| Previous changeset 3:4d4415bcea3c (2013-01-16) Next changeset 5:a8e81a2e6bf8 (2013-01-17) |
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Commit message:
Deleted selected files |
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removed:
peakranger/1.16.tar peakranger/gene_annotation_files/.svn/all-wcprops peakranger/gene_annotation_files/.svn/entries peakranger/gene_annotation_files/.svn/prop-base/dm3refGene.txt.svn-base peakranger/gene_annotation_files/.svn/prop-base/hg19refGene.txt.svn-base peakranger/gene_annotation_files/.svn/prop-base/mm9refGene.txt.svn-base peakranger/gene_annotation_files/.svn/text-base/dm3refGene.txt.svn-base peakranger/gene_annotation_files/.svn/text-base/hg19refGene.txt.svn-base peakranger/gene_annotation_files/.svn/text-base/mm9refGene.txt.svn-base peakranger/gene_annotation_files/dm3refGene.txt peakranger/gene_annotation_files/hg19refGene.txt peakranger/gene_annotation_files/mm9refGene.txt peakranger/ranger_wrapper.py peakranger/ranger_wrapper.xml |
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| diff -r 4d4415bcea3c -r 49542dea5b60 peakranger/1.16.tar |
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| Binary file peakranger/1.16.tar has changed |
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| diff -r 4d4415bcea3c -r 49542dea5b60 peakranger/gene_annotation_files/.svn/all-wcprops --- a/peakranger/gene_annotation_files/.svn/all-wcprops Wed Jan 16 18:25:37 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,23 +0,0 @@ -K 25 -svn:wc:ra_dav:version-url -V 98 -/svn/modencode_galaxy/!svn/ver/288/modENCODE_Galaxy/modENCODE_DCC/peakranger/gene_annotation_files -END -hg19refGene.txt -K 25 -svn:wc:ra_dav:version-url -V 114 -/svn/modencode_galaxy/!svn/ver/288/modENCODE_Galaxy/modENCODE_DCC/peakranger/gene_annotation_files/hg19refGene.txt -END -mm9refGene.txt -K 25 -svn:wc:ra_dav:version-url -V 113 -/svn/modencode_galaxy/!svn/ver/288/modENCODE_Galaxy/modENCODE_DCC/peakranger/gene_annotation_files/mm9refGene.txt -END -dm3refGene.txt -K 25 -svn:wc:ra_dav:version-url -V 113 -/svn/modencode_galaxy/!svn/ver/288/modENCODE_Galaxy/modENCODE_DCC/peakranger/gene_annotation_files/dm3refGene.txt -END |
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| diff -r 4d4415bcea3c -r 49542dea5b60 peakranger/gene_annotation_files/.svn/entries --- a/peakranger/gene_annotation_files/.svn/entries Wed Jan 16 18:25:37 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,130 +0,0 @@ -10 - -dir -338 -https://code.oicr.on.ca/svn/modencode_galaxy/modENCODE_Galaxy/modENCODE_DCC/peakranger/gene_annotation_files -https://code.oicr.on.ca/svn/modencode_galaxy - - - -2012-11-15T21:27:04.538392Z -288 -zzhou - - - - - - - - - - - - - - -7a940d4b-0ac5-471c-bc04-520279569bf3 - -hg19refGene.txt -file - - - - -2012-12-10T20:45:22.000000Z -f165342b892faa371bf37655470271d4 -2012-11-15T21:27:04.538392Z -288 -zzhou -has-props - - - - - - - - - - - - - - - - - - - - -11818959 - -mm9refGene.txt -file - - - - -2012-12-10T20:45:23.000000Z -2d4ef3c4b74401905ee5de7aaffa088a -2012-11-15T21:27:04.538392Z -288 -zzhou -has-props - - - - - - - - - - - - - - - - - - - - -8098919 - -dm3refGene.txt -file - - - - -2012-12-10T20:45:23.000000Z -919f058d6a7b1b28637980d08d80c675 -2012-11-15T21:27:04.538392Z -288 -zzhou -has-props - - - - - - - - - - - - - - - - - - - - -4332934 - |
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| diff -r 4d4415bcea3c -r 49542dea5b60 peakranger/gene_annotation_files/.svn/prop-base/dm3refGene.txt.svn-base --- a/peakranger/gene_annotation_files/.svn/prop-base/dm3refGene.txt.svn-base Wed Jan 16 18:25:37 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -K 14 -svn:executable -V 1 -* -END |
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| diff -r 4d4415bcea3c -r 49542dea5b60 peakranger/gene_annotation_files/.svn/prop-base/hg19refGene.txt.svn-base --- a/peakranger/gene_annotation_files/.svn/prop-base/hg19refGene.txt.svn-base Wed Jan 16 18:25:37 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -K 14 -svn:executable -V 1 -* -END |
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| diff -r 4d4415bcea3c -r 49542dea5b60 peakranger/gene_annotation_files/.svn/prop-base/mm9refGene.txt.svn-base --- a/peakranger/gene_annotation_files/.svn/prop-base/mm9refGene.txt.svn-base Wed Jan 16 18:25:37 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -K 14 -svn:executable -V 1 -* -END |
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| diff -r 4d4415bcea3c -r 49542dea5b60 peakranger/gene_annotation_files/.svn/text-base/dm3refGene.txt.svn-base --- a/peakranger/gene_annotation_files/.svn/text-base/dm3refGene.txt.svn-base Wed Jan 16 18:25:37 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,23964 +0,0 @@\n-585\tNM_001169365\tchr2L\t+\t7528\t9484\t7679\t8610\t2\t7528,8192,\t8116,9484,\t0\tCG11023\tcmpl\tcmpl\t0,2,\n-585\tNM_175941\tchr2L\t+\t7528\t9484\t7679\t9276\t3\t7528,8192,8667,\t8116,8589,9484,\t0\tCG11023\tcmpl\tcmpl\t0,2,0,\n-585\tNM_078715\tchr2L\t-\t9836\t18583\t11214\t17136\t9\t9836,11409,11778,12285,13519,13682,14932,17052,18260,\t11344,11518,12221,12928,13625,14874,15711,17212,18583,\t0\tl(2)gl\tcmpl\tcmpl\t2,1,2,1,0,2,0,0,-1,\n-585\tNM_164349\tchr2L\t-\t9836\t18583\t11214\t17136\t10\t9836,11409,11778,12285,13519,13682,14932,17052,18025,18260,\t11344,11518,12221,12928,13625,14874,15711,17212,18168,18583,\t0\tl(2)gl\tcmpl\tcmpl\t2,1,2,1,0,2,0,0,-1,-1,\n-585\tNM_164348\tchr2L\t-\t9836\t21372\t11214\t19944\t9\t9836,11409,11778,12285,13519,13682,14932,19884,21135,\t11344,11518,12221,12928,13625,14874,15711,20020,21372,\t0\tl(2)gl\tcmpl\tcmpl\t2,1,2,1,0,2,0,0,-1,\n-585\tNM_164350\tchr2L\t-\t9836\t21372\t11214\t15648\t9\t9836,11409,11778,12285,13519,13682,14932,19879,21065,\t11344,11518,12221,12928,13625,14874,15711,20020,21372,\t0\tl(2)gl\tcmpl\tcmpl\t2,1,2,1,0,2,0,-1,-1,\n-585\tNM_164351\tchr2L\t-\t9836\t21372\t11214\t15648\t9\t9836,11409,11778,12285,13519,13682,14932,19879,21065,\t11344,11518,12221,12928,13625,14874,15711,20015,21372,\t0\tl(2)gl\tcmpl\tcmpl\t2,1,2,1,0,2,0,-1,-1,\n-585\tNM_164352\tchr2L\t-\t9836\t21372\t11214\t15648\t10\t9836,11409,11778,12285,13519,13682,14932,19879,21065,21348,\t11344,11518,12221,12928,13625,14874,15711,20020,21200,21372,\t0\tl(2)gl\tcmpl\tcmpl\t2,1,2,1,0,2,0,-1,-1,-1,\n-585\tNM_001103573\tchr2L\t-\t21918\t25151\t21918\t25151\t5\t21918,22742,22993,23928,24746,\t22687,22935,23873,24210,25151,\t0\tIr21a\tcmpl\tcmpl\t2,1,0,0,0,\n-585\tNM_001103574\tchr2L\t-\t25401\t59242\t26520\t58150\t14\t25401,26765,27052,28014,28732,28981,33844,34557,34719,35745,38534,39300,58080,59189,\t26688,26964,27490,28240,28926,29068,34288,34604,35212,38088,38731,39857,58182,59242,\t0\tCda5\tcmpl\tcmpl\t0,2,2,1,2,2,2,0,2,2,0,1,0,-1,\n-585\tNM_001103575\tchr2L\t-\t25401\t59242\t26520\t58150\t13\t25401,26765,27052,28410,28732,28981,33844,34557,34719,38534,39300,58080,59189,\t26688,26964,27490,28639,28926,29068,34288,34604,35212,38731,39857,58182,59242,\t0\tCda5\tcmpl\tcmpl\t0,2,2,1,2,2,2,0,2,0,1,0,-1,\n-585\tNM_164353\tchr2L\t-\t25401\t59242\t26520\t58150\t13\t25401,26765,27052,28014,28732,28981,33844,34557,34719,38534,39300,58080,59189,\t26688,26964,27490,28240,28926,29068,34288,34604,35212,38731,39857,58182,59242,\t0\tCda5\tcmpl\tcmpl\t0,2,2,1,2,2,2,0,2,0,1,0,-1,\n-585\tNM_164354\tchr2L\t-\t25401\t59242\t26520\t58150\t14\t25401,26765,27052,28014,28732,28981,30393,33844,34557,34719,38534,39300,58080,59189,\t26688,26964,27490,28240,28926,29068,33270,34288,34604,35212,38731,39857,58182,59242,\t0\tCda5\tcmpl\tcmpl\t0,2,2,1,2,2,2,2,0,2,0,1,0,-1,\n-585\tNM_134642\tchr2L\t+\t67043\t71390\t67624\t70895\t5\t67043,67568,67891,68084,70606,\t67507,67762,68023,70549,71390,\t0\tdbr\tcmpl\tcmpl\t-1,0,0,0,2,\n-585\tNM_134643\tchr2L\t+\t72387\t76211\t72602\t76098\t3\t72387,74902,75077,\t72977,75018,76211,\t0\tgalectin\tcmpl\tcmpl\t0,0,2,\n-585\tNM_001169367\tchr2L\t+\t73484\t76211\t73569\t76098\t3\t73484,74902,75077,\t73692,75018,76211,\t0\tgalectin\tcmpl\tcmpl\t0,0,2,\n-585\tNM_001169366\tchr2