diff options
Diffstat (limited to 'wqflask/base/webqtlTrait.py')
| -rwxr-xr-x | wqflask/base/webqtlTrait.py | 1152 |
1 files changed, 576 insertions, 576 deletions
diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py index 88226894..812d112a 100755 --- a/wqflask/base/webqtlTrait.py +++ b/wqflask/base/webqtlTrait.py @@ -14,579 +14,579 @@ 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] - print("self.sequence is:", self.sequence) - - - 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': - 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.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 + """ + 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] + print("self.sequence is:", self.sequence) + + + 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': + 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.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 |