| Previous changeset 2:61946b8bd43b (2024-07-25) Next changeset 4:2488bcddaf14 (2024-09-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 06c54e8066ecbc6292167e7c5bdfb8af945a41ba |
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modified:
bigwig_outlier_bed.py bigwig_outlier_bed.xml test-data/bedouthi2_sample test-data/bedouthi_qlo_notset_sample test-data/bedouthi_sample test-data/bedouthilo_sample test-data/bedoutlo_sample test-data/table2_sample test-data/table3_sample test-data/table_only_sample test-data/table_qlo_notset_sample test-data/table_sample |
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added:
test-data/bedouthilo_sample_2 test-data/fake.bed test-data/fake.bigwig |
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removed:
test-data/1.bigwig test-data/bedouthilo2_sample test-data/bedouthilo_qlo_notset_sample test-data/bedoutlo2_sample |
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| diff -r 61946b8bd43b -r 00b3da7776a0 bigwig_outlier_bed.py --- 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 |
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| @@ -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, |
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| diff -r 61946b8bd43b -r 00b3da7776a0 bigwig_outlier_bed.xml --- 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><![CDATA[ |
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| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/1.bigwig |
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| Binary file test-data/1.bigwig has changed |
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| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/bedouthi2_sample --- a/test-data/bedouthi2_sample Thu Jul 25 14:38:34 2024 +0000 +++ b/test-data/bedouthi2_sample Sun Sep 15 17:08:45 2024 +0000 |
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| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/bedouthi_qlo_notset_sample --- a/test-data/bedouthi_qlo_notset_sample Thu Jul 25 14:38:34 2024 +0000 +++ b/test-data/bedouthi_qlo_notset_sample Sun Sep 15 17:08:45 2024 +0000 |
| b |
| b'@@ -1,178 +1,1132 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|
| b |
| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/bedouthi_sample --- a/test-data/bedouthi_sample Thu Jul 25 14:38:34 2024 +0000 +++ b/test-data/bedouthi_sample Sun Sep 15 17:08:45 2024 +0000 |
| b |
| b'@@ -1,1346 +1,5 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n-Merlin\t66169\t66179\tbigwig_sample_24877\t24877\n-Merlin\t66189\t66199\tbigwig_sample_25625\t25625\n-Merlin\t66219\t66249\tbigwig_sample_28698\t28698\n-Merlin\t66269\t66279\tbigwig_sample_31564\t31564\n-Merlin\t66299\t66309\tbigwig_sample_27292\t27292\n-Merlin\t66319\t66329\tbigwig_sample_31338\t31338\n-Merlin\t66429\t66439\tbigwig_sample_30877\t30877\n-Merlin\t66449\t66459\tbigwig_sample_26047\t26047\n-Merlin\t66469