L\t+\t74484\t76211\t74500\t76098\t3\t74484,74902,75077,\t74572,75018,76211,\t0\tgalectin\tcmpl\tcmpl\t0,0,2,\n-585\tNM_134644\tchr2L\t+\t76445\t77639\t76445\t77639\t1\t76445,\t77639,\t0\tCG11374\tcmpl\tcmpl\t0,\n-585\tNM_080081\tchr2L\t-\t82455\t87382\t83267\t87092\t2\t82455,87019,\t84277,87382,\t0\tnet\tcmpl\tcmpl\t1,0,\n-585\tNM_134645\tchr2L\t+\t94751\t102086\t94851\t101918\t12\t94751,94988,95131,95353,97883,98526,99784,100571,100761,101015,101248,101875,\t94892,95070,95301,97833,98470,99723,100516,100703,100942,101194,101619,102086,\t0\tCG11376\tcmpl\tcmpl\t0,2,0,2,1,0,0,0,0,1,0,2,\n-585\tNM_134646\tchr2L\t+\t102381\t104142\t102458\t103763\t3\t102381,103005,103515,\t102906,103434,104142,\t0\tCG11377\tcmpl\tcmpl\t0,1,1,\n-585\tNM_134647\tchr2L\t-\t103961\t106718\t104472\t106642\t5\t103961,105004,105390,105511,105968,\t104947,105336,105455,105915,106718,\t0\tNhe1\tcmpl\tcmpl\t2,0,1,2,0,\n-585\tNM_205880\tchr2L\t+\t106902\t114432\t108685\t113542\t8\t106902,107764,108587,110405,110754,111906,112689,113433,\t107000,107838,108809,110483,110877,112019,113369,114432,\t0\tSam-S\tcm'..b'62\t26430\t5\t14883,22818,23079,24990,26113,\t15008,23006,23272,25362,26444,\t0\tCG12061\tcmpl\tcmpl\t0,1,0,1,1,\n-585\tNM_001015259\tchrXHet\t+\t14883\t26444\t23149\t26430\t5\t14883,22818,23079,24990,26113,\t15008,23006,23177,25362,26444,\t0\tCG12061\tcmpl\tcmpl\t-1,-1,0,1,1,\n-585\tNM_001110997\tchrXHet\t+\t14883\t26444\t14962\t26430\t6\t14883,20025,22818,23079,24990,26113,\t15008,20244,23006,23272,25362,26444,\t0\tCG12061\tcmpl\tcmpl\t0,1,1,0,1,1,\n-585\tNM_001015256\tchrXHet\t+\t47120\t59583\t47415\t58943\t7\t47120,51924,53580,56675,56977,57587,58623,\t47494,52065,53888,56907,57124,57926,59583,\t0\tCG17167\tcmpl\tcmpl\t0,1,1,0,1,1,1,\n-585\tNM_001015257\tchrXHet\t+\t47120\t59583\t47415\t58943\t7\t47120,51921,53580,56675,56977,57587,58623,\t47494,52065,53888,56907,57124,57926,59583,\t0\tCG17167\tcmpl\tcmpl\t0,1,1,0,1,1,1,\n-585\tNM_001015255\tchrXHet\t-\t59688\t61526\t60449\t60947\t3\t59688,60733,60887,\t60677,60820,61526,\t0\tCG17163\tcmpl\tcmpl\t0,0,0,\n-585\tNM_001015254\tchrXHet\t+\t61584\t63394\t61661\t63250\t2\t61584,62544,\t62221,63394,\t0\tCG17168\tcmpl\tcmpl\t0,2,\n-585\tNM_001170391\tchrXHet\t+\t63489\t64354\t63506\t64184\t2\t63489,64076,\t63743,64354,\t0\tCG17169\tcmpl\tcmpl\t0,0,\n-585\tNM_001201441\tchrXHet\t-\t63777\t71448\t68228\t71340\t4\t63777,66121,67532,71032,\t64297,66324,69231,71448,\t0\tCG17159\tcmpl\tcmpl\t-1,-1,2,0,\n-585\tNM_001111000\tchrXHet\t-\t64548\t71449\t65925\t68028\t4\t64548,66121,67532,71032,\t66048,66324,69231,71449,\t0\tCG17162\tcmpl\tcmpl\t0,1,0,-1,\n-585\tNM_001111004\tchrXHet\t-\t64548\t71449\t68228\t71340\t4\t64548,66121,67532,71032,\t66048,66324,69231,71449,\t0\tCG17159\tcmpl\tcmpl\t-1,-1,2,0,\n-585\tNM_001111002\tchrXHet\t-\t64548\t75487\t65925\t68028\t4\t64548,66121,67532,75279,\t66048,66324,69231,75487,\t0\tCG17162\tcmpl\tcmpl\t0,1,0,-1,\n-585\tNM_001111003\tchrXHet\t-\t64548\t75492\t65925\t68028\t4\t64548,66121,67532,75250,\t66048,66324,69231,75492,\t0\tCG17162\tcmpl\tcmpl\t0,1,0,-1,\n-585\tNM_001111001\tchrXHet\t-\t64548\t75522\t65925\t68028\t4\t64548,66121,67532,75430,\t66048,66324,69231,75522,\t0\tCG17162\tcmpl\tcmpl\t0,1,0,-1,\n-585\tNM_001111008\tchrXHet\t-\t64548\t75553\t68228\t75553\t4\t64548,66121,67532,75524,\t66048,66324,69231,75553,\t0\tCG17159\tcmpl\tincmpl\t-1,-1,2,0,\n-585\tNM_001144067\tchrXHet\t-\t64548\t75553\t65925\t68028\t4\t64548,66121,67532,75524,\t66048,66324,69231,75553,\t0\tCG17162\tcmpl\tcmpl\t0,1,0,-1,\n-585\tNM_001015240\tchrXHet\t+\t69194\t80010\t76513\t79925\t10\t69194,76237,76610,77097,77431,78035,78292,78762,79319,79677,\t69305,76549,76933,77373,77831,78227,78706,78870,79620,80010,\t0\tsu(f)\tcmpl\tcmpl\t-1,0,0,2,2,0,0,0,0,1,\n-585\tNM_001111009\tchrXHet\t+\t76209\t80010\t76513\t79925\t9\t76209,76610,77097,77431,78035,78292,78762,79319,79677,\t76549,76933,77373,77735,78227,78706,78870,79620,80010,\t0\tsu(f)\tcmpl\tcmpl\t0,0,2,2,0,0,0,0,1,\n-585\tNM_001111011\tchrXHet\t+\t84842\t87149\t84921\t86148\t2\t84842,85161,\t85101,87149,\t0\tATbp\tcmpl\tcmpl\t0,0,\n-585\tNM_001015499\tchrYHet\t+\t310\t33413\t310\t33413\t15\t310,539,856,1253,1575,1815,2211,2375,2725,15563,16460,16953,30302,30521,33214,\t424,799,1196,1519,1729,2154,2324,2667,2879,15931,16907,19761,30469,31622,33413,\t0\tkl-5\tincmpl\tcmpl\t0,0,2,0,2,0,0,2,0,1,0,0,0,2,2,\n-585\tNM_001111012\tchrYHet\t+\t34289\t65839\t34289\t65582\t9\t34289,35698,39035,52185,52628,53267,62656,63769,65660,\t35635,37083,39370,52593,52993,54728,63619,65605,65839,\t0\tkl-3\tincmpl\tcmpl\t0,2,1,0,0,2,2,2,-1,\n-73\tNM_001015505\tchrYHet\t+\t81208\t148249\t81208\t148243\t11\t81208,122063,122799,135428,138619,140188,141840,145984,146142,147144,147695,\t83052,122745,123184,135872,139940,141784,145922,146089,147085,147638,148249,\t0\tkl-2\tincmpl\tincmpl\t0,2,0,1,1,2,2,1,1,2,1,\n-586\tNM_001015502\tchrYHet\t+\t156741\t206246\t156741\t206246\t7\t156741,160393,161542,161862,191729,191893,206119,\t156949,160677,161792,162113,191814,192065,206246,\t0\tPpr-Y\tcmpl\tcmpl\t0,1,0,1,0,1,2,\n-73\tNM_001015498\tchrYHet\t+\t229032\t271450\t229032\t271450\t5\t229032,232315,232758,233455,271120,\t229342,232495,233402,233594,271450,\t0\tOry\tincmpl\tcmpl\t2,0,0,2,0,\n-587\tNM_001015497\tchrYHet\t+\t279994\t291785\t279994\t291785\t2\t279994,291285,\t280370,291785,\t0\tPp1-Y2\tcmpl\tcmpl\t0,1,\n-587\tNM_001170392\tchrYHet\t+\t305268\t307004\t305331\t307004\t3\t305268,305531,306486,\t305379,306015,307004,\t0\tCG41503\tcmpl\tincmpl\t0,0,1,\n' 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| diff -r 4d4415bcea3c -r 49542dea5b60 peakranger/gene_annotation_files/.svn/text-base/hg19refGene.txt.svn-base --- a/peakranger/gene_annotation_files/.svn/text-base/hg19refGene.txt.svn-base Wed Jan 16 18:25:37 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,41973 +0,0 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845,44886,48107,48651,50281,\t0\tSRSF10\tunk\tunk\t-1,-1,-1,-1,-1,-1,-1,\n-585\tNM_001191009\tchr1_gl000191_random\t-\t36272\t50281\t37488\t50073\t5\t36272,41682,44808,48544,50008,\t37549,41845,44910,48651,50281,\t0\tSRSF10\tcmpl\tcmpl\t2,1,1,2,0,\n-585\tNM_001191007\tchr1_gl000191_random\t-\t36272\t50281\t37488\t50073\t6\t36272,41405,41682,44808,48544,50008,\t37549,41456,41845,44910,48651,50281,\t0\tSRSF10\tcmpl\tcmpl\t2,2,1,1,2,0,\n-585\tNR_038377\tchr4_gl000193_random\t-\t49162\t88375\t88375\t88375\t6\t49162,50561,59868,75048,75487,88199,\t49618,50619,59956,75288,75675,88375,\t0\tMGC39584\tunk\tunk\t-1,-1,-1,-1,-1,-1,\n-585\tNM_001190825\tchr4_gl000194_random\t-\t53588\t115010\t53646\t54021\t3\t53588,112791,114985,\t55676,112850,115010,\t0\tMAFIP\tcmpl\tcmpl\t0,-1,-1,\n-585\tNM_001242480\tchr7_gl000195_random\t-\t42937\t86719\t44723\t49117\t4\t42937,48954,74120,86517,\t44923,49119,74180,86719,\t0\tLOC389831\tcmpl\tcmpl\t1,0,-1,-1,\n-585\tNR_003682\tchr17_gl000205_random\t+\t116622\t119732\t119732\t119732\t1\t116622,\t119732,\t0\tMGC70870\tunk\tunk\t-1,\n-585\tNM_020535\tchr19_gl000209_random\t+\t86690\t96155\t86745\t95742\t8\t86690,87512,88310,89470,91936,94752,95319,95472,\t86779,87548,88595,89764,91987,94857,95372,96155,\t0\tKIR2DL5A\tcmpl\tcmpl\t0,1,1,1,1,1,1,0,\n-585\tNM_001080772\tchr19_gl000209_random\t+\t57208\t68123\t57248\t67307\t8\t57208,57487,58389,59553,62435,66729,67295,67447,\t57288,57523,58674,59847,62486,66833,67348,68123,\t0\tKIR2DL4\tcmpl\tcmpl\t0,1,1,1,1,1,0,-1,\n-585\tNM_014219\tchr19_gl000209_random\t+\t21910\t36449\t21939\t35938\t8\t21910,22881,25353,27167,30730,35046,35610,35761,\t21973,22917,25653,27461,30781,35148,35663,36449,\t0\tKIR2DL2\tcmpl\tcmpl\t0,1,1,1,1,1,1,0,\n-585\tNM_014513\tchr19_gl000209_random\t+\t98111\t113132\t98145\t112480\t8\t98111,99655,102135,103963,107404,111720,112287,112438,\t98179,99691,102435,104257,107455,111825,112340,113132,\t0\tKIR2DS5\tcmpl\tcmpl\t0,1,1,1,1,1,1,0,\n-585\tNM_014512\tchr19_gl000209_random\t+\t115098\t129113\t115111\t128940\t8\t115098,116109,118593,120418,123866,128180,128747,