype, genotype, or user input trait """ def __init__(self, **kw): print("in webqtlTrait") #self.db_conn = db_conn #self.cursor = self.db_conn.cursor() 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 #print("foo") #print("kw in webqtlTrait are:", pf(kw)) #print("printed\n\n") #for name, value in kw.items(): # if self.__dict__.has_key(name): # setattr(self, name, value) # elif name == 'fullname': # name2 = value.split("::") # if len(name2) == 2: # self.dataset, self.name = name2 # elif len(name2) == 3: # self.dataset, self.name, self.cellid = name2 # else: # raise KeyError, repr(value) + ' parameter format error.' # else: # raise KeyError, repr(name) + ' not a valid parameter for this class.' if self.dataset and isinstance(self.dataset, basestring): #assert self.cursor, "Don't have a cursor" self.dataset = create_dataset(self.dataset) #if self.dataset == None, not from a database print("self.dataset is:", self.dataset, type(self.dataset)) if self.dataset: 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.cursor.execute(*query) self.sequence = self.cursor.fetchone()[0] print("self.sequence is:", self.sequence) def getName(self): str = "" if self.dataset and self.name: str = "%s::%s" % (self.dataset, self.name) if self.cellid: str += "::" + self.cellid else: str = self.description return str # # 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 # def getGivenName(self): str = self.name if self.dataset and self.name: if self.dataset.type=='Temp': self.cursor.execute('SELECT description FROM Temp WHERE Name=%s', self.name) desc = self.cursor.fetchone()[0] if desc.__contains__('PCA'): desc = desc[desc.rindex(':')+1:].strip() else: desc = desc[:desc.index('entered')].strip() str = desc return str def displayName(self): str = "" if self.dataset and self.name: if self.dataset.type=='Temp': desc = self.description if desc.__contains__('PCA'): desc = desc[desc.rindex(':')+1:].strip() else: desc = desc[:desc.index('entered')].strip() str = "%s::%s" % (self.dataset, desc) else: str = "%s::%s" % (self.dataset, self.name) if self.cellid: str += "::" + self.cellid else: str = self.description return str #def __str__(self): # #return "%s %s" % (self.getName(), self.group) # return self.getName() #__str__ = getName #__repr__ = __str__ def exportData(self, samplelist, type="val"): """ export data according to samplelist mostly used in calculating correlation """ result = [] for sample in samplelist: if self.data.has_key(sample): if type=='val': result.append(self.data[sample].val) elif type=='var': result.append(self.data[sample].var) elif type=='N': result.append(self.data[sample].N) else: raise KeyError, `type`+' type is incorrect.' else: result.append(None) return result def exportInformative(self, incVar=0): """ export informative sample mostly used in qtl regression """ samples = [] vals = [] 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) vars.append(value.var) return samples, vals, 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 retrieveData(self, samplelist=None): if samplelist == None: samplelist = [] assert self.dataset and self.cursor 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: #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) #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() 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 #else: # pass #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 retrieveInfo(self, QTL = None): assert self.dataset and self.cursor if self.dataset.type == 'Publish': #self.dataset.DisField = ['Name','PubMed_ID','Phenotype','Abbreviation','Authors','Title',\ # 'Abstract', 'Journal','Volume','Pages','Month','Year','Sequence',\ # 'Units', 'comments'] 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) #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' """ % (display_fields_string, self.dataset.name, self.name) #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' """ % (display_fields_string, self.dataset.name, self.name) else: #Temp type query = 'SELECT %s FROM %s WHERE Name = "%s"' % \ (string.join(self.dataset.display_fields,','), self.dataset.type, self.name) 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.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 """ % (self.geneid, self.group) self.cursor.execute(query) result = self.cursor.fetchone() else: result = None if result: self.homologeneid = result[0] if QTL: if self.dataset.type == 'ProbeSet' and not self.cellid: query = ''' 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) 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': query = ''' 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) 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)))