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('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, fc_bigwig, pval_bigwig = macs2( args.ta, args.ctl_ta, args.chrsz, args.gensz, args.pval_thresh, args.fraglen, args.cap_num_peak, args.make_signal, args.out_dir) log.info('Checking if output is empty...') assert_file_not_empty(npeak) 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('Shifted FRiP with fragment length...') frip_qc = frip_shifted( args.ta, bfilt_npeak, 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.')