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encode_task_macs2_signal_track_chip.py
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#!/usr/bin/env python
# ENCODE DCC MACS2 signal track wrapper
# Author: Jin Lee ([email protected])
import sys
import os
import argparse
from encode_lib_common import (
get_num_lines, log, ls_l, mkdir_p, rm_f, run_shell_cmd, strip_ext_ta,
get_gnu_sort_param,
)
from encode_lib_genomic import (
subsample_ta_se, subsample_ta_pe,
)
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE DCC MACS2 signal track',
description='')
parser.add_argument('tas', type=str, nargs='+',
help='Path for TAGALIGN file (first) and control TAGALIGN file (second; optional).')
parser.add_argument('--fraglen', type=int, required=True,
help='Fragment length.')
parser.add_argument('--shift', type=int, default=0,
help='macs2 callpeak --shift.')
parser.add_argument('--chrsz', type=str,
help='2-col chromosome sizes file.')
parser.add_argument('--gensz', type=str,
help='Genome size (sum of entries in 2nd column of \
chr. sizes file, or hs for human, ms for mouse).')
parser.add_argument('--pval-thresh', default=0.01, type=float,
help='P-Value threshold.')
parser.add_argument('--ctl-subsample', default=0, type=int,
help='Subsample control to this read depth '
'(0: no subsampling).')
parser.add_argument('--ctl-paired-end', action="store_true",
help='Paired-end control TA.')
parser.add_argument('--mem-gb', type=float, default=4.0,
help='Max. memory for this job in GB. '
'This will be used to determine GNU sort -S (defaulting to 0.5 of this value). '
'It should be total memory for this task (not memory per thread).')
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()
if len(args.tas) == 1:
args.tas.append('')
log.setLevel(args.log_level)
log.info(sys.argv)
return args
def macs2_signal_track(ta, ctl_ta, chrsz, gensz, pval_thresh, shift, fraglen,
ctl_subsample, ctl_paired_end, mem_gb, out_dir):
basename_ta = os.path.basename(strip_ext_ta(ta))
if ctl_ta:
if ctl_subsample:
if ctl_paired_end:
ctl_ta = subsample_ta_pe(
ctl_ta, ctl_subsample,
non_mito=False, mito_chr_name=None, r1_only=False,
out_dir=out_dir)
else:
ctl_ta = subsample_ta_se(
ctl_ta, ctl_subsample,
non_mito=False, mito_chr_name=None,
out_dir=out_dir)
basename_ctl_ta = os.path.basename(strip_ext_ta(ctl_ta))
basename_prefix = '{}_x_{}'.format(basename_ta, basename_ctl_ta)
if len(basename_prefix) > 200: # UNIX cannot have len(filename) > 255
basename_prefix = '{}_x_control'.format(basename_ta)
else:
basename_prefix = basename_ta
prefix = os.path.join(out_dir, basename_prefix)
fc_bigwig = '{}.fc.signal.bigwig'.format(prefix)
pval_bigwig = '{}.pval.signal.bigwig'.format(prefix)
# temporary files
fc_bedgraph = '{}.fc.signal.bedgraph'.format(prefix)
fc_bedgraph_srt = '{}.fc.signal.srt.bedgraph'.format(prefix)
pval_bedgraph = '{}.pval.signal.bedgraph'.format(prefix)
pval_bedgraph_srt = '{}.pval.signal.srt.bedgraph'.format(prefix)
temp_files = []
run_shell_cmd(
' macs2 callpeak '
'-t {ta} {ctl_param} -f BED -n {prefix} -g {gensz} -p {pval_thresh} '
