| Next changeset 1:54ce44828e1b (2015-06-01) |
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Commit message:
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/fuma commit f56125b28ec44aa28943ed040b7b202fed9c875b-dirty |
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added:
fuma.xml test-data/chimerascan.txt test-data/defuse.txt test-data/edgren_tp.txt test-data/fusion-map.txt test-data/output.txt test-data/refseq_genes_hg19.bed tool_dependencies.xml |
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| diff -r 000000000000 -r a4cfaa0e3e5d fuma.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fuma.xml Thu May 21 09:56:41 2015 -0400 |
| [ |
| b'@@ -0,0 +1,168 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<tool id="fuma" name="FuMa" version="2.7.1.b">\n+\t<description>FuMa (FusionMatcher) matches detected fusion genes based on gene name subset matching (designed in particular for RNA-Seq).</description>\n+\t\n+\t<requirements>\n+\t\t<requirement type="package" version="2.7.1">fuma</requirement>\n+\t</requirements>\n+\t\n+\t<version_command>fuma --version 2>&1 | head -n 1</version_command><!-- -V also works, but is not GNU standard -->\n+\t\n+\t<command>\n+\t\t#import pipes\n+\t\t\n+\t\t#set $gene_annotations = []\n+\t\t#set $samples = []\n+\t\t#set $links = []\n+\t\t\n+\t\t#for $i, $d in enumerate( $datasets )\n+\t\t\t\n+\t\t\t#set $sample_name = pipes.quote(str($d[\'sample\'].name))\n+\t\t\t\n+\t\t\t#set $gene_annotations = $gene_annotations + [ "ga_" + str($i) + ":" + str($d[\'gene_annotation\'].file_name) ]\n+\t\t\t\n+\t\t\t#set $samples = $samples + [ $sample_name + ":" + str($d[\'format\']) + ":" + str($d[\'sample\'].file_name) ]\n+\t\t\t#set $links = $links + [ $sample_name + ":" + str("ga_") + str($i) ]\n+\t\t#end for\n+\t\t\n+\t\t#set $gene_annotations_str = " ".join(gene_annotations)\n+\t\t#set $samples_str = " ".join(samples)\n+\t\t#set $links_str = " ".join(links)\n+\t\t\n+\t\tfuma \n+\t\t -a\n+\t\t $gene_annotations_str\n+\t\t -s\n+\t\t $samples_str\n+\t\t -l\n+\t\t $links_str\n+\t\t#if $output_format.value == "list_boolean"\n+\t\t -f list\n+\t\t#else\n+\t\t -f $output_format.value\n+\t\t#end if\n+\t\t -o $fuma_overview ; \n+\t\t\n+\t\t\n+\t\t\n+\t\t#if $output_format.value == "list_boolean"\n+\t\t\tfuma-list-to-boolean-list -o tmp.txt $fuma_overview &&\n+\t\t\tmv tmp.txt $fuma_overview\n+\t\t#end if\n+\t</command>\n+\t\n+\t<inputs>\n+\t\t<repeat name="datasets" title="FusionGene Datasets" min="2">\n+\t\t\t<param name="sample" type="data" format="txt,tabular" label="Dataset (RNA-Seq fusion gene detection experiment)" />\n+\t\t\t<param name="format" type="select" label="Format of dataset">\n+\t\t\t\t<option value="chimerascan">ChimeraScan</option>\n+\t\t\t\t<option value="defuse">DeFuse</option>\n+\t\t\t\t<option value="complete-genomics">Complete Genomics</option>\n+\t\t\t\t<option value="fusion-catcher_final">Fusion Catcher (final-list file)</option>\n+\t\t\t\t<option value="fusionmap">FusionMap</option>\n+\t\t\t\t<option value="trinity-gmap">GMAP (As step after Trinity)</option>\n+\t\t\t\t<option value="oncofuse">OncoFuse</option>\n+\t\t\t\t<option value="rna-star_chimeric">STAR (chimeric file)</option>\n+\t\t\t\t<option value="tophat-fusion_pre">Tophat Fusion Pre (fusions.out)</option>\n+\t\t\t\t<option value="tophat-fusion_post_potential_fusion">Tophat Fusion Post (potential_fusion.txt)</option>\n+\t\t\t\t<option value="tophat-fusion_post_result">Tophat Fusion Post (result.txt)</option>\n+\t\t\t</param>\n+\t\t\t<param name="gene_annotation" type="data" format="bed" label="Corresponding gene-name annotation file (BED format)" help="Make use of persistent gene annotations! Gene annotations should only be different if different reference genome builds were used." />\n+\t\t</repeat>\n+\t\t\n+\t\t<param name="output_format" type="select" label="Output format">\n+\t\t\t<option value="list_boolean" selected="true">List (Boolean)</option>\n+\t\t\t<option value="list">List</option>\n+\t\t\t<option value="summary">Count summary</option>\n+\t\t</param>\n+\t</inputs>\n+\t\n+\t<outputs>\n+\t\t<data format="tabular" name="fuma_overview" label="${tool.name} on ${\', \'.join([ str(d[\'sample\'].hid)+\': \'+d[\'sample\'].name for d in $datasets ])}" />\n+\t</outputs>\n+\t\n+\t<tests>\n+\t\t<test>\n+\t\t\t<!-- <repeat name="datasets"> -->\n+\t\t\t\t<param name="datasets_0|sample" value="chimerascan.txt" ftype="tabular" />\n+\t\t\t\t<param name="datasets_0|format" value="chimerascan" />\n+\t\t\t\t<param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />\n+\t\t\t<!-- </repeat> -->\n+\t\t\t<!-- <repeat name="datasets"> -->\n+\t\t\t\t<param name="datasets_1|sample" value="defuse.txt" ftype="tabular" />\n+\t\t\t\t<param name="datasets_1|format" value="defuse" />\n+\t\t\t\t<param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />\n+\t\t\t<!-- </repeat> -->\n+\t\t\t<!-- <repeat name="datasets"> -->\n+\t\t\t\t<param name="datasets_'..b'ter should be genome build inspecific.\n+\n+Because RNA-Sequencing deals with samples that may have undergrond splicing, reads may split up because of biological processes. If a fusion event takes place, the same thing may happen. Therefore we hypothesize that using spanning read distances may be unreliable, because there are known introns of > 100kb. Therefore, FuMa translates the breakpoint to gene names, and only overlaps breakpoints with the same genename(s).