def getseqbyfeaturetuple(sequence, gfftuple):
""" """
seqpart = sequence[int(gfftuple[3]) - 1:int(gfftuple[4])]
if gfftuple[5] == '-':
return _reversecomplement(seqpart)
else:
return seqpart
def getseqbyfeaturetuple(sequence,gfftuple):
""" """
seqpart = sequence[int(gfftuple[3])-1:int(gfftuple[4])]
if gfftuple[5] == '-':
return _reversecomplement(seqpart)
else:
return seqpart
def _get_reverse_strand_coords_and_seqs(dnaseq, start, end):
"""
TODO ....
@type dnaseq: string
@param dnaseq: DNA sequence string
@type start: integer
@param start:
@type end: integer
@param end:
@rtype: tuple
@return: (start,end,dnarevseq,protseq)
"""
# obtain position of the exterior stop codons on the other strand
# take care with EOF sequence; after while loop +3; so stop at -6 end
if end >= len(dnaseq) - 6:
# end offset already in the danger zone of reaching EOF sequence
# shift untill in reach (3nt offset) of EOF sequence
while end >= len(dnaseq) - 3:
end -= 3
else:
while end < len(dnaseq) - 6:
if dnaseq[end:end + 3].upper() in REV_STOP_CODONS: break
end += 3
# take care with EOF sequence; after while loop -3; so stop at +6 end
if start < 6:
# start offset already in the danger zone of reaching EOF sequence
# shift untill in reach (3nt offset) of EOF sequence
while start < 3:
start += 3
else:
while start >= 6:
if dnaseq[start - 3:start].upper() in REV_STOP_CODONS: break
start -= 3
# get DNA & Protein sequences on the reverse strand
start -= 3
end += 3
dnarevseq = _reversecomplement(dnaseq[start:end])
protseq = dna2protein(dnarevseq)
# return coords & sequences
return (start, end, dnarevseq, protseq)
def _get_reverse_strand_coords_and_seqs(dnaseq,start,end):
"""
TODO ....
@type dnaseq: string
@param dnaseq: DNA sequence string
@type start: integer
@param start:
@type end: integer
@param end:
@rtype: tuple
@return: (start,end,dnarevseq,protseq)
"""
# obtain position of the exterior stop codons on the other strand
# take care with EOF sequence; after while loop +3; so stop at -6 end
if end >= len(dnaseq)-6:
# end offset already in the danger zone of reaching EOF sequence
# shift untill in reach (3nt offset) of EOF sequence
while end >= len(dnaseq)-3: end-=3
else:
while end < len(dnaseq)-6:
if dnaseq[end:end+3].upper() in REV_STOP_CODONS: break
end += 3
# take care with EOF sequence; after while loop -3; so stop at +6 end
if start < 6:
# start offset already in the danger zone of reaching EOF sequence
# shift untill in reach (3nt offset) of EOF sequence
while start < 3: start += 3
else:
while start >= 6:
if dnaseq[start-3:start].upper() in REV_STOP_CODONS: break
start -= 3
# get DNA & Protein sequences on the reverse strand
start-=3
end+=3
dnarevseq = _reversecomplement(dnaseq[start:end])
protseq = dna2protein(dnarevseq)
# return coords & sequences
return (start,end,dnarevseq,protseq)