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encode_task_trim_adapter.py
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#!/usr/bin/env python
# ENCODE DCC adapter trimmer wrapper
# Author: Jin Lee ([email protected])
import sys
import os
import argparse
import copy
from detect_adapter import detect_most_likely_adapter
from encode_lib_common import (
copy_f_to_dir, log, ls_l, mkdir_p, read_tsv, rm_f,
run_shell_cmd, strip_ext_fastq)
from encode_task_merge_fastq import merge_fastqs
def parse_arguments(debug=False):
parser = argparse.ArgumentParser(prog='ENCODE DCC adapter trimmer.',
description='')
parser.add_argument('fastqs', nargs='+', type=str,
help='TSV file path or list of FASTQs. \
FASTQs must be compressed with gzip (with .gz). \
Use TSV for multiple fastqs to be merged later. \
row=merge_id, col=end_id).')
parser.add_argument(
'--auto-detect-adapter', action='store_true',
help='Automatically detect/trim adapters \
(supported system: Illumina, Nextera and smallRNA).')
parser.add_argument(
'--cutadapt-param', type=str, default='-e 0.1 -m 5',
help='Parameters for cutadapt '
'(default: -e 0.1 -m 5; err_rate=0.1, min_trim_len=5).')
parser.add_argument(
'--adapter', type=str,
help='One adapter to use for all fastqs. '
'This will override individual adapters defined in --adapters.')
parser.add_argument(
'--adapters', nargs='+', type=str,
help='TSV file path or list of adapter strings. '
'Use TSV for multiple fastqs to be merged later. '
'row=merge_id, col=end_id).')
parser.add_argument('--paired-end', action="store_true",
help='Paired-end FASTQs.')
parser.add_argument('--nth', type=int, default=1,
help='Number of threads to parallelize.')
parser.add_argument('--out-dir', default='', type=str,
help='Output directory.')
parser.add_argument('--log-level', default='INFO',
choices=['NOTSET', 'DEBUG', 'INFO',
'WARNING', 'CRITICAL', 'ERROR',
'CRITICAL'],
help='Log level')
args = parser.parse_args()
# parse fastqs command line
if args.fastqs[0].endswith('.gz') or args.fastqs[0].endswith('.fastq') or \
args.fastqs[0].endswith('.fq'): # it's fastq
args.fastqs = [[f] for f in args.fastqs] # make it a matrix
else: # it's TSV
args.fastqs = read_tsv(args.fastqs[0])
# parse --adapters command line
if args.adapters:
if os.path.exists(args.adapters[0]): # it's TSV
args.adapters = read_tsv(args.adapters[0])
else:
args.adapters = [[a] for a in args.adapters] # make it a matrix
# if adapter not given
if args.adapter or not args.adapters: # fill empty string in adapter list
args.adapters = copy.deepcopy(args.fastqs)
for i, adapters in enumerate(args.adapters):
for j, adapter in enumerate(adapters):
args.adapters[i][j] = args.adapter if args.adapter else ''
# check if fastqs, adapers have same/correct dimension
if len(args.adapters) != len(args.fastqs):
raise argparse.ArgumentTypeError(
'fastqs and adapters dimension mismatch.')
for i, fastqs in enumerate(args.fastqs):
if args.paired_end and len(fastqs) != 2:
raise argparse.ArgumentTypeError(
'Need 2 fastqs per replicate for paired end.')
if not args.paired_end and len(fastqs) != 1:
raise argparse.ArgumentTypeError(
'Need 1 fastq per replicate for single end.')
if len(fastqs) != len(args.adapters[i]):
raise argparse.ArgumentTypeError(
'fastqs and adapters dimension mismatch.')
