def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
log.info('Blacklist-filtering peaks...')
bfilt_peak = blacklist_filter(
args.peak, args.blacklist, args.keep_irregular_chr, args.out_dir)
log.info('Checking if output is empty...')
assert_file_not_empty(bfilt_peak)
log.info('Converting peak to bigbed...')
peak_to_bigbed(bfilt_peak, args.peak_type, args.chrsz,
args.keep_irregular_chr, args.out_dir)
log.info('Converting peak to hammock...')
peak_to_hammock(bfilt_peak, args.keep_irregular_chr, args.out_dir)
log.info('Shifted FRiP with fragment length...')
frip_qc = frip_shifted(args.ta, bfilt_peak,
args.chrsz, args.fraglen, args.out_dir)
log.info('Calculating (blacklist-filtered) peak region size QC/plot...')
region_size_qc, region_size_plot = get_region_size_metrics(bfilt_peak)
log.info('Calculating number of peaks (blacklist-filtered)...')
num_peak_qc = get_num_peaks(bfilt_peak)
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.mem_gb,
args.out_dir,
)
log.info('Blacklist-filtering peaks...')
bfilt_overlap_peak = blacklist_filter(overlap_peak, args.blacklist,
args.regex_bfilt_peak_chr_name,
args.out_dir)
log.info('Checking if output is empty...')
assert_file_not_empty(bfilt_overlap_peak)
log.info('Converting peak to bigbed...')
peak_to_bigbed(bfilt_overlap_peak, args.peak_type, args.chrsz, args.mem_gb,
args.out_dir)
log.info('Converting peak to starch...')
peak_to_starch(bfilt_overlap_peak, args.out_dir)
log.info('Converting peak to hammock...')
peak_to_hammock(bfilt_overlap_peak, args.mem_gb, args.out_dir)
if args.ta: # if TAG-ALIGN is given
if args.fraglen: # chip-seq
log.info('Shifted FRiP with fragment length...')
frip_shifted(args.ta, bfilt_overlap_peak, args.chrsz, args.fraglen,
args.out_dir)
else: # atac-seq
log.info('FRiP without fragment length...')
frip(args.ta, bfilt_overlap_peak, 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('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.chrsz,
args.idr_thresh, args.idr_rank, args.mem_gb, args.out_dir,
)
log.info('Checking if output is empty...')
assert_file_not_empty(idr_peak, help=
'No IDR peaks found. IDR threshold might be too stringent '
'or replicates have very poor concordance.')
log.info('Blacklist-filtering peaks...')
bfilt_idr_peak = blacklist_filter(
idr_peak, args.blacklist, args.regex_bfilt_peak_chr_name, args.out_dir)
log.info('Converting peak to bigbed...')
peak_to_bigbed(bfilt_idr_peak, args.peak_type, args.chrsz,
args.mem_gb, args.out_dir)
log.info('Converting peak to starch...')
peak_to_starch(bfilt_idr_peak, args.out_dir)
log.info('Converting peak to hammock...')
peak_to_hammock(bfilt_idr_peak, args.mem_gb, args.out_dir)
if args.ta: # if TAG-ALIGN is given
if args.fraglen: # chip-seq
log.info('Shifted FRiP with fragment length...')
frip_shifted(args.ta, bfilt_idr_peak,
args.chrsz, args.fraglen, args.out_dir)
else: # atac-seq
log.info('FRiP without fragment length...')
frip(args.ta, bfilt_idr_peak, 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('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_shifted(args.ta, bfilt_idr_peak,
args.chrsz, args.fraglen, args.out_dir)
else: # atac-seq
log.info('FRiP without fragment length...')
frip(args.ta, bfilt_idr_peak, 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('Blacklist-filtering peaks...')
bfilt_peak = blacklist_filter(args.peak, args.blacklist,
args.regex_bfilt_peak_chr_name, args.out_dir)
log.info('Checking if output is empty...')
assert_file_not_empty(bfilt_peak)
log.info('Converting peak to bigbed...')
peak_to_bigbed(bfilt_peak, args.peak_type, args.chrsz, args.mem_gb,
args.out_dir)
log.info('Converting peak to starch...')
peak_to_starch(bfilt_peak, args.out_dir)
log.info('Converting peak to hammock...')
peak_to_hammock(bfilt_peak, args.mem_gb, args.out_dir)
log.info('FRiP without fragment length...')
frip(args.ta, bfilt_peak, args.out_dir)
log.info('Calculating (blacklist-filtered) peak region size QC/plot...')
get_region_size_metrics(bfilt_peak)
log.info('Calculating number of peaks (blacklist-filtered)...')
get_num_peaks(bfilt_peak)
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
