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#!/usr/bin/env python
# Copyright (c) 2006, The Regents of the University of California, through
# Lawrence Berkeley National Laboratory (subject to receipt of any required
# approvals from the U.S. Dept. of Energy). All rights reserved.
# This software is distributed under the new BSD Open Source License.
# <http://www.opensource.org/licenses/bsd-license.html>
# Please see the LICENSE.txt file that should have been included
# as part of this package.
""" A tool for converting multiple sequence alignments from
one format to another.
"""
import sys
from optparse import OptionGroup
from weblogo import seq_io
from weblogo.seq import Seq, SeqList, nucleic_alphabet
from weblogo.transform import mask_low_complexity
from weblogo.utils.deoptparse import DeOptionParser
__version__ = "1.0.0"
description = """ A tool for converting multiple sequence alignments from
one format to another. """
def main() -> None:
# ------ Parse Command line ------
parser = _build_option_parser()
(opts, args) = parser.parse_args(sys.argv[1:])
if args:
parser.error("Unparsable arguments: %s " % args)
seqs = opts.reader.read(opts.fin)
if opts.trans_seg:
seqs = SeqList([mask_low_complexity(s) for s in seqs])
if opts.subsample is not None:
from random import random
frac = opts.subsample
ss = []
for s in seqs:
if random() < frac:
ss.append(s)
seqs = SeqList(ss)
if opts.reverse:
seqs = SeqList([s.reverse() for s in seqs])
if opts.complement:
seqs = SeqList([Seq(s, alphabet=nucleic_alphabet) for s in seqs])
seqs = SeqList([s.complement() for s in seqs])
opts.writer.write(opts.fout, seqs)
def _build_option_parser() -> DeOptionParser:
parser = DeOptionParser(
usage="%prog [options] < sequence_data.fa > sequence_logo.eps",
description=description,
version=__version__,
add_verbose_options=False,
)
io_grp = OptionGroup(
parser,
"Input/Output Options",
)
parser.add_option_group(io_grp)
io_grp.add_option(
"-f",
"--fin",
dest="fin",
action="store",
type="file_in",
default=sys.stdin,
help="Sequence input file (default: stdin)",
metavar="FILENAME",
)
io_grp.add_option(
"",
"--format-in",
dest="reader",
action="store",
type="dict",
default=seq_io,
choices=seq_io.format_names(),
help="Multiple sequence alignment format: (%s)"
% ", ".join([f.names[0] for f in seq_io.formats]), # type: ignore
metavar="FORMAT",
)
io_grp.add_option(
"-o",
"--fout",
dest="fout",
type="file_out",
default=sys.stdout,
help="Output file (default: stdout)",
metavar="FILENAME",
)
trans_grp = OptionGroup(
parser,
"Transformations",
)
parser.add_option_group(trans_grp)
trans_grp.add_option(
"",
"--seg",
dest="trans_seg",
action="store_true",
default=False,
help="Mask low complexity regions in protein sequences.",
metavar="TRUE/FALSE",
)
trans_grp.add_option(
"",
"--subsample",
dest="subsample",
action="store",
type="float",
default=None,
help="Return a random subsample of the sequences.",
metavar="FRACTION",
)
trans_grp.add_option(
"",
"--reverse",
dest="reverse",
action="store_true",
default=False,
help="reverse sequences",
metavar="TRUE/FALSE",
)
trans_grp.add_option(
"",
"--complement",
dest="complement",
action="store_true",
default=False,
help="complement DNA sequences",
metavar="TRUE/FALSE",
)
# Writers
out_formats = []
for f in seq_io.formats:
if hasattr(f, "write"):
out_formats.append(f)
out_choices = {}
for f in out_formats:
out_choices[f.names[0]] = f # type: ignore
out_names = [f.names[0] for f in out_formats] # type: ignore
io_grp.add_option(
"-F",
"--format-out",
dest="writer",
action="store",
type="dict",
default=seq_io.fasta_io,
choices=out_choices,
help="Multiple sequence alignment output format: (%s) (Default: fasta)"
% ", ".join(out_names),
metavar="FORMAT",
)
return parser
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