| Previous changeset 0:ebcd48f183b3 (2024-07-05) Next changeset 2:61946b8bd43b (2024-07-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416 |
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modified:
bigwig_outlier_bed.py bigwig_outlier_bed.xml test-data/bedouthi2_sample test-data/bedouthi_sample test-data/bedouthilo2_sample test-data/bedouthilo_sample test-data/bedoutlo2_sample test-data/bedoutlo_sample test-data/table2_sample test-data/table_sample |
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added:
test-data/bedouthi_qlo_notset_sample test-data/bedouthilo_qlo_notset_sample test-data/table3_sample test-data/table_qlo_notset_sample |
| b |
| diff -r ebcd48f183b3 -r 8377a6abb4da bigwig_outlier_bed.py --- a/bigwig_outlier_bed.py Fri Jul 05 06:00:15 2024 +0000 +++ b/bigwig_outlier_bed.py Sun Jul 21 11:03:36 2024 +0000 |
| [ |
| @@ -28,8 +28,6 @@ self.bwnames = args.bigwig self.bwlabels = args.bigwiglabels self.bedwin = args.minwin - self.qlo = args.qlo - self.qhi = args.qhi self.outbeds = args.outbeds self.bedouthi = args.bedouthi self.bedoutlo = args.bedoutlo @@ -37,7 +35,13 @@ self.tableoutfile = args.tableoutfile self.bedwin = args.minwin self.qhi = args.qhi - self.qlo = args.qlo + self.qlo = None + try: + f = float(args.qlo) + self.qlo = f + except Exception as e: + s = str(e) + print(s, ' qlo=', args.qlo) nbw = len(args.bigwig) nlab = len(args.bigwiglabels) if nlab < nbw: @@ -90,13 +94,13 @@ bwmax, ) if self.qhi is not None: - row += "\t%f" % self.bwtop + row += "\t%.2f" % self.bwtop else: - row += "\t" + row += "\tnoqhi" if self.qlo is not None: - row += "\t%f" % self.bwbot + row += "\t%.2f" % self.bwbot else: - row += "\t" + row += "\tnoqlo" return row def makeBed(self): @@ -125,13 +129,31 @@ bwhi = self.processVals(bw, isTop=True) for j, seg in enumerate(bwhi): if seg[1] - seg[0] >= self.bedwin: - bedhi.append((chr, seg[0], seg[1], "%s_hi" % (bwlabel), 1)) + score = np.sum(bw[seg[0]:seg[1]]) + bedhi.append( + ( + chr, + seg[0], + seg[1], + "%s_%d" % (bwlabel, score), + score, + ) + ) if self.qlo is not None: self.bwbot = np.quantile(bw, self.qlo) bwlo = self.processVals(bw, isTop=False) for j, seg in enumerate(bwlo): if seg[1] - seg[0] >= self.bedwin: - bedlo.append((chr, seg[0], seg[1], "%s_lo" % (bwlabel), -1)) + score = -1 * np.sum(bw[seg[0]:seg[1]]) + bedlo.append( + ( + chr, + seg[0], + seg[1], + "%s_%d" % (bwlabel, score), + score, + ) + ) if self.tableoutfile: row = self.makeTableRow(bw, bwlabel, chr) restab.append(copy.copy(row)) @@ -164,7 +186,7 @@ parser = argparse.ArgumentParser() a = parser.add_argument a("-m", "--minwin", default=10, type=int) - a("-l", "--qlo", default=None, type=float) + a("-l", "--qlo", default=None) a("-i", "--qhi", default=None, type=float) a("--bedouthi", default=None) a("--bedoutlo", default=None) |
| b |
| diff -r ebcd48f183b3 -r 8377a6abb4da bigwig_outlier_bed.xml --- a/bigwig_outlier_bed.xml Fri Jul 05 06:00:15 2024 +0000 +++ b/bigwig_outlier_bed.xml Sun Jul 21 11:03:36 2024 +0000 |
| b |