128898,\t115145,116145,118893,120712,123917,128285,128800,129113,\t0\tKIR2DS1\tcmpl\tcmpl\t0,1,1,1,1,1,1,0,\n-585\tNM_001080770\tchr19_gl000209_random\t+\t57208\t68123\t57248\t67717\t7\t57208,57487,58389,59553,62435,67295,67447,\t57288,57523,58674,59847,62486,67348,68123,\t0\tKIR2DL4\tcmpl\tcmpl\t0,1,1,1,1,1,0,\n-585\tNM_012313\tchr19_gl000209_random\t+\t98134\t112667\t98145\t112480\t8\t98134,99656,102135,103963,107404,111720,112287,112438,\t98180,99691,102435,104257,107455,111825,112340,112667,\t0\tKIR2DS3\tcmpl\tcmpl\t0,2,1,1,1,1,1,0,\n-585\tNM_002255\tchr19_gl000209_random\t+\t57208\t68123\t57248\t67717\t8\t57208,57487,58389,59553,62435,66729,67295,67447,\t57288,57523,58674,59847,62486,66834,67348,68123,\t0\tKIR2DL4\tcmpl\tcmpl\t0,1,1,1,1,1,1,0,\n-585\tNM_001083539\tchr19_gl000209_random\t+\t70096\t84658\t70107\t83979\t9\t70096,71140,71920,73693,75573,79037,83368,83936,84085,\t70141,71176,72205,73993,75867,79088,83474,83987,84658,\t0\tKIR3DS1\tcmpl\tcmpl\t0,1,1,1,1,1,1,2,-1,\n-585\tNM_001018081\tchr19_gl000209_random\t+\t86745\t96246\t86745\t95742\t8\t86745,87512,88310,89470,91936,94752,95319,95472,\t86779,87548,88595,89764,91987,94857,95372,96246,\t0\tKIR2DL5B\tcmpl\tcmpl\t0,1,1,1,1,1,1,0,\n-586\tNM_012312\tchr19_gl000209_random\t+\t131448\t145745\t131467\t145120\t8\t131448,132293,134765,136583,140045,144360,144927,145078,\t131501,132329,135065,136877,140096,144465,144980,145745,\t0\tKIR2DS2\tcmpl\tcmpl\t0,1,1,1,1,1,1,0,\n' |
| b |
| diff -r 4d4415bcea3c -r 49542dea5b60 peakranger/gene_annotation_files/.svn/text-base/mm9refGene.txt.svn-base --- a/peakranger/gene_annotation_files/.svn/text-base/mm9refGene.txt.svn-base Wed Jan 16 18:25:37 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,29211 +0,0 @@\n-23\tNM_001042489\tchr5\t+\t122659745\t122692306\t122666351\t122690681\t8\t122659745,122660350,122666240,122683428,122687689,122688414,122690222,122690615,\t122659930,122660401,122666372,122683701,122687794,122688646,122690335,122692306,\t0\tHvcn1\tcmpl\tcmpl\t-1,-1,0,0,0,0,1,0,\n-1669\tNM_001083312\tchr3\t+\t142193301\t142213047\t142197486\t142209538\t11\t142193301,142197480,142199260,142200975,142201685,142204319,142205812,142206885,142208413,142208825,142209283,\t142193403,142197676,142199388,142201085,142201882,142204565,142206093,142207098,142208516,142209019,142213047,\t0\tGbp7\tcmpl\tcmpl\t-1,0,1,0,2,1,1,0,0,1,0,\n-774\tNM_001162485\tchr2\t-\t24780871\t24790801\t24781125\t24790665\t8\t24780871,24781275,24781791,24782064,24782397,24782645,24783248,24790547,\t24781196,24781714,24781968,24782247,24782552,24782696,24783359,24790801,\t0\tArrdc1\tcmpl\tcmpl\t1,0,0,0,1,1,1,0,\n-922\tNM_011729\tchr1\t+\t44204588\t44238105\t44204907\t44237927\t15\t44204588,44213781,44214988,44215649,44217821,44218654,44220721,44223653,44230182,44230756,44231006,44232683,44235018,44235991,44237375,\t44204995,44213957,44215104,44215736,44217882,44218798,44220929,44224727,44230424,44230876,44231220,44232828,44235219,44236076,44238105,\t0\tErcc5\tcmpl\tcmpl\t0,1,0,2,2,0,0,1,1,0,0,1,2,2,0,\n-621\tNR_033530\tchr1\t-\t4763278\t4775807\t4775807\t4775807\t4\t4763278,4767605,4772648,4775653,\t4764597,4767729,4772814,4775807,\t0\tMrpl15\tunk\tunk\t-1,-1,-1,-1,\n-125\tNM_001111052\tchr3\t+\t55265679\t55342990\t55265985\t55337549\t14\t55265679,55266922,55281726,55284255,55291228,55291713,55293671,55303956,55306294,55306730,55310622,55320794,55325771,55337491,\t55266004,55267017,55281811,55284364,55291286,55291833,55293818,55304090,55306372,55306827,55310703,55320908,55325845,55342990,\t0\tDclk1\tcmpl\tcmpl\t0,1,0,1,2,0,0,0,2,2,0,0,0,2,\n-1731\tNM_001115085\tchr7\t+\t150255272\t150256992\t150255861\t150256815\t3\t150255272,150255659,150255840,\t150255418,150255725,150256992,\t0\tTssc4\tcmpl\tcmpl\t-1,-1,0,\n-1514\tNM_001115074\tchr1\t-\t121820095\t121891787\t121820095\t121891787\t23\t121820095,121822137,121824190,121827465,121829350,121830658,121831097,121832667,121833818,121842359,121844628,121846247,121847626,121850177,121850478,121850724,121852225,121858448,121878290,121881306,121881592,121886006,121891648,\t121820204,121822233,121824283,121827557,121829509,121830790,121831205,121832748,121833946,121842465,121844727,121846337,121847714,121850286,121850590,121850842,121852385,121858552,121878391,121881405,121881679,121886107,121891787,\t0\tGm101\tcmpl\tcmpl\t2,2,2,0,0,0,0,0,1,0,0,0,2,1,0,2,1,2,0,0,0,1,0,\n-651\tNM_001160220\tchr12\t+\t8681064\t8759389\t8704914\t8756526\t21\t8681064,8704896,8712738,8716127,8716964,8720165,8720649,8725793,8728470,8730852,8735439,8735661,8740078,8750566,8751142,8751420,8753962,8754916,8755203,8755566,8756394,\t8681286,8704965,8712847,8716315,8717131,8720436,8720743,8725919,8728613,8730985,8735583,8735955,8740315,8750834,8751272,8751549,8754100,8755042,8755325,8755759,8759389,\t0\tPum2\tcmpl\tcmpl\t-1,0,0,1,0,2,0,1,1,0,1,1,1,1,2,0,0,0,0,2,0,\n-1589\tNM_001166206\tchr2\t-\t131679413\t131685483\t131681570\t131682173\t2\t131679413,131685154,\t131682462,131685483,\t0\tErv3\tcmpl\tcmpl\t0,-1,\n-651\tNM_001160219\tchr12\t+\t8681064\t8759389\t8704914\t8756526\t21\t8681064,8704896,8712738,8716127,8716964,8720165,8720649,8725793,8728470,8730852,8735439,8735661,8740078,8750566,8751142,8751420,8753962,8754916,8755203,8755566,8756394,\t8681286,8704965,8712847,8716315,8717131,8720436,8720743,8725919,8728613,8730985,8735583,8735955,8740315,8750834,8751272,8751555,8754100,8755042,8755325,8755759,8759389,\t0\tPum2\tcmpl\tcmpl\t-1,0,0,1,0,2,0,1,1,0,1,1,1,1,2,0,0,0,0,2,0,\n-615\tNM_001085554\tchrX\t-\t3993613\t3995573\t3993991\t3995488\t1\t3993613,\t3995573,\t0\tGm10922\tcmpl\tcmpl\t0,\n-614\tNM_001085543\tchrX\t+\t3907010\t3908970\t3907095\t3908592\t1\t3907010,\t3908970,\t0\tGm14347\tcmpl\tcmpl\t0,\n-887\tNM_001164466\tchr15\t-\t39614242\t39689016\t39616143\t39688908\t10\t39614242,39616114,39624772,39655711,39658409,39659520,39673468,39675403,39678154,39688644,\t39614655,39616260,39624980,39655854,39658551,39659677,39673658,39675583,3967'..b'43L09\tunk\tunk\t-1,-1,-1,\n-1116\tNR_040765\tchr9\t+\t69608952\t69678006\t69678006\t69678006\t5\t69608952,69654593,69668885,69671325,69677487,\t69609019,69654711,69669624,69671517,69678006,\t0\tB230323A14Rik\tunk\tunk\t-1,-1,-1,-1,-1,\n-1260\tNR_040766\tchr9\t-\t88490162\t88494081\t88494081\t88494081\t5\t88490162,88493306,88493718,88493882,88494053,\t88493085,88493402,88493793,88493937,88494081,\t0\t9430037G07Rik\tunk\tunk\t-1,-1,-1,-1,-1,\n-161\tNR_040770\tchr9\t+\t92613553\t92690549\t92690549\t92690549\t5\t92613553,92668281,92676462,92678587,92689441,\t92613916,92668346,92676538,92678683,92690549,\t0\t4933400C23\tunk\tunk\t-1,-1,-1,-1,-1,\n-1293\tNR_040756\tchr9\t-\t92874753\t92900571\t92900571\t92900571\t4\t92874753,92875563,92898642,92900521,\t92875093,92875691,92898741,92900571,\t0\t1700034K08Rik\tunk\tunk\t-1,-1,-1,-1,\n-1347\tNR_040763\tchr9\t+\t99922718\t99935089\t99935089\t99935089\t3\t99922718,99924092,99934969,\t99923098,99924169,99935089,\t0\t4930519F24Rik\tunk\tunk\t-1,-1,-1,\n-1374\tNR_040764\tchr9\t+\t103459419\t103468221\t103468221\t103468221\t3\t103459419,103464701,103467941,\t103461825,103464780,103468221,\t0\t4932413F04Rik\tunk\tunk\t-1,-1,-1,\n-1450\tNR_040760\tchr9\t-\t113405863\t113496270\t113496270\t113496270\t5\t113405863,113408140,113410374,113431528,113496210,\t113407723,113408190,113410471,113431640,113496270,\t0\tAU023762\tunk\tunk\t-1,-1,-1,-1,-1,\n-1506\tNR_040753\tchr9\t-\t120833572\t120839920\t120839920\t120839920\t3\t120833572,120839487,120839877,\t120833814,120839785,120839920,\t0\t4930593C16Rik\tunk\tunk\t-1,-1,-1,\n-1456\tNR_040738\tchr9\t-\t114250228\t114273745\t114273745\t114273745\t6\t114250228,114258847,114264940,114271278,114272869,114273691,\t114250551,114259052,114265110,114271405,114272926,114273745,\t0\t4930525D18Rik\tunk\tunk\t-1,-1,-1,-1,-1,-1,\n-1092\tNM_183119\tchr13\t-\t66519049\t66542054\t66519180\t66541958\t5\t66519049,66519697,66534353,66534614,66541955,\t66519218,66519756,66534414,66534741,66542054,\t0\t2410141K09Rik\tcmpl\tcmpl\t1,2,1,0,0,\n-1348