| Next changeset 1:ddde82ae5dea (2016-12-11) |
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Commit message:
planemo upload |
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added:
countmatrixforedger.xml plotheatmap.xml test-data/annotation test-data/count.matrix test-data/data1 test-data/data2 test-data/data3 test-data/data4 test-data/done test-data/error.log test-data/heatmap.pdf test-data/rerror.log test-data/rscript.log test-data/script.data test-data/script.log test-data/stats.data tools/script.R tools/scrsh.sh |
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| diff -r 000000000000 -r c5a812cdf478 countmatrixforedger.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/countmatrixforedger.xml Fri Dec 09 10:52:35 2016 -0500 |
| [ |
| @@ -0,0 +1,95 @@ +<tool id="countmatrixforedger" name="countMatrixForEdger" version="1.0"> + <description>Make a count matrix for edgeR</description> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ + #for $i, $s in enumerate( $sample )# + echo -e ${s.sample_data}"\t"${s.sample_name}"\t"${s.sample_group} >> script.data; + #end for# + + cat script.data > /tmp/script.data; + $__tool_directory__/tools/scrsh.sh script.data; + + cat count.matrix > $count_matrix; + cat annotation > $annotation; + cat script.log > $log; + cat error.log > $error_log + + ]]> + </command> + <inputs> + <repeat name="sample" title=""> + <param name="sample_data" type="data" format="data" label="" help="" /> + <param name="sample_name" type="text" label="" help="" /> + <param name="sample_group" type="text" label="" help="" /> + </repeat> + </inputs> + <outputs> +<!-- <data name="output" format="data" /> --> + <data name="count_matrix" format="data" /> + <data name="annotation" format="data" /> + <data name="log" format="data" /> + <data name="error_log" format="data" /> + </outputs> + <tests> +<!-- <test> + <param name="sample_0|sample_data" value="data1" /> + <param name="sample_1|sample_data" value="data2" /> + <param name="sample_2|sample_data" value="data3" /> + <param name="sample_3|sample_data" value="data4" /> + <param name="sample_0|sample_name" value="sample1" /> + <param name="sample_1|sample_name" value="sample2" /> + <param name="sample_2|sample_name" value="sample3" /> + <param name="sample_3|sample_name" value="sample4" /> + <param name="sample_0|sample_group" value="gr1" /> + <param name="sample_1|sample_group" value="gr1" /> + <param name="sample_2|sample_group" value="gr2" /> + <param name="sample_3|sample_group" value="gr2" /> + <output name="output" file="output"/> + + </test> --> + <test> + <param name="sample_0|sample_data" value="data1" /> + <param name="sample_1|sample_data" value="data2" /> + <param name="sample_2|sample_data" value="data3" /> + <param name="sample_3|sample_data" value="data4" /> + <param name="sample_0|sample_name" value="sample1" /> + <param name="sample_1|sample_name" value="sample2" /> + <param name="sample_2|sample_name" value="sample3" /> + <param name="sample_3|sample_name" value="sample4" /> + <param name="sample_0|sample_group" value="gr1" /> + <param name="sample_1|sample_group" value="gr1" /> + <param name="sample_2|sample_group" value="gr2" /> + <param name="sample_3|sample_group" value="gr2" /> + <output name="count_matrix" file="count.matrix"/> + <output name="annotation" file="annotation"/> + <output name="log" file="script.log"/> + <output name="error_log" file="error.log"/> + </test> + + </tests> + <help> + <![CDATA[ + +tutaj cos bedzie + ]]> + </help> + <citations> + <citation type="bibtex"> + @article{Berenger2014, + doi = {10.1186/1758-2946-6-23}, + url = {http://dx.doi.org/10.1186/1758-2946-6-23}, + year = {2014}, + publisher = {Springer Nature}, + volume = {6}, + number = {1}, + pages = {23}, + author = {Francois Berenger and Arnout Voet and Xiao Lee and Kam YJ Zhang}, + title = {A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening}, + journal = {Journal of Cheminformatics} + } + </citation> + </citations> +</tool> |
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| diff -r 000000000000 -r c5a812cdf478 plotheatmap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plotheatmap.xml Fri Dec 09 10:52:35 2016 -0500 |
| [ |
| @@ -0,0 +1,57 @@ +<tool id="plotheatmap" name="plotheatmap" version="1.0"> + <description>Make a count matrix for edgeR</description> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ + $__tool_directory__/tools/script.R $count_matrix $stats_matrix $log_fc $log_cpm $pvalue $fdr > $rscript_log 2> $rerror_log + + + + ]]> + </command> + <inputs> + <param name="count_matrix" type="data" format="data" label=""/> + <param name="stats_matrix" type="data" format="data" label=""/> + <param name="log_fc" type="float" value="0.5" label=""/> + <param name="log_cpm" type="float" value="0.5" label=""/> + <param name="pvalue" type="float" value="0.5" label=""/> + <param name="fdr" type="float" value="0.5" label=""/> + + </inputs> + <outputs> +<!-- <data name="output" format="data" /> --> + <data format="pdf" name="haetamappdf" from_work_dir="heatmap.pdf" > + <filter>(outftype == 'pdf')</filter> + </data> + <data name="rscript_log" format="data" /> + <data name="rerror_log" format="data" /> + </outputs> + <tests> + + <test> + <param name="count_matrix" value="count.matrix"/> + <param name="stats_matrix" value="stats.data"/> + <param name="log_fc" value="1"/> + <param name="log_cpm" value="2"/> + <param name="pvalue" value="0.05"/> + <param name="fdr" value="0.1"/> +<!-- <output name="output" file="done"/> --> + <output name="haetamappdf" file="heatmap.pdf" ftype="pdf" compare="sim_size" /> + <output name="rscript_log" file="rscript.log"/> + <output name="rerror_log" file="rerror.log"/> + + </test> + + </tests> + <help> + <![CDATA[ + +tutaj cos bedzie + ]]> + </help> + <citations> + + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r c5a812cdf478 test-data/annotation --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotation Fri Dec 09 10:52:35 2016 -0500 |
