| Previous changeset 17:81faa1567178 (2017-05-31) Next changeset 19:09b34f32dc7d (2017-05-31) |
|
Commit message:
Uploaded 20170531 |
|
added:
._ETn_example ._example ._loadandplot.R ._plotwithscale.R ._testandplot.R ETn_example/._.DS_Store ETn_example/._Control.bed ETn_example/._DESCRIPTION.txt ETn_example/._ETn_fixed.bed ETn_example/._Recombination_hotspots.txt ETn_example/._features.header ETn_example/._regions.header ETn_example/Control.bed ETn_example/DESCRIPTION.txt ETn_example/ETn_fixed.bed ETn_example/Recombination_hotspots.txt ETn_example/features.header ETn_example/regions.header example/._.DS_Store example/._Controls_regions.bed example/._DESCRIPTION.txt example/._Elements1_regions.bed example/._Elements2_regions.bed example/._Elements3_regions.bed example/._Feature1.bed example/._Feature2.bed example/._features.header.bed.txt example/._regions.header.txt example/Controls_regions.bed example/DESCRIPTION.txt example/Elements1_regions.bed example/Elements2_regions.bed example/Elements3_regions.bed example/Feature1.bed example/Feature2.bed example/features.header.bed.txt example/regions.header.txt loadandplot.R loadandplot.xml macros.xml plotwithscale.R plotwithscale.xml testandplot.R testandplot.xml |
|
removed:
iwtomics/ETn_example/._.DS_Store iwtomics/ETn_example/._Control.bed iwtomics/ETn_example/._DESCRIPTION.txt iwtomics/ETn_example/._ETn_fixed.bed iwtomics/ETn_example/._Recombination_hotspots.txt iwtomics/ETn_example/._features.header iwtomics/ETn_example/._regions.header iwtomics/ETn_example/Control.bed iwtomics/ETn_example/DESCRIPTION.txt iwtomics/ETn_example/ETn_fixed.bed iwtomics/ETn_example/Recombination_hotspots.txt iwtomics/ETn_example/features.header iwtomics/ETn_example/regions.header iwtomics/example/._.DS_Store iwtomics/example/._Controls_regions.bed iwtomics/example/._DESCRIPTION.txt iwtomics/example/._Elements1_regions.bed iwtomics/example/._Elements2_regions.bed iwtomics/example/._Elements3_regions.bed iwtomics/example/._Feature1.bed iwtomics/example/._Feature2.bed iwtomics/example/._features.header.bed.txt iwtomics/example/._regions.header.txt iwtomics/example/Controls_regions.bed iwtomics/example/DESCRIPTION.txt iwtomics/example/Elements1_regions.bed iwtomics/example/Elements2_regions.bed iwtomics/example/Elements3_regions.bed iwtomics/example/Feature1.bed iwtomics/example/Feature2.bed iwtomics/example/features.header.bed.txt iwtomics/example/regions.header.txt |
| b |
| diff -r 81faa1567178 -r 565118df598a ._ETn_example |
| b |
| Binary file ._ETn_example has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a ._example |
| b |
| Binary file ._example has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a ._loadandplot.R |
| b |
| Binary file ._loadandplot.R has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a ._plotwithscale.R |
| b |
| Binary file ._plotwithscale.R has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a ._testandplot.R |
| b |
| Binary file ._testandplot.R has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a ETn_example/._.DS_Store |
| b |
| Binary file ETn_example/._.DS_Store has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a ETn_example/._Control.bed |
| b |
| Binary file ETn_example/._Control.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a ETn_example/._DESCRIPTION.txt |
| b |
| Binary file ETn_example/._DESCRIPTION.txt has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a ETn_example/._ETn_fixed.bed |
| b |
| Binary file ETn_example/._ETn_fixed.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a ETn_example/._Recombination_hotspots.txt |
| b |
| Binary file ETn_example/._Recombination_hotspots.txt has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a ETn_example/._features.header |
| b |
| Binary file ETn_example/._features.header has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a ETn_example/._regions.header |
| b |
| Binary file ETn_example/._regions.header has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a ETn_example/Control.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ETn_example/Control.bed Wed May 31 11:07:22 2017 -0400 |
| b |
| b'@@ -0,0 +1,1142 @@\n+chr1\t6743847\t6807847\r\n+chr1\t12755253\t12819253\r\n+chr1\t14459704\t14523704\r\n+chr1\t16989370\t17053370\r\n+chr1\t18859600\t18923600\r\n+chr1\t20393735\t20457735\r\n+chr1\t20457735\t20521735\r\n+chr1\t22357071\t22421071\r\n+chr1\t34267805\t34331805\r\n+chr1\t36860915\t36924915\r\n+chr1\t38084729\t38148729\r\n+chr1\t38513351\t38577351\r\n+chr1\t39997553\t40061553\r\n+chr1\t40484791\t40548791\r\n+chr1\t44015427\t44079427\r\n+chr1\t45327525\t45391525\r\n+chr1\t45420798\t45484798\r\n+chr1\t49687964\t49751964\r\n+chr1\t52202938\t52266938\r\n+chr1\t56924736\t56988736\r\n+chr1\t56988736\t57052736\r\n+chr1\t59226030\t59290030\r\n+chr1\t62745840\t62809840\r\n+chr1\t62809840\t62873840\r\n+chr1\t64105946\t64169946\r\n+chr1\t66424667\t66488667\r\n+chr1\t66554557\t66618557\r\n+chr1\t68388328\t68452328\r\n+chr1\t69038498\t69102498\r\n+chr1\t70745639\t70809639\r\n+chr1\t73940413\t74004413\r\n+chr1\t74387826\t74451826\r\n+chr1\t74451826\t74515826\r\n+chr1\t75349593\t75413593\r\n+chr1\t75413593\t75477593\r\n+chr1\t77371166\t77435166\r\n+chr1\t77480499\t77544499\r\n+chr1\t78114553\t78178553\r\n+chr1\t82603387\t82667387\r\n+chr1\t84801140\t84865140\r\n+chr1\t88807895\t88871895\r\n+chr1\t99596012\t99660012\r\n+chr1\t107880720\t107944720\r\n+chr1\t108229995\t108293995\r\n+chr1\t111850207\t111914207\r\n+chr1\t133368110\t133432110\r\n+chr1\t133798014\t133862014\r\n+chr1\t134191816\t134255816\r\n+chr1\t134443547\t134507547\r\n+chr1\t135090775\t135154775\r\n+chr1\t135590608\t135654608\r\n+chr1\t136621462\t136685462\r\n+chr1\t136924763\t136988763\r\n+chr1\t136988763\t137052763\r\n+chr1\t137229123\t137293123\r\n+chr1\t137689172\t137753172\r\n+chr1\t137771736\t137835736\r\n+chr1\t138803292\t138867292\r\n+chr1\t139778795\t139842795\r\n+chr1\t139995038\t140059038\r\n+chr1\t157022333\t157086333\r\n+chr1\t159052908\t159116908\r\n+chr1\t162345948\t162409948\r\n+chr1\t163888959\t163952959\r\n+chr1\t164146377\t164210377\r\n+chr1\t164593610\t164657610\r\n+chr1\t170078935\t170142935\r\n+chr1\t170185390\t170249390\r\n+chr1\t170249390\t170313390\r\n+chr1\t173284896\t173348896\r\n+chr1\t174231860\t174295860\r\n+chr1\t175209865\t175273865\r\n+chr1\t176812441\t176876441\r\n+chr1\t179114819\t179178819\r\n+chr1\t183090720\t183154720\r\n+chr1\t188499484\t188563484\r\n+chr1\t189459058\t189523058\r\n+chr1\t189774115\t189838115\r\n+chr1\t189838115\t189902115\r\n+chr1\t189902115\t189966115\r\n+chr1\t190477513\t190541513\r\n+chr1\t191934479\t191998479\r\n+chr1\t196512385\t196576385\r\n+chr10\t5474388\t5538388\r\n+chr10\t8440103\t8504103\r\n+chr10\t12363669\t12427669\r\n+chr10\t13778671\t13842671\r\n+chr10\t14108714\t14172714\r\n+chr10\t20382714\t20446714\r\n+chr10\t22896281\t22960281\r\n+chr10\t28142261\t28206261\r\n+chr10\t29331699\t29395699\r\n+chr10\t41896920\t41960920\r\n+chr10\t42699828\t42763828\r\n+chr10\t44063057\t44127057\r\n+chr10\t44127057\t44191057\r\n+chr10\t44393066\t44457066\r\n+chr10\t48942538\t49006538\r\n+chr10\t49490846\t49554846\r\n+chr10\t60233273\t60297273\r\n+chr10\t62294775\t62358775\r\n+chr10\t67544477\t67608477\r\n+chr10\t67608477\t67672477\r\n+chr10\t72718883\t72782883\r\n+chr10\t82994484\t83058484\r\n+chr10\t84328077\t84392077\r\n+chr10\t91514689\t91578689\r\n+chr10\t99772435\t99836435\r\n+chr10\t102459914\t102523914\r\n+chr10\t109462705\t109526705\r\n+chr10\t109595915\t109659915\r\n+chr10\t110902043\t110966043\r\n+chr10\t111748024\t111812024\r\n+chr10\t113960882\t114024882\r\n+chr10\t115695549\t115759549\r\n+chr10\t117239014\t117303014\r\n+chr10\t119851269\t119915269\r\n+chr10\t122527450\t122591450\r\n+chr10\t126452913\t126516913\r\n+chr10\t126866134\t126930134\r\n+chr10\t126985162\t127049162\r\n+chr10\t128302043\t128366043\r\n+chr11\t4600501\t4664501\r\n+chr11\t5031835\t5095835\r\n+chr11\t8334455\t8398455\r\n+chr11\t8428319\t8492319\r\n+chr11\t11551166\t11615166\r\n+chr11\t11615166\t11679166\r\n+chr11\t12267301\t12331301\r\n+chr11\t16683593\t16747593\r\n+chr11\t18764520\t18828520\r\n+chr11\t18877750\t18941750\r\n+chr11\t21882576\t21946576\r\n+chr11\t24000041\t24064041\r\n+chr11\t24178636\t24242636\r\n+chr11\t24750849\t24814849\r\n+chr11\t25545055\t25609055\r\n+chr11\t25743353\t25807353\r\n+chr11\t25960246\t26024246\r\n+chr11\t28338386\t28402386\r\n+chr11\t28555005\t28619005\r\n+chr11\t28755803\t28819803\r\n+chr11\t29629676\t29693676\r\n+chr11\t30033778\t30097778\r\n+chr11\t30689772\t30753772\r\n+chr11\t32102916\t32166916\r\n+chr11\t32554531\t32618531\r\n+chr11\t33072008\t33136008\r\n+chr11\t35342208\t35406208\r\n+chr11\t35813133\t35877133\r\n+chr11\t35877133\t35941133\r\n+chr11\t36051767\t36115767\r\n+chr11\t36150099'..b'\t26489570\r\n+chr7\t28256738\t28320738\r\n+chr7\t29324406\t29388406\r\n+chr7\t29698999\t29762999\r\n+chr7\t30073747\t30137747\r\n+chr7\t31328098\t31392098\r\n+chr7\t31499428\t31563428\r\n+chr7\t34995660\t35059660\r\n+chr7\t37457888\t37521888\r\n+chr7\t38461632\t38525632\r\n+chr7\t51452000\t51516000\r\n+chr7\t52568290\t52632290\r\n+chr7\t52655317\t52719317\r\n+chr7\t53011466\t53075466\r\n+chr7\t56520810\t56584810\r\n+chr7\t56651195\t56715195\r\n+chr7\t77074960\t77138960\r\n+chr7\t77444459\t77508459\r\n+chr7\t79324748\t79388748\r\n+chr7\t80606988\t80670988\r\n+chr7\t85424277\t85488277\r\n+chr7\t86637488\t86701488\r\n+chr7\t87490216\t87554216\r\n+chr7\t94386826\t94450826\r\n+chr7\t94966452\t95030452\r\n+chr7\t98517363\t98581363\r\n+chr7\t99452639\t99516639\r\n+chr7\t100918461\t100982461\r\n+chr7\t102669140\t102733140\r\n+chr7\t103352710\t103416710\r\n+chr7\t103998756\t104062756\r\n+chr7\t105194424\t105258424\r\n+chr7\t105739791\t105803791\r\n+chr7\t107553010\t107617010\r\n+chr7\t110033354\t110097354\r\n+chr7\t110938758\t111002758\r\n+chr7\t122669176\t122733176\r\n+chr7\t122814547\t122878547\r\n+chr7\t122927103\t122991103\r\n+chr7\t123215332\t123279332\r\n+chr7\t127388603\t127452603\r\n+chr7\t133986042\t134050042\r\n+chr7\t134639723\t134703723\r\n+chr7\t134976215\t135040215\r\n+chr7\t139936722\t140000722\r\n+chr7\t144371823\t144435823\r\n+chr7\t144435823\t144499823\r\n+chr7\t146716018\t146780018\r\n+chr7\t149138752\t149202752\r\n+chr7\t149635306\t149699306\r\n+chr7\t149715608\t149779608\r\n+chr8\t6559442\t6623442\r\n+chr8\t6623442\t6687442\r\n+chr8\t7293954\t7357954\r\n+chr8\t11241630\t11305630\r\n+chr8\t11333377\t11397377\r\n+chr8\t12797793\t12861793\r\n+chr8\t17140927\t17204927\r\n+chr8\t17453277\t17517277\r\n+chr8\t18682008\t18746008\r\n+chr8\t24201916\t24265916\r\n+chr8\t26679408\t26743408\r\n+chr8\t32970842\t33034842\r\n+chr8\t33171781\t33235781\r\n+chr8\t34892948\t34956948\r\n+chr8\t35865387\t35929387\r\n+chr8\t39257582\t39321582\r\n+chr8\t39450262\t39514262\r\n+chr8\t49642107\t49706107\r\n+chr8\t49856227\t49920227\r\n+chr8\t50183963\t50247963\r\n+chr8\t50620889\t50684889\r\n+chr8\t51733915\t51797915\r\n+chr8\t59779596\t59843596\r\n+chr8\t64029519\t64093519\r\n+chr8\t72435881\t72499881\r\n+chr8\t72967674\t73031674\r\n+chr8\t73979868\t74043868\r\n+chr8\t74065191\t74129191\r\n+chr8\t80836252\t80900252\r\n+chr8\t83285181\t83349181\r\n+chr8\t86680889\t86744889\r\n+chr8\t87177477\t87241477\r\n+chr8\t87241477\t87305477\r\n+chr8\t87477935\t87541935\r\n+chr8\t90388211\t90452211\r\n+chr8\t90760313\t90824313\r\n+chr8\t92030994\t92094994\r\n+chr8\t93443787\t93507787\r\n+chr8\t96789585\t96853585\r\n+chr8\t97043262\t97107262\r\n+chr8\t97477230\t97541230\r\n+chr8\t111089991\t111153991\r\n+chr8\t111270619\t111334619\r\n+chr8\t111334619\t111398619\r\n+chr8\t111398619\t111462619\r\n+chr8\t117237918\t117301918\r\n+chr8\t125868555\t125932555\r\n+chr8\t126054477\t126118477\r\n+chr8\t127381524\t127445524\r\n+chr9\t7916325\t7980325\r\n+chr9\t10034653\t10098653\r\n+chr9\t21205558\t21269558\r\n+chr9\t27102323\t27166323\r\n+chr9\t28793755\t28857755\r\n+chr9\t28975979\t29039979\r\n+chr9\t29182458\t29246458\r\n+chr9\t29431925\t29495925\r\n+chr9\t30706012\t30770012\r\n+chr9\t32468538\t32532538\r\n+chr9\t36694615\t36758615\r\n+chr9\t36758615\t36822615\r\n+chr9\t41371667\t41435667\r\n+chr9\t42383364\t42447364\r\n+chr9\t43535422\t43599422\r\n+chr9\t44030826\t44094826\r\n+chr9\t44257286\t44321286\r\n+chr9\t44893563\t44957563\r\n+chr9\t45496156\t45560156\r\n+chr9\t45700064\t45764064\r\n+chr9\t47438414\t47502414\r\n+chr9\t47502414\t47566414\r\n+chr9\t47566414\t47630414\r\n+chr9\t47630414\t47694414\r\n+chr9\t48557242\t48621242\r\n+chr9\t56295240\t56359240\r\n+chr9\t56707178\t56771178\r\n+chr9\t57431374\t57495374\r\n+chr9\t59569429\t59633429\r\n+chr9\t62718979\t62782979\r\n+chr9\t63147522\t63211522\r\n+chr9\t63788832\t63852832\r\n+chr9\t69050403\t69114403\r\n+chr9\t69176049\t69240049\r\n+chr9\t69240049\t69304049\r\n+chr9\t71796844\t71860844\r\n+chr9\t74791622\t74855622\r\n+chr9\t79491629\t79555629\r\n+chr9\t79932960\t79996960\r\n+chr9\t84626957\t84690957\r\n+chr9\t96193779\t96257779\r\n+chr9\t107312141\t107376141\r\n+chr9\t107376141\t107440141\r\n+chr9\t107462650\t107526650\r\n+chr9\t107526650\t107590650\r\n+chr9\t107590650\t107654650\r\n+chr9\t107848560\t107912560\r\n+chr9\t107941738\t108005738\r\n+chr9\t108683437\t108747437\r\n+chr9\t108962296\t109026296\r\n+chr9\t109947901\t110011901\r\n+chr9\t110485254\t110549254\r\n+chr9\t110616374\t110680374\r\n+chr9\t111968818\t112032818\r\n+chr9\t113836504\t113900504\r\n+chr9\t118910538\t118974538\r\n+chr9\t121627136\t121691136\r\n' |
| b |
| diff -r 81faa1567178 -r 565118df598a ETn_example/DESCRIPTION.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ETn_example/DESCRIPTION.txt Wed May 31 11:07:22 2017 -0400 |
| b |
| @@ -0,0 +1,21 @@ +This example contains two region datasets "ETn fixed", "Control" and one feature "Recombination hotspots content". +In particular, the region dataset "ETn fixed" contains 1296 genomic regions of 64 kb surrounding +fixed ETns elements (32-kb flanking sequences upstream and 32-kb flanking sequences downstream +of each element). The region dataset "Control" contains 1142 regions of 64 kb without elements, +used as control in the test. The regions are aligned around their center (i.e. around the ETn integration +sites). +Recombination hotspots measurements are associated to each "ETn fixed" and "Control" region. In +particular, this feature is measured in 1-kb windows, so that each region is associated to a recombination +hotspots curve made of 64 values. The measurement used is the feature content, i.e. the +fraction of the 1-kb window that is covered by recombination hotspots + +Data have been collected and pre-processed by: R Campos-Sanchez, MA Cremona, A Pini, F +Chiaromonte and KD Makova (2016). Integration and fixation preferences of human and mouse +endogenous retroviruses uncovered with Functional Data Analysis. PLoS Computational Biology. +12(6): 1-41. +Fixed ETn positions come from: Y Zhang, IA Maksakova, L Gagnier, LN van de Lagemaat, DL +Mager (2008). Genome-wide assessments reveal extremely high levels of polymorphism of two +active families of mouse endogenous retroviral elements. PLoS Genetics. 4: e1000007. +Recombination hotspots data come from: H Brunschwig, L Levi, E Ben-David, RW Williams, +B Yakir, S Shifman (2012). Fine-scale maps of recombination rates and hotspots in the mouse +genome. Genetics. 191: 757-764. \ No newline at end of file |
| b |
| diff -r 81faa1567178 -r 565118df598a ETn_example/ETn_fixed.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ETn_example/ETn_fixed.bed Wed May 31 11:07:22 2017 -0400 |
| b |
| b'@@ -0,0 +1,1296 @@\n+chr1\t3079711\t3144047\r\n+chr1\t3232230\t3302517\r\n+chr1\t3756792\t3826331\r\n+chr1\t4589320\t4653381\r\n+chr1\t5155380\t5219717\r\n+chr1\t5634836\t5704314\r\n+chr1\t5967107\t6035506\r\n+chr1\t6240632\t6304964\r\n+chr1\t7186756\t7250816\r\n+chr1\t7434671\t7504179\r\n+chr1\t7573651\t7643108\r\n+chr1\t7879930\t7944250\r\n+chr1\t7962100\t8026423\r\n+chr1\t8219414\t8283736\r\n+chr1\t9451579\t9515898\r\n+chr1\t10561964\t10626025\r\n+chr1\t10774950\t10844464\r\n+chr1\t11301539\t11365867\r\n+chr1\t11479858\t11543919\r\n+chr1\t11577435\t11646975\r\n+chr1\t11734130\t11798451\r\n+chr1\t12053425\t12117744\r\n+chr1\t12503733\t12568058\r\n+chr1\t12690915\t12755253\r\n+chr1\t13015768\t13080108\r\n+chr1\t13772979\t13840932\r\n+chr1\t14114086\t14178424\r\n+chr1\t15752556\t15816879\r\n+chr1\t15820454\t15889959\r\n+chr1\t16894874\t16964379\r\n+chr1\t17180480\t17250022\r\n+chr1\t17380662\t17444982\r\n+chr1\t17626574\t17695823\r\n+chr1\t18015049\t18079373\r\n+chr1\t18110573\t18174911\r\n+chr1\t19594734\t19659060\r\n+chr1\t22621502\t22685838\r\n+chr1\t26730921\t26795251\r\n+chr1\t29078615\t29142676\r\n+chr1\t29866491\t29930812\r\n+chr1\t31420204\t31484524\r\n+chr1\t32231731\t32295791\r\n+chr1\t32727048\t32791370\r\n+chr1\t41487659\t41551982\r\n+chr1\t42815700\t42880037\r\n+chr1\t44434350\t44498689\r\n+chr1\t44845641\t44915177\r\n+chr1\t45573195\t45637531\r\n+chr1\t46279947\t46344008\r\n+chr1\t47955005\t48019067\r\n+chr1\t48676207\t48745586\r\n+chr1\t50407114\t50471433\r\n+chr1\t50984256\t51048575\r\n+chr1\t52848138\t52912460\r\n+chr1\t54026202\t54090537\r\n+chr1\t55139377\t55203714\r\n+chr1\t55512376\t55576700\r\n+chr1\t60811167\t60880658\r\n+chr1\t63144392\t63208714\r\n+chr1\t64592575\t64656909\r\n+chr1\t72263031\t72327365\r\n+chr1\t79947964\t80012025\r\n+chr1\t81586166\t81651033\r\n+chr1\t83518554\t83582860\r\n+chr1\t84323690\t84388012\r\n+chr1\t87733248\t87797584\r\n+chr1\t89977562\t90048134\r\n+chr1\t90192976\t90257294\r\n+chr1\t90436757\t90502304\r\n+chr1\t90510088\t90574150\r\n+chr1\t90961340\t91030890\r\n+chr1\t92995129\t93064618\r\n+chr1\t93572264\t93636325\r\n+chr1\t94416743\t94481065\r\n+chr1\t95060527\t95124845\r\n+chr1\t96949505\t96993507\r\n+chr1\t97366290\t97430612\r\n+chr1\t102719163\t102788368\r\n+chr1\t104425831\t104490167\r\n+chr1\t105882265\t105946599\r\n+chr1\t106700349\t106764668\r\n+chr1\t107613589\t107658283\r\n+chr1\t110331901\t110395962\r\n+chr1\t113555818\t113625304\r\n+chr1\t116479611\t116543952\r\n+chr1\t117758939\t117823245\r\n+chr1\t118797225\t118861285\r\n+chr1\t119448312\t119513632\r\n+chr1\t130131484\t130195807\r\n+chr1\t132524644\t132588705\r\n+chr1\t133914689\t133978749\r\n+chr1\t136189933\t136254255\r\n+chr1\t136264653\t136334169\r\n+chr1\t137560931\t137625172\r\n+chr1\t138547079\t138611420\r\n+chr1\t148809740\t148874076\r\n+chr1\t149526081\t149590400\r\n+chr1\t149779804\t149844124\r\n+chr1\t152002017\t152072787\r\n+chr1\t155315120\t155379180