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#!/usr/bin/env python
#
# Copyright 2015, Daehwan Kim <infphilo@gmail.com>
#
# This file is part of HISAT 2.
#
# HISAT 2 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.
#
# HISAT 2 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 HISAT 2. If not, see <http://www.gnu.org/licenses/>.
#
import sys, os, subprocess, re, threading
import inspect
import random
import glob
from argparse import ArgumentParser, FileType
import hisatgenotype_typing_common as typing_common
"""
"""
class myThread(threading.Thread):
def __init__(self,
lock,
paths,
reference_type,
region_list,
num_editdist,
max_sample,
assembly,
out_dir,
verbose):
threading.Thread.__init__(self)
self.lock = lock
self.paths = paths
self.reference_type = reference_type
self.region_list = region_list
self.num_editdist = num_editdist
self.max_sample = max_sample
self.assembly = assembly
self.out_dir = out_dir
self.verbose = verbose
def run(self):
global work_idx
while True:
self.lock.acquire()
my_work_idx = work_idx
work_idx += 1
self.lock.release()
if my_work_idx >= len(self.paths) or \
my_work_idx >= self.max_sample:
return
worker(self.lock,
self.paths[my_work_idx],
self.reference_type,
self.region_list,
self.num_editdist,
self.assembly,
self.out_dir,
self.verbose)
"""
"""
work_idx = 0
def worker(lock,
path,
reference_type,
region_list,
num_editdist,
assembly,
out_dir,
verbose):
fq_name = path.split('/')[-1]
read_dir = '/'.join(path.split('/')[:-1])
genome = fq_name.split('.')[0]
if not fq_name.endswith("extracted.1.fq.gz"):
return
read_basename = fq_name[:fq_name.find("extracted.1.fq.gz")]
read_fname_1, read_fname_2 = "%s/%sextracted.1.fq.gz" % \
(read_dir, read_basename), "%s/%sextracted.2.fq.gz" % (read_dir, read_basename)
if not os.path.exists(read_fname_1) or not os.path.exists(read_fname_2):
return
lock.acquire()
print >> sys.stderr, genome
lock.release()
for family, loci in region_list.items():
test_hla_cmd = ["hisatgenotype_locus.py",
"--base", family]
if len(loci) > 0:
test_hla_cmd += ["--locus", ','.join(loci)]
test_hla_cmd += ["--num-editdist", str(num_editdist)]
test_hla_cmd += ["-1", read_fname_1, "-2", read_fname_2]
test_hla_cmd += ["--assembly-base"]
if out_dir != "":
test_hla_cmd += ["%s/%s" % (out_dir, genome)]
else:
test_hla_cmd += [genome]
if assembly:
test_hla_cmd += ["--assembly"]
if verbose:
lock.acquire()
print >> sys.stderr, ' '.join(test_hla_cmd)
lock.release()
proc = subprocess.Popen(test_hla_cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
test_alleles = set()
output_list = []
for line in proc.stdout:
line = line.strip()
if line.find("abundance") == -1:
continue
rank, _, allele, _, abundance = line.split()
output_list.append([allele, abundance[:-2]])
lock.acquire()
for output in output_list:
allele, abundance = output
print >> sys.stdout, "%s\t%s\t%s" % (genome, allele, abundance)
sys.stdout.flush()
lock.release()
"""
"""
def genotyping(read_dir,
reference_type,
region_list,
num_editdist,
nthreads,
max_sample,
assembly,
out_dir,
verbose):
for database_name in region_list:
# Extract variants, backbone sequence, and other sequeces
typing_common.extract_database_if_not_exists(database_name,
[]) # locus_list
# Build HISAT2's graph index
typing_common.build_index_if_not_exists(database_name,
"hisat2",
"graph",
1, # threads
verbose)
if not os.path.exists(read_dir):
print >> sys.stderr, "Error: %s does not exist." % read_dir
sys.exit(1)
if out_dir != "" and not os.path.exists(out_dir):
os.mkdir(out_dir)
# fastq files
fq_fnames = glob.glob("%s/*.extracted.1.fq.gz" % read_dir)
lock = threading.Lock()
threads = []
for t in range(nthreads):
thread = myThread(lock,
fq_fnames,
reference_type,
region_list,
num_editdist,
max_sample,
assembly,
out_dir,
verbose)
thread.start()
threads.append(thread)
for thread in threads:
thread.join()
"""
"""
if __name__ == '__main__':
parser = ArgumentParser(
description='genotyping on many samples')
parser.add_argument("--reference-type",
dest="reference_type",
type=str,
default="gene",
help="Reference type: gene, chromosome, and genome (default: gene)")
parser.add_argument("--region-list",
dest="region_list",
type=str,
default="",
help="A comma-separated list of regions (default: empty)")
parser.add_argument('--read-dir',
dest="read_dir",
type=str,
default="",
help='read directory (e.g. read_input)')
parser.add_argument("--num-editdist",
dest="num_editdist",
type=int,
default=2,
help="Maximum number of mismatches per read alignment to be considered (default: 2)")
parser.add_argument("-p", "--threads",
dest="threads",
type=int,
default=1,
help="Number of threads")
parser.add_argument('--assembly',
dest='assembly',
action='store_true',
help='Perform assembly')
parser.add_argument("--max-sample",
dest="max_sample",
type=int,
default=sys.maxint,
help="Number of samples to be analyzed (default: sys.maxint)")
parser.add_argument("--out-dir",
dest="out_dir",
type=str,
default="",
help='Output directory (default: (empty))')
parser.add_argument('-v', '--verbose',
dest='verbose',
action='store_true',
help='also print some statistics to stderr')
args = parser.parse_args()
if args.read_dir == "":
print >> sys.stderr, "Error: please specify --read-dir."
sys.exit(1)
if not args.reference_type in ["gene", "chromosome", "genome"]:
print >> sys.stderr, "Error: --reference-type (%s) must be one of gene, chromosome, and genome." % (args.reference_type)
sys.exit(1)
region_list = {}
if args.region_list != "":
for region in args.region_list.split(','):
region = region.split('.')
if len(region) < 1 or len(region) > 2:
print >> sys.stderr, "Error: --region-list is incorrectly formatted."
sys.exit(1)
family = region[0].lower()
if len(region) == 2:
locus_name = region[1].upper()
if family not in region_list:
region_list[family] = set()
if len(region) == 2:
region_list[family].add(locus_name)
genotyping(args.read_dir,
args.reference_type,
region_list,
args.num_editdist,
args.threads,
args.max_sample,
args.assembly,
args.out_dir,
args.verbose)
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