encode_task_macs2_signal_track_atac.py

#!/usr/bin/env python

# ENCODE DCC MACS2 signal track wrapper
# Author: Jin Lee (leepc12@gmail.com)

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,
)


def parse_arguments():
    parser = argparse.ArgumentParser(prog='ENCODE DCC MACS2 signal track',
                                     description='')
    parser.add_argument('ta', type=str,
                        help='Path for TAGALIGN file.')
    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('--smooth-win', default=150, type=int,
                        help='Smoothing window size.')
    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()

    log.setLevel(args.log_level)
    log.info(sys.argv)
    return args


def macs2_signal_track(ta, chrsz, gensz, pval_thresh, smooth_win, mem_gb, out_dir):
    prefix = os.path.join(out_dir,
                          os.path.basename(strip_ext_ta(ta)))
    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)

    shiftsize = -int(round(float(smooth_win)/2.0))
    temp_files = []

    run_shell_cmd(
        'macs2 callpeak '
        '-t {ta} -f BED -n {prefix} -g {gensz} -p {pval_thresh} '
        '--shift {shiftsize} --extsize {extsize} '
        '--nomodel -B --SPMR '
        '--keep-dup all --call-summits '.format(
            ta=ta,
            prefix=prefix,
            gensz=gensz,
            pval_thresh=pval_thresh,
            shiftsize=shiftsize,
            extsize=smooth_win,
        )
    )

    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 | '
        '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 | '
        '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.ta,
        args.chrsz,
        args.gensz,
        args.pval_thresh,
        args.smooth_win,
        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()