\r\n+chr1\t157797999\t157862060\r\n+chr1\t158420549\t158462707\r\n+chr1\t158558741\t158623071\r\n+chr1\t158968494\t159020907\r\n+chr1\t159209626\t159273963\r\n+chr1\t162568763\t162633083\r\n+chr1\t170782957\t170847279\r\n+chr1\t172986676\t173051019\r\n+chr1\t173604289\t173668350\r\n+chr1\t173755290\t173826531\r\n+chr1\t175769001\t175833062\r\n+chr1\t176192515\t176256575\r\n+chr1\t181259082\t181323410\r\n+chr1\t182877909\t182941970\r\n+chr1\t184086729\t184151058\r\n+chr1\t190963403\t191027739\r\n+chr1\t192273069\t192337405\r\n+chr1\t192934140\t193005671\r\n+chr1\t193482144\t193546480\r\n+chr10\t3483501\t3547823\r\n+chr10\t3764574\t3828896\r\n+chr10\t3896445\t3960782\r\n+chr10\t4645211\t4715786\r\n+chr10\t5823172\t5887495\r\n+chr10\t6106324\t6174735\r\n+chr10\t7027092\t7091153\r\n+chr10\t8240862\t8305184\r\n+chr10\t9957136\t10021197\r\n+chr10\t15048108\t15112427\r\n+chr10\t15415278\t15479614\r\n+chr10\t15571677\t15635737\r\n+chr10\t19067681\t19132834\r\n+chr10\t21403691\t21468012\r\n+chr10\t21586731\t21658171\r\n+chr10\t21777337\t21847793\r\n+chr10\t22151893\t22221544\r\n+chr10\t22231987\t22296326\r\n+chr10\t23527637\t23591698\r\n+chr10\t23660941\t23725262\r\n+chr10\t24013752\t24083250\r\n+chr10\t24542321\t24615855\r\n+chr10\t24874169\t24938504\r\n+chr10\t25655630\t25719690\r\n+chr10\t29562905\t29627226\r\n+chr10\t29983928\t30053429\r\n+chr10\t30588835\t30659532\r\n+chr10\t34498420\t34562741\r\n+chr10\t34849331\t34913659\r\n+chr10\t35457973\t35527259\r\n+chr10\t35892594\t35956922\r\n+chr10\t38034814\t38099148\r\n+chr10\t38708953\t38773275\r\n+chr10\t40009616\t40077579\r\n+chr10\t40328773\t40393112\r\n+chr10\t41463272\t41527605\r\n+chr10\t41754734\t41819056\r\n+chr10'..b'r7\t64864701\t64929024\r\n+chr7\t86339549\t86403885\r\n+chr7\t88089874\t88153935\r\n+chr7\t88897810\t88961870\r\n+chr7\t91330534\t91394875\r\n+chr7\t92274579\t92338897\r\n+chr7\t92799296\t92871052\r\n+chr7\t96367166\t96431487\r\n+chr7\t97101263\t97165323\r\n+chr7\t97284514\t97348575\r\n+chr7\t97529768\t97599280\r\n+chr7\t97851869\t97916192\r\n+chr7\t100396759\t100461081\r\n+chr7\t102369758\t102433820\r\n+chr7\t110115837\t110185134\r\n+chr7\t110593609\t110657942\r\n+chr7\t111828298\t111892634\r\n+chr7\t113312731\t113382215\r\n+chr7\t113768856\t113840290\r\n+chr7\t115660728\t115732171\r\n+chr7\t117629868\t117694188\r\n+chr7\t120157418\t120221754\r\n+chr7\t121024547\t121088906\r\n+chr7\t125426839\t125490900\r\n+chr7\t127489003\t127553340\r\n+chr7\t130507539\t130571878\r\n+chr7\t134261471\t134325806\r\n+chr7\t138933955\t138998277\r\n+chr7\t139084737\t139149053\r\n+chr7\t140067401\t140131723\r\n+chr7\t140688526\t140759900\r\n+chr7\t143399593\t143469131\r\n+chr7\t145614147\t145678208\r\n+chr7\t147730581\t147794642\r\n+chr7\t149421578\t149485895\r\n+chr8\t3801027\t3865347\r\n+chr8\t4803179\t4867504\r\n+chr8\t7824324\t7888646\r\n+chr8\t15722072\t15793287\r\n+chr8\t18251757\t18315818\r\n+chr8\t18465381\t18529442\r\n+chr8\t19045164\t19112378\r\n+chr8\t22096250\t22137512\r\n+chr8\t24678842\t24743165\r\n+chr8\t25794478\t25858799\r\n+chr8\t26014127\t26078462\r\n+chr8\t26468922\t26533260\r\n+chr8\t28479149\t28543469\r\n+chr8\t30097851\t30161911\r\n+chr8\t30460129\t30524450\r\n+chr8\t30752787\t30817107\r\n+chr8\t31563440\t31627777\r\n+chr8\t36022443\t36086504\r\n+chr8\t36959548\t37023870\r\n+chr8\t39028207\t39092267\r\n+chr8\t41087234\t41151556\r\n+chr8\t41620051\t41689555\r\n+chr8\t42004143\t42068203\r\n+chr8\t43019118\t43083438\r\n+chr8\t47722042\t47786380\r\n+chr8\t59252906\t59322400\r\n+chr8\t60789544\t60853875\r\n+chr8\t61197366\t61261703\r\n+chr8\t61532874\t61596935\r\n+chr8\t63294270\t63358605\r\n+chr8\t64185293\t64253284\r\n+chr8\t64763207\t64827530\r\n+chr8\t67113241\t67177577\r\n+chr8\t69123511\t69187572\r\n+chr8\t70169472\t70233795\r\n+chr8\t72177196\t72241533\r\n+chr8\t75436025\t75500364\r\n+chr8\t76584577\t76648638\r\n+chr8\t77497140\t77561453\r\n+chr8\t77747147\t77811482\r\n+chr8\t79352165\t79416481\r\n+chr8\t80631654\t80703131\r\n+chr8\t83678886\t83743222\r\n+chr8\t87650996\t87722809\r\n+chr8\t88349042\t88413368\r\n+chr8\t94809868\t94874201\r\n+chr8\t95383980\t95448041\r\n+chr8\t102794796\t102859131\r\n+chr8\t103935008\t103999308\r\n+chr8\t109626938\t109691000\r\n+chr8\t109709405\t109773728\r\n+chr8\t116384465\t116448815\r\n+chr8\t120505951\t120570011\r\n+chr8\t121428979\t121493588\r\n+chr8\t125683558\t125747880\r\n+chr8\t128575325\t128644983\r\n+chr9\t4047472\t4116542\r\n+chr9\t4806803\t4870864\r\n+chr9\t4884580\t4954084\r\n+chr9\t6022806\t6092325\r\n+chr9\t6275883\t6339944\r\n+chr9\t7392890\t7457209\r\n+chr9\t7462474\t7526795\r\n+chr9\t7766967\t7837187\r\n+chr9\t8271124\t8335185\r\n+chr9\t8402204\t8466265\r\n+chr9\t8764452\t8828512\r\n+chr9\t11784168\t11855632\r\n+chr9\t12170129\t12234190\r\n+chr9\t12237687\t12309084\r\n+chr9\t12318611\t12382934\r\n+chr9\t12721775\t12785836\r\n+chr9\t13835575\t13899894\r\n+chr9\t15182924\t15247260\r\n+chr9\t17955775\t18020096\r\n+chr9\t18827860\t18898433\r\n+chr9\t24340641\t24404702\r\n+chr9\t24593904\t24658240\r\n+chr9\t27266534\t27330872\r\n+chr9\t30430874\t30495213\r\n+chr9\t35587912\t35657485\r\n+chr9\t35863647\t35935120\r\n+chr9\t37845538\t37909860\r\n+chr9\t38185239\t38249385\r\n+chr9\t38896815\t38961150\r\n+chr9\t41662492\t41726552\r\n+chr9\t43638042\t43702378\r\n+chr9\t45006098\t45070433\r\n+chr9\t47047851\t47112173\r\n+chr9\t49906212\t49970548\r\n+chr9\t50402386\t50472116\r\n+chr9\t52696613\t52760674\r\n+chr9\t53981007\t54045329\r\n+chr9\t55048978\t55113313\r\n+chr9\t55639453\t55703790\r\n+chr9\t57139057\t57203396\r\n+chr9\t58372958\t58437282\r\n+chr9\t59751834\t59816157\r\n+chr9\t59828617\t59892938\r\n+chr9\t67460563\t67524885\r\n+chr9\t69791346\t69855407\r\n+chr9\t72084500\t72148804\r\n+chr9\t73306304\t73370365\r\n+chr9\t75546159\t75615764\r\n+chr9\t76067163\t76131499\r\n+chr9\t78205560\t78269895\r\n+chr9\t79863716\t79932960\r\n+chr9\t83543186\t83607520\r\n+chr9\t83961391\t84025712\r\n+chr9\t84745537\t84816469\r\n+chr9\t87287487\t87351823\r\n+chr9\t88965683\t89029744\r\n+chr9\t89914557\t89978617\r\n+chr9\t95389913\t95454249\r\n+chr9\t98540578\t98604900\r\n+chr9\t104333243\t104397304\r\n+chr9\t105712170\t105776231\r\n+chr9\t105976408\t106040743\r\n+chr9\t108139205\t108203544\r\n+chr9\t111904500\t111968818\r\n+chr9\t113768402\t113832464\r\n+chr9\t120794546\t120858880\r\n+chr9\t122321963\t122386298\r\n' |
| b |
| diff -r 81faa1567178 -r 565118df598a ETn_example/Recombination_hotspots.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ETn_example/Recombination_hotspots.txt Wed May 31 11:07:22 2017 -0400 |
| b |
| b'@@ -0,0 +1,2438 @@\n+chr1\t3079711\t3144047\t1\t1\t1\t1\t0.606\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.394\t1\t0.606\t0\t0\t0\t0\t0\t0\t0.73\t1\t0.27\t0.73\t1\t1\t1\t1\t1\t1\t1\t1\t0.27\t0\t0\t0\t0\t0\t0\t0\t0.73\t1\t1\t1\t1\t1\t1\r\n+chr1\t3232230\t3302517\t1\t1\t1\t0.211\t0\t0\t0\t0\t0\t0.789\t1\t1\t1\t0.211\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.789\t1\t1\t1\t1\t1\t1\t0.924\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t3756792\t3826331\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.11\t1\t1\t1\t1\t1\t0.89\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0.351\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t4589320\t4653381\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.06\t1\t1\t1\t1\t1\t1\t1\t0.94\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.121\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\r\n+chr1\t5155380\t5219717\t1\t0.061\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.939\t1\t1\t1\t1\t1\t1\t1\t0.724\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.276\t1\t1\t1\t1\t1\t1\t1\t1\t0.724\t0\r\n+chr1\t5634836\t5704314\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.873\t1\t1\t1\t0.127\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t5967107\t6035506\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.666\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t6240632\t6304964\t0.191\t1\t1\t1\t0.809\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t7186756\t7250816\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.375\t1\t0.625\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t7434671\t7504179\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t7573651\t7643108\t1\t1\t1\t1\t0.79\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.21\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.79\t0\t0\t0\t0\t0\t0\t0\t0\t0.667\t1\t1\t1\t0.333\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.667\t1\r\n+chr1\t7879930\t7944250\t0.191\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.809\t0\t0\t0\t0.191\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.489\t0\t0\r\n+chr1\t7962100\t8026423\t0.018\t1\t1\t0.982\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.018\t1\t1\t1\t1\t1\t1\t1\t0.659\t0\t0\t0\t0\t0\t0\t0\t0\t0.341\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.659\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t8219414\t8283736\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.295\t0.705\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\r\n+chr1\t9451579\t9515898\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.543\t1\t1\t1\t1\t0.457\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t10561964\t10626025\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.584\t1\t1\t0.416\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t10774950\t10844464\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t11301539\t11365867\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t11479858\t11543919\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t11577435\t11646975\t1\t0.534\t0\t0\t0.466\t1\t1\t0.534\t0.466\t1\t1\t1\t0.534\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.466\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.994\t0.006\t1\t1\t0.994\t0\t0.006\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.994\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t11734130\t11798451\t0\t0\t0\t0.99\t1\t1\t1\t1\t1\t1\t1\t1\t0.01\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.99\t1\t1\t1\t1\t1\t0.689\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.311\t1\t1\t1\t1\t1\r\n+chr1\t12053425\t12117744\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t12503733\t12568058\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t12690915\t12755253\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.188\t1\t1\t0.812\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.526\t1\t1\t1\t1\t1\t0.474\t0\t0\t0\t0.526\t1\t1\t0.474\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr1\t13015768\t13080108\t1\t0.667\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.3'..b'1\t0.233\t0\t0\t0\t0\t0\t0\t0.767\t1\t1\t0.233\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.767\t1\t1\t0.233\t0\t0\t0\t0\t0.767\t1\t1\t1\t1\t0.233\t0\t0\t0\t0\r\n+chr9\t69240049\t69304049\t0\t0\t0\t0\t0\t0.767\t1\t1\t1\t1\t0.233\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.767\t1\t0.233\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr9\t71796844\t71860844\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.562\t1\t1\t0.438\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.562\t1\t1\t1\r\n+chr9\t74791622\t74855622\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.34\t1\t1\t0.66\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr9\t79491629\t79555629\t0\t0\t0\t0\t0\t0.347\t1\t1\t1\t1\t1\t0.653\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.347\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\r\n+chr9\t79932960\t79996960\t0.322\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.678\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.322\t0\t0\t0\t0\t0\t0\t0.678\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\r\n+chr9\t84626957\t84690957\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.675\t1\t1\t0.325\t0\t0\t0\t0\r\n+chr9\t96193779\t96257779\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.949\t1\t1\t0.051\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.949\t1\t1\t0.051\t0\t0\t0\t0\t0\r\n+chr9\t107312141\t107376141\t1\t1\t0.689\t0.311\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.689\t0\t0\t0\t0\t0\t0\t0.311\t1\t1\t1\t1\t0.689\t0\t0\t0\t0.311\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\r\n+chr9\t107376141\t107440141\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.689\t0\t0\t0\t0\t0\t0\t0\t0\t0.311\t1\t1\t0.689\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.311\t1\t1\t1\t1\t1\t1\t1\t1\r\n+chr9\t107462650\t107526650\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.82\t1\t1\t1\t1\t0.18\t0\t0\t0\t0\t0\t0\t0\t0.82\t1\t1\t1\t1\t1\t0.18\t0.82\t1\t0.18\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.82\t1\t1\t0.18\t0\t0.82\t1\t1\t0.18\r\n+chr9\t107526650\t107590650\t0\t0\t0.82\t1\t1\t1\t1\t1\t1\t0.18\t0\t0.82\t1\t1\t1\t1\t1\t1\t0.18\t0\t0.82\t1\t1\t1\t1\t0.18\t0\t0\t0\t0.82\t1\t1\t0.18\t0\t0.82\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.18\t0\t0.82\t1\t0.18\t0\t0\t0\t0\t0\t0.82\t1\t1\r\n+chr9\t107590650\t107654650\t0.18\t0.82\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.18\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.82\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.18\t0\t0\t0\t0\t0\t0.82\t1\t1\t1\t0.18\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.82\r\n+chr9\t107848560\t107912560\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.73\t1\t0.27\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr9\t107941738\t108005738\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.908\t1\t0.092\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr9\t108683437\t108747437\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr9\t108962296\t109026296\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.466\t1\t1\t1\t0.534\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr9\t109947901\t110011901\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr9\t110485254\t110549254\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr9\t110616374\t110680374\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.544\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.456\t0.544\t1\t1\t1\t1\t1\t1\t0.456\t0.544\t1\t1\t0.456\t0.544\t1\t1\t1\r\n+chr9\t111968818\t112032818\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr9\t113836504\t113900504\t0\t0\t0.457\t1\t1\t1\t1\t0.543\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.457\t1\t1\t1\t1\t1\t1\t1\t1\t0.543\t0\t0\t0\t0\t0.457\t1\t1\t1\t1\r\n+chr9\t118910538\t118974538\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.491\t1\t1\t1\t1\t1\t1\t1\t1\t0.509\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+chr9\t121627136\t121691136\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n' |
| b |
| diff -r 81faa1567178 -r 565118df598a ETn_example/features.header --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ETn_example/features.header Wed May 31 11:07:22 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +Recombination_hotspots.txt Recomb_hot Recombination hotspots \ No newline at end of file |
| b |
| diff -r 81faa1567178 -r 565118df598a ETn_example/regions.header --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ETn_example/regions.header Wed May 31 11:07:22 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Control.bed Control Control +ETn_fixed.bed ETn_fixed ETn fixed \ No newline at end of file |
| b |
| diff -r 81faa1567178 -r 565118df598a example/._.DS_Store |
| b |
| Binary file example/._.DS_Store has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a example/._Controls_regions.bed |
| b |
| Binary file example/._Controls_regions.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a example/._DESCRIPTION.txt |
| b |
| Binary file example/._DESCRIPTION.txt has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a example/._Elements1_regions.bed |
| b |
| Binary file example/._Elements1_regions.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a example/._Elements2_regions.bed |
| b |
| Binary file example/._Elements2_regions.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a example/._Elements3_regions.bed |
| b |
| Binary file example/._Elements3_regions.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a example/._Feature1.bed |
| b |
| Binary file example/._Feature1.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a example/._Feature2.bed |
| b |
| Binary file example/._Feature2.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a example/._features.header.bed.txt |
| b |
| Binary file example/._features.header.bed.txt has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a example/._regions.header.txt |
| b |
| Binary file example/._regions.header.txt has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a example/Controls_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/Controls_regions.bed Wed May 31 11:07:22 2017 -0400 |
| b |
| @@ -0,0 +1,35 @@ +chr1 91399892 91499892 +chr1 116447079 116547079 +chr2 231381109 231481109 +chr3 47386633 47486633 +chr3 99195712 99295712 +chr3 116765114 116865114 +chr3 134345017 134445017 +chr4 68064019 68164019 +chr4 137465811 137565811 +chr4 173293016 173393016 +chr5 59044110 59144110 +chr5 94592763 94692763 +chr5 108436006 108536006 +chr5 110836898 110936898 +chr5 146661073 146761073 +chr6 99727306 99827306 +chr7 88291325 88391325 +chr7 120999784 121099784 +chr8 126860366 126960366 +chr8 127636547 127736547 +chr11 41362564 41462564 +chr11 101741527 101841527 +chr12 15210277 15310277 +chr13 91106037 91206037 +chr13 91518822 91618822 +chr13 98959030 99059030 +chr15 39087176 39187176 +chr17 58542142 58642142 +chr18 12199823 12299823 +chr20 8173704 8273704 +chr21 16255112 16355112 +chr21 45089115 45189115 +chrX 23898983 23998983 +chrX 37029585 37129585 +chrX 103593349 103693349 |
| b |
| diff -r 81faa1567178 -r 565118df598a example/DESCRIPTION.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/DESCRIPTION.txt Wed May 31 11:07:22 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +This example contains simulated measurements of two different genomic features, "ftr1" and "ftr2", +corresponding to four different region datasets: "elem1", "elem2", "elem3" and "control". |
| b |
| diff -r 81faa1567178 -r 565118df598a example/Elements1_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/Elements1_regions.bed Wed May 31 11:07:22 2017 -0400 |
| b |