\n+\n+=====\n+Usage\n+=====\n+\n+After you have uploaded the results of your Fusion Gene detection experiment, and selected the format to be *tabular*, you can start the FuMa wrapper. For each dataset you simply have to add another repeat. Then you have to select a corresponding format:\n+\n+*******\n+Formats\n+*******\n+\n++-------------------+-----------------------+-------------------------------------+\n+|Tools | File | Format string |\n++===================+=======================+=====================================+\n+|ChimeraScan | chimeras.bedpe | chimerascan |\n++-------------------+-----------------------+-------------------------------------+\n+|Complete Genomics | highConfidenceJu*.tsv | complete-genomics |\n++-------------------+-----------------------+-------------------------------------+\n+|Complete Genomics | allJunctionsBeta*.tsv | complete-genomics |\n++-------------------+-----------------------+-------------------------------------+\n+|DeFuse | results.txt | defuse |\n++-------------------+-----------------------+-------------------------------------+\n+|DeFuse | results.classify.txt | defuse |\n++-------------------+-----------------------+-------------------------------------+\n+|DeFuse | results.filtered.txt | defuse |\n++-------------------+-----------------------+-------------------------------------+\n+|Fusion Catcher | final-list_cand*.txt | fusion-catcher_final |\n++-------------------+-----------------------+-------------------------------------+\n+|FusionMap | | fusionmap |\n++-------------------+-----------------------+-------------------------------------+\n+|Trinity + GMAP | | trinity-gmap |\n++-------------------+-----------------------+-------------------------------------+\n+|OncoFuse | | oncofuse |\n++-------------------+-----------------------+-------------------------------------+\n+|RNA STAR | Chimeric.out.junction | rna-star_chimeric |\n++-------------------+-----------------------+-------------------------------------+\n+|TopHat Fusion pre | fusions.out | tophat-fusion_pre |\n++-------------------+-----------------------+-------------------------------------+\n+|TopHat Fusion post | potential_fusion.txt | tophat-fusion_post_potential_fusion |\n++-------------------+-----------------------+-------------------------------------+\n+|TopHat Fusion post | result.txt | tophat-fusion_post_result |\n++-------------------+-----------------------+-------------------------------------+\n+\n+To annotate genes upon the breakpoints you must provide a BED file that contains gene annotations for the user genome build. Make sure **your BED file contains one gene per line**. You should use BED files that contain one exon per line only if you want restrict your analysis to fusion genes detected within exons.\n+\n+UCSC genome browser provides a very simple way of obtaining BED files with one gene per line by selecting their *RefSeq Genes*-track and *knownGene*-table and putting the export format to BED. Galaxy should have a built-in UCSC table browser.\n+\n+\t</help>\n+</tool>\n' |
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| diff -r 000000000000 -r a4cfaa0e3e5d test-data/chimerascan.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chimerascan.txt Thu May 21 09:56:41 2015 -0400 |
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| b'@@ -0,0 +1,13347 @@\n+#chrom5p\tstart5p\tend5p\tchrom3p\tstart3p\tend3p\tchimera_cluster_id\tscore\tstrand5p\tstrand3p\n+chr8\t125551265\t125551328\tchr17\t38060847\t38066176\tCLUSTER8432\t278\t-\t-\n+chr20\t49411466\t49411709\tchr17\t59445687\t59470198\tCLUSTER10677\t196\t+\t+\n+chr17\t35479452\t35562785\tchr17\t37366788\t37374425\tCLUSTER11520\t80\t-\t-\n+chr20\t56964174\t56964572\tchr17\t37921198\t37934019\tCLUSTER11559\t43\t+\t-\n+chr17\t57970442\t57970685\tchr17\t47007458\t47018423\tCLUSTER1046\t43\t+\t-\n+chr19\t571324\t580781\tchr19\t13135834\t13209609\tCLUSTER2159\t40\t+\t+\n+chr17\t76778283\t76778375\tchr8\t117657054\t117768035\tCLUSTER3062\t33\t-\t-\n+chr17\t48943418\t48943714\tchr17\t35874899\t35880750\tCLUSTER12009\t30\t-\t-\n+chr20\t45852969\t45905538\tchr20\t34078462\t34099802\tCLUSTER6163\t28\t-\t+\n+chrM\t15503\t15887\tchrM\t235\t367\tCLUSTER3998\t28\t-\t-\n+chr4\t76649459\t76649794\tchr4\t76567952\t76587232\tCLUSTER495\t21\t-\t-\n+chr20\t47538274\t47538546\tchr20\t46286149\t46365685\tCLUSTER6259\t21\t+\t-\n+chr21\t40665736\t40685711\tchr21\t9915249\t9916546\tCLUSTER3440\t19\t-\t-\n+chr1\t144340525\t144340772\tchr1\t145004780\t145005286\tCLUSTER301\t18\t-\t+\n+chr1\t143744200\t143744586\tchr1\t145004780\t145005286\tCLUSTER938\t18\t-\t+\n+chr1\t149576452\t149576699\tchr1\t145004780\t145005286\tCLUSTER2173\t18\t+\t+\n+chr1\t147931723\t147931979\tchr1\t145004780\t145005286\tCLUSTER2320\t18\t-\t+\n+chr8\t145064225\t145064478\tchr16\t22019455\t22098851\tCLUSTER3532\t34\t+\t+\n+chrM\t8366\t14148\tchrM\t235\t367\tCLUSTER8062\t19\t-\t-\n+chr17\t38465422\t38465537\tchr8\t79485045\t79517501\tCLUSTER96\t17\t+\t+\n+chr17\t37607290\t37607526\tchr17\t53218670\t53241448\tCLUSTER3673\t16\t-\t+\n+chr5\t139781398\t139825559\tchr5\t141232672\t141234000\tCLUSTER3292\t15\t+\t-\n+chr10\t5726800\t5727137\tchr10\t5751492\t5754479\tCLUSTER541\t14\t+\t+\n+chr16\t70024499\t70099850\tchr16\t21415197\t21426405\tCLUSTER959\t14\t-\t-\n+chr16\t70024499\t70099850\tchr16\t29497000\t29506927\tCLUSTER5884\t14\t-\t-\n+chr16\t70024499\t70099850\tchr16\t22535140\t22547840\tCLUSTER9215\t14\t-\t+\n+chr16\t70024499\t70099850\tchr16\t30234349\t30246899\tCLUSTER11103\t14\t-\t-\n+chr17\t37856253\t37856563\tchr17\t61509664\t61515530\tCLUSTER328\t13\t+\t-\n+chr20\t56884770\t56886177\tchr19\t17256206\t17324103\tCLUSTER9719\t11\t+\t+\n+chr20\t26189758\t26189868\tchr19\t16345223\t16346155\tCLUSTER9790\t11\t-\t+\n+chr2\t10262694\t10269280\tchr2\t10281980\t10350941\tCLUSTER5168\t10\t+\t+\n+chr3\t4418013\t4508965\tchr3\t37094116\t37170639\tCLUSTER8305\t11\t-\t-\n+chr20\t57226308\t57227142\tchr20\t55929087\t55953518\tCLUSTER10876\t9\t+\t+\n+chr17\t57232491\t57232799\tchr17\t34851598\t34863350\tCLUSTER7548\t9\t-\t-\n+chr4\t120375937\t120376287\tchr7\t56078743\t56088923\tCLUSTER3661\t9\t+\t-\n+chr17\t37595417\t37607526\tchr17\t48548388\t48552199\tCLUSTER7408\t8\t-\t+\n+chr17\t60556385\t60637486\tchr11\t141452\t169051\tCLUSTER7139\t8\t+\t-\n+chr17\t57183958\t57184951\tchr17\t57915655\t57917951\tCLUSTER9133\t8\t+\t+\n+chr17\t60556385\t60637486\tchr3\t197907625\t197907734\tCLUSTER11129\t8\t+\t+\n+chr17\t60556385\t60637486\tchr1\t243219615\t243260600\tCLUSTER11589\t8\t+\t-\n+chr17\t60556385\t60637486\tchr1\t700244\t709659\tCLUSTER13302\t8\t+\t-\n+chr2\t85804613\t85806289\tchr2\t85818847\t85820510\tCLUSTER2615\t8\t+\t+\n+chr17\t60129897\t60142642\tchr17\t59469337\t59470198\tCLUSTER2689\t8\t-\t+\n+chr9\t111754688\t111754848\tchr14\t74178485\t74181127\tCLUSTER598\t12\t-\t-\n+chr7\t45808258\t45808616\tchr7\t55840871\t55841375\tCLUSTER9736\t9\t-\t+\n+chr1\t153934695\t153935797\tchr1\t153920147\t153927641\tCLUSTER4216\t7\t-\t-\n+chr20\t62496580\t62500793\tchr20\t62559687\t62567383\tCLUSTER5323\t7\t+\t+\n+chr13\t32420919\t32520317\tchr13\t32652970\t32870775\tCLUSTER9025\t8\t+\t+\n+chr7\t64126510\t64139713\tchr7\t64144464\t64147263\tCLUSTER3026\t7\t+\t+\n+chr14\