\t66479\tbigwig_sample_26746\t26746\n-Merlin\t66519\t66529\tbigwig_sample_32731\t32731\n-Merlin\t66539\t66559\tbigwig_sample_28810\t28810\n-Merlin\t66579\t66589\tbigwig_sample_25672\t25672\n-Merlin\t66679\t66689\tbigwig_sample_29739\t29739\n-Merlin\t66699\t66709\tbigwig_sample_24375\t24375\n-Merlin\t66729\t66739\tbigwig_sample_29782\t29782\n-Merlin\t66809\t66819\tbigwig_sample_30033\t30033\n-Merlin\t66859\t66869\tbigwig_sample_32552\t32552\n-Merlin\t66879\t66899\tbigwig_sample_28065\t28065\n-Merlin\t66959\t66969\tbigwig_sample_31410\t31410\n-Merlin\t66989\t66999\tbigwig_sample_28381\t28381\n-Merlin\t67049\t67069\tbigwig_sample_30057\t30057\n-Merlin\t67139\t67149\tbigwig_sample_25881\t25881\n-Merlin\t67169\t67179\tbigwig_sample_25665\t25665\n-Merlin\t67189\t67199\tbigwig_sample_30858\t30858\n-Merlin\t67209\t67239\tbigwig_sample_29719\t29719\n-Merlin\t67249\t67259\tbigwig_sample_32335\t32335\n-Merlin\t67309\t67319\tbigwig_sample_29048\t29048\n-Merlin\t67489\t67499\tbigwig_sample_24903\t24903\n-Merlin\t67509\t67519\tbigwig_sample_25376\t25376\n-Merlin\t67529\t67539\tbigwig_sample_31775\t31775\n-Merlin\t67559\t67569\tbigwig_sample_31342\t31342\n-Merlin\t67649\t67659\tbigwig_sample_25712\t25712\n-Merlin\t67669\t67679\tbigwig_sample_31890\t31890\n-Merlin\t67699\t67709\tbigwig_sample_32697\t32697\n-Merlin\t67719\t67729\tbigwig_sample_30825\t30825\n-Merlin\t67829\t67839\tbigwig_sample_30836\t30836\n-Merlin\t67849\t67869\tbigwig_sample_28734\t28734\n-Merlin\t67909\t67919\tbigwig_sample_26236\t26236\n-Merlin\t67959\t67969\tbigwig_sample_28272\t28272\n-Merlin\t67989\t67999\tbigwig_sample_29647\t29647\n-Merlin\t68199\t68209\tbigwig_sample_31849\t31849\n-Merlin\t68299\t68309\tbigwig_sample_30257\t30257\n-Merlin\t68379\t68389\tbigwig_sample_26333\t26333\n-Merlin\t68399\t68409\tbigwig_sample_25571\t25571\n-Merlin\t68439\t68449\tbigwig_sample_25811\t25811\n-Merlin\t68529\t68539\tbigwig_sample_26010\t26010\n-Merlin\t68569\t68579\tbigwig_sample_27683\t27683\n-Merlin\t68599\t68609\tbigwig_sample_29264\t29264\n-Merlin\t68649\t68659\tbigwig_sample_32302\t32302\n-Merlin\t68689\t68699\tbigwig_sample_27504\t27504\n-Merlin\t68749\t68759\tbigwig_sample_29272\t29272\n-Merlin\t68769\t68799\tbigwig_sample_31810\t31810\n-Merlin\t68899\t68909\tbigwig_sample_28642\t28642\n-Merlin\t68919\t68929\tbigwig_sample_26498\t26498\n-Merlin\t68989\t68999\tbigwig_sample_31961\t31961\n-Merlin\t69069\t69079\tbigwig_sample_27897\t27897\n-Merlin\t69099\t69109\tbigwig_sample_25703\t25703\n-Merlin\t69119\t69149\tbigwig_sample_29069\t29069\n-Merlin\t69179\t69189\tbigwig_sample_26934\t26934\n-Merlin\t69199\t69209\tbigwig_sample_25802\t25802\n-Merlin\t69259\t69269\tbigwig_sample_32057\t32057\n-Merlin\t69279\t69289\tbigwig_sample_25180\t25180\n-Merlin\t69329\t69339\tbigwig_sample_28214\t28214\n-Merlin\t69409\t69419\tbigwig_sample_27761\t27761\n-Merlin\t69439\t69459\tbigwig_sample_26146\t26146\n-Merlin\t69509