| @@ -1,5 +1,10 @@ -<tool name="Bigwig extremes to bed features" id="bigwig_outlier_bed" version="0.1.4" profile="22.05"> +<tool name="Bigwig extremes to bed features" id="bigwig_outlier_bed" version="@TOOL_VERSION@" 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> + </macros> <edam_topics> <edam_topic>topic_0157</edam_topic> <edam_topic>topic_0092</edam_topic> @@ -11,9 +16,9 @@ <xref type="bio.tools">bigtools</xref> </xrefs> <requirements> - <requirement type="package" version="3.12.3">python</requirement> - <requirement type="package" version="2.0.0">numpy</requirement> - <requirement type="package" version="0.1.4">pybigtools</requirement> + <requirement type="package" version="@PYTHON_VERSION@">python</requirement> + <requirement type="package" version="@NUMPY_VERSION@">numpy</requirement> + <requirement type="package" version="@TOOL_VERSION@">pybigtools</requirement> </requirements> <required_files> <include path="bigwig_outlier_bed.py"/> @@ -102,15 +107,25 @@ <param name="qlo" value="0.01"/> <param name="tableout" value="create"/> </test> + <test expect_num_outputs="2"> + <output name="bedouthi" value="bedouthi_qlo_notset_sample" compare="diff" lines_diff="0"/> + <output name="tableoutfile" value="table_qlo_notset_sample" compare="diff" lines_diff="0"/> + <param name="outbeds" value="outhi"/> + <param name="bigwig" value="bigwig_sample"/> + <param name="minwin" value="10"/> + <param name="qhi" value="0.99"/> + <param name="qlo" value=""/> + <param name="tableout" value="create"/> + </test> <test expect_num_outputs="3"> <output name="bedouthi" value="bedouthi_sample" compare="diff" lines_diff="0"/> <output name="bedoutlo" value="bedoutlo_sample" compare="diff" lines_diff="0"/> - <output name="tableoutfile" value="table_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="10"/> - <param name="qhi" value="0.99"/> - <param name="qlo" value="0.01"/> + <param name="minwin" value="1"/> + <param name="qhi" value="0.9"/> + <param name="qlo" value="0.1"/> <param name="tableout" value="create"/> </test> <test expect_num_outputs="4"> @@ -120,9 +135,9 @@ <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="10"/> - <param name="qhi" value="0.99"/> - <param name="qlo" value="0.01"/> + <param name="minwin" value="1"/> + <param name="qhi" value="0.9"/> + <param name="qlo" value="0.1"/> <param name="tableout" value="create"/> </test> </tests> |
| b |
| diff -r ebcd48f183b3 -r 8377a6abb4da test-data/bedouthi2_sample --- a/test-data/bedouthi2_sample Fri Jul 05 06:00:15 2024 +0000 +++ b/test-data/bedouthi2_sample Sun Jul 21 11:03:36 2024 +0000 |
| b |
| b'@@ -1,73 +1,1347 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|
| b |
| diff -r ebcd48f183b3 -r 8377a6abb4da test-data/bedouthi_qlo_notset_sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bedouthi_qlo_notset_sample Sun Jul 21 11:03:36 2024 +0000 |
| b |
| b'@@ -0,0 +1,178 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|
| b |
| diff -r ebcd48f183b3 -r 8377a6abb4da test-data/bedouthi_sample --- a/test-data/bedouthi_sample Fri Jul 05 06:00:15 2024 +0000 +++ b/test-data/bedouthi_sample Sun Jul 21 11:03:36 2024 +0000 |
| b |
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|
| b |
| diff -r ebcd48f183b3 -r 8377a6abb4da test-data/bedouthilo2_sample --- a/test-data/bedouthilo2_sample Fri Jul 05 06:00:15 2024 +0000 +++ b/test-data/bedouthilo2_sample Sun Jul 21 11:03:36 2024 +0000 |
| b |
