8 changed files with 423 additions and 483 deletions
@ -1,78 +0,0 @@
|
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# -*- coding: utf-8 -*- |
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# Incenp.Bioutils - Incenp.org's utilities for computational biology |
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# Copyright © 2018,2020 Damien Goutte-Gattat |
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# |
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# This program is free software; you can redistribute it and/or modify |
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# it under the terms of the GNU General Public License as published by |
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# the Free Software Foundation; either version 3 of the License, or |
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# (at your option) any later version. |
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# |
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# This program is distributed in the hope that it will be useful, |
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# but WITHOUT ANY WARRANTY; without even the implied warranty of |
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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# GNU General Public License for more details. |
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# |
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# You should have received a copy of the GNU General Public License |
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# along with this program. If not, see <http://www.gnu.org/licenses/>. |
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|
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"""Dotter wrapper program |
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|
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Wrapper tool to call the seqtools' dotter program on any kind |
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of sequence files instead of only FASTA files. |
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""" |
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|
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from argparse import ArgumentParser |
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from os import unlink |
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from subprocess import call |
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from tempfile import NamedTemporaryFile |
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|
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from Bio.SeqIO import write |
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from incenp.bio.seq.usa import read_usa |
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|
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|
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def dotter(horizontal, vertical): |
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"""Call the dotter program on the specified sequences. |
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|
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:param horizontal: the sequence to plot on the horizontal axis |
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:type: :class:`Bio.SeqRecord.SeqRecord` |
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:param vertical: the sequence to plot on the vertical axis |
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:type: :class:`Bio.SeqRecord.SeqRecord` |
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""" |
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|
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try: |
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hf = NamedTemporaryFile(mode='w', delete=False) |
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vf = NamedTemporaryFile(mode='w', delete=False) |
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|
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write([horizontal], hf, 'fasta') |
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hf.close() |
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|
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write([vertical], vf, 'fasta') |
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vf.close() |
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|
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call(['dotter', hf.name, vf.name]) |
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finally: |
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unlink(hf.name) |
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unlink(vf.name) |
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|
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|
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def main(): |
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parser = ArgumentParser(description="wrapper for the dotter program") |
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parser.add_argument('hseq', help="the horizontal sequence, as a USA") |
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parser.add_argument('vseq', help="the vertical sequence, as a USA") |
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|
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args = parser.parse_args() |
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|
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try: |
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hseq = read_usa(args.hseq)[0] |
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vseq = read_usa(args.vseq)[0] |
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except Exception as e: |
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parser.error("cannot read source sequences: {}".format(e)) |
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|
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try: |
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dotter(hseq, vseq) |
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except Exception as e: |
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parser.error("cannot run dotter: {}".format(e)) |
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|
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|
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if __name__ == '__main__': |
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main() |
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@ -0,0 +1,260 @@
|
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# -*- coding: utf-8 -*- |
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# Incenp.Bioutils - Incenp.org's utilities for computational biology |
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# Copyright © 2020 Damien Goutte-Gattat |
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# |
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# This program is free software; you can redistribute it and/or modify |
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# it under the terms of the GNU General Public License as published by |
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# the Free Software Foundation; either version 3 of the License, or |
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# (at your option) any later version. |
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# |
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# This program is distributed in the hope that it will be useful, |
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# but WITHOUT ANY WARRANTY; without even the implied warranty of |
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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# GNU General Public License for more details. |
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# |
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# You should have received a copy of the GNU General Public License |
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# along with this program. If not, see <http://www.gnu.org/licenses/>. |
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"""A command-line tool to manipulate biological sequence files.""" |
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|
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import sys |
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|
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from Bio.Restriction.Restriction import RestrictionBatch |
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import click |
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from incenp.bio import __version__ |
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from incenp.bio.seq import utils |
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from incenp.bio.seq import wrappers |
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from incenp.bio.seq.plasmidmap import summarize_vector |
