def macs2(ta, ctl_ta, chrsz, gensz, pval_thresh, shift, fraglen, cap_num_peak, ctl_subsample, ctl_paired_end, out_dir): basename_ta = os.path.basename(strip_ext_ta(ta)) if ctl_ta: if ctl_subsample: if ctl_paired_end: ctl_ta = subsample_ta_pe(ctl_ta, ctl_subsample, non_mito=False, mito_chr_name=None, r1_only=False, out_dir=out_dir) else: ctl_ta = subsample_ta_se(ctl_ta, ctl_subsample, non_mito=False, mito_chr_name=None, out_dir=out_dir) basename_ctl_ta = os.path.basename(strip_ext_ta(ctl_ta)) basename_prefix = '{}_x_{}'.format(basename_ta, basename_ctl_ta) if len(basename_prefix) > 200: # UNIX cannot have len(filename) > 255 basename_prefix = '{}_x_control'.format(basename_ta) else: basename_prefix = basename_ta prefix = os.path.join(out_dir, basename_prefix) npeak = '{}.{}.{}.narrowPeak.gz'.format( prefix, 'pval{}'.format(pval_thresh), human_readable_number(cap_num_peak)) npeak_tmp = '{}.tmp'.format(npeak) npeak_tmp2 = '{}.tmp2'.format(npeak) temp_files = [] cmd0 = ' macs2 callpeak ' cmd0 += '-t {} {} -f BED -n {} -g {} -p {} ' cmd0 += '--nomodel --shift {} --extsize {} --keep-dup all -B --SPMR' cmd0 = cmd0.format(ta, '-c {}'.format(ctl_ta) if ctl_ta else '', prefix, gensz, pval_thresh, 0, fraglen) run_shell_cmd(cmd0) cmd1 = 'LC_COLLATE=C sort -k 8gr,8gr "{}"_peaks.narrowPeak | ' cmd1 += 'awk \'BEGIN{{OFS="\\t"}}' cmd1 += '{{$4="Peak_"NR; if ($2<0) $2=0; if ($3<0) $3=0; if ($10==-1) ' cmd1 += '$10=$2+int(($3-$2+1)/2.0); print $0}}\' > {}' cmd1 = cmd1.format(prefix, npeak_tmp) run_shell_cmd(cmd1) cmd2 = 'head -n {} {} > {}'.format(cap_num_peak, npeak_tmp, npeak_tmp2) run_shell_cmd(cmd2) # clip peaks between 0-chromSize. bed_clip(npeak_tmp2, chrsz, npeak) rm_f([npeak_tmp, npeak_tmp2]) # remove temporary files temp_files.append("{}_*".format(prefix)) rm_f(temp_files) return npeak
def idr(basename_prefix, peak1, peak2, peak_pooled, peak_type, chrsz, thresh, rank, out_dir): prefix = os.path.join(out_dir, basename_prefix) prefix += '.idr{}'.format(thresh) idr_peak = '{}.{}.gz'.format(prefix, peak_type) idr_plot = '{}.unthresholded-peaks.txt.png'.format(prefix) idr_stdout = '{}.log'.format(prefix) # temporary idr_12col_bed = '{}.12-col.bed.gz'.format(peak_type) idr_out = '{}.unthresholded-peaks.txt'.format(prefix) idr_tmp = '{}.unthresholded-peaks.txt.tmp'.format(prefix) idr_out_gz = '{}.unthresholded-peaks.txt.gz'.format(prefix) cmd1 = 'idr --samples {} {} --peak-list {} --input-file-type narrowPeak ' cmd1 += '--output-file {} --rank {} --soft-idr-threshold {} ' cmd1 += '--plot --use-best-multisummit-IDR --log-output-file {}' cmd1 = cmd1.format( peak1, peak2, peak_pooled, idr_out, rank, thresh, idr_stdout) run_shell_cmd(cmd1) # clip