t96968712\t96968936\tchr14\t96904171\t96955111\tCLUSTER8583\t7\t+\t+\n+chr20\t61569147\t61569303\tchr20\t36611422\t36634798\tCLUSTER10444\t7\t-\t-\n+chr19\t15443100\t15443341\tchr19\t14072341\t14104706\tCLUSTER11451\t7\t-\t-\n+chr11\t61560108\t61560499\tchr11\t61605249\t61634824\tCLUSTER149\t7\t+\t+\n+chr2\t38829998\t38830177\tchr5\t77781037\t77806220\tCLUSTER7396\t26\t-\t-\n+chr9\t111754688\t111754848\tchr7\t150811764\t150820724\tCLUSTER378\t10\t-\t+\n+chr17\t60556385\t60637486\tchr16\t90196204\t90204398\tCLUSTER1148\t7\t+\t+\n+chr3\t158449928\t158450274\tchr3\t183821969\t183824782\tCLUSTER10641\t7\t-\t+\n+chr1\t114354331\t114355069\tchr1\t114442493\t114443858\tCLUSTER8735\t6\t-\t+\n+chr12\t80211173'..b'\t-\n+chr9\t131186320\t131196891\tchr16\t8946801\t8953191\tCLUSTER13277\t1\t+\t-\n+chr19\t45898693\t45908311\tchr6\t33383586\t33384229\tCLUSTER13278\t1\t-\t+\n+chr17\t62657946\t62658385\tchrM\t7586\t9207\tCLUSTER13279\t1\t-\t+\n+chr7\t75140252\t75157452\tchr7\t75046064\t75115567\tCLUSTER13281\t1\t-\t-\n+chrM\t8366\t14148\tchr20\t34236846\t34243265\tCLUSTER13282\t1\t-\t-\n+chr11\t111625703\t111637168\tchrM\t1755\t4263\tCLUSTER13283\t1\t-\t+\n+chr3\t148709194\t148745455\tchr17\t40465341\t40466879\tCLUSTER13284\t1\t+\t-\n+chr5\t140058646\t140070970\tchrM\t1755\t4263\tCLUSTER13285\t1\t-\t+\n+chr6\t24775158\t24775263\tchr19\t39138266\t39221170\tCLUSTER13286\t1\t+\t+\n+chr10\t27047990\t27150015\tchr17\t26864134\t26865174\tCLUSTER13287\t1\t-\t+\n+chrM\t10472\t12137\tchr7\t97920961\t97922907\tCLUSTER13288\t1\t+\t-\n+chr16\t1383605\t1399441\tchr8\t17827085\t17887456\tCLUSTER13289\t1\t+\t+\n+chr21\t37692486\t37734525\tchrX\t69510540\t69640773\tCLUSTER13290\t1\t+\t+\n+chr9\t117373705\t117373843\tchr16\t30418734\t30425929\tCLUSTER13291\t1\t+\t+\n+chr2\t201994451\t202014557\tchr14\t104200087\t104220580\tCLUSTER13293\t1\t+\t-\n+chr9\t139409934\t139440237\tchrM\t1755\t4263\tCLUSTER13294\t1\t-\t+\n+chr15\t102029696\t102030186\tchr6\t114257319\t114281181\tCLUSTER13295\t1\t-\t-\n+chrM\t8366\t14148\tchr6\t100956607\t101053575\tCLUSTER13296\t1\t-\t-\n+chr2\t120124503\t120130121\tchrX\t147018984\t147032155\tCLUSTER13297\t1\t+\t+\n+chr19\t55967002\t55973048\tchr12\t56552145\t56554578\tCLUSTER13298\t1\t-\t+\n+chr17\t35306174\t35346018\tchr3\t184019324\t184026839\tCLUSTER13299\t1\t+\t+\n+chr6\t32861952\t32862703\tchr1\t151261570\t151264380\tCLUSTER13300\t1\t+\t+\n+chr1\t116935486\t116961243\tchrM\t10059\t10404\tCLUSTER13301\t1\t-\t+\n+chr15\t40509628\t40532881\tchr8\t141668480\t141716303\tCLUSTER13303\t1\t+\t-\n+chr16\t29819965\t29823305\tchrM\t15998\t16570\tCLUSTER13304\t1\t-\t+\n+chr7\t39989958\t40102698\tchr11\t1213089\t1222365\tCLUSTER13305\t1\t+\t+\n+chr1\t9074739\t9086403\tchr2\t242192430\t242196220\tCLUSTER13306\t1\t-\t-\n+chr22\t21119872\t21213099\tchr21\t38123188\t38302732\tCLUSTER13307\t1\t-\t-\n+chr3\t183415605\t183446638\tchr8\t25158091\t25162808\tCLUSTER13308\t1\t+\t+\n+chr15\t44066793\t44068604\tchr8\t67474409\t67504778\tCLUSTER13310\t1\t-\t-\n+chr15\t58932975\t59042176\tchr9\t135766734\t135786075\tCLUSTER13311\t1\t-\t-\n+chr10\t95132686\t95141152\tchr17\t79860776\t79867477\tCLUSTER13312\t1\t-\t-\n+chr9\t35732071\t35732391\tchr14\t61184688\t61190764\tCLUSTER13313\t1\t-\t-\n+chr3\t49148382\t49158370\tchr1\t11166587\t11319479\tCLUSTER13314\t1\t-\t-\n+chr6\t170892144\t170893741\tchr14\t23344263\t23349585\tCLUSTER13315\t1\t-\t+\n+chr2\t99757806\t99757881\tchr9\t131314836\t131315614\tCLUSTER13316\t1\t-\t+\n+chr12\t132628992\t132636364\tchr7\t5566778\t5569293\tCLUSTER13317\t1\t+\t-\n+chr12\t64238540\t64410791\tchr17\t76987801\t76988839\tCLUSTER13318\t1\t+\t-\n+chr6\t44214848\t44221613\tchr10\t5029967\t5040938\tCLUSTER13320\t1\t+\t-\n+chr6\t30886540\t30890330\tchr7\t99661652\t99675055\tCLUSTER13321\t1\t+\t-\n+chr5\t10250281\t10250556\tchr10\t27035524\t27054246\tCLUSTER13322\t1\t+\t-\n+chr7\t26241323\t26246129\tchr10\t14938844\t14946303\tCLUSTER13324\t1\t+\t+\n+chr19\t15484596\t15484875\tchr19\t49458804\t49465054\tCLUSTER13326\t1\t-\t+\n+chr7\t20866916\t20867438\tchr22\t29723668\t29730338\tCLUSTER13327\t1\t+\t-\n+chr3\t49053251\t49058466\tchr9\t20978337\t20995953\tCLUSTER13328\t1\t-\t+\n+chr5\t150415142\t150443307\tchrX\t41206892\t41209523\tCLUSTER13329\t1\t-\t+\n+chr4\t190394298\t190395874\tchr20\t45838380\t45976669\tCLUSTER13330\t1\t+\t-\n+chr16\t55836763\t55867074\tchr2\t128934387\t128953248\tCLUSTER13331\t1\t-\t+\n+chrX\t37430821\t37536749\tchr17\t5289345\t5290429\tCLUSTER13332\t1\t+\t-\n+chr8\t91013579\t91064226\tchr4\t100820709\t100822308\tCLUSTER13333\t1\t+\t-\n+chr16\t2147728\t2153895\tchr16\t14849048\t14859286\tCLUSTER13334\t1\t-\t+\n+chr19\t33968951\t34012798\tchr7\t149576423\t149577786\tCLUSTER13335\t1\t-\t+\n+chr9\t123292255\t123342436\tchrX\t54566567\t54593719\tCLUSTER13337\t1\t-\t+\n+chr5\t1076808\t1112171\tchr22\t38169789\t38172562\tCLUSTER13338\t1\t-\t+\n+chr19\t44130935\t44143990\tchr19\t55602280\t55614935\tCLUSTER13339\t1\t-\t-\n+chr13\t41885340\t41891065\tchr10\t129894924\t129911865\tCLUSTER13341\t1\t+\t-\n+chr11\t47204554\t47207431\tchr6\t43164382\t43192324\tCLUSTER13342\t1\t-\t+\n+chr14\t24911551\t24912006\tchr2\t235401685\t235405692\tCLUSTER13343\t1\t-\t-\n+chr4\t154387497\t154542031\tchr19\t12786530\t12791138\tCLUSTER13344\t1\t+\t-\n+chr7\t102208456\t102213067\tchr19\t34818325\t34846470\tCLUSTER13345\t1\t-\t+\n' 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| b |
| diff -r 000000000000 -r a4cfaa0e3e5d test-data/defuse.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/defuse.txt Thu May 21 09:56:41 2015 -0400 |
| b |