| @@ -0,0 +1,25 @@ +chr2 49960150 50060150 +chr2 55912445 56012445 +chr3 140326750 140426750 +chr4 41772201 41872201 +chr4 70629719 70729719 +chr4 109340735 109440735 +chr5 15025389 15125389 +chr5 43028888 43128888 +chr5 58231354 58331354 +chr5 91277761 91377761 +chr5 119464508 119564508 +chr6 85309170 85409170 +chr6 85762072 85862072 +chr6 134621363 134721363 +chr6 147470164 147570164 +chr7 77195798 77295798 +chr7 77880914 77980914 +chr7 114805399 114905399 +chr10 46350885 46450885 +chr10 67833078 67933078 +chr12 27722692 27822692 +chr12 95518506 95618506 +chr12 117863466 117963466 +chr14 100464166 100564166 +chrX 29266748 29366748 |
| b |
| diff -r 81faa1567178 -r 565118df598a example/Elements2_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/Elements2_regions.bed Wed May 31 11:07:22 2017 -0400 |
| b |
| @@ -0,0 +1,20 @@ +chr1 65942901 66042901 +chr1 117128102 117228102 +chr1 190338169 190438169 +chr2 227365478 227465478 +chr6 50856764 50956764 +chr6 135703067 135803067 +chr7 38228726 38328726 +chr7 51115898 51215898 +chr7 150325760 150425760 +chr8 25475691 25575691 +chr9 73374609 73474609 +chr11 55092625 55192625 +chr11 86581661 86681661 +chr12 12795284 12895284 +chr12 48151882 48251882 +chr12 83109951 83209951 +chr15 31430278 31530278 +chr15 65610815 65710815 +chr17 40766223 40866223 +chr20 17245048 17345048 |
| b |
| diff -r 81faa1567178 -r 565118df598a example/Elements3_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/Elements3_regions.bed Wed May 31 11:07:22 2017 -0400 |
| b |
| @@ -0,0 +1,28 @@ +chr1 49721616 49821616 +chr1 95059425 95159425 +chr1 207236313 207336313 +chr2 73790843 73890843 +chr3 134465321 134565321 +chr4 43433669 43533669 +chr4 122032777 122132777 +chr5 12701747 12801747 +chr5 58501529 58601529 +chr5 152853250 152953250 +chr6 136085023 136185023 +chr6 147019529 147119529 +chr7 14192964 14292964 +chr7 125519883 125619883 +chr8 77652872 77752872 +chr8 108375665 108475665 +chr9 2984971 3084971 +chr10 978822 1078822 +chr11 18395046 18495046 +chr12 47273592 47373592 +chr12 60095778 60195778 +chr12 84854096 84954096 +chr12 95157539 95257539 +chr14 23982000 24082000 +chr16 1875335 1975335 +chr16 66789863 66889863 +chr18 64644131 64744131 +chr21 15966609 16066609 |
| b |
| diff -r 81faa1567178 -r 565118df598a example/Feature1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/Feature1.bed Wed May 31 11:07:22 2017 -0400 |
| b |
| b'@@ -0,0 +1,5400 @@\n+chr1\t91399892\t91401892\t0.914729028492568\n+chr1\t91401892\t91403892\t1.03788669317729\n+chr1\t91403892\t91405892\t1.15695078809331\n+chr1\t91405892\t91407892\t1.05433971377051\n+chr1\t91407892\t91409892\t1.05827244724317\n+chr1\t91409892\t91411892\t1.00216117481117\n+chr1\t91411892\t91413892\t0.873489001753337\n+chr1\t91413892\t91415892\t0.873100412116323\n+chr1\t91415892\t91417892\t0.928712683217515\n+chr1\t91417892\t91419892\t0.94132562114723\n+chr1\t91419892\t91421892\t1.06739894033636\n+chr1\t91421892\t91423892\t0.909275169317382\n+chr1\t91423892\t91425892\t1.10093887463398\n+chr1\t91425892\t91427892\t1.05342912580018\n+chr1\t91427892\t91429892\t0.970074712768588\n+chr1\t91429892\t91431892\t0.742552329847752\n+chr1\t91431892\t91433892\t1.09649292566553\n+chr1\t91433892\t91435892\t0.902578291528885\n+chr1\t91435892\t91437892\t0.821718064516058\n+chr1\t91437892\t91439892\t0.909063175846949\n+chr1\t91439892\t91441892\t1.12598647717153\n+chr1\t91441892\t91443892\t0.962991989888592\n+chr1\t91443892\t91445892\t0.886361985680751\n+chr1\t91445892\t91447892\t1.19735794895968\n+chr1\t91447892\t91449892\t1.1058589065373\n+chr1\t91449892\t91451892\t1.11830938343819\n+chr1\t91451892\t91453892\t0.891849450289035\n+chr1\t91453892\t91455892\t0.921613352575372\n+chr1\t91455892\t91457892\t0.961394603438276\n+chr1\t91457892\t91459892\t0.942120540462845\n+chr1\t91459892\t91461892\t1.04179227745858\n+chr1\t91461892\t91463892\t0.846036296260439\n+chr1\t91463892\t91465892\t0.903782108017989\n+chr1\t91465892\t91467892\t0.926324469715607\n+chr1\t91467892\t91469892\t1.01617788108211\n+chr1\t91469892\t91471892\t1.01871994841433\n+chr1\t91471892\t91473892\t0.86346600407464\n+chr1\t91473892\t91475892\t0.911534382002842\n+chr1\t91475892\t91477892\t0.909397860657818\n+chr1\t91477892\t91479892\t0.882437981483481\n+chr1\t91479892\t91481892\t1.20022730271379\n+chr1\t91481892\t91483892\t1.02286707465404\n+chr1\t91483892\t91485892\t1.00824959158441\n+chr1\t91485892\t91487892\t1.13387236604912\n+chr1\t91487892\t91489892\t0.917808428397605\n+chr1\t91489892\t91491892\t1.00980153326694\n+chr1\t91491892\t91493892\t1.0780078042687\n+chr1\t91493892\t91495892\t1.05789211157318\n+chr1\t91495892\t91497892\t0.983519376160091\n+chr1\t91497892\t91499892\t1.06301499098899\n+chr1\t116447079\t116449079\t0.909510507890661\n+chr1\t116449079\t116451079\t1.04923486926106\n+chr1\t116451079\t116453079\t0.972429435962863\n+chr1\t116453079\t116455079\t0.94348509718749\n+chr1\t116455079\t116457079\t0.877213727110183\n+chr1\t116457079\t116459079\t1.07609955711144\n+chr1\t116459079\t116461079\t1.05964706503259\n+chr1\t116461079\t116463079\t1.08048074104999\n+chr1\t116463079\t116465079\t1.10397643608295\n+chr1\t116465079\t116467079\t0.879172377236955\n+chr1\t116467079\t116469079\t0.952455624542298\n+chr1\t116469079\t116471079\t0.872450868701435\n+chr1\t116471079\t116473079\t0.734632500870684\n+chr1\t116473079\t116475079\t0.975852194327443\n+chr1\t116475079\t116477079\t1.15968481779916\n+chr1\t116477079\t116479079\t1.03479249038231\n+chr1\t116479079\t116481079\t0.958716780567544\n+chr1\t116481079\t116483079\t1.00882150410174\n+chr1\t116483079\t116485079\t0.894048456447358\n+chr1\t116485079\t116487079\t0.862250242465922\n+chr1\t116487079\t116489079\t1.08563273479841\n+chr1\t116489079\t116491079\t1.03570610668607\n+chr1\t116491079\t116493079\t1.282637134762\n+chr1\t116493079\t116495079\t1.05344881721884\n+chr1\t116495079\t116497079\t0.958843714832433\n+chr1\t116497079\t116499079\t0.907730747212707\n+chr1\t116499079\t116501079\t0.964823764805327\n+chr1\t116501079\t116503079\t0.972508803669119\n+chr1\t116503079\t116505079\t0.964761127498888\n+chr1\t116505079\t116507079\t1.21022463445566\n+chr1\t116507079\t116509079\t0.870817357520223\n+chr1\t116509079\t116511079\t0.970216007864307\n+chr1\t116511079\t116513079\t1.09860269791989\n+chr1\t116513079\t116515079\t1.01985884672516\n+chr1\t116515079\t116517079\t1.04151199469522\n+chr1\t116517079\t116519079\t1.10542491108645\n+chr1\t116519079\t116521079\t1.06697958402493\n+chr1\t116521079\t116523079\t0.972137682316022\n+chr1\t116523079\t116525079\t0.900068042346903\n+chr1\t116525079\t116527079\t1.00945179072767\n+chr1\t116527079\t116529079\t0.910760202377398\n+chr1\t116529079\t116531079\t0.960315923931081\n+chr1\t116531079\t116533079\t1.05558603806716\n+chr1\t116533079\t116535079\t0.92038544115'..b'1\t64656131\t0.97369678388939\n+chr18\t64656131\t64658131\t0.910087798040937\n+chr18\t64658131\t64660131\t0.946468289624316\n+chr18\t64660131\t64662131\t1.05842665628809\n+chr18\t64662131\t64664131\t0.927667349376235\n+chr18\t64664131\t64666131\t1.18742333150313\n+chr18\t64666131\t64668131\t1.22205250380213\n+chr18\t64668131\t64670131\t0.880563425486305\n+chr18\t64670131\t64672131\t0.914485239144026\n+chr18\t64672131\t64674131\t1.01034737175594\n+chr18\t64674131\t64676131\t1.62264521151304\n+chr18\t64676131\t64678131\t1.48296645852995\n+chr18\t64678131\t64680131\t1.28681962535927\n+chr18\t64680131\t64682131\t1.53492939742228\n+chr18\t64682131\t64684131\t1.58844790171606\n+chr18\t64684131\t64686131\t1.49033262314301\n+chr18\t64686131\t64688131\t1.31424965988202\n+chr18\t64688131\t64690131\t1.45337032575317\n+chr18\t64690131\t64692131\t1.35217898213701\n+chr18\t64692131\t64694131\t1.77532370910719\n+chr18\t64694131\t64696131\t1.60398303218395\n+chr18\t64696131\t64698131\t1.69307164801575\n+chr18\t64698131\t64700131\t1.54229556388787\n+chr18\t64700131\t64702131\t1.68106575665579\n+chr18\t64702131\t64704131\t1.48714225361666\n+chr18\t64704131\t64706131\t1.55224087444918\n+chr18\t64706131\t64708131\t1.3662045024589\n+chr18\t64708131\t64710131\t1.57624355139023\n+chr18\t64710131\t64712131\t1.44378437443185\n+chr18\t64712131\t64714131\t1.37811537520723\n+chr18\t64714131\t64716131\t1.06551636789331\n+chr18\t64716131\t64718131\t1.04029846172777\n+chr18\t64718131\t64720131\t1.1012560789095\n+chr18\t64720131\t64722131\t1.16248797408295\n+chr18\t64722131\t64724131\t1.10209650363972\n+chr18\t64724131\t64726131\t1.12702540883185\n+chr18\t64726131\t64728131\t1.06158233209566\n+chr18\t64728131\t64730131\t1.24500209867534\n+chr18\t64730131\t64732131\t0.834309455846338\n+chr18\t64732131\t64734131\t0.757289730474966\n+chr18\t64734131\t64736131\t1.10451816307643\n+chr18\t64736131\t64738131\t0.92262846294503\n+chr18\t64738131\t64740131\t0.804253155660302\n+chr18\t64740131\t64742131\t1.00162039935745\n+chr18\t64742131\t64744131\t0.956034285823398\n+chr21\t15966609\t15968609\t1.12440801594939\n+chr21\t15968609\t15970609\t0.958928874609379\n+chr21\t15970609\t15972609\t0.980859325447667\n+chr21\t15972609\t15974609\t0.985836855465142\n+chr21\t15974609\t15976609\t0.924304227149342\n+chr21\t15976609\t15978609\t0.981319441090073\n+chr21\t15978609\t15980609\t0.949853799394529\n+chr21\t15980609\t15982609\t0.858050928062694\n+chr21\t15982609\t15984609\t0.836178837413462\n+chr21\t15984609\t15986609\t1.20633196613812\n+chr21\t15986609\t15988609\t0.969230627046025\n+chr21\t15988609\t15990609\t1.06120061342825\n+chr21\t15990609\t15992609\t0.88573302960608\n+chr21\t15992609\t15994609\t0.987056692659576\n+chr21\t15994609\t15996609\t1.05266019775439\n+chr21\t15996609\t15998609\t1.29745136461899\n+chr21\t15998609\t16000609\t1.3631797211261\n+chr21\t16000609\t16002609\t1.58553521861437\n+chr21\t16002609\t16004609\t1.47800659441217\n+chr21\t16004609\t16006609\t1.75042011315262\n+chr21\t16006609\t16008609\t1.39329136735319\n+chr21\t16008609\t16010609\t1.57255744319984\n+chr21\t16010609\t16012609\t1.20929102513908\n+chr21\t16012609\t16014609\t1.53853232166312\n+chr21\t16014609\t16016609\t1.64985481461386\n+chr21\t16016609\t16018609\t1.59575749789367\n+chr21\t16018609\t16020609\t1.42205668994404\n+chr21\t16020609\t16022609\t1.66053802113289\n+chr21\t16022609\t16024609\t1.70386086339594\n+chr21\t16024609\t16026609\t1.73541878893467\n+chr21\t16026609\t16028609\t1.39682491364686\n+chr21\t16028609\t16030609\t1.43336589770868\n+chr21\t16030609\t16032609\t1.63386317242737\n+chr21\t16032609\t16034609\t1.53233925104548\n+chr21\t16034609\t16036609\t1.53952241603109\n+chr21\t16036609\t16038609\t1.28074961173938\n+chr21\t16038609\t16040609\t1.27922409248079\n+chr21\t16040609\t16042609\t0.962647373836482\n+chr21\t16042609\t16044609\t0.950807449539781\n+chr21\t16044609\t16046609\t1.19549845149275\n+chr21\t16046609\t16048609\t1.03462200267827\n+chr21\t16048609\t16050609\t0.952643344080609\n+chr21\t16050609\t16052609\t1.20946321219477\n+chr21\t16052609\t16054609\t0.965927027586426\n+chr21\t16054609\t16056609\t0.976116334675594\n+chr21\t16056609\t16058609\t1.07756004404963\n+chr21\t16058609\t16060609\t0.987244607153093\n+chr21\t16060609\t16062609\t1.04620355385428\n+chr21\t16062609\t16064609\t1.02761240862396\n+chr21\t16064609\t16066609\t0.870263755617609\n' |
| b |
| diff -r 81faa1567178 -r 565118df598a example/Feature2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/Feature2.bed Wed May 31 11:07:22 2017 -0400 |
| b |
| b'@@ -0,0 +1,5400 @@\n+chr1\t91399892\t91401892\t4.52457845989749\n+chr1\t91401892\t91403892\t4.69885317507985\n+chr1\t91403892\t91405892\t3.62988338998133\n+chr1\t91405892\t91407892\t4.45623107548837\n+chr1\t91407892\t91409892\t4.59364249841659\n+chr1\t91409892\t91411892\t5.70905494693032\n+chr1\t91411892\t91413892\t2.42812136492091\n+chr1\t91413892\t91415892\t3.21325702299381\n+chr1\t91415892\t91417892\t5.83146415223743\n+chr1\t91417892\t91419892\t4.145234941891\n+chr1\t91419892\t91421892\t5.61198015818556\n+chr1\t91421892\t91423892\t3.64586797215646\n+chr1\t91423892\t91425892\t6.20636700257446\n+chr1\t91425892\t91427892\t6.24535453369189\n+chr1\t91427892\t91429892\t5.45642255152577\n+chr1\t91429892\t91431892\t2.25812560771762\n+chr1\t91431892\t91433892\t4.85449016203815\n+chr1\t91433892\t91435892\t3.90115956418853\n+chr1\t91435892\t91437892\t4.73358990127742\n+chr1\t91437892\t91439892\t5.10493877711061\n+chr1\t91439892\t91441892\t6.26626452775677\n+chr1\t91441892\t91443892\t4.50874633533701\n+chr1\t91443892\t91445892\t5.70230938739608\n+chr1\t91445892\t91447892\t5.94455591845681\n+chr1\t91447892\t91449892\t4.52518856675072\n+chr1\t91449892\t91451892\t4.63848705114735\n+chr1\t91451892\t91453892\t4.34603429138827\n+chr1\t91453892\t91455892\t3.03830118655551\n+chr1\t91455892\t91457892\t6.03275619780653\n+chr1\t91457892\t91459892\t5.68223277080844\n+chr1\t91459892\t91461892\t5.50525041823675\n+chr1\t91461892\t91463892\t4.5213830572052\n+chr1\t91463892\t91465892\t5.50133572404842\n+chr1\t91465892\t91467892\t4.91055078504098\n+chr1\t91467892\t91469892\t4.05752990001426\n+chr1\t91469892\t91471892\t5.10897499920239\n+chr1\t91471892\t91473892\t5.43128593940068\n+chr1\t91473892\t91475892\t4.86148316107809\n+chr1\t91475892\t91477892\t4.48947054967865\n+chr1\t91477892\t91479892\t4.04898383490831\n+chr1\t91479892\t91481892\t5.68808370629557\n+chr1\t91481892\t91483892\t3.38402935045047\n+chr1\t91483892\t91485892\t4.55469509198871\n+chr1\t91485892\t91487892\t5.54674749210028\n+chr1\t91487892\t91489892\t6.80643757003305\n+chr1\t91489892\t91491892\t4.36576921982342\n+chr1\t91491892\t91493892\t4.78762392440088\n+chr1\t91493892\t91495892\t4.7968645329394\n+chr1\t91495892\t91497892\t5.2766452300238\n+chr1\t91497892\t91499892\t4.11389723526811\n+chr1\t116447079\t116449079\t3.50479481019937\n+chr1\t116449079\t116451079\t5.80805807123363\n+chr1\t116451079\t116453079\t4.84431415016648\n+chr1\t116453079\t116455079\t3.05704665156576\n+chr1\t116455079\t116457079\t4.08848780835827\n+chr1\t116457079\t116459079\t5.09637693701485\n+chr1\t116459079\t116461079\t5.69818646616106\n+chr1\t116461079\t116463079\t4.19878801898032\n+chr1\t116463079\t116465079\t4.5516661398769\n+chr1\t116465079\t116467079\t4.2453176706507\n+chr1\t116467079\t116469079\t4.67523653585105\n+chr1\t116469079\t116471079\t3.95251471557774\n+chr1\t116471079\t116473079\t4.96923766290807\n+chr1\t116473079\t116475079\t4.96920479716357\n+chr1\t116475079\t116477079\t5.02676539089313\n+chr1\t116477079\t116479079\t5.00052315566\n+chr1\t116479079\t116481079\t4.16809348391652\n+chr1\t116481079\t116483079\t4.59306360967521\n+chr1\t116483079\t116485079\t3.53563628215594\n+chr1\t116485079\t116487079\t4.50469161954188\n+chr1\t116487079\t116489079\t5.56857122702899\n+chr1\t116489079\t116491079\t4.58351619746089\n+chr1\t116491079\t116493079\t4.25823600023412\n+chr1\t116493079\t116495079\t5.90593508834324\n+chr1\t116495079\t116497079\t4.75083460476364\n+chr1\t116497079\t116499079\t2.771628447275\n+chr1\t116499079\t116501079\t3.55096260651244\n+chr1\t116501079\t116503079\t6.17656545119289\n+chr1\t116503079\t116505079\t4.36022614599567\n+chr1\t116505079\t116507079\t3.07947070495695\n+chr1\t116507079\t116509079\t6.00325415448973\n+chr1\t116509079\t116511079\t4.75152529713703\n+chr1\t116511079\t116513079\t4.63430887067622\n+chr1\t116513079\t116515079\t6.20396270678022\n+chr1\t116515079\t116517079\t4.10708349972204\n+chr1\t116517079\t116519079\t6.37204838467736\n+chr1\t116519079\t116521079\t4.20892327541064\n+chr1\t116521079\t116523079\t5.26217726205883\n+chr1\t116523079\t116525079\t4.98426282331262\n+chr1\t116525079\t116527079\t4.54088329611304\n+chr1\t116527079\t116529079\t6.19908300654713\n+chr1\t116529079\t116531079\t4.13307018130982\n+chr1\t116531079\t116533079\t4.81616315789755\n+chr1\t116533079\t116535079\t4.45075212625821\n+chr1\t116535079\t116537079\t5.3278384644649\n+chr1\t11'..b'1\t3.7169759268732\n+chr18\t64654131\t64656131\t5.25442380932218\n+chr18\t64656131\t64658131\t7.45772820471094\n+chr18\t64658131\t64660131\t5.48095406750538\n+chr18\t64660131\t64662131\t3.62733589187025\n+chr18\t64662131\t64664131\t4.55331693366933\n+chr18\t64664131\t64666131\t6.8774312824165\n+chr18\t64666131\t64668131\t5.2001203442027\n+chr18\t64668131\t64670131\t4.95990659880495\n+chr18\t64670131\t64672131\t4.02077893319017\n+chr18\t64672131\t64674131\t4.05668535153819\n+chr18\t64674131\t64676131\t4.23509896158418\n+chr18\t64676131\t64678131\t4.23418796991892\n+chr18\t64678131\t64680131\t5.45699681002164\n+chr18\t64680131\t64682131\t5.19535591598228\n+chr18\t64682131\t64684131\t6.0555950876448\n+chr18\t64684131\t64686131\t3.54284284855037\n+chr18\t64686131\t64688131\t5.0657204197487\n+chr18\t64688131\t64690131\t4.61156619971275\n+chr18\t64690131\t64692131\t4.66622025797826\n+chr18\t64692131\t64694131\t5.34521271919367\n+chr18\t64694131\t64696131\t9.87597953863361\n+chr18\t64696131\t64698131\t7.05091406041253\n+chr18\t64698131\t64700131\t8.00182216055189\n+chr18\t64700131\t64702131\t7.91390780851007\n+chr18\t64702131\t64704131\t6.60478767008177\n+chr18\t64704131\t64706131\t8.42205253797048\n+chr18\t64706131\t64708131\t8.4092636416611\n+chr18\t64708131\t64710131\t7.33893411142367\n+chr18\t64710131\t64712131\t6.44977234209029\n+chr18\t64712131\t64714131\t6.14212509408095\n+chr18\t64714131\t64716131\t7.33470365201403\n+chr18\t64716131\t64718131\t6.14466300830508\n+chr18\t64718131\t64720131\t6.28759018496124\n+chr18\t64720131\t64722131\t6.13121264285508\n+chr18\t64722131\t64724131\t6.25464222302313\n+chr18\t64724131\t64726131\t6.22857474092805\n+chr18\t64726131\t64728131\t6.7164061474755\n+chr18\t64728131\t64730131\t7.71694797882967\n+chr18\t64730131\t64732131\t6.47134532938063\n+chr18\t64732131\t64734131\t5.44078856911433\n+chr18\t64734131\t64736131\t6.72171185147245\n+chr18\t64736131\t64738131\t7.45623695140267\n+chr18\t64738131\t64740131\t6.66053173863693\n+chr18\t64740131\t64742131\t7.26582262622926\n+chr18\t64742131\t64744131\t7.26639325298473\n+chr21\t15966609\t15968609\t3.61661096782077\n+chr21\t15968609\t15970609\t4.73386208722406\n+chr21\t15970609\t15972609\t5.8015549021153\n+chr21\t15972609\t15974609\t4.96167153907388\n+chr21\t15974609\t15976609\t3.95102647749112\n+chr21\t15976609\t15978609\t3.97020922833049\n+chr21\t15978609\t15980609\t5.33786080501161\n+chr21\t15980609\t15982609\t4.36434578068312\n+chr21\t15982609\t15984609\t5.80198476623914\n+chr21\t15984609\t15986609\t5.35739211903602\n+chr21\t15986609\t15988609\t6.08746983525949\n+chr21\t15988609\t15990609\t4.34773396054126\n+chr21\t15990609\t15992609\t5.13949591522979\n+chr21\t15992609\t15994609\t3.73402272260864\n+chr21\t15994609\t15996609\t5.39450798275315\n+chr21\t15996609\t15998609\t5.55466043086729\n+chr21\t15998609\t16000609\t5.28998031818056\n+chr21\t16000609\t16002609\t6.19329925730006\n+chr21\t16002609\t16004609\t2.67150074437477\n+chr21\t16004609\t16006609\t5.16423939358034\n+chr21\t16006609\t16008609\t4.69609507505699\n+chr21\t16008609\t16010609\t5.44942073640721\n+chr21\t16010609\t16012609\t6.03847400860453\n+chr21\t16012609\t16014609\t5.97649168698122\n+chr21\t16014609\t16016609\t5.36013704359642\n+chr21\t16016609\t16018609\t7.92817462773764\n+chr21\t16018609\t16020609\t7.69377454814871\n+chr21\t16020609\t16022609\t8.80647396276848\n+chr21\t16022609\t16024609\t8.52452119781362\n+chr21\t16024609\t16026609\t7.89462789559928\n+chr21\t16026609\t16028609\t6.13805198380259\n+chr21\t16028609\t16030609\t4.64531272265593\n+chr21\t16030609\t16032609\t6.29826676008479\n+chr21\t16032609\t16034609\t7.79487866360525\n+chr21\t16034609\t16036609\t7.31994055340419\n+chr21\t16036609\t16038609\t8.8004479775322\n+chr21\t16038609\t16040609\t8.25854856063076\n+chr21\t16040609\t16042609\t5.04576860851306\n+chr21\t16042609\t16044609\t7.30730130969012\n+chr21\t16044609\t16046609\t7.83870783306589\n+chr21\t16046609\t16048609\t7.63074529828173\n+chr21\t16048609\t16050609\t6.43100021814285\n+chr21\t16050609\t16052609\t7.27551387601485\n+chr21\t16052609\t16054609\t6.26545170591659\n+chr21\t16054609\t16056609\t7.12562466213381\n+chr21\t16056609\t16058609\t6.26895239202312\n+chr21\t16058609\t16060609\t7.3992370168724\n+chr21\t16060609\t16062609\t7.97487587946482\n+chr21\t16062609\t16064609\t6.76355670816454\n+chr21\t16064609\t16066609\t6.11742019669001\n' |