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2100\t9412105\t1.bigwig_0\t0\n+chr21\t9412120\t9412125\t1.bigwig_0\t0\n+chr21\t9412130\t9412135\t1.bigwig_0\t0\n+chr21\t9412140\t9412145\t1.bigwig_0\t0\n+chr21\t9412180\t9412185\t1.bigwig_0\t0\n+chr21\t9412200\t9412210\t1.bigwig_0\t0\n+chr21\t9412225\t9412230\t1.bigwig_0\t0\n+chr21\t9412250\t9412260\t1.bigwig_0\t0\n+chr21\t9412305\t9412310\t1.bigwig_0\t0\n+chr21\t9412360\t9412370\t1.bigwig_0\t0\n+chr21\t9412385\t9412390\t1.bigwig_0\t0\n+chr21\t9412400\t9412415\t1.bigwig_0\t0\n+chr21\t9412440\t9412455\t1.bigwig_0\t0\n+chr21\t9412460\t9412465\t1.bigwig_0\t0\n+chr21\t9412470\t9412480\t1.bigwig_0\t0\n+chr21\t9412485\t9412490\t1.bigwig_0\t0\n+chr21\t9412510\t9412515\t1.bigwig_0\t0\n+chr21\t9412565\t9412570\t1.bigwig_0\t0\n+chr21\t9412590\t9412595\t1.bigwig_0\t0\n+chr21\t9412640\t9412650\t1.bigwig_0\t0\n+chr21\t9412670\t9412675\t1.bigwig_0\t0\n+chr21\t9412690\t9412700\t1.bigwig_0\t0\n+chr21\t9412770\t9412775\t1.bigwig_0\t0\n+chr21\t9412815\t9412820\t1.bigwig_0\t0\n+chr21\t9412835\t9412840\t1.bigwig_0\t0\n+chr21\t9412845\t9412850\t1.bigwig_0\t0\n+chr21\t9412900\t9412905\t1.bigwig_0\t0\n+chr21\t9412970\t9412975\t1.bigwig_0\t0\n+chr21\t9412990\t9412995\t1.bigwig_0\t0\n+chr21\t9413040\t9413045\t1.bigwig_0\t0\n+chr21\t9413055\t9413065\t1.bigwig_0\t0\n+chr21\t9413095\t9413100\t1.bigwig_0\t0\n+chr21\t9413130\t9413135\t1.bigwig_0\t0\n+chr21\t9413155\t9413160\t1.bigwig_0\t0\n+chr21\t9413170\t9413180\t1.bigwig_0\t0\n+chr21\t9413205\t9413210\t1.bigwig_0\t0\n+chr21\t9413250\t9413255\t1.bigwig_0\t0\n+chr21\t9413280\t9413285\t1.bigwig_0\t0\n+chr21\t9413310\t9413315\t1.bigwig_0\t0\n+chr21\t9413345\t9413350\t1.bigwig_0\t0\n+chr21\t9413400\t9413405\t1.bigwig_0\t0\n+chr21\t9413510\t9413515\t1.bigwig_0\t0\n+chr21\t9413665\t9413670\t1.bigwig_0\t0\n+chr21\t9414040\t9414045\t1.bigwig_0\t0\n+chr21\t9414055\t9414060\t1.bigwig_0\t0\n+chr21\t9414100\t9414105\t1.bigwig_0\t0\n+chr21\t9414150\t9414160\t1.bigwig_0\t0\n+chr21\t9414175\t9414180\t1.bigwig_0\t0\n+chr21\t9414215\t9414225\t1.bigwig_0\t0\n+chr21\t9414255\t9414260\t1.bigwig_0\t0\n+chr21\t9414265\t9414270\t1.bigwig_0\t0\n+chr21\t9414280\t9414285\t1.bigwig_0\t0\n+chr21\t9414305\t9414310\t1.bigwig_0\t0\n+chr21\t9414435\t9414440\t1.bigwig_0\t0\n+chr21\t9414525\t9414530\t1.bigwig_0\t0\n+chr21\t9414585\t9414590\t1.bigwig_0\t0\n+chr21\t9414595\t9414600\t1.bigwig_0\t0\n+chr21\t9414655\t9414665\t1.bigwig_0\t0\n+chr21\t9414680\t9414690\t1.bigwig_0\t0\n+chr21\t9414695\t9414700\t1.bigwig_0\t0\n+chr21\t9414705\t9414710\t1.bigwig_0\t0\n+chr21\t9414720\t9414725\t1.bigwig_0\t0\n+chr21\t9414755\t9414760\t1.bigwig_0\t0\n+chr21\t9414775\t9414780\t1.bigwig_0\t0\n+chr21\t9414785\t9414790\t1.bigwig_0\t0\n+chr21\t9414820\t9414825\t1.bigwig_0\t0\n+chr21\t9414835\t9414840\t1.bigwig_0\t0\n+chr21\t9414850\t9414855\t1.bigwig_0\t0\n+chr21\t9414860\t9414870\t1.bigwig_0\t0\n+chr21\t9414905\t9414910\t1.bigwig_0\t0\n+chr21\t9414925\t9414930\t1.bigwig_0\t0\n+chr21\t9414955\t9414960\t1.bigwig_0\t0\n+chr21\t9414975\t9414980\t1.bigwig_0\t0\n+chr21\t9414995\t9415000\t1.bigwig_0\t0\n+chr21\t9415040\t9415055\t1.bigwig_0\t0\n+chr21\t9415065\t9415075\t1.bigwig_0\t0\n+chr21\t9415095\t9415100\t1.bigwig_0\t0\n+chr21\t9415105\t9415115\t1.bigwig_0\t0\n+chr21\t9415135\t9415140\t1.bigwig_0\t0\n+chr21\t9415150\t9415155\t1.bigwig_0\t0\n+chr21\t9415170\t9415175\t1.bigwig_0\t0\n+chr21\t9415270\t9415275\t1.bigwig_0\t0\n+chr21\t9415320\t9415325\t1.bigwig_0\t0\n+chr21\t9415385\t9415390\t1.bigwig_0\t0\n+chr21\t9415470\t9415475\t1.bigwig_0\t0\n+chr21\t9415535\t9415540\t1.bigwig_0\t0\n+chr21\t9415595\t9415600\t1.bigwig_0\t0\n+chr21\t9415665\t9415670\t1.bigwig_0\t0\n+chr21\t9415685\t9415700\t1.bigwig_0\t0\n+chr21\t9415710\t9415715\t1.bigwig_0\t0\n+chr21\t9415820\t9415830\t1.bigwig_0\t0\n+chr21\t9415880\t9415885\t1.bigwig_0\t0\n+chr21\t9416020\t9416025\t1.bigwig_0\t0\n+chr21\t9416080\t9416085\t1.bigwig_0\t0\n+chr21\t9416095\t9416100\t1.bigwig_0\t0\n+chr21\t9416130\t9416135\t1.bigwig_0\t0\n+chr21\t9416150\t9416155\t1.bigwig_0\t0\n+chr21\t9416165\t9416175\t1.bigwig_0\t0\n+chr21\t9416185\t48129895\t1.bigwig_0\t0\n' |
| b |
| diff -r ebcd48f183b3 -r 8377a6abb4da test-data/bedouthilo_qlo_notset_sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bedouthilo_qlo_notset_sample Sun Jul 21 11:03:36 2024 +0000 |
| b |
| @@ -0,0 +1,70 @@ +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 ebcd48f183b3 -r 8377a6abb4da test-data/bedouthilo_sample --- a/test-data/bedouthilo_sample Fri Jul 05 06:00:15 2024 +0000 +++ b/test-data/bedouthilo_sample Sun Jul 21 11:03:36 2024 +0000 |
| b |
| b'@@ -1,139 +1,179 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n+Merlin\t42739\t42749\tbigwig_sample_325060\t325060\n+Merlin\t42759\t42769\tbigwig_sample_322590\t322590\n+Merlin\t43019\t43029\tbigwig_sample_324260\t324260\n+Merlin\t43049\t43059\tbigwig_sample_321650\t321650\n+Merlin\t43919\t43929\tbigwig_sample_327210\t327210\n+Merlin\t44029\t44039\tbigwig_sample_321790\t321790\n+Merlin\t44189\t44199\tbigwig_sample_319430\t319430\n+Merlin\t44679\t44689\tbigwig_sample_325010\t325010\n+Merlin\t45249\t45259\tbigwig_sample_321770\t321770\n+Merlin\t45649\t45659\tbigwig_sample_321720\t321720\n+Merlin\t46019\t46029\tbigwig_sample_324410\t324410\n+Merlin\t46479\t46489\tbigwig_sample_326850\t326850\n+Merlin\t46889\t46899\tbigwig_sample_321120\t321120\n+Merlin\t47439\t47449\tbigwig_sample_320620\t320620\n+Merlin\t49379\t49389\tbigwig_sample_325310\t325310\n+Merlin\t50069\t50079\tbigwig_sample_320990\t320990\n+Merlin\t50319\t50329\tbigwig_sample_326410\t326410\n+Merlin\t50939\t50949\tbigwig_sample_321760\t321760\n+Merlin\t51109\t51119\tbigwig_sample_321510\t321510\n+Merlin\t51549\t51559\tbigwig_sample_323060\t323060\n+Merlin\t52449\t52459\tbigwig_sample_319440\t319440\n+Merlin\t52589\t52599\tbigwig_sample_319130\t319130\n+Merlin\t52989\t52999\tbigwig_sample_326030\t326030\n+Merlin\t53149\t53159\tbigwig_sample_320540\t320540\n+Merlin\t53649\t53659\tbigwig_sample_322240\t322240\n+Merlin\t54459\t54469\tbigwig_sample_323000\t323000\n+Merlin\t54509\t54519\tbigwig_sample_321550\t321550\n+Merlin\t54639\t54649\tbigwig_sample_325760\t325760\n+Merlin\t54759\t54769\tbigwig_sample_323340\t323340\n+Merlin\t54969\t54979\tbigwig_sample_319230\t319230\n+Merlin\t55439\t55449\tbigwig_sample_325210\t325210\n+Merlin\t56209\t56219\tbigwig_sample_319070\t319070\n+Merlin\t56459\t56469\tbigwig_sample_325990\t325990\n+Merlin\t56639\t56649\tbigwig_sample_325740\t325740\n+Merlin\t56719\t56729\tbigwig_sample_320050\t320050\n+Merlin\t57139\t57149\tbigwig_sample_323350\t323350\n+Merlin\t57619\t57629\tbigwig_sample_324660\t324660\n+Merlin\t57799\t57809\tbigwig_sample_324110\t324110\n+Merlin\t57909\t57919\tbigwig_sample_322520\t322520\n+Merlin\t58049\t58059\tbigwig_sample_320380\t320380\n+Merlin\t58739\t58749\tbigwig_sample_327260\t327260\n+Merlin\t59249\t59259\tbigwig_sample_321560\t321560\n+Merlin\t59369\t59379\tbigwig_sample_325920\t325920\n+Merlin\t59459\t59469\tbigwig_sample_326500\t326500\n+Merlin\t60219\t60229\tbigwig_sample_326590\t326590\n+Merlin\t60309\t60319\tbigwig_sample_323670\t323670\n+Merlin\t61119\t61129\tbigwig_sample_325180\t325180\n+Merlin\t61679\t61689\tbigwig_sample_323700\t323700\n+Merlin\t62179\t62189\tbigwig_sample_320550\t320550\n+Merlin\t62479\t62489\tbigwig_sample_325380\t325380\n+Merlin\t63039\t63049\tbigwig_sample_320480\t320480\n+Merlin\t63149\t63159\tbigwig_sample_322560\t322560\n+Merlin\t63339\t63349\tbigwig_sample_327450\t327450\n+Merlin\t63359\t63369\tbigwig_sample_326830\t326830\n+Merlin\t63469\t63479\tbigwig_sample_319260\t319260\n+Merlin\t63519\t63529\tbigwig_sample_319530\t319530\n+Merlin\t63949\t63959\tbigwig_sample_323380\t323380\n+Merlin\t63969\t63979\tbigwig_sample_321670\t321670\n+Merlin\t64359\t64369\tbigwig_sample_321860\t321860\n+Merlin\t65999\t66009\tbigwig_sample_321670\t321670\n+Merlin\t66219\t66229\tbigwig_sample_326610\t326610\n+Merlin\t66519\t66529\tbigwig_sample_327310\t327310\n+Merlin\t66859\t66869\tbigwig_sample_325520\t325520\n+Merlin\t67249\t67259\tbigwig_sample_323350\t323350\n+Merlin\t67699\t67709\tbigwig_sample_326970\t326970\n+Merlin\t68649\t68659\tbigwig_sample_323020\t323020\n+Merlin\t68769\t68789\tbigwig_sample_648580\t648580\n+Merlin\t68989\t68999\tbigwig_sample_319610\t319610\n+Merlin\t69259\t69269\tbigwig_sample_320570\t320570\n+Merlin\t69579\t69589\tbigwig_sample_320980\t320980\n+Merlin\t69819\t69829\tbigwig_sample_320470\t320470\n+Merlin\t69859\t69869\tbigwig_sample_326630\t326630\n+Merlin\t69889\t69899\tbigwig_sample_319940\t319940\n+Merlin\t70049\t180929\tbigwig_sample_0\t0\n' |
| b |
| diff -r ebcd48f183b3 -r 8377a6abb4da test-data/bedoutlo2_sample --- a/test-data/bedoutlo2_sample Fri Jul 05 06:00:15 2024 +0000 +++ b/test-data/bedoutlo2_sample Sun Jul 21 11:03:36 2024 +0000 |
| b |
| @@ -1,91 +1,110 @@ -Merlin 80 90 bigwig_sample_lo -1 -Merlin 430 440 bigwig_sample_lo -1 -Merlin 1230 1240 bigwig_sample_lo -1 -Merlin 2670 2680 bigwig_sample_lo -1 -Merlin 3740 3750 bigwig_sample_lo -1 -Merlin 4700 4710 bigwig_sample_lo -1 -Merlin 5870 5890 bigwig_sample_lo -1 -Merlin 6290 6300 bigwig_sample_lo -1 -Merlin 8860 8870 bigwig_sample_lo -1 -Merlin 10520 10530 bigwig_sample_lo -1 -Merlin 11190 11200 bigwig_sample_lo -1 -Merlin 11380 11390 bigwig_sample_lo -1 -Merlin 11810 11820 bigwig_sample_lo -1 -Merlin 12660 12670 bigwig_sample_lo -1 -Merlin 14160 14170 bigwig_sample_lo -1 -Merlin 14750 14760 bigwig_sample_lo -1 -Merlin 16270 16280 bigwig_sample_lo -1 -Merlin 17240 17250 bigwig_sample_lo -1 -Merlin 18290 18300 bigwig_sample_lo -1 -Merlin 19080 19090 bigwig_sample_lo -1 -Merlin 19220 19230 bigwig_sample_lo -1 -Merlin 20240 20250 bigwig_sample_lo -1 -Merlin 21650 21660 bigwig_sample_lo -1 -Merlin 21810 21820 bigwig_sample_lo -1 -Merlin 23630 23640 bigwig_sample_lo -1 -Merlin 25030 25040 bigwig_sample_lo -1 -Merlin 26260 26270 bigwig_sample_lo -1 -Merlin 26560 26570 bigwig_sample_lo -1 -Merlin 26610 26620 bigwig_sample_lo -1 -Merlin 27670 27680 bigwig_sample_lo -1 -Merlin 27970 27980 bigwig_sample_lo -1 -Merlin 29400 29410 bigwig_sample_lo -1 -Merlin 29910 29920 