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rextraccnt
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#!/usr/bin/env python3
#
# Copyright (C) 2017–2024, Jose Manuel Martí Martínez
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
#
"""
Extract entries from fasta file formatted with accessions as NCBI nt database.
"""
# pylint: disable=no-name-in-module, not-an-iterable
import argparse
import gzip
import os
import sys
import time
from collections import Counter
from typing import Callable, List, Set, TextIO
from Bio import SeqIO
from recentrifuge import __version__, __author__, __date__
from recentrifuge.config import Filename, Id, GZEXT
from recentrifuge.config import LICENSE, NODES_FILE, NAMES_FILE, TAXDUMP_PATH
from recentrifuge.config import gray, red, green, cyan, magenta, blue, yellow
from recentrifuge.rank import Rank, Ranks, TaxLevels
from recentrifuge.taxonomy import Taxonomy
from recentrifuge.trees import TaxTree
# Internal constants
MAX_LENGTH_TAXID_LIST = 32
def main():
"""Main entry point to script."""
def configure_parser():
"""Argument Parser Configuration"""
parser = argparse.ArgumentParser(
description='Extraction from fasta with accessions as NCBI nt DB',
epilog=f'%(prog)s - Release {__version__} - {__date__}' + LICENSE,
formatter_class=argparse.RawDescriptionHelpFormatter
)
parser.add_argument(
'-d', '--debug',
action='store_true',
help='increase output verbosity and perform additional checks'
)
parser.add_argument(
'-l', '--limit',
action='store',
metavar='NUMBER',
type=int,
default=None,
help=('limit of nt DB entries to extract; '
'default: no limit')
)
parser.add_argument(
'-e', '--entrymax',
action='store',
metavar='NUMBER',
type=int,
default=None,
help=('maximum number of nt DB entries to search for the taxa; '
'default: no maximum')
)
parser.add_argument(
'-n', '--nodespath',
action='store',
metavar='PATH',
default=TAXDUMP_PATH,
help=('path for the nodes information files '
'(nodes.dmp and names.dmp from NCBI)')
)
parser_selection = parser.add_argument_group(
'selection',
'Selection of reads based on the taxonomy')
parser_selection.add_argument(
'-i', '--include',
action='append',
metavar='TAXID',
type=Id,
default=[],
help=('NCBI taxid code to include a taxon and all underneath ' +
'(multiple -i is available to include several taxid); ' +
'by default all the taxa is considered for inclusion')
)
parser_selection.add_argument(
'-x', '--exclude',
action='append',
metavar='TAXID',
type=Id,
default=[],
help=('NCBI taxid code to exclude a taxon and all underneath ' +
'(multiple -x is available to exclude several taxid)')
)
parser_in = parser.add_argument_group(
'input', 'Define input files')
parser.add_argument(
'-m', '--mapfile',
action='store',
metavar='FILE',
required=True,
help='Mapping (accession to taxid) file'
)
parser_in.add_argument(
'-f', '--ntfastafile',
action='store',
metavar='FILE',
default=None,
help='NCBI nt formatted FASTA file'
)
parser.add_argument(
'-c', '--compress',
action='store_true',
help='Output FASTA file will be gzipped'
)
parser.add_argument(
'-V', '--version',
action='version',
version=f'%(prog)s release {__version__} ({__date__})'
)
return parser
def check_debug():
"""Check debugging mode"""
if args.debug:
print(blue('INFO:'), gray('Debugging mode activated'))
print(blue('INFO:'), gray('Active parameters:'))
for key, val in vars(args).items():
if val is not None and val is not False and val != []:
print(gray(f'\t{key} ='), f'{val}')
def is_gzipped(fpath: Filename):
"""Check if a file exists and is gzipped"""
try:
with open(fpath, 'rb') as ftest:
return ftest.read(2) == b'\x1f\x8b'
except FileNotFoundError:
return False
def build_out_filename(fname: Filename) -> Filename:
"""Auxiliary function to properly build the output filenames.
Args:
fname: Complete filename of the FASTA input file (gzipped or not)
Returns: Filename of the rextraccnted FASTA output file
"""
# Get filename and extension, accounting for 2 extensions,
# typically found in filename.fname.gz
fastq_filename, fastq_ext = os.path.splitext(fname)
if fastq_ext.casefold() == GZEXT:
fastq_filename, fastq_ext = os.path.splitext(fastq_filename)
if args.compress and not fastq_ext.casefold().endswith(GZEXT):
fastq_ext += GZEXT
output_list: List[str] = [fastq_filename, '_rxnt']
if including:
output_list.append('_incl')
output_list.extend('_'.join(including))
if excluding:
output_list.append('_excl')
output_list.extend('_'.join(excluding))
output_list.append(fastq_ext)
return Filename(''.join(output_list))
# timing initialization
start_time: float = time.time()
# Program header
print(f'\n=-= {sys.argv[0]} =-= v{__version__} - {__date__}'
f' =-= by {__author__} =-=\n')
sys.stdout.flush()
# Parse arguments
argparser = configure_parser()
args = argparser.parse_args()
mapfile = args.mapfile
nodesfile: Filename = Filename(os.path.join(args.nodespath, NODES_FILE))
namesfile: Filename = Filename(os.path.join(args.nodespath, NAMES_FILE))
excluding: Set[Id] = set(args.exclude)
including: Set[Id] = set(args.include)
ntfile: Filename = args.ntfastafile
check_debug()
# Load NCBI nodes, names and build children
ncbi: Taxonomy = Taxonomy(nodesfile, namesfile, None,
False, excluding, including)
# Build taxonomy tree
print(gray('Building taxonomy tree...'), end='')
sys.stdout.flush()
tree = TaxTree()
tree.grow(ontology=ncbi, look_ancestors=False)
print(green(' OK!'))
