def loadExonSequences(self,axisSequenceRef,exons):
numExons=len(exons)
strand=self.strand
for i in range(numExons):
exon=exons[i]
start=exon.begin
length=exon.end-start
exonSeq=axisSequenceRef[start:start+length]
if(len(exonSeq)!=length):
raise Exception("start="+str(start)+", length="+str(length)
+", but substrate "+self.substrate+
" ends at "+len(axisSequenceRef))
if(strand=="-"):
exonSeq=Translation.reverseComplement(exonSeq)
exon.sequence=exonSeq
return True
#filename="/home/bmajoros/1000G/assembly/BRCA1-NA19782.fasta";
filename="/Users/bmajoros/python/test/data/subset.fasta"
print(FastaReader.getSize(filename))
[defline,seq]=FastaReader.firstSequence(filename)
print(len(seq))
#filename="/home/bmajoros/1000G/assembly/test.fasta"
filename="/Users/bmajoros/python/test/data/subset.fasta"
hash=FastaReader.readAllAndKeepDefs(filename)
for key in hash.keys():
[defline,seq]=hash[key]
print(defline)
[id,attrs]=FastaReader.parseDefline(defline)
print("id="+id)
for key,value in attrs.items():
print(key+"="+value)
writer=FastaWriter()
writer.writeFasta(">ABCD","ATCGATCGTAGCTAGTCTGCGCGTATCGTCAGTCTCTATCGATCGTACTGCGATCTAGCTAGCTGATCGTAGCTTCTATGACTGCTAGTCATCTAGCTAGCTGATCGTAGCTGCGCGCGATATATTGCATCTATGCTATCATTGCATGCTAGCTCTAGCTAGTCGATGCTATCTTAGCTAC","test1.fasta")
writer.appendToFasta(">XYZ","GATTACA","test1.fasta")
print(Translation.translate(seq))
print("forward:",seq)
print("revcomp: ",Translation.reverseComplement(seq))
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()
