| Previous changeset 1:5e2a28bee02d (2018-02-17) Next changeset 3:afa81ef5f1c3 (2018-04-19) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2 |
|
modified:
mageck_macros.xml mageck_test.xml test-data/out.count.bam.txt test-data/out.count.fastq.txt test-data/out.count.log.txt test-data/out.countsummary.pdf test-data/out.countsummary.txt test-data/out.mle.log.txt test-data/out.test.R test-data/out.test.log.txt test-data/out.test.normalized.txt test-data/test1.fastq.gz |
|
added:
test-data/in.test.sample.txt test-data/out.count.R test-data/out.count.Rnw test-data/out.count.txt test-data/out.count_multi.txt test-data/out.countsummary_multi.pdf test-data/out.normcounts.txt test-data/out.test.plots.pdf test-data/out.test.report.pdf test-data/output.count_normalized.txt test-data/output_countsummary.Rnw test-data/output_summary.Rnw test-data/test2.fastq.gz |
|
removed:
test-data/out.test.pdf |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 mageck_macros.xml --- a/mageck_macros.xml Sat Feb 17 10:41:53 2018 -0500 +++ b/mageck_macros.xml Wed Apr 04 11:03:59 2018 -0400 |
| [ |
| @@ -1,27 +1,34 @@ <?xml version="1.0"?> <macros> + <token name="@VERSION@">0.5.7</token> + <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">mageck</requirement> - <!-- needed for pdf report outputs --> + <requirement type="package" version="1.14.2">numpy</requirement> <requirement type="package" version="3.0.1">r-gplots</requirement> <requirement type="package" version="1.8_2">r-xtable</requirement> <yield/> </requirements> </xml> + <xml name="version"> - <version_command>mageck -v </version_command> + <version_command><![CDATA[ + echo $(mageck -v )", numpy version" $([python -c "import numpy; numpy.version.version"])", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", xtable version" $(R --vanilla --slave -e "library(xtable); cat(sessionInfo()\$otherPkgs\$xtable\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> </xml> + + <xml name="sort_criteria"> + <param name="sort_criteria" argument="--sort-criteria" type="select" optional="true" label="Sorting criteria"> + <option value="neg" selected="True">Negative selection</option> + <option value="pos">positive selection</option> + </param> + </xml> + <xml name="citations"> <citations> <citation type="doi">10.1186/s13059-014-0554-4</citation> </citations> </xml> - <xml name="sort_criteria"> - <param name="sort_criteria" argument="--sort-criteria" type="select" label="Sorting criteria"> - <option value="neg" selected="True">Negative selection</option> - <option value="pos">positive selection</option> - </param> - </xml> </macros> |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 mageck_test.xml --- a/mageck_test.xml Sat Feb 17 10:41:53 2018 -0500 +++ b/mageck_test.xml Wed Apr 04 11:03:59 2018 -0400 |
| [ |
| b'@@ -24,20 +24,39 @@\n -n output\n \n $out.normcounts\n+\n $out.pdfreport\n \n---norm-method $adv.norm_method\n---gene-test-fdr-threshold $adv.fdr_threshold\n---adjust-method $adv.adjust_method\n+#if $adv.norm_method:\n+ --norm-method $adv.norm_method\n+#end if\n+\n+#if $adv.fdr_threshold:\n+ --gene-test-fdr-threshold $adv.fdr_threshold\n+#end if\n+\n+#if $adv.adjust_method:\n+ --adjust-method $adv.adjust_method\n+#end if\n+\n $adv.var_samples\n---sort-criteria $adv.sort_criteria\n+\n+#if $adv.sort_criteria:\n+ --sort-criteria $adv.sort_criteria\n+#end if\n \n---remove-zero $adv.remove_zero\n+#if $adv.remove_zero:\n+ --remove-zero $adv.remove_zero\n+#end if\n+\n #if $adv.remove_zero_threshold:\n --remove-zero-threshold $adv.remove_zero_threshold\n #end if\n \n---gene-lfc-method $adv.lfc_method\n+#if $adv.lfc_method:\n+ --gene-lfc-method $adv.lfc_method\n+#end if\n+\n #if $adv.control_sgrna:\n --control-sgrna $adv.control_sgrna\n #end if\n@@ -60,46 +79,50 @@\n <option value="control">Control sample</option>\n </param>\n <when value="treated">\n- <param name="treatment_id" argument="--treatment-id" type="text" label="Treated Sample Labels (or Indexes)" help="If sample label is provided, the labels must match the labels in the first line of the count table, separated by comma (,); for example, HL60.final,KBM7.final. For sample index, 0,2 means the 1st and 3rd samples are treatment experiments. See Help below for a detailed description." />\n+ <param name="treatment_id" argument="--treatment-id" type="text" label="Treated Sample Labels (or Indexes)" help="If sample label is provided, the labels must match the labels in the first line of the count table, separated by comma (,); for example, HL60.final,KBM7.final. For sample index, 0,2 means the 1st and 3rd samples are treatment experiments. See Help below for a detailed description.">\n+ <validator type="regex" message="Please only use letters, numbers or underscores in sample labels, and separate labels by commas">^[\\w,]+$</validator>\n+ </param>\n </when>\n <when value="control">\n- <param name="day0_label" argument="--day0-label" type="text" optional="true" value="" label="Control Sample Label" help="Specify the label for the control sample. For every other sample label, the module will treat it as a treatment condition and compare with control sample (usually day 0 or plasmid)" />\n+ <param name="day0_label" argument="--day0-label" type="text" optional="true" value="" label="Control Sample Label" help="Specify the label for the control sample. For every other sample label, the module will treat it as a treatment condition and compare with control sample (usually day 0 or plasmid)">\n+ <validator type="regex" message="Please only use letters, numbers or underscores in sample label">^[\\w]+$</validator>\n+ </param>\n </when>\n </conditional>\n- <param name="control_id" argument="--control-id" type="text" optional="true" label="Control Sample Labels (or Indexes)" help="If sample label is provided, the labels must match the labels in the first line of the count table, separated by comma (,). Default is all the samples not specified in treatment experiments. See Help below for a detailed description." />\n-\n+ <param name="control_id" argument="--control-id" type="text" optional="true" label="Control Sample Labels (or Indexes)" help="If sample