# HG changeset patch # User iuc # Date 1721918314 0 # Node ID 61946b8bd43b9bd80b3f6240b4e19cadfb9fcc56 # Parent 8377a6abb4da380b7efcf2fb96368ceb839e3ac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77 diff -r 8377a6abb4da -r 61946b8bd43b README.md --- a/README.md Sun Jul 21 11:03:36 2024 +0000 +++ b/README.md Thu Jul 25 14:38:34 2024 +0000 @@ -2,9 +2,9 @@ ### 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. -JBrowse2 2.12.3 update will include a plugin for optional colours to distinguish bed features, shown being tested in the screenshots below. +JBrowse2 now includes 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 8377a6abb4da -r 61946b8bd43b bigwig_outlier_bed.py --- a/bigwig_outlier_bed.py Sun Jul 21 11:03:36 2024 +0000 +++ b/bigwig_outlier_bed.py Thu Jul 25 14:38:34 2024 +0000 @@ -13,7 +13,6 @@ """ import argparse -import copy import os import sys from pathlib import Path @@ -22,6 +21,90 @@ import pybigtools +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] + + 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): @@ -34,14 +117,16 @@ self.bedouthilo = args.bedouthilo self.tableoutfile = args.tableoutfile self.bedwin = args.minwin - self.qhi = args.qhi self.qlo = None - try: - f = float(args.qlo) - self.qlo = f - except Exception as e: - s = str(e) - print(s, ' qlo=', args.qlo) + 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: @@ -106,10 +191,11 @@ def makeBed(self): bedhi = [] bedlo = [] + restab = [] bwlabels = self.bwlabels bwnames = self.bwnames - if self.tableoutfile: - restab = ["bigwig\tcontig\tn\tmean\tstd\tmin\tmax\tqtop\tqbot"] + bwnames.sort() + reshead = "bigwig\tcontig\tn\tmean\tstd\tmin\tmax\tqtop\tqbot" for i, bwname in enumerate(bwnames): bwlabel = bwlabels[i].replace(" ", "") fakepath = "in%d.bw" % i @@ -120,16 +206,38 @@ bwf = pybigtools.open(fakepath) chrlist = bwf.chroms() chrs = list(chrlist.keys()) - chrs.sort() for chr in chrs: + first_few = None bw = bwf.values(chr) + 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="%s_%s" % (bwlabel, chr)) + histo = ha.draw() + histo = ( + "\n".join(first_few) + + "\nHistogram of %s bigwig values\n" % bwlabel + + 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 j, seg in enumerate(bwhi): - if seg[1] - seg[0] >= self.bedwin: - score = np.sum(bw[seg[0]:seg[1]]) + seglen = seg[1] - seg[0] + if seglen >= self.bedwin: + score = np.sum(bw[seg[0]:seg[1]]) / float(seglen) bedhi.append( ( chr, @@ -144,7 +252,7 @@ bwlo = self.processVals(bw, isTop=False) for j, seg in enumerate(bwlo): if seg[1] - seg[0] >= self.bedwin: - score = -1 * np.sum(bw[seg[0]:seg[1]]) + score = -1 * np.sum(bw[seg[0]:seg[1]]) / float(seglen) bedlo.append( ( chr, @@ -156,7 +264,15 @@ ) if self.tableoutfile: row = self.makeTableRow(bw, bwlabel, chr) - restab.append(copy.copy(row)) + 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: @@ -175,7 +291,7 @@ allbed = bedlo + bedhi self.writeBed(allbed, self.bedouthilo) some = True - if not some: + 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?" ) diff -r 8377a6abb4da -r 61946b8bd43b bigwig_outlier_bed.xml --- a/bigwig_outlier_bed.xml Sun Jul 21 11:03:36 2024 +0000 +++ b/bigwig_outlier_bed.xml