def ExtendNonMetORFs(predictions, DNAseq):
for p in predictions:
if (p.sequence[0] != 'M' and p.sequence[0] != 'V'): #starting amino acid is not M
#extend upstream in DNAseq until Met found
nextAA = ""
i=0
while(nextAA != 'M'):
nextcodon = ''
if p.strand == '+':
if p.start-i-3 < 0:
break
nextcodon = DNAseq[p.start-i-3 : p.start - i]
else:
if p.stop + i + 3 > len(DNAseq):
break
nextcodon = DNAseq[p.stop + i : p.stop + i + 3]
nextcodon= CommonDNA.reverseComplement(nextcodon)
nextAA = CommonDNA.translate(nextcodon)
if(nextAA == "_"):
break
i+=3
p.sequence = nextAA + p.sequence
if p.strand == "+":
p.start = p.start-i-3
else:
p.stop = p.stop + i + 3
return predictions
def ExtendTruncatedORFs(predictions, DNAseq): #takes in a gene prediction, along with its homologs, and sees if there is an upstream sequence in the DNA that matches for p in predictions: if len(p.homologs) < 1: #skip if no homologs continue else: firstTenAA = "" try: firstTenAA = p.sequence[0:10] except IndexError: continue else: #find first ten AA in other homologs for h in p.homologs: offset = h.sequence.find(firstTenAA) if h.sequence.find(firstTenAA) > 1: #find extra sequence in our DNA input inputMatch = "" if p.strand == "+": inputMatch = DNAseq[p.start: p.start - offset*3] else: inputMatch = DNAseq[p.stop: p.stop + offset*3] inputMatch = CommonDNA.reverseComplement(inputMatch) return predictions