\tNM_001243285\tchrX\t+\t100104243\t100104990\t100104311\t100104905\t3\t100104243,100104526,100104838,\t100104347,100104690,100104990,\t0\t1700011M02Rik\tcmpl\tcmpl\t0,0,2,\n-626\tNM_001243307\tchr19\t-\t5453162\t5457563\t5456984\t5457397\t2\t5453162,5457339,\t5457184,5457563,\t0\tCcdc85b\tcmpl\tcmpl\t1,0,\n-626\tNM_198616\tchr19\t-\t5453162\t5457563\t5456788\t5457397\t1\t5453162,\t5457563,\t0\tCcdc85b\tcmpl\tcmpl\t0,\n-120\tNM_177139\tchr2\t+\t49921948\t50049089\t50021059\t50046337\t5\t49921948,50020988,50029120,50044230,50046169,\t49922104,50021177,50029219,50044361,50049089,\t0\tLypd6\tcmpl\tcmpl\t-1,0,1,1,0,\n-120\tNR_033304\tchr2\t+\t49921948\t50049089\t50049089\t50049089\t6\t49921948,49983889,50020988,50029120,50044230,50046169,\t49922104,49984054,50021177,50029219,50044361,50049089,\t0\tLypd6\tunk\tunk\t-1,-1,-1,-1,-1,-1,\n-1614\tNM_001243305\tchr4\t-\t134925491\t134941587\t134926483\t134932981\t4\t134925491,134927791,134932905,134941444,\t134926625,134927876,134932991,134941587,\t0\tA330049M08Rik\tcmpl\tcmpl\t2,1,0,-1,\n-1614\tNM_001243306\tchr4\t-\t134925491\t134954142\t134926483\t134936083\t6\t134925491,134927791,134932905,134936036,134936566,134953797,\t134926625,134927876,134932988,134936207,134936753,134954142,\t0\tA330049M08Rik\tcmpl\tcmpl\t2,1,2,0,-1,-1,\n-893\tNR_044988\tchr8\t+\t40383333\t40453622\t40453622\t40453622\t4\t40383333,40391916,40432656,40453412,\t40383574,40392002,40432757,40453622,\t0\tGm6213\tunk\tunk\t-1,-1,-1,-1,\n-843\tNR_044989\tchrX\t+\t33943471\t33944649\t33944649\t33944649\t3\t33943471,33944093,33944450,\t33943530,33944135,33944649,\t0\tGm6268\tunk\tunk\t-1,-1,-1,\n-23\tNR_044987\tchr12\t-\t118472993\t118575485\t118575485\t118575485\t3\t118472993,118498486,118575353,\t118473141,118498655,118575485,\t0\tGm5441\tunk\tunk\t-1,-1,-1,\n-966\tNR_045001\tchr16\t+\t49980572\t49997588\t49997588\t49997588\t4\t49980572,49990475,49995718,49996691,\t49980818,49990631,49995851,49997588,\t0\tGm6936\tunk\tunk\t-1,-1,-1,-1,\n-20\tNR_044992\tchr5\t+\t95417718\t95455565\t95455565\t95455565\t4\t95417718,95451908,95452693,95454095,\t95417800,95452202,95453311,95455565,\t0\tGm6367\tunk\tunk\t-1,-1,-1,-1,\n-599\tNR_044992\tchrUn_random\t-\t1919827\t1957720\t1957720\t1957720\t4\t1919827,1922081,1923190,1957638,\t1921297,1922699,1923484,1957720,\t0\tGm6367\tunk\tunk\t-1,-1,-1,-1,\n' |
| b |
| diff -r 4d4415bcea3c -r 49542dea5b60 peakranger/gene_annotation_files/dm3refGene.txt --- a/peakranger/gene_annotation_files/dm3refGene.txt Wed Jan 16 18:25:37 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,23964 +0,0 @@\n-585\tNM_001169365\tchr2L\t+\t7528\t9484\t7679\t8610\t2\t7528,8192,\t8116,9484,\t0\tCG11023\tcmpl\tcmpl\t0,2,\n-585\tNM_175941\tchr2L\t+\t7528\t9484\t7679\t9276\t3\t7528,8192,8667,\t8116,8589,9484,\t0\tCG11023\tcmpl\tcmpl\t0,2,0,\n-585\tNM_078715\tchr2L\t-\t9836\t18583\t11214\t17136\t9\t9836,11409,11778,12285,13519,13682,14932,17052,18260,\t11344,11518,12221,12928,13625,14874,15711,17212,18583,\t0\tl(2)gl\tcmpl\tcmpl\t2,1,2,1,0,2,0,0,-1,\n-585\tNM_164349\tchr2L\t-\t9836\t18583\t11214\t17136\t10\t9836,11409,11778,12285,13519,13682,14932,17052,18025,18260,\t11344,11518,12221,12928,13625,14874,15711,17212,18168,18583,\t0\tl(2)gl\tcmpl\tcmpl\t2,1,2,1,0,2,0,0,-1,-1,\n-585\tNM_164348\tchr2L\t-\t9836\t21372\t11214\t19944\t9\t9836,11409,11778,12285,13519,13682,14932,19884,21135,\t11344,11518,12221,12928,13625,14874,15711,20020,21372,\t0\tl(2)gl\tcmpl\tcmpl\t2,1,2,1,0,2,0,0,-1,\n-585\tNM_164350\tchr2L\t-\t9836\t21372\t11214\t15648\t9\t9836,11409,11778,12285,13519,13682,14932,19879,21065,\t11344,11518,12221,12928,13625,14874,15711,20020,21372,\t0\tl(2)gl\tcmpl\tcmpl\t2,1,2,1,0,2,0,-1,-1,\n-585\tNM_164351\tchr2L\t-\t9836\t21372\t11214\t15648\t9\t9836,11409,11778,12285,13519,13682,14932,19879,21065,\t11344,11518,12221,12928,13625,14874,15711,20015,21372,\t0\tl(2)gl\tcmpl\tcmpl\t2,1,2,1,0,2,0,-1,-1,\n-585\tNM_164352\tchr2L\t-\t9836\t21372\t11214\t15648\t10\t9836,11409,11778,12285,13519,13682,14932,19879,21065,21348,\t11344,11518,12221,12928,13625,14874,15711,20020,21200,21372,\t0\tl(2)gl\tcmpl\tcmpl\t2,1,2,1,0,2,0,-1,-1,-1,\n-585\tNM_001103573\tchr2L\t-\t21918\t25151\t21918\t25151\t5\t21918,22742,22993,23928,24746,\t22687,22935,23873,24210,25151,\t0\tIr21a\tcmpl\tcmpl\t2,1,0,0,0,\n-585\tNM_001103574\tchr2L\t-\t25401\t59242\t26520\t58150\t14\t25401,26765,27052,28014,28732,28981,33844,34557,34719,35745,38534,39300,58080,59189,\t26688,26964,27490,28240,28926,29068,34288,34604,35212,38088,38731,39857,58182,59242,\t0\tCda5\tcmpl\tcmpl\t0,2,2,1,2,2,2,0,2,2,0,1,0,-1,\n-585\tNM_001103575\tchr2L\t-\t25401\t59242\t26520\t58150\t13\t25401,26765,27052,28410,28732,28981,33844,34557,34719,38534,39300,58080,59189,\t26688,26964,27490,28639,28926,29068,34288,34604,35212,38731,39857,58182,59242,\t0\tCda5\tcmpl\tcmpl\t0,2,2,1,2,2,2,0,2,0,1,0,-1,\n-585\tNM_164353\tchr2L\t-\t25401\t59242\t26520\t58150\t13\t25401,26765,27052,28014,28732,28981,33844,34557,34719,38534,39300,58080,59189,\t26688,26964,27490,28240,28926,29068,34288,34604,35212,38731,39857,58182,59242,\t0\tCda5\tcmpl\tcmpl\t0,2,2,1,2,2,2,0,2,0,1,0,-1,\n-585\tNM_164354\tchr2L\t-\t25401\t59242\t26520\t58150\t14\t25401,26765,27052,28014,28732,28981,30393,33844,34557,34719,38534,39300,58080,59189,\t26688,26964,27490,28240,28926,29068,33270,34288,34604,35212,38731,39857,58182,59242,\t0\tCda5\tcmpl\tcmpl\t0,2,2,1,2,2,2,2,0,2,0,1,0,-1,\n-585\tNM_134642\tchr2L\t+\t67043\t71390\t67624\t70895\t5\t67043,67568,67891,68084,70606,\t67507,67762,68023,70549,71390,\t0\tdbr\tcmpl\tcmpl\t-1,0,0,0,2,\n-585\tNM_134643\tchr2L\t+\t72387\t76211\t72602\t76098\t3\t72387,74902,75077,\t72977,75018,76211,\t0\tgalectin\tcmpl\tcmpl\t0,0,2,\n-585\tNM_001169367\tchr2L\t+\t73484\t76211\t73569\t76098\t3\t73484,74902,75077,\t73692,75018,76211,\t0\tgalectin\tcmpl\tcmpl\t0,0,2,\n-585\tNM_001169366\tchr2L\t+\t74484\t76211\t74500\t76098\t3\t74484,74902,75077,\t74572,75018,76211,\t0\tgalectin\tcmpl\tcmpl\t0,0,2,\n-585\tNM_134644\tchr2L\t+\t76445\t77639\t76445\t77639\t1\t76445,\t77639,\t0\tCG11374\tcmpl\tcmpl\t0,\n-585\tNM_080081\tchr2L\t-\t82455\t87382\t83267\t87092\t2\t82455,87019,\t84277,87382,\t0\tnet\tcmpl\tcmpl\t1,0,\n-585\tNM_134645\tchr2L\t+\t94751\t102086\t94851\t101918\t12\t94751,94988,95131,95353,97883,98526,99784,100571,100761,101015,101248,101875,\t94892,95070,95301,97833,98470,99723,100516,100703,100942,101194,101619,102086,\t0\tCG11376\tcmpl\tcmpl\t0,2,0,2,1,0,0,0,0,1,0,2,\n-585\tNM_134646\tchr2L\t+\t102381\t104142\t102458\t103763\t3\t102381,103005,103515,\t102906,103434,104142,\t0\tCG11377\tcmpl\tcmpl\t0,1,1,\n-585\tNM_134647\tchr2L\t-\t103961\t106718\t104472\t106642\t5\t103961,105004,105390,105511,105968,\t104947,105336,105455,105915,106718,\t0\tNhe1\tcmpl\tcmpl\t2,0,1,2,0,\n-585\tNM_205880\tchr2L\t+\t106902\t114432\t108685\t113542\t8\t106902,107764,108587,110405,110754,111906,112689,113433,\t107000,107838,108809,110483,110877,112019,113369,114432,\t0\tSam-S\tcm'..b'62\t26430\t5\t14883,22818,23079,24990,26113,\t15008,23006,23272,25362,26444,\t0\tCG12061\tcmpl\tcmpl\t0,1,0,1,1,\n-585\tNM_001015259\tchrXHet\t+\t14883\t26444\t23149\t26430\t5\t14883,22818,23079,24990,26113,\t15008,23006,23177,25362,26444,\t0\tCG12061\tcmpl\tcmpl\t-1,-1,0,1,1,\n-585\tNM_001110997\tchrXHet\t+\t14883\t26444\t14962\t26430\t6\t14883,20025,22818,23079,24990,26113,\t15008,20244,23006,23272,25362,26444,\t0\tCG12061\tcmpl\tcmpl\t0,1,1,0,1,1,\n-585\tNM_001015256\tchrXHet\t+\t47120\t59583\t47415\t58943\t7\t47120,51924,53580,56675,56977,57587,58623,\t47494,52065,53888,56907,57124,57926,59583,\t0\tCG17167\tcmpl\tcmpl\t0,1,1,0,1,1,1,\n-585\tNM_001015257\tchrXHet\t+\t47120\t59583\t47415\t58943\t7\t47120,51921,53580,56675,56977,57587,58623,\t47494,52065,53888,56907,57124,57926,59583,\t0\tCG17167\tcmpl\tcmpl\t0,1,1,0,1,1,1,\n-585\tNM_001015255\tchrXHet\t-\t59688\t61526\t60449\t60947\t3\t59688,60733,60887,\t60677,60820,61526,\t0\tCG17163\tcmpl\tcmpl\t0,0,0,\n-585\tNM_001015254\tchrXHet\t+\t61584\t63394\t61661\t63250\t2\t61584,62544,\