Thu Jul 25 14:38:34 2024 +0000 @@ -1,9 +1,9 @@ - + Writes high and low bigwig runs as features in a bed file 0.2.0 - 2.0.0 3.12.3 + 0 topic_0157 @@ -17,7 +17,7 @@ python - numpy + numpy pybigtools @@ -50,7 +50,7 @@ #if $qlo: --qlo '$qlo' #end if -#if $tableout == "create": +#if $tableout == "create" or $outbeds == "outtab": --tableoutfile '$tableoutfile' #end if ]]> @@ -58,15 +58,18 @@ - - - + help="Minimum continuous length to count as a bed feature. If windowed bigwig, must be bigger than window size to have any effect"/> + + + + @@ -74,17 +77,17 @@ - @@ -97,6 +100,15 @@ + + + + + + + + + diff -r 8377a6abb4da -r 61946b8bd43b test-data/bedouthi2_sample --- a/test-data/bedouthi2_sample Sun Jul 21 11:03:36 2024 +0000 +++ b/test-data/bedouthi2_sample Thu Jul 25 14:38:34 2024 +0000 @@ -1,1347 +1,1347 @@ -Merlin 19 49 bigwig_sample_921600 921600 -Merlin 79 89 bigwig_sample_302360 302360 -Merlin 199 219 bigwig_sample_612140 612140 -Merlin 259 269 bigwig_sample_298680 298680 -Merlin 289 309 bigwig_sample_640590 640590 -Merlin 329 339 bigwig_sample_273310 273310 -Merlin 359 379 bigwig_sample_549000 549000 -Merlin 389 409 bigwig_sample_525660 525660 -Merlin 419 429 bigwig_sample_294290 294290 -Merlin 499 509 bigwig_sample_244030 244030 -Merlin 519 539 bigwig_sample_596370 596370 -Merlin 559 569 bigwig_sample_314950 314950 -Merlin 649 659 bigwig_sample_296840 296840 -Merlin 699 709 bigwig_sample_314470 314470 -Merlin 719 759 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592880 -Merlin 23089 23099 bigwig_sample_310280 310280 -Merlin 23139 23169 bigwig_sample_877720 877720 -Merlin 23189 23199 bigwig_sample_293670 293670 -Merlin 23279 23309 bigwig_sample_914200 914200 -Merlin 23319 23329 bigwig_sample_278200 278200 -Merlin 23339 23349 bigwig_sample_257330 257330 -Merlin 23369 23389 bigwig_sample_606070 606070 -Merlin 23399 23429 bigwig_sample_864120 864120 -Merlin 23559 23579 bigwig_sample_560930 560930 -Merlin 23589 23599 bigwig_sample_267020 267020 -Merlin 23649 23659 bigwig_sample_311120 311120 -Merlin 23679 23689 bigwig_sample_299320 299320 -Merlin 23699 23719 bigwig_sample_551900 551900 -Merlin 23739 23749 bigwig_sample_312740 312740 -Merlin 23769 23779 bigwig_sample_324230 324230 -Merlin 23829 23859 bigwig_sample_837510 837510 -Merlin 23869 23879 bigwig_sample_271580 271580 -Merlin 23919 23969 bigwig_sample_1345600 1345600 -Merlin 24009 24019 bigwig_sample_310590 310590 -Merlin 24059 24079 bigwig_sample_568810 568810 -Merlin 24109 24119 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test-data/bedouthi_qlo_notset_sample --- a/test-data/bedouthi_qlo_notset_sample Sun Jul 21 11:03:36 2024 +0000 +++ b/test-data/bedouthi_qlo_notset_sample Thu Jul 25 14:38:34 2024 +0000 @@ -1,178 +1,178 @@ -Merlin 29 39 bigwig_sample_324550 324550 -Merlin 199 209 bigwig_sample_325430 325430 -Merlin 299 309 bigwig_sample_322440 322440 -Merlin 1579 1589 bigwig_sample_326050 326050 -Merlin 1729 1749 bigwig_sample_645520 645520 -Merlin 1859 1869 bigwig_sample_325690 325690 -Merlin 1889 1899 bigwig_sample_324060 324060 -Merlin 2589 2599 bigwig_sample_319990 319990 -Merlin 3409 3419 bigwig_sample_327310 327310 -Merlin 