# HG changeset patch # User fubar # Date 1721776343 0 # Node ID eb17eb8a365838499a688da7f5d1b07d23aa1908 # Parent 68cb8e7e266bfeb6a26f3b1887ad6499d1691a58 planemo upload commit 1baff96e75def9248afdcf21edec9bdc7ed42b1f-dirty diff -r 68cb8e7e266b -r eb17eb8a3658 README.md --- a/README.md Mon Jul 01 05:02:05 2024 +0000 +++ b/README.md Tue Jul 23 23:12:23 2024 +0000 @@ -1,10 +1,10 @@ -## bigwig peak outlier to bed +## bigwig peak bed maker ### July 30 2024 for the VGP -This code will soon become a Galaxy tool, for building some of the [NIH MARBL T2T assembly polishing](https://github.com/marbl/training) tools as Galaxy workflows. +This is a Galaxy tool, for building some of the [NIH MARBL T2T assembly polishing](https://github.com/marbl/training) tools as Galaxy workflows. -The next JBrowse2 tool release will include a plugin for optional colours to distinguish bed features, shown being tested in the screenshots below. +JBrowse2 2.12.3 update will include a plugin for optional colours to distinguish bed features, shown being tested in the screenshots below. ### Find and mark BigWig peaks to a bed file for display @@ -29,3 +29,69 @@ better to sample across all chromosomes so as not to lose any systematic differences between them - the current method will hide those differences unfortunately. Sampling might be possible. Looking at the actual quantile values across a couple of test bigwigs suggests that there is not much variation between chromosomes but there's now a tabular report to check them for each input bigwig. + +### Table reports + +The optional table output report gives a crude histogram and the top/bottom 10 values to help +understand what is likely to be informative. In this example, there are 26700 zero values so +using a lower cutoff quantile is likely to have a lot of them, although a large window requirement +will decease the overload... + +Descriptive measures +bigwig test +contig chr10_PATERNAL +n 135711693 +mean 12.178164 +std 7.997467 +min 0.000000 +max 365.000000 +qtop 364.00 +qbot noqlo +First/Last 10 value counts +Value Count +0.00 26700 +1.00 82900 +2.00 261400 +3.00 676993 +4.00 1665500 +5.00 3125700 +6.00 5078000 +7.00 7469000 +8.00 10191700 +9.00 12544600 +355.00 100 +356.00 100 +357.00 300 +358.00 100 +360.00 500 +361.00 300 +362.00 200 +363.00 600 +364.00 900 +365.00 700 +Histogram of bigwig values +chr10_PATERNAL 18.25 | 127,047,593 | ************************************************************************** +chr10_PATERNAL 36.50 | 7,510,000 | **** +chr10_PATERNAL 54.75 | 818,900 | +chr10_PATERNAL 73.00 | 117,200 | +chr10_PATERNAL 91.25 | 51,900 | +chr10_PATERNAL 109.50 | 44,200 | +chr10_PATERNAL 127.75 | 21,600 | +chr10_PATERNAL 146.00 | 17,900 | +chr10_PATERNAL 164.25 | 16,400 | +chr10_PATERNAL 182.50 | 18,600 | +chr10_PATERNAL 200.75 | 5,400 | +chr10_PATERNAL 219.00 | 6,600 | +chr10_PATERNAL 237.25 | 6,200 | +chr10_PATERNAL 255.50 | 3,900 | +chr10_PATERNAL 273.75 | 4,500 | +chr10_PATERNAL 292.00 | 7,100 | +chr10_PATERNAL 310.25 | 3,000 | +chr10_PATERNAL 328.50 | 2,700 | +chr10_PATERNAL 346.75 | 3,500 | +chr10_PATERNAL 365.00 | 4,500 | +chr10_PATERNAL ------------ |------------ | +chr10_PATERNAL N= | 135,711,693 | +chr10_PATERNAL ------------ |------------ | + + diff -r 68cb8e7e266b -r eb17eb8a3658 bigwig_outlier_bed.py --- a/bigwig_outlier_bed.py Mon Jul 01 05:02:05 2024 +0000 +++ b/bigwig_outlier_bed.py Tue Jul 23 23:12:23 2024 +0000 @@ -1,58 +1,149 @@ """ -Ross Lazarus June 2024 for VGP - +Ross Lazarus June 2024 for VGP Bigwigs are great, but hard to reliably "see" small low coverage or small very high coverage regions. Colouring in JB2 tracks will need a new plugin, so this code will find bigwig regions above and below a chosen percentile point. 0.99 and 0.01 work well in testing with a minimum span of 10 bp. - Multiple bigwigs **with the same reference** can be combined - bed segments will be named appropriately Combining multiple references works but is silly because only display will rely on one reference so others will not be shown... - Tricksy numpy method from http://gregoryzynda.com/python/numpy/contiguous/interval/2019/11/29/contiguous-regions.html takes about 95 seconds for a 17MB test wiggle - JBrowse2 bed normally displays ignore the score, so could provide separate low/high bed file outputs as an option. - Update june 30 2024: wrote a 'no-build' plugin for beds to display red/blue if >0/<0 so those are used for scores Bed interval naming must be short for JB2 but needs input bigwig name and (lo or hi). - """ +import argparse +import os +import sys +from pathlib import Path -import argparse import numpy as np import pybigtools -import sys -from pathlib import Path +class asciihist: + + def __init__( + self, + data, + bins=10, + minmax=None, + str_tag="", + scale_output=80, + generate_only=True, + ): + """ + https://gist.github.com/bgbg/608d9ef4fd75032731651257fe67fc81 + Create an ASCII histogram from an interable of numbers. + Author: Boris Gorelik boris@gorelik.net. based on http://econpy.googlecode.com/svn/trunk/pytrix/pytrix.py + License: MIT + """ + self.data = data + self.minmax = minmax + self.str_tag = str_tag + self.bins = bins + self.generate_only = generate_only + self.scale_output = scale_output + self.itarray = np.asanyarray(self.data) + if self.minmax == "auto": + self.minmax = np.percentile(data, [5, 95]) + if self.minmax[0] == self.minmax[1]: + # for very ugly distributions + self.minmax = None + if self.minmax is not None: + # discard values that are outside minmax range + mn = self.minmax[0] + mx = self.minmax[1] + self.itarray = self.itarray[self.itarray >= mn] + self.itarray = self.itarray[self.itarray <= mx] -class findOut(): + def draw(self): + values, counts = np.unique(self.data, return_counts=True) + if len(values) <= 20: + self.bins = len(values) + ret = [] + if self.itarray.size: + total = len(self.itarray) + counts, cutoffs = np.histogram(self.itarray, bins=self.bins) + cutoffs = cutoffs[1:] + if self.str_tag: + self.str_tag = "%s " % self.str_tag + else: + self.str_tag = "" + if self.scale_output is not None: + scaled_counts = counts.astype(float) / counts.sum() * self.scale_output + else: + scaled_counts = counts + footerbar = "{:s}{:s} |{:s} |".format(self.str_tag, "-" * 12, "-" * 12,) + if self.minmax is not None: + ret.append( + "Trimmed to range (%s - %s)" + % (str(self.minmax[0]), str(self.minmax[1])) + ) + for cutoff, original_count, scaled_count in zip( + cutoffs, counts, scaled_counts + ): + ret.append( + "{:s}{:>12.2f} |{:>12,d} | {:s}".format( + self.str_tag, cutoff, original_count, "*" * int(scaled_count) + ) + ) + ret.append(footerbar) + ret.append("{:s}{:>12s} |{:>12,d} |".format(self.str_tag, "N=", total)) + ret.append(footerbar) + ret.append('') + else: + ret = [] + if not self.generate_only: + for line in ret: + print(line) + ret = "\n".join(ret) + return ret + + +class findOut: def __init__(self, args): - self.bwnames=args.bigwig - self.bwlabels=args.bigwiglabels - self.bedwin=args.minwin - self.qlo=args.qlo - self.qhi=args.qhi - self.bedouthilo=args.bedouthilo - self.bedouthi=args.bedouthi - self.bedoutlo=args.bedoutlo - self.tableout = args.tableout + self.bwnames = args.bigwig + self.bwlabels = args.bigwiglabels + self.bedwin = args.minwin + self.outbeds = args.outbeds + self.bedouthi = args.bedouthi + self.bedoutlo = args.bedoutlo + self.bedouthilo = args.bedouthilo + self.tableoutfile = args.tableoutfile self.bedwin = args.minwin - self.qhi = args.qhi - self.qlo = args.qlo + self.qlo = None + self.qhi = None + if args.outbeds != "outtab": + self.qhi = args.qhi + if args.qlo: + try: + f = float(args.qlo) + self.qlo = f + except Exception: + print('qlo not provided') + nbw = len(args.bigwig) + nlab = len(args.bigwiglabels) + if nlab < nbw: + self.bwlabels += ["Nolabel"] * (nbw - nlab) self.makeBed() def processVals(self, bw, isTop): - # http://gregoryzynda.com/python/numpy/contiguous/interval/2019/11/29/contiguous-regions.html + """ + idea from http://gregoryzynda.com/python/numpy/contiguous/interval/2019/11/29/contiguous-regions.html + Fast segmentation into regions by taking np.diff on the boolean array of over (under) cutpoint indicators in bwex. + This only gives non-zero values at the segment boundaries where there's a change, so those zeros are all removed in bwexdnz + leaving an array of segment start/end positions. That's twisted around into an array of start/end coordinates. + Magical. Fast. Could do the same for means or medians over windows for sparse bigwigs like repeat regions. + """ if isTop: - bwex = np.r_[False, bw >= self.bwtop, False] # extend with 0s + bwex = np.r_[False, bw >= self.bwtop, False] # extend with 0s else: bwex = np.r_[False, bw <= self.bwbot, False] bwexd = np.diff(bwex) bwexdnz = bwexd.nonzero()[0] - bwregions = np.reshape(bwexdnz, (-1,2)) + bwregions = np.reshape(bwexdnz, (-1, 2)) return bwregions def writeBed(self, bed, bedfname): @@ -60,89 +151,151 @@ potentially multiple """ bed.sort() - beds = ['%s\t%d\t%d\t%s\t%d' % x for x in bed] + beds = ["%s\t%d\t%d\t%s\t%d" % x for x in bed] with open(bedfname, "w") as bedf: - bedf.write('\n'.join(beds)) - bedf.write('\n') - print('Wrote %d bed regions to %s' % (len(bed), bedfname)) - + bedf.write("\n".join(beds)) + bedf.write("\n") + + def makeTableRow(self, bw, bwlabel, chr): + """ + called for every contig, but messy inline + """ + bwmean = np.mean(bw) + bwstd = np.std(bw) + bwmax = np.max(bw) + nrow = np.size(bw) + bwmin = np.min(bw) + row = "%s\t%s\t%d\t%f\t%f\t%f\t%f" % ( + bwlabel, + chr, + nrow, + bwmean, + bwstd, + bwmin, + bwmax, + ) + if self.qhi is not None: + row += "\t%.2f" % self.bwtop + else: + row += "\tnoqhi" + if self.qlo is not None: + row += "\t%.2f" % self.bwbot + else: + row += "\tnoqlo" + return row + def makeBed(self): bedhi = [] bedlo = [] + restab = [] bwlabels = self.bwlabels bwnames = self.bwnames - print('bwnames=', bwnames, "bwlabs=", bwlabels) + reshead = "bigwig\tcontig\tn\tmean\tstd\tmin\tmax\tqtop\tqbot" for i, bwname in enumerate(bwnames): - bwlabel = bwlabels[i].replace(" ",'') - p = Path('in.bw') - p.symlink_to( bwname ) # required by pybigtools (!) - bwf = pybigtools.open('in.bw') + bwlabel = bwlabels[i].replace(" ", "") + fakepath = "in%d.bw" % i + if os.path.isfile(fakepath): + os.remove(fakepath) + p = Path(fakepath) + p.symlink_to(bwname) # required by pybigtools (!) + bwf = pybigtools.open(fakepath) chrlist = bwf.chroms() chrs = list(chrlist.keys()) - chrs.sort() - restab = ["contig\tn\tmean\tstd\tmin\tmax\tqtop\tqbot"] for chr in chrs: + first_few = None bw = bwf.values(chr) - bw = bw[~np.isnan(bw)] # some have NaN if parts of a contig not covered + values, counts = np.unique(bw, return_counts=True) + nvalues = len(values) + if nvalues <= 20: + histo = '\n'.join(['%s: %f occurs %d times' % (chr, values[x], counts[x]) for x in range(len(values))]) + else: + last10 = range(nvalues-10, nvalues) + first_few = ['%.2f\t%d' % (values[x],counts[x]) for x in range(10)] + first_few += ['%.2f\t%d' % (values[x],counts[x]) for x in last10] + first_few.insert(0,'First/Last 10 value counts\nValue\tCount') + ha = asciihist(data=bw, bins=20, str_tag=chr) + histo = ha.draw() + histo = '\n'.join(first_few) + '\nHistogram of bigwig values\n' + histo + bw = bw[~np.isnan(bw)] # some have NaN if parts of a contig not covered if self.qhi is not None: self.bwtop = np.quantile(bw, self.qhi) bwhi = self.processVals(bw, isTop=True) - for i, seg in enumerate(bwhi): - if seg[1] - seg[0] >= self.bedwin: - bedhi.append((chr, seg[0], seg[1], '%s_hi' % (bwlabel), 1)) + for j, seg in enumerate(bwhi): + seglen = seg[1] - seg[0] + if seglen >= self.bedwin: + score = np.sum(bw[seg[0]:seg[1]])/float(seglen) + bedhi.append( + ( + chr, + seg[0], + seg[1], + "%s_%d" % (bwlabel, score), + score, + ) + ) if self.qlo is not None: self.bwbot = np.quantile(bw, self.qlo) - bwlo = self.processVals(bw, isTop=False) - for i, seg in enumerate(bwlo): + bwlo = self.processVals(bw, isTop=False) + for j, seg in enumerate(bwlo): if seg[1] - seg[0] >= self.bedwin: - bedlo.append((chr, seg[0], seg[1], '%s_lo' % (bwlabel), -1)) - bwmean = np.mean(bw) - bwstd = np.std(bw) - bwmax = np.max(bw) - nrow = np.size(bw) - bwmin = np.min(bw) - restab.append('%s\t%d\t%f\t%f\t%f\t%f\t%f\t%f' % (chr,nrow,bwmean,bwstd,bwmin,bwmax,self.bwtop,self.bwbot)) - print('\n'.join(restab), '\n') - if self.tableout: - with open(self.tableout) as t: - t.write('\n'.join(restab)) - t.write('\n') - if self.bedoutlo: - if self.qlo: + score = -1 * np.sum(bw[seg[0]:seg[1]])/float(seglen) + bedlo.append( + ( + chr, + seg[0], + seg[1], + "%s_%d" % (bwlabel, score), + score, + ) + ) + if self.tableoutfile: + row = self.makeTableRow(bw, bwlabel, chr) + resheadl = reshead.split('\t') + rowl = row.split() + desc = ['%s\t%s' % (resheadl[x], rowl[x]) for x in range(len(rowl))] + desc.insert(0, 'Descriptive measures') + descn = '\n'.join(desc) + restab.append(descn) + restab.append(histo) + if os.path.isfile(fakepath): + os.remove(fakepath) + if self.tableoutfile: + stable = "\n".join(restab) + with open(self.tableoutfile, "w") as t: + t.write(stable) + t.write("\n") + some = False + if self.qlo: + if self.outbeds in ["outall", "outlo", "outlohi"]: self.writeBed(bedlo, self.bedoutlo) - if self.bedouthi: - if self.qhi: + some = True + if self.qhi: + if self.outbeds in ["outall", "outlohi", "outhi"]: self.writeBed(bedhi, self.bedouthi) - if self.bedouthilo: + some = True + if self.outbeds in ["outall", "outhilo"]: allbed = bedlo + bedhi self.writeBed(allbed, self.bedouthilo) - return restab - + some = True + if not ((self.outbeds == 'outtab') or some): + sys.stderr.write( + "Invalid configuration - no output could be created. Was qlo missing and only low output requested for example?" + ) + sys.exit(2) + if __name__ == "__main__": parser = argparse.ArgumentParser() a = parser.add_argument - a('-m', '--minwin',default=10, type=int) - a('-l', '--qlo',default=None, type=float) - a('-i', '--qhi',default=None, type=float) - a('-w', '--bigwig', nargs='+') - a('-n', '--bigwiglabels', nargs='+') - a('-o', '--bedouthilo', default=None, help="optional high and low combined bed") - a('-u', '--bedouthi', default=None, help="optional high only bed") - a('-b', '--bedoutlo', default=None, help="optional low only bed") - a('-t', '--tableout', default=None) + a("-m", "--minwin", default=10, type=int) + a("-l", "--qlo", default=None) + a("-i", "--qhi", default=None, type=float) + a("--bedouthi", default=None) + a("--bedoutlo", default=None) + a("--bedouthilo", default=None) + a("-w", "--bigwig", nargs="+") + a("-n", "--bigwiglabels", nargs="+") + a("-o", "--outbeds", default="outhilo", help="optional high and low combined bed") + a("-t", "--tableoutfile", default=None) args = parser.parse_args() - print('args=', args) - if not (args.bedouthilo or args.bedouthi or args.bedoutlo): - sys.stderr.write("bigwig_outlier_bed.py cannot usefully run - need a bed output choice - must be one of low only, high only or both combined") - sys.exit(2) - if not (args.qlo or args.qhi): - sys.stderr.write("bigwig_outlier_bed.py cannot usefully run - need one or both of quantile cutpoints qhi and qlo") - sys.exit(2) - restab = findOut(args) - if args.tableout: - with open(args.tableout, 'w') as tout: - tout.write('\n'.join(restab)) - tout.write('\n') - - + findOut(args) diff -r 68cb8e7e266b -r eb17eb8a3658 bigwig_outlier_bed.xml --- a/bigwig_outlier_bed.xml Mon Jul 01 05:02:05 2024 +0000 +++ b/bigwig_outlier_bed.xml Tue Jul 23 23:12:23 2024 +0000 @@ -1,208 +1,198 @@ - - - - Writes high and low bigwig regions as features in a bed file + + Writes high and low bigwig runs as features in a bed file + + 0.2.0 + 2.0.0 + 3.12.3 + topic_0157 topic_0092 operation_0337 - + + + bigtools + - python - numpy - pybigtools + python + numpy + pybigtools + + + - - - 0/<0 so those are used for scores -Bed interval naming must be short for JB2 but needs input bigwig name and (lo or hi). -""" - -import argparse -import numpy as np -import pybigtools -import sys -from pathlib import Path - - -class findOut(): - def __init__(self, args): - self.bwnames=args.bigwig - self.bwlabels=args.bigwiglabels - self.bedwin=args.minwin - self.qlo=args.qlo - self.qhi=args.qhi - self.bedouthilo=args.bedouthilo - self.bedouthi=args.bedouthi - self.bedoutlo=args.bedoutlo - self.tableout = args.tableout - self.bedwin = args.minwin - self.qhi = args.qhi - self.qlo = args.qlo - self.makeBed() - - def processVals(self, bw, isTop): - # http://gregoryzynda.com/python/numpy/contiguous/interval/2019/11/29/contiguous-regions.html - if isTop: - bwex = np.r_[False, bw >= self.bwtop, False] # extend with 0s - else: - bwex = np.r_[False, bw <= self.bwbot, False] - bwexd = np.diff(bwex) - bwexdnz = bwexd.nonzero()[0] - bwregions = np.reshape(bwexdnz, (-1,2)) - return bwregions - - def writeBed(self, bed, bedfname): - """ - potentially multiple - """ - bed.sort() - beds = ['%s\t%d\t%d\t%s\t%d' % x for x in bed] - with open(bedfname, "w") as bedf: - bedf.write('\n'.join(beds)) - bedf.write('\n') - print('Wrote %d bed regions to %s' % (len(bed), bedfname)) - - def makeBed(self): - bedhi = [] - bedlo = [] - bwlabels = self.bwlabels - bwnames = self.bwnames - print('bwnames=', bwnames, "bwlabs=", bwlabels) - for i, bwname in enumerate(bwnames): - bwlabel = bwlabels[i].replace(" ",'') - p = Path('in.bw') - p.symlink_to( bwname ) # required by pybigtools (!) - bwf = pybigtools.open('in.bw') - chrlist = bwf.chroms() - chrs = list(chrlist.keys()) - chrs.sort() - restab = ["contig\tn\tmean\tstd\tmin\tmax\tqtop\tqbot"] - for chr in chrs: - bw = bwf.values(chr) - bw = bw[~np.isnan(bw)] # some have NaN if parts of a contig not covered - if self.qhi is not None: - self.bwtop = np.quantile(bw, self.qhi) - bwhi = self.processVals(bw, isTop=True) - for i, seg in enumerate(bwhi): - if seg[1] - seg[0] >= self.bedwin: - bedhi.append((chr, seg[0], seg[1], '%s_hi' % (bwlabel), 1)) - if self.qlo is not None: - self.bwbot = np.quantile(bw, self.qlo) - bwlo = self.processVals(bw, isTop=False) - for i, seg in enumerate(bwlo): - if seg[1] - seg[0] >= self.bedwin: - bedlo.append((chr, seg[0], seg[1], '%s_lo' % (bwlabel), -1)) - bwmean = np.mean(bw) - bwstd = np.std(bw) - bwmax = np.max(bw) - nrow = np.size(bw) - bwmin = np.min(bw) - restab.append('%s\t%d\t%f\t%f\t%f\t%f\t%f\t%f' % (chr,nrow,bwmean,bwstd,bwmin,bwmax,self.bwtop,self.bwbot)) - print('\n'.join(restab), '\n') - if self.tableout: - with open(self.tableout) as t: - t.write('\n'.join(restab)) - t.write('\n') - if self.bedoutlo: - if self.qlo: - self.writeBed(bedlo, self.bedoutlo) - if self.bedouthi: - if self.qhi: - self.writeBed(bedhi, self.bedouthi) - if self.bedouthilo: - allbed = bedlo + bedhi - self.writeBed(allbed, self.bedouthilo) - return restab - - -if __name__ == "__main__": - parser = argparse.ArgumentParser() - a = parser.add_argument - a('-m', '--minwin',default=10, type=int) - a('-l', '--qlo',default=None, type=float) - a('-i', '--qhi',default=None, type=float) - a('-w', '--bigwig', nargs='+') - a('-n', '--bigwiglabels', nargs='+') - a('-o', '--bedouthilo', default=None, help="optional