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)
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()
BIGWIG = args.bigwig
DNASE = args.dnase
OUTPUT_PREFIX = os.path.join(args.out_dir,
os.path.basename(strip_ext_bigwig(BIGWIG)))
REG2MAP_BED = args.reg2map_bed if args.reg2map_bed and os.path.basename(
args.reg2map_bed) != 'null' else DNASE
REG2MAP = args.reg2map if args.reg2map and os.path.basename(
args.reg2map) != 'null' else ''
ROADMAP_META = args.roadmap_meta if args.roadmap_meta and os.path.basename(
args.roadmap_meta) != 'null' else ''
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
compare_to_roadmap(BIGWIG, REG2MAP_BED, REG2MAP, ROADMAP_META,
OUTPUT_PREFIX)
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)
# generate read length file
log.info('Generating read length file...')
make_read_length_file(args.fastq, args.out_dir)
log.info('Running samtools index...')
samtools_index(args.bam, args.nth, args.out_dir)
log.info('SAMstat on raw BAM...')
samstat(args.bam, args.nth, args.out_dir)
if args.chrsz:
log.info('SAMstat on non-mito BAM...')
non_mito_out_dir = os.path.join(args.out_dir, 'non_mito')
mkdir_p(non_mito_out_dir)
non_mito_bam = remove_chrs_from_bam(args.bam, [args.mito_chr_name],
args.chrsz, args.nth,
non_mito_out_dir)
samstat(non_mito_bam, args.nth, non_mito_out_dir)
rm_f(non_mito_bam)
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)
# update array with trimmed fastqs
fastqs_R1 = []
fastqs_R2 = []
for fastqs in args.fastqs:
fastqs_R1.append(fastqs[0])
if args.paired_end:
fastqs_R2.append(fastqs[1])
log.info('Merging fastqs...')
log.info('R1 to be merged: {}'.format(fastqs_R1))
merge_fastqs(fastqs_R1, 'R1', args.out_dir)
if args.paired_end:
log.info('R2 to be merged: {}'.format(fastqs_R2))
merge_fastqs(fastqs_R2, 'R2', 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 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)
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)
# declare temp arrays
temp_files = [] # files to deleted later at the end
log.info('Subsampling TAGALIGN for xcor...')
if args.paired_end:
ta_subsampled = subsample_ta_pe(args.ta, args.subsample, True,
args.mito_chr_name, True, args.out_dir)
else:
ta_subsampled = subsample_ta_se(args.ta, args.subsample, True,
args.mito_chr_name, args.out_dir)
temp_files.append(ta_subsampled)
log.info('Cross-correlation analysis...')
xcor_plot_pdf, xcor_plot_png, xcor_score, fraglen_txt = xcor(
ta_subsampled, args.speak, args.mito_chr_name, args.nth, args.out_dir,
args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max)
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('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_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)
# declare temp arrays
temp_files = [] # files to deleted later at the end
# if bowtie2 index is tarball then unpack it
if args.bowtie2_index_prefix_or_tar.endswith('.tar') or \
args.bowtie2_index_prefix_or_tar.endswith('.tar.gz'):
log.info('Unpacking bowtie2 index tar...')
tar = args.bowtie2_index_prefix_or_tar
# untar
untar(tar, args.out_dir)
bowtie2_index_prefix = find_bowtie2_index_prefix(args.out_dir)
temp_files.append('{}*'.format(
bowtie2_index_prefix))
else:
bowtie2_index_prefix = args.bowtie2_index_prefix_or_tar
# check if bowties indices are unpacked on out_dir
chk_bowtie2_index(bowtie2_index_prefix)
# bowtie2
log.info('Running bowtie2...')
if args.paired_end:
bam, align_log = bowtie2_pe(
args.fastqs[0], args.fastqs[1],
bowtie2_index_prefix,
args.multimapping, args.nth,
args.out_dir)
else:
bam, align_log = bowtie2_se(
args.fastqs[0],
bowtie2_index_prefix,
args.multimapping, args.nth,
args.out_dir)
log.info('Removing temporary files...')
print(temp_files)
rm_f(temp_files)
log.info('Showing align log...')
run_shell_cmd('cat {}'.format(align_log))
log.info('Checking if BAM file is empty...')
if not int(run_shell_cmd('samtools view -c {}'.format(bam))):
raise ValueError('BAM file is empty, no reads found.')
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)
frac_mito(args.non_mito_samstat, args.mito_samstat, args.out_dir)
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
def merge_fastqs(fastqs, end, out_dir):
out_dir = os.path.join(out_dir, end)
mkdir_p(out_dir)
prefix = os.path.join(out_dir,
os.path.basename(strip_ext_fastq(fastqs[0])))
merged = '{}.merged.fastq.gz'.format(prefix)
if len(fastqs) > 1:
cmd = 'zcat -f {} | gzip -nc > {}'.format(' '.join(fastqs), merged)
run_shell_cmd(cmd)
return merged
else:
return hard_link(fastqs[0], merged)
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
# if bwa index is tarball then unpack it
if args.bwa_index_prefix_or_tar.endswith('.tar') or \
args.bwa_index_prefix_or_tar.endswith('.tar.gz'):
log.info('Unpacking bwa index tar...')