peaks between 0-chromSize. bed_clip(idr_out, chrsz, idr_tmp, no_gz=True) col = get_npeak_col_by_rank(rank) neg_log10_thresh = -math.log10(thresh) # LC_COLLATE=C cmd2 = 'awk \'BEGIN{{OFS="\\t"}} $12>={} ' cmd2 += '{{if ($2<0) $2=0; ' cmd2 += 'print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}}\' {} ' cmd2 += '| sort | uniq | sort -grk{},{} | gzip -nc > {}' cmd2 = cmd2.format( neg_log10_thresh, idr_tmp, col, col, idr_12col_bed) run_shell_cmd(cmd2) cmd3 = 'zcat {} | ' cmd3 += 'awk \'BEGIN{{OFS="\\t"}} ' cmd3 += '{{print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}}\' | ' cmd3 += 'gzip -nc > {}' cmd3 = cmd3.format( idr_12col_bed, idr_peak) run_shell_cmd(cmd3) cmd4 = 'cat {} | gzip -nc > {}'.format(idr_tmp, idr_out_gz) run_shell_cmd(cmd4) rm_f([idr_out, idr_tmp, idr_12col_bed]) rm_f('{}.*.noalternatesummitpeaks.png'.format(prefix)) return idr_peak, idr_plot, idr_out_gz, idr_stdout
def macs2(ta, chrsz, gensz, pval_thresh, smooth_win, cap_num_peak, mem_gb, out_dir): prefix = os.path.join(out_dir, os.path.basename(strip_ext_ta(ta))) npeak = '{}.{}.{}.narrowPeak.gz'.format( prefix, 'pval{}'.format(pval_thresh), human_readable_number(cap_num_peak)) # temporary files npeak_tmp = '{}.tmp'.format(npeak) npeak_tmp2 = '{}.tmp2'.format(npeak) shiftsize = -int(round(float(smooth_win) / 2.0)) temp_files = [] run_shell_cmd('macs2 callpeak ' '-t {ta} -f BED -n {prefix} -g {gensz} -p {pval_thresh} ' '--shift {shiftsize} --extsize {extsize} ' '--nomodel -B --SPMR --keep-dup all --call-summits'.format( ta=ta, prefix=prefix, gensz=gensz, pval_thresh=pval_thresh, shiftsize=shiftsize, extsize=smooth_win, )) run_shell_cmd( 'LC_COLLATE=C sort -k 8gr,8gr {sort_param} "{prefix}"_peaks.narrowPeak | ' 'awk \'BEGIN{{OFS="\\t"}}' '{{$4="Peak_"NR; if ($2<0) $2=0; if ($3<0) $3=0; if ($10==-1) ' '$10=$2+int(($3-$2+1)/2.0); print $0}}\' > {npeak_tmp}'.format( sort_param=get_gnu_sort_param(mem_gb * 1024**3, ratio=0.5), prefix=prefix, npeak_tmp=npeak_tmp, )) run_shell_cmd('head -n {cap_num_peak} {npeak_tmp} > {npeak_tmp2}'.format( cap_num_peak=cap_num_peak, npeak_tmp=npeak_tmp, npeak_tmp2=npeak_tmp2, )) # clip peaks between 0-chromSize. bed_clip(npeak_tmp2, chrsz, npeak) rm_f([npeak_tmp, npeak_tmp2]) # remove temporary files temp_files.append("{prefix}_*".format(prefix=prefix)) rm_f(temp_files) return npeak