| b'@@ -0,0 +1,916 @@\n+cluster_id\tsplitr_sequence\tsplitr_count\tsplitr_span_pvalue\tsplitr_pos_pvalue\tsplitr_min_pvalue\tadjacent\taltsplice\tbreak_adj_entropy1\tbreak_adj_entropy2\tbreak_adj_entropy_min\tbreakpoint_homology\tbreakseqs_estislands_percident\tcdna_breakseqs_percident\tconcordant_ratio\tdeletion\test_breakseqs_percident\teversion\texonboundaries\texpression1\texpression2\tgene1\tgene2\tgene_align_strand1\tgene_align_strand2\tgene_chromosome1\tgene_chromosome2\tgene_end1\tgene_end2\tgene_location1\tgene_location2\tgene_name1\tgene_name2\tgene_start1\tgene_start2\tgene_strand1\tgene_strand2\tgenome_breakseqs_percident\tgenomic_break_pos1\tgenomic_break_pos2\tgenomic_strand1\tgenomic_strand2\tinterchromosomal\tinterrupted_index1\tinterrupted_index2\tinversion\tlibrary_name\tmax_map_count\tmax_repeat_proportion\tmean_map_count\tmin_map_count\tnum_multi_map\tnum_splice_variants\torf\tread_through\n+23092\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t14006\t8407\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23115\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t11706\t5320\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+25612\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t12\t12\t\t\t\t\t\t\t\t\t\t\t\t6457893\t6443410\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tY\n+31848\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t8\t10\t\t\t\t\t\t\t\t\t\t\t\t43035551\t8925081\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23019\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t343\t7686\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+16995\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t14\t1\t\t\t\t\t\t\t\t\t\t\t\t43723013\t91853147\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+27652\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t14\t5\t\t\t\t\t\t\t\t\t\t\t\t102551038\t118309569\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+25508\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t12\t12\t\t\t\t\t\t\t\t\t\t\t\t52628954\t53298489\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+9682\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t17\t17\t\t\t\t\t\t\t\t\t\t\t\t37682566\t37700499\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tY\n+10165\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t17\tX\t\t\t\t\t\t\t\t\t\t\t\t33478116\t108297810\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33747\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t4\t19\t\t\t\t\t\t\t\t\t\t\t\t38637596\t8451051\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+20438\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t16\t6\t\t\t\t\t\t\t\t\t\t\t\t33964132\t150665062\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+10624\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t17\t9\t\t\t\t\t\t\t\t\t\t\t\t80049211\t5684298\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23005\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t4000\t14769\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33840\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t19\t19\t\t\t\t\t\t\t\t\t\t\t\t580782\t13135835\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+16823\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t12\t1\t\t\t\t\t\t\t\t\t\t\t\t52632491\t565697\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+16074\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t3\t1\t\t\t\t\t\t\t\t\t\t\t\t63898900\t106758926\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+13382\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t7\t1\t\t\t\t\t\t\t\t\t\t\t\t26235516\t566899\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+16017\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t1\tX\t\t\t\t\t\t\t\t\t\t\t\t91853147\t108297892\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+26187\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t12\t19\t\t\t\t\t\t\t\t\t\t\t\t46752889\t56299731\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33085\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t9\t\t\t\t\t\t\t\t\t\t\t\t24184164\t79483765\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+13938\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t1\t2\t\t\t\t\t\t\t\t\t\t\t\t566950\t133012886\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+27355\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t14\t14\t\t\t\t\t\t\t\t\t\t\t\t75287839\t75321919\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tY\n+17825\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t1\t19\t\t\t\t\t\t\t\t\t\t\t\t565801\t11777312\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+8499\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t17\t21\t\t\t\t\t\t\t\t\t\t\t\t38151526\t9826993\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23047\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t3484\t14450\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+8015\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t5\t2\t\t\t\t\t\t\t\t\t\t\t\t71146755\t133038453\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23073\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t8586\t14763\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+25540\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t12\t12\t\t\t\t\t\t\t\t\t\t\t\t50506081\t50558806\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tY\n+19272\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t3\t13\t\t\t\t\t\t\t\t\t\t\t\t58551170\t72249657\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+17206\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t20\t1\t\t\t\t\t\t\t\t\t\t\t\t3765920\t565772\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23102\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t8931\t14449\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+2551\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t11\t12\t\t\t\t\t\t\t\t\t\t\t\t110167262\t34372608\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+34931\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t5\t5\t\t\t\t\t\t\t\t\t\t\t\t118309571\t170814948\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23113\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t12104\t5263\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+26300\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t12\t5\t\t\t\t\t\t\t\t\t\t\t\t53858625\t91139848\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23128\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t12103\t3340\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+15225\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t1\t1\t\t\t\t\t\t\t\t\t\t\t\t2473653'..b'\t\t\t\t\t\t\t\t33141546\t108113634\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+3168\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t11\t5\t\t\t\t\t\t\t\t\t\t\t\t2019011\t134259999\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+12433\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t5\t17\t\t\t\t\t\t\t\t\t\t\t\t34955886\t29119901\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23330