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from incenp.bio.seq.usa import read_usa, write_usa |
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from reportlab.pdfgen.canvas import Canvas |
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|
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prog_name = "seqtool" |
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prog_notice = f"""\ |
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{prog_name} {__version__} |
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Copyright © 2020 Damien Goutte-Gattat |
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|
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This program is released under the GNU General Public License. |
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See the COPYING file or <http://www.gnu.org/licenses/gpl.html>. |
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""" |
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|
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|
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@click.group(context_settings={'help_option_names': ['-h', '--help']}) |
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@click.version_option(version=__version__, message=prog_notice) |
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@click.pass_context |
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def seqtool(ctx): |
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pass |
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|
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|
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@seqtool.command() |
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@click.argument('sequences', nargs=-1) |
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@click.option('--output', '-o', default='genbank::stdout', metavar="USA", |
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help="""Write to the specified USA instead of standard |
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output.""") |
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@click.option('--name', '-n', metavar="NAME", help="Set the sequence name.") |
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@click.option('--accession', '-a', metavar="ACC", help="Set the sequence ID.") |
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@click.option('--description', '-d', help="Set the sequence description.") |
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@click.option('--circular', '-c', 'topology', flag_value='circular', |
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help="Force circular topology.") |
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@click.option('--linear', 'topology', flag_value='linear', default=True, |
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help="Force linear topology.") |
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@click.option('--division', '-D', metavar="DIV", |
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help="""The data file division to use if none is already |
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assigned to the sequence.""") |
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@click.option('--clean', '-C', is_flag=True, |
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help="Clean the output sequence.") |
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@click.option('--remove-external-features', '-r', is_flag=True, |
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help="Remove features referring to an external sequence.") |
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@click.pass_context |
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def cat(ctx, sequences, output, name, accession, description, topology, |
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division, clean, remove_external_features): |
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"""Read and write sequences. |
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|
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This tool reads the specified input SEQUENCES and catenate them into |
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a single written to standard output. |
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""" |
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|
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inputs = [] |
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for f in sequences: |
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try: |
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inputs.extend(read_usa(f)) |
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except Exception as e: |
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raise click.ClickException(f"Cannot read {f}: {e}") |
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|
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if len(inputs) == 0: |
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ctx.exit() |
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outrec = inputs[0] |
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for record in inputs[1:]: |
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outrec += record |
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if clean: |
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utils.clean(outrec, div=division, topology=topology) |
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if remove_external_features: |
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utils.remove_external_features(outrec) |
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if name: |
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outrec.name = name |
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if accession: |
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outrec.id = accession |
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if description: |
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outrec.description = description |
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try: |
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write_usa([outrec], output) |
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except Exception as e: |
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raise click.ClickException(f"Cannot write to {output}: {e}") |
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|
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|
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@seqtool.command() |
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@click.argument('source') |
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@click.option('--output', '-o', metavar="USA", default='fasta::stdout', |
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help="""Write to the specified USA instead of standard |
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output.""") |
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@click.pass_context |
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def siresist(ctx, source, output): |
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"""Silently mutate a CDS. |
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|
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Creates a variant of the SOURCE sequence with silent mutations. |
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""" |
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try: |
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source = read_usa(source)[0] |
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except Exception as e: |
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raise click.ClickException(f"Cannot read {source}: {e}") |
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source.seq = utils.silently_mutate(source.seq) |
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try: |
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write_usa([source], output) |
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except Exception as e: |
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raise click.ClickException(f"Cannot write to {output}: {e}") |
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|
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|
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@seqtool.command() |
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@click.argument('source') |
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@click.argument('destination') |
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@click.option('--output', '-o', metavar="USA", |
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help="""Write to the specified USA instead of standard |
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output.""") |