3659 3669 bigwig_sample_320520 320520 -Merlin 4039 4049 bigwig_sample_326360 326360 -Merlin 4409 4419 bigwig_sample_319410 319410 -Merlin 7129 7139 bigwig_sample_324490 324490 -Merlin 7269 7279 bigwig_sample_322880 322880 -Merlin 7869 7879 bigwig_sample_327240 327240 -Merlin 8079 8089 bigwig_sample_320310 320310 -Merlin 8289 8299 bigwig_sample_325450 325450 -Merlin 8739 8749 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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 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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 8377a6abb4da -r 61946b8bd43b test-data/bedoutlo2_sample --- a/test-data/bedoutlo2_sample Sun Jul 21 11:03:36 2024 +0000 +++ b/test-data/bedoutlo2_sample Thu Jul 25 14:38:34 2024 +0000 @@ -1,110 +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 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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 +Merlin 0 9 1.bigwig_0 0 +Merlin 70049 180929 1.bigwig_0 0 +chr21 0 9411190 bigwig_sample_0 0 +chr21 9411785 9411790 bigwig_sample_0 0 +chr21 9411800 9411815 bigwig_sample_0 0 +chr21 9411860 9411865 bigwig_sample_0 0 +chr21 9411900 9411905 bigwig_sample_0 0 +chr21 9412005 9412010 bigwig_sample_0 0 +chr21 9412050 9412055 bigwig_sample_0 0 +chr21 9412065 9412070 bigwig_sample_0 0 +chr21 9412080 9412085 bigwig_sample_0 0 +chr21 9412100 9412105 bigwig_sample_0 0 +chr21 9412120 9412125 bigwig_sample_0 0 +chr21 9412130 9412135 bigwig_sample_0 0 +chr21 9412140 9412145 bigwig_sample_0 0 +chr21 9412180 9412185 bigwig_sample_0 0 +chr21 9412200 9412210 bigwig_sample_0 0 +chr21 9412225 9412230 bigwig_sample_0 0 +chr21 9412250 9412260 bigwig_sample_0 0 +chr21 9412305 9412310 bigwig_sample_0 0 +chr21 9412360 9412370 bigwig_sample_0 0 +chr21 9412385 9412390 bigwig_sample_0 0 +chr21 9412400 9412415 bigwig_sample_0 0 +chr21 9412440 9412455 bigwig_sample_0 0 +chr21 9412460 9412465 bigwig_sample_0 0 +chr21 9412470 9412480 bigwig_sample_0 0 +chr21 9412485 9412490 bigwig_sample_0 0 +chr21 9412510 9412515 bigwig_sample_0 0 +chr21 9412565 9412570 bigwig_sample_0 0 +chr21 9412590 9412595 bigwig_sample_0 0 +chr21 9412640 9412650 bigwig_sample_0 0 +chr21 9412670 9412675 bigwig_sample_0 0 +chr21 9412690 9412700 bigwig_sample_0 0 +chr21 9412770 9412775 bigwig_sample_0 0 +chr21 9412815 9412820 bigwig_sample_0 0 +chr21 9412835 9412840 bigwig_sample_0 0 +chr21 9412845 9412850 bigwig_sample_0 0 +chr21 9412900 9412905 bigwig_sample_0 0 +chr21 9412970 9412975 bigwig_sample_0 0 +chr21 9412990 9412995 bigwig_sample_0 0 +chr21 9413040 9413045 bigwig_sample_0 0 +chr21 9413055 9413065 bigwig_sample_0 0 +chr21 9413095 9413100 bigwig_sample_0 0 +chr21 9413130 9413135 bigwig_sample_0 0 +chr21 9413155 9413160 bigwig_sample_0 0 +chr21 9413170 9413180 bigwig_sample_0 0 +chr21 9413205 9413210 bigwig_sample_0 0 +chr21 9413250 9413255 bigwig_sample_0 0 +chr21 9413280 9413285 bigwig_sample_0 0 +chr21 9413310 9413315 bigwig_sample_0 0 +chr21 9413345 9413350 bigwig_sample_0 0 +chr21 9413400 9413405 bigwig_sample_0 0 +chr21 9413510 9413515 bigwig_sample_0 0 +chr21 9413665 9413670 bigwig_sample_0 0 +chr21 9414040 9414045 