label is provided, the labels must match the labels in the first line of the count table, separated by comma (,). Default is all the samples not specified in treatment experiments. See Help below for a detailed description.">\n+ <validator type="regex" message="Please only use letters, numbers or underscores in sample labels, and separate labels by commas">^[\\w,]+$</validator>\n+ </param>\n <section name="out" title="Output Options">\n '..b'</option>\n <option value="alphamedian">Alphamedian</option>\n <option value="mean">Mean</option>\n@@ -121,35 +144,41 @@\n <data name="normcounts" format="tabular" from_work_dir="output.normalized.txt" label="${tool.name} on ${on_string}: sgRNA Normalized Counts">\n <filter>out[\'normcounts\'] is True</filter>\n </data>\n- <data name="pdfreport" format="pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: PDF Report">\n+ <data name="plots" format="pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: PDF Report">\n <filter>out[\'pdfreport\'] is True</filter>\n </data>\n- <data name="rscript" format="txt" from_work_dir="output.R" label="${tool.name} on ${on_string}: RScript">\n- <filter>out[\'rscriptOpt\'] is True</filter>\n+ <data name="rscript" format="txt" from_work_dir="output.R" label="${tool.name} on ${on_string}: R file" >\n+ <filter>out[\'rfilesOpt\'] is True</filter>\n+ </data>\n+ <data name="rnwfile" format="txt" from_work_dir="output_summary.Rnw" label="${tool.name} on ${on_string}: Rnw file" >\n+ <filter>out[\'rfilesOpt\'] is True</filter>\n </data>\n </outputs>\n <tests>\n- <test><!-- Ensure MAGeCK\'s default output works -->\n- <param name="count_table" value="demo/demo1/sample.txt" ftype="tabular" />\n- <param name="treatment_id" value="HL60.final,KBM7.final" />\n- <param name="control_id" value="HL60.initial,KBM7.initial" />\n+ <!-- Ensure MAGeCK\'s default output works -->\n+ <test expect_num_outputs="2">\n+ <param name="count_table" value="in.test.sample.txt" ftype="tabular" />\n+ <param name="treatment_id" value="HL60_final,KBM7_final" />\n+ <param name="control_id" value="HL60_initial,KBM7_initial" />\n <output name="gene_summary" file="out.test.gene_summary.txt"/>\n <output name="sgrna_summary" file="out.test.sgrna_summary.txt"/>\n </test>\n- <test><!-- Ensure MAGeCK\'s additional outputs works -->\n- <param name="count_table" value="demo/demo1/sample.txt" ftype="tabular" />\n- <param name="treatment_id" value="HL60.final,KBM7.final" />\n- <param name="control_id" value="HL60.initial,KBM7.initial" />\n+ <!-- Ensure MAGeCK\'s additional outputs works -->\n+ <test expect_num_outputs="7">\n+ <param name="count_table" value="in.test.sample.txt" ftype="tabular" />\n+ <param name="treatment_id" value="HL60_final,KBM7_final" />\n+ <param name="control_id" value="HL60_initial,KBM7_initial" />\n <param name="out_log" value="True" />\n <param name="normcounts" value="True" />\n <param name="pdfreport" value="True" />\n- <param name="rscriptOpt" value="True" />\n+ <param name="rfilesOpt" value="True" />\n <output name="gene_summary" file="out.test.gene_summary.txt"/>\n <output name="sgrna_summary" file="out.test.sgrna_summary.txt"/>\n <output name="normcounts" file="out.test.normalized.txt"/>\n <output name="log" file="out.test.log.txt" compare="sim_size"/>\n- <output name="pdfreport" file="out.test.pdf" compare="sim_size"/>\n+ <output name="plots" file="out.test.plots.pdf" compare="sim_size"/>\n <output name="rscript" file="out.test.R" />\n+ <output name="rnwfile" file="output_summary.Rnw" />\n </test>\n </tests>\n \n@@ -210,6 +239,18 @@\n \n **Outputs**\n \n+This tool outputs\n+\n+ * a ranked sgRNA Summary file\n+ * a ranked Gene Summary file\n+\n+Optionally, under **Output Options** you can choose to output\n+\n+ * a Normalized Counts table\n+ * a PDF of the plots\n+ * the .R and .Rnw files to generate the report\n+ * a Log file of the analysis\n+\n **sgRNA Summary file**\n \n An example of the sgRNA ranking output is as follows:\n' |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/in.test.sample.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in.test.sample.txt Wed Apr 04 11:03:59 2018 -0400 |
| b |
| b'@@ -0,0 +1,1000 @@\n+sgRNA\tGene\tHL60_initial\tKBM7_initial\tHL60_final\tKBM7_final\n+A1CF_m52595977\tA1CF\t213\t274\t883\t175\n+A1CF_m52596017\tA1CF\t294\t412\t1554\t1891\n+A1CF_m52596056\tA1CF\t421\t368\t566\t759\n+A1CF_m52603842\tA1CF\t274\t243\t314\t855\n+A1CF_m52603847\tA1CF\t0\t50\t145\t266\n+A1CF_p52595870\tA1CF\t623\t583\t1503\t1117\n+A1CF_p52595881\tA1CF\t486\t378\t1775\t1585\n+A1CF_p52596023\tA1CF\t195\t429\t783\t774\n+A1CF_p52601638\tA1CF\t744\t459\t1233\t2407\n+A1CF_p52603829\tA1CF\t76\t142\t332\t471\n+AAAS_m53714382\tAAAS\t704\t671\t799\t1426\n+AAAS_m53715169\tAAAS\t651\t627\t797\t1690\n+AAAS_m53715176\tAAAS\t545\t89\t392\t664\n+AAAS_m53715212\tAAAS\t254\t340\t429\t742\n+AAAS_m53715238\tAAAS\t32\t135\t421\t77\n+AAAS_p53714367\tAAAS\t323\t328\t652\t469\n+AAAS_p53714374\tAAAS\t293\t261\t856\t968\n+AAAS_p53714391\tAAAS\t283\t399\t954\t940\n+AAAS_p53714405\tAAAS\t1119\t856\t2212\t2715\n+AAAS_p53714441\tAAAS\t273\t327\t1093\t829\n+AAK1_m69870049\tAAK1\t364\t465\t693\t2006\n+AAK1_m69870056\tAAK1\t635\t707\t2234\t3515\n+AAK1_m69870103\tAAK1\t485\t452\t914\t629\n+AAK1_m69870119\tAAK1\t405\t275\t806\t837\n+AAK1_m69870125\tAAK1\t274\t350\t1822\t2101\n+AAK1_m69870131\tAAK1\t754\t763\t1411\t2637\n+AAK1_m69870137\tAAK1\t905\t294\t512\t798\n+AAK1_p69870063\tAAK1\t330\t167\t364\t1139\n+AAK1_p69870070\tAAK1\t991\t718\t1790\t1682\n+AAK1_p69870105\tAAK1\t190\t163\t922\t1118\n+AATF_m35306444\tAATF\t449\t456\t1396\t1402\n+AATF_m35306475\tAATF\t493\t612\t1102\t537\n+AATF_m35306482\tAATF\t569\t726\t743\t311\n+AATF_m35306509\tAATF\t250\t322\t476\t204\n+AATF_m35307516\tAATF\t353\t356\t995\t540\n+AATF_m35307525\tAATF\t276\t146\t514\t291\n+AATF_p35306410\tAATF\t1426\t1104\t2494\t1101\n+AATF_p35306466\tAATF\t189\t245\t289\t0\n+AATF_p35307505\tAATF\t677\t269\t1154\t481\n+AATF_p35307527\tAATF\t1487\t835\t2761\t3255\n+AATK_m79102275\tAATK\t621\t435\t4568\t1109\n+AATK_m79102281\tAATK\t465\t460\t1736\t2651\n+AATK_m79102298\tAATK\t726\t798\t2538\t2676\n+AATK_m79102320\tAATK\t1003\t655\