high and low combined bed") - a('-u', '--bedouthi', default=None, help="optional high only bed") - a('-b', '--bedoutlo', default=None, help="optional low only bed") - a('-t', '--tableout', default=None) - args = parser.parse_args() - print('args=', args) - if not (args.bedouthilo or args.bedouthi or args.bedoutlo): - sys.stderr.write("bigwig_outlier_bed.py cannot usefully run - need a bed output choice - must be one of low only, high only or both combined") - sys.exit(2) - if not (args.qlo or args.qhi): - sys.stderr.write("bigwig_outlier_bed.py cannot usefully run - need one or both of quantile cutpoints qhi and qlo") - sys.exit(2) - restab = findOut(args) - if args.tableout: - with open(args.tableout, 'w') as tout: - tout.write('\n'.join(restab)) - tout.write('\n') -#end raw]]> - +#for bw in $bigwig: + '$bw.name' +#end for +--outbeds '$outbeds' +#if $outbeds in ['outhilo', 'outall']: + --bedouthilo '$bedouthilo' +#end if +#if $outbeds in ['outhi', 'outall', 'outlohi']: + --bedouthi '$bedouthi' +#end if +#if $outbeds in ['outlo', 'outall', 'outlohi']: + --bedoutlo '$bedoutlo' +#end if +--minwin '$minwin' +#if $qhi: +--qhi '$qhi' +#end if +#if $qlo: +--qlo '$qlo' +#end if +#if $tableout == "create" or $outbeds == "outtab": + --tableoutfile '$tableoutfile' +#end if +]]> - - - - - - - + + + + + + + + + + + - + + + + - - + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 68cb8e7e266b -r eb17eb8a3658 bigwigtobed.python.txt --- a/bigwigtobed.python.txt Mon Jul 01 05:02:05 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,131 +0,0 @@ -#raw -""" -Ross Lazarus June 2024 for VGP -Bigwigs are great, but hard to reliably "see" small low coverage or small very high coverage regions. -Colouring in JB2 tracks will need a new plugin, so this code will find bigwig regions above and below a chosen percentile point. -0.99 and 0.01 work well in testing with a minimum span of 10 bp. -Multiple bigwigs **with the same reference** can be combined - bed segments will be named appropriately -Combining multiple references works but is silly because only display will rely on one reference so others will not be shown... -Tricksy numpy method from http://gregoryzynda.com/python/numpy/contiguous/interval/2019/11/29/contiguous-regions.html -takes about 95 seconds for a 17MB test wiggle -JBrowse2 bed normally displays ignore the score, so could provide separate low/high bed file outputs as an option. -Update june 30 2024: wrote a 'no-build' plugin for beds to display red/blue if >0/<0 so those are used for scores -Bed interval naming must be short for JB2 but needs input bigwig name and (lo or hi). -""" -import argparse -import numpy as np -import pybigtools -import sys -from pathlib import Path -class findOut(): - def __init__(self, args): - self.bwnames=args.bigwig - self.bwlabels=args.bigwiglabels - self.bedwin=args.minwin - self.qlo=args.qlo - self.qhi=args.qhi - self.bedouthilo=args.bedouthilo - self.bedouthi=args.bedouthi - self.bedoutlo=args.bedoutlo - self.tableout = args.tableout - self.bedwin = args.minwin - self.qhi = args.qhi - self.qlo = args.qlo - self.makeBed() - def processVals(self, bw, isTop): - # http://gregoryzynda.com/python/numpy/contiguous/interval/2019/11/29/contiguous-regions.html - if isTop: - bwex = np.r_[False, bw >= self.bwtop, False] # extend with 0s - else: - bwex = np.r_[False, bw <= self.bwbot, False] - bwexd = np.diff(bwex) - bwexdnz = bwexd.nonzero()[0] - bwregions = np.reshape(bwexdnz, (-1,2)) - return bwregions - def writeBed(self, bed, bedfname): - """ - potentially multiple - """ - bed.sort() - beds = ['%s\t%d\t%d\t%s\t%d' % x for x in bed] - with open(bedfname, "w") as bedf: - bedf.write('\n'.join(beds)) - bedf.write('\n') - print('Wrote %d bed regions to %s' % (len(bed), bedfname)) - def makeBed(self): - bedhi = [] - bedlo = [] - bwlabels = self.bwlabels - bwnames = self.bwnames - print('bwnames=', bwnames, "bwlabs=", bwlabels) - for i, bwname in enumerate(bwnames): - bwlabel = bwlabels[i].replace(" ",'') - p = Path('in.bw') - p.symlink_to( bwname ) # required by pybigtools (!) - bwf = pybigtools.open('in.bw') - chrlist = bwf.chroms() - chrs = list(chrlist.keys()) - chrs.sort() - restab = ["contig\tn\tmean\tstd\tmin\tmax\tqtop\tqbot"] - for chr in chrs: - bw = bwf.values(chr) - bw = bw[~np.isnan(bw)] # some have NaN if parts of a contig not covered - if self.qhi is not None: - self.bwtop = np.quantile(bw, self.qhi) - bwhi = self.processVals(bw, isTop=True) - for i, seg in enumerate(bwhi): - if seg[1] - seg[0] >= self.bedwin: - bedhi.append((chr, seg[0], seg[1], '%s_hi' % (bwlabel), 1)) - if self.qlo is not None: - self.bwbot = np.quantile(bw, self.qlo) - bwlo = self.processVals(bw, isTop=False) - for i, seg in enumerate(bwlo): - if seg[1] - seg[0] >= self.bedwin: - bedlo.append((chr, seg[0], seg[1], '%s_lo' % (bwlabel), -1)) - bwmean = np.mean(bw) - bwstd = np.std(bw) - bwmax = np.max(bw) - nrow = np.size(bw) - bwmin = np.min(bw) - restab.append('%s\t%d\t%f\t%f\t%f\t%f\t%f\t%f' % (chr,nrow,bwmean,bwstd,bwmin,bwmax,self.bwtop,self.bwbot)) - print('\n'.join(restab), '\n') - if self.tableout: - with open(self.tableout) as t: - t.write('\n'.join(restab)) - t.write('\n') - if self.bedoutlo: - if self.qlo: - self.writeBed(bedlo, self.bedoutlo) - if self.bedouthi: - if self.qhi: - self.writeBed(bedhi, self.bedouthi) - if self.bedouthilo: - allbed = bedlo + bedhi - self.writeBed(allbed, self.bedouthilo) - return restab -if __name__ == "__main__": - parser = argparse.ArgumentParser() - a = parser.add_argument - a('-m', '--minwin',default=10, type=int) - a('-l', '--qlo',default=None, type=float) - a('-i', '--qhi',default=None, type=float) - a('-w', '--bigwig', nargs='+') - a('-n', '--bigwiglabels', nargs='+') - a('-o', '--bedouthilo', default=None, help="optional high and low combined bed") - a('-u', '--bedouthi', default=None, help="optional high only bed") - a('-b', '--bedoutlo', default=None, help="optional low only bed") - a('-t', '--tableout', default=None) - args = parser.parse_args() - print('args=', args) - if not (args.bedouthilo or args.bedouthi or args.bedoutlo): - sys.stderr.write("bigwig_outlier_bed.py cannot usefully run - need a bed output choice - must be one of low only, high only or both combined") - sys.exit(2) - if not (args.qlo or