def bidirectional_alignment(forward, reverse):
"""Align forward and reverse sequence of bidirectional Sanger reads.
forward and reverse sequences must already be in the same 'sense' (i.e.,
reverse should be revcomped if necessary so that both strands in alignment
are '+').
Forces alignment of both ends (right end of forward, and left end of
reverse).
...FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR...
Uses exonerate.
"""
# perform alignment
cmd = exonerate.ExonerateCommand('findend', 'parsable', 'bestonly')
rawaln = exonerate.run_exonerate2(cmd, forward, reverse)
aln = exonerate.parse_aln(rawaln)
# check that both strands are + orientation
if aln['query_strand'] != '+':
raise ValueError, "query strand has been reversed"
if aln['target_strand'] != '+':
raise ValueError, "target strand has been reversed"
# check that right end of forward and left end of reverse are placed
if aln['query_len'] != aln['query_aln_end']:
raise ValueError, "failed to align right-end of forward sequence"
if aln['query_aln_begin'] != 0:
raise ValueError, "failed to align left-end of right sequence"
def bidirectional_alignment(forward,reverse):
"""Align forward and reverse sequence of bidirectional Sanger reads.
forward and reverse sequences must already be in the same 'sense' (i.e.,
reverse should be revcomped if necessary so that both strands in alignment
are '+').
Forces alignment of both ends (right end of forward, and left end of
reverse).
...FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR...
Uses exonerate.
"""
# perform alignment
cmd = exonerate.ExonerateCommand('findend','parsable','bestonly')
rawaln = exonerate.run_exonerate2(cmd,forward,reverse)
aln = exonerate.parse_aln(rawaln)
# check that both strands are + orientation
if aln['query_strand'] != '+':
raise ValueError, "query strand has been reversed"
if aln['target_strand'] != '+':
raise ValueError, "target strand has been reversed"
# check that right end of forward and left end of reverse are placed
if aln['query_len'] != aln['query_aln_end']:
raise ValueError, "failed to align right-end of forward sequence"
if aln['query_aln_begin'] != 0:
raise ValueError, "failed to align left-end of right sequence"
def trimright(right, read):
"""Align 2 seqs, forcing alignment of left-end of right.
...DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD...
(forced aln here) -> RRRRRRRRRRRRRRRRRRRRRRRRRRRRR...
Uses exonerate.
"""
# perform alignment
cmd = exonerate.ExonerateCommand('findend', 'parsable', 'bestonly')
rawaln = exonerate.run_exonerate2(cmd, right, read)
if rawaln == '': return read
aln = exonerate.parse_aln(rawaln)
# check that the left-end of right was successfully placed
if aln['query_aln_begin'] != 0:
raise ValueError, "failed to align left-end of right sequence"
# check that both strands are + orientation
if aln['query_strand'] != '+':
raise ValueError, "query strand has been reversed"
if aln['target_strand'] != '+':
raise ValueError, "target strand has been reversed"
# return trimmed sequence
return read[:aln['target_aln_begin']]
def trimright(right,read):
"""Align 2 seqs, forcing alignment of left-end of right.
...DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD...
(forced aln here) -> RRRRRRRRRRRRRRRRRRRRRRRRRRRRR...
Uses exonerate.
"""
# perform alignment
cmd = exonerate.ExonerateCommand('findend','parsable','bestonly')
rawaln = exonerate.run_exonerate2(cmd,right,read)
if rawaln == '': return read
aln = exonerate.parse_aln(rawaln)
# check that the left-end of right was successfully placed
if aln['query_aln_begin'] != 0:
raise ValueError, "failed to align left-end of right sequence"
# check that both strands are + orientation
if aln['query_strand'] != '+':
raise ValueError, "query strand has been reversed"
if aln['target_strand'] != '+':
raise ValueError, "target strand has been reversed"
# return trimmed sequence
return read[:aln['target_aln_begin']]