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authorzsloan2015-03-27 20:28:51 +0000
committerzsloan2015-03-27 20:28:51 +0000
commitd0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/webqtl/base/webqtlTrait.py
parenta840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
downloadgenenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz
Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'
Diffstat (limited to 'web/webqtl/base/webqtlTrait.py')
-rw-r--r--web/webqtl/base/webqtlTrait.py590
1 files changed, 0 insertions, 590 deletions
diff --git a/web/webqtl/base/webqtlTrait.py b/web/webqtl/base/webqtlTrait.py
deleted file mode 100644
index 2469504f..00000000
--- a/web/webqtl/base/webqtlTrait.py
+++ /dev/null
@@ -1,590 +0,0 @@
-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 __future__ import print_function, division
-
-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):
- 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
-
- debug_file = open("/home/zas1024/gn/web/traitlist_debug.txt", "w")
- debug_file.write("strianlist is:" + strainlist + "\n")
-
- 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
-
- debug_file.write("self.data is:", pf(self.data) + "\n")
-
- 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
-
-