def setTranscriptConsequences(self, transcriptConsequences):
''' Expect transcriptConsequences as dict from JSON '''
# print "biomine::variant::vepvariant::setTranscriptConsequence"
#if not transcriptConsequences:
# return
for consequence in transcriptConsequences: #list of dict's
otherVar = vepconsequencevariant(parentVariant=self)
otherVar.parseTranscriptConsequence(consequence)
self.consequences.append(otherVar)
if otherVar.canonical:
self.gene = otherVar.gene
def setTranscriptConsequences( self , transcriptConsequences ): ''' Expect transcriptConsequences as dict from JSON ''' # print "biomine::variant::vepvariant::setTranscriptConsequence" #if not transcriptConsequences: # return try: for consequence in transcriptConsequences: #list of dict's otherVar = vepconsequencevariant( parentVariant=self ) otherVar.parseTranscriptConsequence( consequence ) self.consequences.append( otherVar ) if otherVar.canonical: self.gene = otherVar.gene except: print( "BioMine Warning: Cannot set transcript consequences - no consequence for " + self.genomicVar() ) pass
def setTranscriptConsequences( self , transcriptConsequences ): ''' Expect transcriptConsequences as dict from JSON ''' # print "biomine::variant::vepvariant::setTranscriptConsequence" #if not transcriptConsequences: # return try: for consequence in transcriptConsequences: #list of dict's otherVar = vepconsequencevariant( parentVariant=self ) otherVar.parseTranscriptConsequence( consequence ) self.consequences.append( otherVar ) if otherVar.canonical: self.gene = otherVar.gene except: print( "BioMine Warning: Cannot set transcript consequences - no consequence for " + self.genomicVar() ) pass
def getCSQ(self, var, record, begin, end, ref, alt, alti, **kwargs):
info = record.INFO
csq = info.get('CSQ', "noCSQ")
preVEP = []
if not csq == "noCSQ":
vepDone = True
exacDone = True
var.vepVariant = vepvariant()
for thisCSQ in csq:
values = thisCSQ.split("|")
var.vcfInfo = values
aas = [None, None]
if self.getVCFKeyIndex(values,
"Amino_acids"): #8 => Amino_acids
aas = self.getVCFKeyIndex(values, "Amino_acids").split("/")
if len(aas) > 1:
aas[0] = mafvariant().convertAA(aas[0])
aas[1] = mafvariant().convertAA(aas[1])
else:
#28 => HGVSc
#29 => HGVSp
hgvsp = self.getVCFKeyIndex(values, "HGVSp").split(":")
changep = None
if len(hgvsp) > 1:
changep = re.match("p\.", hgvsp[1])
if changep:
aas = mafvariant().splitHGVSp(hgvsp[1])
aas[0] = mafvariant().convertAA(aas[0])
aas[2] = mafvariant().convertAA(aas[2])
else:
aas.append(None)
needVEP = True
preVEP.append(var)
exons = [None, None]
if self.getVCFKeyIndex(values, "EXON"): #25 => EXON
exons = self.getVCFKeyIndex(values, "EXON").split("/")
if len(exons) == 1:
exons.append(None)
introns = [None, None]
if self.getVCFKeyIndex(values, "INTRON"): #26 => INTRON
introns = self.getVCFKeyIndex(values, "INTRON").split("/")
if len(introns) == 1:
introns.append(None)
siftStuff = [None, None]
if self.getVCFKeyIndex(values, "SIFT"):
siftStuff = self.getVCFKeyIndex(values, "SIFT").split("(")
if len(siftStuff) == 1:
siftStuff.append(None)
else:
siftStuff[1] = siftStuff[1].rstrip(")")
polyPhenStuff = [None, None]
if self.getVCFKeyIndex(values, "PolyPhen"):
polyPhenStuff = self.getVCFKeyIndex(values,
"PolyPhen").split("(")
if len(polyPhenStuff) == 1:
polyPhenStuff.append(None)
else:
polyPhenStuff[1] = polyPhenStuff[1].rstrip(")")
vcv = vepconsequencevariant( \
chromosome = record.CHROM , \
start = begin , \
stop = end , \
dbsnp = record.ID , \
reference = ref , \
alternate = alt , \
gene_id=self.getVCFKeyIndex( values , "Gene" ) , \
transcriptCodon=self.getVCFKeyIndex( values , "Feature" ) , \
consequence_terms=self.getVCFKeyIndex( values , "Consequence" ).split( "&" ) , \
positionCodon=self.getVCFKeyIndex( values , "cDNA_position" ) , \
positionPeptide=self.getVCFKeyIndex( values , "Protein_position" ) , \
referencePeptide=aas[0] , \
alternatePeptide=aas[1] , \
strand=self.getVCFKeyIndex( values , "STRAND" ) , \
gene=self.getVCFKeyIndex( values , "SYMBOL" ) , \
gene_symbol_source=self.getVCFKeyIndex( values , "SYMBOL_SOURCE" ) , \
hgnc_id=self.getVCFKeyIndex( values , "HGNC_ID" ) , \
biotype=self.getVCFKeyIndex( values , "BIOTYPE" ) , \
canonical=self.getVCFKeyIndex( values , "CANONICAL" ) , \
ccds=self.getVCFKeyIndex( values , "CCDS" ) , \
transcriptPeptide=self.getVCFKeyIndex( values , "ENSP" ) , \
predictionSIFT=siftStuff[0] , \
scoreSIFT=siftStuff[1] , \
predictionPolyphen=polyPhenStuff[0] , \
scorePolyphen=polyPhenStuff[1] , \
exon=exons[0] , \
totalExons=exons[1] , \
intron=introns[0] , \
totalIntrons=introns[1] , \
)
var.alleleFrequency = self.getVCFKeyIndex(values, "GMAF")
var.vepVariant.consequences.append(vcv)
self.determineMostSevere(var, **kwargs)
self.setAlleleMeasures(var, info, **kwargs)
return None