def loadGFF_UTR(self,fields,line,transcriptBeginEnd,GFF,
transcripts,readOrder,genes):
exonBegin=int(fields[3])-1
exonEnd=int(fields[4])
exonScore=fields[5]
strand=fields[6]
frame=fields[7]
transcriptId=None
rex=Rex()
if(rex.find('transgrp[:=]\s*(\S+)',line)): transcriptId=rex[1]
elif(rex.find('transcript_id[:=]?\s*"?([^\s";]+)"?',line)):
transcriptId=rex[1]
elif(rex.find('Parent=([^;,\s]+)',line)): transcriptId=rex[1]
geneId=None
if(rex.find('genegrp=(\S+)',line)): geneId=rex[1]
elif(rex.find('gene_id[:=]?\s*"?([^\s\;"]+)"?',line)): geneId=rex[1]
if(transcriptId is None): transcriptId=geneId
if(geneId is None): geneId=transcriptId
if(transcriptId is None):
raise Exception(line+" : no transcript ID found")
if(rex.find("(\S+);$",transcriptId)): transcriptId=rex[1]
if(rex.find("(\S+);$",geneId)): geneId=rex[1]
extra=""
for i in range(8,len(fields)): extra+=fields[i]+" "
if(exonBegin>exonEnd): (exonBegin,exonEnd)=(exonEnd,exonBegin)
transcript=transcripts.get(transcriptId,None)
if(not transcript):
transcripts[transcriptId]=transcript= \
Transcript(transcriptId,strand)
transcript.setStopCodons(self.stopCodons)
transcript.readOrder=readOrder
readOrder+=1
transcript.substrate=fields[0]
transcript.source=fields[1]
if(transcriptBeginEnd.get(transcriptId,None) is not None):
(begin,end)=transcriptBeginEnd[transcriptId]
transcript.setBegin(begin)
transcript.setEnd(end)
else:
transcript.setBegin(exonBegin)
transcript.setEnd(exonEnd)
transcript.geneId=geneId
gene=genes.get(geneId,None)
if(gene is None):
genes[geneId]=gene=Gene(); gene.setId(geneId)
transcript.setGene(gene)
exon=Exon(exonBegin,exonEnd,transcript)
exon.extraFields=extra
if(transcript.rawExons is not None):
exon.frame=frame
exon.score=exonScore
exon.type=fields[2]
transcript.rawExons.append(exon)
elif(not transcript.exonOverlapsExon(exon)):
exon.frame=frame
exon.score=exonScore
exon.type=fields[2]
transcript.UTR.append(exon) # OK -- we sort later
gene.addTranscript(transcript)
def loadGFF_CDS(self,fields,line,transcriptBeginEnd,GFF,
transcripts,readOrder,genes):
exonBegin=int(fields[3])-1
exonEnd=int(fields[4])
exonScore=fields[5]
strand=fields[6]
frame=fields[7]
transcriptId=None
rex=Rex()
if(rex.find('transgrp[:=]\s*(\S+)',line)): transcriptId=rex[1]
elif(rex.find('transcript_id[:=]?\s*"?([^\s";]+)"?',line)):
transcriptId=rex[1]
elif(rex.find('Parent=([^;,\s]+)',line)): transcriptId=rex[1]
geneId=None
if(rex.find('genegrp=(\S+)',line)): geneId=rex[1]
elif(rex.find('gene_id[:=]?\s*"?([^\s\;"]+)"?',line)): geneId=rex[1]
if(transcriptId is None): transcriptId=geneId
if(geneId is None): geneId=transcriptId
if(transcriptId is None):
raise Exception(line+" : no transcript ID found")
if(rex.find('(\S+);$',transcriptId)): transcriptId=rex[1]
if(rex.find('(\S+);$',geneId)): geneId=rex[1]
extra=""
for i in range(8,len(fields)): extra+=fields[i]+" "
if(exonBegin>exonEnd): (exonBegin,exonEnd)=(exonEnd,exonBegin)
transcript=transcripts.get(transcriptId,None)
if(transcript is None):
transcripts[transcriptId]=transcript= \
Transcript(transcriptId,strand)
transcript.setStopCodons(self.stopCodons)
transcript.readOrder=readOrder
readOrder+=1
transcript.substrate=fields[0]
transcript.source=fields[1]
if(transcriptBeginEnd.get(transcriptId,None) is not None):
(begin,end)=transcriptBeginEnd[transcriptId]
transcript.setBegin(begin)
transcript.setEnd(end)
transcript.geneId=geneId
gene=genes.get(geneId,None)
if(gene is None):
genes[geneId]=gene=Gene(); gene.setId(geneId)
transcript.setGene(gene)
exon=Exon(exonBegin,exonEnd,transcript)
exon.extraFields=extra
if(not transcript.exonOverlapsExon(exon)):
exon.frame=frame
exon.score=exonScore
exon.type=fields[2]
transcript.exons.append(exon) # OK -- we sort later