tar = args.bwa_index_prefix_or_tar
# untar
untar(tar, args.out_dir)
bwa_index_prefix = find_bwa_index_prefix(args.out_dir)
temp_files.append('{}*'.format(
bwa_index_prefix))
else:
bwa_index_prefix = args.bwa_index_prefix_or_tar
# check if bowties indices are unpacked on out_dir
chk_bwa_index(bwa_index_prefix)
# bwa
log.info('Running bwa...')
if args.paired_end:
bam = bwa_pe(
args.fastqs[0], args.fastqs[1],
bwa_index_prefix, args.nth, args.mem_gb, args.use_bwa_mem_for_pe,
args.bwa_mem_read_len_limit, args.rescue_reads_for_bwa_mem,
args.out_dir)
else:
bam = bwa_se(
args.fastqs[0],
bwa_index_prefix, args.nth, args.mem_gb,
args.out_dir)
log.info('Removing temporary files...')
rm_f(temp_files)
log.info('Checking if BAM file is empty...')
if bam_is_empty(bam, args.nth):
raise ValueError('BAM file is empty, no reads found.')
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...')
# make out_dir (root of all outputs)
mkdir_p(args.out_dir)
# reproducibility QC
log.info('Filtering peak with blacklist...')
blacklist_filter(args.peak, args.blacklist, args.keep_irregular_chr,
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('Generating count signal tracks...')
pos_bw, neg_bw = count_signal_track(args.ta, args.chrsz, 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('Pooling TAGALIGNs...')
pool_ta(args.tas, args.col, args.prefix, args.out_dir)
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
def merge_fastqs(fastqs, end, out_dir):
"""make merged fastqs on $out_dir/R1, $out_dir/R2
"""
out_dir = os.path.join(out_dir, end)
mkdir_p(out_dir)
prefix = os.path.join(out_dir,
os.path.basename(strip_ext_fastq(fastqs[0])))
merged = '{}.merged.fastq.gz'.format(prefix)
if len(fastqs) > 1:
cmd = 'zcat -f {} | gzip -nc > {}'.format(' '.join(fastqs), merged)
run_shell_cmd(cmd)
return merged
else:
return copy_f_to_f(fastqs[0], merged)
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)
if args.fraglen:
frip_shifted(args.ta, args.peak, args.chrsz, args.fraglen,
args.out_dir)
else:
frip(args.ta, args.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('Calling peaks and generating signal tracks with MACS2...')
fc_bigwig, pval_bigwig = macs2_signal_track(args.ta, args.chrsz,
args.gensz, args.pval_thresh,
args.smooth_win, 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)
# 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 and generating signal tracks with MACS2...')
fc_bigwig, pval_bigwig = macs2_signal_track(
args.tas[0], args.tas[1], args.chrsz, args.gensz, args.pval_thresh,
args.shift, args.fraglen, args.ctl_subsample, args.ctl_paired_end,
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
# if bwa index is tarball then unpack it
if args.bwa_index_prefix_or_tar.endswith('.tar') or \
args.bwa_index_prefix_or_tar.endswith('.tar.gz'):
log.info('Unpacking bwa index tar...')
tar = args.bwa_index_prefix_or_tar
# untar
untar(tar, args.out_dir)
bwa_index_prefix = os.path.join(args.out_dir,
os.path.basename(strip_ext_tar(tar)))
temp_files.append('{}.*'.format(bwa_index_prefix))
else:
bwa_index_prefix = args.bwa_index_prefix_or_tar
# check if bowties indices are unpacked on out_dir
chk_bwa_index(bwa_index_prefix)
# bwa
log.info('Running bwa...')
if args.paired_end:
bam = bwa_pe(args.fastqs[0], args.fastqs[1], bwa_index_prefix,
args.nth, args.use_bwa_mem_for_pe, args.out_dir)
else:
bam = bwa_se(args.fastqs[0], bwa_index_prefix, args.nth, args.out_dir)
log.info('Removing temporary files...')
rm_f(temp_files)
log.info('Checking if BAM file is empty...')
if not int(run_shell_cmd('samtools view -c {}'.format(bam))):
raise ValueError('BAM file is empty, no reads found.')
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()
CHROMSIZES = args.chrsz
TSS = args.tss if args.tss and os.path.basename(args.tss) != 'null' else ''
FINAL_BAM = args.nodup_bam
OUTPUT_PREFIX = os.path.join(args.out_dir,
os.path.basename(strip_ext_bam(FINAL_BAM)))
samtools_index(FINAL_BAM) # make an index first
RG_FREE_FINAL_BAM = remove_read_group(FINAL_BAM)
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
# Also get read length
# read_len = get_read_length(FASTQ)
if args.read_len_log:
with open(args.read_len_log, 'r') as fp:
read_len = int(fp.read().strip())
elif args.read_len:
read_len = args.read_len
else:
read_len = None
# Enrichments: V plot for enrichment
# Use final to avoid duplicates
tss_plot, tss_large_plot, tss_enrich_qc = \
make_tss_plot(FINAL_BAM,
TSS,
OUTPUT_PREFIX,
CHROMSIZES,
read_len)
# remove temporary files
rm_f(RG_FREE_FINAL_BAM)
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.')