\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t9\t9\t\t\t\t\t\t\t\t\t\t\t\t139372139\t139378921\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tY\n+14232\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t1\t2\t\t\t\t\t\t\t\t\t\t\t\t569011\t207284336\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+31817\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t20\t10\t\t\t\t\t\t\t\t\t\t\t\t32664993\t21811145\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+17006\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t1\t14\t\t\t\t\t\t\t\t\t\t\t\t151738242\t50329313\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+16784\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t1\t12\t\t\t\t\t\t\t\t\t\t\t\t91852672\t127650989\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+3290\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t11\t5\t\t\t\t\t\t\t\t\t\t\t\t2019030\t134263539\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+9360\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t17\t17\t\t\t\t\t\t\t\t\t\t\t\t37359262\t56769000\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+12747\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t11\t1\t\t\t\t\t\t\t\t\t\t\t\t10830376\t569766\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+10164\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t17\tX\t\t\t\t\t\t\t\t\t\t\t\t33478114\t108297713\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23851\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t12\t2\t\t\t\t\t\t\t\t\t\t\t\t54677629\t88124624\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33050\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t7\t\t\t\t\t\t\t\t\t\t\t\t9361819\t97599083\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+12227\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t17\t\t\t\t\t\t\t\t\t\t\t\t24184163\t60142706\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+12282\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t19\t17\t\t\t\t\t\t\t\t\t\t\t\t11945083\t37868701\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+8398\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t2\t5\t\t\t\t\t\t\t\t\t\t\t\t232576633\t134260383\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+14515\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t17\t1\t\t\t\t\t\t\t\t\t\t\t\t37828494\t569305\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+9626\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t17\t17\t\t\t\t\t\t\t\t\t\t\t\t57232492\t34863351\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+15768\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t1\tX\t\t\t\t\t\t\t\t\t\t\t\t568364\t108297446\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23135\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t6472\t10858\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+9691\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t17\t17\t\t\t\t\t\t\t\t\t\t\t\t37360941\t33478228\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+25777\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t20\t12\t\t\t\t\t\t\t\t\t\t\t\t2451398\t3560214\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33699\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t4\t19\t\t\t\t\t\t\t\t\t\t\t\t38629661\t33185000\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+14138\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t2\t1\t\t\t\t\t\t\t\t\t\t\t\t232577176\t565851\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23083\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t13987\t6324\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+16016\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t1\tX\t\t\t\t\t\t\t\t\t\t\t\t91853050\t108297687\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+12950\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t11\t1\t\t\t\t\t\t\t\t\t\t\t\t2017954\t568203\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+15652\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t6\t1\t\t\t\t\t\t\t\t\t\t\t\t75950980\t566931\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+15640\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t1\t6\t\t\t\t\t\t\t\t\t\t\t\t224548265\t937525\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33433\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t2\t19\t\t\t\t\t\t\t\t\t\t\t\t204055493\t24184153\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23003\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t5490\t14115\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33615\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t19\t8\t\t\t\t\t\t\t\t\t\t\t\t1478773\t145981626\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+4672\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t21\t2\t\t\t\t\t\t\t\t\t\t\t\t9827191\t88124672\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33263\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t19\t2\t\t\t\t\t\t\t\t\t\t\t\t24184077\t230045634\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23075\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\tMT\tMT\t\t\t\t\t\t\t\t\t\t\t\t7768\t14653\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+8397\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t2\t5\t\t\t\t\t\t\t\t\t\t\t\t232576639\t134263192\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+33953\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t5\t\t\t\t\t\t\t\t\t\t\t\t24184164\t139666182\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+18059\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t1\t5\t\t\t\t\t\t\t\t\t\t\t\t569446\t177482956\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+32486\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t3\t\t\t\t\t\t\t\t\t\t\t\t14606850\t129324128\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+2368\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t12\t11\t\t\t\t\t\t\t\t\t\t\t\t76443552\t125938478\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+1042\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t11\t17\t\t\t\t\t\t\t\t\t\t\t\t810235\t33478232\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+7322\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t20\t2\t\t\t\t\t\t\t\t\t\t\t\t48807862\t133038722\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+17868\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t+\t19\t1\t\t\t\t\t\t\t\t\t\t\t\t13054352\t568203\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+30812\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t11\t10\t\t\t\t\t\t\t\t\t\t\t\t2018875\t69423263\t+\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+34942\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t-\t5\t5\t\t\t\t\t\t\t\t\t\t\t\t134260436\t177482849\t+\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+14718\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t+\t+\t1\t17\t\t\t\t\t\t\t\t\t\t\t\t568222\t33478228\t-\t+\t\t\t\t\t\t\t\t\t\t\t\t\tN\n+23748\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t-\t-\t2\t12\t\t\t\t\t\t\t\t\t\t\t\t203500040\t124069216\t-\t-\t\t\t\t\t\t\t\t\t\t\t\t\tN\n' |