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@click.option('--reaction', '-r', type=click.Choice(['BP', 'LR']), |
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default='LR', |
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help="Specify the type of Gateway reaction.") |
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@click.option('--name', '-n', metavar="NAME", help="Set the sequence name.") |
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@click.option('--accession', '-a', metavar="ACC", help="Set the sequence ID.") |
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@click.option('--description', '-d', help="Set the sequence description.") |
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@click.option('--clean', '-c', is_flag=True, help="Clean the output sequence.") |
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@click.pass_context |
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def gateway(ctx, source, destination, output, reaction, name, accession, |
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description, clean): |
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"""Perform in-silico Gateway cloning.""" |
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|
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try: |
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source = read_usa(source)[0] |
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destination = read_usa(destination)[0] |
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except Exception as e: |
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raise click.ClickException(f"Cannot read input sequences: {e}") |
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|
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clone = utils.gateway(source, destination, reaction, sys.stderr) |
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if not clone: |
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raise click.ClickException("Gateway cloning not possible") |
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clone.name = name or source.name |
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clone.id = accession or source.id |
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clone.description = description or source.description |
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clone.annotations['date'] = utils.genbank_date() |
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|
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if clean: |
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utils.clean(clone) |
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|
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try: |
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write_usa([clone], output) |
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except Exception as e: |
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raise click.ClickException(f"Cannot write output: {e}") |
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|
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|
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@seqtool.command() |
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@click.argument('sequences') |
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@click.option('--output', '-o', metavar="FILE", default='plasmm.pdf', |
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help="Write to the specified file.", show_default=True) |
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@click.option('--enzymes', '-e', help="Specify the enzymes to display.") |
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@click.pass_context |
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def plasmm(ctx, sequences, output, enzymes): |
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"""Draw plasmid maps.""" |
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|
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if enzymes: |
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_enzymes = RestrictionBatch() |
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for enz in enzymes.split(','): |
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_enzymes.add(enz) |
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|
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records = [] |
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for f in sequences: |
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try: |
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records.extend(read_usa(f)) |
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except Exception as e: |
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raise click.ClickException(f"Cannot read {f}: {e}") |
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|
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c = Canvas(output) |
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for record in records: |
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if record.annotations.get('molecule_type', 'DNA') == 'protein': |
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continue |
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summarize_vector(c, record) |
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|
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try: |
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c.save() |
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except Exception as e: |
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raise click.ClickException(f"Cannot write output: {e}") |
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|
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|
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@seqtool.command() |
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@click.argument('subject') |
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@click.argument('query') |
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@click.option('--type', '-t', 'blast_type', default='blastn', |
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type=click.Choice(['blastn', 'blastp', 'blastx', 'tblastn', |
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'tblastx']), |
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help="The type of alignment to perform.") |
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@click.option('--database', '-d', is_flag=True, |
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help="Treat SUBJECT as a database name.") |
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@click.option('--short', '-s', is_flag=True, |
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help="Optimize BLAST for short matches.") |
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def blast(ctx, subject, query, blast_type, database, short): |
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"""Wrapper for the BLAST programs. |
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|
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SUBJECT and QUERY should be USAs representing the subject and query |
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sequences, respectively. |
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""" |
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|
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try: |
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if not database: |
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subject = read_usa(subject)[0] |
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query = read_usa(query)[0] |
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except Exception as e: |
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raise click.ClickException(f"Cannot read source sequences: {e}") |
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|
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try: |
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stdout, _ = wrappers.blast(query, subject, blast_type, database, short) |
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print(stdout) |
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except BrokenPipeError: |
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pass |
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except Exception as e: |
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raise click.ClickException(f"Cannot run blast: {e}") |
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|
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|
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@seqtool.command() |
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@click.argument('hseq') |
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@click.argument('vseq') |
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@click.pass_context |
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def dotter(ctx, hseq, vseq): |
