def __init__(self, genetic_code=None, path=None):
self.genetic_code = get_genetic_code(genetic_code)
self.__sequences = {}
self.headers = []
self.items = []
if path:
self.read(path)
def __init__(self, genetic_code=None, path=None):
self.genetic_code = get_genetic_code(genetic_code)
self.__sequences = {}
self.headers = []
self.items = []
if path:
self.read(path)
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 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)