t1932\t3223\n+AATK_m79102325\tAATK\t633\t722\t1874\t2030\n+AATK_p79102286\tAATK\t1284\t562\t1844\t1624\n+AATK_p79102311\tAATK\t73\t184\t843\t281\n+AATK_p79104850\tAATK\t298\t316\t507\t602\n+AATK_p79104858\tAATK\t284\t346\t905\t852\n+AATK_p79104864\tAATK\t597\t640\t2244\t2543\n+ABCB8_m150725643\tABCB8\t407\t583\t1738\t2951\n+ABCB8_m150725669\tABCB8\t821\t425\t1510\t1077\n+ABCB8_m150730720\tABCB8\t100\t150\t464\t433\n+ABCB8_p150725600\tABCB8\t298\t225\t350\t482\n+ABCB8_p150725605\tABCB8\t102\t146\t1396\t428\n+ABCB8_p150725612\tABCB8\t251\t107\t1110\t685\n+ABCB8_p150725675\tABCB8\t642\t426\t975\t2565\n+ABCB8_p150730680\tABCB8\t526\t481\t1012\t1108\n+ABCB8_p150730705\tABCB8\t743\t522\t1400\t2105\n+ABCB8_p150730712\tABCB8\t170\t215\t999\t1004\n+ABCC1_m16043636\tABCC1\t48\t208\t563\t817\n+ABCC1_m16043645\tABCC1\t1095\t551\t1280\t1793\n+ABCC1_m16101705\tABCC1\t873\t593\t1320\t1374\n+ABCC1_m16101777\tABCC1\t476\t410\t1487\t1117\n+ABCC1_m16101788\tABCC1\t453\t296\t754\t857\n+ABCC1_m16101799\tABCC1\t497\t511\t779\t1023\n+ABCC1_p16043597\tABCC1\t209\t232\t484\t581\n+ABCC1_p16101667\tABCC1\t218\t140\t392\t695\n+ABCC1_p16101710\tABCC1\t36\t15\t323\t392\n+ABCC1_p16101721\tABCC1\t1007\t684\t1399\t2741\n+ABCF1_m30539291\tABCF1\t147\t163\t305\t871\n+ABCF1_p30539251\tABCF1\t767\t675\t589\t647\n+ABCF1_p30539272\tABCF1\t756\t585\t1503\t1612\n+ABCF1_p30545181\tABCF1\t792\t678\t2674\t3651\n+ABCF1_p30545587\tABCF1\t33\t140\t1055\t435\n+ABCF1_p30545605\tABCF1\t341\t218\t692\t550\n+ABCF1_p30545610\tABCF1\t1344\t1012\t2581\t2254\n+ABCF1_p30545638\tABCF1\t145\t212\t641\t844\n+ABCF1_p30545878\tABCF1\t1369\t1120\t1687\t755\n+ABCF1_p30545888\tABCF1\t180\t199\t701\t335\n+ABHD14B_m52004073\tABHD14B\t322\t191\t616\t546\n+ABHD14B_m52004106\tABHD14B\t304\t222\t823\t595\n+ABHD14B_m52004113\tABHD14B\t394\t367\t1469\t905\n+ABHD14B_m52004122\tABHD14B\t1220\t1034\t1559\t2275\n+ABHD14B_p52004005\tABHD14B\t127\t234\t529\t826\n+ABHD14B_p52004011\tABHD14B\t341\t358\t1060\t1399\n+ABHD14B_p52004019\tABHD14B\t28\t160\t268\t454\n+ABHD14B_p52004061\tABHD14B\t265\t341\t598\t324\n+ABHD14B_p52004076\tABHD14B\t1415\t1062\t3286\t2836\n+ABHD14B_p52004124\tABHD14B\t584\t546\t1254\t1988\n+ABI1_m27149710\tABI1\t433\t671\t1145\t574\n+ABI1_m27149743\tABI1\t961\t396\t1282\t1685\n+ABI1_m27149751\tABI1\t839\t489\t1142\t929\n+ABI1_m27149764\tABI1\t139\t187\t322\t470\n+ABI1_p27112164\tABI1\t1163\t932\t1935\t2368\n+ABI1_p27112174\tABI1\t1010\t740\t3367\t2458\n+ABI1_p27112180\tABI1\t310\t214\t532\t667\n+ABI1_p27149695\tABI1\t158\t43\t242\t324\n+ABI1_p27149701\tABI1\t475\t439\t2839\t1808\n+ABI1_p27149733\tABI1\t84\t265\t395'..b'5\t754\t1109\t1690\t2331\n+AGFG1_m228337138\tAGFG1\t714\t564\t2746\t1557\n+AGFG1_m228337178\tAGFG1\t374\t575\t1247\t1529\n+AGFG1_m228337201\tAGFG1\t635\t496\t1007\t1334\n+AGFG1_m228337208\tAGFG1\t457\t440\t879\t1340\n+AGFG1_m228337217\tAGFG1\t229\t348\t573\t750\n+AGFG1_m228337248\tAGFG1\t669\t378\t1071\t587\n+AGFG1_m228337276\tAGFG1\t1621\t1273\t2485\t2620\n+AGFG1_p228337142\tAGFG1\t0\t24\t0\t137\n+AGFG1_p228337168\tAGFG1\t454\t376\t780\t1240\n+AGFG1_p228337221\tAGFG1\t306\t241\t1131\t1122\n+AGL_m100327112\tAGL\t777\t539\t1842\t2115\n+AGL_m100327128\tAGL\t83\t140\t505\t640\n+AGL_m100327135\tAGL\t151\t67\t664\t807\n+AGL_m100327186\tAGL\t94\t90\t635\t232\n+AGL_m100327263\tAGL\t516\t261\t650\t368\n+AGL_p100327060\tAGL\t497\t260\t523\t675\n+AGL_p100327074\tAGL\t413\t555\t1032\t899\n+AGL_p100327114\tAGL\t32\t83\t380\t54\n+AGL_p100327219\tAGL\t134\t162\t66\t137\n+AGL_p100327246\tAGL\t315\t143\t320\t626\n+AGPAT3_m45379563\tAGPAT3\t179\t141\t81\t288\n+AGPAT3_m45379570\tAGPAT3\t87\t130\t303\t281\n+AGPAT3_m45379578\tAGPAT3\t69\t88\t328\t395\n+AGPAT3_m45379590\tAGPAT3\t819\t918\t2207\t1744\n+AGPAT3_m45379606\tAGPAT3\t256\t166\t527\t358\n+AGPAT3_p45379552\tAGPAT3\t710\t651\t2228\t2263\n+AGPAT3_p45379592\tAGPAT3\t734\t254\t476\t439\n+AGPAT3_p45379613\tAGPAT3\t407\t172\t740\t481\n+AGPAT3_p45379618\tAGPAT3\t40\t396\t699\t1463\n+AGPAT3_p45379648\tAGPAT3\t701\t370\t934\t719\n+AGPAT5_m6566202\tAGPAT5\t195\t321\t307\t227\n+AGPAT5_m6566212\tAGPAT5\t1668\t1381\t3410\t4278\n+AGPAT5_m6566223\tAGPAT5\t782\t1145\t2701\t2379\n+AGPAT5_m6566233\tAGPAT5\t2271\t2181\t4502\t4135\n+AGPAT5_m6566240\tAGPAT5\t546\t898\t1383\t1661\n+AGPAT5_m6566254\tAGPAT5\t520\t268\t586\t1373\n+AGPAT5_m6566307\tAGPAT5\t196\t141\t369\t188\n+AGPAT5_p6566182\tAGPAT5\t329\t233\t790\t1033\n+AGPAT5_p6566257\tAGPAT5\t941\t738\t1815\t1921\n+AGPAT5_p6566262\tAGPAT5\t474\t274\t1506\t1191\n+AGTPBP1_m88296213\tAGTPBP1\t531\t492\t2269\t2580\n+AGTPBP1_m88296222\tAGTPBP1\t1138\t509\t1909\t2637\n+AGTPBP1_m88307605\tAGTPBP1\t495\t251\t796\t824\n+AGTPBP1_m88307687\tAGTPBP1\t1353\t700\t2269\t2760\n+AGTPBP1_m88307696\tAGTPBP1\t0\t204\t694\t669\n+AGTPBP1_p88296203\tAGTPBP1\t298\t192\t727\t1188\n+AGTPBP1_p88307644\tAGTPBP1\t206\t189\t435\t608\n+AGTPBP1_p88307675\tAGTPBP1\t800\t646\t1441\t2138\n+AGTPBP1_p88307700\tAGTPBP1\t107\t67\t64\t1054\n+AGTPBP1_p88307705\tAGTPBP1\t446\t253\t716\t903\n+AHCTF1_m247067252\tAHCTF1\t134\t170\t672\t60\n+AHCTF1_m247068844\tAHCTF1\t753\t595\t2763\t1411\n+AHCTF1_m247068867\tAHCTF1\t509\t275\t380\t835\n+AHCTF1_m247068886\tAHCTF1\t745\t497\t1328\t638\n+AHCTF1_m247068945\tAHCTF1\t461\t178\t973\t1432\n+AHCTF1_m247070906\tAHCTF1\t734\t906\t553\t339\n+AHCTF1_m247070995\tAHCTF1\t978\t617\t508\t282\n+AHCTF1_m247094617\tAHCTF1\t575\t372\t858\t1120\n+AHCTF1_p247076572\tAHCTF1\t375\t417\t1749\t1088\n+AHCTF1_p247079429\tAHCTF1\t409\t507\t1166\t1318\n+AHCY_m32883210\tAHCY\t205\t370\t362\t240\n+AHCY_m32883247\tAHCY\t777\t619\t179\t176\n+AHCY_m32883267\tAHCY\t537\t378\t1147\t1029\n+AHCY_m32883301\tAHCY\t267\t232\t530\t374\n+AHCY_m32883330\tAHCY\t1367\t1259\t3863\t3387\n+AHCY_p32883227\tAHCY\t729\t229\t1023\t611\n+AHCY_p32883238\tAHCY\t42\t123\t974\t791\n+AHCY_p32883253\tAHCY\t443\t495\t376\t33\n+AHCY_p32883304\tAHCY\t1106\t794\t3402\t3472\n+AHCY_p32883309\tAHCY\t717\t497\t169\t185\n+AHNAK2_m105423801\tAHNAK2\t827\t932\t2364\t2698\n+AHNAK2_m105423809\tAHNAK2\t275\t265\t776\t1124\n+AHNAK2_m105423822\tAHNAK2\t215\t414\t1125\t1162\n+AHNAK2_m105423829\tAHNAK2\t502\t495\t890\t704\n+AHNAK2_m105423836\tAHNAK2\t200\t460\t2170\t1886\n+AHNAK2