args.qhi): - sys.stderr.write("bigwig_outlier_bed.py cannot usefully run - need one or both of quantile cutpoints qhi and qlo") - sys.exit(2) - restab = findOut(args) - if args.tableout: - with open(args.tableout, 'w') 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bigwig_sample_hi 1 +Merlin 63330 63340 bigwig_sample_hi 1 +Merlin 63350 63360 bigwig_sample_hi 1 +Merlin 66210 66220 bigwig_sample_hi 1 +Merlin 66510 66520 bigwig_sample_hi 1 +Merlin 66850 66860 bigwig_sample_hi 1 +Merlin 67690 67700 bigwig_sample_hi 1 +Merlin 68760 68780 bigwig_sample_hi 1 +Merlin 69850 69860 bigwig_sample_hi 1 diff -r 68cb8e7e266b -r eb17eb8a3658 test-data/bedouthilo_sample --- a/test-data/bedouthilo_sample Mon Jul 01 05:02:05 2024 +0000 +++ b/test-data/bedouthilo_sample Tue Jul 23 23:12:23 2024 +0000 @@ -1,139 +1,179 @@ -Merlin 20 30 outbed_hi 1 -Merlin 80 90 outbed_lo -1 -Merlin 190 200 outbed_hi 1 -Merlin 430 440 outbed_lo -1 -Merlin 1230 1240 outbed_lo -1 -Merlin 1570 1580 outbed_hi 1 -Merlin 1730 1740 outbed_hi 1 -Merlin 1850 1860 outbed_hi 1 -Merlin 1880 1890 outbed_hi 1 -Merlin 2670 2680 outbed_lo -1 -Merlin 3400 3410 outbed_hi 1 -Merlin 3740 3750 outbed_lo -1 -Merlin 4030 4040 outbed_hi 1 -Merlin 4700 4710 outbed_lo -1 -Merlin 5870 5890 outbed_lo -1 -Merlin 6290 6300 outbed_lo -1 -Merlin 7120 7130 outbed_hi 1 -Merlin 7860 7870 outbed_hi 1 -Merlin 8280 8290 outbed_hi 1 -Merlin 8860 8870 outbed_lo -1 -Merlin 10520 10530 outbed_lo -1 -Merlin 10820 10830 outbed_hi 1 -Merlin 11190 11200 outbed_lo -1 -Merlin 11380 11390 outbed_lo -1 -Merlin 11810 11820 outbed_lo -1 -Merlin 12660 12670 outbed_lo -1 -Merlin 13310 13320 outbed_hi 1 -Merlin 14160 14170 outbed_lo -1 -Merlin 14750 14760 outbed_lo -1 -Merlin 16270 16280 outbed_lo -1 -Merlin 17240 17250 outbed_lo -1 -Merlin 17570 17580 outbed_hi 1 -Merlin 17940 17950 outbed_hi 1 -Merlin 18290 18300 outbed_lo -1 -Merlin 18340 18350 outbed_hi 1 -Merlin 18810 18820 outbed_hi 1 -Merlin 19080 19090 outbed_lo -1 -Merlin 19220 19230 outbed_lo -1 -Merlin 20240 20250 outbed_lo -1 -Merlin 21650 21660 outbed_lo -1 -Merlin 21810 21820 outbed_lo -1 -Merlin 22310 22320 outbed_hi 1 -Merlin 23630 23640 outbed_lo -1 -Merlin 23760 23770 outbed_hi 1 -Merlin 24580 24590 outbed_hi 1 -Merlin 24860 24870 outbed_hi 1 -Merlin 25030 25040 outbed_lo -1 -Merlin 25700 25710 outbed_hi 1 -Merlin 26260 26270 outbed_lo -1 -Merlin 26450 26460 outbed_hi 1 -Merlin 26560 26570 outbed_lo -1 -Merlin 26610 26620 outbed_lo -1 -Merlin 27220 27230 outbed_hi 1 -Merlin 27280 27290 outbed_hi 1 -Merlin 27670 27680 outbed_lo -1 -Merlin 27970 27980 outbed_lo -1 -Merlin 28500 28510 outbed_hi 1 -Merlin 29400 29410 outbed_lo -1 -Merlin 29740 29750 outbed_hi 1 -Merlin 29910 29920 outbed_lo -1 -Merlin 31540 31550 outbed_hi 1 -Merlin 31890 31900 outbed_hi 1 -Merlin 32970 32980 outbed_hi 1 -Merlin 33460 33470 outbed_lo -1 -Merlin 33910 33920 outbed_lo -1 -Merlin 33980 33990 outbed_hi 1 -Merlin 34470 34490 outbed_lo -1 -Merlin 35320 35330 outbed_lo -1 -Merlin 35440 35450 outbed_hi 1 -Merlin 35620 35630 outbed_lo -1 -Merlin 35880 35890 outbed_lo -1 -Merlin 36510 36520 outbed_hi 1 -Merlin 36810 36820 outbed_lo -1 -Merlin 37230 37240 outbed_lo -1 -Merlin 37560 37570 outbed_lo -1 -Merlin 37750 37760 outbed_lo -1 -Merlin 38330 38340 outbed_lo -1 -Merlin 39600 39610 outbed_lo -1 -Merlin 39690 39700 outbed_hi 1 -Merlin 40350 40360 outbed_hi 1 -Merlin 40550 40560 outbed_hi 1 -Merlin 40780 40790 outbed_hi 1 -Merlin 41390 41400 outbed_hi 1 -Merlin 41900 41910 outbed_lo -1 -Merlin 41940 41950 outbed_hi 1 -Merlin 42050 42060 outbed_lo -1 -Merlin 42470 42480 outbed_hi 1 -Merlin 42560 42570 outbed_hi 1 -Merlin 42730 42740 outbed_hi 1 -Merlin 43010 43020 outbed_hi 1 -Merlin 43910 43920 outbed_hi 1 -Merlin 44440 44450 outbed_lo -1 -Merlin 44670 44680 outbed_hi 1 -Merlin 46010 46020 outbed_hi 1 -Merlin 46470 46480 outbed_hi 1 -Merlin 46610 46620 outbed_lo -1 -Merlin 49290 49300 outbed_lo -1 -Merlin 49370 49380 outbed_hi 1 -Merlin 50310 50320 outbed_hi 1 -Merlin 50880 50890 outbed_lo -1 -Merlin 52230 52240 outbed_lo -1 -Merlin 52460 52470 outbed_lo -1 -Merlin 52740 52750 outbed_lo -1 -Merlin 52770 52780 outbed_lo -1 -Merlin 52980 52990 outbed_hi 1 -Merlin 53150 53160 outbed_lo -1 -Merlin 54630 54640 outbed_hi 1 -Merlin 54830 54840 outbed_lo -1 -Merlin 55430 55440 outbed_hi 1 -Merlin 56020 56030 outbed_lo -1 -Merlin 56450 56460 outbed_hi 1 -Merlin 56630 56640 outbed_hi 1 -Merlin 57220 57230 outbed_lo -1 -Merlin 57610 57620 outbed_hi 1 -Merlin 57790 57800 outbed_hi 1 -Merlin 58730 58740 outbed_hi 1 -Merlin 59360 59370 outbed_hi 1 -Merlin 59450 59460 outbed_hi 1 -Merlin 60210 60220 outbed_hi 1 -Merlin 61110 61120 outbed_hi 1 -Merlin 61250 61260 outbed_lo -1 -Merlin 62470 62480 outbed_hi 1 -Merlin 63190 63200 outbed_lo -1 -Merlin 63290 63300 outbed_lo -1 -Merlin 63330 63340 outbed_hi 1 -Merlin 63350 63360 outbed_hi 1 -Merlin 64660 64670 outbed_lo -1 -Merlin 65050 65060 outbed_lo -1 -Merlin 66210 66220 outbed_hi 1 -Merlin 66510 66520 outbed_hi 1 -Merlin 66660 66670 outbed_lo -1 -Merlin 66850 66860 outbed_hi 1 -Merlin 66900 66910 outbed_lo -1 -Merlin 67150 67160 outbed_lo -1 -Merlin 67690 67700 outbed_hi 1 -Merlin 68760 68780 outbed_hi 1 -Merlin 68790 68800 outbed_lo -1 -Merlin 69660 69670 outbed_lo -1 -Merlin 69850 69860 outbed_hi 1 +Merlin 29 39 bigwig_sample_32455 32455 +Merlin 199 209 bigwig_sample_32543 32543 +Merlin 299 309 bigwig_sample_32244 32244 +Merlin 1579 1589 bigwig_sample_32605 32605 +Merlin 1729 1749 bigwig_sample_32276 32276 +Merlin 1859 1869 bigwig_sample_32569 32569 +Merlin 1889 1899 bigwig_sample_32406 32406 +Merlin 2589 2599 bigwig_sample_31999 31999 +Merlin 3409 3419 bigwig_sample_32731 32731 +Merlin 3659 3669 bigwig_sample_32052 32052 +Merlin 4039 4049 bigwig_sample_32636 32636 +Merlin 4409 4419 bigwig_sample_31941 31941 +Merlin 7129 7139 bigwig_sample_32449 32449 +Merlin 7269 7279 bigwig_sample_32288 32288 +Merlin 7869 7879 bigwig_sample_32724 32724 +Merlin 8079 8089 bigwig_sample_32031 32031 +Merlin 8289 8299 bigwig_sample_32545 32545 +Merlin 8739 8749 bigwig_sample_32005 32005 +Merlin 9039 9049 bigwig_sample_32217 32217 +Merlin 9259 9269 bigwig_sample_32114 32114 +Merlin 9459 9469 bigwig_sample_32260 32260 +Merlin 9549 9559 bigwig_sample_32108 32108 +Merlin 10209 10219 bigwig_sample_32107 32107 +Merlin 10829 10839 bigwig_sample_32766 32766 +Merlin 11219 11229 bigwig_sample_32089 