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...')
npeak, fc_bigwig, pval_bigwig = macs2(args.tas[0], args.tas[1], args.chrsz,
args.gensz, args.pval_thresh,
args.fraglen, args.cap_num_peak,
args.make_signal, args.out_dir)
log.info('Blacklist-filtering peaks...')
bfilt_npeak = blacklist_filter(npeak, args.blacklist,
args.keep_irregular_chr, args.out_dir)
log.info('Checking if output is empty...')
assert_file_not_empty(bfilt_npeak)
log.info('Converting peak to bigbed...')
peak_to_bigbed(bfilt_npeak, 'narrowPeak', args.chrsz,
args.keep_irregular_chr, args.out_dir)
log.info('Converting peak to hammock...')
peak_to_hammock(bfilt_npeak, args.out_dir)
log.info('Shifted FRiP with fragment length...')
frip_qc = frip_shifted(args.tas[0], bfilt_npeak, args.chrsz, args.fraglen,
args.out_dir)
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
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...')
npeak, fc_bigwig, pval_bigwig = macs2(args.ta, args.chrsz, args.gensz,
args.pval_thresh, args.smooth_win,
args.cap_num_peak, args.make_signal,
args.out_dir)
if args.blacklist:
log.info('Blacklist-filtering peaks...')
bfilt_npeak = blacklist_filter(npeak, args.blacklist, False,
args.out_dir)
else:
bfilt_npeak = npeak
if args.ta: # if TAG-ALIGN is given
log.info('FRiP without fragment length...')
frip_qc = frip(args.ta, bfilt_npeak, args.out_dir)
else:
frip_qc = '/dev/null'
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
log.info('Do naive overlap...')
overlap_peak = naive_overlap(args.prefix, args.peak1, args.peak2,
args.peak_pooled, args.peak_type,
args.nonamecheck, args.out_dir)
log.info('Blacklist-filtering peaks...')
bfilt_overlap_peak = blacklist_filter(overlap_peak, args.blacklist, False,
args.out_dir)
log.info('Converting peak to bigbed...')
peak_to_bigbed(bfilt_overlap_peak, args.peak_type, args.chrsz,
args.out_dir)
if args.ta: # if TAG-ALIGN is given
if args.fraglen: # chip-seq
log.info('Shifted FRiP with fragment length...')
frip_qc = frip_shifted(args.ta, bfilt_overlap_peak, args.chrsz,
args.fraglen, args.out_dir)
else: # atac-seq
log.info('FRiP without fragment length...')
frip_qc = frip(args.ta, bfilt_overlap_peak, args.out_dir)
else:
frip_qc = '/dev/null'
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
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 spp...')
rpeak = spp(args.tas[0], args.tas[1],
args.fraglen, args.cap_num_peak, args.nth, args.out_dir)
log.info('Checking if output is empty...')
assert_file_not_empty(rpeak)
log.info('Blacklist-filtering peaks...')
bfilt_rpeak = blacklist_filter(
rpeak, args.blacklist, False, args.out_dir)
log.info('Converting peak to bigbed...')
peak_to_bigbed(bfilt_rpeak, 'regionPeak', args.chrsz, args.out_dir)
log.info('Converting peak to hammock...')
peak_to_hammock(bfilt_rpeak, args.out_dir)
log.info('Shifted FRiP with fragment length...')
frip_qc = frip_shifted( args.tas[0], bfilt_rpeak,
args.chrsz, args.fraglen, args.out_dir)
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
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...')
npeak = macs2(args.ta, args.chrsz, args.gensz, args.pval_thresh,
args.smooth_win, args.cap_num_peak, args.out_dir)
log.info('Blacklist-filtering peaks...')
bfilt_npeak = blacklist_filter(npeak, args.blacklist,
args.keep_irregular_chr, args.out_dir)
log.info('Checking if output is empty...')
assert_file_not_empty(bfilt_npeak)
log.info('Converting peak to bigbed...')
peak_to_bigbed(bfilt_npeak, 'narrowPeak', args.chrsz,
args.keep_irregular_chr, args.out_dir)
log.info('Converting peak to hammock...')
peak_to_hammock(bfilt_npeak, args.keep_irregular_chr, args.out_dir)
if args.ta: # if TAG-ALIGN is given
log.info('FRiP without fragment length...')
frip_qc = frip(args.ta, bfilt_npeak, args.out_dir)
else:
frip_qc = '/dev/null'
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
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 spp...')
rpeak = spp(args.ta, args.ctl_ta, args.fraglen, args.cap_num_peak,
args.nth, args.out_dir)
log.info('Checking if output is empty...')
assert_file_not_empty(rpeak)
if args.blacklist:
log.info('Blacklist-filtering peaks...')
bfilt_rpeak = blacklist_filter(rpeak, args.blacklist, False,
args.out_dir)
else:
bfilt_rpeak = rpeak
if args.ta: # if TAG-ALIGN is given
log.info('Shifted FRiP with fragment length...')
frip_qc = frip_shifted(args.ta, bfilt_rpeak, args.chrsz, args.fraglen,
args.out_dir)
else:
frip_qc = '/dev/null'
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
log.info('Do IDR...')
idr_peak, idr_plot, idr_out_gz, idr_stdout = idr(
args.prefix,
args.peak1, args.peak2, args.peak_pooled, args.peak_type,
args.idr_thresh, args.idr_rank, args.out_dir)
if args.blacklist:
log.info('Blacklist-filtering peaks...')
bfilt_idr_peak = blacklist_filter(
idr_peak, args.blacklist, False, args.out_dir)
else:
bfilt_idr_peak = idr_peak
if args.ta: # if TAG-ALIGN is given
if args.fraglen: # chip-seq
log.info('Shifted FRiP with fragment length...')
frip_qc = frip_shifted( args.ta, bfilt_idr_peak,
args.chrsz, args.fraglen, args.out_dir)
else: # atac-seq
log.info('FRiP without fragment length...')
frip_qc = frip( args.ta, bfilt_idr_peak, args.out_dir)
else:
frip_qc = '/dev/null'
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
log.info('Do IDR...')
idr_peak, idr_plot, idr_out_gz, idr_stdout = idr(
args.prefix, args.peak1, args.peak2, args.peak_pooled, args.peak_type,
args.idr_thresh, args.idr_rank, args.out_dir)
log.info('Blacklist-filtering peaks...')
bfilt_idr_peak = blacklist_filter(idr_peak, args.blacklist,
args.keep_irregular_chr, args.out_dir)
log.info('Checking if output is empty...')
assert_file_not_empty(bfilt_idr_peak)
log.info('Converting peak to bigbed...')
peak_to_bigbed(bfilt_idr_peak, args.peak_type, args.chrsz,
args.keep_irregular_chr, args.out_dir)
log.info('Converting peak to hammock...')
peak_to_hammock(bfilt_idr_peak, args.keep_irregular_chr, args.out_dir)
if args.ta: # if TAG-ALIGN is given
if args.fraglen: # chip-seq
log.info('Shifted FRiP with fragment length...')
frip_qc = frip_shifted(args.ta, bfilt_idr_peak, args.chrsz,
args.fraglen, args.out_dir)
else: # atac-seq
log.info('FRiP without fragment length...')
frip_qc = frip(args.ta, bfilt_idr_peak, args.out_dir)
else:
frip_qc = '/dev/null'
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