_m105444536\tAHNAK2\t260\t256\t1122\t1064\n+AHNAK2_m105444541\tAHNAK2\t518\t374\t1342\t1589\n+AHNAK2_m105444555\tAHNAK2\t343\t156\t257\t1290\n+AHNAK2_p105423957\tAHNAK2\t460\t311\t497\t1143\n+AHNAK2_p105423983\tAHNAK2\t247\t219\t1549\t972\n+AHNAK_m62303488\tAHNAK\t272\t284\t1238\t1124\n+AHNAK_m62303507\tAHNAK\t79\t133\t464\t34\n+AHNAK_m62303523\tAHNAK\t122\t168\t238\t534\n+AHNAK_m62303528\tAHNAK\t181\t449\t1074\t1467\n+AHNAK_m62303548\tAHNAK\t591\t552\t1143\t573\n+AHNAK_m62303560\tAHNAK\t479\t540\t1629\t2630\n+AHNAK_p62303470\tAHNAK\t258\t412\t1397\t1743\n+AHNAK_p62303477\tAHNAK\t446\t282\t879\t831\n+AHNAK_p62303510\tAHNAK\t322\t254\t948\t862\n+AHNAK_p62303551\tAHNAK\t35\t23\t186\t55\n+AHRR_m344006\tAHRR\t235\t92\t752\t841\n+AHRR_m344069\tAHRR\t283\t210\t337\t610\n+AHRR_m353878\tAHRR\t1\t47\t0\t110\n+AHRR_m353892\tAHRR\t239\t85\t458\t728\n+AHRR_m353898\tAHRR\t382\t96\t316\t720\n+AHRR_p344008\tAHRR\t171\t125\t2480\t2626\n+AHRR_p344030\tAHRR\t501\t503\t1767\t803\n+AHRR_p344036\tAHRR\t230\t342\t600\t114\n+AHRR_p344042\tAHRR\t837\t296\t1327\t1652\n' |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.count.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.count.R Wed Apr 04 11:03:59 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +Sweave("output_countsummary.Rnw"); +library(tools); + +texi2dvi("output_countsummary.tex",pdf=TRUE); + |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.count.Rnw --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.count.Rnw Wed Apr 04 11:03:59 2018 -0400 |
| [ |
| @@ -0,0 +1,237 @@ +% This is a template file for Sweave used in MAGeCK +% Author: Wei Li, Shirley Liu lab +% Do not modify lines beginning with "#__". +\documentclass{article} + +\usepackage{amsmath} +\usepackage{amscd} +\usepackage[tableposition=top]{caption} +\usepackage{ifthen} +\usepackage{fullpage} +\usepackage[utf8]{inputenc} +% \usepackage{longtable} + +\begin{document} +\setkeys{Gin}{width=0.9\textwidth} + +\title{MAGeCK Count Report} +\author{Wei Li} + +\maketitle + + +\tableofcontents + +\section{Summary} + +%Function definition +<<label=funcdef,include=FALSE,echo=FALSE>>= +genreporttable<-function(filelist,labellist,reads,mappedreads){ + xtb=data.frame(Label=labellist,Reads=reads,MappedReads=mappedreads,MappedPercentage=mappedreads/reads); + colnames(xtb)=c("Label","Reads","Mapped","Percentage"); + return (xtb); +} +genreporttable2<-function(filelist,labellist,sgrnas,zerocounts,gini){ + xtb=data.frame(Label=labellist,TotalsgRNAs=sgrnas,ZeroCounts=zerocounts,GiniIndex=gini); + colnames(xtb)=c("Label","TotalsgRNA","ZeroCounts","GiniIndex"); + return (xtb); +} +genreporttable3<-function(filelist,labellist){ + xtb=data.frame(File=filelist,Label=labellist); + colnames(xtb)=c("File","Label"); + return (xtb); +} + + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F"); + + + +genboxplot<-function(filename,...){ + #slmed=read.table(filename,header=T) + slmed=read.table(filename,header=T) + slmat=as.matrix(slmed[,c(-1,-2)]) + slmat_log=log2(slmat+1) + + boxplot(slmat_log,pch='.',las=2,ylab='log2(read counts)',cex.axis=0.8,...) +} + + +genhistplot<-function(filename,isfile=T,...){ + if(isfile){ + slmed=read.table(filename,header=T) + }else{ + slmed=filename; + } + tabsmat=as.matrix(log2(slmed[,c(-1,-2)]+1)) + colnames(tabsmat)=colnames(slmed)[c(-1,-2)] + samplecol=colors[((1:ncol(tabsmat)) %% length(colors)) ] + if(ncol(tabsmat)>=1){ + histlist=lapply(1:ncol(tabsmat),function(X){ return (hist(tabsmat[,X],plot=F,breaks=40)) }) + xrange=range(unlist(lapply(histlist,function(X){X$mids}))) + yrange=range(unlist(lapply(histlist,function(X){X$counts}))) + hst1=histlist[[1]] + plot(hst1$mids,hst1$counts,type='b',pch=20,xlim=c(0,xrange[2]*1.2),ylim=c(0,yrange[2]*1.2),xlab='log2(counts)',ylab='Frequency',main='Distribution of read counts',col = samplecol[1], ... ) + } + if(ncol(tabsmat)>=2){ + for(i in 2:ncol(tabsmat)){ + hstn=histlist[[i]] + lines(hstn$mids,hstn$counts,type='b',pch=20,col=samplecol[i]) + } + } + legend('topright',colnames(tabsmat),pch=20,lwd=1,col=samplecol) +} + + + +genclustering<-function(filename,...){ + #slmed=read.table(filename,header=T) + slmed=read.table(filename,header=T) + slmat=as.matrix(slmed[,c(-1,-2)]) + slmat_log=log2(slmat+1) + + result=tryCatch({ + library(gplots); + heatmap.2(cor(slmat_log),trace = 'none',density.info = 'none',cexRow = 0.8,cexCol = 0.8,offsetRow = -0.2,offsetCol = -0.2) + }, error=function(e){ + heatmap(cor(slmat_log),scale='none',cexRow = 0.8,cexCol = 0.8,cex.axis=0.8,...) + }); +} + +ctfit_tx=0; + + +panel.plot<-function(x,y,textnames=names(x),...){ + par(new=TRUE) + m<-cbind(x,y) + plot(m,pch=20,xlim = range(x)*1.1,ylim=range(y)*1.1,...) + text(x,y,textnames,...) +} + + +genpcaplot<-function(filename,...){ + #slmed=read.table(filename,header=T) + slmed=read.table(filename,header=T) + slmat=as.matrix(slmed[,c(-1,-2)]) + slmat_log=log2(slmat+1) + ctfit_tx<<-prcomp(t(slmat_log),center=TRUE) + + # par(mfrow=c(2,1)); + samplecol=colors[((1:ncol(slmat)) %% length(colors)) ] + # first 2 PCA + #plot(ctfit_tx$x[,1],ctfit_tx$x[,2],xlab='PC1',ylab='PC2',main='First 2 PCs',col=samplecol,xlim=1.1*range(ctfit_tx$x[,1]),ylim=1.1*range(ctfit_tx$x[,2])); + #text(ctfit_tx$x[,1],ctfit_tx$x[,2],rownames(ctfit_tx$x),col=samplecol); + # par(mfrow=c(1,1)); + if(length(samplecol)>2){ + pairs(ctfit_tx$x[,1:3],panel=panel.plot,textnames=rownames(ctfit_tx$x),main='First 3 principle components',col=samplecol) + }else{ + if(length(samplecol)>1){ + pairs(ctfit_tx$x[,1:2],panel=panel.plot,textnames=rownames(ctfit_tx$x),main='First 2 principle components',col=samplecol) + } + } + + +} + +genpcavar<-function(){ + # % variance + varpca=ctfit_tx$sdev^2 + varpca=varpca/sum(varpca)*100; + if(length(varpca)>10){ + varpca=varpca[1:10]; + } + plot(varpca,type='b',lwd=2,pch=20,xlab='PCs',ylab='% Variance explained'); +} + +@ + +%__FILE_SUMMARY__ + +The statistics of comparisons are listed in Table 1 and Table 2. +The corresponding fastq files in each row are listed in Table 