Mercurial > repos > iuc > bigwig_outlier_bed
changeset 2:61946b8bd43b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
| author | iuc |
|---|---|
| date | Thu, 25 Jul 2024 14:38:34 +0000 |
| parents | 8377a6abb4da |
| children | |
| files | README.md bigwig_outlier_bed.py bigwig_outlier_bed.xml test-data/bedouthi2_sample test-data/bedouthi_qlo_notset_sample test-data/bedouthi_sample test-data/bedouthilo2_sample test-data/bedouthilo_sample test-data/bedoutlo2_sample test-data/table2_sample test-data/table3_sample test-data/table_only_sample test-data/table_qlo_notset_sample test-data/table_sample |
| diffstat | 14 files changed, 5160 insertions(+), 4656 deletions(-) [+] |
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--- 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 ------------ |------------ | + +
--- 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?" )
--- 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 @@ -<tool name="Bigwig extremes to bed features" id="bigwig_outlier_bed" version="@TOOL_VERSION@" profile="22.05"> +<tool name="Bigwig extremes to bed features" id="bigwig_outlier_bed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> <description>Writes high and low bigwig runs as features in a bed file</description> <macros> <token name="@TOOL_VERSION@">0.2.0</token> - <token name="@NUMPY_VERSION@">2.0.0</token> <token name="@PYTHON_VERSION@">3.12.3</token> + <token name="@VERSION_SUFFIX@">0</token> </macros> <edam_topics> <edam_topic>topic_0157</edam_topic> @@ -17,7 +17,7 @@ </xrefs> <requirements> <requirement type="package" version="@PYTHON_VERSION@">python</requirement> - <requirement type="package" version="@NUMPY_VERSION@">numpy</requirement> + <requirement type="package" version="2.0.0">numpy</requirement> <requirement type="package" version="@TOOL_VERSION@">pybigtools</requirement> </requirements> <required_files> @@ -50,7 +50,7 @@ #if $qlo: --qlo '$qlo' #end if -#if $tableout == "create": +#if $tableout == "create" or $outbeds == "outtab": --tableoutfile '$tableoutfile' #end if ]]></command> @@ -58,15 +58,18 @@ <param name="bigwig" type="data" optional="false" label="Choose one or more bigwig file(s) to return outlier regions as a bed file" help="If more than one, MUST all use the same reference sequence to be displayable. Feature names will include the bigwig label." format="bigwig" multiple="true"/> <param name="minwin" type="integer" value="10" label="Minimum continuous bases to count as a high or low bed feature" - help="Continuous features as long or longer than this window size will appear as bed features"/> - <param name="qhi" type="float" value="0.99" label="Quantile cutoff for a high region - 0.99 will cut off at or above the 99th percentile" help="Required" optional="false"/> - <param name="qlo" type="float" value="0.01" label="Quantile cutoff for a low region - 0.01 will cut off at or below the 1st percentile." help="Optional" optional="true"/> - <param name="outbeds" type="select" label="Select the required bed file outputs" help="Any combination of the 3 different kinds of bed file output can be made"> + help="Minimum continuous length to count as a bed feature. If windowed bigwig, must be bigger than window size to have any effect"/> + <param name="qhi" type="float" value="0.99999" label="Quantile cutoff for a high region - 0.99999 will cut off at about 1 in 100,000" + help="1 per 100k might be a few thousand features in a 200M chromosome - depends on the distribution - see the table output" optional="false"/> + <param name="qlo" type="float" value="0.00001" label="Quantile cutoff for a low region - 0.01 will cut off at or below the 1st percentile." help="Optional" optional="true"/> + <param name="outbeds" type="select" label="Select the required bed file outputs or none for a bigwig value distribution report" + help="Any combination of the 3 different kinds of bed file output can be made"> <option value="outhilo" selected="true">Make 1 bed output with both low and high regions</option> <option value="outhi">Make 1 bed output with high regions only</option> <option value="outlo">Make 1 bed output with low regions only</option> <option value="outall">Make 3 bed outputs with low and high together in one, high in one and low in the other</option> <option value="outlohi">Make 2 bed outputs with high in one and low in the other</option> + <option value="outtab">NO bed outputs. Report bigwig value distribution only</option> </param> <param name="tableout" type="select" label="Write a table showing contig statistics for each bigwig input" help=""> <option value="donotmake">Do not create this report</option> @@ -74,17 +77,17 @@ </param> </inputs> <outputs> - <data name="bedouthilo" format="bed" label="High_and_low_bed" hidden="false"> + <data name="bedouthilo" format="bed" label="High_and_low_bed"> <filter>outbeds in ["outall", "outhilo"]</filter> </data> - <data name="bedouthi" format="bed" label="High bed" hidden="false"> + <data name="bedouthi" format="bed" label="High bed"> <filter>outbeds in ["outall", "outlohi", "outhi"]</filter> </data> - <data name="bedoutlo" format="bed" label="Low bed" hidden="false"> + <data name="bedoutlo" format="bed" label="Low bed"> <filter>outbeds in ["outall", "outlohi", "outlo"]</filter> </data> - <data name="tableoutfile" format="tabular" label="Contig statistics" hidden="false"> - <filter>tableout == "create"</filter> + <data name="tableoutfile" format="txt" label="Contig statistics"> + <filter>tableout == "create" or outbeds == "outtab"</filter> </data> </outputs> <tests> @@ -97,6 +100,15 @@ <param name="qlo" value="0.01"/> <param name="tableout" value="donotmake"/> </test> + <test expect_num_outputs="1"> + <output name="tableoutfile" value="table_only_sample" compare="diff" lines_diff="0"/> + <param name="outbeds" value="outtab"/> + <param name="bigwig" value="bigwig_sample,1.bigwig"/> + <param name="minwin" value="10"/> + <param name="qhi" value="0.99"/> + <param name="qlo" value="0.01"/> + <param name="tableout" value="create"/> + </test> <test expect_num_outputs="2"> <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/> <output name="tableoutfile" value="table_sample" compare="diff" lines_diff="0"/>
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--- 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 bigwig_sample_320050 320050 -Merlin 9039 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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
--- 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 ------------ |------------ | +
--- 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 ------------ |------------ | +
--- /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
--- 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 ------------ |------------ | +
--- 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 ------------ |------------ | +