\t69519\tbigwig_sample_26219\t26219\n-Merlin\t69579\t69589\tbigwig_sample_32098\t32098\n-Merlin\t69769\t69779\tbigwig_sample_28162\t28162\n-Merlin\t69809\t69829\tbigwig_sample_31848\t31848\n-Merlin\t69859\t69869\tbigwig_sample_32663\t32663\n-Merlin\t69879\t69909\tbigwig_sample_27935\t27935\n-Merlin\t69949\t69959\tbigwig_sample_30960\t30960\n-Merlin\t69979\t69989\tbigwig_sample_30973\t30973\n+chr1\t0\t10\tfake.bigwig_1\t1\n+chr1\t20\t30\tfake.bigwig_1\t1\n+chr1\t40\t50\tfake.bigwig_1\t1\n+chr1\t60\t70\tfake.bigwig_1\t1\n+chr1\t200\t1000\tfake.bigwig_1\t1\n' |
| b |
| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/bedouthilo2_sample --- a/test-data/bedouthilo2_sample Thu Jul 25 14:38:34 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1457 +0,0 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|
| b |
| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/bedouthilo_qlo_notset_sample --- a/test-data/bedouthilo_qlo_notset_sample Thu Jul 25 14:38:34 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,70 +0,0 @@ -Merlin 20 30 bigwig_sample_hi 1 -Merlin 190 200 bigwig_sample_hi 1 -Merlin 1570 1580 bigwig_sample_hi 1 -Merlin 1730 1740 bigwig_sample_hi 1 -Merlin 1850 1860 bigwig_sample_hi 1 -Merlin 1880 1890 bigwig_sample_hi 1 -Merlin 3400 3410 bigwig_sample_hi 1 -Merlin 4030 4040 bigwig_sample_hi 1 -Merlin 7120 7130 bigwig_sample_hi 1 -Merlin 7860 7870 bigwig_sample_hi 1 -Merlin 8280 8290 bigwig_sample_hi 1 -Merlin 10820 10830 bigwig_sample_hi 1 -Merlin 13310 13320 bigwig_sample_hi 1 -Merlin 17570 17580 bigwig_sample_hi 1 -Merlin 17940 17950 bigwig_sample_hi 1 -Merlin 18340 18350 bigwig_sample_hi 1 -Merlin 18810 18820 bigwig_sample_hi 1 -Merlin 22310 22320 bigwig_sample_hi 1 -Merlin 23760 23770 bigwig_sample_hi 1 -Merlin 24580 24590 bigwig_sample_hi 1 -Merlin 24860 24870 bigwig_sample_hi 1 -Merlin 25700 25710 bigwig_sample_hi 1 -Merlin 26450 26460 bigwig_sample_hi 1 -Merlin 27220 27230 bigwig_sample_hi 1 -Merlin 27280 27290 bigwig_sample_hi 1 -Merlin 28500 28510 bigwig_sample_hi 1 -Merlin 29740 29750 bigwig_sample_hi 1 -Merlin 31540 31550 bigwig_sample_hi 1 -Merlin 31890 31900 bigwig_sample_hi 1 -Merlin 32970 32980 bigwig_sample_hi 1 -Merlin 33980 33990 bigwig_sample_hi 1 -Merlin 35440 35450 bigwig_sample_hi 1 -Merlin 36510 36520 bigwig_sample_hi 1 -Merlin 39690 39700 bigwig_sample_hi 1 -Merlin 40350 40360 bigwig_sample_hi 1 -Merlin 40550 40560 bigwig_sample_hi 1 -Merlin 40780 40790 bigwig_sample_hi 1 -Merlin 41390 41400 bigwig_sample_hi 1 -Merlin 41940 41950 bigwig_sample_hi 1 -Merlin 42470 42480 bigwig_sample_hi 1 -Merlin 42560 42570 bigwig_sample_hi 1 -Merlin 42730 42740 bigwig_sample_hi 1 -Merlin 43010 43020 bigwig_sample_hi 1 -Merlin 43910 43920 bigwig_sample_hi 1 -Merlin 44670 44680 bigwig_sample_hi 1 -Merlin 46010 46020 bigwig_sample_hi 1 -Merlin 46470 46480 bigwig_sample_hi 1 -Merlin 49370 49380 bigwig_sample_hi 1 -Merlin 50310 50320 