from __future__ import division, print_function import string from htmlgen import HTMLgen2 as HT import webqtlConfig from webqtlCaseData import webqtlCaseData from webqtlDataset import webqtlDataset from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil from pprint import pformat as pf class webqtlTrait: """ Trait class defines a trait in webqtl, can be either Microarray, Published phenotype, genotype, or user input trait """ def __init__(self, cursor = None, **kw): print("in webqtlTrait") self.cursor = cursor self.db = None # database object self.name = '' # Trait ID, ProbeSet ID, Published ID, etc. self.cellid = '' self.identification = 'un-named trait' self.riset = '' self.haveinfo = 0 self.sequence = '' # Blat sequence, available for ProbeSet self.data = {} 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.db, self.name = name2 elif len(name2) == 3: self.db, 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.db and isinstance(self.db, basestring): assert self.cursor, "Don't have a cursor" self.db = webqtlDataset(self.db, self.cursor) #if self.db == None, not from a database print("self.db is:", self.db, type(self.db)) if self.db: if self.db.type == "Temp": self.cursor.execute(''' SELECT InbredSet.Name FROM InbredSet, Temp WHERE Temp.InbredSetId = InbredSet.Id AND Temp.Name = "%s" ''', self.name) self.riset = self.cursor.fetchone()[0] else: self.riset = self.db.getRISet() # # 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.db: if self.db.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.db.name) print("query is:", query) self.cursor.execute(query) self.sequence = self.cursor.fetchone()[0] def getName(self): str = "" if self.db and self.name: str = "%s::%s" % (self.db, 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.db and self.name: if self.db.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.db and self.name: if self.db.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.db, desc) else: str = "%s::%s" % (self.db, self.name) if self.cellid: str += "::" + self.cellid else: str = self.description return str #def __str__(self): # #return "%s %s" % (self.getName(), self.riset) # return self.getName() __str__ = getName __repr__ = __str__ def exportData(self, strainlist, type="val"): """ export data according to strainlist mostly used in calculating correlation """ result = [] for strain in strainlist: if self.data.has_key(strain): if type=='val': result.append(self.data[strain].val) elif type=='var': result.append(self.data[strain].var) elif type=='N': result.append(self.data[strain].N) else: raise KeyError, `type`+' type is incorrect.' else: result.append(None) return result def exportInformative(self, incVar=0): """ export informative strain mostly used in qtl regression """ strains = [] vals = [] vars = [] for strain, value in self.data.items(): if value.val != None: if not incVar or value.var != None: strains.append(strain) vals.append(value.val) vars.append(value.var) return strains, 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.db.type == 'ProbeSet': query = ''' 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.db.name) self.cursor.execute(query) results = self.fetchone() return results[0] def retrieveData(self, strainlist=[]): assert self.db and self.cursor if self.db.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.db.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.db.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.db.name) #XZ, 03/02/2009: Xiaodong added this block for ProbeSetData and ProbeSetSE elif self.db.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.db.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.db.riset), self.name, self.db.name) self.cursor.execute(query) results = self.cursor.fetchall() self.data.clear() if results: self.mysqlid = results[0][-1] if strainlist: for item in results: if item[0] in strainlist: val = item[1] if val != None: var = item[2] ndata = None if self.db.type in ('Publish', 'Temp'): ndata = item[3] self.data[item[0]] = webqtlCaseData(val, var, ndata) #end for else: for item in results: val = item[1] if val != None: var = item[2] ndata = None if self.db.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.db and self.cursor if self.db.type == 'Publish': #self.db.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.db.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.db.type == 'ProbeSet': disfieldString = string.join(self.db.disfield,',ProbeSet.') disfieldString = 'ProbeSet.' + disfieldString 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' """ % (disfieldString, self.db.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.db.type == 'Geno': disfieldString = string.join(self.db.disfield,',Geno.') disfieldString = 'Geno.' + disfieldString 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' """ % (disfieldString, self.db.name, self.name) else: #Temp type query = 'SELECT %s FROM %s WHERE Name = "%s"' % \ (string.join(self.db.disfield,','), self.db.type, self.name) self.cursor.execute(query) traitInfo = self.cursor.fetchone() if traitInfo: self.haveinfo = 1 #XZ: assign SQL query result to trait attributes. for i, field in enumerate(self.db.disfield): setattr(self, field, traitInfo[i]) if self.db.type == 'Publish': self.confidential = 0 if self.pre_publication_description and not self.pubmed_id: self.confidential = 1 self.homologeneid = None if self.db.type == 'ProbeSet' and self.riset 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.riset) self.cursor.execute(query) result = self.cursor.fetchone() else: result = None if result: self.homologeneid = result[0] if QTL: if self.db.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.db.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.db.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.db.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.db.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.db.name, self.name), Class = "fs14") else: setDescription2 = HT.Href(url="javascript:showDatabase2('%s','%s','')" % (self.db.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.db.type == 'Temp': setDescription = HT.Href(text="%s" % (self.description),url="javascript:showDatabase2\ ('%s','%s','')" % (self.db.name,self.name), Class = "fs14") setDescription = HT.Span(setDescription) elif self.db.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.db.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.db.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.db.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.db.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.db.name,self.name), \ Class = "fs14") else: setDescription = HT.Href(text="ProbeSet/%s" % self.name, url=\ "javascript:showDatabase2('%s','%s','')" % (self.db.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.db.type != 'Temp' and dispFromDatabase: setDescription.append( ' --- FROM : ') setDescription.append(self.db.genHTML(Class='cori')) return setDescription