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|
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| diff -r 000000000000 -r c5a812cdf478 test-data/count.matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count.matrix Fri Dec 09 10:52:35 2016 -0500 |
| b |
| b'@@ -0,0 +1,1681 @@\n+#\tgr1:gr1\tgr1:gr1\tgr2:gr2\tgr2:gr2\n+#Feature\tsample1\tsample2\tsample3\tsample4\n+Cj0001\t416\t407\t516\t506\n+Cj0002\t1818\t1778\t2774\t2645\n+Cj0003\t3067\t3039\t2904\t2873\n+Cj0004c\t42\t36\t60\t59\n+Cj0005c\t215\t229\t235\t216\n+Cj0006\t208\t201\t216\t228\n+Cj0007\t3190\t3015\t3058\t3067\n+Cj0008\t2059\t2058\t1783\t1815\n+Cj0009\t2369\t2426\t1803\t1772\n+Cj0010c\t261\t271\t224\t203\n+Cj0011c\t2347\t2313\t2225\t2331\n+Cj0012c\t22026\t21796\t20028\t19844\n+Cj0013\t713\t755\t578\t612\n+Cj0014c\t582\t552\t687\t700\n+Cj0015c\t942\t902\t880\t846\n+Cj0016\t266\t279\t312\t309\n+Cj0017c\t364\t386\t350\t339\n+Cj0018c\t77\t80\t34\t49\n+Cj0019c\t1128\t1168\t1338\t1279\n+Cj0020c\t769\t794\t1258\t1199\n+Cj0021c\t330\t348\t357\t358\n+Cj0022c\t67\t62\t62\t67\n+Cj0023\t1243\t1292\t1355\t1287\n+Cj0024\t1722\t1626\t1657\t1578\n+Cj0025c\t92\t93\t76\t82\n+Cj0026c\t416\t386\t306\t291\n+Cj0027\t2958\t2930\t3305\t3106\n+Cj0028\t589\t609\t568\t643\n+Cj0029\t274\t229\t229\t226\n+Cj0030\t175\t167\t214\t197\n+Cj0031\t455\t429\t443\t465\n+Cj0033\t347\t326\t315\t272\n+Cj0034c\t661\t585\t487\t509\n+Cj0035c\t76\t62\t50\t68\n+Cj0036\t724\t737\t774\t712\n+Cj0037c\t976\t1062\t1175\t1136\n+Cj0038c\t56\t53\t92\t116\n+Cj0039c\t2107\t2168\t1869\t1899\n+Cj0040\t583\t556\t712\t705\n+Cj0041\t1199\t1198\t996\t1000\n+Cj0042\t717\t736\t792\t816\n+Cj0043\t1084\t1027\t942\t973\n+Cj0044c\t990\t998\t1149\t1065\n+Cj0045c\t491\t494\t497\t485\n+Cj0053c\t556\t555\t482\t437\n+Cj0054c\t577\t489\t609\t637\n+Cj0055c\t342\t297\t496\t481\n+Cj0056c\t628\t586\t693\t679\n+Cj0057\t107\t87\t120\t113\n+Cj0058\t85\t95\t108\t123\n+Cj0059c\t456\t379\t432\t418\n+Cj0060c\t357\t338\t398\t398\n+Cj0061c\t481\t452\t417\t376\n+Cj0062c\t543\t523\t562\t568\n+Cj0063c\t672\t707\t922\t890\n+Cj0064c\t1215\t1239\t1167\t1117\n+Cj0065c\t452\t419\t239\t201\n+Cj0066c\t1053\t1091\t693\t754\n+Cj0067\t293\t296\t474\t409\n+Cj0068\t140\t111\t126\t103\n+Cj0069\t4382\t4382\t4565\t4364\n+Cj0070c\t46\t47\t45\t49\n+Cj0073c\t4150\t4181\t4789\t4752\n+Cj0074c\t16990\t16764\t13677\t13480\n+Cj0075c\t7511\t7456\t5857\t5921\n+Cj0076c\t10698\t10831\t10024\t9861\n+Cj0077c\t107\t88\t94\t96\n+Cj0078c\t279\t290\t317\t296\n+Cj0079c\t356\t369\t270\t279\n+Cj0080\t32\t37\t30\t26\n+Cj0081\t227\t264\t292\t258\n+Cj0082\t233\t197\t191\t208\n+Cj0085c\t461\t491\t530\t542\n+Cj0086c\t300\t302\t366\t336\n+Cj0087\t13092\t12857\t12609\t12257\n+Cj0088\t6614\t6636\t5357\t5250\n+Cj0089\t1546\t1572\t2069\t1999\n+Cj0090\t217\t186\t208\t221\n+Cj0091\t1058\t1021\t731\t701\n+Cj0092\t702\t719\t699\t674\n+Cj0093\t602\t656\t700\t691\n+Cj0094\t4440\t4542\t4809\t4757\n+Cj0095\t4239\t4229\t5271\t5133\n+Cj0096\t187\t197\t241\t206\n+Cj0097\t161\t180\t160\t159\n+Cj0098\t128\t151\t123\t138\n+Cj0099\t872\t887\t2327\t2232\n+Cj0100\t1185\t1086\t1375\t1366\n+Cj0101\t571\t537\t751\t702\n+Cj0102\t1935\t1958\t2539\t2472\n+Cj0103\t1098\t1205\t1281\t1266\n+Cj0104\t662\t710\t1136\t1041\n+Cj0105\t3419\t3533\t4488\t4474\n+Cj0106\t1107\t1169\t1445\t1400\n+Cj0107\t6338\t6201\t5494\t5364\n+Cj0108\t283\t286\t282\t286\n+Cj0109\t444\t459\t384\t372\n+Cj0110\t174\t167\t147\t147\n+Cj0111\t302\t330\t336\t343\n+Cj0112\t682\t676\t767\t762\n+Cj0113\t5780\t5822\t6496\t6260\n+Cj0114\t2240\t2320\t2674\t2574\n+Cj0115\t1920\t2000\t2089\t2015\n+Cj0116\t899\t858\t1513\t1597\n+Cj0117\t426\t412\t489\t495\n+Cj0118\t433\t481\t426\t411\n+Cj0119\t143\t121\t113\t136\n+Cj0120\t27\t29\t40\t45\n+Cj0121\t34\t28\t36\t36\n+Cj0122\t55\t64\t96\t87\n+Cj0123c\t97\t121\t102\t122\n+Cj0124c\t258\t262\t325\t283\n+Cj0125c\t165\t151\t155\t159\n+Cj0126c\t217\t232\t219\t234\n+Cj0127c\t696\t701\t806\t837\n+Cj0128c\t105\t82\t106\t110\n+Cj0129c\t1859\t1872\t2101\t2043\n+Cj0130\t256\t249\t255\t251\n+Cj0131\t1855\t1830\t2423\t2332\n+Cj0132\t846\t880\t928\t901\n+Cj0133\t189\t151\t255\t276\n+Cj0134\t158\t150\t137\t136\n+Cj0135\t160\t155\t201\t146\n+Cj0136\t3506\t3422\t3497\t3481\n+Cj0137\t213\t229\t239\t247\n+Cj0138\t214\t193\t175\t183\n+Cj0139\t708\t738\t889\t860\n+Cj0140\t382\t369\t222\t205\n+Cj0141c\t198\t184\t164\t160\n+Cj0142c\t330\t310\t260\t297\n+Cj0143c\t917\t949\t1025\t1011\n+Cj0144\t3419\t3409\t4208\t4102\n+Cj0145\t194\t163\t204\t195\n+Cj0146c\t618\t631\t671\t680\n+Cj0147c\t1867\t1795\t2243\t2239\n+Cj0148c\t182\t165\t217\t197\n+Cj0149c\t820\t795\t885\t923\n+Cj0150c\t895\t858\t1170\t1147\n+Cj0151c\t498\