bigwig_sample_hi 1 -Merlin 52980 52990 bigwig_sample_hi 1 -Merlin 54630 54640 bigwig_sample_hi 1 -Merlin 55430 55440 bigwig_sample_hi 1 -Merlin 56450 56460 bigwig_sample_hi 1 -Merlin 56630 56640 bigwig_sample_hi 1 -Merlin 57610 57620 bigwig_sample_hi 1 -Merlin 57790 57800 bigwig_sample_hi 1 -Merlin 58730 58740 bigwig_sample_hi 1 -Merlin 59360 59370 bigwig_sample_hi 1 -Merlin 59450 59460 bigwig_sample_hi 1 -Merlin 60210 60220 bigwig_sample_hi 1 -Merlin 61110 61120 bigwig_sample_hi 1 -Merlin 62470 62480 bigwig_sample_hi 1 -Merlin 63330 63340 bigwig_sample_hi 1 -Merlin 63350 63360 bigwig_sample_hi 1 -Merlin 66210 66220 bigwig_sample_hi 1 -Merlin 66510 66520 bigwig_sample_hi 1 -Merlin 66850 66860 bigwig_sample_hi 1 -Merlin 67690 67700 bigwig_sample_hi 1 -Merlin 68760 68780 bigwig_sample_hi 1 -Merlin 69850 69860 bigwig_sample_hi 1 |
| b |
| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/bedouthilo_sample --- a/test-data/bedouthilo_sample Thu Jul 25 14:38:34 2024 +0000 +++ b/test-data/bedouthilo_sample Sun Sep 15 17:08:45 2024 +0000 |
| b |
| b'@@ -1,179 +1,9 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|
| b |
| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/bedouthilo_sample_2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bedouthilo_sample_2 Sun Sep 15 17:08:45 2024 +0000 |
| b |
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le_24515\t24515\n+Merlin\t65869\t65909\tbigwig_sample_19404\t19404\n+Merlin\t65919\t65959\tbigwig_sample_17683\t17683\n+Merlin\t65969\t66049\tbigwig_sample_25033\t25033\n+Merlin\t66059\t66079\tbigwig_sample_15162\t15162\n+Merlin\t66099\t66149\tbigwig_sample_17443\t17443\n+Merlin\t66159\t66339\tbigwig_sample_22446\t22446\n+Merlin\t66349\t66379\tbigwig_sample_20486\t20486\n+Merlin\t66389\t66419\tbigwig_sample_20880\t20880\n+Merlin\t66429\t66459\tbigwig_sample_22615\t22615\n+Merlin\t66469\t66509\tbigwig_sample_21289\t21289\n+Merlin\t66519\t66559\tbigwig_sample_27462\t27462\n+Merlin\t66569\t66599\tbigwig_sample_23016\t23016\n+Merlin\t66609\t66619\tbigwig_sample_20196\t20196\n+Merlin\t66639\t66669\tbigwig_sample_13156\t13156\n+Merlin\t66679\t66719\tbigwig_sample_23166\t23166\n+Merlin\t66729\t66799\tbigwig_sample_17423\t17423\n+Merlin\t66809\t66829\tbigwig_sample_21352\t21352\n+Merlin\t66839\t66909\tbigwig_sample_21896\t21896\n+Merlin\t66919\t66939\tbigwig_sample_16781\t16781\n+Merlin\t66949\t67069\tbigwig_sample_20514\t20514\n+Merlin\t67079\t67119\tbigwig_sample_13168\t13168\n+Merlin\t67129\t67159\tbigwig_sample_23519\t23519\n+Merlin\t67169\t67349\tbigwig_sample_21280\t21280\n+Merlin\t67359\t67379\tbigwig_sample_13757\t13757\n+Merlin\t67399\t67439\tbigwig_sample_18254\t18254\n+Merlin\t67449\t67469\tbigwig_sample_13060\t13060\n+Merlin\t67489\t67499\tbigwig_sample_24903\t24903\n+Merlin\t67509\t67549\tbigwig_sample_24981\t24981\n+Merlin\t67559\t67679\tbigwig_sample_19499\t19499\n+Merlin\t67689\t67749\tbigwig_sample_