# Get the taxa
print(gray('Filtering taxa...'), end='')
sys.stdout.flush()
ranks: Ranks = Ranks({})
tree.get_taxa(ranks=ranks,
include=including,
exclude=excluding)
print(green(' OK!'))
taxids: Set[Id] = set(ranks)
taxlevels: TaxLevels = Rank.ranks_to_taxlevels(ranks)
num_taxlevels = Counter({rank: len(taxlevels[rank])
for rank in taxlevels})
num_taxlevels = +num_taxlevels
# Statistics about including taxa
print(f' {len(taxids)}', gray('taxid selected in '), end='')
print(f'{len(num_taxlevels)}', gray('different taxonomic levels:'))
for rank in num_taxlevels:
print(f' Number of different {rank}: {num_taxlevels[rank]}')
assert taxids, red('ERROR! No taxids to search for!')
# Get the accessions from the mapping file
accessions: List[str] = []
num_maps: int = 0
# timing initialization
start_time_load: float = time.perf_counter()
print(gray('Parsing acc->tid mapping file'), mapfile,
gray('...\nMmaps: '), end='')
sys.stdout.flush()
try:
with open(mapfile, 'rt', newline=None) as file:
for num_maps, mapp in enumerate(file):
acc, tid = mapp.strip().split(maxsplit=1)
if not num_maps % 10_000_000:
print(f'{num_maps // 1_000_000:_d}', end='')
sys.stdout.flush()
elif not num_maps % 1_000_000:
print('_', end='')
sys.stdout.flush()
if tid not in taxids:
continue
else:
accessions.append(acc)
except (FileNotFoundError, ValueError):
raise Exception(red('ERROR!') + 'Cannot process "' + mapfile + '"')
print(green(' OK!'))
# Basic accessions statistics (or exit if no matching read)
print(gray(' Parse elapsed time: ') +
f'{time.perf_counter() - start_time_load:.3g}' + gray(' sec'))
if num_maps:
print(gray(f' Selected accessions: '), f'{len(accessions):_d}\t',
gray('('), f'{len(accessions) / num_maps:.4%}', gray('of DB )'))
sys.stdout.flush()
else:
print(yellow('WARNING!'), 'No matching accession found! Exiting.')
sys.exit(1)
# Deals with NCBI nt formatted FASTA file
records_ids: Set[str] = set(accessions)
extracted: int = 0
nts: int = 0
i: int = 0
print(gray('Processing DB (nt FASTA)'), f'{ntfile}', gray('...\nMseqs: '),
end='')
sys.stdout.flush()
outfilename: Filename = build_out_filename(ntfile)
outhandler: Callable[..., TextIO]
if args.compress:
outhandler = gzip.open
else:
outhandler = open
dbhandler: Callable[..., TextIO]
if is_gzipped(ntfile):
dbhandler = gzip.open
else:
dbhandler = open
try:
with dbhandler(ntfile, 'rt') as nt, \
outhandler(outfilename, 'wt') as out:
for i, rec in enumerate(SeqIO.parse(nt, 'fasta')):
if not records_ids:
print(green(' [all accessions found]'), end='')
break
elif args.entrymax and i >= args.entrymax:
print(yellow(' [stopping by entrymax limit]!'), end='')
break
elif args.limit and extracted >= args.limit:
print(yellow(f' [stopping by {extracted} limit]!'),
end='')
break
elif not i % 1_000_000:
print(f'{i // 1_000_000:_d}', end='')
sys.stdout.flush()
elif not i % 100_000:
print('.', end='')
sys.stdout.flush()
try:
records_ids.remove(rec.id)
except KeyError:
pass
else:
SeqIO.write(rec, out, 'fasta-2line')
nts += len(rec.seq)
extracted += 1
except FileNotFoundError:
raise Exception('\n\033[91mERROR!\033[0m Cannot read nt DB FASTA file')
print(cyan(f' {i / 1e+6:.3g} Mseqs'), green('OK! '))
print(gray('Wrote'), magenta(f'{extracted}'), gray('extracted entries ('),
magenta(f'{nts / 1e+9:.3g}'), gray('Gnucs and'),
magenta(f'{extracted / i:.4%}'), gray('of DB )\n\t'),
magenta('gzipped' if args.compress else ''),
gray('in'), outfilename)
# Timing results
print(gray('Total elapsed time:'), time.strftime(
"%H:%M:%S", time.gmtime(time.time() - start_time)))
if __name__ == '__main__':
main()