def spp(ta, ctl_ta, chrsz, fraglen, cap_num_peak, fdr_thresh, ctl_subsample, ctl_paired_end, nth, out_dir): basename_ta = os.path.basename(strip_ext_ta(ta)) if ctl_subsample: if ctl_paired_end: ctl_ta = subsample_ta_pe(ctl_ta, ctl_subsample, non_mito=False, mito_chr_name=None, r1_only=False, out_dir=out_dir) else: ctl_ta = subsample_ta_se(ctl_ta, ctl_subsample, non_mito=False, mito_chr_name=None, out_dir=out_dir) basename_ctl_ta = os.path.basename(strip_ext_ta(ctl_ta)) basename_prefix = '{}_x_{}'.format(basename_ta, basename_ctl_ta) if len(basename_prefix) > 200: # UNIX cannot have filename > 255 basename_prefix = '{}_x_control'.format(basename_ta) nth_param = '-p={}'.format(nth) if nth >= 2 else '' prefix = os.path.join(out_dir, basename_prefix) rpeak = '{}.{}.regionPeak.gz'.format(prefix, human_readable_number(cap_num_peak)) rpeak_tmp_prefix = '{}.tmp'.format(rpeak) rpeak_tmp_gz = '{}.tmp.gz'.format(rpeak) rpeak_tmp2 = '{}.tmp2'.format(rpeak) cmd0 = 'Rscript --max-ppsize=500000 $(which run_spp.R) -c={} -i={} ' cmd0 += '-npeak={} -odir={} -speak={} -savr={} -fdr={} -rf {}' cmd0 = cmd0.format(ta, ctl_ta, cap_num_peak, os.path.abspath(out_dir), fraglen, rpeak_tmp_prefix, fdr_thresh, nth_param) run_shell_cmd(cmd0) # if we have scientific representation of chr coord. then convert it to int cmd1 = 'zcat -f {} | awk \'BEGIN{{OFS="\\t"}}' cmd1 += '{{if ($2<0) $2=0; ' cmd1 += 'print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}}\' > {}' cmd1 = cmd1.format(rpeak_tmp_gz, rpeak_tmp2) run_shell_cmd(cmd1) rm_f(rpeak_tmp_gz) # clip peaks between 0-chromSize. bed_clip(rpeak_tmp2, chrsz, rpeak) rm_f(rpeak_tmp2) return rpeak
def macs2(ta, chrsz, gensz, pval_thresh, smooth_win, cap_num_peak, out_dir): prefix = os.path.join(out_dir, os.path.basename(strip_ext_ta(ta))) npeak = '{}.{}.{}.narrowPeak.gz'.format( prefix, 'pval{}'.format(pval_thresh), human_readable_number(cap_num_peak)) # temporary files npeak_tmp = '{}.tmp'.format(npeak) npeak_tmp2 = '{}.tmp2'.format(npeak) shiftsize = -int(round(float(smooth_win) / 2.0)) temp_files = [] cmd0 = 'macs2 callpeak ' cmd0 += '-t {} -f BED -n {} -g {} -p {} ' cmd0 += '--shift {} --extsize {} ' cmd0 += '--nomodel -B --SPMR ' cmd0 += '--keep-dup all --call-summits ' cmd0 = cmd0.format(ta, prefix, gensz, pval_thresh, shiftsize, smooth_win) run_shell_cmd(cmd0) cmd1 = 'LC_COLLATE=C sort -k 8gr,8gr "{}"_peaks.narrowPeak | ' cmd1 += 'awk \'BEGIN{{OFS="\\t"}}' cmd1 += '{{$4="Peak_"NR; if ($2<0) $2=0; if ($3<0) $3=0; if ($10==-1) ' cmd1 += '$10=$2+int(($3-$2+1)/2.0); print $0}}\' > {}' cmd1 = cmd1.format(prefix, npeak_tmp) run_shell_cmd(cmd1) cmd2 = 'head -n {} {} > {}'.format(cap_num_peak, npeak_tmp, npeak_tmp2) run_shell_cmd(cmd2) # clip peaks between 0-chromSize. bed_clip(npeak_tmp2, chrsz, npeak) rm_f([npeak_tmp, npeak_tmp2]) # remove temporary files temp_files.append("{}_*".format(prefix)) rm_f(temp_files) return npeak