bigwig_sample_lo -1 -Merlin 33460 33470 bigwig_sample_lo -1 -Merlin 33910 33920 bigwig_sample_lo -1 -Merlin 34470 34490 bigwig_sample_lo -1 -Merlin 35320 35330 bigwig_sample_lo -1 -Merlin 35620 35630 bigwig_sample_lo -1 -Merlin 35880 35890 bigwig_sample_lo -1 -Merlin 36810 36820 bigwig_sample_lo -1 -Merlin 37230 37240 bigwig_sample_lo -1 -Merlin 37560 37570 bigwig_sample_lo -1 -Merlin 37750 37760 bigwig_sample_lo -1 -Merlin 38330 38340 bigwig_sample_lo -1 -Merlin 39600 39610 bigwig_sample_lo -1 -Merlin 41900 41910 bigwig_sample_lo -1 -Merlin 42050 42060 bigwig_sample_lo -1 -Merlin 44440 44450 bigwig_sample_lo -1 -Merlin 46610 46620 bigwig_sample_lo -1 -Merlin 49290 49300 bigwig_sample_lo -1 -Merlin 50880 50890 bigwig_sample_lo -1 -Merlin 52230 52240 bigwig_sample_lo -1 -Merlin 52460 52470 bigwig_sample_lo -1 -Merlin 52740 52750 bigwig_sample_lo -1 -Merlin 52770 52780 bigwig_sample_lo -1 -Merlin 53150 53160 bigwig_sample_lo -1 -Merlin 54830 54840 bigwig_sample_lo -1 -Merlin 56020 56030 bigwig_sample_lo -1 -Merlin 57220 57230 bigwig_sample_lo -1 -Merlin 61250 61260 bigwig_sample_lo -1 -Merlin 63190 63200 bigwig_sample_lo -1 -Merlin 63290 63300 bigwig_sample_lo -1 -Merlin 64660 64670 bigwig_sample_lo -1 -Merlin 65050 65060 bigwig_sample_lo -1 -Merlin 66660 66670 bigwig_sample_lo -1 -Merlin 66900 66910 bigwig_sample_lo -1 -Merlin 67150 67160 bigwig_sample_lo -1 -Merlin 68790 68800 bigwig_sample_lo -1 -Merlin 69660 69670 bigwig_sample_lo -1 -chr21 610 625 1.bigwig_lo -1 -chr21 1010 1020 1.bigwig_lo -1 -chr21 1060 1070 1.bigwig_lo -1 -chr21 1170 1180 1.bigwig_lo -1 -chr21 1210 1225 1.bigwig_lo -1 -chr21 1250 1265 1.bigwig_lo -1 -chr21 1280 1290 1.bigwig_lo -1 -chr21 1450 1460 1.bigwig_lo -1 -chr21 1500 1510 1.bigwig_lo -1 -chr21 1865 1875 1.bigwig_lo -1 -chr21 1980 1990 1.bigwig_lo -1 -chr21 2960 2970 1.bigwig_lo -1 -chr21 3025 3035 1.bigwig_lo -1 -chr21 3465 3475 1.bigwig_lo -1 -chr21 3490 3500 1.bigwig_lo -1 -chr21 3670 3680 1.bigwig_lo -1 -chr21 3850 3865 1.bigwig_lo -1 -chr21 3875 3885 1.bigwig_lo -1 -chr21 3915 3925 1.bigwig_lo -1 -chr21 4495 4510 1.bigwig_lo -1 -chr21 4630 4640 1.bigwig_lo -1 -chr21 4975 4985 1.bigwig_lo -1 +Merlin 0 9 bigwig_sample_0 0 +Merlin 70049 180929 bigwig_sample_0 0 +chr21 0 9411190 1.bigwig_0 0 +chr21 9411785 9411790 1.bigwig_0 0 +chr21 9411800 9411815 1.bigwig_0 0 +chr21 9411860 9411865 1.bigwig_0 0 +chr21 9411900 9411905 1.bigwig_0 0 +chr21 9412005 9412010 1.bigwig_0 0 +chr21 9412050 9412055 1.bigwig_0 0 +chr21 9412065 9412070 1.bigwig_0 0 +chr21 9412080 9412085 1.bigwig_0 0 +chr21 9412100 9412105 1.bigwig_0 0 +chr21 9412120 9412125 1.bigwig_0 0 +chr21 9412130 9412135 1.bigwig_0 0 +chr21 9412140 9412145 1.bigwig_0 0 +chr21 9412180 9412185 1.bigwig_0 0 +chr21 9412200 9412210 1.bigwig_0 0 +chr21 9412225 9412230 1.bigwig_0 0 +chr21 9412250 9412260 1.bigwig_0 0 +chr21 9412305 9412310 1.bigwig_0 0 +chr21 9412360 9412370 1.bigwig_0 0 +chr21 9412385 9412390 1.bigwig_0 0 +chr21 9412400 9412415 1.bigwig_0 0 +chr21 9412440 9412455 1.bigwig_0 0 +chr21 9412460 9412465 1.bigwig_0 0 +chr21 9412470 9412480 1.bigwig_0 0 +chr21 9412485 9412490 1.bigwig_0 0 +chr21 9412510 9412515 1.bigwig_0 0 +chr21 9412565 9412570 1.bigwig_0 0 +chr21 9412590 9412595 1.bigwig_0 0 +chr21 9412640 9412650 1.bigwig_0 0 +chr21 9412670 9412675 