| b |
| diff -r 000000000000 -r a4cfaa0e3e5d test-data/edgren_tp.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/edgren_tp.txt Thu May 21 09:56:41 2015 -0400 |
| b |
| @@ -0,0 +1,28 @@ +FusionID all.UniqueCuttingPositionCount all.SeedCount all.RescuedCount Strand Chromosome1 Position1 Chromosome2 Position2 KnownGene1 KnownTranscript1 KnownExonNumber1 KnownTranscriptStrand1 KnownGene2 KnownTranscript2 KnownExonNumber2 KnownTranscriptStrand2 FusionJunctionSequence SplicePattern FusionGene FrameShift +Edgren_ACACA_STAC2 -- chr17 35604416 chr17 37374457 +Edgren_ANKHD1_PCDH1 +- chr5 139855281 chr5 141245875 +Edgren_BSG_NFIX ++ chr19 577395 chr19 13158016 +Edgren_CCDC85C_SETD3 -- chr14 100023983 chr14 99905650 +Edgren_CPNE1_PI3 -+ chr20 34233416 chr20 43804351 +Edgren_CSE1L_ENSG00000236127 ++ chr20 47688169 chr20 47951036 +Edgren_CYTH1_EIF3H -- chr17 76724255 chr8 117716767 +Edgren_DHX35_ITCH ++ chr20 37629654 chr20 33025120 +Edgren_DIDO1_KIAA0406 -- chr20 61539197 chr20 36636628 +Edgren_GLB1_CMTM7 -+ chr3 33088411 chr3 32478861 +Edgren_LAMP1_MCF2L2 +- chr13 113964772 chr3 183021199 +Edgren_NFS1_PREX1 -- chr20 34271629 chr20 47342605 +Edgren_NOTCH1_NUP214 -+ chr9 139414605 chr9 134055503 +Edgren_PPP1R12A_SEPT10 -- chr12 80248292 chr2 110336171 +Edgren_RAB22A_MYO9B ++ chr20 56913658 chr19 17255969 +Edgren_RARA_PKIA ++ chr17 38489269 chr8 79472938 +Edgren_RPS6KB1_SNF8 +- chr17 57999186 chr17 47014579 +Edgren_SKA2_MYO19 -- chr17 57209971 chr17 34875381 +Edgren_STARD3_DOK5 ++ chr17 37806528 chr20 53179923 +Edgren_SUMF1_LRRFIP2 -- chr3 4125732 chr3 37159649 +Edgren_TATDN1_GSDMB -- chr8 125526213 chr17 38068478 +Edgren_VAPB_IKZF3 +- chr20 56995168 chr17 37970820 +Edgren_WDR67_ZNF704 +- chr8 124096521 chr8 81733797 +Edgren_ZMYND8_CEP250 -+ chr20 45911713 chr20 34071395 +Edgren_BCAS4_BCAS3 ++ chr20 49452573 chr17 59112507 +Edgren_ARFGEF2_SULF2 +- chr20 47595829 chr20 46350226 +Edgren_RPS6KB1_TMEM49 ++ chr17 57999186 chr17 57851408 |
| b |
| diff -r 000000000000 -r a4cfaa0e3e5d test-data/fusion-map.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fusion-map.txt Thu May 21 09:56:41 2015 -0400 |
| b |
| @@ -0,0 +1,70 @@ +FusionID all.UniqueCuttingPositionCount all.SeedCount all.RescuedCount Strand Chromosome1 Position1 Chromosome2 Position2 KnownGene1 KnownTranscript1 KnownExonNumber1 KnownTranscriptStrand1 KnownGene2 KnownTranscript2 KnownExonNumber2 KnownTranscriptStrand2 FusionJunctionSequence SplicePattern FusionGene FrameShift +FUS_26799002_2222102817(--) -- 1 26799003 12 56527458 +FUS_27652879_2794310094(-+) -+ 1 27652880 17 79477135 +FUS_27677421_1106763499(--) -- 1 27677422 6 44221420 +FUS_52818775_491865792(++) ++ 1 52818776 2 242615169 +FUS_109756747_2844503161(++) ++ 1 109756748 18 48474938 +FUS_162336993_162351680(++) ++ 1 162336994 1 162351681 +FUS_204162041_204183009(++) ++ 1 204162042 1 204183010 +FUS_260933576_260947203(++) ++ 2 11682953 2 11696580 +FUS_317729880_2671195661(--) -- 2 68479257 16 46717518 +FUS_431341885_488240973(++) ++ 2 182091262 2 238990350 +FUS_468401284_468407812(++) ++ 2 219150661 2 219157189 +FUS_481827274_1095808311(-+) -+ 2 232576651 6 33266232 +FUS_535356398_535379077(++) ++ 3 42906351 3 42929030 +FUS_564945819_2208207316(++) ++ 3 72495772 12 42631957 +FUS_622049449_622062384(++) ++ 3 129599402 3 129612337 +FUS_641333884_641344084(++) ++ 3 148883837 3 148894037 +FUS_642753372_2640297172(++) ++ 3 150303325 16 15819029 +FUS_650628845_650704928(++) ++ 3 158178798 3 158254881 +FUS_688959544_1831692166(-+) -+ 3 196509497 X 151302279 +FUS_690560141_1289758805(-+) -+ 4 87630 7 56101654 +FUS_844223288_2907008396(--) -- 4 153750777 19 32902925 +FUS_950027061_1496638003(+-) +- 5 68400246 8 103842164 +FUS_1021452375_1022860816(+-) +- 5 139825560 5 141234001 +FUS_1093233534_2218149952(-+) -+ 6 30691455 12 52574593 +FUS_1096426187_3038889284(--) -- 6 33884108 21 42629253 +FUS_1136770263_2286212600(++) ++ 6 74228184 12 120637241 +FUS_1136770312_2883379228(-+) -+ 6 74228233 19 9273757 +FUS_1136770987_1980946407(+-) +- 6 74228908 10 85912360 +FUS_1233435659_2723113969(--) -- 6 170893580 17 8281010 +FUS_1309258884_2298001199(++) ++ 7 75601733 12 132425840 +FUS_1325089044_1999508485(+-) +- 7 91431893 10 104474438 +FUS_1472280885_2753298497(--) -- 8 79485046 17 38465538 +FUS_1518347105_2752895197(--) -- 8 125551266 17 38062238 +FUS_1518347105_2752895483(--) -- 8 125551266 17 38062524 +FUS_1518347105_2752896199(--) -- 8 125551266 17 38063240 +FUS_1518347105_2752899136(--) -- 8 125551266 17 38066177 +FUS_1536899619_2586923912(++) ++ 8 144103780 15 64977161 +FUS_1625744006_2750144109(-+) -+ 9 86584135 17 35311150 +FUS_1654638612_1662879517(--) -- 9 115478741 9 123719646 +FUS_1669121216_1669132845(++) ++ 9 129961345 9 129972974 +FUS_1670521420_3062528544(++) ++ 9 131361549 22 18138593 +FUS_1799397243_2485431458(+-) +- X 119007356 14 70834275 +FUS_1900761185_1900785540(++) ++ 10 5727138 10 5751493 +FUS_1908751091_1908769529(++) ++ 10 13717044 10 13735482 +FUS_2018880080_2591692014(--) -- 10 123846033 15 69745263 +FUS_2041405408_2909026952(-+) -+ 11 10836577 19 34921481 +FUS_2088954897_2955778536(-+) -+ 11 58386066 20 22544041 +FUS_2123194535_2562850433(++) ++ 11 92625704 15 40903682 +FUS_2172555288_2751715570(--) -- 12 6979929 17 36882611 +FUS_2217352725_2217359993(++) ++ 12 51777366 12 51784634 +FUS_2220354100_2220360378(++) ++ 12 54778741 12 54785019 +FUS_2345398656_2640249892(-+) -+ 13 45971393 16 15771749 +FUS_2412983948_2413096340(++) ++ 13 113556685 13 113669077 +FUS_2439284820_2439298041(++) ++ 14 24687637 14 24700858 +FUS_2451742910_2913912193(-+) -+ 14 37145727 19 39806722 +FUS_2489891478_2508003573(+-) +- 14 75294295 14 93406390 +FUS_2749696310_2772065451(++) ++ 17 34863351 17 57232492 +FUS_2749696722_2772065451(++) ++ 17 34863763 17 57232492 +FUS_2750312412_2752207385(--) -- 17 35479453 17 37374426 +FUS_2752428377_2763381348(-+) -+ 17 37595418 17 48548389 +FUS_2758316408_2758339948(++) ++ 17 43483449 17 43506989 +FUS_2774302297_2774962857(-+) -+ 17 59469338 17 60129898 +FUS_2780655412_2781079288(++) ++ 17 65822453 17 66246329 +FUS_2788733755_2966381512(-+) -+ 17 73900796 20 33147017 +FUS_2792979986_2792985266(++) ++ 17 78147027 17 78152307 +FUS_2893652499_2893681620(++) ++ 19 19547028 19 19576149 +FUS_2914960146_2914976931(++) ++ 19 40854675 19 40871460 +FUS_2979600181_2980773042(+-) +- 20 46365686 20 47538547 +FUS_3006176578_3036925768(++) ++ 21 9916547 21 40665737 |