bigwig_sample_0 0 +chr21 9414055 9414060 bigwig_sample_0 0 +chr21 9414100 9414105 bigwig_sample_0 0 +chr21 9414150 9414160 bigwig_sample_0 0 +chr21 9414175 9414180 bigwig_sample_0 0 +chr21 9414215 9414225 bigwig_sample_0 0 +chr21 9414255 9414260 bigwig_sample_0 0 +chr21 9414265 9414270 bigwig_sample_0 0 +chr21 9414280 9414285 bigwig_sample_0 0 +chr21 9414305 9414310 bigwig_sample_0 0 +chr21 9414435 9414440 bigwig_sample_0 0 +chr21 9414525 9414530 bigwig_sample_0 0 +chr21 9414585 9414590 bigwig_sample_0 0 +chr21 9414595 9414600 bigwig_sample_0 0 +chr21 9414655 9414665 bigwig_sample_0 0 +chr21 9414680 9414690 bigwig_sample_0 0 +chr21 9414695 9414700 bigwig_sample_0 0 +chr21 9414705 9414710 bigwig_sample_0 0 +chr21 9414720 9414725 bigwig_sample_0 0 +chr21 9414755 9414760 bigwig_sample_0 0 +chr21 9414775 9414780 bigwig_sample_0 0 +chr21 9414785 9414790 bigwig_sample_0 0 +chr21 9414820 9414825 bigwig_sample_0 0 +chr21 9414835 9414840 bigwig_sample_0 0 +chr21 9414850 9414855 bigwig_sample_0 0 +chr21 9414860 9414870 bigwig_sample_0 0 +chr21 9414905 9414910 bigwig_sample_0 0 +chr21 9414925 9414930 bigwig_sample_0 0 +chr21 9414955 9414960 bigwig_sample_0 0 +chr21 9414975 9414980 bigwig_sample_0 0 +chr21 9414995 9415000 bigwig_sample_0 0 +chr21 9415040 9415055 bigwig_sample_0 0 +chr21 9415065 9415075 bigwig_sample_0 0 +chr21 9415095 9415100 bigwig_sample_0 0 +chr21 9415105 9415115 bigwig_sample_0 0 +chr21 9415135 9415140 bigwig_sample_0 0 +chr21 9415150 9415155 bigwig_sample_0 0 +chr21 9415170 9415175 bigwig_sample_0 0 +chr21 9415270 9415275 bigwig_sample_0 0 +chr21 9415320 9415325 bigwig_sample_0 0 +chr21 9415385 9415390 bigwig_sample_0 0 +chr21 9415470 9415475 bigwig_sample_0 0 +chr21 9415535 9415540 bigwig_sample_0 0 +chr21 9415595 9415600 bigwig_sample_0 0 +chr21 9415665 9415670 bigwig_sample_0 0 +chr21 9415685 9415700 bigwig_sample_0 0 +chr21 9415710 9415715 bigwig_sample_0 0 +chr21 9415820 9415830 bigwig_sample_0 0 +chr21 9415880 9415885 bigwig_sample_0 0 +chr21 9416020 9416025 bigwig_sample_0 0 +chr21 9416080 9416085 bigwig_sample_0 0 +chr21 9416095 9416100 bigwig_sample_0 0 +chr21 9416130 9416135 bigwig_sample_0 0 +chr21 9416150 9416155 bigwig_sample_0 0 +chr21 9416165 9416175 bigwig_sample_0 0 +chr21 9416185 48129895 bigwig_sample_0 0 diff -r 8377a6abb4da -r 61946b8bd43b test-data/table2_sample --- a/test-data/table2_sample Sun Jul 21 11:03:36 2024 +0000 +++ b/test-data/table2_sample Thu Jul 25 14:38:34 2024 +0000 @@ -1,3 +1,74 @@ -bigwig contig n mean std min max qtop qbot -bigwig_sample Merlin 180929 6354.313736 9951.749936 0.000000 32767.000000 24359.00 0.00 -1.bigwig chr21 48129895 0.003446 0.400601 0.000000 100.000000 0.00 0.00 +Descriptive measures +bigwig bigwig_sample +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 +Descriptive measures +bigwig 1.bigwig +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 1.bigwig bigwig values +1.bigwig_Merlin 1638.35 | 114,349 | ************************************************** +1.bigwig_Merlin 3276.70 | 3,650 | * +1.bigwig_Merlin 4915.05 | 3,620 | * +1.bigwig_Merlin 6553.40 | 3,570 | * +1.bigwig_Merlin 8191.75 | 3,570 | * +1.bigwig_Merlin 9830.10 | 3,410 | * +1.bigwig_Merlin 11468.45 | 3,610 | * +1.bigwig_Merlin 13106.80 | 3,170 | * +1.bigwig_Merlin 14745.15 | 3,310 | * +1.bigwig_Merlin 16383.50 | 3,390 | * +1.bigwig_Merlin 18021.85 | 3,270 | * +1.bigwig_Merlin 19660.20 | 3,680 | * +1.bigwig_Merlin 21298.55 | 3,560 | * +1.bigwig_Merlin 22936.90 | 3,490 | * +1.bigwig_Merlin 24575.25 | 3,530 | * +1.bigwig_Merlin 26213.60 | 3,460 | * +1.bigwig_Merlin 27851.95 | 3,470 | * +1.bigwig_Merlin 29490.30 | 3,500 | * +1.bigwig_Merlin 31128.65 | 3,920 | * +1.bigwig_Merlin 32767.00 | 3,400 | * +1.bigwig_Merlin ------------ |------------ | +1.bigwig_Merlin N= | 180,929 | +1.bigwig_Merlin ------------ |------------ | + diff -r 8377a6abb4da -r 61946b8bd43b test-data/table3_sample --- a/test-data/table3_sample Sun Jul 21 11:03:36 2024 +0000 +++ b/test-data/table3_sample Thu Jul 25 14:38:34 2024 +0000 @@ -1,2 +1,57 @@ -bigwig contig n mean std min max qtop qbot -bigwig_sample Merlin 180929 6354.313736 9951.749936 0.000000 32767.000000 24359.00 0.00 +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_sample bigwig values +bigwig_sample_Merlin 1638.35 | 114,349 | ************************************************** +bigwig_sample_Merlin 3276.70 | 3,650 | * +bigwig_sample_Merlin 4915.05 | 3,620 | * +bigwig_sample_Merlin 6553.40 | 3,570 | * +bigwig_sample_Merlin 8191.75 | 3,570 | * +bigwig_sample_Merlin 9830.10 | 3,410 | * +bigwig_sample_Merlin 11468.45 | 3,610 | * +bigwig_sample_Merlin 13106.80 | 3,170 | * +bigwig_sample_Merlin 14745.15 | 3,310 | * +bigwig_sample_Merlin 16383.50 | 3,390 | * +bigwig_sample_Merlin 18021.85 | 3,270 | * +bigwig_sample_Merlin 19660.20 | 3,680 | * +bigwig_sample_Merlin 21298.55 | 3,560 | * +bigwig_sample_Merlin 22936.90 | 3,490 | * +bigwig_sample_Merlin 24575.25 | 3,530 | * +bigwig_sample_Merlin 26213.60 | 3,460 | * +bigwig_sample_Merlin 27851.95 | 3,470 | * +bigwig_sample_Merlin 29490.30 | 3,500 | * +bigwig_sample_Merlin 31128.65 | 3,920 | * +bigwig_sample_Merlin 32767.00 | 3,400 | * +bigwig_sample_Merlin ------------ |------------ | +bigwig_sample_Merlin N= | 180,929 | +bigwig_sample_Merlin ------------ |------------ | + diff -r 8377a6abb4da -r 61946b8bd43b test-data/table_only_sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/table_only_sample Thu Jul 25 14:38:34 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_sample bigwig values +bigwig_sample_Merlin 1638.35 | 114,349 | ************************************************** +bigwig_sample_Merlin 3276.70 | 3,650 | * +bigwig_sample_Merlin 4915.05 | 3,620 | * +bigwig_sample_Merlin 6553.40 | 3,570 | * +bigwig_sample_Merlin 8191.75 | 3,570 | * +bigwig_sample_Merlin 9830.10 | 3,410 | * +bigwig_sample_Merlin 11468.45 | 3,610 | * +bigwig_sample_Merlin 13106.80 | 3,170 | * +bigwig_sample_Merlin 14745.15 | 3,310 | * +bigwig_sample_Merlin 16383.50 | 3,390 | * +bigwig_sample_Merlin 18021.85 | 3,270 | * +bigwig_sample_Merlin 19660.20 | 3,680 | * +bigwig_sample_Merlin 21298.55 | 3,560 | * +bigwig_sample_Merlin 22936.90 | 3,490 | * +bigwig_sample_Merlin 24575.25 | 3,530 | * +bigwig_sample_Merlin 26213.60 | 3,460 | * +bigwig_sample_Merlin 27851.95 | 3,470 | * +bigwig_sample_Merlin 29490.30 | 3,500 | * +bigwig_sample_Merlin 31128.65 | 3,920 | * +bigwig_sample_Merlin 32767.00 | 3,400 | * +bigwig_sample_Merlin ------------ |------------ | +bigwig_sample_Merlin N= | 180,929 | +bigwig_sample_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 8377a6abb4da -r 61946b8bd43b test-data/table_qlo_notset_sample --- a/test-data/table_qlo_notset_sample Sun Jul 21 11:03:36 2024 +0000 +++ b/test-data/table_qlo_notset_sample Thu Jul 25 14:38:34 2024 +0000 @@ -1,2 +1,57 @@ -bigwig contig n mean std min max qtop qbot -bigwig_sample Merlin 180929 6354.313736 9951.749936 0.000000 32767.000000 31906.72 noqlo +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_sample bigwig values +bigwig_sample_Merlin 1638.35 | 114,349 | ************************************************** +bigwig_sample_Merlin 3276.70 | 3,650 | * +bigwig_sample_Merlin 4915.05 | 3,620 | * +bigwig_sample_Merlin 6553.40 | 3,570 | * +bigwig_sample_Merlin 8191.75 | 3,570 | * +bigwig_sample_Merlin 9830.10 | 3,410 | * +bigwig_sample_Merlin 11468.45 | 3,610 | * +bigwig_sample_Merlin 13106.80 | 3,170 | * +bigwig_sample_Merlin 14745.15 | 3,310 | * +bigwig_sample_Merlin 16383.50 | 3,390 | * +bigwig_sample_Merlin 18021.85 | 3,270 | * +bigwig_sample_Merlin 19660.20 | 3,680 | * +bigwig_sample_Merlin 21298.55 | 3,560 | * +bigwig_sample_Merlin 22936.90 | 3,490 | * +bigwig_sample_Merlin 24575.25 | 3,530 | * +bigwig_sample_Merlin 26213.60 | 3,460 | * +bigwig_sample_Merlin 27851.95 | 3,470 | * +bigwig_sample_Merlin 29490.30 | 3,500 | * +bigwig_sample_Merlin 31128.65 | 3,920 | * +bigwig_sample_Merlin 32767.00 | 3,400 | * +bigwig_sample_Merlin ------------ |------------ | +bigwig_sample_Merlin N= | 180,929 | +bigwig_sample_Merlin ------------ |------------ | + diff -r 8377a6abb4da -r 61946b8bd43b test-data/table_sample --- a/test-data/table_sample Sun Jul 21 11:03:36 2024 +0000 +++ b/test-data/table_sample Thu Jul 25 14:38:34 2024 +0000 @@ -1,2 +1,57 @@ -bigwig contig n mean std min max qtop qbot -bigwig_sample Merlin 180929 6354.313736 9951.749936 0.000000 32767.000000 31906.72 0.00 +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_sample bigwig values +bigwig_sample_Merlin 1638.35 | 114,349 | ************************************************** +bigwig_sample_Merlin 3276.70 | 3,650 | * +bigwig_sample_Merlin 4915.05 | 3,620 | * +bigwig_sample_Merlin 6553.40 | 3,570 | * +bigwig_sample_Merlin 8191.75 | 3,570 | * +bigwig_sample_Merlin 9830.10 | 3,410 | * +bigwig_sample_Merlin 11468.45 | 3,610 | * +bigwig_sample_Merlin 13106.80 | 3,170 | * +bigwig_sample_Merlin 14745.15 | 3,310 | * +bigwig_sample_Merlin 16383.50 | 3,390 | * +bigwig_sample_Merlin 18021.85 | 3,270 | * +bigwig_sample_Merlin 19660.20 | 3,680 | * +bigwig_sample_Merlin 21298.55 | 3,560 | * +bigwig_sample_Merlin 22936.90 | 3,490 | * +bigwig_sample_Merlin 24575.25 | 3,530 | * +bigwig_sample_Merlin 26213.60 | 3,460 | * +bigwig_sample_Merlin 27851.95 | 3,470 | * +bigwig_sample_Merlin 29490.30 | 3,500 | * +bigwig_sample_Merlin 31128.65 | 3,920 | * +bigwig_sample_Merlin 32767.00 | 3,400 | * +bigwig_sample_Merlin ------------ |------------ | +bigwig_sample_Merlin N= | 180,929 | +bigwig_sample_Merlin ------------ |------------ | +