t441\t588\t567\n+Cj0152c\t1911\t1883\t2152\t2107\n+Cj0153c\t1286\t1175\t1522\t1396\n+Cj0154c\t143\t121\t139\t168\n+Cj0155c\t378\t365\t401\t369\n+Cj0156c\t109\t130\t129\t132\n+Cj0157c\t254\t274\t259\t242\n+Cj0158c\t334\t264\t223\t204\n+Cj0159c\t296\t285\t292\t258\n+Cj0160c\t154\t140\t206\t197\n+Cj0161c\t247\t213\t298\t312\n+Cj0162c\t197\t218\t259\t232\n+Cj0163c\t207\t222\t194\t189\n+Cj0164c\t301\t284\t268\t241\n+Cj0166\t191\t170\t261\t270\n+Cj0167c\t64\t'..b'\n+Cj1614\t22\t19\t16\t12\n+Cj1615\t19\t20\t21\t23\n+Cj1616\t3\t5\t5\t6\n+Cj1617\t32\t27\t36\t25\n+Cj1618c\t96\t94\t164\t135\n+Cj1619\t757\t715\t731\t693\n+Cj1620c\t159\t155\t139\t127\n+Cj1621\t740\t678\t726\t749\n+Cj1622\t180\t144\t115\t112\n+Cj1623\t449\t473\t498\t418\n+Cj1624c\t9284\t9224\t9353\t9042\n+Cj1625c\t4309\t4290\t4604\t4477\n+Cj1626c\t1145\t1141\t1002\t955\n+Cj1627c\t314\t280\t230\t237\n+Cj1628\t2\t0\t2\t0\n+Cj1629\t9\t2\t2\t1\n+Cj1630\t45\t38\t47\t46\n+Cj1631c\t876\t890\t1050\t995\n+Cj1632c\t139\t116\t124\t127\n+Cj1633\t265\t259\t258\t257\n+Cj1634c\t346\t373\t349\t381\n+Cj1635c\t219\t232\t232\t224\n+Cj1636c\t274\t297\t274\t267\n+Cj1637c\t653\t715\t1024\t976\n+Cj1638\t361\t354\t348\t359\n+Cj1639\t1637\t1594\t1888\t1772\n+Cj1640\t446\t457\t555\t545\n+Cj1641\t542\t566\t646\t622\n+Cj1642\t332\t331\t316\t313\n+Cj1643\t527\t490\t609\t590\n+Cj1644\t189\t208\t181\t201\n+Cj1645\t470\t487\t538\t474\n+Cj1646\t103\t83\t113\t124\n+Cj1647\t61\t44\t84\t85\n+Cj1648\t85\t88\t80\t80\n+Cj1649\t60\t63\t80\t94\n+Cj1650\t155\t176\t178\t192\n+Cj1651c\t378\t370\t465\t417\n+Cj1652c\t123\t117\t137\t123\n+Cj1653c\t259\t263\t205\t237\n+Cj1654c\t885\t893\t934\t927\n+Cj1655c\t965\t1022\t977\t984\n+Cj1656c\t1988\t1995\t2292\t2267\n+Cj1658\t31\t40\t30\t27\n+Cj1659\t35\t45\t48\t40\n+Cj1660\t28\t24\t35\t25\n+Cj1661\t15\t20\t15\t15\n+Cj1662\t7\t18\t14\t22\n+Cj1663\t28\t27\t17\t22\n+Cj1664\t16\t20\t13\t5\n+Cj1665\t54\t54\t56\t67\n+Cj1666c\t189\t202\t184\t154\n+Cj1667c\t0\t0\t0\t0\n+Cj1668c\t90\t57\t61\t68\n+Cj1669c\t118\t132\t99\t101\n+Cj1670c\t365\t363\t451\t434\n+Cj1671c\t274\t275\t423\t404\n+Cj1672c\t3104\t3039\t3540\t3294\n+Cj1673c\t4945\t4917\t4231\t4255\n+Cj1674\t246\t249\t243\t211\n+Cj1675\t45\t53\t46\t41\n+Cj1676\t83\t81\t95\t101\n+Cj1677\t943\t901\t911\t878\n+Cj1679\t269\t293\t263\t310\n+Cj1680c\t559\t506\t1646\t1629\n+Cj1681c\t463\t446\t367\t338\n+Cj1682c\t2874\t2645\t3685\t3618\n+Cj1684c\t180\t156\t212\t197\n+Cj1685c\t258\t243\t229\t218\n+Cj1686c\t798\t718\t756\t725\n+Cj1687\t139\t139\t188\t189\n+Cj1688c\t1473\t1439\t1095\t1055\n+Cj1689c\t1138\t1131\t1086\t1029\n+Cj1690c\t1203\t1209\t1313\t1302\n+Cj1691c\t1851\t1905\t2648\t2644\n+Cj1692c\t1925\t1890\t1528\t1498\n+Cj1693c\t722\t698\t717\t698\n+Cj1694c\t491\t484\t632\t596\n+Cj1695c\t2294\t2366\t1687\t1708\n+Cj1696c\t1249\t1262\t582\t584\n+Cj1697c\t1316\t1283\t1073\t965\n+Cj1698c\t656\t671\t514\t523\n+Cj1699c\t996\t1056\t879\t851\n+Cj1700c\t2216\t2133\t2446\t2355\n+Cj1701c\t2898\t2781\t2887\t2808\n+Cj1702c\t2100\t2123\t2141\t2141\n+Cj1703c\t1255\t1224\t1176\t1143\n+Cj1704c\t4911\t4712\t3669\t3693\n+Cj1705c\t601\t635\t769\t803\n+Cj1706c\t2484\t2455\t2694\t2618\n+Cj1707c\t2235\t2121\t2070\t2040\n+Cj1708c\t1271\t1256\t1359\t1381\n+Cj1709c\t58\t50\t58\t53\n+Cj1710c\t480\t422\t526\t539\n+Cj1711c\t212\t188\t250\t236\n+Cj1712\t137\t145\t91\t78\n+Cj1713\t42\t48\t31\t41\n+Cj1714\t6\t4\t3\t8\n+Cj1715\t83\t83\t66\t60\n+Cj1716c\t63\t62\t58\t59\n+Cj1717c\t225\t212\t211\t204\n+Cj1718c\t128\t113\t115\t118\n+Cj1719c\t170\t151\t152\t144\n+Cj1720\t786\t765\t790\t791\n+Cj1721c\t95\t104\t119\t104\n+Cj1722c\t4\t6\t6\t6\n+Cj1723c\t36\t39\t27\t38\n+Cj1724c\t365\t373\t341\t307\n+Cj1725\t629\t664\t692\t678\n+Cj1726c\t462\t417\t493\t493\n+Cj1727c\t442\t464\t503\t471\n+Cj1728c\t2\t2\t3\t6\n+Cj1729c\t4646\t4704\t5157\t4871\n+Cj1731c\t81\t77\t63\t63\n+Cjp01\t20\t21\t25\t21\n+Cjp02\t353\t362\t332\t313\n+Cjp03\t288\t330\t279\t273\n+Cjp04\t20\t21\t25\t21\n+Cjp05\t353\t362\t332\t313\n+Cjp06\t124\t120\t127\t119\n+Cjp07\t182\t174\t170\t153\n+Cjp08\t18\t21\t28\t11\n+Cjp09\t147\t177\t163\t194\n+Cjp10\t973\t978\t878\t889\n+Cjp11\t9427\t9126\t12373\t12282\n+Cjp12\t70\t53\t57\t54\n+Cjp13\t228\t249\t190\t208\n+Cjp14\t20\t21\t25\t21\n+Cjp15\t353\t362\t332\t313\n+Cjp16\t43\t40\t27\t33\n+Cjp17\t6\t4\t6\t6\n+Cjp19\t53\t55\t37\t38\n+Cjp20\t42\t40\t40\t39\n+Cjp21\t95\t96\t100\t90\n+Cjp22\t285\t278\t259\t243\n+Cjp23\t14\t13\t15\t7\n+Cjp24\t17\t14\t19\t13\n+Cjp25\t105\t92\t110\t108\n+Cjp26\t256\t268\t239\t248\n+Cjp27\t15\t13\t9\t7\n+Cjp28\t74\t103\t83\t75\n+Cjp29\t28\t18\t43\t37\n+Cjp30\t32\t40\t31\t38\n+Cjp32\t162\t170\t160\t166\n+Cjp33\t60\t52\t47\t46\n+Cjp34\t176\t161\t132\t138\n+Cjp35\t38\t37\t25\t33\n+Cjp36\t17\t15\t20\t9\n+Cjr01\t32453\t31605\t31153\t31081\n+Cjr02\t199051\t195254\t206408\t204396\n+Cjr03\t1584\t1599\t1782\t1708\n+Cjr04\t32453\t31605\t31153\t31081\n+Cjr05\t199060\t195263\t206415\t204401\n+Cjr06\t1086\t1085\t1305\t1238\n+Cjr07\t32453\t31605\t31153\t31081\n+Cjr08\t199060\t195263\t206415\t204401\n+Cjr09\t1056\t1056\t1274\t1210\n+Cjs01\t12294\t11902\t14430\t14462\n+Cjs02\t15\t19\t23\t28\n+Cjs03\t2680\t2690\t3212\t3083\n+Cjt01\t77\t84\t95\t85\n+Cjt02\t70\t70\t66\t68\n+Cjt03\t50\t55\t36\t37\n+Cjt04\t32\t40\t40\t39\n+Cjt05\t270\t252\t237\t233\n+Cjt06\t36\t35\t46\t36\n+Cjt1\t47\t55\t66\t78\n+Cjt2\t77\t74\t72\t73\n+Cjt3\t73\t85\t65\t54\n+Cjt4\t85\t78\t77\t63\n' |
