def main():
"""
main function
"""
opts = get_options()
genetic_code = None if opts.aa else get_genetic_code(opts.code)
sequences = parse_fasta(opts.fastafile, genetic_code)
tmp_dir = dirname(
opts.outfile) + ('/tmp' if '/' in opts.outfile else 'tmp')
Popen('mkdir -p ' + tmp_dir, shell=True).communicate()
### if we need to align:
# write sense and anti-sense translated sequences
this = 'seq' if opts.aa else 'prot'
write_rfasta(sequences, tmp_dir + '/prot.fasta', what=this)
if opts.align == 2:
write_rfasta(sequences, tmp_dir + '/torp.fasta', what=this, rev=True)
# run alignment
if opts.align:
run_alignments(tmp_dir, opts.cpus, opts.quiet, opts.align)
# merge all in one, keep only sites with score better than m_coffee cut
aligners = [ali for ali in BINARIES if 'fun' in BINARIES[ali]]
if len(aligners) > 1 or opts.align == 2:
merge_mcoffee(tmp_dir, opts.mcoffee_cut, sequences, aa=opts.aa)
else:
aa_ali = parse_fasta(tmp_dir + '/prot.fasta_' + aligners[0])
for seq in sequences:
sequences[seq]['aa_ali'] = aa_ali[seq]['seq']
for elt in xrange(len(sequences[seq]['aa_ali'])):
if sequences[seq]['aa_ali'][elt] == '-':
sequences[seq]['codon'].insert(elt, '---')
continue
# trimal
if opts.trimseq:
trim_sequences(tmp_dir,
opts.outfile,
sequences,
opts.trimseq,
quiet=opts.quiet)
if opts.trimcol != 'None':
trim_columns(sequences, opts, tmp_dir)
# write codon sequences
if opts.aa:
write_fasta(sequences, opts.outfile, what='aa_ali')
else:
write_fasta(sequences, opts.outfile, what='codon')
# print map
if opts.printmap:
printmap(sequences, opts.outfile + '.map', opts.pymap)
def run_alignments(path, cpus=1, quiet=False, tries=2):
"""
"""
procs = []
files = []
aligners = [ali for ali in BINARIES if 'fun' in BINARIES[ali]]
for ali in sorted(
aligners,
key=lambda x: ['probcons', 'dialign', 'muscle', 'mafft'].index(x)):
if not quiet:
print 'Aligning with: ' + ali
for sense in ['prot', 'torp'][:tries]:
if not quiet:
print ' -> ' + ('sense' if sense == 'prot' else 'anti-sense')
files.append('%s.fasta_%s' % (sense, ali))
procs.append(BINARIES[ali]['fun'](path + '/%s.fasta' % (sense)))
if len(procs) < cpus: continue
while len(procs) != 0:
out, err = procs.pop(0).communicate()
if 'ERROR' in err:
print >> stderr, out, err
raise Exception('\nERROR: running alignments')
while len(procs) != 0:
out, err = procs.pop(0).communicate()
if 'ERROR' in err:
print >> stderr, out, err
raise Exception('\nERROR: running alignments')
for fil in files:
if fil.startswith('torp'):
seqs = parse_fasta(path + '/' + fil)
for seq in seqs:
seqs[seq]['seq'] = seqs[seq]['seq'][::-1]
write_rfasta(seqs, path + '/' + fil)
def trim_sequences(path, seq_path, seqs, trimseq, quiet=True):
trimsq_path = path + '/seq_trimmed.fasta'
proc = Popen([
BINARIES['trimal']['bin'], '-in', seq_path, '-out', trimsq_path,
'-resoverlap',
str(trimseq[1]), '-seqoverlap',
str(trimseq[2]), '-cons', '100'
],
stdout=PIPE)
if proc.communicate()[1] is not None:
print >> stderr, proc.communicate()[0]
exit('\nERROR: trimming sequences')
trimmed = parse_fasta(trimsq_path)
for seq in trimmed:
seqs[seq]['ali'] = trimmed[seq]['seq']
trimmed = filter(lambda x: not seqs[x].has_key('ali'), seqs)
if not quiet:
print >> stderr, 'WARNING: trimmed sequences: \n\t' + \
'\n\t'.join(trimmed)
LOG.append('')
if len(trimmed) > 0:
LOG[-1] += '->trimmed sequences: \n\t' + \
'\n\t'.join(trimmed) + '\n'
else:
LOG[-1] += '->no trimmed sequences\n'
for s in seqs.keys():
if s in trimmed:
del (seqs[s])
return trimsq_path