| b |
| diff -r 81faa1567178 -r 565118df598a example/features.header.bed.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/features.header.bed.txt Wed May 31 11:07:22 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Feature1.bed ftr1 Feature 1 +Feature2.bed ftr2 Feature 2 \ No newline at end of file |
| b |
| diff -r 81faa1567178 -r 565118df598a example/regions.header.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example/regions.header.txt Wed May 31 11:07:22 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Elements1_regions.bed elem1 Elements 1 +Elements2_regions.bed elem2 Elements 2 +Elements3_regions.bed elem3 Elements 3 +Controls_regions.bed control Controls \ No newline at end of file |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/._.DS_Store |
| b |
| Binary file iwtomics/ETn_example/._.DS_Store has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/._Control.bed |
| b |
| Binary file iwtomics/ETn_example/._Control.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/._DESCRIPTION.txt |
| b |
| Binary file iwtomics/ETn_example/._DESCRIPTION.txt has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/._ETn_fixed.bed |
| b |
| Binary file iwtomics/ETn_example/._ETn_fixed.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/._Recombination_hotspots.txt |
| b |
| Binary file iwtomics/ETn_example/._Recombination_hotspots.txt has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/._features.header |
| b |
| Binary file iwtomics/ETn_example/._features.header has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/._regions.header |
| b |
| Binary file iwtomics/ETn_example/._regions.header has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/Control.bed --- a/iwtomics/ETn_example/Control.bed Wed May 31 11:06:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1142 +0,0 @@\n-chr1\t6743847\t6807847\r\n-chr1\t12755253\t12819253\r\n-chr1\t14459704\t14523704\r\n-chr1\t16989370\t17053370\r\n-chr1\t18859600\t18923600\r\n-chr1\t20393735\t20457735\r\n-chr1\t20457735\t20521735\r\n-chr1\t22357071\t22421071\r\n-chr1\t34267805\t34331805\r\n-chr1\t36860915\t36924915\r\n-chr1\t38084729\t38148729\r\n-chr1\t38513351\t38577351\r\n-chr1\t39997553\t40061553\r\n-chr1\t40484791\t40548791\r\n-chr1\t44015427\t44079427\r\n-chr1\t45327525\t45391525\r\n-chr1\t45420798\t45484798\r\n-chr1\t49687964\t49751964\r\n-chr1\t52202938\t52266938\r\n-chr1\t56924736\t56988736\r\n-chr1\t56988736\t57052736\r\n-chr1\t59226030\t59290030\r\n-chr1\t62745840\t62809840\r\n-chr1\t62809840\t62873840\r\n-chr1\t64105946\t64169946\r\n-chr1\t66424667\t66488667\r\n-chr1\t66554557\t66618557\r\n-chr1\t68388328\t68452328\r\n-chr1\t69038498\t69102498\r\n-chr1\t70745639\t70809639\r\n-chr1\t73940413\t74004413\r\n-chr1\t74387826\t74451826\r\n-chr1\t74451826\t74515826\r\n-chr1\t75349593\t75413593\r\n-chr1\t75413593\t75477593\r\n-chr1\t77371166\t77435166\r\n-chr1\t77480499\t77544499\r\n-chr1\t78114553\t78178553\r\n-chr1\t82603387\t82667387\r\n-chr1\t84801140\t84865140\r\n-chr1\t88807895\t88871895\r\n-chr1\t99596012\t99660012\r\n-chr1\t107880720\t107944720\r\n-chr1\t108229995\t108293995\r\n-chr1\t111850207\t111914207\r\n-chr1\t133368110\t133432110\r\n-chr1\t133798014\t133862014\r\n-chr1\t134191816\t134255816\r\n-chr1\t134443547\t134507547\r\n-chr1\t135090775\t135154775\r\n-chr1\t135590608\t135654608\r\n-chr1\t136621462\t136685462\r\n-chr1\t136924763\t136988763\r\n-chr1\t136988763\t137052763\r\n-chr1\t137229123\t137293123\r\n-chr1\t137689172\t137753172\r\n-chr1\t137771736\t137835736\r\n-chr1\t138803292\t138867292\r\n-chr1\t139778795\t139842795\r\n-chr1\t139995038\t140059038\r\n-chr1\t157022333\t157086333\r\n-chr1\t159052908\t159116908\r\n-chr1\t162345948\t162409948\r\n-chr1\t163888959\t163952959\r\n-chr1\t164146377\t164210377\r\n-chr1\t164593610\t164657610\r\n-chr1\t170078935\t170142935\r\n-chr1\t170185390\t170249390\r\n-chr1\t170249390\t170313390\r\n-chr1\t173284896\t173348896\r\n-chr1\t174231860\t174295860\r\n-chr1\t175209865\t175273865\r\n-chr1\t176812441\t176876441\r\n-chr1\t179114819\t179178819\r\n-chr1\t183090720\t183154720\r\n-chr1\t188499484\t188563484\r\n-chr1\t189459058\t189523058\r\n-chr1\t189774115\t189838115\r\n-chr1\t189838115\t189902115\r\n-chr1\t189902115\t189966115\r\n-chr1\t190477513\t190541513\r\n-chr1\t191934479\t191998479\r\n-chr1\t196512385\t196576385\r\n-chr10\t5474388\t5538388\r\n-chr10\t8440103\t8504103\r\n-chr10\t12363669\t12427669\r\n-chr10\t13778671\t13842671\r\n-chr10\t14108714\t14172714\r\n-chr10\t20382714\t20446714\r\n-chr10\t22896281\t22960281\r\n-chr10\t28142261\t28206261\r\n-chr10\t29331699\t29395699\r\n-chr10\t41896920\t41960920\r\n-chr10\t42699828\t42763828\r\n-chr10\t44063057\t44127057\r\n-chr10\t44127057\t44191057\r\n-chr10\t44393066\t44457066\r\n-chr10\t48942538\t49006538\r\n-chr10\t49490846\t49554846\r\n-chr10\t60233273\t60297273\r\n-chr10\t62294775\t62358775\r\n-chr10\t67544477\t67608477\r\n-chr10\t67608477\t67672477\r\n-chr10\t72718883\t72782883\r\n-chr10\t82994484\t83058484\r\n-chr10\t84328077\t84392077\r\n-chr10\t91514689\t91578689\r\n-chr10\t99772435\t99836435\r\n-chr10\t102459914\t102523914\r\n-chr10\t109462705\t109526705\r\n-chr10\t109595915\t109659915\r\n-chr10\t110902043\t110966043\r\n-chr10\t111748024\t111812024\r\n-chr10\t113960882\t114024882\r\n-chr10\t115695549\t115759549\r\n-chr10\t117239014\t117303014\r\n-chr10\t119851269\t119915269\r\n-chr10\t122527450\t122591450\r\n-chr10\t126452913\t126516913\r\n-chr10\t126866134\t126930134\r\n-chr10\t126985162\t127049162\r\n-chr10\t128302043\t128366043\r\n-chr11\t4600501\t4664501\r\n-chr11\t5031835\t5095835\r\n-chr11\t8334455\t8398455\r\n-chr11\t8428319\t8492319\r\n-chr11\t11551166\t11615166\r\n-chr11\t11615166\t11679166\r\n-chr11\t12267301\t12331301\r\n-chr11\t16683593\t16747593\r\n-chr11\t18764520\t18828520\r\n-chr11\t18877750\t18941750\r\n-chr11\t21882576\t21946576\r\n-chr11\t24000041\t24064041\r\n-chr11\t24178636\t24242636\r\n-chr11\t24750849\t24814849\r\n-chr11\t25545055\t25609055\r\n-chr11\t25743353\t25807353\r\n-chr11\t25960246\t26024246\r\n-chr11\t28338386\t28402386\r\n-chr11\t28555005\t28619005\r\n-chr11\t28755803\t28819803\r\n-chr11\t29629676\t29693676\r\n-chr11\t30033778\t30097778\r\n-chr11\t30689772\t30753772\r\n-chr11\t32102916\t32166916\r\n-chr11\t32554531\t32618531\r\n-chr11\t33072008\t33136008\r\n-chr11\t35342208\t35406208\r\n-chr11\t35813133\t35877133\r\n-chr11\t35877133\t35941133\r\n-chr11\t36051767\t36115767\r\n-chr11\t36150099'..b'\t26489570\r\n-chr7\t28256738\t28320738\r\n-chr7\t29324406\t29388406\r\n-chr7\t29698999\t29762999\r\n-chr7\t30073747\t30137747\r\n-chr7\t31328098\t31392098\r\n-chr7\t31499428\t31563428\r\n-chr7\t34995660\t35059660\r\n-chr7\t37457888\t37521888\r\n-chr7\t38461632\t38525632\r\n-chr7\t51452000\t51516000\r\n-chr7\t52568290\t52632290\r\n-chr7\t52655317\t52719317\r\n-chr7\t53011466\t53075466\r\n-chr7\t56520810\t56584810\r\n-chr7\t56651195\t56715195\r\n-chr7\t77074960\t77138960\r\n-chr7\t77444459\t77508459\r\n-chr7\t79324748\t79388748\r\n-chr7\t80606988\t80670988\r\n-chr7\t85424277\t85488277\r\n-chr7\t86637488\t86701488\r\n-chr7\t87490216\t87554216\r\n-chr7\t94386826\t94450826\r\n-chr7\t94966452\t95030452\r\n-chr7\t98517363\t98581363\r\n-chr7\t99452639\t99516639\r\n-chr7\t100918461\t100982461\r\n-chr7\t102669140\t102733140\r\n-chr7\t103352710\t103416710\r\n-chr7\t103998756\t104062756\r\n-chr7\t105194424\t105258424\r\n-chr7\t105739791\t105803791\r\n-chr7\t107553010\t107617010\r\n-chr7\t110033354\t110097354\r\n-chr7\t110938758\t111002758\r\n-chr7\t122669176\t122733176\r\n-chr7\t122814547\t122878547\r\n-chr7\t122927103\t122991103\r\n-chr7\t123215332\t123279332\r\n-chr7\t127388603\t127452603\r\n-chr7\t133986042\t134050042\r\n-chr7\t134639723\t134703723\r\n-chr7\t134976215\t135040215\r\n-chr7\t139936722\t140000722\r\n-chr7\t144371823\t144435823\r\n-chr7\t144435823\t144499823\r\n-chr7\t146716018\t146780018\r\n-chr7\t149138752\t149202752\r\n-chr7\t149635306\t149699306\r\n-chr7\t149715608\t149779608\r\n-chr8\t6559442\t6623442\r\n-chr8\t6623442\t6687442\r\n-chr8\t7293954\t7357954\r\n-chr8\t11241630\t11305630\r\n-chr8\t11333377\t11397377\r\n-chr8\t12797793\t12861793\r\n-chr8\t17140927\t17204927\r\n-chr8\t17453277\t17517277\r\n-chr8\t18682008\t18746008\r\n-chr8\t24201916\t24265916\r\n-chr8\t26679408\t26743408\r\n-chr8\t32970842\t33034842\r\n-chr8\t33171781\t33235781\r\n-chr8\t34892948\t34956948\r\n-chr8\t35865387\t35929387\r\n-chr8\t39257582\t39321582\r\n-chr8\t39450262\t39514262\r\n-chr8\t49642107\t49706107\r\n-chr8\t49856227\t49920227\r\n-chr8\t50183963\t50247963\r\n-chr8\t50620889\t50684889\r\n-chr8\t51733915\t51797915\r\n-chr8\t59779596\t59843596\r\n-chr8\t64029519\t64093519\r\n-chr8\t72435881\t72499881\r\n-chr8\t72967674\t73031674\r\n-chr8\t73979868\t74043868\r\n-chr8\t74065191\t74129191\r\n-chr8\t80836252\t80900252\r\n-chr8\t83285181\t83349181\r\n-chr8\t86680889\t86744889\r\n-chr8\t87177477\t87241477\r\n-chr8\t87241477\t87305477\r\n-chr8\t87477935\t87541935\r\n-chr8\t90388211\t90452211\r\n-chr8\t90760313\t90824313\r\n-chr8\t92030994\t92094994\r\n-chr8\t93443787\t93507787\r\n-chr8\t96789585\t96853585\r\n-chr8\t97043262\t97107262\r\n-chr8\t97477230\t97541230\r\n-chr8\t111089991\t111153991\r\n-chr8\t111270619\t111334619\r\n-chr8\t111334619\t111398619\r\n-chr8\t111398619\t111462619\r\n-chr8\t117237918\t117301918\r\n-chr8\t125868555\t125932555\r\n-chr8\t126054477\t126118477\r\n-chr8\t127381524\t127445524\r\n-chr9\t7916325\t7980325\r\n-chr9\t10034653\t10098653\r\n-chr9\t21205558\t21269558\r\n-chr9\t27102323\t27166323\r\n-chr9\t28793755\t28857755\r\n-chr9\t28975979\t29039979\r\n-chr9\t29182458\t29246458\r\n-chr9\t29431925\t29495925\r\n-chr9\t30706012\t30770012\r\n-chr9\t32468538\t32532538\r\n-chr9\t36694615\t36758615\r\n-chr9\t36758615\t36822615\r\n-chr9\t41371667\t41435667\r\n-chr9\t42383364\t42447364\r\n-chr9\t43535422\t43599422\r\n-chr9\t44030826\t44094826\r\n-chr9\t44257286\t44321286\r\n-chr9\t44893563\t44957563\r\n-chr9\t45496156\t45560156\r\n-chr9\t45700064\t45764064\r\n-chr9\t47438414\t47502414\r\n-chr9\t47502414\t47566414\r\n-chr9\t47566414\t47630414\r\n-chr9\t47630414\t47694414\r\n-chr9\t48557242\t48621242\r\n-chr9\t56295240\t56359240\r\n-chr9\t56707178\t56771178\r\n-chr9\t57431374\t57495374\r\n-chr9\t59569429\t59633429\r\n-chr9\t62718979\t62782979\r\n-chr9\t63147522\t63211522\r\n-chr9\t63788832\t63852832\r\n-chr9\t69050403\t69114403\r\n-chr9\t69176049\t69240049\r\n-chr9\t69240049\t69304049\r\n-chr9\t71796844\t71860844\r\n-chr9\t74791622\t74855622\r\n-chr9\t79491629\t79555629\r\n-chr9\t79932960\t79996960\r\n-chr9\t84626957\t84690957\r\n-chr9\t96193779\t96257779\r\n-chr9\t107312141\t107376141\r\n-chr9\t107376141\t107440141\r\n-chr9\t107462650\t107526650\r\n-chr9\t107526650\t107590650\r\n-chr9\t107590650\t107654650\r\n-chr9\t107848560\t107912560\r\n-chr9\t107941738\t108005738\r\n-chr9\t108683437\t108747437\r\n-chr9\t108962296\t109026296\r\n-chr9\t109947901\t110011901\r\n-chr9\t110485254\t110549254\r\n-chr9\t110616374\t110680374\r\n-chr9\t111968818\t112032818\r\n-chr9\t113836504\t113900504\r\n-chr9\t118910538\t118974538\r\n-chr9\t121627136\t121691136\r\n' |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/DESCRIPTION.txt --- a/iwtomics/ETn_example/DESCRIPTION.txt Wed May 31 11:06:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,21 +0,0 @@ -This example contains two region datasets "ETn fixed", "Control" and one feature "Recombination hotspots content". -In particular, the region dataset "ETn fixed" contains 1296 genomic regions of 64 kb surrounding -fixed ETns elements (32-kb flanking sequences upstream and 32-kb flanking sequences downstream -of each element). The region dataset "Control" contains 1142 regions of 64 kb without elements, -used as control in the test. The regions are aligned around their center (i.e. around the ETn integration -sites). -Recombination hotspots measurements are associated to each "ETn fixed" and "Control" region. In -particular, this feature is measured in 1-kb windows, so that each region is associated to a recombination -hotspots curve made of 64 values. The measurement used is the feature content, i.e. the -fraction of the 1-kb window that is covered by recombination hotspots - -Data have been collected and pre-processed by: R Campos-Sanchez, MA Cremona, A Pini, F -Chiaromonte and KD Makova (2016). Integration and fixation preferences of human and mouse -endogenous retroviruses uncovered with Functional Data Analysis. PLoS Computational Biology. -12(6): 1-41. -Fixed ETn positions come from: Y Zhang, IA Maksakova, L Gagnier, LN van de Lagemaat, DL -Mager (2008). Genome-wide assessments reveal extremely high levels of polymorphism of two -active families of mouse endogenous retroviral elements. PLoS Genetics. 4: e1000007. -Recombination hotspots data come from: H Brunschwig, L Levi, E Ben-David, RW Williams, -B Yakir, S Shifman (2012). Fine-scale maps of recombination rates and hotspots in the mouse -genome. Genetics. 191: 757-764. \ No newline at end of file |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/ETn_fixed.bed --- a/iwtomics/ETn_example/ETn_fixed.bed Wed May 31 11:06:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1296 +0,0 @@\n-chr1\t3079711\t3144047\r\n-chr1\t3232230\t3302517\r\n-chr1\t3756792\t3826331\r\n-chr1\t4589320\t4653381\r\n-chr1\t5155380\t5219717\r\n-chr1\t5634836\t5704314\r\n-chr1\t5967107\t6035506\r\n-chr1\t6240632\t6304964\r\n-chr1\t7186756\t7250816\r\n-chr1\t7434671\t7504179\r\n-chr1\t7573651\t7643108\r\n-chr1\t7879930\t7944250\r\n-chr1\t7962100\t8026423\r\n-chr1\t8219414\t8283736\r\n-chr1\t9451579\t9515898\r\n-chr1\t10561964\t10626025\r\n-chr1\t10774950\t10844464\r\n-chr1\t11301539\t11365867\r\n-chr1\t11479858\t11543919\r\n-chr1\t11577435\t11646975\r\n-chr1\t11734130\t11798451\r\n-chr1\t12053425\t12117744\r\n-chr1\t12503733\t12568058\r\n-chr1\t12690915\t12755253\r\n-chr1\t13015768\t13080108\r\n-chr1\t13772979\t13840932\r\n-chr1\t14114086\t14178424\r\n-chr1\t15752556\t15816879\r\n-chr1\t15820454\t15889959\r\n-chr1\t16894874\t16964379\r\n-chr1\t17180480\t17250022\r\n-chr1\t17380662\t17444982\r\n-chr1\t17626574\t17695823\r\n-chr1\t18015049\t18079373\r\n-chr1\t18110573\t18174911\r\n-chr1\t19594734\t19659060\r\n-chr1\t22621502\t22685838\r\n-chr1\t26730921\t26795251\r\n-chr1\t29078615\t29142676\r\n-chr1\t29866491\t29930812\r\n-chr1\t31420204\t31484524\r\n-chr1\t32231731\t32295791\r\n-chr1\t32727048\t32791370\r\n-chr1\t41487659\t41551982\r\n-chr1\t42815700\t42880037\r\n-chr1\t44434350\t44498689\r\n-chr1\t44845641\t44915177\r\n-chr1\t45573195\t45637531\r\n-chr1\t46279947\t46344008\r\n-chr1\t47955005\t48019067\r\n-chr1\t48676207\t48745586\r\n-chr1\t50407114\t50471433\r\n-chr1\t50984256\t51048575\r\n-chr1\t52848138\t52912460\r\n-chr1\t54026202\t54090537\r\n-chr1\t55139377\t55203714\r\n-chr1\t55512376\t55576700\r\n-chr1\t60811167\t60880658\r\n-chr1\t63144392\t63208714\r\n-chr1\t64592575\t64656909\r\n-chr1\t72263031\t72327365\r\n-chr1\t79947964\t80012025\r\n-chr1\t81586166\t81651033\r\n-chr1\t83518554\t83582860\r\n-chr1\t84323690\t84388012\r\n-chr1\t87733248\t87797584\r\n-chr1\t89977562\t90048134\r\n-chr1\t90192976\t90257294\r\n-chr1\t90436757\t90502304\r\n-chr1\t90510088\t90574150\r\n-chr1\t90961340\t91030890\r\n-chr1\t92995129\t93064618\r\n-chr1\t93572264\t93636325\r\n-chr1\t94416743\t94481065\r\n-chr1\t95060527\t95124845\r\n-chr1\t96949505\t96993507\r\n-chr1\t97366290\t97430612\r\n-chr1\t102719163\t102788368\r\n-chr1\t104425831\t104490167\r\n-chr1\t105882265\t105946599\r\n-chr1\t106700349\t106764668\r\n-chr1\t107613589\t107658283\r\n-chr1\t110331901\t110395962\r\n-chr1\t113555818\t113625304\r\n-chr1\t116479611\t116543952\r\n-chr1\t117758939\t117823245\r\n-chr1\t118797225\t118861285\r\n-chr1\t119448312\t119513632\r\n-chr1\t130131484\t130195807\r\n-chr1\t132524644\t132588705\r\n-chr1\t133914689\t133978749\r\n-chr1\t136189933\t136254255\r\n-chr1\t136264653\t136334169\r\n-chr1\t137560931\t137625172\r\n-chr1\t138547079\t138611420\r\n-chr1\t148809740\t148874076\r\n-chr1\t149526081\t149590400\r\n-chr1\t149779804\t149844124\r\n-chr1\t152002017\t152072787\r\n-chr1\t155315120\t155379180\r\n-chr1\t157797999\t157862060\r\n-chr1\t158420549\t158462707\r\n-chr1\t158558741\t158623071\r\n-chr1\t158968494\t159020907\r\n-chr1\t159209626\t159273963\r\n-chr1\t162568763\t162633083\r\n-chr1\t170782957\t170847279\r\n-chr1\t172986676\t173051019\r\n-chr1\t173604289\t173668350\r\n-chr1\t173755290\t173826531\r\n-chr1\t175769001\t175833062\r\n-chr1\t176192515\t176256575\r\n-chr1\t181259082\t181323410\r\n-chr1\t182877909\t182941970\r\n-chr1\t184086729\t184151058\r\n-chr1\t190963403\t191027739\r\n-chr1\t192273069\t192337405\r\n-chr1\t192934140\t193005671\r\n-chr1\t193482144\t193546480\r\n-chr10\t3483501\t3547823\r\n-chr10\t3764574\t3828896\r\n-chr10\t3896445\t3960782\r\n-chr10\t4645211\