t62221,63394,\t0\tCG17168\tcmpl\tcmpl\t0,2,\n-585\tNM_001170391\tchrXHet\t+\t63489\t64354\t63506\t64184\t2\t63489,64076,\t63743,64354,\t0\tCG17169\tcmpl\tcmpl\t0,0,\n-585\tNM_001201441\tchrXHet\t-\t63777\t71448\t68228\t71340\t4\t63777,66121,67532,71032,\t64297,66324,69231,71448,\t0\tCG17159\tcmpl\tcmpl\t-1,-1,2,0,\n-585\tNM_001111000\tchrXHet\t-\t64548\t71449\t65925\t68028\t4\t64548,66121,67532,71032,\t66048,66324,69231,71449,\t0\tCG17162\tcmpl\tcmpl\t0,1,0,-1,\n-585\tNM_001111004\tchrXHet\t-\t64548\t71449\t68228\t71340\t4\t64548,66121,67532,71032,\t66048,66324,69231,71449,\t0\tCG17159\tcmpl\tcmpl\t-1,-1,2,0,\n-585\tNM_001111002\tchrXHet\t-\t64548\t75487\t65925\t68028\t4\t64548,66121,67532,75279,\t66048,66324,69231,75487,\t0\tCG17162\tcmpl\tcmpl\t0,1,0,-1,\n-585\tNM_001111003\tchrXHet\t-\t64548\t75492\t65925\t68028\t4\t64548,66121,67532,75250,\t66048,66324,69231,75492,\t0\tCG17162\tcmpl\tcmpl\t0,1,0,-1,\n-585\tNM_001111001\tchrXHet\t-\t64548\t75522\t65925\t68028\t4\t64548,66121,67532,75430,\t66048,66324,69231,75522,\t0\tCG17162\tcmpl\tcmpl\t0,1,0,-1,\n-585\tNM_001111008\tchrXHet\t-\t64548\t75553\t68228\t75553\t4\t64548,66121,67532,75524,\t66048,66324,69231,75553,\t0\tCG17159\tcmpl\tincmpl\t-1,-1,2,0,\n-585\tNM_001144067\tchrXHet\t-\t64548\t75553\t65925\t68028\t4\t64548,66121,67532,75524,\t66048,66324,69231,75553,\t0\tCG17162\tcmpl\tcmpl\t0,1,0,-1,\n-585\tNM_001015240\tchrXHet\t+\t69194\t80010\t76513\t79925\t10\t69194,76237,76610,77097,77431,78035,78292,78762,79319,79677,\t69305,76549,76933,77373,77831,78227,78706,78870,79620,80010,\t0\tsu(f)\tcmpl\tcmpl\t-1,0,0,2,2,0,0,0,0,1,\n-585\tNM_001111009\tchrXHet\t+\t76209\t80010\t76513\t79925\t9\t76209,76610,77097,77431,78035,78292,78762,79319,79677,\t76549,76933,77373,77735,78227,78706,78870,79620,80010,\t0\tsu(f)\tcmpl\tcmpl\t0,0,2,2,0,0,0,0,1,\n-585\tNM_001111011\tchrXHet\t+\t84842\t87149\t84921\t86148\t2\t84842,85161,\t85101,87149,\t0\tATbp\tcmpl\tcmpl\t0,0,\n-585\tNM_001015499\tchrYHet\t+\t310\t33413\t310\t33413\t15\t310,539,856,1253,1575,1815,2211,2375,2725,15563,16460,16953,30302,30521,33214,\t424,799,1196,1519,1729,2154,2324,2667,2879,15931,16907,19761,30469,31622,33413,\t0\tkl-5\tincmpl\tcmpl\t0,0,2,0,2,0,0,2,0,1,0,0,0,2,2,\n-585\tNM_001111012\tchrYHet\t+\t34289\t65839\t34289\t65582\t9\t34289,35698,39035,52185,52628,53267,62656,63769,65660,\t35635,37083,39370,52593,52993,54728,63619,65605,65839,\t0\tkl-3\tincmpl\tcmpl\t0,2,1,0,0,2,2,2,-1,\n-73\tNM_001015505\tchrYHet\t+\t81208\t148249\t81208\t148243\t11\t81208,122063,122799,135428,138619,140188,141840,145984,146142,147144,147695,\t83052,122745,123184,135872,139940,141784,145922,146089,147085,147638,148249,\t0\tkl-2\tincmpl\tincmpl\t0,2,0,1,1,2,2,1,1,2,1,\n-586\tNM_001015502\tchrYHet\t+\t156741\t206246\t156741\t206246\t7\t156741,160393,161542,161862,191729,191893,206119,\t156949,160677,161792,162113,191814,192065,206246,\t0\tPpr-Y\tcmpl\tcmpl\t0,1,0,1,0,1,2,\n-73\tNM_001015498\tchrYHet\t+\t229032\t271450\t229032\t271450\t5\t229032,232315,232758,233455,271120,\t229342,232495,233402,233594,271450,\t0\tOry\tincmpl\tcmpl\t2,0,0,2,0,\n-587\tNM_001015497\tchrYHet\t+\t279994\t291785\t279994\t291785\t2\t279994,291285,\t280370,291785,\t0\tPp1-Y2\tcmpl\tcmpl\t0,1,\n-587\tNM_001170392\tchrYHet\t+\t305268\t307004\t305331\t307004\t3\t305268,305531,306486,\t305379,306015,307004,\t0\tCG41503\tcmpl\tincmpl\t0,0,1,\n' |
| b |
| diff -r 4d4415bcea3c -r 49542dea5b60 peakranger/gene_annotation_files/hg19refGene.txt --- a/peakranger/gene_annotation_files/hg19refGene.txt Wed Jan 16 18:25:37 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,41973 +0,0 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845,44886,48107,48651,50281,\t0\tSRSF10\tunk\tunk\t-1,-1,-1,-1,-1,-1,-1,\n-585\tNM_001191009\tchr1_gl000191_random\t-\t36272\t50281\t37488\t50073\t5\t36272,41682,44808,48544,50008,\t37549,41845,44910,48651,50281,\t0\tSRSF10\tcmpl\tcmpl\t2,1,1,2,0,\n-585\tNM_001191007\tchr1_gl000191_random\t-\t36272\t50281\t37488\t50073\t6\t36272,41405,41682,44808,48544,50008,\t37549,41456,41845,44910,48651,50281,\t0\tSRSF10\tcmpl\tcmpl\t2,2,1,1,2,0,\n-585\tNR_038377\tchr4_gl000193_random\t-\t49162\t88375\t88375\t88375\t6\t49162,50561,59868,75048,75487,88199,\t49618,50619,59956,75288,75675,88375,\t0\tMGC39584\tunk\tunk\t-1,-1,-1,-1,-1,-1,\n-585\tNM_001190825\tchr4_gl000194_random\t-\t53588\t115010\t53646\t54021\t3\t53588,112791,114985,\t55676,112850,115010,\t0\tMAFIP\tcmpl\tcmpl\t0,-1,-1,\n-585\tNM_001242480\tchr7_gl000195_random\t-\t42937\t86719\t44723\t49117\t4\t42937,48954,74120,86517,\t44923,49119,74180,86719,\t0\tLOC389831\tcmpl\tcmpl\t1,0,-1,-1,\n-585\tNR_003682\tchr17_gl000205_random\t+\t116622\t119732\t119732\t119732\t1\t116622,\t119732,\t0\tMGC70870\tunk\tunk\t-1,\n-585\tNM_020535\tchr19_gl000209_random\t+\t86690\t96155\t86745\t95742\t8\t86690,87512,88310,89470,91936,94752,95319,95472,\t86779,87548,88595,89764,91987,94857,95372,96155,\t0\tKIR2DL5A\tcmpl\tcmpl\t0,1,1,1,1,1,1,0,\n-585\tNM_001080772\tchr19_gl000209_random\t+\t57208\t68123\t57248\t67307\t8\t57208,57487,58389,59553,62435,66729,67295,67447,\t57288,57523,58674,59847,62486,66833,67348,68123,\t0\tKIR2DL4\tcmpl\tcmpl\t0,1,1,1,1,1,0,-1,\n-585\tNM_014219\tchr19_gl000209_random\t+\t21910\t36449\t21939\t35938\t8\t21910,22881,25353,27167,30730,35046,35610,35761,\t21973,22917,25653,27461,30781,35148,35663,36449,\t0\tKIR2DL2\tcmpl\tcmpl\t0,1,1,1,1,1,1,0,\n-585\tNM_014513\tchr19_gl000209_random\t+\t98111\t113132\t98145\t112480\t8\t98111,99655,102135,103963,107404,111720,112287,112438,\t98179,99691,102435,104257,107455,111825,112340,113132,\t0\tKIR2DS5\tcmpl\tcmpl\t0,1,1,1,1,1,1,0,\n-585\tNM_014512\tchr19_gl000209_random\t+\t115098\t129113\t115111\t128940\t8\t115098,116109,118593,120418,123866,128180,128747,128898,\t115145,116145,118893,120712,123917,128285,128800,129113,\t0\tKIR2DS1\tcmpl\tcmpl\t0,1,1,1,1,1,1,0,\n-585\tNM_001080770\tchr19_gl000209_random\t+\t57208\t68123\t57248\t67717\t7\t57208,57487,58389,59553,62435,67295,67447,\t57288,57523,58674,59847,62486,67348,68123,\t0\tKIR2DL4\tcmpl\tcmpl\t0,1,1,1,1,1,0,\n-585\tNM_012313\tchr19_gl000209_random\t+\t98134\t112667\t98145\t112480\t8\t98134,99656,102135,103963,107404,111720,112287,112438,\t98180,99691,102435,104257,107455,111825,112340,112667,\t0\tKIR2DS3\tcmpl\tcmpl\t0,2,1,1,1,1,1,0,\n-585\tNM_002255\tchr19_gl000209_random\t+\t57208\t68123\t57248\t67717\t8\t57208,57487,58389,59553,62435,66729,67295,67447,\t57288,57523,58674,59847,62486,66834,67348,68123,\t0\tKIR2DL4\tcmpl\tcmpl\t0,1,1,1,1,1,1,0,\n-585\tNM_001083539\tchr19_gl000209_random\t+\t70096\t84658\t70107\t83979\t9\t70096,71140,71920,73693,75573,79037,83368,83936,84085,\t70141,71176,72205,73993,75867,79088,83474,83987,84658,\t0\tKIR3DS1\tcmpl\tcmpl\t0,1,1,1,1,1,1,2,-1,\n-585\tNM_001018081\tchr19_gl000209_random\t+\t86745\t96246\t86745\t95742\t8\t86745,87512,88310,89470,91936,94752,95319,95472,\t86779,87548,88595,89764,91987,94857,95372,96246,\t0\tKIR2DL5B\tcmpl\tcmpl\t0,1,1,1,1,1,1,0,\n-586\tNM_012312\tchr19_gl000209_random\t+\t131448\t145745\t131467\t145120\t8\t131448,132293,134765,136583,140045,144360,144927,145078,\t131501,132329,135065,136877,140096,144465,144980,145745,\t0\tKIR2DS2\tcmpl\tcmpl\t0,1,1,1,1,1,1,0,\n' |
| b |