gene.addTranscript(transcript)
def __init__(self,id,strand=None):
if(type(id)!=EssexNode): # not an EssexNode
self.transcriptId=id
self.strand=strand
self.exons=[]
self.UTR=[]
self.rawExons=None
self.stopCodons={"TAG":1,"TGA":1,"TAA":1}
self.startCodon=None
self.extraFields=None
else: # EssexNode
essex=id
self.transcriptId=essex.getAttribute("ID")
self.strand=essex.getAttribute("strand")
self.source=essex.getAttribute("source")
self.begin=essex.getAttribute("begin")
self.end=essex.getAttribute("end")
self.geneId=essex.getAttribute("gene")
self.substrate=essex.getAttribute("substrate")
self.exons=[]
self.UTR=[]
self.rawExons=None
self.startCodon=None
self.extraFields=None
self.stopCodons={"TAG":1,"TGA":1,"TAA":1}
exons=self.exons
UTR=self.UTR
exonsElem=essex.findChild("exons")
if(exonsElem):
n=exonsElem.numElements()
for i in range(0,n):
exon=exonsElem.getIthElem(i)
begin=int(exon.getIthElem(0))
end=int(exon.getIthElem(1))
exon=Exon(begin,end,self)
exons.append(exon)
utrElem=essex.findChild("UTR")
if(utrElem):
n=utrElem.numElements()
for i in range(0,n):
exon=utrElem.getIthElem(i)
begin=int(exon.getIthElem(0))
end=int(exon.getIthElem(1))
exon=Exon(begin,end,self)
UTR.append(exon)
def makeExon(self, root):
begin = int(root["begin"])
end = int(root["end"])
exon = Exon(begin, end, None)
exon.strand = root["strand"]
exon.frame = root["frame"]
exon.type = root["type"]
exon.score = root["score"]
exon.substrate = root["substrate"]
extra = root["extra"]
exon.extraFields = ""
for key in extra:
exon.extraFields += key + "=" + extra[key] + ";"
return exon
def makeExon(self,root):
begin=int(root["begin"])
end=int(root["end"])
exon=Exon(begin,end,None)
exon.strand=root["strand"]
exon.frame=root["frame"]
exon.type=root["type"]
exon.score=root["score"]
exon.substrate=root["substrate"]
extra=root["extra"]
exon.extraFields=""
for key in extra:
exon.extraFields+=key+"="+extra[key]+";"
return exon
def organize_features( self, isoform, bool_exon = True ):
"""
Args:
isoform = cruzdb object that contains information for a specific isoform
Function: this will organize the feats, cds, & reading frame for a specific gene
"""
#hash_feats = will contain feats sorted by start position (key = index, value = feat)
hash_feats = {} #key = string that is feat range (chrom:start-end), value = feat object
#get reading frames
##TEST:: print "organize_feats: isoform = ", isoform.feats
if bool_exon:
list_features = isoform.exons
feat_frames = map( int, [x for x in isoform.exonFrames.split(',') if x] )
else:
list_features = isoform.introns
for i, feat in enumerate( list_features ): #i = feat number
#check to see if the key_range exists
key_range = Isoform.make_key_range( self.chrom, feat[0], feat[1] )
#calculate the feat number
# feat_num = i if self.strand == 1 else ( len(list_features) - i - 1 ) #for 0-based exons, use this
# feat_num = i + 1 if self.strand == 1 else ( len(list_features) - i ) #for 1-based exons, use this
feat_num = i + exon_base if self.strand == 1 else ( len(list_features) - i - ( exon_base - 1 ) ) #this handles both 0-based & 1-based
#NOTE: UCSC has 0-based genome, meaning the first position of the feat is actually the last position in the previous intron, that is why I add '+1'
if bool_exon:
feat_info = self.get_feat_info( feat[0], feat[1], feat_frames[i], feat_num, True, 'exon' )
else:
feat_info = self.get_feat_info( feat[0], feat[1], None, feat_num, True, 'intron' )
hash_feats[ key_range ] = Exon( feat_info )
#go through all cds, assign CDS to each feat
if bool_exon:
for each_cds in isoform.cds: #each_cd = tuple where [0] = start position & [1] = end position
hash_feats = self.organize_exons_cds( each_cds[0], each_cds[1], hash_feats )
return hash_feats