| b |
| diff -r 000000000000 -r c5a812cdf478 test-data/data1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data1 Fri Dec 09 10:52:35 2016 -0500 |
| b |
| b'@@ -0,0 +1,1681 @@\n+gene_ID start_coord end_coord average_cov #reads RPKM\n+\n+Cj0001 1 1323 11.6 416 157\n+Cj0002 1483 2550 63.0 1818 851\n+Cj0003 2579 4888 49.1 3067 663\n+Cj0004c 4916 5257 4.5 42 61\n+Cj0005c 5260 6498 6.4 215 87\n+Cj0006 6703 8010 5.9 208 79\n+Cj0007 8144 12634 26.3 3190 355\n+Cj0008 12644 14395 43.5 2059 587\n+Cj0009 14398 15843 60.6 2369 819\n+Cj0010c 15844 16419 16.8 261 226\n+Cj0011c 16452 16691 361.8 2347 4887\n+Cj0012c 16756 17403 1257.7 22026 16986\n+Cj0013 17563 19239 15.7 713 212\n+Cj0014c 19251 19775 41.0 582 554\n+Cj0015c 19867 21093 28.4 942 384\n+Cj0016 21159 21833 14.6 266 197\n+Cj0017c 21854 23380 8.8 364 119\n+Cj0018c 23392 23559 16.9 77 229\n+Cj0019c 23665 25443 23.5 1128 317\n+Cj0020c 25433 26347 31.1 769 420\n+Cj0021c 26411 27289 13.9 330 188\n+Cj0022c 27402 28304 2.8 67 0\n+Cj0023 28382 29710 34.6 1243 467\n+Cj0024 29726 32095 26.9 1722 363\n+Cj0025c 32134 33519 2.5 92 0\n+Cj0026c 33639 34262 24.7 416 333\n+Cj0027 34382 36013 67.1 2958 906\n+Cj0028 36000 37571 13.9 589 187\n+Cj0029 37667 38662 10.2 274 137\n+Cjr01 39249 40761 793.6 32453 10719\n+Cjp01 40866 40941 9.9 20 132\n+Cjp02 40950 41026 169.8 353 2291\n+Cjr02 41568 44457 2548.4 199051 34419\n+Cjr03 44741 44860 488.6 1584 6596\n+Cj0030 44966 46363 4.6 175 63\n+Cj0031 46424 50156 4.5 455 61\n+Cj0033 50156 51937 7.2 347 97\n+Cj0034c 51967 52668 34.8 661 471\n'..b'2294 2100\n+Cj1696c 1615195 1615428 197.5 1249 2667\n+Cj1697c 1615428 1615796 132.0 1316 1782\n+Cj1698c 1615796 1616047 96.4 656 1301\n+Cj1699c 1616057 1616242 198.2 996 2676\n+Cj1700c 1616229 1616654 192.4 2216 2600\n+Cj1701c 1616657 1617358 152.7 2898 2063\n+Cj1702c 1617358 1617783 182.4 2100 2463\n+Cj1703c 1617794 1618075 164.7 1255 2224\n+Cj1704c 1618077 1618907 218.7 4911 2953\n+Cj1705c 1618909 1619190 78.9 601 1065\n+Cj1706c 1619193 1619807 149.5 2484 2018\n+Cj1707c 1619804 1620379 143.6 2235 1939\n+Cj1708c 1620389 1620700 150.8 1271 2036\n+Cj1709c 1620899 1621660 2.8 58 0\n+Cj1710c 1621696 1623690 8.9 480 120\n+Cj1711c 1623659 1624459 9.8 212 132\n+Cj1712 1624541 1625077 9.4 137 127\n+Cj1713 1625100 1626170 1.4 42 0\n+Cj1714 1626167 1626265 2.1 6 0\n+Cjp34 1626279 1626355 84.7 176 1142\n+Cjt06 1626491 1626578 15.1 36 204\n+Cjp35 1626625 1626700 18.4 38 250\n+Cjp36 1626704 1626779 8.3 17 112\n+Cj1715 1626807 1627337 5.8 83 78\n+Cj1716c 1627317 1627919 3.9 63 52\n+Cj1717c 1627921 1629333 5.9 225 80\n+Cj1718c 1629320 1630396 4.4 128 59\n+Cj1719c 1630393 1631928 4.1 170 55\n+Cj1720 1632248 1632877 46.2 786 623\n+Cj1721c 1632901 1633545 5.5 95 74\n+Cj1722c 1633791 1633892 1.5 4 0\n+Cj1723c 1633895 1634119 5.9 36 80\n+Cj1724c 1634296 1634679 35.2 365 475\n+Cj1725 1634839 1635438 38.8 629 524\n+Cj1726c 1635443 1636324 19.4 462 262\n+Cj1727c 1636407 1637678 12.9 442 174\n+Cj1728c 1637923 1638078 0.5 2 0\n+Cj1729c 1638104 1640701 66.2 4646 894\n+Cj1731c 1640904 1641386 6.2 81 84\n' |
| b |
| diff -r 000000000000 -r c5a812cdf478 test-data/data2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data2 Fri Dec 09 10:52:35 2016 -0500 |
| b |
| b'@@ -0,0 +1,1681 @@\n+gene_ID start_coord end_coord average_cov #reads RPKM\n+\n+Cj0001 1 1323 11.4 407 154\n+Cj0002 1483 2550 61.6 1778 835\n+Cj0003 2579 4888 48.7 3039 660\n+Cj0004c 4916 5257 3.9 36 53\n+Cj0005c 5260 6498 6.8 229 93\n+Cj0006 6703 8010 5.7 201 77\n+Cj0007 8144 12634 24.8 3015 337\n+Cj0008 12644 14395 43.5 2058 589\n+Cj0009 14398 15843 62.1 2426 842\n+Cj0010c 15844 16419 17.4 271 236\n+Cj0011c 16452 16691 356.6 2313 4834\n+Cj0012c 16756 17403 1244.6 21796 16872\n+Cj0013 17563 19239 16.6 755 226\n+Cj0014c 19251 19775 38.9 552 527\n+Cj0015c 19867 21093 27.2 902 369\n+Cj0016 21159 21833 15.3 279 207\n+Cj0017c 21854 23380 9.4 386 127\n+Cj0018c 23392 23559 17.7 80 239\n+Cj0019c 23665 25443 24.3 1168 329\n+Cj0020c 25433 26347 32.1 794 435\n+Cj0021c 26411 27289 14.6 348 199\n+Cj0022c 27402 28304 2.6 62 0\n+Cj0023 28382 29710 36.0 1292 488\n+Cj0024 29726 32095 25.4 1626 344\n+Cj0025c 32134 33519 2.5 93 0\n+Cj0026c 33639 34262 22.9 386 310\n+Cj0027 34382 36013 66.4 2930 901\n+Cj0028 36000 37571 14.3 609 194\n+Cj0029 37667 38662 8.5 229 115\n+Cjr01 39249 40761 772.9 31605 10478\n+Cjp01 40866 40941 10.1 21 139\n+Cjp02 40950 41026 174.0 362 2358\n+Cjr02 41568 44457 2499.8 195254 33890\n+Cjr03 44741 44860 493.0 1599 6684\n+Cj0030 44966 46363 4.4 167 60\n+Cj0031 46424 50156 4.2 429 58\n+Cj0033 50156 51937 6.8 326 92\n+Cj0034c 51967 52668 30.8 585 418\n'..b'2366 2174\n+Cj1696c 1615195 1615428 199.5 1262 2705\n+Cj1697c 1615428 1615796 128.7 1283 1744\n+Cj1698c 1615796 1616047 98.6 671 1336\n+Cj1699c 1616057 1616242 210.0 1056 2848\n+Cj1700c 1616229 1616654 185.2 2133 2512\n+Cj1701c 1616657 1617358 146.6 2781 1987\n+Cj1702c 1617358 1617783 184.4 2123 2500\n+Cj1703c 1617794 1618075 160.6 1224 2177\n+Cj1704c 1618077 1618907 209.8 4712 2844\n+Cj1705c 1618909 1619190 83.3 635 1130\n+Cj1706c 1619193 1619807 147.7 2455 2002\n+Cj1707c 1619804 1620379 136.2 2121 1847\n+Cj1708c 1620389 1620700 148.9 1256 2019\n+Cj1709c 1620899 1621660 2.4 50 0\n+Cj1710c 1621696 1623690 7.8 422 106\n+Cj1711c 1623659 1624459 8.7 188 118\n+Cj1712 