# HG changeset patch # User fubar # Date 1719795181 0 # Node ID 2fbbc1be66556b3bf12bbf443fb98107719398c0 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty diff -r 000000000000 -r 2fbbc1be6655 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Mon Jul 01 00:53:01 2024 +0000 @@ -0,0 +1,31 @@ +## bigwig peak outlier to bed + +### 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. + +The next JBrowse2 tool release 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 + +In the spirit of DeepTools, but finding contiguous regions where the bigwig value is either above or below a given centile. +0.99 and 0.01 for example. These quantile cut point values are found and applied over each chromosome using some [cunning numpy code](http://gregoryzynda.com/python/numpy/contiguous/interval/2019/11/29/contiguous-regions.html) + +![image](https://github.com/fubar2/bigwig_peak_bed/assets/6016266/cdee3a2b-ae31-4282-b744-992c15fb49db) + +![image](https://github.com/fubar2/bigwig_peak_bed/assets/6016266/59d1564b-0c34-42a3-b437-44332cf1b2f0) + +Big differences between chromosomes 14,15,21,22 and Y in this "all contigs" view - explanations welcomed: + +![image](https://github.com/fubar2/bigwig_peak_bed/assets/6016266/162bf681-2977-4eb8-8d6f-9dad5b3931f8) + + +[pybedtools](https://github.com/jackh726/bigtools) is used for the bigwig interface. Optionally allow +multiple bigwigs to be processed into a single bed - the bed features have the bigwig name in the label for viewing. + +### Note on quantiles per chromosome rather than quantiles for the whole bigwig + +It is just not feasible to hold all contigs in the entire decoded bigwig in RAM to estimate quantiles. It may be +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. diff -r 000000000000 -r 2fbbc1be6655 bigslowtest.bw Binary file bigslowtest.bw has changed diff -r 000000000000 -r 2fbbc1be6655 bigslowtest.bw.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bigslowtest.bw.bed Mon Jul 01 00:53:01 2024 +0000 @@ -0,0 +1,76170 @@ +Superscaffold_1 0 6000 bar_lo -1 +Superscaffold_1 8900 9700 bar_lo -1 +Superscaffold_1 22700 29800 bar_lo -1 +Superscaffold_1 30400 48200 bar_lo -1 +Superscaffold_1 51700 52900 bar_hi 1 +Superscaffold_1 53000 53700 bar_hi 1 +Superscaffold_1 60700 60900 bar_lo -1 +Superscaffold_1 64000 69300 bar_lo -1 +Superscaffold_1 71600 80200 bar_lo -1 +Superscaffold_1 85800 97100 bar_lo -1 +Superscaffold_1 103400 103600 bar_lo -1 +Superscaffold_1 116700 118100 bar_lo -1 +Superscaffold_1 120900 121000 bar_lo -1 +Superscaffold_1 122500 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53734400 53734800 foo_hi 1 +chr9_PATERNAL 53734900 53738000 foo_hi 1 +chr9_PATERNAL 53982200 53982500 foo_hi 1 +chr9_PATERNAL 53982900 53983400 foo_hi 1 +chr9_PATERNAL 53984400 53999500 foo_hi 1 +chr9_PATERNAL 53999600 53999900 foo_hi 1 +chr9_PATERNAL 54000400 54000500 foo_hi 1 +chr9_PATERNAL 54001300 54002600 foo_hi 1 +chr9_PATERNAL 54002800 54003000 foo_hi 1 +chr9_PATERNAL 54005700 54006800 foo_hi 1 +chr9_PATERNAL 54010700 54012300 foo_hi 1 +chr9_PATERNAL 54012500 54034900 foo_hi 1 +chr9_PATERNAL 54035000 54038900 foo_hi 1 +chr9_PATERNAL 54039100 54039400 foo_hi 1 +chr9_PATERNAL 54039800 54041500 foo_hi 1 +chr9_PATERNAL 54047700 54048200 foo_hi 1 +chr9_PATERNAL 54048300 54048400 foo_hi 1 +chr9_PATERNAL 54052700 54053100 foo_hi 1 +chr9_PATERNAL 54053200 54054900 foo_hi 1 +chr9_PATERNAL 54055000 54055100 foo_hi 1 +chr9_PATERNAL 54056600 54058500 foo_hi 1 +chr9_PATERNAL 54061900 54062100 foo_hi 1 +chr9_PATERNAL 54063200 54063400 foo_hi 1 +chr9_PATERNAL 54063500 54064100 foo_hi 1 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+scaffold_99_arrow_ctg1 26100 28400 bar_lo -1 +scaffold_99_arrow_ctg1 30700 32300 bar_lo -1 +scaffold_99_arrow_ctg1 34000 34028 bar_lo -1 +scaffold_9_arrow_ctg1 0 200 bar_lo -1 +scaffold_9_arrow_ctg1 1600 1800 bar_lo -1 +scaffold_9_arrow_ctg1 13900 14100 bar_hi 1 +scaffold_9_arrow_ctg1 14200 14500 bar_hi 1 +scaffold_9_arrow_ctg1 43800 44275 bar_lo -1 diff -r 000000000000 -r 2fbbc1be6655 bigwig_outlier_bed.