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-rw-r--r--web/webqtl/base/webqtlTrait.py581
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diff --git a/web/webqtl/base/webqtlTrait.py b/web/webqtl/base/webqtlTrait.py
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+++ b/web/webqtl/base/webqtlTrait.py
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+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
+
+
+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):
+ 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 = {}
+ 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, `value` + ' parameter format error.'
+ else:
+ raise KeyError, `name`+' not a valid parameter for this class.'
+
+ if self.db and type(self.db) == type("1"):
+ assert self.cursor
+ self.db = webqtlDataset(self.db, self.cursor)
+
+ #if self.db == None, not from a database
+ 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':
+ 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)
+ 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
+
+
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 09:18:18 +0000