1624541 1625077 10.0 145 135\n+Cj1713 1625100 1626170 1.6 48 0\n+Cj1714 1626167 1626265 1.7 4 0\n+Cjp34 1626279 1626355 77.1 161 1049\n+Cjt06 1626491 1626578 14.6 35 200\n+Cjp35 1626625 1626700 18.2 37 244\n+Cjp36 1626704 1626779 7.1 15 99\n+Cj1715 1626807 1627337 5.8 83 78\n+Cj1716c 1627317 1627919 3.8 62 52\n+Cj1717c 1627921 1629333 5.6 212 75\n+Cj1718c 1629320 1630396 3.9 113 53\n+Cj1719c 1630393 1631928 3.6 151 49\n+Cj1720 1632248 1632877 44.9 765 609\n+Cj1721c 1632901 1633545 6.0 104 81\n+Cj1722c 1633791 1633892 2.0 6 0\n+Cj1723c 1633895 1634119 6.4 39 87\n+Cj1724c 1634296 1634679 36.0 373 487\n+Cj1725 1634839 1635438 41.0 664 555\n+Cj1726c 1635443 1636324 17.5 417 237\n+Cj1727c 1636407 1637678 13.5 464 183\n+Cj1728c 1637923 1638078 0.5 2 0\n+Cj1729c 1638104 1640701 67.0 4704 908\n+Cj1731c 1640904 1641386 5.9 77 80\n' |
| b |
| diff -r 000000000000 -r c5a812cdf478 test-data/data3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data3 Fri Dec 09 10:52:35 2016 -0500 |
| b |
| b'@@ -0,0 +1,1681 @@\n+gene_ID start_coord end_coord average_cov #reads RPKM\n+\n+Cj0001 1 1323 14.4 516 189\n+Cj0002 1483 2550 96.1 2774 1258\n+Cj0003 2579 4888 46.5 2904 609\n+Cj0004c 4916 5257 6.5 60 85\n+Cj0005c 5260 6498 7.0 235 92\n+Cj0006 6703 8010 6.1 216 80\n+Cj0007 8144 12634 25.2 3058 330\n+Cj0008 12644 14395 37.7 1783 493\n+Cj0009 14398 15843 46.1 1803 604\n+Cj0010c 15844 16419 14.4 224 188\n+Cj0011c 16452 16691 343.0 2225 4491\n+Cj0012c 16756 17403 1143.6 20028 14971\n+Cj0013 17563 19239 12.8 578 167\n+Cj0014c 19251 19775 48.4 687 634\n+Cj0015c 19867 21093 26.5 880 347\n+Cj0016 21159 21833 17.1 312 224\n+Cj0017c 21854 23380 8.5 350 111\n+Cj0018c 23392 23559 7.4 34 98\n+Cj0019c 23665 25443 27.8 1338 364\n+Cj0020c 25433 26347 50.9 1258 666\n+Cj0021c 26411 27289 15.0 357 197\n+Cj0022c 27402 28304 2.6 62 0\n+Cj0023 28382 29710 37.7 1355 494\n+Cj0024 29726 32095 25.9 1657 339\n+Cj0025c 32134 33519 2.0 76 0\n+Cj0026c 33639 34262 18.2 306 238\n+Cj0027 34382 36013 74.9 3305 981\n+Cj0028 36000 37571 13.4 568 175\n+Cj0029 37667 38662 8.5 229 111\n+Cjr01 39249 40761 761.8 31153 9974\n+Cjp01 40866 40941 12.3 25 159\n+Cjp02 40950 41026 159.7 332 2089\n+Cjr02 41568 44457 2642.6 206408 34596\n+Cjr03 44741 44860 549.3 1782 7193\n+Cj0030 44966 46363 5.7 214 74\n+Cj0031 46424 50156 4.4 443 57\n+Cj0033 50156 51937 6.5 315 86\n+Cj0034c 51967 52668 25.6 487 336\n'..b'1687 1497\n+Cj1696c 1615195 1615428 92.0 582 1205\n+Cj1697c 1615428 1615796 107.6 1073 1409\n+Cj1698c 1615796 1616047 75.5 514 988\n+Cj1699c 1616057 1616242 174.9 879 2289\n+Cj1700c 1616229 1616654 212.4 2446 2781\n+Cj1701c 1616657 1617358 152.2 2887 1992\n+Cj1702c 1617358 1617783 186.0 2141 2434\n+Cj1703c 1617794 1618075 154.3 1176 2020\n+Cj1704c 1618077 1618907 163.4 3669 2139\n+Cj1705c 1618909 1619190 101.0 769 1321\n+Cj1706c 1619193 1619807 162.1 2694 2122\n+Cj1707c 1619804 1620379 133.0 2070 1741\n+Cj1708c 1620389 1620700 161.2 1359 2110\n+Cj1709c 1620899 1621660 2.8 58 0\n+Cj1710c 1621696 1623690 9.7 526 128\n+Cj1711c 1623659 1624459 11.6 250 151\n+Cj1712 1624541 1625077 6.3 91 82\n+Cj1713 1625100 1626170 1.1 31 0\n+Cj1714 1626167 1626265 1.1 3 0\n+Cjp34 1626279 1626355 63.4 132 830\n+Cjt06 1626491 1626578 19.2 46 253\n+Cjp35 1626625 1626700 12.2 25 159\n+Cjp36 1626704 1626779 9.9 20 127\n+Cj1715 1626807 1627337 4.6 66 60\n+Cj1716c 1627317 1627919 3.6 58 47\n+Cj1717c 1627921 1629333 5.5 211 72\n+Cj1718c 1629320 1630396 4.0 115 52\n+Cj1719c 1630393 1631928 3.7 152 48\n+Cj1720 1632248 1632877 46.4 790 607\n+Cj1721c 1632901 1633545 6.8 119 89\n+Cj1722c 1633791 1633892 2.3 6 0\n+Cj1723c 1633895 1634119 4.5 27 58\n+Cj1724c 1634296 1634679 32.9 341 430\n+Cj1725 1634839 1635438 42.7 692 559\n+Cj1726c 1635443 1636324 20.7 493 271\n+Cj1727c 1636407 1637678 14.6 503 192\n+Cj1728c 1637923 1638078 0.7 3 0\n+Cj1729c 1638104 1640701 73.5 5157 962\n+Cj1731c 1640904 1641386 4.8 63 63\n' |
| b |
| diff -r 000000000000 -r c5a812cdf478 test-data/data4 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data4 Fri Dec 09 10:52:35 2016 -0500 |
| b |
| b'@@ -0,0 +1,1681 @@\n+gene_ID start_coord end_coord average_cov #reads RPKM\n+\n+Cj0001 1 1323 14.1 506 188\n+Cj0002 1483 2550 91.7 2645 1219\n+Cj0003 2579 4888 46.0 2873 612\n+Cj0004c 4916 5257 6.4 59 85\n+Cj0005c 5260 6498 6.4 216 86\n+Cj0006 6703 8010 6.4 228 86\n+Cj0007 8144 12634 25.3 3067 336\n+Cj0008 12644 14395 38.3 1815 510\n+Cj0009 14398 15843 45.3 1772 603\n+Cj0010c 15844 16419 13.1 203 174\n+Cj0011c 16452 16691 359.4 2331 4782\n+Cj0012c 16756 17403 1133.1 19844 15077\n+Cj0013 17563 19239 13.5 612 180\n+Cj0014c 19251 19775 49.3 700 656\n+Cj0015c 19867 21093 25.5 846 339\n+Cj0016 21159 21833 16.9 309 225\n+Cj0017c 21854 23380 8.2 339 109\n+Cj0018c 23392 23559 10.8 49 144\n+Cj0019c 23665 25443 26.6 1279 354\n+Cj0020c 25433 26347 48.5 1199 645\n+Cj0021c 26411 27289 15.1 358 201\n+Cj0022c 27402 28304 2.7 67 0\n+Cj0023 28382 29710 35.8 1287 477\n+Cj0024 29726 32095 24.6 1578 328\n+Cj0025c 32134 33519 2.2 82 0\n+Cj0026c 33639 34262 17.2 291 230\n+Cj0027 34382 36013 70.4 3106 937\n+Cj0028 36000 37571 15.1 643 201\n+Cj0029 37667 38662 8.4 226 112\n+Cjr01 39249 40761 760.1 31081 10114\n+Cjp01 40866 40941 10.0 21 136\n+Cjp02 40950 41026 150.6 313 2001\n+Cjr02 41568 44457 2616.8 204396 34820\n+Cjr03 44741 44860 526.7 1708 