def walkCdsFwd(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.start
if self.frame == 1:
i=i+1
if self.frame == 2:
i= i+2
while (i +3 < self.end):
sequence =twobit[self.seqname][i:i+3]
sequence=sequence.upper()
yield sequence, codonTable.translateCodon(sequence), i, i+3
i=i+3
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
def walkExonSequence(sequence):
while (i < len(sequence) ):
yield sequence[i:i+3], codonTable.translateCodon(sequence[i:i+3])
i+=3
