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, cov_bigwig = macs2(
args.tas[0], args.tas[1], args.chrsz, args.gensz, args.pval_thresh,
args.shift, 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 = 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('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.')
def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
log.info('Reproducibility QC...')
# description for variables
# N: list of number of peaks in peak files from pseudo replicates
# Nt: top number of peaks in peak files from true replicates (rep-x_vs_rep-y)
# Np: number of peaks in peak files from pooled pseudo replicate
N = [get_num_lines(peak) for peak in args.peaks_pr]
if len(args.peaks):
# multiple replicate case
num_rep = infer_n_from_nC2(len(args.peaks))
num_peaks_tr = [get_num_lines(peak) for peak in args.peaks]
Nt = max(num_peaks_tr)
Np = get_num_lines(args.peak_ppr)
rescue_ratio = float(max(Np,Nt))/float(min(Np,Nt))
self_consistency_ratio = float(max(N))/float(min(N))
Nt_idx = num_peaks_tr.index(Nt)
label_tr = infer_pair_label_from_idx(num_rep, Nt_idx)
conservative_set = label_tr
conservative_peak = make_hard_link(args.peaks[Nt_idx], args.out_dir)
N_conservative = Nt
if Nt>Np:
optimal_set = conservative_set
optimal_peak = conservative_peak
N_optimal = N_conservative
else:
optimal_set = "ppr"
optimal_peak = make_hard_link(args.peak_ppr, args.out_dir)
N_optimal = Np
else:
# single replicate case
num_rep = 1
Nt = 0
Np = 0
rescue_ratio = 0.0
self_consistency_ratio = 1.0
conservative_set = 'rep1-pr'
conservative_peak = make_hard_link(args.peaks_pr[0], args.out_dir)
N_conservative = N[0]
optimal_set = conservative_set
optimal_peak = conservative_peak
N_optimal = N_conservative
reproducibility = 'pass'
if rescue_ratio>2.0 or self_consistency_ratio>2.0:
reproducibility = 'borderline'
if rescue_ratio>2.0 and self_consistency_ratio>2.0:
reproducibility = 'fail'
log.info('Writing optimal/conservative peak files...')
optimal_peak_file = os.path.join(args.out_dir, 'optimal_peak.{}.gz'.format(args.peak_type))
conservative_peak_file = os.path.join(args.out_dir, 'conservative_peak.{}.gz'.format(args.peak_type))
copy_f_to_f(optimal_peak, optimal_peak_file)
copy_f_to_f(conservative_peak, conservative_peak_file)
if args.chrsz:
log.info('Converting peak to bigbed...')
peak_to_bigbed(optimal_peak_file, args.peak_type, args.chrsz, args.keep_irregular_chr, args.out_dir)
peak_to_bigbed(conservative_peak_file, args.peak_type, args.chrsz, args.keep_irregular_chr, args.out_dir)
log.info('Converting peak to hammock...')
peak_to_hammock(optimal_peak_file, args.keep_irregular_chr, args.out_dir)
peak_to_hammock(conservative_peak_file, args.keep_irregular_chr, args.out_dir)
log.info('Writing reproducibility QC log...')
if args.prefix:
reproducibility_qc = '{}.reproducibility.qc'.format(args.prefix)
else:
reproducibility_qc = 'reproducibility.qc'
reproducibility_qc = os.path.join(args.out_dir, reproducibility_qc)
with open(reproducibility_qc,'w') as fp:
header = '{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n'.format(
'Nt',
'\t'.join(['N{}'.format(i+1) for i in range(num_rep)]),
'Np',
'N_opt',
'N_consv',
'opt_set',
'consv_set',
'rescue_ratio',
'self_consistency_ratio',
'reproducibility',
)
line = '{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n'.format(
Nt,
'\t'.join([str(i) for i in N]),
Np,
N_optimal,
N_conservative,
optimal_set,
conservative_set,
rescue_ratio,
self_consistency_ratio,
reproducibility)
fp.write(header)
fp.write(line)
log.info('All done.')