21397\t21397\n+Merlin\t67769\t67779\tbigwig_sample_19775\t19775\n+Merlin\t67789\t67809\tbigwig_sample_10614\t10614\n+Merlin\t67829\t67839\tbigwig_sample_30836\t30836\n+Merlin\t67849\t67869\tbigwig_sample_28734\t28734\n+Merlin\t67889\t67919\tbigwig_sample_19830\t19830\n+Merlin\t67949\t67999\tbigwig_sample_22137\t22137\n+Merlin\t68009\t68029\tbigwig_sample_15201\t15201\n+Merlin\t68049\t68059\tbigwig_sample_22812\t22812\n+Merlin\t68079\t68209\tbigwig_sample_15934\t15934\n+Merlin\t68219\t68229\tbigwig_sample_8170\t8170\n+Merlin\t68249\t68269\tbigwig_sample_16653\t16653\n+Merlin\t68299\t68359\tbigwig_sample_17040\t17040\n+Merlin\t68369\t68419\tbigwig_sample_18176\t18176\n+Merlin\t68439\t68469\tbigwig_sample_21687\t21687\n+Merlin\t68499\t68509\tbigwig_sample_17839\t17839\n+Merlin\t68529\t68609\tbigwig_sample_15825\t15825\n+Merlin\t68619\t68659\tbigwig_sample_20922\t20922\n+Merlin\t68669\t68699\tbigwig_sample_22089\t22089\n+Merlin\t68709\t68719\tbigwig_sample_10207\t10207\n+Merlin\t68739\t68799\tbigwig_sample_27086\t27086\n+Merlin\t68809\t68819\tbigwig_sample_17481\t17481\n+Merlin\t68839\t68909\tbigwig_sample_15691\t15691\n+Merlin\t68919\t68979\tbigwig_sample_17502\t17502\n+Merlin\t68989\t69009\tbigwig_sample_22744\t22744\n+Merlin\t69019\t69039\tbigwig_sample_13195\t13195\n+Merlin\t69049\t69169\tbigwig_sample_21374\t21374\n+Merlin\t69179\t69239\tbigwig_sample_22329\t22329\n+Merlin\t69259\t69289\tbigwig_sample_25619\t25619\n+Merlin\t69299\t69309\tbigwig_sample_18813\t18813\n+Merlin\t69329\t69349\tbigwig_sample_25571\t25571\n+Merlin\t69359\t69369\tbigwig_sample_19190\t19190\n+Merlin\t69389\t69419\tbigwig_sample_18133\t18133\n+Merlin\t69429\t69469\tbigwig_sample_22535\t22535\n+Merlin\t69489\t69589\tbigwig_sample_16166\t16166\n+Merlin\t69599\t69649\tbigwig_sample_14415\t14415\n+Merlin\t69659\t69669\tbigwig_sample_22113\t22113\n+Merlin\t69689\t69739\tbigwig_sample_17369\t17369\n+Merlin\t69749\t69759\tbigwig_sample_11081\t11081\n+Merlin\t69769\t69789\tbigwig_sample_20422\t20422\n+Merlin\t69799\t69839\tbigwig_sample_24162\t24162\n+Merlin\t69849\t69909\tbigwig_sample_24912\t24912\n+Merlin\t69919\t69929\tbigwig_sample_17370\t17370\n+Merlin\t69939\t69999\tbigwig_sample_19347\t19347\n+Merlin\t70009\t70019\tbigwig_sample_8066\t8066\n+Merlin\t70029\t70049\tbigwig_sample_19091\t19091\n+Merlin\t70049\t180929\tbigwig_sample_0\t0\n' |
| b |
| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/bedoutlo2_sample --- a/test-data/bedoutlo2_sample Thu Jul 25 14:38:34 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,110 +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 |
| b |
| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/bedoutlo_sample --- a/test-data/bedoutlo_sample Thu Jul 25 14:38:34 2024 +0000 +++ b/test-data/bedoutlo_sample Sun Sep 15 17:08:45 2024 +0000 |
| b |
| @@ -1,2 +1,1 @@ -Merlin 0 9 bigwig_sample_0 0 -Merlin 70049 180929 bigwig_sample_0 0 +chr1 0 1000 fake.bigwig_0 0 |