7008\n+Cj0030 44966 46363 5.2 197 69\n+Cj0031 46424 50156 4.6 465 61\n+Cj0033 50156 51937 5.6 272 75\n+Cj0034c 51967 52668 26.8 509 357\n'..b'1708 1540\n+Cj1696c 1615195 1615428 92.3 584 1229\n+Cj1697c 1615428 1615796 96.7 965 1288\n+Cj1698c 1615796 1616047 76.8 523 1022\n+Cj1699c 1616057 1616242 169.3 851 2253\n+Cj1700c 1616229 1616654 204.5 2355 2722\n+Cj1701c 1616657 1617358 148.0 2808 1969\n+Cj1702c 1617358 1617783 186.0 2141 2474\n+Cj1703c 1617794 1618075 150.0 1143 1996\n+Cj1704c 1618077 1618907 164.4 3693 2188\n+Cj1705c 1618909 1619190 105.4 803 1402\n+Cj1706c 1619193 1619807 157.5 2618 2096\n+Cj1707c 1619804 1620379 131.0 2040 1744\n+Cj1708c 1620389 1620700 163.8 1381 2179\n+Cj1709c 1620899 1621660 2.6 53 0\n+Cj1710c 1621696 1623690 10.0 539 133\n+Cj1711c 1623659 1624459 10.9 236 145\n+Cj1712 1624541 1625077 5.4 78 72\n+Cj1713 1625100 1626170 1.4 41 0\n+Cj1714 1626167 1626265 2.9 8 0\n+Cjp34 1626279 1626355 66.2 138 882\n+Cjt06 1626491 1626578 15.1 36 201\n+Cjp35 1626625 1626700 16.1 33 214\n+Cjp36 1626704 1626779 4.5 9 58\n+Cj1715 1626807 1627337 4.2 60 56\n+Cj1716c 1627317 1627919 3.6 59 48\n+Cj1717c 1627921 1629333 5.3 204 71\n+Cj1718c 1629320 1630396 4.0 118 54\n+Cj1719c 1630393 1631928 3.5 144 46\n+Cj1720 1632248 1632877 46.5 791 618\n+Cj1721c 1632901 1633545 5.9 104 79\n+Cj1722c 1633791 1633892 2.1 6 0\n+Cj1723c 1633895 1634119 6.2 38 83\n+Cj1724c 1634296 1634679 29.6 307 394\n+Cj1725 1634839 1635438 41.8 678 556\n+Cj1726c 1635443 1636324 20.7 493 275\n+Cj1727c 1636407 1637678 13.7 471 182\n+Cj1728c 1637923 1638078 1.4 6 0\n+Cj1729c 1638104 1640701 69.4 4871 923\n+Cj1731c 1640904 1641386 4.9 63 64\n' |
| b |
| diff -r 000000000000 -r c5a812cdf478 test-data/done --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/done Fri Dec 09 10:52:35 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +DONE |
| b |
| diff -r 000000000000 -r c5a812cdf478 test-data/error.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/error.log Fri Dec 09 10:52:35 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ + |
| b |
| diff -r 000000000000 -r c5a812cdf478 test-data/heatmap.pdf |
| b |
| Binary file test-data/heatmap.pdf has changed |
| b |
| diff -r 000000000000 -r c5a812cdf478 test-data/rerror.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rerror.log Fri Dec 09 10:52:35 2016 -0500 |
| [ |
| @@ -0,0 +1,12 @@ +Loading required package: preprocessCore +Loading required package: gplots + +Attaching package: ‘gplots’ + +The following object is masked from ‘package:stats’: + + lowess + +Warning message: +In heatmap.2(countDataNormLog[wh, ], density.info = c("none"), hclustfun = function(x) hclust(x, : + Discrepancy: Colv is FALSE, while dendrogram is `both'. Omitting column dendogram. |
| b |
| diff -r 000000000000 -r c5a812cdf478 test-data/rscript.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rscript.log Fri Dec 09 10:52:35 2016 -0500 |
| b |
| @@ -0,0 +1,2 @@ +null device + 1 |
| b |
| diff -r 000000000000 -r c5a812cdf478 test-data/script.data --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/script.data Fri Dec 09 10:52:35 2016 -0500 |
| b |
| @@ -0,0 +1,4 @@ +sample1 sample1 gr1 +sample2 sample2 gr1 +sample3 sample3 gr2 +sample4 sample4 gr2 |
| b |
| diff -r 000000000000 -r c5a812cdf478 test-data/stats.data --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stats.data Fri Dec 09 10:52:35 2016 -0500 |
| b |
| b'@@ -0,0 +1,1680 @@\n+Feature\tgr2-gr1:logFC\tgr2-gr1:logCPM\tgr2-gr1:PValue\tgr2-gr1:FDR\n+Cj0001\t0.251163140624812\t7.450466899601\t0.000210979477327028\t0.000648781213245567\n+Cj0002\t0.530387367681972\t9.73328197799141\t3.92647017615346e-62\t1.43316161429601e-60\n+Cj0003\t-0.141096118617414\t10.1328696827574\t3.23730270556559e-07\t1.49736397868998e-06\n+Cj0004c\t0.546789320738327\t4.27438964069929\t0.0101429432128199\t0.0223216152515204\n+Cj0005c\t-0.0386100455851845\t6.41352518261495\t0.713021814662884\t0.801314341913642\n+Cj0006\t0.0572262525537494\t6.34479964715941\t0.583897736817362\t0.685569440640805\n+Cj0007\t-0.0798748935714388\t10.1859689943891\t0.00666385884081241\t0.0156265628403967\n+Cj0008\t-0.255567171662445\t9.51034236301575\t5.54315407636418e-14\t4.11812198859091e-13\n+Cj0009\t-0.484759400409196\t9.62822097543145\t9.67052427932554e-50\t2.61884036532058e-48\n+Cj0010c\t-0.378190664513606\t6.51239940649276\t5.36839159626876e-05\t0.000183155708236247\n+Cj0011c\t-0.0936887877353404\t9.76634066448534\t0.00440155038839324\t0.0106487076399312\n+Cj0012c\t-0.197456901899823\t12.949347565317\t3.16490585700577e-60\t1.08446468039034e-58\n+Cj0013\t-0.364006157463179\t7.97565692061486\t2.10110931097026e-10\t1.246559198982e-09\n+Cj0014c\t0.229302522931033\t7.89915141545952\t7.3889787523684e-05\t0.000247133373012481\n+Cj0015c\t-0.156583554909941\t8.4000051205571\t0.00125756904417107\t0.003422136831707\n+Cj0016\t0.127083234386439\t6.79211799297971\t0.143007733647566\t0.22208899226952\n+Cj0017c\t-0.18352203902824\t7.09385501458378\t0.0164829285531994\t0.0345072781057629\n+Cj0018c\t-0.978590636036807\t4.54920036252744\t4.20719576672574e-07\t1.92476340390532e-06\n+Cj0019c\t0.127578640965301\t8.85951692547961\t0.00209796126661611\t0.00539585506454568\n+Cj0020c\t0.591304518222515\t8.57021062747079\t5.91328316644171e-38\t1.18195267100662e-36\n+Cj0021c\t0.015453274