t4715786\r\n-chr10\t5823172\t5887495\r\n-chr10\t6106324\t6174735\r\n-chr10\t7027092\t7091153\r\n-chr10\t8240862\t8305184\r\n-chr10\t9957136\t10021197\r\n-chr10\t15048108\t15112427\r\n-chr10\t15415278\t15479614\r\n-chr10\t15571677\t15635737\r\n-chr10\t19067681\t19132834\r\n-chr10\t21403691\t21468012\r\n-chr10\t21586731\t21658171\r\n-chr10\t21777337\t21847793\r\n-chr10\t22151893\t22221544\r\n-chr10\t22231987\t22296326\r\n-chr10\t23527637\t23591698\r\n-chr10\t23660941\t23725262\r\n-chr10\t24013752\t24083250\r\n-chr10\t24542321\t24615855\r\n-chr10\t24874169\t24938504\r\n-chr10\t25655630\t25719690\r\n-chr10\t29562905\t29627226\r\n-chr10\t29983928\t30053429\r\n-chr10\t30588835\t30659532\r\n-chr10\t34498420\t34562741\r\n-chr10\t34849331\t34913659\r\n-chr10\t35457973\t35527259\r\n-chr10\t35892594\t35956922\r\n-chr10\t38034814\t38099148\r\n-chr10\t38708953\t38773275\r\n-chr10\t40009616\t40077579\r\n-chr10\t40328773\t40393112\r\n-chr10\t41463272\t41527605\r\n-chr10\t41754734\t41819056\r\n-chr10'..b'r7\t64864701\t64929024\r\n-chr7\t86339549\t86403885\r\n-chr7\t88089874\t88153935\r\n-chr7\t88897810\t88961870\r\n-chr7\t91330534\t91394875\r\n-chr7\t92274579\t92338897\r\n-chr7\t92799296\t92871052\r\n-chr7\t96367166\t96431487\r\n-chr7\t97101263\t97165323\r\n-chr7\t97284514\t97348575\r\n-chr7\t97529768\t97599280\r\n-chr7\t97851869\t97916192\r\n-chr7\t100396759\t100461081\r\n-chr7\t102369758\t102433820\r\n-chr7\t110115837\t110185134\r\n-chr7\t110593609\t110657942\r\n-chr7\t111828298\t111892634\r\n-chr7\t113312731\t113382215\r\n-chr7\t113768856\t113840290\r\n-chr7\t115660728\t115732171\r\n-chr7\t117629868\t117694188\r\n-chr7\t120157418\t120221754\r\n-chr7\t121024547\t121088906\r\n-chr7\t125426839\t125490900\r\n-chr7\t127489003\t127553340\r\n-chr7\t130507539\t130571878\r\n-chr7\t134261471\t134325806\r\n-chr7\t138933955\t138998277\r\n-chr7\t139084737\t139149053\r\n-chr7\t140067401\t140131723\r\n-chr7\t140688526\t140759900\r\n-chr7\t143399593\t143469131\r\n-chr7\t145614147\t145678208\r\n-chr7\t147730581\t147794642\r\n-chr7\t149421578\t149485895\r\n-chr8\t3801027\t3865347\r\n-chr8\t4803179\t4867504\r\n-chr8\t7824324\t7888646\r\n-chr8\t15722072\t15793287\r\n-chr8\t18251757\t18315818\r\n-chr8\t18465381\t18529442\r\n-chr8\t19045164\t19112378\r\n-chr8\t22096250\t22137512\r\n-chr8\t24678842\t24743165\r\n-chr8\t25794478\t25858799\r\n-chr8\t26014127\t26078462\r\n-chr8\t26468922\t26533260\r\n-chr8\t28479149\t28543469\r\n-chr8\t30097851\t30161911\r\n-chr8\t30460129\t30524450\r\n-chr8\t30752787\t30817107\r\n-chr8\t31563440\t31627777\r\n-chr8\t36022443\t36086504\r\n-chr8\t36959548\t37023870\r\n-chr8\t39028207\t39092267\r\n-chr8\t41087234\t41151556\r\n-chr8\t41620051\t41689555\r\n-chr8\t42004143\t42068203\r\n-chr8\t43019118\t43083438\r\n-chr8\t47722042\t47786380\r\n-chr8\t59252906\t59322400\r\n-chr8\t60789544\t60853875\r\n-chr8\t61197366\t61261703\r\n-chr8\t61532874\t61596935\r\n-chr8\t63294270\t63358605\r\n-chr8\t64185293\t64253284\r\n-chr8\t64763207\t64827530\r\n-chr8\t67113241\t67177577\r\n-chr8\t69123511\t69187572\r\n-chr8\t70169472\t70233795\r\n-chr8\t72177196\t72241533\r\n-chr8\t75436025\t75500364\r\n-chr8\t76584577\t76648638\r\n-chr8\t77497140\t77561453\r\n-chr8\t77747147\t77811482\r\n-chr8\t79352165\t79416481\r\n-chr8\t80631654\t80703131\r\n-chr8\t83678886\t83743222\r\n-chr8\t87650996\t87722809\r\n-chr8\t88349042\t88413368\r\n-chr8\t94809868\t94874201\r\n-chr8\t95383980\t95448041\r\n-chr8\t102794796\t102859131\r\n-chr8\t103935008\t103999308\r\n-chr8\t109626938\t109691000\r\n-chr8\t109709405\t109773728\r\n-chr8\t116384465\t116448815\r\n-chr8\t120505951\t120570011\r\n-chr8\t121428979\t121493588\r\n-chr8\t125683558\t125747880\r\n-chr8\t128575325\t128644983\r\n-chr9\t4047472\t4116542\r\n-chr9\t4806803\t4870864\r\n-chr9\t4884580\t4954084\r\n-chr9\t6022806\t6092325\r\n-chr9\t6275883\t6339944\r\n-chr9\t7392890\t7457209\r\n-chr9\t7462474\t7526795\r\n-chr9\t7766967\t7837187\r\n-chr9\t8271124\t8335185\r\n-chr9\t8402204\t8466265\r\n-chr9\t8764452\t8828512\r\n-chr9\t11784168\t11855632\r\n-chr9\t12170129\t12234190\r\n-chr9\t12237687\t12309084\r\n-chr9\t12318611\t12382934\r\n-chr9\t12721775\t12785836\r\n-chr9\t13835575\t13899894\r\n-chr9\t15182924\t15247260\r\n-chr9\t17955775\t18020096\r\n-chr9\t18827860\t18898433\r\n-chr9\t24340641\t24404702\r\n-chr9\t24593904\t24658240\r\n-chr9\t27266534\t27330872\r\n-chr9\t30430874\t30495213\r\n-chr9\t35587912\t35657485\r\n-chr9\t35863647\t35935120\r\n-chr9\t37845538\t37909860\r\n-chr9\t38185239\t38249385\r\n-chr9\t38896815\t38961150\r\n-chr9\t41662492\t41726552\r\n-chr9\t43638042\t43702378\r\n-chr9\t45006098\t45070433\r\n-chr9\t47047851\t47112173\r\n-chr9\t49906212\t49970548\r\n-chr9\t50402386\t50472116\r\n-chr9\t52696613\t52760674\r\n-chr9\t53981007\t54045329\r\n-chr9\t55048978\t55113313\r\n-chr9\t55639453\t55703790\r\n-chr9\t57139057\t57203396\r\n-chr9\t58372958\t58437282\r\n-chr9\t59751834\t59816157\r\n-chr9\t59828617\t59892938\r\n-chr9\t67460563\t67524885\r\n-chr9\t69791346\t69855407\r\n-chr9\t72084500\t72148804\r\n-chr9\t73306304\t73370365\r\n-chr9\t75546159\t75615764\r\n-chr9\t76067163\t76131499\r\n-chr9\t78205560\t78269895\r\n-chr9\t79863716\t79932960\r\n-chr9\t83543186\t83607520\r\n-chr9\t83961391\t84025712\r\n-chr9\t84745537\t84816469\r\n-chr9\t87287487\t87351823\r\n-chr9\t88965683\t89029744\r\n-chr9\t89914557\t89978617\r\n-chr9\t95389913\t95454249\r\n-chr9\t98540578\t98604900\r\n-chr9\t104333243\t104397304\r\n-chr9\t105712170\t105776231\r\n-chr9\t105976408\t106040743\r\n-chr9\t108139205\t108203544\r\n-chr9\t111904500\t111968818\r\n-chr9\t113768402\t113832464\r\n-chr9\t120794546\t120858880\r\n-chr9\t122321963\t122386298\r\n' |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/Recombination_hotspots.txt --- a/iwtomics/ETn_example/Recombination_hotspots.txt Wed May 31 11:06:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2438 +0,0 @@\n-chr1\t3079711\t3144047\t1\t1\t1\t1\t0.606\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.394\t1\t0.606\t0\t0\t0\t0\t0\t0\t0.73\t1\t0.27\t0.73\t1\t1\t1\t1\t1\t1\t1\t1\t0.27\t0\t0\t0\t0\t0\t0\t0\t0.73\t1\t1\t1\t1\t1\t1\r\n-chr1\t3232230\t3302517\t1\t1\t1\t0.211\t0\t0\t0\t0\t0\t0.789\t1\t1\t1\t0.211\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.789\t1\t1\t1\t1\t1\t1\t0.924\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t3756792\t3826331\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.11\t1\t1\t1\t1\t1\t0.89\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0.351\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t4589320\t4653381\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.06\t1\t1\t1\t1\t1\t1\t1\t0.94\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.121\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\r\n-chr1\t5155380\t5219717\t1\t0.061\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.939\t1\t1\t1\t1\t1\t1\t1\t0.724\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.276\t1\t1\t1\t1\t1\t1\t1\t1\t0.724\t0\r\n-chr1\t5634836\t5704314\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.873\t1\t1\t1\t0.127\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t5967107\t6035506\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.666\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t6240632\t6304964\t0.191\t1\t1\t1\t0.809\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t7186756\t7250816\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.375\t1\t0.625\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t7434671\t7504179\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t7573651\t7643108\t1\t1\t1\t1\t0.79\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.21\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.79\t0\t0\t0\t0\t0\t0\t0\t0\t0.667\t1\t1\t1\t0.333\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.667\t1\r\n-chr1\t7879930\t7944250\t0.191\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.809\t0\t0\t0\t0.191\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.489\t0\t0\r\n-chr1\t7962100\t8026423\t0.018\t1\t1\t0.982\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.018\t1\t1\t1\t1\t1\t1\t1\t0.659\t0\t0\t0\t0\t0\t0\t0\t0\t0.341\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.659\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t8219414\t8283736\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.295\t0.705\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\r\n-chr1\t9451579\t9515898\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.543\t1\t1\t1\t1\t0.457\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t10561964\t10626025\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.584\t1\t1\t0.416\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t10774950\t10844464\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t11301539\t11365867\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t11479858\t11543919\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t11577435\t11646975\t1\t0.534\t0\t0\t0.466\t1\t1\t0.534\t0.466\t1\t1\t1\t0.534\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.466\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.994\t0.006\t1\t1\t0.994\t0\t0.006\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.994\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t11734130\t11798451\t0\t0\t0\t0.99\t1\t1\t1\t1\t1\t1\t1\t1\t0.01\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.99\t1\t1\t1\t1\t1\t0.689\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.311\t1\t1\t1\t1\t1\r\n-chr1\t12053425\t12117744\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t12503733\t12568058\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t12690915\t12755253\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.188\t1\t1\t0.812\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.526\t1\t1\t1\t1\t1\t0.474\t0\t0\t0\t0.526\t1\t1\t0.474\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr1\t13015768\t13080108\t1\t0.667\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.3'..b'1\t0.233\t0\t0\t0\t0\t0\t0\t0.767\t1\t1\t0.233\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.767\t1\t1\t0.233\t0\t0\t0\t0\t0.767\t1\t1\t1\t1\t0.233\t0\t0\t0\t0\r\n-chr9\t69240049\t69304049\t0\t0\t0\t0\t0\t0.767\t1\t1\t1\t1\t0.233\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.767\t1\t0.233\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr9\t71796844\t71860844\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.562\t1\t1\t0.438\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.562\t1\t1\t1\r\n-chr9\t74791622\t74855622\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.34\t1\t1\t0.66\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr9\t79491629\t79555629\t0\t0\t0\t0\t0\t0.347\t1\t1\t1\t1\t1\t0.653\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.347\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\r\n-chr9\t79932960\t79996960\t0.322\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.678\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.322\t0\t0\t0\t0\t0\t0\t0.678\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\r\n-chr9\t84626957\t84690957\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.675\t1\t1\t0.325\t0\t0\t0\t0\r\n-chr9\t96193779\t96257779\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.949\t1\t1\t0.051\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.949\t1\t1\t0.051\t0\t0\t0\t0\t0\r\n-chr9\t107312141\t107376141\t1\t1\t0.689\t0.311\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.689\t0\t0\t0\t0\t0\t0\t0.311\t1\t1\t1\t1\t0.689\t0\t0\t0\t0.311\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\r\n-chr9\t107376141\t107440141\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.689\t0\t0\t0\t0\t0\t0\t0\t0\t0.311\t1\t1\t0.689\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.311\t1\t1\t1\t1\t1\t1\t1\t1\r\n-chr9\t107462650\t107526650\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.82\t1\t1\t1\t1\t0.18\t0\t0\t0\t0\t0\t0\t0\t0.82\t1\t1\t1\t1\t1\t0.18\t0.82\t1\t0.18\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.82\t1\t1\t0.18\t0\t0.82\t1\t1\t0.18\r\n-chr9\t107526650\t107590650\t0\t0\t0.82\t1\t1\t1\t1\t1\t1\t0.18\t0\t0.82\t1\t1\t1\t1\t1\t1\t0.18\t0\t0.82\t1\t1\t1\t1\t0.18\t0\t0\t0\t0.82\t1\t1\t0.18\t0\t0.82\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.18\t0\t0.82\t1\t0.18\t0\t0\t0\t0\t0\t0.82\t1\t1\r\n-chr9\t107590650\t107654650\t0.18\t0.82\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.18\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.82\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.18\t0\t0\t0\t0\t0\t0.82\t1\t1\t1\t0.18\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.82\r\n-chr9\t107848560\t107912560\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.73\t1\t0.27\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr9\t107941738\t108005738\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.908\t1\t0.092\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr9\t108683437\t108747437\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr9\t108962296\t109026296\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.466\t1\t1\t1\t0.534\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr9\t109947901\t110011901\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr9\t110485254\t110549254\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr9\t110616374\t110680374\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.544\t1\t1\t1\t1\t1\t1\t1\t1\t1\t0.456\t0.544\t1\t1\t1\t1\t1\t1\t0.456\t0.544\t1\t1\t0.456\t0.544\t1\t1\t1\r\n-chr9\t111968818\t112032818\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr9\t113836504\t113900504\t0\t0\t0.457\t1\t1\t1\t1\t0.543\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.457\t1\t1\t1\t1\t1\t1\t1\t1\t0.543\t0\t0\t0\t0\t0.457\t1\t1\t1\t1\r\n-chr9\t118910538\t118974538\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.491\t1\t1\t1\t1\t1\t1\t1\t1\t0.509\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n-chr9\t121627136\t121691136\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n' |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/features.header --- a/iwtomics/ETn_example/features.header Wed May 31 11:06:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -Recombination_hotspots.txt Recomb_hot Recombination hotspots \ No newline at end of file |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/regions.header --- a/iwtomics/ETn_example/regions.header Wed May 31 11:06:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Control.bed Control Control -ETn_fixed.bed ETn_fixed ETn fixed \ No newline at end of file |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/._.DS_Store |
| b |
| Binary file iwtomics/example/._.DS_Store has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/._Controls_regions.bed |
| b |
| Binary file iwtomics/example/._Controls_regions.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/._DESCRIPTION.txt |
| b |
| Binary file iwtomics/example/._DESCRIPTION.txt has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/._Elements1_regions.bed |
| b |
| Binary file iwtomics/example/._Elements1_regions.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/._Elements2_regions.bed |
| b |
| Binary file iwtomics/example/._Elements2_regions.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/._Elements3_regions.bed |
| b |
| Binary file iwtomics/example/._Elements3_regions.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/._Feature1.bed |
| b |
| Binary file iwtomics/example/._Feature1.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/._Feature2.bed |
| b |
| Binary file iwtomics/example/._Feature2.bed has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/._features.header.bed.txt |
| b |
| Binary file iwtomics/example/._features.header.bed.txt has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/._regions.header.txt |
| b |