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def trim_adapter_se(fastq, adapter, adapter_for_all, cutadapt_param, out_dir):
if adapter:
prefix = os.path.join(out_dir,
os.path.basename(strip_ext_fastq(fastq)))
trimmed = '{}.trim.fastq.gz'.format(prefix)
cmd = 'cutadapt {} -a {} {} | gzip -nc > {}'.format(
cutadapt_param,
adapter_for_all if adapter_for_all else adapter,
fastq,
trimmed)
run_shell_cmd(cmd)
return trimmed
else:
return copy_f_to_dir(fastq, out_dir)
def trim_adapter_pe(fastq1, fastq2, adapter1, adapter2, adapter_for_all,
cutadapt_param, out_dir):
if adapter1 and adapter2:
prefix1 = os.path.join(out_dir,
os.path.basename(strip_ext_fastq(fastq1)))
prefix2 = os.path.join(out_dir,
os.path.basename(strip_ext_fastq(fastq2)))
trimmed1 = '{}.trim.fastq.gz'.format(prefix1)
trimmed2 = '{}.trim.fastq.gz'.format(prefix2)
cmd = 'cutadapt {} -a {} -A {} {} {} -o {} -p {}'.format(
cutadapt_param,
adapter_for_all if adapter_for_all else adapter1,
adapter_for_all if adapter_for_all else adapter2,
fastq1, fastq2,
trimmed1, trimmed2)
run_shell_cmd(cmd)
return [trimmed1, trimmed2]
else:
fq1 = copy_f_to_dir(fastq1, out_dir)
fq2 = copy_f_to_dir(fastq2, out_dir)
return [fq1, fq2]
def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
# declare temp arrays
temp_files = [] # files to deleted later at the end
log.info('Detecting adapters...')
for i in range(len(args.fastqs)):
# for each fastq to be merged later
log.info('Detecting adapters for merge_id={}...'.format(
i+1))
fastqs = args.fastqs[i] # R1 and R2
adapters = args.adapters[i]
if args.paired_end:
if not args.adapter and args.auto_detect_adapter and \
not (adapters[0] and adapters[1]):
args.adapters[i][0] = detect_most_likely_adapter(fastqs[0])
args.adapters[i][1] = detect_most_likely_adapter(fastqs[1])
log.info('Detected adapters for merge_id={}, '
'R1: {}, R2: {}'.format(
i+1, args.adapters[i][0], args.adapters[i][1]))
else:
if not args.adapter and args.auto_detect_adapter and \
not adapters[0]:
args.adapters[i][0] = detect_most_likely_adapter(fastqs[0])
log.info('Detected adapter for merge_id={}, R1: {}'.format(
i+1, args.adapters[i][0]))
log.info('Trimming adapters...')
trimmed_fastqs_R1 = []
trimmed_fastqs_R2 = []
for i in range(len(args.fastqs)):
# for each fastq to be merged later
fastqs = args.fastqs[i] # R1 and R2
adapters = args.adapters[i]
if args.paired_end:
fastqs = trim_adapter_pe(
fastqs[0], fastqs[1],
adapters[0], adapters[1],
args.adapter,
args.cutadapt_param,
args.out_dir)
trimmed_fastqs_R1.append(fastqs[0])
trimmed_fastqs_R2.append(fastqs[1])
else:
fastq = trim_adapter_se(
fastqs[0],
adapters[0],
args.adapter,
args.cutadapt_param,
args.out_dir)
trimmed_fastqs_R1.append(fastq)
log.info('Merging fastqs...')
log.info('R1 to be merged: {}'.format(trimmed_fastqs_R1))
merge_fastqs(trimmed_fastqs_R1, 'R1', args.out_dir)
if args.paired_end:
log.info('R2 to be merged: {}'.format(trimmed_fastqs_R2))
merge_fastqs(trimmed_fastqs_R2, 'R2', args.out_dir)
temp_files.extend(trimmed_fastqs_R1)
temp_files.extend(trimmed_fastqs_R2)
log.info('Removing temporary files...')
rm_f(temp_files)
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
if __name__ == '__main__':
main()