3. + +<<label=tab1,echo=FALSE,results=tex>>= +library(xtable) +filelist=c("input_0.gz"); +labellist=c("test1_fastq_gz"); +reads=c(2500); +mappedreads=c(1453); +totalsgrnas=c(2550); +zerocounts=c(1276); +giniindex=c(0.5266899931488773); + +cptable=genreporttable(filelist,labellist,reads,mappedreads); +print(xtable(cptable, caption = "Summary of comparisons", label = "tab:one", + digits = c(0, 0, 0, 0,2), + align=c('c', 'c','c', 'c', 'c'), + table.placement = "tbp", + caption.placement = "top")) +@ + +<<label=tab2,echo=FALSE,results=tex>>= +library(xtable) +cptable=genreporttable2(filelist,labellist,totalsgrnas,zerocounts,giniindex); +print(xtable(cptable, caption = "Summary of comparisons", label = "tab:two", + digits = c(0, 0,0, 0,2), + align=c('c', 'c','c', 'c', 'c'), + table.placement = "tbp", + caption.placement = "top")) +@ + + + + + +<<label=tab3,echo=FALSE,results=tex>>= +library(xtable) +cptable=genreporttable3(filelist,labellist); +print(xtable(cptable, caption = "Summary of samples", label = "tab:three", + digits = c(0,0, 0), + align=c('c', 'p{9cm}', 'c'), + table.placement = "tbp", + caption.placement = "top")) +@ + + + + +The meanings of the columns are as follows. + +\begin{itemize} +\item \textbf{Row}: The row number in the table; +\item \textbf{File}: The filename of fastq file; +\item \textbf{Label}: Assigned label; +\item \textbf{Reads}: The total read count in the fastq file; +\item \textbf{Mapped}: Reads that can be mapped to gRNA library; +\item \textbf{Percentage}: The percentage of mapped reads; +\item \textbf{TotalsgRNAs}: The number of sgRNAs in the library; +\item \textbf{ZeroCounts}: The number of sgRNA with 0 read counts; +\item \textbf{GiniIndex}: The Gini Index of the read count distribution. Gini index can be used to measure the evenness of the read counts, and a smaller value means a more even distribution of the read counts. +\end{itemize} + + + +\newpage\section{Normalized read count distribution of all samples} +The following figure shows the distribution of median-normalized read counts in all samples. + + +<<fig=TRUE,echo=FALSE,width=4.5,height=4.5>>= +genboxplot("output.count_normalized.txt"); +@ + +The following figure shows the histogram of median-normalized read counts in all samples. + + +<<fig=TRUE,echo=FALSE,width=4.5,height=4.5>>= +genhistplot("output.count_normalized.txt"); +@ + +%__INDIVIDUAL_PAGE__ + + + +\end{document} + |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.count.bam.txt --- a/test-data/out.count.bam.txt Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.count.bam.txt Wed Apr 04 11:03:59 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -sgRNA Gene test1.bam +sgRNA Gene test1_bam s_10007 CCNA1 0 s_10008 CCNA1 0 s_10027 CCNC 0 |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.count.fastq.txt --- a/test-data/out.count.fastq.txt Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.count.fastq.txt Wed Apr 04 11:03:59 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -sgRNA Gene test1.fastq.gz +sgRNA Gene test1_fastq_gz s_47512 RNF111 1 s_24835 HCFC1R1 1 s_14784 CYP4B1 4 |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.count.log.txt --- a/test-data/out.count.log.txt Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.count.log.txt Wed Apr 04 11:03:59 2018 -0400 |
| b |
| @@ -1,46 +1,43 @@ -INFO @ Wed, 14 Feb 2018 01:52:58: Parameters: /home/maria/miniconda3/envs/mulled-v1-0142cfe25b04f0c1d6899e250fb2f311b2d84778259938a0f6bd1d2ee743fa71/bin/mageck count -l /tmp/tmpqZ84Xc/files/000/dataset_7.dat --fastq input.gz -n output --pdf-report --keep-tmp --unmapped-to-file --norm-method median --sgrna-len 20 -INFO @ Wed, 14 Feb 2018 01:52:58: Welcome to MAGeCK v0.5.7. Command: count -INFO @ Wed, 14 Feb 2018 01:52:58: Loading 2550 predefined sgRNAs. -WARNING @ Wed, 14 Feb 2018 01:52:58: There are 0 sgRNAs with duplicated sequences. -INFO @ Wed, 14 Feb 2018 01:52:58: Parsing FASTQ file input.gz... -INFO @ Wed, 14 Feb 2018 01:52:58: Determining the trim-5 length of FASTQ file input.gz... -INFO @ Wed, 14 Feb 2018 01:52:58: Possible gRNA lengths:20 -INFO @ Wed, 14 Feb 2018 01:52:58: Processing 0M reads ... -INFO @ Wed, 14 Feb 2018 01:52:58: Read length:30 -INFO @ Wed, 14 Feb 2018 01:52:58: Total tested reads: 2500, mapped: 1453(0.5812) -INFO @ Wed, 14 Feb 2018 01:52:58: --trim-5 test data: (trim_length reads fraction) -INFO @ Wed, 14 Feb 2018 01:52:58: 0 1453 1.0 -INFO @ Wed, 14 Feb 2018 01:52:58: Auto determination of trim5 results: 0 -INFO @ Wed, 14 Feb 2018 01:52:58: Possible gRNA lengths:20 -INFO @ Wed, 14 Feb 2018 01:52:58: Processing 0M reads .. -INFO @ Wed, 14 Feb 2018 01:52:58: Total: 2500. -INFO @ Wed, 14 Feb 2018 01:52:58: Mapped: 1453. -DEBUG @ Wed, 14 Feb 2018 01:52:58: Initial (total) size factor: 1.0 -DEBUG @ Wed, 14 Feb 2018 01:52:58: Median factor: 2.0 -INFO @ Wed, 14 Feb 2018 01:52:58: Final size factor: 2.0 -INFO @ Wed, 14 Feb 2018 01:52:58: Summary of file input.gz: -INFO @ Wed, 14 Feb 2018 01:52:58: label sample1 -INFO @ Wed, 14 Feb 2018 01:52:58: reads 2500 -INFO @ Wed, 14 Feb 2018 01:52:58: mappedreads 1453 -INFO @ Wed, 14 Feb 2018 01:52:58: totalsgrnas 2550 -INFO @ Wed, 14 Feb 2018 01:52:58: zerosgrnas 1276 -INFO @ Wed, 14 Feb 2018 01:52:58: giniindex 0.5266899931488773 -INFO @ Wed, 14 Feb 2018 01:52:58: Loading Rnw template file: /home/maria/miniconda3/envs/mulled-v1-0142cfe25b04f0c1d6899e250fb2f311b2d84778259938a0f6bd1d2ee743fa71/lib/python3.6/site-packages/mageck/fastq_template.Rnw. -DEBUG @ Wed, 14 Feb 2018 01:52:58: Setting up the visualization module... -INFO @ Wed, 14 Feb 2018 01:52:58: Running command: cd ./; Rscript output_countsummary.R -INFO @ Wed, 14 Feb 2018 01:52:58: Command message: -INFO @ Wed, 14 Feb 2018 01:52:58: Writing to file output_countsummary.tex -INFO @ Wed, 14 Feb 2018 01:52:58: Processing code chunks with options ... -INFO @ Wed, 14 Feb 2018 01:52:58: 1 : keep.source term verbatim (label = funcdef, output_countsummary.Rnw:28) -INFO @ Wed, 14 Feb 2018 01:52:58: 2 : keep.source term tex (label = tab1, output_countsummary.Rnw:156) -INFO @ Wed, 14 Feb 2018 01:52:58: 3 : keep.source term tex (label = tab2, output_countsummary.Rnw:174) -INFO @ Wed, 14 Feb 2018 01:52:58: 4 : keep.source term tex (label = tab3, output_countsummary.Rnw:188) -INFO @ Wed, 14 Feb 2018 