262304\t7.04717719970582\t0.872325116787744\t0.922313520835405\n+Cj0022c\t-0.0610807618230194\t4.65022647688166\t0.755664352572265\t0.836913224253848\n+Cj0023\t-0.00155879292653441\t8.93505784928644\t0.977619840313746\t1\n+Cj0024\t-0.11073341579623\t9.28136807636078\t0.0026924493181347\t0.00677754483530458\n+Cj0025c\t-0.288377536563003\t5.0502940017973\t0.0750668237772794\t0.128740752933659\n+Cj0026c\t-0.486893832008047\t7.05351465527707\t3.74572338965654e-10\t2.20669107762573e-09\n+Cj0027\t0.0615279240104964\t10.1819388112351\t0.029781050546858\t0.0580747780118173\n+Cj0028\t-0.0454073637059376\t7.83399574924162\t0.514654351321527\t0.624804523404804\n+Cj0029\t-0.205750222309521\t6.51086679060757\t0.0445561029712139\t0.0819383317510056\n+Cj0030\t0.203806772126169\t6.16664584501197\t0.0580593877928865\t0.103155250903975\n+Cj0031\t-0.022546617798866\t7.40873794226012\t0.758862272204966\t0.839900959151047\n+Cj0033\t-0.258372446631317\t6.90334794900954\t0.00201223850231749\t0.0052138093293072\n+Cj0034c\t-0.384103076190169\t7.73087023750986\t1.48504736931912e-08\t7.74346128287829e-08\n+Cj0035c\t-0.286286710162699\t4.63935723534391\t0.156641404154039\t0.239527247335729\n+Cj0036\t-0.036715548339173\t8.12389305588524\t0.498866673463925\t0.612726514078954\n+Cj0037c\t0.120131023920956\t8.6839310127116\t0.00951372918057541\t0.0210732866677917\n+Cj0038c\t0.869835832472237\t4.93917190533352\t1.23975792218773e-06\t5.32366637174731e-06\n+Cj0039c\t-0.243295673978174\t9.57034537165025\t4.4783463764191e-13\t3.18607778220664e-12\n+Cj0040\t0.253822924348461\t7.91895715827187\t1.00139722177811e-05\t3.76983393579695e-05\n+Cj0041\t-0.325279908421266\t8.69890329220657\t9.2596052853717e-14\t6.73024990222471e-13\n+Cj0042\t0.0850199671165459\t8.17843963926571\t0.106812978809227\t0.173946645412893\n+Cj0043\t-0.201750388999392\t8.57314218916993\t1.16907543313394e-05\t4.36195033829308e-05\n+Cj0044c\t0.09412638483492\t8.63442847229589\t0.0364988448933533\t0.069480227410363\n+Cj0045c\t-0.0655832609551803\t7.54260707321925\t0.324224706788124\t0.437364144790227\n+Cj0053c\t-0.33483860585757\t7.58803703245217\t1.82073447037724e-07\t8.63563044000955e-07\n+Cj0054c\t0.164049771960829\t7.77475968350957\t0.0241552526527\t0.0483969799569014\n+Cj0055c\t0.551168041619309\t7.26004484056475\t3.83461866183206e-14\t2.88714113597132e-13\n+Cj0056c\t0.11529059'..b'\n+Cjp07\t-0.201393832690504\t6.01913520892501\t0.0774727844265827\t0.132057670103789\n+Cjp08\t-0.0610565292975918\t3.02119869200662\t0.911902320795614\t0.956329791765044\n+Cjp09\t0.0789492050345755\t6.02329713096144\t0.551039972472727\t0.65523804092189\n+Cjp10\t-0.204083169510766\t8.45854384462665\t1.76391328367489e-05\t6.39656674576703e-05\n+Cjp11\t0.349068919311388\t11.9923156784728\t2.44148200321706e-81\t1.24219644951559e-79\n+Cjp12\t-0.208848577045457\t4.51381269704339\t0.301685213879788\t0.412584514937022\n+Cjp13\t-0.322231225736962\t6.38128949105107\t0.00107780166219975\t0.00296174957583205\n+Cjp14\t0.104210823178076\t3.16479010904796\t0.830375874138309\t0.893718649152705\n+Cjp15\t-0.209766151010146\t7.01286048574317\t0.00789098456236578\t0.0179768834195552\n+Cjp16\t-0.527469323690171\t3.83336481231359\t0.0368575810313408\t0.0698463640537486\n+Cjp17\t0.197329320131585\t1.50182740629166\t0.831812631474571\t0.894118699261078\n+Cjp19\t-0.585630413256889\t4.17239585352498\t0.00761744618229388\t0.017568258434164\n+Cjp20\t-0.114614424829157\t3.99582222380107\t0.636456459735365\t0.733332848591807\n+Cjp21\t-0.0686823737490038\t5.19856866137998\t0.681991688267342\t0.772126800135447\n+Cjp22\t-0.226540237060962\t6.66243106472528\t0.0110000844678772\t0.0240337364745386\n+Cjp23\t-0.353025723104197\t2.42783006043204\t0.391607487160007\t0.504611643086455\n+Cjp24\t-0.0152743402303605\t2.74468336782184\t0.999999999999776\t1\n+Cjp25\t0.0848310092076146\t5.31944191023014\t0.588852855180689\t0.69042174849747\n+Cjp26\t-0.166761557958878\t6.58792537916917\t0.0731730109983744\t0.126137048733337\n+Cjp27\t-0.858268961181644\t2.29538700484784\t0.0724567718900572\t0.125030750260438\n+Cjp28\t-0.224851950084201\t5.01702220568239\t0.217001981820457\t0.31167350511253\n+Cjp29\t0.734109496851576\t3.66100088606691\t0.00704870545765388\t0.0164143917661593\n+Cjp30\t-0.122166326183728\t3.81411418090365\t0.674943147226437\t0.765983072710674\n+Cjp32\t-0.0874439451768363\t5.97433497049163\t0.45896096308337\t0.575500714725152\n+Cjp33\t-0.328588828011158\t4.32966509182498\t0.124211315818702\t0.197866033453132\n+Cjp34\t-0.380671920243272\t5.85944326037467\t0.00133854890531683\t0.00361903963289366\n+Cjp35\t-0.430399681435943\t3.73450743410787\t0.100374637588678\t0.164579117686904\n+Cjp36\t-0.201563169939485\t2.70346212180279\t0.608925025674964\t0.708513595362623\n+Cjr01\t-0.102775882095673\t13.5422910142694\t7.20756779798992e-10\t4.17293321821554e-09\n+Cjr02\t-0.00199342109653863\t16.21381505212\t0.870136632410869\t0.921562930750092\n+Cjr03\t0.0716348479862328\t9.30066612687491\t0.0445037148480824\t0.0819317294187833\n+Cjr04\t-0.10277590228244\t13.5422910142694\t7.11640659274934e-10\t4.13441061218898e-09\n+Cjr05\t-0.00201720063842253\t16.2138690187805\t0.868521430782704\t0.921562930750092\n+Cjr06\t0.166954322200703\t8.79992007728668\t7.93557714601454e-05\t0.000263838297587295\n+Cjr07\t-0.102775979976485\t13.5422910142