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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 tool to access a BioSQL-based sequence database.""" |
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import sys |
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from configparser import ConfigParser |
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from hashlib import md5 |
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from subprocess import run |
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from tempfile import NamedTemporaryFile |
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from Bio import SeqIO |
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from BioSQL.BioSeqDatabase import open_database |
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import click |
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from click_shell import shell |
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from incenp.bio import __version__ |
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from incenp.bio.seq import vault |
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from incenp.bio.seq.usa import read_usa, write_usa |
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prog_name = "seqvault" |
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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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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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def _get_database(ctx, _, value): |
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try: |
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return ctx.obj[value] |
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except KeyError: |
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raise click.BadParameter(f"No {value!r} database on the server") |
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@shell(context_settings={'help_option_names': ['-h', '--help']}, |
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prompt=f"{prog_name}> ") |
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@click.option('--config', '-c', type=click.Path(exists=True), |
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default='{}/seqvault.rc'.format(click.get_app_dir('seqvault')), |
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help="Path to the configuration file.") |
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@click.option('--driver', metavar="DRIVER", |
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help="Specify the database driver.") |
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@click.option('--host', '-H', metavar="HOST", |
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help="Specify the database host.") |
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@click.option('--user', '-u', metavar="USER", |
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help="Specify the database user name.") |
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@click.option('--name', '-n', metavar="NAME", |
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help="Specify the database name.") |
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@click.version_option(version=__version__, message=prog_notice) |
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@click.pass_context |
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def seqvault(ctx, config, driver, host, user, name): |
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"""Access a BioSQL sequence database.""" |
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cfg = ConfigParser() |
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cfg.add_section('Server') |
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cfg.set('Server', 'driver', 'psycopg2') |
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cfg.set('Server', 'host', 'localhost') |
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cfg.set('Server', 'user', 'seqvault') |
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cfg.set('Server', 'database', 'seqvault') |
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cfg.read(config) |
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if driver: |
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cfg.set('Server', 'driver', driver) |
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if host: |
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cfg.set('Server', 'host', host) |
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if user: |
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cfg.set('Server', 'user', user) |
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if name: |
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cfg.set('Server', 'database', name) |
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server = open_database(**dict(cfg.items('Server'))) |
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server.__class__ = vault.Server |
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ctx.obj = server |
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@seqvault.command() |
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@click.pass_obj |
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def listdb(server): |
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"""List databases. |
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This command prints information about the databases available on the |
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server. |
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""" |
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print("NAME PREFIX ENTRIES") |
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for db in server.values(): |
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print(f"{db.name:16}{db.get_prefix():8}{len(db)}") |
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@seqvault.command() |
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@click.argument('database', callback=_get_database) |
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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 output.") |
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def export(database, output): |
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"""Export sequences from a database. |
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This command exports all the sequences contained in the specified |
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DATABASE. |
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""" |
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write_usa(database.get_unique_Seqs(), output) |
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@seqvault.command('list') |
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@click.argument('database', callback=_get_database) |
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@click.option('--all', '-a', 'show_all', is_flag=True, |
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help="Include obsolete sequences.") |
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def list_records(database, show_all): |
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"""List database contents. |
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This command list all the sequences contained in the specified |
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DATABASE. |
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""" |
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if show_all: |
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entries = database.values() |
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else: |
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entries = database.get_unique_seqs() |
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for entry in entries: |
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print(f"{entry.name:17}{entry.id:15}{entry.description}") |
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@seqvault.command() |
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@click.argument('accessions', nargs=-1) |
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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 output.") |
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@click.pass_obj |
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def get(server, accessions, output): |
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"""Extract sequences from a database. |
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This command extract sequences with the specified ACCESSIONS from |
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any database on the server. |
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""" |
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records = [] |
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for accession in accessions: |
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records.append(server.get_Seq_by_accession(accession)) |
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if len(records) > 0: |
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write_usa(records, output) |
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@seqvault.command() |
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@click.argument('database', callback=_get_database) |
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@click.argument('sequences', nargs=-1) |
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@click.pass_obj |
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def add(server, database, sequences): |
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"""Add sequences to a database. |
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This command imports the specified SEQUENCES (as USAs) into the |
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specified DATABASE. |
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""" |
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try: |
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records = [] |
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for usa in sequences: |
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records.extend(read_usa(usa)) |
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except Exception as e: |
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raise click.ClickException(f"Cannot read sequences: {e}") |
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try: |
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database.load(records) |
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server.commit() |
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except Exception as e: |
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raise click.ClickException(f"Cannot load sequences: {e}") |
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# Extract newly inserted records and write them out |
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extracted = [] |
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try: |
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for record in records: |
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rid = str(record.annotations['gi']) |
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extracted.append(database.lookup(gi=rid)) |
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write_usa(extracted, 'genbank::stdout') |
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except Exception as e: |
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raise click.ClickException(f"Cannot write sequences: {e}") |
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@seqvault.command() |
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@click.argument('accession') |
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@click.option('--editor', '-e', default='/usr/bin/gvim --nofork', |
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help="The editor command to use.") |
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@click.option('--read-only', '-r', is_flag=True, |
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help="View the record only, do not store back any change.") |
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@click.pass_obj |
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def edit(server, accession, editor, read_only): |
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"""Edit a record. |
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This command extracts the sequence with the specified ACCESSION |
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number and fires up an external editor to view and edit the |
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sequence before saving any changes back to the database. |
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""" |
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record = server.get_Seq_by_accession(accession) |
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tmpfile = NamedTemporaryFile(mode='w', delete=False) |
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SeqIO.write(record, tmpfile, 'genbank') |
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tmpfile.close() |
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if not read_only: |
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h1 = md5(open(tmpfile.name, 'rb').read()).hexdigest() |
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command = editor.split() |
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command.append(tmpfile.name) |
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run(command) |
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if not read_only: |
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h2 = md5(open(tmpfile.name, 'rb').read()).hexdigest() |
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if h1 != h2: |
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new_record = SeqIO.read(tmpfile.name, 'genbank') |
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db = server.get_database_by_prefix(new_record.id[:3]) |
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db.load([new_record]) |
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server.commit() |
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extracted = db.lookup(gi=str(new_record.annotations['gi'])) |
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write_usa([extracted], 'genbank::stdout') |
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if __name__ == '__main__': |
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try: |
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seqvault() |
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except Exception as e: |
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print(f"seqvault: Unexpected error: {e}", file=sys.stderr) |
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