Mercurial > repos > iuc > bigwig_outlier_bed
changeset 3:00b3da7776a0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 06c54e8066ecbc6292167e7c5bdfb8af945a41ba
| author | iuc |
|---|---|
| date | Sun, 15 Sep 2024 17:08:45 +0000 |
| parents | 61946b8bd43b |
| children | 2488bcddaf14 |
| files | bigwig_outlier_bed.py bigwig_outlier_bed.xml test-data/1.bigwig test-data/bedouthi2_sample test-data/bedouthi_qlo_notset_sample test-data/bedouthi_sample test-data/bedouthilo2_sample test-data/bedouthilo_qlo_notset_sample test-data/bedouthilo_sample test-data/bedouthilo_sample_2 test-data/bedoutlo2_sample test-data/bedoutlo_sample test-data/fake.bed test-data/fake.bigwig test-data/table2_sample test-data/table3_sample test-data/table_only_sample test-data/table_qlo_notset_sample test-data/table_sample |
| diffstat | 19 files changed, 2471 insertions(+), 4883 deletions(-) [+] |
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--- a/bigwig_outlier_bed.py Thu Jul 25 14:38:34 2024 +0000 +++ b/bigwig_outlier_bed.py Sun Sep 15 17:08:45 2024 +0000 @@ -146,7 +146,7 @@ else: bwex = np.r_[False, bw <= self.bwbot, False] bwexd = np.diff(bwex) - bwexdnz = bwexd.nonzero()[0] + bwexdnz = bwexd.nonzero()[0] # start and end transition of each segment - nice! bwregions = np.reshape(bwexdnz, (-1, 2)) return bwregions @@ -155,10 +155,9 @@ 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") + for b in bed: + bedf.write("%s\t%d\t%d\t%s\t%d\n" % b) def makeTableRow(self, bw, bwlabel, chr): """ @@ -194,7 +193,6 @@ restab = [] bwlabels = self.bwlabels bwnames = self.bwnames - bwnames.sort() reshead = "bigwig\tcontig\tn\tmean\tstd\tmin\tmax\tqtop\tqbot" for i, bwname in enumerate(bwnames): bwlabel = bwlabels[i].replace(" ", "") @@ -251,8 +249,11 @@ self.bwbot = np.quantile(bw, self.qlo) bwlo = self.processVals(bw, isTop=False) for j, seg in enumerate(bwlo): + seglen = seg[1] - seg[0] if seg[1] - seg[0] >= self.bedwin: - score = -1 * np.sum(bw[seg[0]:seg[1]]) / float(seglen) + score = ( + -1 * np.sum(bw[seg[0]:seg[1]]) / float(seglen) + ) bedlo.append( ( chr,
--- a/bigwig_outlier_bed.xml Thu Jul 25 14:38:34 2024 +0000 +++ b/bigwig_outlier_bed.xml Sun Sep 15 17:08:45 2024 +0000 @@ -3,7 +3,7 @@ <macros> <token name="@TOOL_VERSION@">0.2.0</token> <token name="@PYTHON_VERSION@">3.12.3</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <edam_topics> <edam_topic>topic_0157</edam_topic> @@ -25,13 +25,13 @@ </required_files> <version_command><![CDATA[python -c "import pybigtools; from importlib.metadata import version; print(version('pybigtools'))"]]></version_command> <command><![CDATA[python '${__tool_directory__}/bigwig_outlier_bed.py' ---bigwig -#for bw in $bigwig: - '$bw' +#set bwns = [x.name for x in $bigwig] +#set bwfs = [x for x in $bigwig] +#for $bwf in $bwfs: +--bigwig '$bwf' #end for ---bigwiglabels -#for bw in $bigwig: - '$bw.name' +#for $bwn in $bwns: +--bigwiglabels '$bwn' #end for --outbeds '$outbeds' #if $outbeds in ['outhilo', 'outall']: @@ -94,29 +94,29 @@ <test expect_num_outputs="1"> <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/> <param name="outbeds" value="outhilo"/> - <param name="bigwig" value="bigwig_sample"/> + <param name="bigwig" value="fake.bigwig"/> <param name="minwin" value="10"/> - <param name="qhi" value="0.99"/> + <param name="qhi" value="0.6"/> <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="bigwig" value="fake.bigwig"/> <param name="minwin" value="10"/> - <param name="qhi" value="0.99"/> - <param name="qlo" value="0.01"/> + <param name="qhi" value="0.7"/> + <param name="qlo" value="0.3"/> <param name="tableout" value="create"/> </test> <test expect_num_outputs="2"> - <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/> + <output name="bedouthilo" value="bedouthilo_sample_2" compare="diff" lines_diff="0"/> <output name="tableoutfile" value="table_sample" compare="diff" lines_diff="0"/> <param name="outbeds" value="outhilo"/> <param name="bigwig" value="bigwig_sample"/> <param name="minwin" value="10"/> - <param name="qhi" value="0.99"/> - <param name="qlo" value="0.01"/> + <param name="qhi" value="0.7"/> + <param name="qlo" value="0.3"/> <param name="tableout" value="create"/> </test> <test expect_num_outputs="2"> @@ -125,7 +125,7 @@ <param name="outbeds" value="outhi"/> <param name="bigwig" value="bigwig_sample"/> <param name="minwin" value="10"/> - <param name="qhi" value="0.99"/> + <param name="qhi" value="0.69"/> <param name="qlo" value=""/> <param name="tableout" value="create"/> </test> @@ -134,24 +134,25 @@ <output name="bedoutlo" value="bedoutlo_sample" compare="diff" lines_diff="0"/> <output name="tableoutfile" value="table3_sample" compare="diff" lines_diff="0"/> <param name="outbeds" value="outlohi"/> - <param name="bigwig" value="bigwig_sample"/> - <param name="minwin" value="1"/> - <param name="qhi" value="0.9"/> - <param name="qlo" value="0.1"/> + <param name="bigwig" value="fake.bigwig"/> + <param name="minwin" value="10"/> + <param name="qhi" value="0.5"/> + <param name="qlo" value="0.5"/> <param name="tableout" value="create"/> </test> - <test expect_num_outputs="4"> - <output name="bedouthilo" value="bedouthilo2_sample" compare="diff" lines_diff="0"/> - <output name="bedoutlo" value="bedoutlo2_sample" compare="diff" lines_diff="0"/> + <test expect_num_outputs="2"> <output name="bedouthi" value="bedouthi2_sample" compare="diff" lines_diff="0"/> <output name="tableoutfile" value="table2_sample" compare="diff" lines_diff="0"/> - <param name="outbeds" value="outall"/> - <param name="bigwig" value="bigwig_sample,1.bigwig"/> - <param name="minwin" value="1"/> - <param name="qhi" value="0.9"/> - <param name="qlo" value="0.1"/> + <param name="outbeds" value="outhi"/> + <param name="bigwig" value="fake.bigwig,bigwig_sample"/> + <param name="minwin" value="10"/> + <param name="qhi" value="0.5"/> + <param name="qlo" value="0.5"/> <param name="tableout" value="create"/> </test> + + + </tests> <help><