def isWellFormed(self,seq):
"""if(transcript.isWellFormed(sequence)) ...
This procedure iterates through the codons of this transcript,
starting at the start codon (attribute startCodon specifies this
offset within the transcript, not counting intron bases), and
continuing until either an in-frame stop codon is encountered,
or the end of the transcript is reached. The transcript is
considered well-formed only if a stop-codon is encountered.
"""
stopCodons=self.stopCodons
# 1. Check whether any exons overlap each other
exons=self.exons
numExons=len(exons)
for i in range(1,numExons):
exon=exons[i]
prevExon=exons[i-1]
if(exon.overlaps(prevExon)): return 0
# 2. Check that there is an in-frame stop-codon
iterator=CodonIterator(self,seq,stopCodons)
codons=iterator.getAllCodons()
n=len(codons)
if(n==0): return False
lastCodon=codons[n-1]
isStop=stopCodons.get(lastCodon.triplet,None)
return True if isStop else False
def trimUTR(self,axisSequenceRef):
self.adjustOrders()
stopCodons=self.stopCodons
sequence=self.sequence
strand=self.strand
numExons=self.numExons()
startCodon=self.startCodon
if(not startCodon):
raise Exception("can't trim UTR, because startCodon is not set")
for j in(numExons):
exon=self.getIthExon(j)
length=exon.getLength()
if(length<=startCodon):
self.deleteExon(j)
numExons-=1
j-=1
startCodon-=length
self.adjustOrders() ### 4/1/03
else:
if(strand=="+"):
exon.trimInitialPortion(startCodon)
self.begin=exon.begin
else:
exon.trimInitialPortion(startCodon)### ???
self.end=exon.end
exon.type="initial-exon" if numExons>1 else "single-exon"
self.startCodon=0
break
# Find in-frame stop codon
codonIterator=CodonIterator(self,axisSequenceRef,stopCodons)
stopCodonFound=False
while(True):
codon=codonIterator.nextCodon()
if(not codon): break
if(stopCodons.get(codon.triplet,None)):
exon=codon.exon
coord=codon.absoluteCoord
trimBases=0
if(strand=="+"): trimBases=exon.end-coord-3
else: trimBases=coord-exon.begin-3
if(trimBases>=0):
exon.trimFinalPortion(trimBases)
exon.type="single-exon" if exon.order==0 else "final-exon"
j=numExons-1
while(j>exon.order):
self.deleteExon(j)
j-=1
stopCodonFound=True
break
else: # codon is interrupted; trim the next exon
nextExon=self.getSuccessor(exon)
if(not nextExon):
raise Exception("exon successor not found")
nextExon.trimFinalPortion(nextExon.getLength()+trimBases)
nextExon.type="final-exon"
j=numExons-1
while(j>nextExon.order):
self.deleteExon(j)
j-=1
stopCodonFound=True
break
if(not stopCodonFound):
### sometimes the GFF coords don't include the stop codon...
numExons=self.numExons()
lastExon=self.getIthExon(numExons-1)
lastExonEnd=lastExon.getEnd()
seq=axisSequenceRef
if(strand=="+"):
stopCodonBegin=lastExonEnd
stopCodon=seq[stopCodonBegin:stopCodonBegin+3]
if(stopCodon!="TAG" and stopCodon!="TAA" and stopCodon!="TGA"):
print("Warning! No stop codon found for",
self.transcriptId,self.strand,
"strand , unable to trim UTR")
else: # strand="-"
stopCodonBegin=lastExon.getBegin()-3
stopCodon=seq[stopCodonBegin,stopCodonBegin+3]
stopCodon=Translation.reverseComplement(stopCodon)
if(stopCodon!="TAG" and stopCodon!= "TAA" and stopCodon!="TGA"):
print("Warning! No stop codon found for",
self.transcriptId,self.strand,
"strand , unable to trim UTR")
self.recomputeBoundaries()