| diff -r 4d4415bcea3c -r 49542dea5b60 peakranger/gene_annotation_files/mm9refGene.txt --- a/peakranger/gene_annotation_files/mm9refGene.txt Wed Jan 16 18:25:37 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,29211 +0,0 @@\n-23\tNM_001042489\tchr5\t+\t122659745\t122692306\t122666351\t122690681\t8\t122659745,122660350,122666240,122683428,122687689,122688414,122690222,122690615,\t122659930,122660401,122666372,122683701,122687794,122688646,122690335,122692306,\t0\tHvcn1\tcmpl\tcmpl\t-1,-1,0,0,0,0,1,0,\n-1669\tNM_001083312\tchr3\t+\t142193301\t142213047\t142197486\t142209538\t11\t142193301,142197480,142199260,142200975,142201685,142204319,142205812,142206885,142208413,142208825,142209283,\t142193403,142197676,142199388,142201085,142201882,142204565,142206093,142207098,142208516,142209019,142213047,\t0\tGbp7\tcmpl\tcmpl\t-1,0,1,0,2,1,1,0,0,1,0,\n-774\tNM_001162485\tchr2\t-\t24780871\t24790801\t24781125\t24790665\t8\t24780871,24781275,24781791,24782064,24782397,24782645,24783248,24790547,\t24781196,24781714,24781968,24782247,24782552,24782696,24783359,24790801,\t0\tArrdc1\tcmpl\tcmpl\t1,0,0,0,1,1,1,0,\n-922\tNM_011729\tchr1\t+\t44204588\t44238105\t44204907\t44237927\t15\t44204588,44213781,44214988,44215649,44217821,44218654,44220721,44223653,44230182,44230756,44231006,44232683,44235018,44235991,44237375,\t44204995,44213957,44215104,44215736,44217882,44218798,44220929,44224727,44230424,44230876,44231220,44232828,44235219,44236076,44238105,\t0\tErcc5\tcmpl\tcmpl\t0,1,0,2,2,0,0,1,1,0,0,1,2,2,0,\n-621\tNR_033530\tchr1\t-\t4763278\t4775807\t4775807\t4775807\t4\t4763278,4767605,4772648,4775653,\t4764597,4767729,4772814,4775807,\t0\tMrpl15\tunk\tunk\t-1,-1,-1,-1,\n-125\tNM_001111052\tchr3\t+\t55265679\t55342990\t55265985\t55337549\t14\t55265679,55266922,55281726,55284255,55291228,55291713,55293671,55303956,55306294,55306730,55310622,55320794,55325771,55337491,\t55266004,55267017,55281811,55284364,55291286,55291833,55293818,55304090,55306372,55306827,55310703,55320908,55325845,55342990,\t0\tDclk1\tcmpl\tcmpl\t0,1,0,1,2,0,0,0,2,2,0,0,0,2,\n-1731\tNM_001115085\tchr7\t+\t150255272\t150256992\t150255861\t150256815\t3\t150255272,150255659,150255840,\t150255418,150255725,150256992,\t0\tTssc4\tcmpl\tcmpl\t-1,-1,0,\n-1514\tNM_001115074\tchr1\t-\t121820095\t121891787\t121820095\t121891787\t23\t121820095,121822137,121824190,121827465,121829350,121830658,121831097,121832667,121833818,121842359,121844628,121846247,121847626,121850177,121850478,121850724,121852225,121858448,121878290,121881306,121881592,121886006,121891648,\t121820204,121822233,121824283,121827557,121829509,121830790,121831205,121832748,121833946,121842465,121844727,121846337,121847714,121850286,121850590,121850842,121852385,121858552,121878391,121881405,121881679,121886107,121891787,\t0\tGm101\tcmpl\tcmpl\t2,2,2,0,0,0,0,0,1,0,0,0,2,1,0,2,1,2,0,0,0,1,0,\n-651\tNM_001160220\tchr12\t+\t8681064\t8759389\t8704914\t8756526\t21\t8681064,8704896,8712738,8716127,8716964,8720165,8720649,8725793,8728470,8730852,8735439,8735661,8740078,8750566,8751142,8751420,8753962,8754916,8755203,8755566,8756394,\t8681286,8704965,8712847,8716315,8717131,8720436,8720743,8725919,8728613,8730985,8735583,8735955,8740315,8750834,8751272,8751549,8754100,8755042,8755325,8755759,8759389,\t0\tPum2\tcmpl\tcmpl\t-1,0,0,1,0,2,0,1,1,0,1,1,1,1,2,0,0,0,0,2,0,\n-1589\tNM_001166206\tchr2\t-\t131679413\t131685483\t131681570\t131682173\t2\t131679413,131685154,\t131682462,131685483,\t0\tErv3\tcmpl\tcmpl\t0,-1,\n-651\tNM_001160219\tchr12\t+\t8681064\t8759389\t8704914\t8756526\t21\t8681064,8704896,8712738,8716127,8716964,8720165,8720649,8725793,8728470,8730852,8735439,8735661,8740078,8750566,8751142,8751420,8753962,8754916,8755203,8755566,8756394,\t8681286,8704965,8712847,8716315,8717131,8720436,8720743,8725919,8728613,8730985,8735583,8735955,8740315,8750834,8751272,8751555,8754100,8755042,8755325,8755759,8759389,\t0\tPum2\tcmpl\tcmpl\t-1,0,0,1,0,2,0,1,1,0,1,1,1,1,2,0,0,0,0,2,0,\n-615\tNM_001085554\tchrX\t-\t3993613\t3995573\t3993991\t3995488\t1\t3993613,\t3995573,\t0\tGm10922\tcmpl\tcmpl\t0,\n-614\tNM_001085543\tchrX\t+\t3907010\t3908970\t3907095\t3908592\t1\t3907010,\t3908970,\t0\tGm14347\tcmpl\tcmpl\t0,\n-887\tNM_001164466\tchr15\t-\t39614242\t39689016\t39616143\t39688908\t10\t39614242,39616114,39624772,39655711,39658409,39659520,39673468,39675403,39678154,39688644,\t39614655,39616260,39624980,39655854,39658551,39659677,39673658,39675583,3967'..b'43L09\tunk\tunk\t-1,-1,-1,\n-1116\tNR_040765\tchr9\t+\t69608952\t69678006\t69678006\t69678006\t5\t69608952,69654593,69668885,69671325,69677487,\t69609019,69654711,69669624,69671517,69678006,\t0\tB230323A14Rik\tunk\tunk\t-1,-1,-1,-1,-1,\n-1260\tNR_040766\tchr9\t-\t88490162\t88494081\t88494081\t88494081\t5\t88490162,88493306,88493718,88493882,88494053,\t88493085,88493402,88493793,88493937,88494081,\t0\t9430037G07Rik\tunk\tunk\t-1,-1,-1,-1,-1,\n-161\tNR_040770\tchr9\t+\t92613553\t92690549\t92690549\t92690549\t5\t92613553,92668281,92676462,92678587,92689441,\t92613916,92668346,92676538,92678683,92690549,\t0\t4933400C23\tunk\tunk\t-1,-1,-1,-1,-1,\n-1293\tNR_040756\tchr9\t-\t92874753\t92900571\t92900571\t92900571\t4\t92874753,92875563,92898642,92900521,\t92875093,92875691,92898741,92900571,\t0\t1700034K08Rik\tunk\tunk\t-1,-1,-1,-1,\n-1347\tNR_040763\tchr9\t+\t99922718\t99935089\t99935089\t99935089\t3\t99922718,99924092,99934969,\t99923098,99924169,99935089,\t0\t4930519F24Rik\tunk\tunk\t-1,-1,-1,\n-1374\tNR_040764\tchr9\t+\t103459419\t103468221\t103468221\t103468221\t3\t103459419,103464701,103467941,\t103461825,103464780,103468221,\t0\t4932413F04Rik\tunk\tunk\t-1,-1,-1,\n-1450\tNR_040760\tchr9\t-\t113405863\t113496270\t113496270\t113496270\t5\t113405863,113408140,113410374,113431528,113496210,\t113407723,113408190,113410471,113431640,113496270,\t0\tAU023762\tunk\tunk\t-1,-1,-1,-1,-1,\n-1506\tNR_040753\tchr9\t-\t120833572\t120839920\t120839920\t120839920\t3\t120833572,120839487,120839877,\t120833814,120839785,120839920,\t0\t4930593C16Rik\tunk\tunk\t-1,-1,-1,\n-1456\tNR_040738\tchr9\t-\t114250228\t114273745\t114273745\t114273745\t6\t114250228,114258847,114264940,114271278,114272869,114273691,\t114250551,114259052,114265110,114271405,114272926,114273745,\t0\t4930525D18Rik\tunk\tunk\t-1,-1,-1,-1,-1,-1,\n-1092\tNM_183119\tchr13\t-\t66519049\t66542054\t66519180\t66541958\t5\t66519049,66519697,66534353,66534614,66541955,\t66519218,66519756,66534414,66534741,66542054,\t0\t2410141K09Rik\tcmpl\tcmpl\t1,2,1,0,0,\n-1348\tNM_001243285\tchrX\t+\t100104243\t100104990\t100104311\t100104905\t3\t100104243,100104526,100104838,\t100104347,100104690,100104990,\t0\t1700011M02Rik\tcmpl\tcmpl\t0,0,2,\n-626\tNM_001243307\tchr19\t-\t5453162\t5457563\t5456984\t5457397\t2\t5453162,5457339,\t5457184,5457563,\t0\tCcdc85b\tcmpl\tcmpl\t1,0,\n-626\tNM_198616\tchr19\t-\t5453162\t5457563\t5456788\t5457397\t1\t5453162,\t5457563,\t0\tCcdc85b\tcmpl\tcmpl\t0,\n-120\tNM_177139\tchr2\t+\t49921948\t50049089\t50021059\t50046337\t5\t49921948,50020988,50029120,50044230,50046169,\t49922104,50021177,50029219,50044361,50049089,\t0\tLypd6\tcmpl\tcmpl\t-1,0,1,1,0,\n-120\tNR_033304\tchr2\t+\t49921948\t50049089\t50049089\t50049089\t6\t49921948,49983889,50020988,50029120,50044230,50046169,\t49922104,49984054,50021177,50029219,50044361,50049089,\t0\tLypd6\tunk\tunk\t-1,-1,-1,-1,-1,-1,\n-1614\tNM_001243305\tchr4\t-\t134925491\t134941587\t134926483\t134932981\t4\t134925491,134927791,134932905,134941444,\t134926625,134927876,134932991,134941587,\t0\tA330049M08Rik\tcmpl\tcmpl\t2,1,0,-1,\n-1614\tNM_001243306\tchr4\t-\t134925491\t134954142\t134926483\t134936083\t6\t134925491,134927791,134932905,134936036,134936566,134953797,\t134926625,134927876,134932988,134936207,134936753,134954142,\t0\tA330049M08Rik\tcmpl\tcmpl\t2,1,2,0,-1,-1,\n-893\tNR_044988\tchr8\t+\t40383333\t40453622\t40453622\t40453622\t4\t40383333,40391916,40432656,40453412,\t40383574,40392002,40432757,40453622,\t0\tGm6213\tunk\tunk\t-1,-1,-1,-1,\n-843\tNR_044989\tchrX\t+\t33943471\t33944649\t33944649\t33944649\t3\t33943471,33944093,33944450,\t33943530,33944135,33944649,\t0\tGm6268\tunk\tunk\t-1,-1,-1,\n-23\tNR_044987\tchr12\t-\t118472993\t118575485\t118575485\t118575485\t3\t118472993,118498486,118575353,\t118473141,118498655,118575485,\t0\tGm5441\tunk\tunk\t-1,-1,-1,\n-966\tNR_045001\tchr16\t+\t49980572\t49997588\t49997588\t49997588\t4\t49980572,49990475,49995718,49996691,\t49980818,49990631,49995851,49997588,\t0\tGm6936\tunk\tunk\t-1,-1,-1,-1,\n-20\tNR_044992\tchr5\t+\t95417718\t95455565\t95455565\t95455565\t4\t95417718,95451908,95452693,95454095,\t95417800,95452202,95453311,95455565,\t0\tGm6367\tunk\tunk\t-1,-1,-1,-1,\n-599\tNR_044992\tchrUn_random\t-\t1919827\t1957720\t1957720\t1957720\t4\t1919827,1922081,1923190,1957638,\t1921297,1922699,1923484,1957720,\t0\tGm6367\tunk\tunk\t-1,-1,-1,-1,\n' |