1.bigwig_0 0 +chr21 9412690 9412700 1.bigwig_0 0 +chr21 9412770 9412775 1.bigwig_0 0 +chr21 9412815 9412820 1.bigwig_0 0 +chr21 9412835 9412840 1.bigwig_0 0 +chr21 9412845 9412850 1.bigwig_0 0 +chr21 9412900 9412905 1.bigwig_0 0 +chr21 9412970 9412975 1.bigwig_0 0 +chr21 9412990 9412995 1.bigwig_0 0 +chr21 9413040 9413045 1.bigwig_0 0 +chr21 9413055 9413065 1.bigwig_0 0 +chr21 9413095 9413100 1.bigwig_0 0 +chr21 9413130 9413135 1.bigwig_0 0 +chr21 9413155 9413160 1.bigwig_0 0 +chr21 9413170 9413180 1.bigwig_0 0 +chr21 9413205 9413210 1.bigwig_0 0 +chr21 9413250 9413255 1.bigwig_0 0 +chr21 9413280 9413285 1.bigwig_0 0 +chr21 9413310 9413315 1.bigwig_0 0 +chr21 9413345 9413350 1.bigwig_0 0 +chr21 9413400 9413405 1.bigwig_0 0 +chr21 9413510 9413515 1.bigwig_0 0 +chr21 9413665 9413670 1.bigwig_0 0 +chr21 9414040 9414045 1.bigwig_0 0 +chr21 9414055 9414060 1.bigwig_0 0 +chr21 9414100 9414105 1.bigwig_0 0 +chr21 9414150 9414160 1.bigwig_0 0 +chr21 9414175 9414180 1.bigwig_0 0 +chr21 9414215 9414225 1.bigwig_0 0 +chr21 9414255 9414260 1.bigwig_0 0 +chr21 9414265 9414270 1.bigwig_0 0 +chr21 9414280 9414285 1.bigwig_0 0 +chr21 9414305 9414310 1.bigwig_0 0 +chr21 9414435 9414440 1.bigwig_0 0 +chr21 9414525 9414530 1.bigwig_0 0 +chr21 9414585 9414590 1.bigwig_0 0 +chr21 9414595 9414600 1.bigwig_0 0 +chr21 9414655 9414665 1.bigwig_0 0 +chr21 9414680 9414690 1.bigwig_0 0 +chr21 9414695 9414700 1.bigwig_0 0 +chr21 9414705 9414710 1.bigwig_0 0 +chr21 9414720 9414725 1.bigwig_0 0 +chr21 9414755 9414760 1.bigwig_0 0 +chr21 9414775 9414780 1.bigwig_0 0 +chr21 9414785 9414790 1.bigwig_0 0 +chr21 9414820 9414825 1.bigwig_0 0 +chr21 9414835 9414840 1.bigwig_0 0 +chr21 9414850 9414855 1.bigwig_0 0 +chr21 9414860 9414870 1.bigwig_0 0 +chr21 9414905 9414910 1.bigwig_0 0 +chr21 9414925 9414930 1.bigwig_0 0 +chr21 9414955 9414960 1.bigwig_0 0 +chr21 9414975 9414980 1.bigwig_0 0 +chr21 9414995 9415000 1.bigwig_0 0 +chr21 9415040 9415055 1.bigwig_0 0 +chr21 9415065 9415075 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 |
| b |
| diff -r ebcd48f183b3 -r 8377a6abb4da test-data/bedoutlo_sample --- a/test-data/bedoutlo_sample Fri Jul 05 06:00:15 2024 +0000 +++ b/test-data/bedoutlo_sample Sun Jul 21 11:03:36 2024 +0000 |
| b |
| @@ -1,69 +1,2 @@ -Merlin 80 90 bigwig_sample_lo -1 -Merlin 430 440 bigwig_sample_lo -1 -Merlin 1230 1240 bigwig_sample_lo -1 -Merlin 2670 2680 bigwig_sample_lo -1 -Merlin 3740 3750 bigwig_sample_lo -1 -Merlin 4700 4710 bigwig_sample_lo -1 -Merlin 5870 5890 bigwig_sample_lo -1 -Merlin 6290 6300 bigwig_sample_lo -1 -Merlin 8860 8870 bigwig_sample_lo -1 -Merlin 10520 10530 bigwig_sample_lo -1 -Merlin 11190 11200 bigwig_sample_lo -1 -Merlin 11380 11390 bigwig_sample_lo -1 -Merlin 11810 11820 bigwig_sample_lo -1 -Merlin 12660 12670 bigwig_sample_lo -1 -Merlin 14160 14170 bigwig_sample_lo -1 -Merlin 14750 14760 bigwig_sample_lo -1 -Merlin 16270 16280 bigwig_sample_lo -1 -Merlin 17240 17250 bigwig_sample_lo -1 -Merlin 18290 18300 bigwig_sample_lo -1 -Merlin 19080 19090 bigwig_sample_lo -1 -Merlin 19220 19230 bigwig_sample_lo -1 -Merlin 20240 20250 bigwig_sample_lo -1 -Merlin 21650 21660 bigwig_sample_lo -1 -Merlin 21810 21820 bigwig_sample_lo -1 -Merlin 23630 23640 bigwig_sample_lo -1 -Merlin 25030 25040 bigwig_sample_lo -1 -Merlin 26260 26270 