694\t6.77618864736138e-10\t3.95042386768047e-09\n+Cjr08\t-0.00201719911428346\t16.2138690187805\t0.86854118978017\t0.921562930750092\n+Cjr09\t0.172836846375826\t8.7634083905036\t5.48033049240918e-05\t0.000186264674023381\n+Cjs01\t0.194800216436614\t12.2901088394379\t2.34683500730423e-23\t2.83477408436245e-22\n+Cjs02\t0.520621450537711\t3.13408724707507\t0.128402772795709\t0.203193454782277\n+Cjs03\t0.168063147710577\t10.1054046632285\t2.1180899514834e-09\t1.19338021091967e-08\n+Cjt01\t0.0995906789925662\t5.04200992251548\t0.588231919020598\t0.690175675776089\n+Cjt02\t-0.124166329208327\t4.7344995351148\t0.506444192273288\t0.618864482406733\n+Cjt03\t-0.583941660254936\t4.13412515205323\t0.0085236436529396\t0.0191582298437558\n+Cjt04\t0.0724165206745971\t3.90781846125343\t0.870782546926074\t0.921562930750092\n+Cjt05\t-0.212480888910792\t6.56077639094446\t0.0223001487916176\t0.045165198819211\n+Cjt06\t0.146126727543698\t3.92584585167676\t0.62778126057736\t0.72542652202986\n+Cjt1\t0.435399237792385\t4.58359947584301\t0.0212662026694545\t0.0432799445842596\n+Cjt2\t-0.119492910275624\t4.842875582846\t0.522681436188141\t0.63078490717773\n+Cjt3\t-0.469303073374358\t4.74978787712401\t0.00808820116400837\t0.0184012056292277\n+Cjt4\t-0.280180139875651\t4.87572672286493\t0.107580248404089\t0.1745190696333\n' |
| b |
| diff -r 000000000000 -r c5a812cdf478 tools/script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/script.R Fri Dec 09 10:52:35 2016 -0500 |
| [ |
| @@ -0,0 +1,68 @@ +#!/usr/bin/env Rscript + +args = commandArgs(TRUE) +countDataPath = args[1] +statsDataPath = args[2] +logFC = args[3] +logCPM = args[4] +pValue = args[5] +fdr = args[6] + +require(preprocessCore) +require(gplots) + +#prepare counts data -------------------------------------------------------- +countData = read.table(countDataPath, comment = "", + sep = "\t") + +groups = sapply(as.character(countData[1, -1]), strsplit, ":") +groups = as.vector(t(countData[1, -1])) + +names = as.vector(t(countData[2, -1])) + +countData = countData[-c(1,2), ] +rownames(countData) = countData[, 1] +countData = countData[, -1] +colnames(countData) = names + +countData = countData[, order(groups, names)] + +# prepare stats data ------------------------------------------------------ + +statsData = read.table(statsDataPath, sep = "\t", + header = T) + +colnames(statsData)[-1] = sapply(colnames(statsData)[-1], function(x){ + unlist(strsplit(x, ".", fixed = T))[3] +}) + +wh = which(abs(statsData$logFC) >= logFC & statsData$logCPM >= logCPM & statsData$PValue <= pValue & statsData$FDR <= fdr) + +for(i in 1:ncol(countData)){ + countData[,i] = as.numeric(countData[,i]) +} + +countDataNorm = normalize.quantiles(as.matrix(countData), copy = T) +countDataNormLog = log(countDataNorm + 1, 2) + +colnames(countDataNormLog) = colnames(countData) +rownames(countDataNormLog) = rownames(countData) + +#svg("heatmap.svg", width = 3+length(names), height = 1/2*length(wh)) +pdf("heatmap.pdf") + +heatmap.2( + countDataNormLog[wh, ], + density.info=c("none"), + hclustfun = function(x) hclust(x, method = "average"), + distfun = function(x) as.dist(1-cor(t(x))), + col = bluered(50), + scale = 'row', + trace = "none", #lwid = c(1, length(names)), lhei = c(1,1/3*length(wh)), +# Rowv=NA, + Colv = NA, + margins = c(7, 8) +) + +dev.off() + |
| b |
| diff -r 000000000000 -r c5a812cdf478 tools/scrsh.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/scrsh.sh Fri Dec 09 10:52:35 2016 -0500 |
| [ |
| @@ -0,0 +1,56 @@ +#!/bin/bash + +#sample_data=(tmp tmp1 tmp2 tmp3) +sample_data=(`cat $1 | cut -f1 | sed ':a;N;$!ba;s/\n/ /g'`) +#sample_name=(sample1 sample2 sample3 sample4) +sample_name=(`cat $1 | cut -f2 | sed ':a;N;$!ba;s/\n/ /g'`) +#sample_group=(gr1 gr1 gr2 gr2) +sample_group=(`cat $1 | cut -f3 | sed ':a;N;$!ba;s/\n/ /g'`) + + +group=('#') +sample=('#Feature') + +touch anno.tmp +touch count.tmp + +nsamples=`expr ${#sample_data[@]} - 1` + +for i in `seq 0 1 $nsamples`; do + group+=(${sample_group[i]}:${sample_group[i]}) + sample+=(${sample_name[i]}) + + cat ${sample_data[i]} | tail -n+3 > dataWithoutHeader 2>> script.log + + cat dataWithoutHeader | sort -k1 > dataWithoutHeader.sorted 2>> script.log + + cat dataWithoutHeader.sorted | awk '{print $1}' > anno.sample 2>> script.log + cat dataWithoutHeader.sorted | awk '{print $5}' > count.sample 2>> script.log + + paste -d"\t" count.tmp count.sample > count 2>> script.log + paste -d"\t" anno.tmp anno.sample > anno 2>> script.log + + cat count > count.tmp 2>> script.log + cat anno > anno.tmp 2>> script.log + +done + +echo ${group[*]} | sed -e 's/ /\t/g' > count.matrix 2>> script.log +echo ${sample[*]} | sed -e 's/ /\t/g' >> count.matrix 2>> script.log + +cat count | cut -f 2- > count.tmp 2>> script.log + +paste -d"\t" anno.sample count.tmp >> count.matrix 2>> script.log + +cat anno.tmp | cut -f 2- | awk '{for (i=2; i<=NF; i++){if ($1!=$i){print "error"; break}}}' > control.data 2>> script.log + +echo -e "gene_ID\tstart_coord\tend_coord" > annotation 2>> script.log +cat dataWithoutHeader.sorted | awk '{print $1"\t"$2"\t"$3}' >> annotation 2>> script.log + +if [[ -s control.data ]]; then + echo "kolumny nie sa w odpowiedniej kolejnosci" > error.log + echo "" > count.matrix + echo "" > annotation +else + echo "" > error.log +fi |