01:52:58: 5 : keep.source term verbatim pdf (output_countsummary.Rnw:221) -INFO @ Wed, 14 Feb 2018 01:52:58: 6 : keep.source term verbatim pdf (output_countsummary.Rnw:228) -INFO @ Wed, 14 Feb 2018 01:52:58: -INFO @ Wed, 14 Feb 2018 01:52:58: You can now run (pdf)latex on ‘output_countsummary.tex’ -INFO @ Wed, 14 Feb 2018 01:52:58: Error in texi2dvi("output_countsummary.tex", pdf = TRUE) : -INFO @ Wed, 14 Feb 2018 01:52:58: pdflatex is not available -INFO @ Wed, 14 Feb 2018 01:52:58: Execution halted -INFO @ Wed, 14 Feb 2018 01:52:58: -INFO @ Wed, 14 Feb 2018 01:52:58: End command message. +INFO @ Sun, 25 Mar 2018 15:51:06: Parameters: /Users/doylemaria/miniconda3/envs/mulled-v1-5ed9647f14e9d3e99564d31bed2eb19cd32ee8b9da66a89bea59b64a8983b1d6/bin/mageck count -l /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmp0EKzNL/files/000/dataset_2.dat --fastq input_0.gz --sample-label test1_fastq_gz -n output --pdf-report --keep-tmp --unmapped-to-file +INFO @ Sun, 25 Mar 2018 15:51:06: Welcome to MAGeCK v0.5.7. Command: count +INFO @ Sun, 25 Mar 2018 15:51:06: Loading 2550 predefined sgRNAs. +WARNING @ Sun, 25 Mar 2018 15:51:06: There are 0 sgRNAs with duplicated sequences. +INFO @ Sun, 25 Mar 2018 15:51:06: Parsing FASTQ file input_0.gz... +INFO @ Sun, 25 Mar 2018 15:51:06: Determining the trim-5 length of FASTQ file input_0.gz... +INFO @ Sun, 25 Mar 2018 15:51:06: Possible gRNA lengths:20 +INFO @ Sun, 25 Mar 2018 15:51:06: Processing 0M reads ... +INFO @ Sun, 25 Mar 2018 15:51:06: Read length:30 +INFO @ Sun, 25 Mar 2018 15:51:06: Total tested reads: 2500, mapped: 1453(0.5812) +INFO @ Sun, 25 Mar 2018 15:51:06: --trim-5 test data: (trim_length reads fraction) +INFO @ Sun, 25 Mar 2018 15:51:06: 0 1453 1.0 +INFO @ Sun, 25 Mar 2018 15:51:06: Auto determination of trim5 results: 0 +INFO @ Sun, 25 Mar 2018 15:51:06: Possible gRNA lengths:20 +INFO @ Sun, 25 Mar 2018 15:51:06: Processing 0M reads .. +INFO @ Sun, 25 Mar 2018 15:51:06: Total: 2500. +INFO @ Sun, 25 Mar 2018 15:51:06: Mapped: 1453. +DEBUG @ Sun, 25 Mar 2018 15:51:06: Initial (total) size factor: 1.0 +DEBUG @ Sun, 25 Mar 2018 15:51:06: Median factor: 2.0 +INFO @ Sun, 25 Mar 2018 15:51:06: Final size factor: 2.0 +INFO @ Sun, 25 Mar 2018 15:51:06: Summary of file input_0.gz: +INFO @ Sun, 25 Mar 2018 15:51:06: label test1_fastq_gz +INFO @ Sun, 25 Mar 2018 15:51:06: reads 2500 +INFO @ Sun, 25 Mar 2018 15:51:06: mappedreads 1453 +INFO @ Sun, 25 Mar 2018 15:51:06: totalsgrnas 2550 +INFO @ Sun, 25 Mar 2018 15:51:06: zerosgrnas 1276 +INFO @ Sun, 25 Mar 2018 15:51:06: giniindex 0.5266899931488773 +INFO @ Sun, 25 Mar 2018 15:51:06: Loading Rnw template file: /Users/doylemaria/miniconda3/envs/mulled-v1-5ed9647f14e9d3e99564d31bed2eb19cd32ee8b9da66a89bea59b64a8983b1d6/lib/python3.6/site-packages/mageck/fastq_template.Rnw. +DEBUG @ Sun, 25 Mar 2018 15:51:06: Setting up the visualization module... +INFO @ Sun, 25 Mar 2018 15:51:06: Running command: cd ./; Rscript output_countsummary.R +INFO @ Sun, 25 Mar 2018 15:51:11: Command message: +INFO @ Sun, 25 Mar 2018 15:51:11: Writing to file output_countsummary.tex +INFO @ Sun, 25 Mar 2018 15:51:11: Processing code chunks with options ... +INFO @ Sun, 25 Mar 2018 15:51:11: 1 : keep.source term verbatim (label = funcdef, output_countsummary.Rnw:28) +INFO @ Sun, 25 Mar 2018 15:51:11: 2 : keep.source term tex (label = tab1, output_countsummary.Rnw:156) +INFO @ Sun, 25 Mar 2018 15:51:11: 3 : keep.source term tex (label = tab2, output_countsummary.Rnw:174) +INFO @ Sun, 25 Mar 2018 15:51:11: 4 : keep.source term tex (label = tab3, output_countsummary.Rnw:188) +INFO @ Sun, 25 Mar 2018 15:51:11: 5 : keep.source term verbatim pdf (output_countsummary.Rnw:221) +INFO @ Sun, 25 Mar 2018 15:51:11: 6 : keep.source term verbatim pdf (output_countsummary.Rnw:228) +INFO @ Sun, 25 Mar 2018 15:51:11: +INFO @ Sun, 25 Mar 2018 15:51:11: You can now run (pdf)latex on ‘output_countsummary.tex’ +INFO @ Sun, 25 Mar 2018 15:51:11: +INFO @ Sun, 25 Mar 2018 15:51:11: End command message. |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.count.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.count.txt Wed Apr 04 11:03:59 2018 -0400 |
| b |
| b'@@ -0,0 +1,2551 @@\n+sgRNA\tGene\ttest1_fastq_gz\n+s_47512\tRNF111\t1\n+s_24835\tHCFC1R1\t1\n+s_14784\tCYP4B1\t4\n+s_51146\tSLC18A1\t1\n+s_58960\tTRIM5\t1\n+s_48256\tRPRD2\t1\n+s_30297\tKRTAP5-5\t1\n+s_14555\tCYB5B\t1\n+s_39959\tPAAF1\t1\n+s_45293\tPUF60\t1\n+s_49358\tSCN8A\t1\n+s_64995\tZYG11A\t1\n+s_4029\tASTE1\t1\n+s_45554\tR3HDML\t1\n+s_34264\tMMRN1\t1\n+s_37459\tNOL6\t1\n+s_23990\tGPX7\t1\n+s_20268\tFANCC\t1\n+s_14157\tCTLA4\t1\n+s_36773\tNEURL4\t18\n+s_18804\tETFB\t1\n+s_782\tACSS1\t1\n+s_18272\tENPP2\t1\n+s_46620\tRCN1\t1\n+s_55436\tTAS2R3\t1\n+s_57947\tTMPRSS2\t1\n+s_6438\tC14orf159\t1\n+s_33846\tMGST2\t1\n+s_16328\tDNAH6\t1\n+s_17875\tEIF4G1\t1\n+s_2305\tANAPC11\t1\n+s_2500\tANKRD2\t1\n+s_82\tAARSD1\t1\n+s_55329\tTAL1\t1\n+s_57926\tTMPRSS11E\t8\n+s_38414\tNUP98\t4\n+s_50044\tSERPINF1\t1\n+s_9257\tCASR\t1\n+s_63396\tZNF182\t1\n+s_56478\tTHBS3\t1\n+s_17191\tDYRK1A\t1\n+s_11988\tCIR1\t1\n+s_43313\tPPARD\t1\n+s_44681\tPSMA4\t1\n+s_10387\tCD320\t1\n+s_64869\tZPBP\t1\n+s_54385\tSTK17B\t1\n+s_25423\tHIST1H4D\t1\n+s_54172\tST8SIA4\t9\n+s_1161\tADCY10\t1\n+s_29184\tKIAA0913\t1\n+s_42977\tPOLD3\t1\n+s_49449\tSCUBE1\t1\n+s_24181\tGRM4\t1\n+s_52507\tSMARCA5\t1\n+s_28674\tKCNJ10\t1\n+s_61074\tVAMP2\t4\n+s_3954\tASIC2\t1\n+s_2385\tANK1\t1\n+s_18397\tEPDR1\t1\n+s_18377\tEPB41L4B\t1\n+s_34580\tMRAP2\t1\n+s_48676\tRUFY3\t10\n+s_691\tACP1\t1\n+s_30460\tLAMP2\t1\n+s_42637\tPLRG1\t1\n+s_12695\tCNOT6\t1\n+s_33316\tMECOM\t2\n+s_35081\tMSRB2\t1\n+s_58512\tTPD52L2\t1\n+s_19912\tFAM22F\t1\n+s_45517\tQSOX2\t1\n+s_56705\tTINAG\t1\n+s_10946\tCDKL5\t1\n+s_57473\tTMEM211\t2\n+s_57657\tTMEM44\t1\n+s_43200\tPOT1\t1\n+s_19436\tFAM135A\t1\n+s_184\tABCB9\t1\n+s_30171\tKRT84\t1\n+s_44758\tPSMC3IP\t1\n+s_48313\tRPS3\t1\n+s_58142\tTNFSF12\t6\n+s_59718\tTTLL6\t7\n+s_9725\tCCDC43\t1\n+s_5135\tBCKDHA\t1\n+s_36539\tNDUFC2\t1\n+s_27251\tIL27RA\t1\n+s_48939\tSAMD10\t1\n+s_27343\tIL5RA\t1\n+s_28386\tKANK2\t1\n+s_27610\tINSRR\t1\n+s_2769\tAOC3\t2\n+s_58632\tTRA2B\t12\n