def main():
out_fmt, infiles, opts = common.parse_args('alignment')
for in_path in infiles:
dir, base, ext = common.dir_base_ext(in_path)
in_fmt = (opts.input_format or EXT_TO_FORMAT.get(ext, '')).lower()
assert (in_fmt), "no known input format specified"
# calculate output format and name
out_path = common.make_out_path(
dir, base, opts.output_extension or FORMAT_TO_EXT[out_fmt])
# open & read infile
in_hndl = open(in_path, 'rb')
in_alns = [x for x in AlignIO.parse(in_hndl, in_fmt)]
in_hndl.close()
assert (in_alns), \
'''No alignments read from %s. Perhaps the file is not in %s format.''' % (file_name, in_fmt)
# write out
out_hndl = open(out_path, 'wb')
if opts.seqtype:
for s in in_alns:
s._alphabet = opts.seqtype
AlignIO.write(in_alns, out_hndl, out_fmt)
out_hndl.close()
def main():
out_fmt, infiles, opts = common.parse_args('biosequence')
for in_path in infiles:
dir, base, ext = common.dir_base_ext(in_path)
in_fmt = (opts.input_format or EXT_TO_FORMAT.get(ext, '')).lower()
assert (in_fmt), "no known input format specified"
# calculate output format and name
out_path = common.make_out_path(
dir, base, opts.output_extension or FORMAT_TO_EXT[out_fmt])
# open & read infile
in_hndl = open(in_path, 'rb')
in_seqs = [x for x in SeqIO.parse(in_hndl, in_fmt)]
in_hndl.close()
assert (in_seqs), \
'''No sequences read from %s. Perhaps the file is not in %s format.''' % (file_name, in_fmt)
# write out
out_hndl = open(out_path, 'wb')
if opts.seqtype:
for s in in_seqs:
s.alphabet = opts.seqtype
if out_fmt in ['nexus']:
# need to hack to handle this crap
from Bio.Align import MultipleSeqAlignment
aln = MultipleSeqAlignment(in_seqs,
alphabet=opts.seqtype
or BIOSEQ_ALPHABET_PROTEIN)
AlignIO.write(aln, out_hndl, out_fmt)
else:
SeqIO.write(in_seqs, out_hndl, out_fmt)
out_hndl.close()
def main():
out_fmt, infiles, opts = common.parse_args('biosequence')
for in_path in infiles:
dir, base, ext = common.dir_base_ext (in_path)
in_fmt = (opts.input_format or EXT_TO_FORMAT.get (ext, '')).lower()
assert (in_fmt), "no known input format specified"
# calculate output format and name
out_path = common.make_out_path (dir, base,
opts.output_extension or FORMAT_TO_EXT[out_fmt])
# open & read infile
in_hndl = open (in_path, 'rb')
in_seqs = [x for x in SeqIO.parse (in_hndl, in_fmt)]
in_hndl.close()
assert (in_seqs), \
'''No sequences read from %s. Perhaps the file is not in %s format.''' % (file_name, in_fmt)
# write out
out_hndl = open (out_path, 'wb')
if opts.seqtype:
for s in in_seqs:
s.alphabet = opts.seqtype
if out_fmt in ['nexus']:
# need to hack to handle this crap
from Bio.Align import MultipleSeqAlignment
aln = MultipleSeqAlignment(in_seqs,
alphabet=opts.seqtype or BIOSEQ_ALPHABET_PROTEIN)
AlignIO.write (aln, out_hndl, out_fmt)
else:
SeqIO.write (in_seqs, out_hndl, out_fmt)
out_hndl.close()
def main():
out_fmt, infiles, opts = common.parse_args("alignment")
for in_path in infiles:
dir, base, ext = common.dir_base_ext(in_path)
in_fmt = (opts.input_format or EXT_TO_FORMAT.get(ext, "")).lower()
assert in_fmt, "no known input format specified"
# calculate output format and name
out_path = common.make_out_path(dir, base, opts.output_extension or FORMAT_TO_EXT[out_fmt])
# open & read infile
in_hndl = open(in_path, "rb")
in_alns = [x for x in AlignIO.parse(in_hndl, in_fmt)]
in_hndl.close()
assert in_alns, """No alignments read from %s. Perhaps the file is not in %s format.""" % (file_name, in_fmt)
# write out
out_hndl = open(out_path, "wb")
if opts.seqtype:
for s in in_alns:
s._alphabet = opts.seqtype
AlignIO.write(in_alns, out_hndl, out_fmt)
out_hndl.close()