| b |
| diff -r 4d4415bcea3c -r 49542dea5b60 peakranger/ranger_wrapper.py --- a/peakranger/ranger_wrapper.py Wed Jan 16 18:25:37 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,184 +0,0 @@\n-#purpose: python wrapper to run peak ranger\n-#author: Ziru Zhou\n-#Date: November 2012\n-\n-import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip\n-from galaxy import eggs\n-import pkg_resources\n-pkg_resources.require( "simplejson" )\n-import simplejson\n-import glob\n-import datetime\n-\n-CHUNK_SIZE = 1024\n-\n-def main():\n- options = simplejson.load( open( sys.argv[1] ) )\n- outputs = simplejson.load( open( sys.argv[2] ) )\n-\n-\n- #sets experiment name and sets the chip/input files\n- #======================================================================================== \n- experiment_name = \'_\'.join( options[\'experiment_name\'].split() ) #save experiment name\n-\n- #cmdline = "bash /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC_tools/peakranger/peakranger %s -d %s --format bam" % ( options[\'action\'], options[\'chip_file\'] )\n- cmdline = "peakranger %s -d %s" % ( options[\'action\'], options[\'chip_file\'] )\n- if \'input_file\' in options:\n- cmdline = "%s -c %s" % ( cmdline, options[\'input_file\'] )\n-\n- #set additional options\n- #========================================================================================\n- if (options[\'action\'] == "nr"):\n-\toutput_ranger_file = outputs[\'output_ranger_file\']\n-\n-\tcmdline = "%s --format bam -l %s --verbose > default_output.txt" % ( cmdline, options[\'extension\'] ) \n- elif (options[\'action\'] == "lc"):\n-\toutput_ranger_file = outputs[\'output_ranger_file\']\n-\n-\tcmdline = "%s --verbose > default_output.txt" % ( cmdline )\n- elif (options[\'action\'] == "wig"):\n-\toutput_wigzip_file = outputs[\'output_wigzip_file\']\n-\n-\tcmdline = "%s --format bam -l %s %s %s %s -o ranger_wig" % ( cmdline, options[\'extension\'], options[\'split\'], options[\'strand\'], options[\'gzip\'] ) \n- elif (options[\'action\'] == "wigpe"):\n-\toutput_wigzip_file = outputs[\'output_wigzip_file\']\n-\n-\tcmdline = "%s -l %s %s %s %s -o ranger_wig" % ( cmdline, options[\'extension\'], options[\'split\'], options[\'strand\'], options[\'gzip\'] ) \n- elif (options[\'action\'] == "ranger"):\n-\toutput_summit_file = outputs[\'output_summit_file\']\n-\toutput_region_file = outputs[\'output_region_file\']\n-\toutput_details_file = outputs[\'output_details_file\']\n-\toutput_report_file = outputs[\'output_report_file\']\n-\n-\tif (options[\'gene_annotate_file\'] != "None"):\n-\t\tgene_annotate_file = "--gene_annot_file /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC_tools/peakranger/gene_annotation_files/%s" % options[\'gene_annotate_file\']\n-\t\treport = "--report"\n-\telif (options[\'gene_annotate_file\'] == "Upload"):\n-\t\tgene_annotate_file = options[\'usr_annot_file\']\n-\t\treport = "--report"\n-\telse:\n-\t\tgene_annotate_file = ""\n-\t\treport = ""\n-\n-\tcmdline = "%s -t %s --format bam %s --plot_region %s -l %s -p %s -q %s -r %s -b %s %s %s -o ranger_peak" % ( cmdline, options[\'threads\'], gene_annotate_file, options[\'plot_region\'], options[\'extension\'], options[\'pvalue\'], options[\'fdr\'], options[\'delta\'], options[\'bandwith\'], options[\'pad\'], report )\n- elif (options[\'action\'] == "ccat"):\n-\toutput_summit_file = outputs[\'output_summit_file\']\n-\toutput_region_file = outputs[\'output_region_file\']\n-\toutput_details_file = outputs[\'output_details_file\']\n-\toutput_report_file = outputs[\'output_report_file\']\n-\toutput_ranger_file = outputs[\'output_ranger_file\']\n-\t\n-\tif (options[\'gene_annotate_file\'] != "None"):\n-\t\tgene_annotate_file = "--gene_annot_file /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC_tools/peakranger/gene_annotation_files/%s" % options[\'gene_annotate_file\']\n-\t\treport = "--report"\n-\telif (options[\'gene_annotate_file\'] == "Upload"):\n-\t\tgene_annotate_file = options[\'usr_annot_file\']\n-\t\treport = "--report"\n-\telse:\n-\t\tgene_annotate_file = ""\n-\t\treport = ""\n-\n-\tcmdline = "%s --format bam %s --plot_region %s -l %s -q %s --win_size %s --win_step %s --min_count %s --min_score %s %s -o ranger_peak > default_output.txt" % ( cmdline, gene_annotate_file, options[\'plot_region\'], options[\'extension\'], options[\'fdr\'], options[\'winsize'..b'uts are there, copy them to the appropriate dir and filename\n- #========================================================================================\n- if(options[\'action\'] == "nr" or options[\'action\'] == "lc" or options[\'action\'] == "ccat"):\n-\tcreated_ranger_file = os.path.join( tmp_dir, "default_output.txt" )\n- if os.path.exists( created_ranger_file ):\n- \tshutil.move( created_ranger_file, output_ranger_file )\n-\n- if(options[\'action\'] == "wig" or options[\'action\'] == "wigpe"):\n-\tif(options[\'split\'] == "-s" or options[\'strand\'] == "-x"):\n-\t\tif(options[\'gzip\'] == "-z"):\n-\t\t\tfiles = str( glob.glob(\'%s/*.wig.gz\' % tmp_dir) )\n-\t\t\tfiles = files.replace("[", "")\n-\t\t\tfiles = files.replace("]", "")\n-\t\t\tfiles = files.replace(",", "")\n-\t\t\tfiles = files.replace("\'", "")\n-\t\t\tcmd = "zip -j %s/ranger_wig.zip %s > /dev/null" % (tmp_dir, files)\n-\t\t\t#cmd = "tar -czvf %s/ranger_wig.tar %s > /dev/null" % (tmp_dir, files)\n-\t\t\tos.system(cmd)\n-\t\t\tcreated_wigzip_file = os.path.join( tmp_dir, "ranger_wig.zip" )\n-\t\telse:\n-\t\t\tfiles = str( glob.glob(\'%s/*.wig\' % tmp_dir) )\n-\t\t\tfiles = files.replace("[", "")\n-\t\t\tfiles = files.replace("]", "")\n-\t\t\tfiles = files.replace(",", "")\n-\t\t\tfiles = files.replace("\'", "")\n-\t\t\tcmd = "zip -j %s/ranger_wig.zip %s > /dev/null" % (tmp_dir, files)\n-\t\t\t#cmd = "tar -czvf %s/ranger_wig.tar %s > /dev/null" % (tmp_dir, files)\n-\t\t\tos.system(cmd)\n-\t\t\tcreated_wigzip_file = os.path.join( tmp_dir, "ranger_wig.zip" )\n-\telse:\n-\t\tif(options[\'gzip\'] == "-z"):\n-\t\t\tcreated_wigzip_file = os.path.join( tmp_dir, "ranger_wig.wig.gz" )\n-\t\telse:\n-\t\t\tcreated_wigzip_file = os.path.join( tmp_dir, "ranger_wig.wig" )\n- \n-\tif os.path.exists( created_wigzip_file ):\n- \tshutil.move( created_wigzip_file, output_wigzip_file )\n- \n- if(options[\'action\'] == "ranger" or options[\'action\'] == "ccat"):\t\n-\tcreated_summit_file = os.path.join( tmp_dir, "ranger_peak_summit.bed" )\n-\tif os.path.exists( created_summit_file ):\n- \tshutil.move( created_summit_file, output_summit_file )\n-\n-\tcreated_region_file = os.path.join( tmp_dir, "ranger_peak_region.bed" )\n-\tif os.path.exists( created_region_file ):\n- \tshutil.move( created_region_file, output_region_file )\n-\n-\tcreated_details_file = os.path.join( tmp_dir, "ranger_peak_details" )\n-\tif os.path.exists( created_details_file ):\n- \tshutil.move( created_details_file, output_details_file )\n-\n-\t#zips the html report and puts it in history, whole report is too big and display in galaxy is very unformatted \n-\tfilename = os.path.splitext(os.path.basename(options[\'chip_file\']))[0]\n-\tfilename = filename.upper()\n-\textension = os.path.splitext(options[\'chip_file\'])[1]\n-\textension = extension.replace(".", "")\n-\textension = extension.upper()\n-\tnow = datetime.datetime.now()\n-\tdate = now.strftime("%Y-%m-%d")\n-\tfoldername = "%s_%s_REPORT_%s" % (filename, extension, date)\n-\n-\tcreated_report_file = os.path.join( tmp_dir, foldername )\n-\tif os.path.exists ( created_report_file ):\n-\t\t#os.system("cp -rf %s %s" % (created_report_file, "/mnt/galaxyData/files/000/"))\n-\t\tos.system("cp -rf %s ." % created_report_file)\n-\t\tos.system("zip -r created_report.zip %s > /dev/null" % foldername)\n-\t\t#os.system("zip -r created_report.zip /mnt/galaxyData/files/000/%s > /dev/null" % foldername)\n-\t\tshutil.move( "created_report.zip", output_report_file)\n-\n-\n-\t\t#os.system("ln -fs %s/index.html %s" %( foldername, output_report_file ))\n-\t\t#datafoldername = os.path.splitext(os.path.basename(output_report_file))\n-\t\t#datafolder = os.path.join ("/mnt/galaxyData/files/000/" datafoldername)\n-\t\t#print "datafolder %s" % datafolder\n-\t\t#if os.path.exists( datafolder )\n-\t\t#\tos.system("rm -rf %s" % datafolder)\n-\t\t#\tos.system("cp -rf %s/%s/imgs /mnt/galaxyData/files/000/%s" % (tmp_dir, foldername, datafolder))\n-\t\t#\tos.system("cp -rf %s/%s/scripts /mnt/galaxyData/files/000/%s" % (tmp_dir, foldername, datafolder))\n-\n- os.unlink( stderr_name )\n- shutil.rmtree( tmp_dir )\n-\n-if __name__ == "__main__": main()\n' |
