def getSequence(self, twobit):
""" return sequence of Gtf object's feature given a bx seq twobit object"""
sequence=''
try:
sequence = twobit[self.seqname][self.start:self.end]
sequence=sequence.upper()
except:
sys.stderr.write("Unable to fetch the sequence\n")
if self.strand == '-':
return codonTable.reverse_complement(sequence)
return sequence
def walkCdsMinus(self, twobit):
""" given a twobit object generator to walk CDS feature and yield codon, aa & codonStart, codonEnd intervals """
#walk the CDS feature in frame, so adjust the counter variable i if needed
i=self.end
if self.frame == 1:
i=i-1
if self.frame == 2:
i=i-2
while ( i > self.start+1):
sequence=twobit[self.seqname][i-3:i]
sequence=sequence.upper()
sequence=codonTable.reverse_complement(sequence)
yield sequence, codonTable.translateCodon(sequence), i-3, i
i=i-3