| b |
| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/fake.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fake.bed Sun Sep 15 17:08:45 2024 +0000 |
| b |
| @@ -0,0 +1,7 @@ +chr1 0 10 100 100 + +chr1 20 30 100 100 + +chr1 40 50 100 100 + +chr1 60 70 100 100 + +chr1 200 300 100 100 + +chr1 300 400 0 0 + +chr1 400 1000 100 100 + |
| b |
| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/fake.bigwig |
| b |
| Binary file test-data/fake.bigwig has changed |
| b |
| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/table2_sample --- a/test-data/table2_sample Thu Jul 25 14:38:34 2024 +0000 +++ b/test-data/table2_sample Sun Sep 15 17:08:45 2024 +0000 |
| b |
| @@ -1,29 +1,12 @@ 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 +qtop 0.00 qbot 0.00 First/Last 10 value counts Value Count @@ -47,28 +30,28 @@ 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 ------------ |------------ | +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 ------------ |------------ | |
| b |
| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/table3_sample --- a/test-data/table3_sample Thu Jul 25 14:38:34 2024 +0000 +++ b/test-data/table3_sample Sun Sep 15 17:08:45 2024 +0000 |
| b |
| @@ -1,57 +1,12 @@ Descriptive measures -bigwig bigwig_sample -contig Merlin -n 180929 -mean 6354.313736 -std 9951.749936 +bigwig fake.bigwig +contig chr1 +n 1000 +mean 0.840000 +std 0.366606 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 ------------ |------------ | - +max 1.000000 +qtop 1.00 +qbot 1.00 +chr1: 0.000000 occurs 160 times +chr1: 1.000000 occurs 840 times |
| b |
| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/table_only_sample --- a/test-data/table_only_sample Thu Jul 25 14:38:34 2024 +0000 +++ b/test-data/table_only_sample Sun Sep 15 17:08:45 2024 +0000 |
| b |
| @@ -1,74 +1,12 @@ Descriptive measures -bigwig bigwig_sample -contig Merlin -n 180929 -mean 6354.313736 -std 9951.749936 +bigwig fake.bigwig +contig chr1 +n 1000 +mean 0.840000 +std 0.366606 min 0.000000 -max 32767.000000 +max 1.000000 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 +chr1: 0.000000 occurs 160 times +chr1: 1.000000 occurs 840 times |
| b |
| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/table_qlo_notset_sample --- a/test-data/table_qlo_notset_sample Thu Jul 25 14:38:34 2024 +0000 +++ b/test-data/table_qlo_notset_sample Sun Sep 15 17:08:45 2024 +0000 |
| b |
| @@ -6,7 +6,7 @@ std 9951.749936 min 0.000000 max 32767.000000 -qtop 31906.72 +qtop 6436.00 qbot noqlo First/Last 10 value counts Value Count |
| b |
| diff -r 61946b8bd43b -r 00b3da7776a0 test-data/table_sample --- a/test-data/table_sample Thu Jul 25 14:38:34 2024 +0000 +++ b/test-data/table_sample Sun Sep 15 17:08:45 2024 +0000 |
| b |
| @@ -6,7 +6,7 @@ std 9951.749936 min 0.000000 max 32767.000000 -qtop 31906.72 +qtop 7293.00 qbot 0.00 First/Last 10 value counts Value Count |