| b |
| diff -r 4d4415bcea3c -r 49542dea5b60 peakranger/ranger_wrapper.xml --- a/peakranger/ranger_wrapper.xml Wed Jan 16 18:25:37 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,254 +0,0 @@\n-<tool id="modencode_peakcalling_ranger" name="PeakRanger" version="1.16">\n- <description>multi-purpose, ultrafast ChIP Seq peak caller</description>\n- <command interpreter="python">ranger_wrapper.py $options_file $outputs_file</command>\n- <requirements>\n- <requirement type="package">peakranger</requirement>\n- </requirements>\n- <inputs>\n- <param name="experiment_name" type="text" value="PeakRanger in Galaxy" size="50" label="Experiment Name"/> \n-\n- <conditional name="major_command">\n- <param name="major_command_selector" type="select" label="Select action to be performed">\n- <option value="nr">Estimate data quality (nr)</option>\n- <option value="lc">Calculate library complexity (lc)</option>\n- <option value="wig">Generate coverage wiggle file (wig)</option>\n- <option value="wigpe">Generate coverage wiggle file using block models (wigpe)</option>\n- <option value="ranger">Peak calling for sharp peaks (ranger)</option>\n- <option value="ccat">Peak calling for broad peaks (ccat)</option>\n- </param>\n- <when value="nr">\n- <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />\n- <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />\n-\n- <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>\n- </when>\n- <when value="lc">\n- <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />\n- </when>\n- <when value="wig">\n- <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />\n-\n- <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>\n-\n- <param name="split" truevalue="-s" falsevalue="" type="boolean" checked="False" label="Generate one wig file per chromosome" help="output will be in .zip format (-s)"/>\n- <param name="strand" truevalue="-x" falsevalue="" type="boolean" checked="False" label="Generate one wig file per strand" help="output will be in .zip format (-x)"/>\n- <param name="gzip" truevalue="-z" falsevalue="" type="boolean" checked="False" label="Compress the output" help="(-z)"/>\n- </when>\n- <when value="wigpe">\n- <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />\n-\n- <param name="extension" type="integer" value="0" label="Read extension length" help="default=0 (-l)"/>\n-\n- <param name="split" truevalue="-s" falsevalue="" type="boolean" checked="False" label="Generate one wig file per chromosome" help="(-s)"/>\n- <param name="strand" truevalue="-x" falsevalue="" type="boolean" checked="False" label="Generate one wig file per strand" help="(-x)"/>\n- <param name="gzip" truevalue="-z" falsevalue="" type="boolean" checked="False" label="Compress the output" help="(-z)"/>\n- </when>\n- <when value="ranger">\n- <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />\n- <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />\n-\n-\t<conditional name="gene_annotate_file">\n-\t <param name="gene_annotate_file_selector" type="select" label="Select the gene annotation file">\n-\t <option value="dm3refGene.txt">dm3refGene.txt</option>\n-\t <option value="hg19refGene.txt">hg19refGene.txt</option>\n-\t <option value="mm9refGene.txt">mm9refGene.txt</option>\n-\t <option value="Upload">Select from history</option>\n-\t <option value="None">None</option>\n-\t </param>\n-\t <when value="upload">\n- <param name="usr_annot_file" type="data" format="txt" label="Select gene annotation file" />\n-\t </when>\n-\t'..b" \t#set $__options['input_file'] = str( $major_command.input_control_file1 )\n-\n- #set $__options['gene_annotate_file'] = str( $major_command.gene_annotate_file.gene_annotate_file_selector )\n-\t#if str( $major_command.gene_annotate_file.gene_annotate_file_selector ) == 'Upload'\n-\t\t#set $__options['usr_annot_file'] = str( $major_command.gene_annotate_file.usr_annot_file ) \n-\t#end if\n-\n- #set $__options['plot_region'] = str( $major_command.plot_region )\n- #set $__options['pvalue'] = str( $major_command.pvalue )\n- #set $__options['fdr'] = str( $major_command.fdr )\n- #set $__options['extension'] = str( $major_command.extension )\n- #set $__options['delta'] = str( $major_command.delta )\n-\t#set $__options['threads'] = str( $major_command.threads )\n- #set $__options['bandwith'] = str( $major_command.bandwith )\n- #set $__options['pad'] = str( $major_command.pad )\n-#end if\n-##=============================================================================\n-#if str($major_command.major_command_selector) == 'ccat':\n- #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )\n- \t#set $__options['input_file'] = str( $major_command.input_control_file1 )\n-\n- #set $__options['gene_annotate_file'] = str( $major_command.gene_annotate_file.gene_annotate_file_selector )\n-\t#if str( $major_command.gene_annotate_file.gene_annotate_file_selector ) == 'Upload'\n-\t\t#set $__options['usr_annot_file'] = str( $major_command.gene_annotate_file.usr_annot_file ) \n-\t#end if\n-\n- #set $__options['plot_region'] = str( $major_command.plot_region )\n- #set $__options['fdr'] = str( $major_command.fdr )\n- #set $__options['extension'] = str( $major_command.extension )\n- #set $__options['winsize'] = str( $major_command.winsize )\n- #set $__options['winstep'] = str( $major_command.winstep )\n- #set $__options['mincount'] = str( $major_command.mincount )\n- #set $__options['minscore'] = str( $major_command.minscore )\n-#end if\n-##=============================================================================\n-${ simplejson.dumps( __options ) }\n- </configfile>\n- </configfiles>\n- <tests>\n-\t<!--none yet for macs2-->\n- </tests>\n- <help>\n-**What it does**\n-\n-PeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data. The suite contains the following tools:\n-\n-View the modified PeakRanger documentation: http://ranger.sourceforge.net/manualv116.html#introduction\n-\n-------\n-\n-**Usage**\n-\n-**nr:** noise rate estimator. Estimates signal to noise ratio which is an indicator for ChIP enrichment\n-\n-**lc:** library complexity calculator. Calculates the ratio of unique reads over total reads. Only accepts bam files.\n-\n-**wig:** coverage file generator. Generates variable step format wiggle file\n-\n-**wigpe:** coverage file generator. Generates bedGraph format wiggle file and supports spliced alignments and thus only supports bam files\n-\n- wigpe can also generate coverage files for bam files containing spliced reads, such as those from RNA-Seq experiments.\n-\n-**ranger:** ChIP-Seq peak caller. It is able to identify enriched genomic regions while at the same time discover summits within these regions.\n-\n-**ccat:** ChIP-Seq peak caller. Tuned for the discovery of broad peaks\n-\n- Both ranger and ccat supports generating HTML-based annotation reports.\n-\n-------\n-\n-**Citation**\n-\n-If you use PeakRanger in your research, please cite:\n-Feng X, Grossman R, Stein L: PeakRanger:A cloud-enabled peak caller for ChIP-seq data.BMC Bioinformatics 2011, 12(1):139.\n-\n-if you use the ccat tool, please also cite:\n-Xu, H., L. Handoko, et al. (2010).A signal-noise model for significance analysis of ChIP-seq with negative control.Bioinformatics 26(9): 1199-1204.\n-\n-\n-Integration of PeakRanger with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to help@modencode.org.\n- </help>\n-</tool>\n" |