| Binary file iwtomics/example/._regions.header.txt has changed |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/Controls_regions.bed --- a/iwtomics/example/Controls_regions.bed Wed May 31 11:06:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,35 +0,0 @@ -chr1 91399892 91499892 -chr1 116447079 116547079 -chr2 231381109 231481109 -chr3 47386633 47486633 -chr3 99195712 99295712 -chr3 116765114 116865114 -chr3 134345017 134445017 -chr4 68064019 68164019 -chr4 137465811 137565811 -chr4 173293016 173393016 -chr5 59044110 59144110 -chr5 94592763 94692763 -chr5 108436006 108536006 -chr5 110836898 110936898 -chr5 146661073 146761073 -chr6 99727306 99827306 -chr7 88291325 88391325 -chr7 120999784 121099784 -chr8 126860366 126960366 -chr8 127636547 127736547 -chr11 41362564 41462564 -chr11 101741527 101841527 -chr12 15210277 15310277 -chr13 91106037 91206037 -chr13 91518822 91618822 -chr13 98959030 99059030 -chr15 39087176 39187176 -chr17 58542142 58642142 -chr18 12199823 12299823 -chr20 8173704 8273704 -chr21 16255112 16355112 -chr21 45089115 45189115 -chrX 23898983 23998983 -chrX 37029585 37129585 -chrX 103593349 103693349 |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/DESCRIPTION.txt --- a/iwtomics/example/DESCRIPTION.txt Wed May 31 11:06:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -This example contains simulated measurements of two different genomic features, "ftr1" and "ftr2", -corresponding to four different region datasets: "elem1", "elem2", "elem3" and "control". |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/Elements1_regions.bed --- a/iwtomics/example/Elements1_regions.bed Wed May 31 11:06:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,25 +0,0 @@ -chr2 49960150 50060150 -chr2 55912445 56012445 -chr3 140326750 140426750 -chr4 41772201 41872201 -chr4 70629719 70729719 -chr4 109340735 109440735 -chr5 15025389 15125389 -chr5 43028888 43128888 -chr5 58231354 58331354 -chr5 91277761 91377761 -chr5 119464508 119564508 -chr6 85309170 85409170 -chr6 85762072 85862072 -chr6 134621363 134721363 -chr6 147470164 147570164 -chr7 77195798 77295798 -chr7 77880914 77980914 -chr7 114805399 114905399 -chr10 46350885 46450885 -chr10 67833078 67933078 -chr12 27722692 27822692 -chr12 95518506 95618506 -chr12 117863466 117963466 -chr14 100464166 100564166 -chrX 29266748 29366748 |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/Elements2_regions.bed --- a/iwtomics/example/Elements2_regions.bed Wed May 31 11:06:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,20 +0,0 @@ -chr1 65942901 66042901 -chr1 117128102 117228102 -chr1 190338169 190438169 -chr2 227365478 227465478 -chr6 50856764 50956764 -chr6 135703067 135803067 -chr7 38228726 38328726 -chr7 51115898 51215898 -chr7 150325760 150425760 -chr8 25475691 25575691 -chr9 73374609 73474609 -chr11 55092625 55192625 -chr11 86581661 86681661 -chr12 12795284 12895284 -chr12 48151882 48251882 -chr12 83109951 83209951 -chr15 31430278 31530278 -chr15 65610815 65710815 -chr17 40766223 40866223 -chr20 17245048 17345048 |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/Elements3_regions.bed --- a/iwtomics/example/Elements3_regions.bed Wed May 31 11:06:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,28 +0,0 @@ -chr1 49721616 49821616 -chr1 95059425 95159425 -chr1 207236313 207336313 -chr2 73790843 73890843 -chr3 134465321 134565321 -chr4 43433669 43533669 -chr4 122032777 122132777 -chr5 12701747 12801747 -chr5 58501529 58601529 -chr5 152853250 152953250 -chr6 136085023 136185023 -chr6 147019529 147119529 -chr7 14192964 14292964 -chr7 125519883 125619883 -chr8 77652872 77752872 -chr8 108375665 108475665 -chr9 2984971 3084971 -chr10 978822 1078822 -chr11 18395046 18495046 -chr12 47273592 47373592 -chr12 60095778 60195778 -chr12 84854096 84954096 -chr12 95157539 95257539 -chr14 23982000 24082000 -chr16 1875335 1975335 -chr16 66789863 66889863 -chr18 64644131 64744131 -chr21 15966609 16066609 |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/Feature1.bed --- a/iwtomics/example/Feature1.bed Wed May 31 11:06:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5400 +0,0 @@\n-chr1\t91399892\t91401892\t0.914729028492568\n-chr1\t91401892\t91403892\t1.03788669317729\n-chr1\t91403892\t91405892\t1.15695078809331\n-chr1\t91405892\t91407892\t1.05433971377051\n-chr1\t91407892\t91409892\t1.05827244724317\n-chr1\t91409892\t91411892\t1.00216117481117\n-chr1\t91411892\t91413892\t0.873489001753337\n-chr1\t91413892\t91415892\t0.873100412116323\n-chr1\t91415892\t91417892\t0.928712683217515\n-chr1\t91417892\t91419892\t0.94132562114723\n-chr1\t91419892\t91421892\t1.06739894033636\n-chr1\t91421892\t91423892\t0.909275169317382\n-chr1\t91423892\t91425892\t1.10093887463398\n-chr1\t91425892\t91427892\t1.05342912580018\n-chr1\t91427892\t91429892\t0.970074712768588\n-chr1\t91429892\t91431892\t0.742552329847752\n-chr1\t91431892\t91433892\t1.09649292566553\n-chr1\t91433892\t91435892\t0.902578291528885\n-chr1\t91435892\t91437892\t0.821718064516058\n-chr1\t91437892\t91439892\t0.909063175846949\n-chr1\t91439892\t91441892\t1.12598647717153\n-chr1\t91441892\t91443892\t0.962991989888592\n-chr1\t91443892\t91445892\t0.886361985680751\n-chr1\t91445892\t91447892\t1.19735794895968\n-chr1\t91447892\t91449892\t1.1058589065373\n-chr1\t91449892\t91451892\t1.11830938343819\n-chr1\t91451892\t91453892\t0.891849450289035\n-chr1\t91453892\t91455892\t0.921613352575372\n-chr1\t91455892\t91457892\t0.961394603438276\n-chr1\t91457892\t91459892\t0.942120540462845\n-chr1\t91459892\t91461892\t1.04179227745858\n-chr1\t91461892\t91463892\t0.846036296260439\n-chr1\t91463892\t91465892\t0.903782108017989\n-chr1\t91465892\t91467892\t0.926324469715607\n-chr1\t91467892\t91469892\t1.01617788108211\n-chr1\t91469892\t91471892\t1.01871994841433\n-chr1\t91471892\t91473892\t0.86346600407464\n-chr1\t91473892\t91475892\t0.911534382002842\n-chr1\t91475892\t91477892\t0.909397860657818\n-chr1\t91477892\t91479892\t0.882437981483481\n-chr1\t91479892\t91481892\t1.20022730271379\n-chr1\t91481892\t91483892\t1.02286707465404\n-chr1\t91483892\t91485892\t1.00824959158441\n-chr1\t91485892\t91487892\t1.13387236604912\n-chr1\t91487892\t91489892\t0.917808428397605\n-chr1\t91489892\t91491892\t1.00980153326694\n-chr1\t91491892\t91493892\t1.0780078042687\n-chr1\t91493892\t91495892\t1.05789211157318\n-chr1\t91495892\t91497892\t0.983519376160091\n-chr1\t91497892\t91499892\t1.06301499098899\n-chr1\t116447079\t116449079\t0.909510507890661\n-chr1\t116449079\t116451079\t1.04923486926106\n-chr1\t116451079\t116453079\t0.972429435962863\n-chr1\t116453079\t116455079\t0.94348509718749\n-chr1\t116455079\t116457079\t0.877213727110183\n-chr1\t116457079\t116459079\t1.07609955711144\n-chr1\t116459079\t116461079\t1.05964706503259\n-chr1\t116461079\t116463079\t1.08048074104999\n-chr1\t116463079\t116465079\t1.10397643608295\n-chr1\t116465079\t116467079\t0.879172377236955\n-chr1\t116467079\t116469079\t0.952455624542298\n-chr1\t116469079\t116471079\t0.872450868701435\n-chr1\t116471079\t116473079\t0.734632500870684\n-chr1\t116473079\t116475079\t0.975852194327443\n-chr1\t116475079\t116477079\t1.15968481779916\n-chr1\t116477079\t116479079\t1.03479249038231\n-chr1\t116479079\t116481079\t0.958716780567544\n-chr1\t116481079\t116483079\t1.00882150410174\n-chr1\t116483079\t116485079\t0.894048456447358\n-chr1\t116485079\t116487079\t0.862250242465922\n-chr1\t116487079\t116489079\t1.08563273479841\n-chr1\t116489079\t116491079\t1.03570610668607\n-chr1\t116491079\t116493079\t1.282637134762\n-chr1\t116493079\t116495079\t1.05344881721884\n-chr1\t116495079\t116497079\t0.958843714832433\n-chr1\t116497079\t116499079\t0.907730747212707\n-chr1\t116499079\t116501079\t0.964823764805327\n-chr1\t116501079\t116503079\t0.972508803669119\n-chr1\t116503079\t116505079\t0.964761127498888\n-chr1\t116505079\t116507079\t1.21022463445566\n-chr1\t116507079\t116509079\t0.870817357520223\n-chr1\t116509079\t116511079\t0.970216007864307\n-chr1\t116511079\t116513079\t1.09860269791989\n-chr1\t116513079\t116515079\t1.01985884672516\n-chr1\t116515079\t116517079\t1.04151199469522\n-chr1\t116517079\t116519079\t1.10542491108645\n-chr1\t116519079\t116521079\t1.06697958402493\n-chr1\t116521079\t116523079\t0.972137682316022\n-chr1\t116523079\t116525079\t0.900068042346903\n-chr1\t116525079\t116527079\t1.00945179072767\n-chr1\t116527079\t116529079\t0.910760202377398\n-chr1\t116529079\t116531079\t0.960315923931081\n-chr1\t116531079\t116533079\t1.05558603806716\n-chr1\t116533079\t116535079\t0.92038544115'..b'1\t64656131\t0.97369678388939\n-chr18\t64656131\t64658131\t0.910087798040937\n-chr18\t64658131\t64660131\t0.946468289624316\n-chr18\t64660131\t64662131\t1.05842665628809\n-chr18\t64662131\t64664131\t0.927667349376235\n-chr18\t64664131\t64666131\t1.18742333150313\n-chr18\t64666131\t64668131\t1.22205250380213\n-chr18\t64668131\t64670131\t0.880563425486305\n-chr18\t64670131\t64672131\t0.914485239144026\n-chr18\t64672131\t64674131\t1.01034737175594\n-chr18\t64674131\t64676131\t1.62264521151304\n-chr18\t64676131\t64678131\t1.48296645852995\n-chr18\t64678131\t64680131\t1.28681962535927\n-chr18\t64680131\t64682131\t1.53492939742228\n-chr18\t64682131\t64684131\t1.58844790171606\n-chr18\t64684131\t64686131\t1.49033262314301\n-chr18\t64686131\t64688131\t1.31424965988202\n-chr18\t64688131\t64690131\t1.45337032575317\n-chr18\t64690131\t64692131\t1.35217898213701\n-chr18\t64692131\t64694131\t1.77532370910719\n-chr18\t64694131\t64696131\t1.60398303218395\n-chr18\t64696131\t64698131\t1.69307164801575\n-chr18\t64698131\t64700131\t1.54229556388787\n-chr18\t64700131\t64702131\t1.68106575665579\n-chr18\t64702131\t64704131\t1.48714225361666\n-chr18\t64704131\t64706131\t1.55224087444918\n-chr18\t64706131\t64708131\t1.3662045024589\n-chr18\t64708131\t64710131\t1.57624355139023\n-chr18\t64710131\t64712131\t1.44378437443185\n-chr18\t64712131\t64714131\t1.37811537520723\n-chr18\t64714131\t64716131\t1.06551636789331\n-chr18\t64716131\t64718131\t1.04029846172777\n-chr18\t64718131\t64720131\t1.1012560789095\n-chr18\t64720131\t64722131\t1.16248797408295\n-chr18\t64722131\t64724131\t1.10209650363972\n-chr18\t64724131\t64726131\t1.12702540883185\n-chr18\t64726131\t64728131\t1.06158233209566\n-chr18\t64728131\t64730131\t1.24500209867534\n-chr18\t64730131\t64732131\t0.834309455846338\n-chr18\t64732131\t64734131\t0.757289730474966\n-chr18\t64734131\t64736131\t1.10451816307643\n-chr18\t64736131\t64738131\t0.92262846294503\n-chr18\t64738131\t64740131\t0.804253155660302\n-chr18\t64740131\t64742131\t1.00162039935745\n-chr18\t64742131\t64744131\t0.956034285823398\n-chr21\t15966609\t15968609\t1.12440801594939\n-chr21\t15968609\t15970609\t0.958928874609379\n-chr21\t15970609\t15972609\t0.980859325447667\n-chr21\t15972609\t15974609\t0.985836855465142\n-chr21\t15974609\t15976609\t0.924304227149342\n-chr21\t15976609\t15978609\t0.981319441090073\n-chr21\t15978609\t15980609\t0.949853799394529\n-chr21\t15980609\t15982609\t0.858050928062694\n-chr21\t15982609\t15984609\t0.836178837413462\n-chr21\t15984609\t15986609\t1.20633196613812\n-chr21\t15986609\t15988609\t0.969230627046025\n-chr21\t15988609\t15990609\t1.06120061342825\n-chr21\t15990609\t15992609\t0.88573302960608\n-chr21\t15992609\t15994609\t0.987056692659576\n-chr21\t15994609\t15996609\t1.05266019775439\n-chr21\t15996609\t15998609\t1.29745136461899\n-chr21\t15998609\t16000609\t1.3631797211261\n-chr21\t16000609\t16002609\t1.58553521861437\n-chr21\t16002609\t16004609\t1.47800659441217\n-chr21\t16004609\t16006609\t1.75042011315262\n-chr21\t16006609\t16008609\t1.39329136735319\n-chr21\t16008609\t16010609\t1.57255744319984\n-chr21\t16010609\t16012609\t1.20929102513908\n-chr21\t16012609\t16014609\t1.53853232166312\n-chr21\t16014609\t16016609\t1.64985481461386\n-chr21\t16016609\t16018609\t1.59575749789367\n-chr21\t16018609\t16020609\t1.42205668994404\n-chr21\t16020609\t16022609\t1.66053802113289\n-chr21\t16022609\t16024609\t1.70386086339594\n-chr21\t16024609\t16026609\t1.73541878893467\n-chr21\t16026609\t16028609\t1.39682491364686\n-chr21\t16028609\t16030609\t1.43336589770868\n-chr21\t16030609\t16032609\t1.63386317242737\n-chr21\t16032609\t16034609\t1.53233925104548\n-chr21\t16034609\t16036609\t1.53952241603109\n-chr21\t16036609\t16038609\t1.28074961173938\n-chr21\t16038609\t16040609\t1.27922409248079\n-chr21\t16040609\t16042609\t0.962647373836482\n-chr21\t16042609\t16044609\t0.950807449539781\n-chr21\t16044609\t16046609\t1.19549845149275\n-chr21\t16046609\t16048609\t1.03462200267827\n-chr21\t16048609\t16050609\t0.952643344080609\n-chr21\t16050609\t16052609\t1.20946321219477\n-chr21\t16052609\t16054609\t0.965927027586426\n-chr21\t16054609\t16056609\t0.976116334675594\n-chr21\t16056609\t16058609\t1.07756004404963\n-chr21\t16058609\t16060609\t0.987244607153093\n-chr21\t16060609\t16062609\t1.04620355385428\n-chr21\t16062609\t16064609\t1.02761240862396\n-chr21\t16064609\t16066609\t0.870263755617609\n' |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/Feature2.bed --- a/iwtomics/example/Feature2.bed Wed May 31 11:06:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5400 +0,0 @@\n-chr1\t91399892\t91401892\t4.52457845989749\n-chr1\t91401892\t91403892\t4.69885317507985\n-chr1\t91403892\t91405892\t3.62988338998133\n-chr1\t91405892\t91407892\t4.45623107548837\n-chr1\t91407892\t91409892\t4.59364249841659\n-chr1\t91409892\t91411892\t5.70905494693032\n-chr1\t91411892\t91413892\t2.42812136492091\n-chr1\t91413892\t91415892\t3.21325702299381\n-chr1\t91415892\t91417892\t5.83146415223743\n-chr1\t91417892\t91419892\t4.145234941891\n-chr1\t91419892\t91421892\t5.61198015818556\n-chr1\t91421892\t91423892\t3.64586797215646\n-chr1\t91423892\t91425892\t6.20636700257446\n-chr1\t91425892\t91427892\t6.24535453369189\n-chr1\t91427892\t91429892\t5.45642255152577\n-chr1\t91429892\t91431892\t2.25812560771762\n-chr1\t91431892\t91433892\t4.85449016203815\n-chr1\t91433892\t91435892\t3.90115956418853\n-chr1\t91435892\t91437892\t4.73358990127742\n-chr1\t91437892\t91439892\t5.10493877711061\n-chr1\t91439892\t91441892\t6.26626452775677\n-chr1\t91441892\t91443892\t4.50874633533701\n-chr1\t91443892\t91445892\t5.70230938739608\n-chr1\t91445892\t91447892\t5.94455591845681\n-chr1\t91447892\t91449892\t4.52518856675072\n-chr1\t91449892\t91451892\t4.63848705114735\n-chr1\t91451892\t91453892\t4.34603429138827\n-chr1\t91453892\t91455892\t3.03830118655551\n-chr1\t91455892\t91457892\t6.03275619780653\n-chr1\t91457892\t91459892\t5.68223277080844\n-chr1\t91459892\t91461892\t5.50525041823675\n-chr1\t91461892\t91463892\t4.5213830572052\n-chr1\t91463892\t91465892\t5.50133572404842\n-chr1\t91465892\t91467892\t4.91055078504098\n-chr1\t91467892\t91469892\t4.05752990001426\n-chr1\t91469892\t91471892\t5.10897499920239\n-chr1\t91471892\t91473892\t5.43128593940068\n-chr1\t91473892\t91475892\t4.86148316107809\n-chr1\t91475892\t91477892\t4.48947054967865\n-chr1\t91477892\t91479892\t4.04898383490831\n-chr1\t91479892\t91481892\t5.68808370629557\n-chr1\t91481892\t91483892\t3.38402935045047\n-chr1\t91483892\t91485892\t4.55469509198871\n-chr1\t91485892\t91487892\t5.54674749210028\n-chr1\t91487892\t91489892\t6.80643757003305\n-chr1\t91489892\t91491892\t4.36576921982342\n-chr1\t91491892\t91493892\t4.78762392440088\n-chr1\t91493892\t91495892\t4.7968645329394\n-chr1\t91495892\t91497892\t5.2766452300238\n-chr1\t91497892\t91499892\t4.11389723526811\n-chr1\t116447079\t116449079\t3.50479481019937\n-chr1\t116449079\t116451079\t5.80805807123363\n-chr1\t116451079\t116453079\t4.84431415016648\n-chr1\t116453079\t116455079\t3.05704665156576\n-chr1\t116455079\t116457079\t4.08848780835827\n-chr1\t116457079\t116459079\t5.09637693701485\n-chr1\t116459079\t116461079\t5.69818646616106\n-chr1\t116461079\t116463079\t4.19878801898032\n-chr1\t116463079\t116465079\t4.5516661398769\n-chr1\t116465079\t116467079\t4.2453176706507\n-chr1\t116467079\t116469079\t4.67523653585105\n-chr1\t116469079\t116471079\t3.95251471557774\n-chr1\t116471079\t116473079\t4.96923766290807\n-chr1\t116473079\t116475079\t4.96920479716357\n-chr1\t116475079\t116477079\t5.02676539089313\n-chr1\t116477079\t116479079\t5.00052315566\n-chr1\t116479079\t116481079\t4.16809348391652\n-chr1\t116481079\t116483079\t4.59306360967521\n-chr1\t116483079\t116485079\t3.53563628215594\n-chr1\t116485079\t116487079\t4.50469161954188\n-chr1\t116487079\t116489079\t5.56857122702899\n-chr1\t116489079\t116491079\t4.58351619746089\n-chr1\t116491079\t116493079\t4.25823600023412\n-chr1\t116493079\t116495079\t5.90593508834324\n-chr1\t116495079\t116497079\t4.75083460476364\n-chr1\t116497079\t116499079\t2.771628447275\n-chr1\t116499079\t116501079\t3.55096260651244\n-chr1\t116501079\t116503079\t6.17656545119289\n-chr1\t116503079\t116505079\t4.36022614599567\n-chr1\t116505079\t116507079\t3.07947070495695\n-chr1\t116507079\t116509079\t6.00325415448973\n-chr1\t116509079\t116511079\t4.75152529713703\n-chr1\t116511079\t116513079\t4.63430887067622\n-chr1\t116513079\t116515079\t6.20396270678022\n-chr1\t116515079\t116517079\t4.10708349972204\n-chr1\t116517079\t116519079\t6.37204838467736\n-chr1\t116519079\t116521079\t4.20892327541064\n-chr1\t116521079\t116523079\t5.26217726205883\n-chr1\t116523079\t116525079\t4.98426282331262\n-chr1\t116525079\t116527079\t4.54088329611304\n-chr1\t116527079\t116529079\t6.19908300654713\n-chr1\t116529079\t116531079\t4.13307018130982\n-chr1\t116531079\t116533079\t4.81616315789755\n-chr1\t116533079\t116535079\t4.45075212625821\n-chr1\t116535079\t116537079\t5.3278384644649\n-chr1\t11'..b'1\t3.7169759268732\n-chr18\t64654131\t64656131\t5.25442380932218\n-chr18\t64656131\t64658131\t7.45772820471094\n-chr18\t64658131\t64660131\t5.48095406750538\n-chr18\t64660131\t64662131\t3.62733589187025\n-chr18\t64662131\t64664131\t4.55331693366933\n-chr18\t64664131\t64666131\t6.8774312824165\n-chr18\t64666131\t64668131\t5.2001203442027\n-chr18\t64668131\t64670131\t4.95990659880495\n-chr18\t64670131\t64672131\t4.02077893319017\n-chr18\t64672131\t64674131\t4.05668535153819\n-chr18\t64674131\t64676131\t4.23509896158418\n-chr18\t64676131\t64678131\t4.23418796991892\n-chr18\t64678131\t64680131\t5.45699681002164\n-chr18\t64680131\t64682131\t5.19535591598228\n-chr18\t64682131\t64684131\t6.0555950876448\n-chr18\t64684131\t64686131\t3.54284284855037\n-chr18\t64686131\t64688131\t5.0657204197487\n-chr18\t64688131\t64690131\t4.61156619971275\n-chr18\t64690131\t64692131\t4.66622025797826\n-chr18\t64692131\t64694131\t5.34521271919367\n-chr18\t64694131\t64696131\t9.87597953863361\n-chr18\t64696131\t64698131\t7.05091406041253\n-chr18\t64698131\t64700131\t8.00182216055189\n-chr18\t64700131\t64702131\t7.91390780851007\n-chr18\t64702131\t64704131\t6.60478767008177\n-chr18\t64704131\t64706131\t8.42205253797048\n-chr18\t64706131\t64708131\t8.4092636416611\n-chr18\t64708131\t64710131\t7.33893411142367\n-chr18\t64710131\t64712131\t6.44977234209029\n-chr18\t64712131\t64714131\t6.14212509408095\n-chr18\t64714131\t64716131\t7.33470365201403\n-chr18\t64716131\t64718131\t6.14466300830508\n-chr18\t64718131\t64720131\t6.28759018496124\n-chr18\t64720131\t64722131\t6.13121264285508\n-chr18\t64722131\t64724131\t6.25464222302313\n-chr18\t64724131\t64726131\t6.22857474092805\n-chr18\t64726131\t64728131\t6.7164061474755\n-chr18\t64728131\t64730131\t7.71694797882967\n-chr18\t64730131\t64732131\t6.47134532938063\n-chr18\t64732131\t64734131\t5.44078856911433\n-chr18\t64734131\t64736131\t6.72171185147245\n-chr18\t64736131\t64738131\t7.45623695140267\n-chr18\t64738131\t64740131\t6.66053173863693\n-chr18\t64740131\t64742131\t7.26582262622926\n-chr18\t64742131\t64744131\t7.26639325298473\n-chr21\t15966609\t15968609\t3.61661096782077\n-chr21\t15968609\t15970609\t4.73386208722406\n-chr21\t15970609\t15972609\t5.8015549021153\n-chr21\t15972609\t15974609\t4.96167153907388\n-chr21\t15974609\t15976609\t3.95102647749112\n-chr21\t15976609\t15978609\t3.97020922833049\n-chr21\t15978609\t15980609\t5.33786080501161\n-chr21\t15980609\t15982609\t4.36434578068312\n-chr21\t15982609\t15984609\t5.80198476623914\n-chr21\t15984609\t15986609\t5.35739211903602\n-chr21\t15986609\t15988609\t6.08746983525949\n-chr21\t15988609\t15990609\t4.34773396054126\n-chr21\t15990609\t15992609\t5.13949591522979\n-chr21\t15992609\t15994609\t3.73402272260864\n-chr21\t15994609\t15996609\t5.39450798275315\n-chr21\t15996609\t15998609\t5.55466043086729\n-chr21\t15998609\t16000609\t5.28998031818056\n-chr21\t16000609\t16002609\t6.19329925730006\n-chr21\t16002609\t16004609\t2.67150074437477\n-chr21\t16004609\t16006609\t5.16423939358034\n-chr21\t16006609\t16008609\t4.69609507505699\n-chr21\t16008609\t16010609\t5.44942073640721\n-chr21\t16010609\t16012609\t6.03847400860453\n-chr21\t16012609\t16014609\t5.97649168698122\n-chr21\t16014609\t16016609\t5.36013704359642\n-chr21\t16016609\t16018609\t7.92817462773764\n-chr21\t16018609\t16020609\t7.69377454814871\n-chr21\t16020609\t16022609\t8.80647396276848\n-chr21\t16022609\t16024609\t8.52452119781362\n-chr21\t16024609\t16026609\t7.89462789559928\n-chr21\t16026609\t16028609\t6.13805198380259\n-chr21\t16028609\t16030609\t4.64531272265593\n-chr21\t16030609\t16032609\t6.29826676008479\n-chr21\t16032609\t16034609\t7.79487866360525\n-chr21\t16034609\t16036609\t7.31994055340419\n-chr21\t16036609\t16038609\t8.8004479775322\n-chr21\t16038609\t16040609\t8.25854856063076\n-chr21\t16040609\t16042609\t5.04576860851306\n-chr21\t16042609\t16044609\t7.30730130969012\n-chr21\t16044609\t16046609\t7.83870783306589\n-chr21\t16046609\t16048609\t7.63074529828173\n-chr21\t16048609\t16050609\t6.43100021814285\n-chr21\t16050609\t16052609\t7.27551387601485\n-chr21\t16052609\t16054609\t6.26545170591659\n-chr21\t16054609\t16056609\t7.12562466213381\n-chr21\t16056609\t16058609\t6.26895239202312\n-chr21\t16058609\t16060609\t7.3992370168724\n-chr21\t16060609\t16062609\t7.97487587946482\n-chr21\t16062609\t16064609\t6.76355670816454\n-chr21\t16064609\t16066609\t6.11742019669001\n' |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/features.header.bed.txt --- a/iwtomics/example/features.header.bed.txt Wed May 31 11:06:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -Feature1.bed ftr1 Feature 1 -Feature2.bed ftr2 Feature 2 \ No newline at end of file |