+s_6674\tC16orf86\t1\n+s_22902\tGJD4\t1\n+s_48278\tRPS15A\t1\n+s_61998\tWIPF2\t1\n+s_4937\tBAIAP3\t2\n+s_54471\tSTOML1\t2\n+s_19157\tFABP12\t1\n+s_5434\tBIN1\t2\n+s_42042\tPIP5K1A\t1\n+s_7794\tC3orf18\t1\n+s_54846\tSVIL\t1\n+s_62273\tXPA\t1\n+s_45859\tRACGAP1\t1\n+s_53626\tSPOCK3\t1\n+s_43295\tPPAP2C\t7\n+s_11788\tCHRDL1\t2\n+s_50636\tSHQ1\t1\n+s_16705\tDPF1\t1\n+s_39741\tOTOF\t1\n+s_27505\tINHBE\t1\n+s_707\tACPL2\t1\n+s_15418\tDDX3Y\t6\n+s_56018\tTEAD4\t1\n+s_44367\tPRR12\t1\n+s_25875\tHOXB5\t1\n+s_49360\tSCN9A\t1\n+s_16244\tDMPK\t1\n+s_3909\tASCC2\t1\n+s_55088\tSYT6\t1\n+s_54311\tSTAU1\t1\n+s_53890\tSRP72\t1\n+s_11035\tCDX1\t1\n+s_18178\tEMR3\t2\n+s_16084\tDLD\t1\n+s_47207\tRHOBTB1\t1\n+s_40267\tPARK2\t6\n+s_43104\tPOLR3B\t1\n+s_2200\tAMDHD2\t1\n+s_12738\tCNRIP1\t1\n+s_17842\tEIF4A3\t1\n+s_57950\tTMPRSS3\t1\n+s_62146\tWRN\t1\n+s_11055\tCEACAM1\t1\n+s_54580\tSTX2\t1\n+s_29277\tKIAA1407\t1\n+s_33428\tMEF2A\t1\n+s_59797\tTUBB\t1\n+s_18113\tEME1\t1\n+s_29839\tKLHL8\t1\n+s_18058\tELP2\t1\n+s_49497\tSDCBP2\t3\n+s_16874\tDRP2\t1\n+s_13572\tCREBL2\t1\n+s_20540\tFBXO30\t1\n+s_64380\tZNF646\t1\n+s_50366\tSH2B1\t1\n+s_2548\tANKRD33B\t1\n+s_41183\tPDXP\t1\n+s_16315\tDNAH12\t1\n+s_19996\tFAM49B\t1\n+s_30751\tLDLRAD3\t1\n+s_36960\tNGEF\t1\n+s_39015\tOR2A2\t1\n+s_26302\tHSPB2\t1\n+s_64297\tZNF611\t5\n+s_730\tACSBG1\t1\n+s_50271\tSFXN4\t1\n+s_8592\tCA6\t2\n+s_13683\tCRMP1\t1\n+s_51103\tSLC16A7\t1\n+s_63785\tZNF384\t1\n+s_16339\tDNAH9\t1\n+s_55936\tTCTEX1D1\t1\n+s_14497\tCXorf40A\t1\n+s_1123\tADAT1\t1\n+s_41304\tPERP\t1\n+s_18719\tESAM\t1\n+s_35118\tMSX2\t1\n+s_30128\tKRT6A\t1\n+s_402\tABTB1\t1\n+s_32578\tMAP1LC3A\t1\n+s_45063\tPTMA\t1\n+s_43551\tPPP1R14D\t1\n+s_2538\tANKRD32\t1\n+s_40384\tPAX1\t1\n+s_29076\tKIAA0101\t1\n+s_40482\tPCDH10\t1\n+s_2348\tANGPT2\t1\n+s_59756\tTTYH3\t1\n+s_34330\tMOB4\t1\n+s_49331\tSCN2B\t1\n+s_54905\tSYDE1\t1\n+s_39101\tOR2T1\t1\n+s_36623\tNEDD4L\t1\n+s_40500\tPCDH15\t2\n+s_10660\tCDC42SE2\t1\n+s_30867\tLGALS13\t1\n+s_24322\tGSTK1\t2\n+s_59167\tTRPC1\t1\n+s_57440\tTMEM201\t1\n+s_50539\tSHC1\t1\n+s_37087\tNIT1\t1\n+s_56345\tTGFB2\t1\n+s_55388\tTARM1\t1\n+s_1224\tADD2\t1\n+s_5256\tBCOR\t2\n+s_51731\tSLC35B3\t1\n+s_12987\tCOL6A6\t1\n+s_56745\tTJP3\t1\n+s_19340\tFAM120AOS\t1\n+s_53904\tSRPR\t1\n+s_1588\tAGXT\t1\n+s_46157\tRASA3\t1\n+s_19166\tFABP3\t7\n+s_22330\tGATM\t1\n+s_10731\tCDH13\t1\n+s_2329\tANAPC5\t1\n+s_46045\tRANGAP1\t1\n+s_54814\tSUV39H2\t1\n+s_56169\tTEX14\t1\n+s_3433\tARHGEF26\t1\n+s_48032\tRP4-811H24.6\t1\n+s_51930\tSLC41A3\t1\n+s_63893\tZNF433\t1\n+s_46996\tRGCC\t1\n+s_13863\tCSF3R\t1\n+s_26337\tHSPH1\t1\n+s_12983\tCOL6A3\t1\n+s_1376\tADSS\t1\n+s_45449\tPYHIN1\t1\n+s_49629\tSEC22C\t1\n+s_20204\tFAM86A\t1\n+s_24920\tHDAC9\t1\n+s_14961\tDAPK1\t1\n+s_'..b'A\t0\n+s_57422\tTMEM198\t0\n+s_57429\tTMEM2\t0\n+s_57475\tTMEM212\t0\n+s_57531\tTMEM231\t0\n+s_57568\tTMEM245\t0\n+s_57700\tTMEM54\t0\n+s_57873\tTMF1\t0\n+s_57992\tTMUB1\t0\n+s_58180\tTNIP1\t0\n+s_58211\tTNKS2\t0\n+s_58237\tTNNT1\t0\n+s_58256\tTNPO2\t0\n+s_58259\tTNPO3\t0\n+s_58309\tTOM1\t0\n+s_58485\tTP73\t0\n+s_58503\tTPD52\t0\n+s_58533\tTPI1\t0\n+s_5857\tBSPRY\t0\n+s_58612\tTPSG1\t0\n+s_58633\tTRA2B\t0\n+s_58655\tTRAF3\t0\n+s_58668\tTRAF3IP2\t0\n+s_58690\tTRAK1\t0\n+s_58809\tTRIB2\t0\n+s_58962\tTRIM50\t0\n+s_58968\tTRIM52\t0\n+s_59050\tTRIO\t0\n+s_59107\tTRMT1L\t0\n+s_59133\tTRMT61B\t0\n+s_59160\tTROVE2\t0\n+s_59173\tTRPC4\t0\n+s_59196\tTRPM1\t0\n+s_59204\tTRPM3\t0\n+s_59311\tTSEN54\t0\n+s_59332\tTSHB\t0\n+s_59340\tTSHZ2\t0\n+s_59360\tTSNARE1\t0\n+s_5952\tBTG4\t0\n+s_59539\tTTC21A\t0\n+s_59602\tTTC39A\t0\n+s_59654\tTTC9C\t0\n+s_59717\tTTLL6\t0\n+s_5974\tBTN3A1\t0\n+s_59748\tTTYH1\t0\n+s_59807\tTUBB2B\t0\n+s_59859\tTULP1\t0\n+s_59870\tTULP3\t0\n+s_59955\tTXNDC8\t0\n+s_59983\tTXNRD2\t0\n+s_600\tACE\t0\n+s_60169\tUBE2H\t0\n+s_60209\tUBE2Q2\t0\n+s_60237\tUBE2V2\t0\n+s_60248\tUBE3A\t0\n+s_60250\tUBE3B\t0\n+s_60373\tUBXN6\t0\n+s_60396\tUCKL1\t0\n+s_60423\tUEVLD\t0\n+s_60438\tUFSP1\t0\n+s_60449\tUGDH\t0\n+s_60517\tUGT2A1\t0\n+s_60542\tUGT3A1\t0\n+s_60603\tUMODL1\t0\n+s_60614\tUNC119\t0\n+s_60649\tUNC5B\t0\n+s_6068\tC10orf125\t0\n+s_6071\tC10orf128\t0\n+s_60753\tUQCRC2\t0\n+s_60780\tURM1\t0\n+s_60839\tUSP15\t0\n+s_60851\tUSP19\t0\n+s_60925\tUSP4\t0\n+s_6100\tC10orf53\t0\n+s_6106\tC10orf54\t0\n+s_61149\tVAV2\t0\n+s_61173\tVCAM1\t0\n+s_61178\tVCAN\t0\n+s_61221\tVEPH1\t0\n+s_61263\tVIL1\t0\n+s_61341\tVPS13C\t0\n+s_61344\tVPS13D\t0\n+s_61367\tVPS29\t0\n+s_61529\tVWA5A\t0\n+s_61531\tVWA5A\t0\n+s_61587\tWBP1\t0\n+s_61595\tWBP2\t0\n+s_61623\tWDFY1\t0\n+s_61640\tWDHD1\t0\n+s_61662\tWDR16\t0\n+s_61695\tWDR26\t0\n+s_61739\tWDR44\t0\n+s_6200\tC11orf49\t0\n+s_62019\tWISP1\t0\n+s_62098\tWNT5B\t0\n+s_62114\tWNT8A\t0\n+s_62171\tWTAP\t0\n+s_62249\tXKR3\t0\n+s_62257\tXKR6\t0\n+s_62275\tXPC\t0\n+s_62320\tXRCC4\t0\n+s_62361\tYAE1D1\t0\n+s_62550\tZBBX\t0\n+s_62559\tZBED6\t0\n+s_62567\tZBTB1\t0\n+s_62624\tZBTB37\t0\n+s_62657\tZBTB47\t0\n+s_62759\tZC3H7A\t0\n+s_62845\tZDHHC11\t0\n+s_62862\tZDHHC16\t0\n+s_62881\tZDHHC2\t0\n+s_6292\tC12orf23\t0\n+s_62975\tZFC3H1\t0\n+s_63034\tZFP64\t0\n+s_63104\tZFYVE27\t0\n+s_63107\tZFYVE27\t0\n+s_63114\tZFYVE28\t0\n+s_63217\tZMIZ2\t0\n+s_63228\tZMYM3\t0\n+s_63234\tZMYM3\t0\n+s_6326\tC12orf49\t0\n+s_63302\tZNF132\t0\n+s_63362\tZNF167\t0\n+s_63435\tZNF200\t0\n+s_63487\tZNF223\t0\n+s_63594\tZNF276\t0\n+s_636\tACO1\t0\n+s_63746\tZNF354B\t0\n+s_63755\tZNF362\t0\n+s_6376\tC12orf74\t0\n+s_63903\tZNF436\t0\n+s_63905\tZNF438\t0\n+s_63923\tZNF442\t0\n+s_63934\tZNF445\t0\n+s_63935\tZNF446\t0\n+s_63964\tZNF469\t0\n+s_63983\tZNF480\t0\n+s_6409\tC14orf105\t0\n+s_64137\tZNF554\t0\n+s_64241\tZNF586\t0\n+s_6427\tC14orf133\t0\n+s_64356\tZNF639\t0\n+s_64393\tZNF655\t0\n+s_64396\tZNF655\t0\n+s_64419\tZNF668\t0\n+s_64424\tZNF669\t0\n+s_64459\tZNF682\t0\n+s_64479\tZNF688\t0\n+s_64581\tZNF746\t0\n+s_64627\tZNF772\t0\n+s_64638\tZNF776\t0\n+s_64652\tZNF780A\t0\n+s_64791\tZNF85\t0\n+s_64851\tZNRF3\t0\n+s_64871\tZPBP\t0\n+s_64878\tZPLD1\t0\n+s_64898\tZSCAN10\t0\n+s_64930\tZSCAN30\t0\n+s_64997\tZYG11A\t0\n+s_6525\tC15orf39\t0\n+s_6592\tC16orf13\t0\n+s_6639\tC16orf62\t0\n+s_6707\tC17orf102\t0\n+s_6710\tC17orf104\t0\n+s_6728\tC17orf112\t0\n+s_6736\tC17orf39\t0\n+s_6794\tC17orf72\t0