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('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.')
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.')