32089 +Merlin 12049 12059 bigwig_sample_32371 32371 +Merlin 12169 12179 bigwig_sample_32170 32170 +Merlin 12509 12519 bigwig_sample_32254 32254 +Merlin 12969 12979 bigwig_sample_31932 31932 +Merlin 13319 13329 bigwig_sample_32695 32695 +Merlin 13749 13759 bigwig_sample_32364 32364 +Merlin 14419 14429 bigwig_sample_32029 32029 +Merlin 14469 14479 bigwig_sample_32250 32250 +Merlin 14749 14759 bigwig_sample_32248 32248 +Merlin 15499 15509 bigwig_sample_32125 32125 +Merlin 15979 15989 bigwig_sample_32079 32079 +Merlin 16559 16569 bigwig_sample_32302 32302 +Merlin 16589 16599 bigwig_sample_32385 32385 +Merlin 17579 17589 bigwig_sample_32463 32463 +Merlin 17949 17959 bigwig_sample_32580 32580 +Merlin 17989 17999 bigwig_sample_32248 32248 +Merlin 18349 18359 bigwig_sample_32737 32737 +Merlin 18819 18829 bigwig_sample_32544 32544 +Merlin 19159 19169 bigwig_sample_32005 32005 +Merlin 19999 20009 bigwig_sample_32199 32199 +Merlin 20509 20519 bigwig_sample_32129 32129 +Merlin 20799 20809 bigwig_sample_32326 32326 +Merlin 21149 21159 bigwig_sample_32335 32335 +Merlin 21169 21179 bigwig_sample_32184 32184 +Merlin 21309 21319 bigwig_sample_32352 32352 +Merlin 21329 21339 bigwig_sample_32337 32337 +Merlin 21569 21579 bigwig_sample_32207 32207 +Merlin 22319 22329 bigwig_sample_32613 32613 +Merlin 22369 22379 bigwig_sample_32335 32335 +Merlin 22729 22739 bigwig_sample_31965 31965 +Merlin 22799 22809 bigwig_sample_32271 32271 +Merlin 22879 22889 bigwig_sample_31918 31918 +Merlin 23289 23299 bigwig_sample_32003 32003 +Merlin 23769 23779 bigwig_sample_32423 32423 +Merlin 23939 23949 bigwig_sample_32246 32246 +Merlin 24449 24459 bigwig_sample_31981 31981 +Merlin 24589 24599 bigwig_sample_32701 32701 +Merlin 24869 24879 bigwig_sample_32403 32403 +Merlin 24899 24919 bigwig_sample_32209 32209 +Merlin 25709 25719 bigwig_sample_32499 32499 +Merlin 25769 25779 bigwig_sample_32324 32324 +Merlin 26459 26469 bigwig_sample_32436 32436 +Merlin 26559 26569 bigwig_sample_32203 32203 +Merlin 27229 27239 bigwig_sample_32509 32509 +Merlin 27289 27299 bigwig_sample_32767 32767 +Merlin 27529 27539 bigwig_sample_32210 32210 +Merlin 27919 27929 bigwig_sample_31926 31926 +Merlin 28509 28519 bigwig_sample_32628 32628 +Merlin 28589 28599 bigwig_sample_32192 32192 +Merlin 29069 29079 bigwig_sample_31921 31921 +Merlin 29189 29199 bigwig_sample_31939 31939 +Merlin 29749 29759 bigwig_sample_32709 32709 +Merlin 29849 29859 bigwig_sample_32376 32376 +Merlin 29889 29899 bigwig_sample_32142 32142 +Merlin 30299 30309 bigwig_sample_32382 32382 +Merlin 31549 31559 bigwig_sample_32387 32387 +Merlin 31899 31909 bigwig_sample_32572 32572 +Merlin 32049 32059 bigwig_sample_32097 32097 +Merlin 32949 32959 bigwig_sample_32019 32019 +Merlin 32979 32989 bigwig_sample_32536 32536 +Merlin 33729 33739 bigwig_sample_32063 32063 +Merlin 33989 33999 bigwig_sample_32571 32571 +Merlin 35449 35459 bigwig_sample_32451 32451 +Merlin 36159 36169 bigwig_sample_32188 32188 +Merlin 36399 36409 bigwig_sample_31933 31933 +Merlin 36519 36529 bigwig_sample_32686 32686 +Merlin 36589 36599 bigwig_sample_32354 32354 +Merlin 37939 37949 bigwig_sample_32111 32111 +Merlin 38549 38559 bigwig_sample_31918 31918 +Merlin 39529 39539 bigwig_sample_32165 32165 +Merlin 39699 39709 bigwig_sample_32615 32615 +Merlin 40149 40159 bigwig_sample_32224 32224 +Merlin 40359 40369 bigwig_sample_32728 32728 +Merlin 40559 40569 bigwig_sample_32597 32597 +Merlin 40699 40709 bigwig_sample_32298 32298 +Merlin 40789 40799 bigwig_sample_32612 32612 +Merlin 41399 41409 bigwig_sample_32730 32730 +Merlin 41949 41959 bigwig_sample_32397 32397 +Merlin 42479 42489 bigwig_sample_32390 32390 +Merlin 42569 42579 bigwig_sample_32399 32399 +Merlin 42739 42749 bigwig_sample_32506 32506 +Merlin 42759 42769 bigwig_sample_32259 32259 +Merlin 43019 43029 bigwig_sample_32426 32426 +Merlin 43049 43059 bigwig_sample_32165 32165 +Merlin 43919 43929 bigwig_sample_32721 32721 +Merlin 44029 44039 bigwig_sample_32179 32179 +Merlin 44189 44199 bigwig_sample_31943 31943 +Merlin 44679 44689 bigwig_sample_32501 32501 +Merlin 45249 45259 bigwig_sample_32177 32177 +Merlin 45649 45659 bigwig_sample_32172 32172 +Merlin 46019 46029 bigwig_sample_32441 32441 +Merlin 46479 46489 bigwig_sample_32685 32685 +Merlin 46889 46899 bigwig_sample_32112 32112 +Merlin 47439 47449 bigwig_sample_32062 32062 +Merlin 49379 49389 bigwig_sample_32531 32531 +Merlin 50069 50079 bigwig_sample_32099 32099 +Merlin 50319 50329 bigwig_sample_32641 32641 +Merlin 50939 50949 bigwig_sample_32176 32176 +Merlin 51109 51119 bigwig_sample_32151 32151 +Merlin 51549 51559 bigwig_sample_32306 32306 +Merlin 52449 52459 bigwig_sample_31944 31944 +Merlin 52589 52599 bigwig_sample_31913 31913 +Merlin 52989 52999 bigwig_sample_32603 32603 +Merlin 53149 53159 bigwig_sample_32054 32054 +Merlin 53649 53659 bigwig_sample_32224 32224 +Merlin 54459 54469 bigwig_sample_32300 32300 +Merlin 54509 54519 bigwig_sample_32155 32155 +Merlin 54639 54649 bigwig_sample_32576 32576 +Merlin 54759 54769 bigwig_sample_32334 32334 +Merlin 54969 54979 bigwig_sample_31923 31923 +Merlin 55439 55449 bigwig_sample_32521 32521 +Merlin 56209 56219 bigwig_sample_31907 31907 +Merlin 56459 56469 bigwig_sample_32599 32599 +Merlin 56639 56649 bigwig_sample_32574 32574 +Merlin 56719 56729 bigwig_sample_32005 32005 +Merlin 57139 57149 bigwig_sample_32335 32335 +Merlin 57619 57629 bigwig_sample_32466 32466 +Merlin 57799 57809 bigwig_sample_32411 32411 +Merlin 57909 57919 bigwig_sample_32252 32252 +Merlin 58049 58059 bigwig_sample_32038 32038 +Merlin 58739 58749 bigwig_sample_32726 32726 +Merlin 59249 59259 bigwig_sample_32156 32156 +Merlin 59369 59379 bigwig_sample_32592 32592 +Merlin 59459 59469 bigwig_sample_32650 32650 +Merlin 60219 60229 bigwig_sample_32659 32659 +Merlin 60309 60319 bigwig_sample_32367 32367 +Merlin 61119 61129 bigwig_sample_32518 32518 +Merlin 61679 61689 bigwig_sample_32370 32370 +Merlin 62179 62189 bigwig_sample_32055 32055 +Merlin 62479 62489 bigwig_sample_32538 32538 +Merlin 63039 63049 bigwig_sample_32048 32048 +Merlin 63149 63159 bigwig_sample_32256 32256 +Merlin 63339 63349 bigwig_sample_32745 32745 +Merlin 63359 63369 bigwig_sample_32683 32683 +Merlin 63469 63479 bigwig_sample_31926 31926 +Merlin 63519 63529 bigwig_sample_31953 31953 +Merlin 63949 63959 bigwig_sample_32338 32338 +Merlin 63969 63979 bigwig_sample_32167 32167 +Merlin 64359 64369 bigwig_sample_32186 32186 +Merlin 65999 66009 bigwig_sample_32167 32167 +Merlin 66219 66229 bigwig_sample_32661 32661 +Merlin 66519 66529 bigwig_sample_32731 32731 +Merlin 66859 66869 bigwig_sample_32552 32552 +Merlin 67249 67259 bigwig_sample_32335 32335 +Merlin 67699 67709 bigwig_sample_32697 32697 +Merlin 68649 68659 bigwig_sample_32302 32302 +Merlin 68769 68789 bigwig_sample_32429 32429 +Merlin 68989 68999 bigwig_sample_31961 31961 +Merlin 69259 69269 bigwig_sample_32057 32057 +Merlin 69579 69589 bigwig_sample_32098 32098 +Merlin 69819 69829 bigwig_sample_32047 32047 +Merlin 69859 69869 bigwig_sample_32663 32663 +Merlin 69889 69899 bigwig_sample_31994 31994 +Merlin 70049 180929 bigwig_sample_0 0 diff -r 68cb8e7e266b -r eb17eb8a3658 test-data/bedoutlo2_sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bedoutlo2_sample Tue Jul 23 23:12:23 2024 +0000 @@ -0,0 +1,110 @@ +Merlin 0 9 bigwig_sample_0 0 +Merlin 70049 180929 bigwig_sample_0 0 +chr21 0 9411190 1.bigwig_0 0 +chr21 9411785 9411790 1.bigwig_0 0 +chr21 9411800 9411815 1.bigwig_0 0 +chr21 9411860 9411865 1.bigwig_0 0 +chr21 9411900 9411905 1.bigwig_0 0 +chr21 9412005 9412010 1.bigwig_0 0 +chr21 9412050 9412055 1.bigwig_0 0 +chr21 9412065 9412070 1.bigwig_0 0 +chr21 9412080 9412085 1.bigwig_0 0 +chr21 9412100 9412105 1.bigwig_0 0 +chr21 9412120 9412125 1.bigwig_0 0 +chr21 9412130 9412135 1.bigwig_0 0 +chr21 9412140 9412145 1.bigwig_0 0 +chr21 9412180 9412185 1.bigwig_0 0 +chr21 9412200 9412210 1.bigwig_0 0 +chr21 9412225 9412230 1.bigwig_0 0 +chr21 9412250 9412260 1.bigwig_0 0 +chr21 9412305 9412310 1.bigwig_0 0 +chr21 9412360 9412370 1.bigwig_0 0 +chr21 9412385 9412390 1.bigwig_0 0 +chr21 9412400 9412415 1.bigwig_0 0 +chr21 9412440 9412455 1.bigwig_0 0 +chr21 9412460 9412465 1.bigwig_0 0 +chr21 9412470 9412480 1.bigwig_0 0 +chr21 9412485 9412490 1.bigwig_0 0 +chr21 9412510 9412515 1.bigwig_0 0 +chr21 9412565 9412570 1.bigwig_0 0 +chr21 9412590 9412595 1.bigwig_0 0 +chr21 9412640 9412650 1.bigwig_0 0 +chr21 9412670 9412675 1.bigwig_0 0 +chr21 9412690 9412700 1.bigwig_0 0 +chr21 9412770 9412775 1.bigwig_0 0 +chr21 9412815 9412820 1.bigwig_0 0 +chr21 9412835 9412840 1.bigwig_0 0 +chr21 9412845 9412850 1.bigwig_0 0 +chr21 9412900 9412905 1.bigwig_0 0 +chr21 9412970 9412975 1.bigwig_0 0 +chr21 9412990 9412995 1.bigwig_0 0 +chr21 9413040 9413045 1.bigwig_0 0 +chr21 9413055 9413065 1.bigwig_0 0 +chr21 9413095 9413100 1.bigwig_0 0 +chr21 9413130 9413135 1.bigwig_0 0 +chr21 9413155 9413160 1.bigwig_0 0 +chr21 9413170 9413180 1.bigwig_0 0 +chr21 9413205 9413210 1.bigwig_0 0 +chr21 9413250 9413255 1.bigwig_0 0 +chr21 9413280 9413285 1.bigwig_0 0 +chr21 9413310 9413315 1.bigwig_0 0 +chr21 9413345 9413350 1.bigwig_0 0 +chr21 9413400 9413405 1.bigwig_0 0 +chr21 9413510 9413515 1.bigwig_0 0 +chr21 9413665 9413670 1.bigwig_0 0 +chr21 9414040 9414045 1.bigwig_0 0 +chr21 9414055 9414060 1.bigwig_0 0 +chr21 9414100 9414105 1.bigwig_0 0 +chr21 9414150 9414160 1.bigwig_0 0 +chr21 9414175 9414180 1.bigwig_0 0 +chr21 9414215 9414225 1.bigwig_0 0 +chr21 9414255 9414260 1.bigwig_0 0 +chr21 9414265 9414270 1.bigwig_0 0 +chr21 9414280 9414285 1.bigwig_0 0 +chr21 9414305 9414310 1.bigwig_0 0 +chr21 9414435 9414440 1.bigwig_0 0 +chr21 9414525 9414530 1.bigwig_0 0 +chr21 9414585 9414590 1.bigwig_0 0 +chr21 9414595 9414600 1.bigwig_0 0 +chr21 9414655 9414665 1.bigwig_0 0 +chr21 9414680 9414690 1.bigwig_0 0 +chr21 9414695 9414700 1.bigwig_0 0 +chr21 9414705 9414710 1.bigwig_0 0 +chr21 9414720 9414725 1.bigwig_0 0 +chr21 9414755 9414760 1.bigwig_0 0 +chr21 9414775 9414780 1.bigwig_0 0 +chr21 9414785 9414790 1.bigwig_0 0 +chr21 9414820 9414825 1.bigwig_0 0 +chr21 9414835 9414840 1.bigwig_0 0 +chr21 9414850 9414855 1.bigwig_0 0 +chr21 9414860 9414870 1.bigwig_0 0 +chr21 9414905 9414910 1.bigwig_0 0 +chr21 9414925 9414930 1.bigwig_0 0 +chr21 9414955 9414960 1.bigwig_0 0 +chr21 9414975 9414980 1.bigwig_0 0 +chr21 9414995 9415000 1.bigwig_0 0 +chr21 9415040 9415055 1.bigwig_0 0 +chr21 9415065 9415075 1.bigwig_0 0 +chr21 9415095 9415100 1.bigwig_0 0 +chr21 9415105 9415115 1.bigwig_0 0 +chr21 9415135 9415140 1.bigwig_0 0 +chr21 9415150 9415155 1.bigwig_0 0 +chr21 9415170 9415175 1.bigwig_0 0 +chr21 9415270 9415275 1.bigwig_0 0 +chr21 9415320 9415325 1.bigwig_0 0 +chr21 9415385 9415390 1.bigwig_0 0 +chr21 9415470 9415475 1.bigwig_0 0 +chr21 9415535 9415540 1.bigwig_0 0 +chr21 9415595 9415600 1.bigwig_0 0 +chr21 9415665 9415670 1.bigwig_0 0 +chr21 9415685 9415700 1.bigwig_0 0 +chr21 9415710 9415715 1.bigwig_0 0 +chr21 9415820 9415830 1.bigwig_0 0 +chr21 9415880 9415885 1.bigwig_0 0 +chr21 9416020 9416025 1.bigwig_0 0 +chr21 9416080 9416085 1.bigwig_0 0 +chr21 9416095 9416100 1.bigwig_0 0 +chr21 9416130 9416135 1.bigwig_0 0 +chr21 9416150 9416155 1.bigwig_0 0 +chr21 9416165 9416175 1.bigwig_0 0 +chr21 9416185 48129895 1.bigwig_0 0 diff -r 68cb8e7e266b -r eb17eb8a3658 test-data/bedoutlo_sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bedoutlo_sample Tue Jul 23 23:12:23 2024 +0000 @@ -0,0 +1,2 @@ +Merlin 0 9 bigwig_sample_0 0 +Merlin 70049 180929 bigwig_sample_0 0 diff -r 68cb8e7e266b -r eb17eb8a3658 test-data/table2_sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/table2_sample Tue Jul 23 23:12:23 2024 +0000 @@ -0,0 +1,74 @@ +Descriptive measures +bigwig bigwig_sample +contig Merlin +n 180929 +mean 6354.313736 +std 9951.749936 +min 0.000000 +max 32767.000000 +qtop 24359.00 +qbot 0.00 +First/Last 10 value counts +Value Count +0.00 110889 +13.00 30 +22.00 10 +26.00 10 +29.00 10 +40.00 10 +43.00 10 +53.00 10 +57.00 10 +60.00 20 +32721.00 10 +32724.00 10 +32726.00 10 +32728.00 10 +32730.00 10 +32731.00 20 +32737.00 10 +32745.00 10 +32766.00 10 +32767.00 10 +Histogram of bigwig values +Merlin 1638.35 | 114,349 | ************************************************** +Merlin 3276.70 | 3,650 | * +Merlin 4915.05 | 3,620 | * +Merlin 6553.40 | 3,570 | * +Merlin 8191.75 | 3,570 | * +Merlin 9830.10 | 3,410 | * +Merlin 11468.45 | 3,610 | * +Merlin 13106.80 | 3,170 | * +Merlin 14745.15 | 3,310 | * +Merlin 16383.50 | 3,390 | * +Merlin 18021.85 | 3,270 | * +Merlin 19660.20 | 3,680 | * +Merlin 21298.55 | 3,560 | * +Merlin 22936.90 | 3,490 | * +Merlin 24575.25 | 3,530 | * +Merlin 26213.60 | 3,460 | * +Merlin 27851.95 | 3,470 | * +Merlin 29490.30 | 3,500 | * +Merlin 31128.65 | 3,920 | * +Merlin 32767.00 | 3,400 | * +Merlin ------------ |------------ | +Merlin N= | 180,929 | +Merlin ------------ |------------ | + +Descriptive measures +bigwig 1.bigwig +contig chr21 +n 48129895 +mean 0.003446 +std 0.400601 +min 0.000000 +max 100.000000 +qtop 0.00 +qbot 0.00 +chr21: 0.000000 occurs 48125565 times +chr21: 20.000000 occurs 1660 times +chr21: 40.000000 occurs 1610 times +chr21: 50.000000 occurs 5 times +chr21: 60.000000 occurs 840 times +chr21: 80.000000 occurs 195 times +chr21: 100.000000 occurs 20 times diff -r 68cb8e7e266b -r eb17eb8a3658 test-data/table3_sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/table3_sample Tue Jul 23 23:12:23 2024 +0000 @@ -0,0 +1,57 @@ +Descriptive measures +bigwig bigwig_sample +contig Merlin +n 180929 +mean 6354.313736 +std 9951.749936 +min 0.000000 +max 32767.000000 +qtop 24359.00 +qbot 0.00 +First/Last 10 value counts +Value Count +0.00 110889 +13.00 30 +22.00 10 +26.00 10 +29.00 10 +40.00 10 +43.00 10 +53.00 10 +57.00 10 +60.00 20 +32721.00 10 +32724.00 10 +32726.00 10 +32728.00 10 +32730.00 10 +32731.00 20 +32737.00 10 +32745.00 10 +32766.00 10 +32767.00 10 +Histogram of bigwig values +Merlin 1638.35 | 114,349 | ************************************************** +Merlin 3276.70 | 3,650 | * +Merlin 4915.05 | 3,620 | * +Merlin 6553.40 | 3,570 | * +Merlin 8191.75 | 3,570 | * +Merlin 9830.10 | 3,410 | * +Merlin 11468.45 | 3,610 | * +Merlin 13106.80 | 3,170 | * +Merlin 14745.15 | 3,310 | * +Merlin 16383.50 | 3,390 | * +Merlin 18021.85 | 3,270 | * +Merlin 19660.20 | 3,680 | * +Merlin 21298.55 | 3,560 | * +Merlin 22936.90 | 3,490 | * +Merlin 24575.25 | 3,530 | * +Merlin 26213.60 | 3,460 | * +Merlin 27851.95 | 3,470 | * +Merlin 29490.30 | 3,500 | * +Merlin 31128.65 | 3,920 | * +Merlin 32767.00 | 3,400 | * +Merlin ------------ |------------ | +Merlin N= | 180,929 | +Merlin ------------ |------------ | + diff -r 68cb8e7e266b -r eb17eb8a3658 test-data/table_only_sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/table_only_sample Tue Jul 23 23:12:23 2024 +0000 @@ -0,0 +1,74 @@ +Descriptive measures +bigwig bigwig_sample +contig Merlin +n 180929 +mean 6354.313736 +std 9951.749936 +min 0.000000 +max 32767.000000 +qtop noqhi +qbot noqlo +First/Last 10 value counts +Value Count +0.00 110889 +13.00 30 +22.00 10 +26.00 10 +29.00 10 +40.00 10 +43.00 10 +53.00 10 +57.00 10 +60.00 20 +32721.00 10 +32724.00 10 +32726.00 10 +32728.00 10 +32730.00 10 +32731.00 20 +32737.00 10 +32745.00 10 +32766.00 10 +32767.00 10 +Histogram of bigwig values +Merlin 1638.35 | 114,349 | ************************************************** +Merlin 3276.70 | 3,650 | * +Merlin 4915.05 | 3,620 | * +Merlin 6553.40 | 3,570 | * +Merlin 8191.75 | 3,570 | * +Merlin 9830.10 | 3,410 | * +Merlin 11468.45 | 3,610 | * +Merlin 13106.80 | 3,170 | * +Merlin 14745.15 | 3,310 | * +Merlin 16383.50 | 3,390 | * +Merlin 18021.85 | 3,270 | * +Merlin 19660.20 | 3,680 | * +Merlin 21298.55 | 3,560 | * +Merlin 22936.90 | 3,490 | * +Merlin 24575.25 | 3,530 | * +Merlin 26213.60 | 3,460 | * +Merlin 27851.95 | 3,470 | * +Merlin 29490.30 | 3,500 | * +Merlin 31128.65 | 3,920 | * +Merlin 32767.00 | 3,400 | * +Merlin ------------ |------------ | +Merlin N= | 180,929 | +Merlin ------------ |------------ | + +Descriptive measures +bigwig 1.bigwig +contig chr21 +n 48129895 +mean 0.003446 +std 0.400601 +min 0.000000 +max 100.000000 +qtop noqhi +qbot noqlo +chr21: 0.000000 occurs 48125565 times +chr21: 20.000000 occurs 1660 times +chr21: 40.000000 occurs 1610 times +chr21: 50.000000 occurs 5 times +chr21: 60.000000 occurs 840 times +chr21: 80.000000 occurs 195 times +chr21: 100.000000 occurs 20 times diff -r 68cb8e7e266b -r eb17eb8a3658 test-data/table_qlo_notset_sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/table_qlo_notset_sample Tue Jul 23 23:12:23 2024 +0000 @@ -0,0 +1,57 @@ +Descriptive measures +bigwig bigwig_sample +contig Merlin +n 180929 +mean 6354.313736 +std 9951.749936 +min 0.000000 +max 32767.000000 +qtop 31906.72 +qbot noqlo +First/Last 10 value counts +Value Count +0.00 110889 +13.00 30 +22.00 10 +26.00 10 +29.00 10 +40.00 10 +43.00 10 +53.00 10 +57.00 10 +60.00 20 +32721.00 10 +32724.00 10 +32726.00 10 +32728.00 10 +32730.00 10 +32731.00 20 +32737.00 10 +32745.00 10 +32766.00 10 +32767.00 10 +Histogram of bigwig values +Merlin 1638.35 | 114,349 | ************************************************** +Merlin 3276.70 | 3,650 | * +Merlin 4915.05 | 3,620 | * +Merlin 6553.40 | 3,570 | * +Merlin 8191.75 | 3,570 | * +Merlin 9830.10 | 3,410 | * +Merlin 11468.45 | 3,610 | * +Merlin 13106.80 | 3,170 | * +Merlin 14745.15 | 3,310 | * +Merlin 16383.50 | 3,390 | * +Merlin 18021.85 | 3,270 | * +Merlin 19660.20 | 3,680 | * +Merlin 21298.55 | 3,560 | * +Merlin 22936.90 | 3,490 | * +Merlin 24575.25 | 3,530 | * +Merlin 26213.60 | 3,460 | * +Merlin 27851.95 | 3,470 | * +Merlin 29490.30 | 3,500 | * +Merlin 31128.65 | 3,920 | * +Merlin 32767.00 | 3,400 | * +Merlin ------------ |------------ | +Merlin N= | 180,929 | +Merlin ------------ |------------ | + diff -r 68cb8e7e266b -r eb17eb8a3658 test-data/table_sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/table_sample Tue Jul 23 23:12:23 2024 +0000 @@ -0,0 +1,57 @@ +Descriptive measures +bigwig bigwig_sample +contig Merlin +n 180929 +mean 6354.313736 +std 9951.749936 +min 0.000000 +max 32767.000000 +qtop 31906.72 +qbot 0.00 +First/Last 10 value counts +Value Count +0.00 110889 +13.00 30 +22.00 10 +26.00 10 +29.00 10 +40.00 10 +43.00 10 +53.00 10 +57.00 10 +60.00 20 +32721.00 10 +32724.00 10 +32726.00 10 +32728.00 10 +32730.00 10 +32731.00 20 +32737.00 10 +32745.00 10 +32766.00 10 +32767.00 10 +Histogram of bigwig values +Merlin 1638.35 | 114,349 | ************************************************** +Merlin 3276.70 | 3,650 | * +Merlin 4915.05 | 3,620 | * +Merlin 6553.40 | 3,570 | * +Merlin 8191.75 | 3,570 | * +Merlin 9830.10 | 3,410 | * +Merlin 11468.45 | 3,610 | * +Merlin 13106.80 | 3,170 | * +Merlin 14745.15 | 3,310 | * +Merlin 16383.50 | 3,390 | * +Merlin 18021.85 | 3,270 | * +Merlin 19660.20 | 3,680 | * +Merlin 21298.55 | 3,560 | * +Merlin 22936.90 | 3,490 | * +Merlin 24575.25 | 3,530 | * +Merlin 26213.60 | 3,460 | * +Merlin 27851.95 | 3,470 | * +Merlin 29490.30 | 3,500 | * +Merlin 31128.65 | 3,920 | * +Merlin 32767.00 | 3,400 | * +Merlin ------------ |------------ | +Merlin N= | 180,929 | +Merlin ------------ |------------ | +