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"""Wrapper for the dotter program.""" |
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|
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try: |
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hseq = read_usa(hseq)[0] |
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vseq = read_usa(vseq)[0] |
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except Exception as e: |
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raise click.ClickException(f"Cannot read source sequences: {e}") |
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|
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try: |
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wrappers.dotter(hseq, vseq) |
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except Exception as e: |
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raise click.ClickException(f"Cannot run dotter: {e}") |
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|
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|
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if __name__ == '__main__': |
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seqtool() |
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@ -1,166 +0,0 @@
|
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# -*- coding: utf-8 -*- |
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# Incenp.Bioutils - Incenp.org's utilities for computational biology |
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# Copyright © 2018,2020 Damien Goutte-Gattat |
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# |
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# This program is free software; you can redistribute it and/or modify |
||||
# it under the terms of the GNU General Public License as published by |
||||
# the Free Software Foundation; either version 3 of the License, or |
||||
# (at your option) any later version. |
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# |
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# This program is distributed in the hope that it will be useful, |
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of |
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
||||
# GNU General Public License for more details. |
||||
# |
||||
# You should have received a copy of the GNU General Public License |
||||
# along with this program. If not, see <http://www.gnu.org/licenses/>. |
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|
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"""Utility functions for working on biological sequences |
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|
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This module is intended to provide various helper functions |
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for working on sequence files. |
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""" |
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|
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from argparse import ArgumentParser |
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from datetime import datetime |
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|
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from incenp.bio.seq.usa import read_usa, write_usa |
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|
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|
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def genbank_date(date=None): |
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if date is None: |
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date = datetime.now() |
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return date.strftime('%d-%b-%Y').upper() |
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|
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|
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def remove_external_features(record): |
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for feature in [f for f in record.features[:] if f.ref is not None]: |
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record.features.remove(feature) |
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|
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|
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def clean(record, div='UNK', topology='linear'): |
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# Set the data division if needed |
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if (not 'data_file_division' in record.annotations |
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or record.annotations['data_file_division'].isspace()): |
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record.annotations['data_file_division'] = div |
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|
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# Fix topology |
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if not 'topology' in record.annotations: |
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record.annotations['topology'] = topology |
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|
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# Fix missing molecule type |
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if not 'molecule_type' in record.annotations: |
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record.annotations['molecule_type'] = guess_molecule_type(record.seq) |
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|
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# Translate CDS |
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for cds in [f for f in record.features if f.type == 'CDS']: |
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if 'translation' in cds.qualifiers: |
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continue |
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if record.annotations['molecule_type'] == 'protein': |
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continue |
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seq = record.seq[cds.location.start.position:cds.location.end.position] |
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if cds.strand == -1: |
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seq = seq.reverse_complement() |
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cds.qualifiers['translation'] = str(seq.translate()) |
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|
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# Remove Ugene stuff |
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for feature in [f for f in record.features[:] if 'ugene_name' in f.qualifiers]: |
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# Restriction site features |
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if 'cut' in feature.qualifiers: |
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record.features.remove(feature) |
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|
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# Fragments |
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if 'ugene_group' in feature.qualifiers and 'fragments' in feature.qualifiers['ugene_group']: |
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record.features.remove(feature) |
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|
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# Source |
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if 'source' in feature.qualifiers['ugene_name']: |
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record.features.remove(feature) |
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|
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feature.qualifiers.pop('ugene_name', None) |
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feature.qualifiers.pop('ugene_group', None) |
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|
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# Remove SerialCloner stuff |
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for feature in record.features: |
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feature.qualifiers.pop('SerialCloner_Color', None) |
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feature.qualifiers.pop('SerialCloner_Show', None) |
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feature.qualifiers.pop('SerialCloner_Protect', None) |
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feature.qualifiers.pop('SerialCloner_Arrow', None) |
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|
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|
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_alphabets = { |
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'DNA': 'ACGTRYSWKMBDHVN', |
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'RNA': 'ACGURYSWKMBDHVN', |
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'protein': 'ACDEFGHIKLMNPQRSTVWY*' |