'--nomodel --shift {shiftsize} --extsize {extsize} --keep-dup all -B --SPMR'.format(
ta=ta,
ctl_param='-c {ctl_ta}'.format(ctl_ta=ctl_ta) if ctl_ta else '',
prefix=prefix,
gensz=gensz,
pval_thresh=pval_thresh,
shiftsize=0,
extsize=fraglen,
)
)
run_shell_cmd(
'macs2 bdgcmp -t "{prefix}_treat_pileup.bdg" '
'-c "{prefix}_control_lambda.bdg" '
'--o-prefix "{prefix}" -m FE '.format(
prefix=prefix,
)
)
run_shell_cmd(
'bedtools slop -i "{prefix}_FE.bdg" -g {chrsz} -b 0 | '
'awk \'{{if ($3 != -1) print $0}}\' |'
'bedClip stdin {chrsz} {fc_bedgraph}'.format(
prefix=prefix,
chrsz=chrsz,
fc_bedgraph=fc_bedgraph,
)
)
# sort and remove any overlapping regions in bedgraph by comparing two lines in a row
run_shell_cmd(
'LC_COLLATE=C sort -k1,1 -k2,2n {sort_param} {fc_bedgraph} | '
'awk \'BEGIN{{OFS="\\t"}}{{if (NR==1 || NR>1 && (prev_chr!=$1 || '
'prev_chr==$1 && prev_chr_e<=$2)) '
'{{print $0}}; prev_chr=$1; prev_chr_e=$3;}}\' > {fc_bedgraph_srt}'.format(
sort_param=get_gnu_sort_param(mem_gb * 1024 ** 3, ratio=0.5),
fc_bedgraph=fc_bedgraph,
fc_bedgraph_srt=fc_bedgraph_srt
)
)
rm_f(fc_bedgraph)
run_shell_cmd(
'bedGraphToBigWig {fc_bedgraph_srt} {chrsz} {fc_bigwig}'.format(
fc_bedgraph_srt=fc_bedgraph_srt,
chrsz=chrsz,
fc_bigwig=fc_bigwig,
)
)
rm_f(fc_bedgraph_srt)
# sval counts the number of tags per million in the (compressed) BED file
sval = float(get_num_lines(ta))/1000000.0
run_shell_cmd(
'macs2 bdgcmp -t "{prefix}_treat_pileup.bdg" '
'-c "{prefix}_control_lambda.bdg" '
'--o-prefix {prefix} -m ppois -S {sval}'.format(
prefix=prefix,
sval=sval,
)
)
run_shell_cmd(
'bedtools slop -i "{prefix}_ppois.bdg" -g {chrsz} -b 0 | '
'awk \'{{if ($3 != -1) print $0}}\' |'
'bedClip stdin {chrsz} {pval_bedgraph}'.format(
prefix=prefix,
chrsz=chrsz,
pval_bedgraph=pval_bedgraph,
)
)
# sort and remove any overlapping regions in bedgraph by comparing two lines in a row
run_shell_cmd(
'LC_COLLATE=C sort -k1,1 -k2,2n {sort_param} {pval_bedgraph} | '
'awk \'BEGIN{{OFS="\\t"}}{{if (NR==1 || NR>1 && (prev_chr!=$1 || '
'prev_chr==$1 && prev_chr_e<=$2)) '
'{{print $0}}; prev_chr=$1; prev_chr_e=$3;}}\' > {pval_bedgraph_srt}'.format(
sort_param=get_gnu_sort_param(mem_gb * 1024 ** 3, ratio=0.5),
pval_bedgraph=pval_bedgraph,
pval_bedgraph_srt=pval_bedgraph_srt,
)
)
rm_f(pval_bedgraph)
run_shell_cmd(
'bedGraphToBigWig {pval_bedgraph_srt} {chrsz} {pval_bigwig}'.format(
pval_bedgraph_srt=pval_bedgraph_srt,
chrsz=chrsz,
pval_bigwig=pval_bigwig
)
)
rm_f(pval_bedgraph_srt)
# remove temporary files
temp_files.append("{prefix}_*".format(prefix=prefix))
rm_f(temp_files)
return fc_bigwig, pval_bigwig
def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
log.info('Calling peaks and generating signal tracks with MACS2...')
fc_bigwig, pval_bigwig = macs2_signal_track(
args.tas[0], args.tas[1], args.chrsz, args.gensz, args.pval_thresh,
args.shift, args.fraglen, args.ctl_subsample, args.ctl_paired_end,
args.mem_gb, args.out_dir)
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
if __name__ == '__main__':
main()