Mercurial > repos > iuc > bigwig_outlier_bed
changeset 4:2488bcddaf14 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
| author | iuc |
|---|---|
| date | Mon, 30 Sep 2024 01:42:34 +0000 |
| parents | 00b3da7776a0 |
| children | |
| files | bigwig_outlier_bed.py bigwig_outlier_bed.xml test-data/bedoutzero_sample |
| diffstat | 3 files changed, 47 insertions(+), 9 deletions(-) [+] |
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--- a/bigwig_outlier_bed.py Sun Sep 15 17:08:45 2024 +0000 +++ b/bigwig_outlier_bed.py Mon Sep 30 01:42:34 2024 +0000 @@ -117,6 +117,7 @@ self.bedouthilo = args.bedouthilo self.tableoutfile = args.tableoutfile self.bedwin = args.minwin + self.bedoutzero = args.bedoutzero self.qlo = None self.qhi = None if args.outbeds != "outtab": @@ -133,7 +134,7 @@ self.bwlabels += ["Nolabel"] * (nbw - nlab) self.makeBed() - def processVals(self, bw, isTop): + def processVals(self, bw, isTop, isZero): """ 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. @@ -143,6 +144,8 @@ """ if isTop: bwex = np.r_[False, bw >= self.bwtop, False] # extend with 0s + elif isZero: + bwex = np.r_[False, bw == 0, False] # extend with 0s else: bwex = np.r_[False, bw <= self.bwbot, False] bwexd = np.diff(bwex) @@ -190,6 +193,7 @@ def makeBed(self): bedhi = [] bedlo = [] + bedzero = [] restab = [] bwlabels = self.bwlabels bwnames = self.bwnames @@ -229,9 +233,24 @@ + histo ) bw = bw[~np.isnan(bw)] # some have NaN if parts of a contig not covered + if self.bedoutzero is not None: + bwzero = self.processVals(bw, isTop=False, isZero=True) + for j, seg in enumerate(bwzero): + seglen = seg[1] - seg[0] + if seglen >= self.bedwin: + score = seglen + bedzero.append( + ( + chr, + seg[0], + seg[1], + "%s_%d" % (bwlabel, score), + score, + ) + ) if self.qhi is not None: self.bwtop = np.quantile(bw, self.qhi) - bwhi = self.processVals(bw, isTop=True) + bwhi = self.processVals(bw, isTop=True, isZero=False) for j, seg in enumerate(bwhi): seglen = seg[1] - seg[0] if seglen >= self.bedwin: @@ -247,7 +266,7 @@ ) if self.qlo is not None: self.bwbot = np.quantile(bw, self.qlo) - bwlo = self.processVals(bw, isTop=False) + bwlo = self.processVals(bw, isTop=False, isZero=False) for j, seg in enumerate(bwlo): seglen = seg[1] - seg[0] if seg[1] - seg[0] >= self.bedwin: @@ -280,6 +299,9 @@ t.write(stable) t.write("\n") some = False + if self.outbeds in ["outzero"]: + self.writeBed(bedzero, self.bedoutzero) + some = True if self.qlo: if self.outbeds in ["outall", "outlo", "outlohi"]: self.writeBed(bedlo, self.bedoutlo) @@ -308,6 +330,7 @@ a("--bedouthi", default=None) a("--bedoutlo", default=None) a("--bedouthilo", default=None) + a("--bedoutzero", default=None) a("-w", "--bigwig", nargs="+") a("-n", "--bigwiglabels", nargs="+") a("-o", "--outbeds", default="outhilo", help="optional high and low combined bed")
--- a/bigwig_outlier_bed.xml Sun Sep 15 17:08:45 2024 +0000 +++ b/bigwig_outlier_bed.xml Mon Sep 30 01:42:34 2024 +0000 @@ -1,9 +1,9 @@ -<tool name="Bigwig extremes to bed features" id="bigwig_outlier_bed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> +<tool name="Bigwig outliers 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="@PYTHON_VERSION@">3.12.3</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> </macros> <edam_topics> <edam_topic>topic_0157</edam_topic> @@ -43,6 +43,9 @@ #if $outbeds in ['outlo', 'outall', 'outlohi']: --bedoutlo '$bedoutlo' #end if +#if $outbeds in ['outzero']: + --bedoutzero '$bedoutzero' +#end if --minwin '$minwin' #if $qhi: --qhi '$qhi' @@ -67,9 +70,10 @@ <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="outzero">Make 1 bed output for regions with contiguous zero values 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> + <option value="outtab">NO bed outputs. Report bigwig value distribution table 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> @@ -86,6 +90,9 @@ <data name="bedoutlo" format="bed" label="Low bed"> <filter>outbeds in ["outall", "outlohi", "outlo"]</filter> </data> + <data name="bedoutzero" format="bed" label="Zeros only bed"> + <filter>outbeds in ["outzero"]</filter> + </data> <data name="tableoutfile" format="txt" label="Contig statistics"> <filter>tableout == "create" or outbeds == "outtab"</filter> </data> @@ -150,9 +157,15 @@ <param name="qlo" value="0.5"/> <param name="tableout" value="create"/> </test> - - - + <test expect_num_outputs="1"> + <output name="bedoutzero" value="bedoutzero_sample" compare="diff" lines_diff="0"/> + <param name="outbeds" value="outzero"/> + <param name="bigwig" value="fake.bigwig,bigwig_sample"/> + <param name="minwin" value="2"/> + <param name="qhi" value="0.5"/> + <param name="qlo" value="0.5"/> + <param name="tableout" value="donotmake"/> + </test> </tests> <help><![CDATA[