def test_bed_clip(tmp_path): chrsz = tmp_path / 'chrsz' chrsz.write_text(CHRSZ_HG38) out_bed = tmp_path / 'out.bed' # no change if it's inside 0-chrsz bed_in = tmp_path / 'test.in.bed' bed_in.write_text('chrM\t2\t10000\n') bed_clip(str(bed_in), str(chrsz), str(out_bed), no_gz=True) assert out_bed.read_text() == 'chrM\t2\t10000\n' # out-of-bound error should occur bed_oob1 = tmp_path / 'test.oob1.bed' bed_oob1.write_text('chrM\t-10\t-1\n') with pytest.raises(Exception): bed_clip(str(bed_oob1), str(chrsz), str(out_bed), no_gz=True) # should be truncated to 0 (left) or chrsz (right) bed_left_crossing = tmp_path / 'test.lc.bed' bed_left_crossing.write_text('chrM\t-1\t13000\n') bed_right_crossing = tmp_path / 'test.rc.bed' bed_right_crossing.write_text('chrM\t13000\t17000\n') bed_larger = tmp_path / 'test.l.bed' bed_larger.write_text('chrM\t-1\t17000\n') bed_clip(str(bed_left_crossing), str(chrsz), str(out_bed), no_gz=True) assert out_bed.read_text() == 'chrM\t0\t13000\n' bed_clip(str(bed_right_crossing), str(chrsz), str(out_bed), no_gz=True) assert out_bed.read_text() == 'chrM\t13000\t16569\n' bed_clip(str(bed_larger), str(chrsz), str(out_bed), no_gz=True) assert out_bed.read_text() == 'chrM\t0\t16569\n' # test no_gz flag out_bed = tmp_path / 'out.bed.gz' bed_clip(str(bed_larger), str(chrsz), str(out_bed), no_gz=False) with gzip.open(str(out_bed), 'rb') as fp: assert fp.read().decode() == 'chrM\t0\t16569\n'
def macs2(ta, ctl_ta, chrsz, gensz, pval_thresh, shift, fraglen, cap_num_peak, ctl_subsample, ctl_paired_end, mem_gb, out_dir): basename_ta = os.path.basename(strip_ext_ta(ta)) if ctl_ta: if ctl_subsample: if ctl_paired_end: ctl_ta = subsample_ta_pe(ctl_ta, ctl_subsample, non_mito=False, mito_chr_name=None, r1_only=False, out_dir=out_dir) else: ctl_ta = subsample_ta_se(ctl_ta, ctl_subsample, non_mito=False, mito_chr_name=None, out_dir=out_dir) basename_ctl_ta = os.path.basename(strip_ext_ta(ctl_ta)) basename_prefix = '{}_x_{}'.format(basename_ta, basename_ctl_ta) if len(basename_prefix) > 200: # UNIX cannot have len(filename) > 255 basename_prefix = '{}_x_control'.format(basename_ta) else: basename_prefix = basename_ta prefix = os.path.join(out_dir, basename_prefix) npeak = '{}.{}.{}.narrowPeak.gz'.format( prefix, 'pval{}'.format(pval_thresh), human_readable_number(cap_num_peak)) npeak_tmp = '{}.tmp'.format(npeak) npeak_tmp2 = '{}.tmp2'.format(npeak) temp_files = [] run_shell_cmd( ' macs2 callpeak ' '-t {ta} {ctl_param} -f BED -n {prefix} -g {gensz} -p {pval_thresh} ' '--nomodel --shift {shiftsize} --extsize {extsize} --keep-dup all -B --SPMR' .format( ta=ta, ctl_param='-c {ctl_ta}'.format(ctl_ta=ctl_ta) if ctl_ta else '', prefix=prefix, gensz=gensz, pval_thresh=pval_thresh, shiftsize=0, extsize=fraglen, )) run_shell_cmd( 'LC_COLLATE=C sort -k 