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} |
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|
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|
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def guess_molecule_type(sequence, alphabets=_alphabets): |
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seqset = set(str(sequence).upper()) |
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for typename in alphabets.keys(): |
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leftover = seqset - set(alphabets[typename]) |
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if not leftover: |
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return typename |
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return 'DNA' |
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|
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|
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def main(): |
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parser = ArgumentParser(description="read and write sequences") |
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|
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igroup = parser.add_argument_group(title="input/output") |
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igroup.add_argument('sequences', nargs='+', |
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help="the input sequences, as USAs") |
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igroup.add_argument('-o', '--output', nargs='?', default='genbank::stdout', |
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help="""write to the specified file (as USA) instead |
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of standard output""") |
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|
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sgroup = parser.add_argument_group(title="output sequence properties") |
||||
sgroup.add_argument('-n', '--name', help="set the sequence name") |
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sgroup.add_argument('-a', '--accession', help="set the sequence ID") |
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sgroup.add_argument('-d', '--description', help="set the sequence description") |
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sgroup.add_argument('-c', '--circular', action='store_const', |
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dest='topology', const='circular', default='linear', |
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help="force circular topology if needed") |
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sgroup.add_argument('-D', '--division', nargs='?', |
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help="""data file division to use if none is already |
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assigned to the sequence""") |
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|
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ogroup = parser.add_argument_group(title="optional features") |
||||
ogroup.add_argument('-C', '--clean', action='store_true', |
||||
help="clean the output sequence") |
||||
ogroup.add_argument('-r', '--remove-external-features', dest='remove_ext_feat', |
||||
action='store_true', |
||||
help="remove features referring to an external sequence") |
||||
|
||||
args = parser.parse_args() |
||||
|
||||
inputs = [] |
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for f in args.sequences: |
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try: |
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inputs.extend(read_usa(f)) |
||||
except Exception as e: |
||||
parser.error("cannot read {}: {}".format(f, e)) |
||||
|
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output = inputs[0] |
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for record in inputs[1:]: |
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output += record |
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|
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if args.clean: |
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clean(output, div=args.division, topology=args.topology) |
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if args.remove_ext_feat: |
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remove_external_features(output) |
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if args.name: |
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output.name = args.name |
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if args.accession: |
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output.id = args.accession |
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if args.description: |
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output.description = args.description |
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|
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try: |
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write_usa([output], args.output) |
||||
except Exception as e: |
||||
parser.error("cannot write to {}: {}".format(args.output, e)) |
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|
||||
|
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if __name__ == '__main__': |
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main() |
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@ -1,97 +0,0 @@
|
||||
# -*- coding: utf-8 -*- |
||||
# Incenp.Bioutils - Incenp.org's utilities for computational biology |
||||
# Copyright © 2018,2020 Damien Goutte-Gattat |
||||
# |
||||
# This program is free software; you can redistribute it and/or modify |
||||
# it under the terms of the GNU General Public License as published by |
||||
# the Free Software Foundation; either version 3 of the License, or |
||||
# (at your option) any later version. |
||||
# |
||||
# This program is distributed in the hope that it will be useful, |
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of |
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
||||
# GNU General Public License for more details. |
||||
# |
||||
# You should have received a copy of the GNU General Public License |
||||
# along with this program. If not, see <http://www.gnu.org/licenses/>. |
||||
|
||||
"""Functions to work on siRNA and similar stuff.""" |
||||
|
||||
import argparse |
||||
from random import sample |
||||
|
||||
from Bio.Data import CodonTable |
||||
from Bio.Seq import MutableSeq |
||||
from incenp.bio.seq.usa import read_usa, write_usa |
||||
|
||||
_reverse_codon_tables = {} |
||||
|
||||
|
||||
def _build_reverse_codon_table(code): |
||||
rt = {} |
||||
for residue in code.forward_table.values(): |
||||
codons_list = [] |
||||
for k, v in code.forward_table.items(): |
||||
if v == residue: |
||||
codons_list.append(k) |
||||
rt[residue] = codons_list |
||||
return rt |
||||
|
||||
|
||||
def silently_mutate(sequence, code=None): |
||||
"""Mutate a CDS without changing its translation. |
||||
|
||||
Generate a mutated sequence by altering all possible codons |
||||
without introducing any changes in the aminoacids translation. |
||||
|
||||
:param sequence: the sequence to mutate |
||||
:type: :class:`Bio.Seq.Seq` |
||||
:param code: the codon table to use (defaults to the “standard” genetic code) |
||||
:type: :class:`Bio.Data.CodonTable` |
||||
:return: the mutated sequence |
||||
:rtype: :class:`Bio.Seq.Seq` |
||||
""" |
||||
|
||||
if not code: |
||||
code = CodonTable.unambiguous_dna_by_name['Standard'] |
||||
if not code in _reverse_codon_tables: |
||||
_reverse_codon_tables[code] = _build_reverse_codon_table(code) |
||||
rt = _reverse_codon_tables[code] |
||||
|
||||
output = MutableSeq('') |
||||
for i in range(int(len(sequence) / 3)): |
||||
codon = str(sequence[i * 3:(i * 3) + 3]) |
||||
if codon in code.forward_table: |
||||
residue = code.forward_table[codon] |
||||
possible_codons = rt[residue] |
||||
if len(possible_codons) > 1: |
||||
codon = sample([a for a in possible_codons if a != codon], 1)[0] |
||||
output += codon |
||||
|
||||
return output |
||||
|
||||
|
||||
def main(): |
||||
parser = argparse.ArgumentParser(description="silently mutate a CDS") |
||||
parser.add_argument('source', help="the source sequence, as a USA") |
||||
parser.add_argument('--output', '-o', nargs='?', default='fasta::stdout', |
||||
help="""write to the specified file (as USA) instead |
||||
of standard output""") |
||||
|
||||
args = parser.parse_args() |
||||
|
||||
try: |
||||
source = read_usa(args.source)[0] |
||||
except Exception as e: |
||||
parser.error("cannot read {}: {}".format(args.source, e)) |
||||
|
||||
source.seq = silently_mutate(source.seq) |
||||
|
||||
try: |
||||
write_usa([source], args.output) |
||||
except Exception as e: |
||||
parser.error("cannot write to {}: {}".format(args.output, e)) |
||||
|
||||
|
||||
if __name__ == '__main__': |
||||
main() |
||||
Loading…
Reference in new issue