| b |
| diff -r 000000000000 -r a4cfaa0e3e5d test-data/output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.txt Thu May 21 09:56:41 2015 -0400 |
| b |
| @@ -0,0 +1,23 @@ + chimerascan.txt (10914) defuse.txt (258) fusion-map.txt (58) edgren_tp.txt (25) +chimerascan.txt (10914) 32/10914 (0.29%) : 32/258 (12.4%) 17/10914 (0.16%) : 17/58 (29.31%) 18/10914 (0.16%) : 18/25 (72.0%) +defuse.txt (258) 32/258 (12.4%) : 32/10914 (0.29%) 9/258 (3.49%) : 9/58 (15.52%) 17/258 (6.59%) : 17/25 (68.0%) +fusion-map.txt (58) 17/58 (29.31%) : 17/10914 (0.16%) 9/58 (15.52%) : 9/258 (3.49%) 6/58 (10.34%) : 6/25 (24.0%) +edgren_tp.txt (25) 18/25 (72.0%) : 18/10914 (0.16%) 17/25 (68.0%) : 17/258 (6.59%) 6/25 (24.0%) : 6/58 (10.34%) + + + chimerascan.txt (10914) defuse.txt (258) fusion-map.txt (58) edgren_tp.txt (25) +chimerascan.txt & defuse.txt (32) 8/32 (25.0%) : 8/58 (13.79%) 15/32 (46.88%) : 15/25 (60.0%) +chimerascan.txt & fusion-map.txt (17) 8/17 (47.06%) : 8/258 (3.1%) 5/17 (29.41%) : 5/25 (20.0%) +chimerascan.txt & edgren_tp.txt (18) 15/18 (83.33%) : 15/258 (5.81%) 5/18 (27.78%) : 5/58 (8.62%) +defuse.txt & fusion-map.txt (9) 8/9 (88.89%) : 8/10914 (0.07%) 6/9 (66.67%) : 6/25 (24.0%) +defuse.txt & edgren_tp.txt (17) 15/17 (88.24%) : 15/10914 (0.14%) 6/17 (35.29%) : 6/58 (10.34%) +fusion-map.txt & edgren_tp.txt (6) 5/6 (83.33%) : 5/10914 (0.05%) 6/6 (100.0%) : 6/258 (2.33%) + + + chimerascan.txt (10914) defuse.txt (258) fusion-map.txt (58) edgren_tp.txt (25) +chimerascan.txt & defuse.txt & fusion-map.txt (8) 5/8 (62.5%) : 5/25 (20.0%) +chimerascan.txt & defuse.txt & edgren_tp.txt (15) 5/15 (33.33%) : 5/58 (8.62%) +chimerascan.txt & fusion-map.txt & edgren_tp.txt (5) 5/5 (100.0%) : 5/258 (1.94%) +defuse.txt & fusion-map.txt & edgren_tp.txt (6) 5/6 (83.33%) : 5/10914 (0.05%) + + |
| b |
| diff -r 000000000000 -r a4cfaa0e3e5d test-data/refseq_genes_hg19.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refseq_genes_hg19.bed Thu May 21 09:56:41 2015 -0400 |
| b |
| b'@@ -0,0 +1,49305 @@\n+chr1\t66999824\t67210768\tNM_032291\n+chr1\t48998526\t50489626\tNM_032785\n+chr1\t16767166\t16786584\tNM_001145277\n+chr1\t16767166\t16786584\tNM_001145278\n+chr1\t16767166\t16786584\tNM_018090\n+chr1\t25071759\t25170815\tNM_013943\n+chr1\t33546713\t33585995\tNM_052998\n+chr1\t8384389\t8404227\tNM_001080397\n+chr1\t92145899\t92371559\tNM_001195684\n+chr1\t92145899\t92351836\tNM_001195683\n+chr1\t92145899\t92351836\tNM_003243\n+chr1\t100652477\t100715409\tNM_001918\n+chr1\t92145899\t92351836\tNR_036634\n+chr1\t175913961\t176176380\tNM_001286644\n+chr1\t175913961\t176176380\tNM_022457\n+chr1\t184356149\t184598155\tNM_030806\n+chr1\t150980972\t151008189\tNM_021222\n+chr1\t175913961\t176176380\tNM_001001740\n+chr1\t226418849\t226497204\tNM_001270409\n+chr1\t226418849\t226497204\tNM_173083\n+chr1\t226418849\t226497449\tNM_001270410\n+chr1\t2985741\t3355185\tNM_199454\n+chr1\t2985741\t3355185\tNM_022114\n+chr1\t2005424\t2116834\tNM_001242874\n+chr1\t6845383\t7829766\tNM_015215\n+chr1\t6281252\t6296044\tNM_012405\n+chr1\t1017197\t1051736\tNM_017891\n+chr1\t2036154\t2116834\tNM_001033582\n+chr1\t2005085\t2116834\tNM_001033581\n+chr1\t1981908\t2116834\tNM_002744\n+chr1\t22004791\t22109688\tNM_032236\n+chr1\t20959947\t20978004\tNM_032409\n+chr1\t23037330\t23241823\tNM_017449\n+chr1\t23037330\t23241823\tNM_004442\n+chr1\t20969149\t20978686\tNR_046507\n+chr1\t29213602\t29446558\tNM_001166005\n+chr1\t32479294\t32509482\tNM_001271878\n+chr1\t29213602\t29446558\tNM_004437\n+chr1\t27248212\t27273362\tNM_006600\n+chr1\t28296854\t28415148\tNM_001990\n+chr1\t29241087\t29391733\tNM_001166006\n+chr1\t28296854\t28415148\tNM_001282561\n+chr1\t29213602\t29446558\tNM_001166007\n+chr1\t31404352\t31538564\tNM_014676\n+chr1\t28296854\t28415148\tNM_001282562\n+chr1\t32479294\t32509482\tNM_006559\n+chr1\t26210676\t26232993\tNM_001145454\n+chr1\t28303783\t28415148\tNM_001282560\n+chr1\t29213602\t29446558\tNM_203343\n+chr1\t32479294\t32526460\tNR_073499\n+chr1\t32479294\t32509482\tNR_073498\n+chr1\t29213602\t29446558\tNM_203342\n+chr1\t31404352\t31538564\tNM_001020658\n+chr1\t39549838\t39952810\tNM_012090\n+chr1\t36690016\t36770957\tNM_005119\n+chr1\t35649200\t35658743\tNM_005066\n+chr1\t33979598\t34630875\tNM_001281956\n+chr1\t33979598\t34631443\tNM_052896\n+chr1\t43996546\t44089343\tNM_002840\n+chr1\t48226199\t48462562\tNM_001194986\n+chr1\t44870959\t45117396\tNM_018150\n+chr1\t43996546\t44089343\tNM_130440\n+chr1\t46092975\t46152302\tNM_021639\n+chr1\t50906934\t51425936\tNM_007051\n+chr1\t55532031\t55681039\tNM_015306\n+chr1\t53392900\t53517289\tNM_002979\n+chr1\t53392900\t53517289\tNM_001193599\n+chr1\t53392900\t53517289\tNM_001193600\n+chr1\t53392900\t53517289\tNM_001193617\n+chr1\t54519273\t54565416\tNM_153035\n+chr1\t52373627\t52456436\tNM_002867\n+chr1\t57463578\t58716211\tNM_021080\n+chr1\t61542945\t61928460\tNM_001145511\n+chr1\t64936475\t65158741\tNM_020925\n+chr1\t65991371\t66091917\tNM_001198688\n+chr1\t65991371\t66101111\tNM_001198689\n+chr1\t65886334\t66103176\tNM_002303\n+chr1\t61547533\t61928460\tNM_001145512\n+chr1\t61547979\t61928460\tNM_005595\n+chr1\t63906440\t63988944\tNM_014288\n+chr1\t59762624\t60228402\tNM_001113411\n+chr1\t59762624\t60228402\tNM_018291\n+chr1\t61547979\t61928460\tNM_001134673\n+chr1\t63906440\t63988944\tNR_045147\n+chr1\t62902382\t62917475\tNM_003368\n+chr1\t65991371\t66096095\tNM_001198687\n+chr1\t63906440\t63988944\tNM_001206739\n+chr1\