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#! python
# encoding: utf-8
# Wellcome Trust Sanger Institute and Imperial College London
# Copyright (C) 2020 Imperial College London and Imperial College London
#
# 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 2
# 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, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#
# Generic imports
import sys
import os
import argparse
import subprocess
from multiprocessing import Pool
from functools import partial
from shutil import which
# command line parsing
def get_options():
parser = argparse.ArgumentParser(description='Generate a ska2 alignment from a list '
'of assemblies',
prog='generate_ska_alignment')
# input options
parser.add_argument('--reference',
help = 'Name of reference sequence to use for alignment',
required = True)
parser.add_argument('--input',
help = 'List of sequence data; one row per isolate, with first column being the isolate name',
default = None,
required = False)
parser.add_argument('--out',
help = 'Name of output alignment',
required = True)
parser.add_argument('--k',
help = 'Split kmer size',
type = int,
default = 17)
parser.add_argument('--threads',
help = 'Number of threads to use',
type = int,
default = 1)
parser.add_argument('--no-cleanup',
help = 'Do not remove intermediate files',
action = 'store_true',
default = False)
return parser.parse_args()
def map_fasta_sequence(seq, k = None, names = None):
subprocess.check_output('ska fasta -o ' + names[seq] + ' -k ' + str(k) + ' ' + seq,
shell = True)
def map_fastq_sequence(read_pair, k = None, names = None):
subprocess.check_output('ska fastq -o ' + names[read_pair[0]] + ' -k ' + str(k) + ' ' + \
read_pair[0] + ' ' + read_pair[1],
shell = True)
def ska_map_sequences(seq, k = None, ref = None):
subprocess.check_output('ska map -o ' + seq + '.map -k ' + str(k) + ' -r ' + ref + \
' ' + seq + '.skf',
shell = True)
# main code
if __name__ == "__main__":
__spec__ = None
# Get command line options
args = get_options()
# Check if ska is installed
if which('ska') is None:
sys.stderr.write('ska2 cannot be found on PATH; install with "conda install ska2"')
sys.exit(1)
# Check if k value is acceptable:
if (args.k % 2) == 0 or args.k < 5 or args.k > 63:
sys.stderr.write('k must be odd and between 5 and 63\n')
sys.exit(1)
# Build ska sketch
subprocess.check_output('ska build -o ' + args.out + ' -k ' + str(args.k) + \
' -f ' + args.input + ' --threads ' + str(args.threads),
shell = True)
# Remove repetitive sequences
if not os.path.exists(args.reference):
sys.stderr.write('Reference file missing: ' + args.reference + '\n')
sys.exit(1)
# Run ska mapping
if os.path.exists(args.out + '.skf'):
tmp_aln = os.path.join(os.path.dirname(args.out), 'tmp.' + os.path.basename(args.out))
subprocess.check_output('ska map -o ' + tmp_aln + ' --threads ' + str(args.threads) + ' --repeat-mask ' + \
args.reference + ' ' + args.out + '.skf',
shell = True)
else:
sys.stderr.write('ska building failed\n')
sys.exit(1)
# Clean alignment to prep for Gubbins
subprocess.check_output('gubbins_alignment_checker.py --aln ' + tmp_aln + ' --out-aln ' + args.out + \
' --out ' + args.out + '.csv',
shell = True)
sys.stderr.write("Completed generating alignment with ska2 (https://github.com/bacpop/ska.rust)\nPlease cite https://doi.org/10.1101/2024.03.25.586631\n")
# Clean up
if not args.no_cleanup:
subprocess.check_output('rm ' + args.out + '.skf ' + tmp_aln,
shell = True)
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