8gr,8gr {sort_param} "{prefix}_peaks.narrowPeak" | ' 'awk \'BEGIN{{OFS="\\t"}}' '{{$4="Peak_"NR; if ($2<0) $2=0; if ($3<0) $3=0; if ($10==-1) ' '$10=$2+int(($3-$2+1)/2.0); print $0}}\' > {npeak_tmp}'.format( sort_param=get_gnu_sort_param(mem_gb * 1024**3, ratio=0.5), prefix=prefix, npeak_tmp=npeak_tmp, )) run_shell_cmd('head -n {cap_num_peak} {npeak_tmp} > {npeak_tmp2}'.format( cap_num_peak=cap_num_peak, npeak_tmp=npeak_tmp, npeak_tmp2=npeak_tmp2, )) # clip peaks between 0-chromSize. bed_clip(npeak_tmp2, chrsz, npeak) rm_f([npeak_tmp, npeak_tmp2]) # remove temporary files temp_files.append("{prefix}_*".format(prefix=prefix)) rm_f(temp_files) return npeak
def idr(basename_prefix, peak1, peak2, peak_pooled, peak_type, chrsz, thresh, rank, mem_gb, out_dir): prefix = os.path.join(out_dir, basename_prefix) prefix += '.idr{}'.format(thresh) idr_peak = '{}.{}.gz'.format(prefix, peak_type) idr_plot = '{}.unthresholded-peaks.txt.png'.format(prefix) idr_stdout = '{}.log'.format(prefix) # temporary idr_12col_bed = '{}.12-col.bed.gz'.format(peak_type) idr_out = '{}.unthresholded-peaks.txt'.format(prefix) idr_tmp = '{}.unthresholded-peaks.txt.tmp'.format(prefix) idr_out_gz = '{}.unthresholded-peaks.txt.gz'.format(prefix) run_shell_cmd( 'idr --samples {peak1} {peak2} --peak-list {peak_pooled} --input-file-type narrowPeak ' '--output-file {idr_out} --rank {rank} --soft-idr-threshold {thresh} ' '--plot --use-best-multisummit-IDR --log-output-file {idr_stdout}'.format( peak1=peak1, peak2=peak2, peak_pooled=peak_pooled, idr_out=idr_out, rank=rank, thresh=thresh, idr_stdout=idr_stdout, ) ) # clip peaks between 0-chromSize. bed_clip(idr_out, chrsz, idr_tmp, no_gz=True) col = get_npeak_col_by_rank(rank) neg_log10_thresh = -math.log10(thresh) # LC_COLLATE=C run_shell_cmd( 'awk \'BEGIN{{OFS="\\t"}} $12>={neg_log10_thresh} ' '{{if ($2<0) $2=0; ' 'print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}}\' {idr_tmp} ' '| sort {sort_param} | uniq | sort -grk{col},{col} {sort_param} | gzip -nc > {idr_12col_bed}'.format( neg_log10_thresh=neg_log10_thresh, idr_tmp=idr_tmp, sort_param=get_gnu_sort_param(mem_gb * 1024 ** 3, ratio=0.5), col=col, idr_12col_bed=idr_12col_bed, ) ) run_shell_cmd( 'zcat {idr_12col_bed} | ' 'awk \'BEGIN{{OFS="\\t"}} ' '{{print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}}\' | ' 'gzip -nc > {idr_peak}'.format( idr_12col_bed=idr_12col_bed, idr_peak=idr_peak, ) ) run_shell_cmd( 'cat {idr_tmp} | gzip -nc > {idr_out_gz}'.format( idr_tmp=idr_tmp, idr_out_gz=idr_out_gz, ) ) rm_f([idr_out, idr_tmp, idr_12col_bed]) rm_f('{prefix}.*.noalternatesummitpeaks.png'.format(prefix=prefix)) return idr_peak, idr_plot, idr_out_gz, idr_stdout