| b |
| diff -r 81faa1567178 -r 565118df598a iwtomics/example/regions.header.txt --- a/iwtomics/example/regions.header.txt Wed May 31 11:06:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -Elements1_regions.bed elem1 Elements 1 -Elements2_regions.bed elem2 Elements 2 -Elements3_regions.bed elem3 Elements 3 -Controls_regions.bed control Controls \ No newline at end of file |
| b |
| diff -r 81faa1567178 -r 565118df598a loadandplot.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/loadandplot.R Wed May 31 11:07:22 2017 -0400 |
| [ |
| @@ -0,0 +1,146 @@ +if (require("IWTomics",character.only = TRUE,quietly = FALSE)) { + require(tools,quietly = FALSE) + args=commandArgs(TRUE) + + for (i in seq_along(args)) { + message(args[[i]]) + } + + # get args names and values + args_values=strsplit(args,'=') + args_names=unlist(lapply(args_values,function(arg) arg[1])) + names(args_values)=args_names + args_values=lapply(args_values,function(arg) arg[2]) + # read filenames + outrdata=args_values$outrdata + outregions=args_values$outregions + outfeatures=args_values$outfeatures + outpdf=args_values$outpdf + regionspaths=unlist(strsplit(args_values$regionspaths,'\\|')) + if("regionsheaderfile" %in% args_names){ + # the file regionsheaderfile must contain as first column the (unique) regionsfilenames, + # as second column the corresponding ids and as third column the names + tryCatch({ + regionsheader=read.delim(args_values$regionsheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t") + regionsfilenames=unlist(strsplit(args_values$regionsfilenames,'\\|')) + if(length(setdiff(regionsfilenames,row.names(regionsheader)))) { + quit(save="no", status=11) + stop('Not all regionsfilenames are present in the first column of regionsheader.') + } + id_regions=regionsheader[regionsfilenames,1] + name_regions=regionsheader[regionsfilenames,2] + }, error = function(err) { + quit(save="no", status=10) #error on header file + stop(err) + }) + }else{ + eval(parse(text=args[[which(args_names=='regionsgalaxyids')]])) + id_regions=paste0('data_',regionsgalaxyids) + name_regions=paste0('data_',regionsgalaxyids) + } + featurespaths=unlist(strsplit(args_values$featurespaths,'\\|')) + if("featuresheaderfile" %in% args_names){ + # the file featuresheaderfile must contain as first column the (unique) featuresfilenames, + # as second column the corresponding ids and as third column the names + tryCatch({ + featuresheader=read.delim(args_values$featuresheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t") + featuresfilenames=unlist(strsplit(args_values$featuresfilenames,'\\|')) + if(length(setdiff(featuresfilenames,row.names(featuresheader)))) { + quit(save="no", status=21) + stop('Not all featuresfilenames are present in the first column of featuresheader.') + } + id_features=featuresheader[featuresfilenames,1] + name_features=featuresheader[featuresfilenames,2] + }, error = function(err) { + quit(save="no", status=20) #error on header file + stop(err) + }) + }else{ + eval(parse(text=args[[which(args_names=='featuresgalaxyids')]])) + id_features=paste0('data_',featuresgalaxyids) + name_features=paste0('data_',featuresgalaxyids) + } + # read parameters (from smoothing on) + i_smoothing=which(args_names=='smoothing') + for(i in i_smoothing:length(args)){ + eval(parse(text=args[[i]])) + } + + # load data + tryCatch({ + regionsFeatures=IWTomicsData(regionspaths,featurespaths,alignment, + id_regions,name_regions,id_features,name_features,start.are.0based=start.are.0based) + }, error = function(err) { + if(grepl('invalid format',err$message)){ + quit(save="no", status=31) # error, not enough columns in input file + }else if(grepl('duplicated regions',err$message)){ + quit(save="no", status=32) # error, duplicated regions in region file + }else if(grepl('duplicated windows',err$message)){ + quit(save="no", status=33) # error, duplicated windows in feature file + }else if(grepl('overlapping windows',err$message)){ + quit(save="no", status=34) # error, overlapping windows in feature file + }else if(grepl('not all regions in datasets',err$message)){ + quit(save="no", status=35) # error, windows in feature files do not cover all regions in region files + }else if(grepl('ifferent size windows',err$message)){ + quit(save="no", status=36) # error, all windows in a feature files must have the same size + } + #error loading data + + stop(err) + + quit(save="no", status=30) + + }) + + # smooth data + if(smoothing!='no'){ + tryCatch({ + if(smoothing=='locpoly'){ + dist_knots=10 + }else if(smoothing=='kernel'){ + degree=3 + dist_knots=10 + }else if(smoothing=='splines'){ + bandwidth=5 + } + if(alignment=='scale'){ + if(scale==0){ + regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps, + bandwidth=bandwidth,degree=degree,dist_knots=dist_knots) + }else{ + regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps, + bandwidth=bandwidth,degree=degree,dist_knots=dist_knots,scale_grid=scale) + } + }else{ + regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps, + bandwidth=bandwidth,degree=degree,dist_knots=dist_knots) + } + }, error = function(err) { + quit(save="no", status=40) #error on smoothing + stop(err) + }) + } + + # plot data + pdf(outpdf,width=10,height=8) + if(plottype=='boxplot'){ + # fix repeated probs + probs=sort(unique(probs)) + }else{ + probs=c(0.25,0.5,0.75) + } + plot(regionsFeatures,type=plottype,probs=probs,average=average,size=size,ask=FALSE) + dev.off() + + # create output + #write.table(cbind(unlist(strsplit(args_values$regionsfilenames,'\\|')),idRegions(regionsFeatures),nameRegions(regionsFeatures)), + #file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE) + write.table(as.data.frame(t(idRegions(regionsFeatures))),file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE) + #write.table(cbind(unlist(strsplit(args_values$featuresfilenames,'\\|')),idFeatures(regionsFeatures),nameFeatures(regionsFeatures)), + #file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE) + write.table(as.data.frame(t(idFeatures(regionsFeatures))),file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE) + save(regionsFeatures,file=outrdata) +}else{ + quit(save="no", status=255) + stop("Missing IWTomics package") +} \ No newline at end of file |
| b |
| diff -r 81faa1567178 -r 565118df598a loadandplot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/loadandplot.xml Wed May 31 11:07:22 2017 -0400 |
| [ |
| b'@@ -0,0 +1,325 @@\n+<tool id="loadandplot" name="IWTomics Load" version="@VERSION@.0">\n+ <description>Smooth and Plot</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <stdio>\n+ <exit_code range="255" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />\n+ <exit_code range="10" source="both" level="fatal" description="An error has occurred reading the header file for regions. Please try again." />\n+ <exit_code range="11" source="both" level="fatal" description="Not all region files are present in the first column of header file for regions." />\n+ <exit_code range="20" source="both" level="fatal" description="An error has occurred reading the header file for features. Please try again." />\n+ <exit_code range="21" source="both" level="fatal" description="Not all feature files are present in the first column of header file for features." />\n+ <exit_code range="30" source="both" level="fatal" description="An error has occurred reading the data. Please try again." />\n+ <exit_code range="31" source="both" level="fatal" description="Not enough columns in input file." />\n+ <exit_code range="32" source="both" level="fatal" description="Duplicated regions in region file." />\n+ <exit_code range="33" source="both" level="fatal" description="Duplicated windows in feature file." />\n+ <exit_code range="34" source="both" level="fatal" description="Overlapping windows in feature file." />\n+ <exit_code range="35" source="both" level="fatal" description="Windows in feature files do not cover all regions in region files." />\n+ <exit_code range="36" source="both" level="fatal" description="All windows in a feature file must have the same size." />\n+ <exit_code range="40" source="both" level="fatal" description="An error has occurred smoothing the data. Please try again." />\n+ <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />\n+ </stdio>\n+\n+ <command>\n+<![CDATA[\n+ Rscript $__tool_directory__/loadandplot.R outrdata="${outrdata}" outregions="${outregions}" outfeatures="${outfeatures}" outpdf="${outpdf}"\n+\n+ #set region_paths = \'"\\\\|"\'.join( [ str( $r ) for $r in $regions ] )\n+ regionspaths="${region_paths}"\n+ #set region_galaxyids = \'","\'.join( [ str( $r.hid ) for $r in $regions ] )\n+ regionsgalaxyids="c(${region_galaxyids})"\n+ #set region_names = \'"\\\\|"\'.join( [ str( $r.name ) for $r in $regions ] )\n+ regionsfilenames="${region_names}"\n+ #set region_header = \'"\\\\|"\'.join( [ str( $rh.regionsheader ) for $rh in $regionsheaderrepeat ] )\n+ #if $region_header != "":\n+ regionsheaderfile="${region_header}"\n+ #end if\n+\n+ #set feature_paths = \'"\\\\|"\'.join( [ str( $f ) for $f in $features ] )\n+ featurespaths="${feature_paths}"\n+ #set feature_galaxyids = \'","\'.join( [ str( $f.hid ) for $f in $features ] )\n+ featuresgalaxyids="c(${feature_galaxyids})"\n+ #set feature_names = \'"\\\\|"\'.join( [ str( $f.name ) for $f in $features ] )\n+ featuresfilenames="${feature_names}"\n+ #set feature_header = \'"\\\\|"\'.join( [ str( $fh.featuresheader ) for $fh in $featuresheaderrepeat ] )\n+ #if $feature_header != "":\n+ featuresheaderfile="${feature_header}"\n+ #end if\n+\n+ smoothing="\'${conditionaltype.smoothing}\'"\n+ start.are.0based="${zerobased}"\n+ #if $conditionaltype.smoothing == \'no\':\n+ alignment="\'${conditionaltype.alignment}\'"\n+ #elif $conditionaltype.smoothing == \'locpoly\':\n+ alignment="\'${conditionaltype.locpolyconditionalscale.alignment}\'"\n+ #if $conditionaltype.locpolyconditionalscale.alignment == \'scale\':\n+ scale="${conditionaltype.locpolyconditionalscale.scalegrid}"\n+ #end if\n+ bandwidth="${conditionaltype.locpolybandwidth}"\n+ degree="${conditionaltype.locpolydegr'..b'/section>\n+ </inputs>\n+\n+ <outputs>\n+ <!--<data format="txt" name="stackerr" label="iwtomics.loadandplot.stackerr.txt" from_work_dir="iwtomics.loadandplot.stackerr.txt" />-->\n+ <data format="rdata" name="outrdata" label="${tool.name} on ${on_string}: IWTomicsData Object" from_work_dir="iwtomics.loadandplot.RData" />\n+ <data format="tabular" name="outregions" label="${tool.name} on ${on_string}: Region Dataset IDs" from_work_dir="iwtomics.loadandplot.regions.txt" />\n+ <data format="tabular" name="outfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.loadandplot.features.txt" />\n+ <data format="pdf" name="outpdf" label="${tool.name} on ${on_string}: Plotted Data" from_work_dir="iwtomics.loadandplot.pdf" />\n+ </outputs>\n+\n+ <help>\n+This tool imports a collection of genomic region datasets, and associates to each region\n+multiple genomic feature measurements. It allows to align the regions in multiple ways\n+(center, left, right or scale alignment), to smooth the feature curves (possibly filling gaps in the\n+measurements) and to create a graphical representation of the feature measurements in each\n+region datasets (aligned curves or pointwise quantile curves).\n+\n+-----\n+\n+**Region datasets**\n+\n+Each region dataset can be provided as a BED or Tabular file with tab delimited columns chr\n+start end (extra columns present in the input file are ignored). Regions can be of different\n+length::\n+\n+ chr2 49960150 50060150\n+ chr2 55912445 56012445\n+ ...\n+\n+-----\n+\n+**Feature measurements**\n+\n+Feature measurements corresponding to all the regions can be provided as a BED or Tabular\n+file with tab delimited columns chr start end value::\n+\n+ chr2 49960150 49962150 0.9426\n+ chr2 49962150 49964150 0.7816\n+ ...\n+\n+Each feature must be measured in windows of a fixed size inside all the regions (missing\n+values must be indicated as NA). Another way to import feature measurements is from a\n+Tabular file with the first three columns chr start end corresponding to the different genomic\n+regions, followed on the same row by all the measurements in fixed-size windows::\n+\n+ chr2 49960150 50060150 0.9426 0.7816 0.8921 ... ... 1.2063\n+ chr2 55912445 56012445 0.8719 0.9975 1.1619 ... ... 0.9601\n+ ...\n+\n+-----\n+\n+**Output**\n+\n+The tool returns:\n+\n+1. RData with the IWTomicsData object, that stores the aligned genomic region datasets, and their associated feature measurements;\n+2. Region dataset identifiers;\n+3. Feature identifiers;\n+4. PDF file with the plotted data.\n+\n+1-3 can be used as input of the tool *IWTomics Test and Plot*\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Notes**\n+\n+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).\n+\n+It implements a simplified version of the methods *smooth* and *plot* for *IWTomicsData* objects.\n+The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).\n+\n+.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf\n+ </help>\n+\n+ <citations>\n+ <citation type="bibtex">\n+ @ARTICLE{\n+ iwt-functional-data,\n+ author = {Pini, Alessia and Vantini, Simone},\n+ title = {Interval-Wise Testing for functional data},\n+ journal = {Journal of Nonparametric Statistics},\n+ year = {2017},\n+ volume = {29},\n+ number = {2},\n+ pages = {407-424}\n+ }\n+ </citation>\n+ <citation type="bibtex">\n+ @MANUAL{\n+ iwtomics,\n+ author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},\n+ title = {IWTomics: Interval-Wise Testing for Omics Data},\n+ note = {R package version 0.99.12},\n+ year = {2017}\n+ }\n+ </citation>\n+ </citations>\n+\n+</tool>\n' |
| b |
| diff -r 81faa1567178 -r 565118df598a macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed May 31 11:07:22 2017 -0400 |
| b |
| @@ -0,0 +1,9 @@ +<macros> + <token name="@VERSION@">1.0.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="3.3.1">R</requirement> + <requirement type="package" version="@VERSION">bioconductor-iwtomics</requirement> + </requirements> + </xml> +</macros> \ No newline at end of file |
| b |
| diff -r 81faa1567178 -r 565118df598a plotwithscale.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plotwithscale.R Wed May 31 11:07:22 2017 -0400 |
| [ |
| @@ -0,0 +1,117 @@ +if (require("IWTomics",character.only = TRUE,quietly = FALSE)) { + args=commandArgs(TRUE) + + # get args names and values + args_values=strsplit(args,'=') + args_names=unlist(lapply(args_values,function(arg) arg[1])) + names(args_values)=args_names + args_values=lapply(args_values,function(arg) arg[2]) + # read filenames + adjustedpvalue=args_values$adjustedpvalue + iwtomicsrespdf=args_values$iwtomicsrespdf + iwtomicssumpdf=args_values$iwtomicssumpdf + iwtomicsrdata=args_values$iwtomicsrdata + iwtomicstests=args_values$iwtomicstests + iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures + test_subset=paste0('c(',strsplit(args_values$test_subset,'\\|')[[1]],')') + feature_subset=paste0('c(',strsplit(args_values$feature_subset,'\\|')[[1]],')') + # read parameters (from test_subset on) + i_scale_subset=which(args_names=='scale_subset') + for(i in i_scale_subset:length(args)){ + eval(parse(text=args[[i]])) + } + + # load RData + load(iwtomicsrdata) + # read testids and featureids and check them + unlisted=lapply(seq_along(test_subset), + function(i){ + test_subset_i=eval(parse(text=test_subset[i])) + feature_subset_i=eval(parse(text=feature_subset[i])) + test_subset_i=rep(test_subset_i,each=length(feature_subset_i)) + feature_subset_i=rep(feature_subset_i,length.out=length(test_subset_i)) + scale_subset_i=rep(scale_subset[i],length(test_subset_i)) + return(list(test_subset=test_subset_i,feature_subset=feature_subset_i,scale_subset=scale_subset_i)) + }) + test_subset=unlist(lapply(unlisted,function(l) l$test_subset)) + feature_subset=unlist(lapply(unlisted,function(l) l$feature_subset)) + scale_subset=unlist(lapply(unlisted,function(l) l$scale_subset)) + testids=as.character(read.delim(iwtomicstests,header=FALSE,sep='\t',stringsAsFactors=FALSE)) + featureids=as.character(read.delim(iwtomicsselectedfeatures,header=FALSE,sep='\t',stringsAsFactors=FALSE)) + id_features_subset=featureids[feature_subset] + if(sum(testids!=paste(testInput(regionsFeatures_test)$id_region1,'vs',testInput(regionsFeatures_test)$id_region2))){ + quit(save="no", status=10) + stop('Wrong test ids') + } + if(sum(featureids!=idFeatures(regionsFeatures_test))){ + quit(save="no", status=20) + stop('Wrong feature ids') + } + # retrieve test and features_subset ids + id_features_subset=featureids[feature_subset] + if(sum(duplicated(paste0(test_subset,id_features_subset)))){ + quit(save="no", status=30) + stop('Two scale thresholds selected for the same test and feature.') + } + # If scale_subset=0, do not change the threshold + default=(scale_subset==0) + scale_subset=scale_subset[!default] + test_subset=test_subset[!default] + id_features_subset=id_features_subset[!default] + + # get scale threshold + scale_threshold=lapply(regionsFeatures_test@test$result, + function(result) unlist(lapply(result,function(feature) feature$max_scale))) + for(i in seq_along(test_subset)){ + if(scale_threshold[[test_subset[i]]][id_features_subset[i]]<scale_subset[i]){ + quit(save="no", status=40) + stop('Scale threshold too high.') + } + scale_threshold[[test_subset[i]]][id_features_subset[i]]=scale_subset[i] + } + + # create adjustedvalue output + pval=adjusted_pval(regionsFeatures_test,scale_threshold=scale_threshold) + for(test in seq_along(pval)){ + for(id_feature in idFeatures(regionsFeatures_test)){ + write(paste0('Test: ',testids[test],', on feature ',id_feature), + file=adjustedpvalue,append=TRUE,sep='\t') + pval_i=as.data.frame(t(pval[[test]][[id_feature]])) + row.names(pval_i)=paste('Scale',scale_threshold[[test]][[id_feature]]) + write.table(pval_i,file=adjustedpvalue,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE) + write('',file=adjustedpvalue,append=TRUE,sep='\t') + } + } + + + # plot test results + pdf(iwtomicsrespdf,width=5,height=7) + if(plottype=='boxplot'){ + # fix repeated probs + probs=sort(unique(probs)) + }else{ + probs=c(0.25,0.5,0.75) + } + plotTest(regionsFeatures_test,alpha=testalpha,type=plottype,probs=probs,average=average,size=size,scale_threshold=scale_threshold,ask=FALSE) + dev.off() + + # plot summary results + if(groupby!='none'){ + tryCatch({ + pdf(iwtomicssumpdf,width=15,height=10) + plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,scale_threshold=scale_threshold,ask=FALSE,append=TRUE) + dev.off() + }, error = function(err) { + if (grepl('selected features with different resolution',err$message)) { + quit(save="no", status=50) #error: groupby 'test' but selected features with different resolution. + stop(err) + } + quit(save="no", status=60) #error + stop(err) + }) + } + +}else{ + quit(save="no", status=255) + stop("Missing IWTomics package") +} \ No newline at end of file |