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bigwig_outlier_bed.py Mon Jul 01 00:53:01 2024 +0000 @@ -0,0 +1,148 @@ +""" +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') as tout: + tout.write('\n'.join(restab)) + tout.write('\n') + + diff -r 000000000000 -r 2fbbc1be6655 bigwig_outlier_bed.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bigwig_outlier_bed.xml Mon Jul 01 00:53:01 2024 +0000 @@ -0,0 +1,212 @@ + + + + Writes high and low bigwig regions as features in a bed file + + topic_0157 + topic_0092 + + + operation_0337 + + + 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]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1093/bioinformatics/btae350 + + + diff -r 000000000000 -r 2fbbc1be6655 bigwig_outlier_bed_slow1.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bigwig_outlier_bed_slow1.py Mon Jul 01 00:53:01 2024 +0000 @@ -0,0 +1,88 @@ +import os +import pyBigWig + + +class findOut(): + + def __init__(self, bwname="test.bw", bedname="test.bed", sd_lo=3, sd_hi=3, bedwin=10): + self.bedwin = bedwin + self.bwf = pyBigWig.open(bwname, "r") + self.chrlist = self.bwf.chroms() + self.bedf = open(bedname, "w") + self.sd_lo = sd_lo + self.sd_hi = sd_hi + self.makeBed(self.chrlist) + + def makeBed(self, chrlist): + bed = [] + for chr in chrlist: + print(chr) + gm = self.bwf.stats(chr, 0, type="mean")[0] + gstd = self.bwf.stats(chr, 0, type="std")[0] + cutlow = gm - (self.sd_lo * gstd) + cuthi = gm + (self.sd_hi * gstd) + chr_len = self.chrlist[chr] + nb = chr_len // self.bedwin + means = self.bwf.stats(chr, 0, chr_len, type="mean", nBins=nb) + inlo = False + inhi = False + reg_start = None + reg_end = None + reg_means = [] + print('got %d means, gm=%f, lo=%f, hi=%f' % (len(means), gm, cutlow, cuthi)) + for i, m in enumerate(means): + bend = min(chr_len, (i + 1) * self.bedwin) + featname = "%s_%d" % (chr,i) + if m and (m < cutlow or m > cuthi): + if inlo: + if m < cutlow: # extend + reg_end = bend + reg_means.append(m) + else: # high so close + rm = sum(reg_means) / len(reg_means) + bed.append( + "%s\t%d\t%d\t%s\t%.3f\n" + % (chr, reg_start, reg_end, featname, rm) + ) + inlo = False + reg_means = [] + elif inhi: + if m > cuthi: # extend + reg_end = bend + reg_means.append(m) + else: + rm = sum(reg_means) / len(reg_means) + bed.append( + "%s\t%d\t%d\t%s\t%.3f\n" + % (chr, reg_start, reg_end, featname, rm) + ) + inhi = False + reg_means = [] + elif m < cutlow: # start new low region + inlo = True + reg_start = i * self.bedwin + reg_end = bend + reg_means = [m] + elif m > cuthi: + inhi = True + reg_start = i * self.bedwin + reg_end = bend + reg_means = [m] + else: # not out of range - write current extended bed region + if inhi or inlo: + inhi = False + inlo = False + rm = sum(reg_means) / len(reg_means) + bed.append( + "%s\t%d\t%d\t%s\t%.3f\n" + % (chr, reg_start, reg_end, featname, rm) + ) + reg_means = [] + reg_start = None + reg_end = None + self.bedf.write(''.join(bed)) + self.bedf.close() + + +if __name__ == "__main__": + fo = findOut(bwname="test.bw", bedname="test.bed", sd_lo=2, sd_hi=2, bedwin=100) diff -r 000000000000 -r 2fbbc1be6655 bigwigtobed.python.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bigwigtobed.python.txt Mon Jul 01 00:53:01 2024 +0000 @@ -0,0 +1,131 @@ +#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') as tout: + tout.write('\n'.join(restab)) + tout.write('\n') +#end raw diff -r 000000000000 -r 2fbbc1be6655 merlin.bw Binary file merlin.bw has changed diff -r 000000000000 -r 2fbbc1be6655 merlin.bw.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/merlin.bw.bed Mon Jul 01 00:53:01 2024 +0000 @@ -0,0 +1,16 @@ 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