def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
log.info('Making self-pseudo replicates...')
if args.paired_end:
ta_pr1, ta_pr2 = spr_pe(
args.ta,
args.pseudoreplication_random_seed,
args.out_dir,
)
else:
ta_pr1, ta_pr2 = spr_se(
args.ta,
args.pseudoreplication_random_seed,
args.out_dir,
)
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('Checking if output is empty...')
assert_file_not_empty(ta_pr1)
assert_file_not_empty(ta_pr2)
log.info('All done.')
def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
if args.paired_end:
subsampled_ta = subsample_ta_pe(args.ta,
args.subsample,
non_mito=False,
mito_chr_name=None,
r1_only=False,
out_dir=args.out_dir)
else:
subsampled_ta = subsample_ta_se(args.ta,
args.subsample,
non_mito=False,
mito_chr_name=None,
out_dir=args.out_dir)
log.info('Checking if output is empty...')
assert_file_not_empty(subsampled_ta)
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.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('Calling peaks with macs2...')
npeak = macs2(
args.tas[0],
args.tas[1],
args.chrsz,
args.gensz,
args.pval_thresh,
args.shift,
args.fraglen,
args.cap_num_peak,
args.ctl_subsample,
args.ctl_paired_end,
args.mem_gb,
args.out_dir,
)
log.info('Checking if output is empty...')
assert_file_not_empty(npeak)
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_R1)
if args.paired_end:
mkdir_p(args.out_dir_R2)
log.info('Cropping fastqs ({} bp) with Trimmomatic...'.format(
args.crop_length))
if args.paired_end:
cropped_R1, cropped_R2 = trimmomatic_pe(args.fastq1, args.fastq2,
args.crop_length,
args.out_dir_R1,
args.out_dir_R2, args.nth,
args.trimmomatic_java_heap)
else:
cropped_R1 = trimmomatic_se(args.fastq1, args.crop_length,
args.out_dir_R1, args.nth,
args.trimmomatic_java_heap)
log.info('List all files in output directory...')
ls_l(args.out_dir_R1)
if args.paired_end:
ls_l(args.out_dir_R2)
log.info('Checking if output is empty...')
assert_file_not_empty(
cropped_R1,
help='No reads in FASTQ after cropping. crop_length might be too high? '
'While cropping, Trimmomatic (with MINLEN) excludes all reads '
'SHORTER than crop_length.')
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 macs2...')
npeak = macs2(
args.ta,
args.chrsz,
args.gensz,
args.pval_thresh,
args.smooth_win,
args.cap_num_peak,
args.mem_gb,
args.out_dir,
)
log.info('Checking if output is empty...')
assert_file_not_empty(npeak)
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('Trimming fastqs ({} bp)...'.format(args.trim_bp))
trimmed = trim_fastq(args.fastq, args.trim_bp, args.out_dir)
assert_file_not_empty(trimmed)
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)
# declare temp arrays
temp_files = [] # files to deleted later at the end
log.info('Converting BAM to TAGALIGN...')
if args.paired_end:
ta = bam2ta_pe(args.bam, args.nth, args.out_dir)
else:
ta = bam2ta_se(args.bam, args.out_dir)
if args.subsample:
log.info('Subsampling TAGALIGN...')
if args.paired_end:
subsampled_ta = subsample_ta_pe(ta, args.subsample, False,
args.mito_chr_name, False,
args.out_dir)
else:
subsampled_ta = subsample_ta_se(ta, args.subsample, False,
args.mito_chr_name, args.out_dir)
temp_files.append(ta)
else:
subsampled_ta = ta
if args.disable_tn5_shift:
shifted_ta = subsampled_ta
else:
log.info("TN5-shifting TAGALIGN...")
shifted_ta = tn5_shift_ta(subsampled_ta, args.out_dir)
temp_files.append(subsampled_ta)
log.info('Checking if output is empty...')
assert_file_not_empty(shifted_ta)
log.info('Removing temporary files...')
rm_f(temp_files)
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 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('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 with spp...')
rpeak = spp(args.tas[0], args.tas[1],
args.fraglen, args.cap_num_peak, args.fdr_thresh,
args.nth, args.out_dir)
log.info('Checking if output is empty...')
assert_file_not_empty(rpeak, help=
'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
'might be too stringent or poor quality sample?')
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.')