| b |
| diff -r 81faa1567178 -r 565118df598a plotwithscale.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plotwithscale.xml Wed May 31 11:07:22 2017 -0400 |
| [ |
| b'@@ -0,0 +1,201 @@\n+<tool id="plotwithscale" name="IWTomics Plot with Threshold" version="@VERSION@.0">\n+ <description>on Test Scale</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <stdio>\n+ <exit_code range="-1" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />\n+ <exit_code range="10" source="both" level="fatal" description="Wrong test ids." />\n+ <exit_code range="20" source="both" level="fatal" description="Wrong feature ids." />\n+ <exit_code range="30" source="both" level="fatal" description="Two scale thresholds selected for the same test and feature." />\n+ <exit_code range="40" source="both" level="fatal" description="Scale threshold too high." />\n+ <exit_code range="50" source="both" level="fatal" description="Group by \'test\' but selected features with different resolution." />\n+ <exit_code range="60" source="both" level="fatal" description="Summary plot error. Please try again." />\n+ <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />\n+ </stdio>\n+\n+ <command>\n+<![CDATA[\n+ Rscript $__tool_directory__/plotwithscale.R adjustedpvalue="${adjustedpvalue}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}"\n+ iwtomicsrdata="${rdata}"\n+ iwtomicstests="${testids}"\n+ iwtomicsselectedfeatures="${featureids}"\n+\n+ #set test_subset = \'"\\\\|"\'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )\n+ test_subset="${test_subset}"\n+ #set feature_subset = \'"\\\\|"\'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )\n+ feature_subset="${feature_subset}"\n+ #set scale_subset = \'","\'.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )\n+ scale_subset="c(${scale_subset})"\n+\n+ testalpha="${plotres.alpha}"\n+ average="${plotres.average}"\n+ size="${plotres.size}"\n+ plottype="\'${plotres.conditionalplottype.plottype}\'"\n+ #if $plotres.conditionalplottype.plottype == \'boxplot\':\n+ #set probs = \'","\'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )\n+ #if $probs != "":\n+ probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})"\n+ #else:\n+ probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})"\n+ #end if\n+ #end if\n+\n+ groupby="\'${plotsum.conditionalgroupby.groupby}\'"\n+ #if $plotsum.conditionalgroupby.groupby == "test":\n+ summaryalpha="${plotsum.conditionalgroupby.testalphaplot}"\n+ only_significant="${plotsum.conditionalgroupby.testonlysig}"\n+ #elif $plotsum.conditionalgroupby.groupby == "feature":\n+ summaryalpha="${plotsum.conditionalgroupby.featurealphaplot}"\n+ only_significant="${plotsum.conditionalgroupby.featureonlysig}"\n+ #end if\n+\n+ >& /dev/null\n+]]>\n+ <!--\n+ to print the stack add the following line at the end of the command and enable the corresponding entry in output\n+ 2> "${stackerr}"\n+ -->\n+ </command>\n+\n+ <inputs>\n+ <help>\n+ ...\n+ </help>\n+\n+ <!-- RData -->\n+ <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object with test results" help="File created by \'IWTomics Test and Plot\'." />\n+ <!-- test IDs -->\n+ <param format="tabular" name="testids" type="data" label="Select test IDs" help="File created by \'IWTomics Test and Plot\'." />\n+ <!-- feature IDs -->\n+ <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by \'IWTomics Test and Plot\'." />\n+\n+ <!-- rep'..b'epeat>\n+ </section>\n+ </when>\n+ </conditional>\n+ </section>\n+\n+ <!-- summary plot -->\n+ <section name="plotsum" title="Summary plot" expanded="True">\n+ <!-- conditional group by -->\n+ <conditional name="conditionalgroupby">\n+ <!-- group by -->\n+ <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">\n+ <option value="none">No plot</option>\n+ <option value="test">Group by test</option>\n+ <option value="feature">Group by feature</option>\n+ </param>\n+ <when value="test">\n+ <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />\n+ <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />\n+ </when>\n+ <when value="feature">\n+ <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />\n+ <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />\n+ </when>\n+ </conditional>\n+ </section>\n+ </inputs>\n+\n+ <outputs>\n+ <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.testandplot.stackerr.txt" />-->\n+ <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.testandplot.adjustedpvalue.txt" />\n+ <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" />\n+ <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" />\n+ </outputs>\n+\n+ <help>\n+This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves\n+for the different tests performed at the selected scale, and it creates a graphical representation of the\n+Interval-Wise Testing results and a summary plot (optional) at the selected scale.\n+\n+-----\n+\n+**Input files**\n+\n+RData file with the IWTomicsData object with test results, tabular files with test IDs and feature IDs.\n+These files are created by the tool *IWTomics Test and Plot*.\n+\n+-----\n+\n+**Output**\n+\n+The tool returns:\n+\n+1. TXT file with an adjusted p-value curve for every test performed at the selected scale;\n+2. PDF file with the plotted test results;\n+3. PDF file with the summary plot.\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Notes**\n+\n+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).\n+\n+It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.\n+The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).\n+\n+.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf\n+ </help>\n+\n+ <citations>\n+ <citation type="bibtex">\n+ @ARTICLE{\n+ iwt-functional-data,\n+ author = {A Pini and S. Vantini},\n+ title = {Interval-Wise Testing for functional data},\n+ journal = {Journal of Nonparametric Statistics},\n+ year = {2017},\n+ volume = {29},\n+ number = {2},\n+ pages = {407-424}\n+ }\n+ </citation>\n+ <citation type="bibtex">\n+ @MANUAL{\n+ iwtomics,\n+ author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},\n+ title = {IWTomics: Interval-Wise Testing for Omics Data},\n+ note = {R package version 0.99.12},\n+ year = {2017}\n+ }\n+ </citation>\n+ </citations>\n+\n+</tool>\n' |
| b |
| diff -r 81faa1567178 -r 565118df598a testandplot.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/testandplot.R Wed May 31 11:07:22 2017 -0400 |
| [ |
| @@ -0,0 +1,99 @@ +if (require("IWTomics",character.only = TRUE,quietly = FALSE)) { + args=commandArgs(TRUE) + + # get args names and values + args_values=strsplit(args,'=') + args_names=unlist(lapply(args_values,function(arg) arg[1])) + names(args_values)=args_names + args_values=lapply(args_values,function(arg) arg[2]) + # read filenames + adjustedpvaluematrix=args_values$adjustedpvaluematrix + iwtomicsrespdf=args_values$iwtomicsrespdf + iwtomicssumpdf=args_values$iwtomicssumpdf + regionids=args_values$regionids + featureids=args_values$featureids + rdatafile=args_values$rdatafile + iwtomicsrdata=args_values$iwtomicsrdata + iwtomicstests=args_values$iwtomicstests + iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures + # read parameters (from region1 on) + i_region1=which(args_names=='region1') + for(i in i_region1:length(args)){ + eval(parse(text=args[[i]])) + } + + # load RData + load(rdatafile) + # read regionids and featureids + regionids=as.character(read.delim(regionids,header=FALSE,sep='\t',stringsAsFactors=FALSE)) + featureids=as.character(read.delim(featureids,header=FALSE,sep='\t',stringsAsFactors=FALSE)) + # retrieve region1, region2 and features_subset ids and check they are in the RData + id_region1=regionids[region1] + id_region2=regionids[region2] + id_features_subset=featureids[features_subset] + if(length(setdiff(c(id_region1,id_region2),idRegions(regionsFeatures)))!=0){ + quit(save="no", status=10) + stop('Wrong region ids') + } + if(length(setdiff(id_features_subset,idFeatures(regionsFeatures)))!=0){ + quit(save="no", status=20) + stop('Wrong feature ids') + } + if(sum(duplicated(paste0(id_region1,id_region2)))){ + quit(save="no", status=30) + stop('Same test repeated multiple times.') + } + + # perform test + tryCatch({ + # fix repeated probs + if(statistics=='quantile'){ + # fix repeated probs + testprobs=sort(unique(testprobs)) + }else{ + testprobs=0.5 + } + regionsFeatures_test=IWTomicsTest(regionsFeatures,id_region1,id_region2,id_features_subset, + statistics=statistics,probs=testprobs,B=B) + # create adjustedvaluematrix output + for(test in seq_along(id_region1)){ + for(id_feature in id_features_subset){ + write(paste0('Test: ',id_region1[test],' vs ',id_region2[test],', on feature ',id_feature), + file=adjustedpvaluematrix,append=TRUE,sep='\t') + pval=regionsFeatures_test@test$result[[test]][[id_feature]]$adjusted_pval_matrix + row.names(pval)=paste('Scale',rev(seq_len(nrow(pval)))) + write.table(pval,file=adjustedpvaluematrix,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE) + write('',file=adjustedpvaluematrix,append=TRUE,sep='\t') + } + } + }, error = function(err) { + quit(save="no", status=40) #error testing + stop(err) + }) + + # plot test results + pdf(iwtomicsrespdf,width=5,height=7) + if(plottype=='boxplot'){ + # fix repeated probs + probs=sort(unique(probs)) + }else{ + probs=c(0.25,0.5,0.75) + } + plotTest(regionsFeatures_test,alpha=testalpha,type=plottype,probs=probs,average=average,size=size,ask=FALSE) + dev.off() + + # plot summary results + if(groupby!='none'){ + pdf(iwtomicssumpdf,width=15,height=10) + plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,ask=FALSE,append=TRUE) + dev.off() + } + + # create output + write.table(as.data.frame(t(paste(id_region1,'vs',id_region2))),file=iwtomicstests,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE) + write.table(as.data.frame(t(idFeatures(regionsFeatures_test))),file=iwtomicsselectedfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE) + save(regionsFeatures_test,file=iwtomicsrdata) +}else{ + quit(save="no", status=255) + stop("Missing IWTomics package") +} \ No newline at end of file |
| b |
| diff -r 81faa1567178 -r 565118df598a testandplot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/testandplot.xml Wed May 31 11:07:22 2017 -0400 |
| [ |
| b'@@ -0,0 +1,239 @@\n+<tool id="testandplot" name="IWTomics Test" version="@VERSION@.0">\n+ <description>and Plot</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <stdio>\n+ <exit_code range="-1" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />\n+ <exit_code range="10" source="both" level="fatal" description="Wrong region ids." />\n+ <exit_code range="20" source="both" level="fatal" description="Wrong feature ids." />\n+ <exit_code range="30" source="both" level="fatal" description="Same test repeated multiple times." />\n+ <exit_code range="40" source="both" level="fatal" description="Testing error." />\n+ <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />\n+ </stdio>\n+\n+ <command>\n+<![CDATA[\n+ Rscript $__tool_directory__/testandplot.R adjustedpvaluematrix="${adjustedpvaluematrix}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}" iwtomicsrdata="${iwtomicsrdata}" iwtomicstests="${iwtomicstests}" iwtomicsselectedfeatures="${iwtomicsselectedfeatures}"\n+ regionids="${regionids}"\n+ featureids="${featureids}"\n+ rdatafile="${rdata}"\n+\n+ #set region1 = \'","\'.join( [ str( $r.region0 ) for $r in $regionssection.regions ] )\n+ #set region2 = \'","\'.join( [ str( $r.region1 ) for $r in $regionssection.regions ] )\n+ region1="c(${region1})"\n+ region2="c(${region2})"\n+\n+ features_subset="c(${featureslist})"\n+\n+ statistics="\'${conditionalstatistics.statistics}\'"\n+ #if $conditionalstatistics.statistics == "quantile":\n+ #set probabilities = \'","\'.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] )\n+ testprobs="c(${probabilities})"\n+ #end if\n+\n+ B="${permutations}"\n+\n+ testalpha="${plotres.alpha}"\n+ average="${plotres.average}"\n+ size="${plotres.size}"\n+ plottype="\'${plotres.conditionalplottype.plottype}\'"\n+ #if $plotres.conditionalplottype.plottype == \'boxplot\':\n+ #set probs = \'","\'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )\n+ #if $probs != "":\n+ probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})"\n+ #else:\n+ probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})"\n+ #end if\n+ #end if\n+\n+ groupby="\'${plotsum.conditionalgroupby.groupby}\'"\n+ #if $plotsum.conditionalgroupby.groupby == "test":\n+ summaryalpha="${plotsum.conditionalgroupby.testalphaplot}"\n+ only_significant="${plotsum.conditionalgroupby.testonlysig}"\n+ #elif $plotsum.conditionalgroupby.groupby == "feature":\n+ summaryalpha="${plotsum.conditionalgroupby.featurealphaplot}"\n+ only_significant="${plotsum.conditionalgroupby.featureonlysig}"\n+ #end if\n+\n+ >& /dev/null\n+]]>\n+ <!--\n+ to print the stack add the following line at the end of the command and enable the corresponding entry in output\n+ 2> "${stackerr}"\n+ -->\n+ </command>\n+\n+ <inputs>\n+ <!-- RData -->\n+ <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object" help="File created by \'IWTomics Load Smooth and Plot\'." />\n+ <!-- region IDs -->\n+ <param format="tabular" name="regionids" type="data" label="Select region dataset IDs" help="File created by \'IWTomics Load Smooth and Plot\'." />\n+ <!-- feature IDs -->\n+ <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by \'IWTomics Load Smooth and Plot\'." />\n+\n+ <!-- repeat region ids -->\n+ <sectio'..b' </conditional>\n+ </section>\n+ </inputs>\n+\n+ <outputs>\n+ <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.testandplot.stackerr.txt" />-->\n+ <data format="txt" name="adjustedpvaluematrix" label="${tool.name} on ${on_string}: Adjusted p-value Matrix" from_work_dir="iwtomics.testandplot.adjustedpvalue.matrix.txt" />\n+ <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" />\n+ <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" />\n+ <data format="rdata" name="iwtomicsrdata" label="${tool.name} on ${on_string}: IWTomicsData Object with Test Results" from_work_dir="iwtomics.testandplot.RData" />\n+ <data format="tabular" name="iwtomicstests" label="${tool.name} on ${on_string}: Test IDs" from_work_dir="iwtomics.testandplot.tests.txt" />\n+ <data format="tabular" name="iwtomicsselectedfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.testandplot.selectedfeatures.txt" />\n+ </outputs>\n+\n+ <help>\n+This tool statistically evaluates differences in genomic features between groups of regions along the genome.\n+In particular, it implements the Interval-Wise Testing for omics data, an extended version of the Interval-Wise\n+Testing for functional data presented in Pini and Vantini (2017). It allows to perform multiple two sample permutation\n+tests between pairs of region datasets, on several features. It returns the adjusted p-value curves for every test\n+and all possible scales. Moreover, it creates a graphical representation of the Interval-Wise Testing results\n+and a summary plot (optional) with p-values at the maximum scale. The tool *IWTomics Plot with Threshold on Test Scale*\n+permits to select the scale to be used in the plots.\n+\n+-----\n+\n+**Input files**\n+\n+RData file with the IWTomicsData object, tabular files with region dataset IDs and feature IDs.\n+These files are created by the tool *IWTomics Load Smooth and Plot*.\n+\n+-----\n+\n+**Output**\n+\n+The tool returns:\n+\n+1. TXT file with an adjusted p-value matrix for every test performed. Each matrix contains a p-value curve (row) for every scale considered in the test;\n+2. PDF file with the plotted test results;\n+3. PDF file with the summary plot;\n+4. RData with the IWTomicsData object with the test results;\n+5. Test identifiers;\n+6. Feature identifiers.\n+\n+4-6 can be used as input of the tool *IWTomics Plot with Threshold on Test Scale*\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Notes**\n+\n+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).\n+\n+It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.\n+The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).\n+\n+.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf\n+ </help>\n+\n+ <citations>\n+ <citation type="bibtex">\n+ @ARTICLE{\n+ iwt-functional-data,\n+ author = {A Pini and S. Vantini},\n+ title = {Interval-Wise Testing for functional data},\n+ journal = {Journal of Nonparametric Statistics},\n+ year = {2017},\n+ volume = {29},\n+ number = {2},\n+ pages = {407-424}\n+ }\n+ </citation>\n+ <citation type="bibtex">\n+ @MANUAL{\n+ iwtomics,\n+ author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},\n+ title = {IWTomics: Interval-Wise Testing for Omics Data},\n+ note = {R package version 0.99.12},\n+ year = {2017}\n+ }\n+ </citation>\n+ </citations>\n+\n+</tool>\n' |