bigwig_sample_lo -1 -Merlin 26560 26570 bigwig_sample_lo -1 -Merlin 26610 26620 bigwig_sample_lo -1 -Merlin 27670 27680 bigwig_sample_lo -1 -Merlin 27970 27980 bigwig_sample_lo -1 -Merlin 29400 29410 bigwig_sample_lo -1 -Merlin 29910 29920 bigwig_sample_lo -1 -Merlin 33460 33470 bigwig_sample_lo -1 -Merlin 33910 33920 bigwig_sample_lo -1 -Merlin 34470 34490 bigwig_sample_lo -1 -Merlin 35320 35330 bigwig_sample_lo -1 -Merlin 35620 35630 bigwig_sample_lo -1 -Merlin 35880 35890 bigwig_sample_lo -1 -Merlin 36810 36820 bigwig_sample_lo -1 -Merlin 37230 37240 bigwig_sample_lo -1 -Merlin 37560 37570 bigwig_sample_lo -1 -Merlin 37750 37760 bigwig_sample_lo -1 -Merlin 38330 38340 bigwig_sample_lo -1 -Merlin 39600 39610 bigwig_sample_lo -1 -Merlin 41900 41910 bigwig_sample_lo -1 -Merlin 42050 42060 bigwig_sample_lo -1 -Merlin 44440 44450 bigwig_sample_lo -1 -Merlin 46610 46620 bigwig_sample_lo -1 -Merlin 49290 49300 bigwig_sample_lo -1 -Merlin 50880 50890 bigwig_sample_lo -1 -Merlin 52230 52240 bigwig_sample_lo -1 -Merlin 52460 52470 bigwig_sample_lo -1 -Merlin 52740 52750 bigwig_sample_lo -1 -Merlin 52770 52780 bigwig_sample_lo -1 -Merlin 53150 53160 bigwig_sample_lo -1 -Merlin 54830 54840 bigwig_sample_lo -1 -Merlin 56020 56030 bigwig_sample_lo -1 -Merlin 57220 57230 bigwig_sample_lo -1 -Merlin 61250 61260 bigwig_sample_lo -1 -Merlin 63190 63200 bigwig_sample_lo -1 -Merlin 63290 63300 bigwig_sample_lo -1 -Merlin 64660 64670 bigwig_sample_lo -1 -Merlin 65050 65060 bigwig_sample_lo -1 -Merlin 66660 66670 bigwig_sample_lo -1 -Merlin 66900 66910 bigwig_sample_lo -1 -Merlin 67150 67160 bigwig_sample_lo -1 -Merlin 68790 68800 bigwig_sample_lo -1 -Merlin 69660 69670 bigwig_sample_lo -1 +Merlin 0 9 bigwig_sample_0 0 +Merlin 70049 180929 bigwig_sample_0 0 |
| b |
| diff -r ebcd48f183b3 -r 8377a6abb4da test-data/table2_sample --- a/test-data/table2_sample Fri Jul 05 06:00:15 2024 +0000 +++ b/test-data/table2_sample Sun Jul 21 11:03:36 2024 +0000 |
| b |
| @@ -1,3 +1,3 @@ bigwig contig n mean std min max qtop qbot -bigwig_sample Merlin 70040 16414.614934 9523.634628 13.000000 32767.000000 32387.000000 323.000000 -1.bigwig chr21 4995 33.203203 21.071159 0.000000 100.000000 80.000000 0.000000 +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 |
| b |
| diff -r ebcd48f183b3 -r 8377a6abb4da test-data/table3_sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/table3_sample Sun Jul 21 11:03:36 2024 +0000 |
| b |
| @@ -0,0 +1,2 @@ +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 |
| b |
| diff -r ebcd48f183b3 -r 8377a6abb4da test-data/table_qlo_notset_sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/table_qlo_notset_sample Sun Jul 21 11:03:36 2024 +0000 |
| b |
| @@ -0,0 +1,2 @@ +bigwig contig n mean std min max qtop qbot +bigwig_sample Merlin 180929 6354.313736 9951.749936 0.000000 32767.000000 31906.72 noqlo |
| b |
| diff -r ebcd48f183b3 -r 8377a6abb4da test-data/table_sample --- a/test-data/table_sample Fri Jul 05 06:00:15 2024 +0000 +++ b/test-data/table_sample Sun Jul 21 11:03:36 2024 +0000 |
| b |
| @@ -1,2 +1,2 @@ bigwig contig n mean std min max qtop qbot -bigwig_sample Merlin 70040 16414.614934 9523.634628 13.000000 32767.000000 32387.000000 323.000000 +bigwig_sample Merlin 180929 6354.313736 9951.749936 0.000000 32767.000000 31906.72 0.00 |