t59762683\t60165066\tNR_103473\n+chr1\t62901974\t62917475\tNM_001017416\n+chr1\t62901974\t62917475\tNM_001017415\n+chr1\t65886334\t66096095\tNM_001003680\n+chr1\t65886334\t66101111\tNM_001003679\n+chr1\t71868624\t72748277\tNM_173808\n+chr1\t70225857\t70589171\tNM_020794\n+chr1\t76540388\t77042892\tNM_001160011\n+chr1\t76540388\t77096669\tNM_152996\n+chr1\t77554666\t77685132\tNM_005482\n+chr1\t90098643\t90185094\tNM_032270\n+chr1\t85784167\t86044046\tNM_001134445\n+chr1\t87012758\t87046432\tNM_012128\n+chr1\t87012758\t87046432\tNR_024602\n+chr1\t94352589\t94375012\tNM_002061\n+chr1\t93307716\t93427079\tNM_001252269\n+chr1\t93307716\t93427079\tNM_001252270\n+chr1\t95393583\t95428826\tNR_033998\n+chr1\t93307716\t93342707\tNM_001252271\n+chr1\t93298285\t93427079\tNM_001252273\n+chr1\t93307716\t93427079\tNM_001006605\n+chr1\t107682628\t108024475\tNM_001113226\n+chr1\t107682628\t108024475\tNM_001113228\n+chr1\t107682744\t108024475\tNM_014917\n+chr1\t111136201\t111174096\tNM_001204269\n+chr1\t113243748\t11325'..b'000228\t86059\t87439\tNM_033178\n+chrUn_gl000228\t82753\t84133\tNM_033178\n+chrUn_gl000228\t79447\t80827\tNM_033178\n+chrUn_gl000228\t102589\t103969\tNM_033178\n+chrUn_gl000228\t105895\t107275\tNM_033178\n+chrUn_gl000228\t109201\t110581\tNM_033178\n+chr17_ctg5_hap1\t954314\t1170453\tNM_001256299\n+chr17_ctg5_hap1\t596065\t760700\tNM_015443\n+chr17_ctg5_hap1\t762280\t895830\tNM_001123066\n+chr17_ctg5_hap1\t391611\t454187\tNM_001103154\n+chr17_ctg5_hap1\t762280\t895830\tNM_001203252\n+chr17_ctg5_hap1\t762280\t895830\tNM_001123067\n+chr17_ctg5_hap1\t894693\t946818\tNR_024559\n+chr17_ctg5_hap1\t128327\t183214\tNM_014798\n+chr17_ctg5_hap1\t391582\t454600\tNM_016632\n+chr17_ctg5_hap1\t762280\t895830\tNM_005910\n+chr17_ctg5_hap1\t596171\t760700\tNM_001193466\n+chr17_ctg5_hap1\t762280\t895830\tNM_016841\n+chr17_ctg5_hap1\t391611\t414020\tNM_001039083\n+chr17_ctg5_hap1\t762280\t895830\tNM_016835\n+chr17_ctg5_hap1\t762280\t895830\tNM_016834\n+chr17_ctg5_hap1\t128327\t183214\tNR_027774\n+chr17_ctg5_hap1\t197720\t424115\tNR_002940\n+chr17_ctg5_hap1\t762280\t895830\tNM_001203251\n+chr17_ctg5_hap1\t391582\t462618\tNM_001288812\n+chr17_ctg5_hap1\t391582\t418517\tNM_001113738\n+chr17_ctg5_hap1\t391582\t444217\tNM_001288811\n+chr17_ctg5_hap1\t563497\t760700\tNM_001193465\n+chr17_ctg5_hap1\t128327\t183214\tNR_027782\n+chr17_ctg5_hap1\t391582\t444217\tNM_001288813\n+chr17_ctg5_hap1\t1524912\t1574839\tNR_033799\n+chr17_ctg5_hap1\t121842\t125407\tNM_174919\n+chr17_ctg5_hap1\t86403\t118136\tNM_199282\n+chr17_ctg5_hap1\t86403\t122788\tNM_001282290\n+chr17_ctg5_hap1\t236131\t236665\tNM_016632\n+chr17_ctg5_hap1\t195720\t200597\tNM_001113738\n+chr17_ctg5_hap1\t167791\t167864\tNR_036199\n+chr17_ctg5_hap1\t167791\t167864\tNR_036271\n+chr17_ctg5_hap1\t197705\t240669\tNM_001006607\n+chr17_ctg5_hap1\t266211\t380618\tNM_006178\n+chr17_ctg5_hap1\t330260\t380553\tNR_033799\n+chr17_ctg5_hap1\t266211\t380618\tNR_040116\n+chr17_ctg5_hap1\t415626\t458604\tNM_014834\n+chr17_ctg5_hap1\t592235\t595386\tNR_034172\n+chr17_ctg5_hap1\t543725\t545984\tNR_026901\n+chr17_ctg5_hap1\t891433\t894424\tNR_024560\n+chr17_ctg5_hap1\t790688\t791133\tNM_001007532\n+chr17_ctg5_hap1\t943101\t945284\tNM_175882\n+chr17_ctg5_hap1\t954314\t1005883\tNM_001145148\n+chr17_ctg5_hap1\t954314\t1005883\tNM_001145146\n+chr17_ctg5_hap1\t954314\t1005883\tNM_001145147\n+chr17_ctg5_hap1\t954314\t1005883\tNM_004382\n+chr17_ctg5_hap1\t1151951\t1170451\tNR_026680\n+chr17_ctg5_hap1\t1147639\t1150972\tNR_026905\n+chr17_ctg5_hap1\t1151951\t1170182\tNR_027295\n+chr17_ctg5_hap1\t1143725\t1150972\tNR_026906\n+chr17_ctg5_hap1\t1188438\t1190693\tNR_026901\n+chr17_ctg5_hap1\t1407998\t1410253\tNR_026901\n+chr17_ctg5_hap1\t1450905\t1513884\tNM_016632\n+chr17_ctg5_hap1\t1461295\t1513884\tNM_001288813\n+chr17_ctg5_hap1\t1486976\t1513884\tNM_001113738\n+chr17_ctg5_hap1\t1481376\t1489848\tNR_002940\n+chr17_ctg5_hap1\t1461295\t1513884\tNM_001288811\n+chr1_gl000191_random\t36272\t50281\tNM_006625\n+chr1_gl000191_random\t38911\t50281\tNM_001191005\n+chr1_gl000191_random\t36272\t50281\tNM_001191009\n+chr1_gl000191_random\t36272\t50281\tNM_001191006\n+chr1_gl000191_random\t38911\t50281\tNM_054016\n+chr1_gl000191_random\t36272\t50281\tNR_034035\n+chr1_gl000191_random\t36272\t50281\tNM_001191007\n+chr1_gl000192_random\t132568\t407510\tNR_103556\n+chr4_gl000193_random\t49162\t88375\tNR_038377\n+chr4_gl000194_random\t53588\t115071\tNR_046441\n+chr4_gl000194_random\t53588\t115071\tNR_046440\n+chr4_gl000194_random\t61659\t115071\tNR_046442\n+chr4_gl000194_random\t53588\t115071\tNR_046439\n+chr7_gl000195_random\t42937\t86719\tNM_001242480\n+chr17_gl000205_random\t116622\t119732\tNR_003682\n+chr19_gl000209_random\t21910\t36449\tNM_014219\n+chr19_gl000209_random\t86690\t96155\tNM_020535\n+chr19_gl000209_random\t70070\t84658\tNM_001282171\n+chr19_gl000209_random\t115098\t129113\tNM_014512\n+chr19_gl000209_random\t57208\t68123\tNM_002255\n+chr19_gl000209_random\t57208\t68123\tNM_001080770\n+chr19_gl000209_random\t98134\t112667\tNM_012313\n+chr19_gl000209_random\t57208\t68123\tNM_001080772\n+chr19_gl000209_random\t98111\t113132\tNM_014513\n+chr19_gl000209_random\t46645\t68123\tNM_001258383\n+chr19_gl000209_random\t86745\t96246\tNM_001018081\n+chr19_gl000209_random\t70070\t84658\tNM_001282170\n+chr19_gl000209_random\t70070\t84658\tNM_001083539\n+chr19_gl000209_random\t131432\t145745\tNM_012312\n' |
| b |
| diff -r 000000000000 -r a4cfaa0e3e5d tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu May 21 09:56:41 2015 -0400 |
| b |
| @@ -0,0 +1,29 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="fuma" version="2.7.1"> + <install version="1.0"> + <actions> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="make_directory">$INSTALL_DIR/lib64/python</action> + + <action type="shell_command"> + git clone https://github.com/yhoogstrate/fuma.git fuma && + cd fuma && + git reset --hard 3d9a0532209d4ad10283cac324788b4fecfd2675 && + + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python && + python setup.py build && + python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin + </action> + + <action type="set_environment"> + <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + Downloads and installs Fuma; requires python pip and get to be installed. + </readme> + </package> +</tool_dependency> |