\n+s_6814\tC17orf80\t0\n+s_6849\tC18orf21\t0\n+s_6859\tC18orf32\t0\n+s_6862\tC18orf34\t0\n+s_6906\tC19orf38\t0\n+s_7053\tC1QTNF7\t0\n+s_7128\tC1orf122\t0\n+s_7144\tC1orf130\t0\n+s_7162\tC1orf144\t0\n+s_7234\tC1orf198\t0\n+s_7341\tC1orf63\t0\n+s_747\tACSL1\t0\n+s_76\tAARS2\t0\n+s_7674\tC2orf57\t0\n+s_7681\tC2orf62\t0\n+s_7692\tC2orf63\t0\n+s_77\tAARSD1\t0\n+s_78\tAARSD1\t0\n+s_781\tACSS1\t0\n+s_786\tACSS2\t0\n+s_7940\tC4orf26\t0\n+s_7970\tC4orf37\t0\n+s_8000\tC4orf52\t0\n+s_804\tACTB\t0\n+s_8073\tC5orf51\t0\n+s_8141\tC6orf162\t0\n+s_8227\tC7orf10\t0\n+s_8281\tC7orf59\t0\n+s_8318\tC8A\t0\n+s_8403\tC9orf100\t0\n+s_8470\tC9orf24\t0\n+s_8699\tCACNA1G\t0\n+s_8705\tCACNA1I\t0\n+s_871\tACTR8\t0\n+s_874\tACTR8\t0\n+s_8757\tCACNG5\t0\n+s_8797\tCADPS\t0\n+s_8879\tCALR\t0\n+s_8910\tCAMK2B\t0\n+s_893\tACVR1B\t0\n+s_8930\tCAMKK1\t0\n+s_8954\tCAMSAP1\t0\n+s_9064\tCAPRIN1\t0\n+s_9077\tCAPSL\t0\n+s_9109\tCARD17\t0\n+s_913\tACY1\t0\n+s_9171\tCASD1\t0\n+s_9196\tCASP10\t0\n+s_9285\tCATSPER3\t0\n+s_9506\tCCDC120\t0\n+s_9507\tCCDC121\t0\n+s_952\tADAM12\t0\n+s_9584\tCCDC149\t0\n+s_964\tADAM18\t0\n+s_9646\tCCDC170\t0\n+s_9710\tCCDC40\t0\n+s_9732\tCCDC48\t0\n+s_976\tADAM21\t0\n+s_9763\tCCDC62\t0\n+s_9868\tCCDC89\t0\n+s_991\tADAM30\t0\n+s_9925\tCCL1\t0\n+s_9973\tCCL26\t0\n' |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.count_multi.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.count_multi.txt Wed Apr 04 11:03:59 2018 -0400 |
| b |
| b'@@ -0,0 +1,2551 @@\n+sgRNA\tGene\ttest1_fastq_gz\ttest2_fastq_gz\n+s_47512\tRNF111\t1\t0\n+s_24835\tHCFC1R1\t1\t0\n+s_14784\tCYP4B1\t4\t0\n+s_51146\tSLC18A1\t1\t0\n+s_58960\tTRIM5\t1\t0\n+s_48256\tRPRD2\t1\t0\n+s_30297\tKRTAP5-5\t1\t0\n+s_14555\tCYB5B\t1\t0\n+s_39959\tPAAF1\t1\t1\n+s_45293\tPUF60\t1\t0\n+s_49358\tSCN8A\t1\t1\n+s_64995\tZYG11A\t1\t0\n+s_4029\tASTE1\t1\t0\n+s_45554\tR3HDML\t1\t0\n+s_34264\tMMRN1\t1\t0\n+s_37459\tNOL6\t1\t0\n+s_23990\tGPX7\t1\t0\n+s_20268\tFANCC\t1\t0\n+s_14157\tCTLA4\t1\t0\n+s_36773\tNEURL4\t18\t3\n+s_18804\tETFB\t1\t0\n+s_782\tACSS1\t1\t0\n+s_18272\tENPP2\t1\t0\n+s_46620\tRCN1\t1\t0\n+s_55436\tTAS2R3\t1\t0\n+s_57947\tTMPRSS2\t1\t1\n+s_6438\tC14orf159\t1\t0\n+s_33846\tMGST2\t1\t0\n+s_16328\tDNAH6\t1\t0\n+s_17875\tEIF4G1\t1\t0\n+s_2305\tANAPC11\t1\t0\n+s_2500\tANKRD2\t1\t0\n+s_82\tAARSD1\t1\t0\n+s_55329\tTAL1\t1\t0\n+s_57926\tTMPRSS11E\t8\t0\n+s_38414\tNUP98\t4\t0\n+s_50044\tSERPINF1\t1\t0\n+s_9257\tCASR\t1\t0\n+s_63396\tZNF182\t1\t0\n+s_56478\tTHBS3\t1\t0\n+s_17191\tDYRK1A\t1\t0\n+s_11988\tCIR1\t1\t0\n+s_43313\tPPARD\t1\t0\n+s_44681\tPSMA4\t1\t0\n+s_10387\tCD320\t1\t0\n+s_64869\tZPBP\t1\t0\n+s_54385\tSTK17B\t1\t0\n+s_25423\tHIST1H4D\t1\t0\n+s_54172\tST8SIA4\t9\t0\n+s_1161\tADCY10\t1\t0\n+s_29184\tKIAA0913\t1\t0\n+s_42977\tPOLD3\t1\t0\n+s_49449\tSCUBE1\t1\t0\n+s_24181\tGRM4\t1\t1\n+s_52507\tSMARCA5\t1\t0\n+s_28674\tKCNJ10\t1\t0\n+s_61074\tVAMP2\t4\t0\n+s_3954\tASIC2\t1\t0\n+s_2385\tANK1\t1\t0\n+s_18397\tEPDR1\t1\t0\n+s_18377\tEPB41L4B\t1\t0\n+s_34580\tMRAP2\t1\t0\n+s_48676\tRUFY3\t10\t0\n+s_691\tACP1\t1\t0\n+s_30460\tLAMP2\t1\t0\n+s_42637\tPLRG1\t1\t0\n+s_12695\tCNOT6\t1\t0\n+s_33316\tMECOM\t2\t0\n+s_35081\tMSRB2\t1\t0\n+s_58512\tTPD52L2\t1\t0\n+s_19912\tFAM22F\t1\t0\n+s_45517\tQSOX2\t1\t0\n+s_56705\tTINAG\t1\t0\n+s_10946\tCDKL5\t1\t0\n+s_57473\tTMEM211\t2\t0\n+s_57657\tTMEM44\t1\t0\n+s_43200\tPOT1\t1\t0\n+s_19436\tFAM135A\t1\t0\n+s_184\tABCB9\t1\t0\n+s_30171\tKRT84\t1\t0\n+s_44758\tPSMC3IP\t1\t0\n+s_48313\tRPS3\t1\t0\n+s_58142\tTNFSF12\t6\t0\n+s_59718\tTTLL6\t7\t0\n+s_9725\tCCDC43\t1\t0\n+s_5135\tBCKDHA\t1\t0\n+s_36539\tNDUFC2\t1\t0\n+s_27251\tIL27RA\t1\t0\n+s_48939\tSAMD10\t1\t0\n+s_27343\tIL5RA\t1\t0\n+s_28386\tKANK2\t1\t0\n+s_27610\tINSRR\t1\t0\n+s_2769\tAOC3\t2\t0\n+s_58632\tTRA2B\t12\t0\n+s_6674\tC16orf86\t1\t0\n+s_22902\tGJD4\t1\t0\n+s_48278\tRPS15A\t1\t0\n+s_61998\tWIPF2\t1\t0\n+s_4937\tBAIAP3\t2\t0\n+s_54471\tSTOML1\t2\t1\n+s_19157\tFABP12\t1\t0\n+s_5434\tBIN1\t2\t0\n+s_42042\tPIP5K1A\t1\t0\n+s_7794\tC3orf18\t1\t0\n+s_54846\tSVIL\t1\t0\n+s_62273\tXPA\t1\t0\n+s_45859\tRACGAP1\t1\t0\n+s_53626\tSPOCK3\t1\t0\n+s_43295\tPPAP2C\t7\t0\n+s_11788\tCHRDL1\t2\t0\n+s_50636\tSHQ1\t1\t0\n+s_16705\tDPF1\t1\t0\n+s_39741\tOTOF\t1\t0\n+s_27505\tINHBE\t1\t0\n+s_707\tACPL2\t1\t0\n+s_15418\tDDX3Y\t6\t0\n+s_56018\tTEAD4\t1\t0\n+s_44367\tPRR12\t1\t0\n+s_25875\tHOXB5\t1\t0\n+s_49360\tSCN9A\t1\t0\n+s_16244\tDMPK\t1\t0\n+s_3909\tASCC2\t1\t0\n+s_55088\tSYT6\t1\t1\n+s_54311\tSTAU1\t1\t0\n+s_53890\tSRP72\t1\t0\n+s_11035\tCDX1\t1\t0\n+s_18178\tEMR3\t2\t0\n+s_16084\tDLD\t1\t0\n+s_47207\tRHOBTB1\t1\t0\n+s_40267\tPARK2\t6\t0\n+s_43104\tPOLR3B\t1\t0\n+s_2200\tAMDHD2\t1\t0\n+s_12738\tCNRIP1\t1\t0\n+s_17842\tEIF4A3\t1\t0\n+s_57950\tTMPRSS3\t1\t0\n+s_62146\tWRN\t1\t0\n+s_11055\tCEACAM1\t1\t0\n+s_54580\tSTX2\t1\t0\n+s_29277\tKIAA1407\t1\t0\n+s_33428\tMEF2A\t1\t0\n+s_59797\tTUBB\t1\t0\n+s_18113\tEME1\t1\t1\n+s_29839\tKLHL8\t1\t0\n+s_18058\tELP2\t1\t0\n+s_49497\tSDCBP2\t3\t0\n+s_16874\tDRP2\t1\t0\n+s_13572\tCREBL2\t1\t0\n+s_20540\tFBXO30\t1\t0\n+s_64380\tZNF646\t1\t0\n+s_50366\tSH2B1\t1\t0\n+s_2548\tANKRD33B\t1\t0\n+s_41183\tPDXP\t1\t1\n+s_16315\tDNAH12\t1\t0\n+s_19996\tFAM49B\t1\t0\n+s_30751\tLDLRAD3\t1\t0\n+s_36960\tNGEF\t1\t0\n+s_39015\tOR2A2\t1\t0\n+s_26302\tHSPB2\t1\t0\n+s_64297\tZNF611\t5\t0\n+s_730\tACSBG1\t1\t0\n+s_50271\tSFXN4\t1\t0\n+s_8592\tCA6\t2\t0\n+s_13683\tCRMP1\t1\t0\n+s_51103\tSLC16A7\t1\t0\n+s_63785\tZNF384\t1\t0\n+s_16339\tDNAH9\t1\t0\n+s_55936\tTCTEX1D1\t1\t0\n+s_14497\tCXorf40A\t1\t0\n+s_1123\tADAT1\t1\t0\n+s_41304\tPERP\t1\t0\n+s_18719\tESAM\t1\t0\n+s_35118\tMSX2\t1\t0\n+s_30128\tKRT6A\t1\t0\n+s_402\tABTB1\t1\t0\n+s_32578\tMAP1LC3A\t1\t0\n+s_45063\tPTMA\t1\t2\n+s_43551\tPPP1R14D\t1\t0\n+s_2538\tANKRD32\t1\t0\n+s_40384\tPAX1\t1\t0\n+s_29076\tKIAA0101\t1\t0\n+s_40482\tPCDH10\t1\t0\n+s_2348\tANGPT2\t1\t0\n+s_59756\tTTYH3\t1\t0\n+s_34330\tMOB4\t1\t0\n+s_49331\tSCN2B\t1\t0\n+s_54905\tSYDE1\t1\t0\n+s_39101\tOR2T1\t1\t0\n+s_36623\tNEDD4L\t1\t0\n+s_40500\tPCDH15\t2\t2\n+s_10660\tCDC42SE2\t1\t0\n+s_30867\tLGALS13\t1\t0\n+s_24322\tGSTK1\t2\t0\n+s_59167\tTRPC1\t1\t0\n+s_57440\tTMEM201\t1\t0\n+s_50539\tSHC1\t1\t0\n+s_37087\tNIT1\t1\t0\n+s_56345\tTGFB2\t1\t1\n+s_55388\tTARM1\t1\t0\n+s_1224\tADD2\t1\t0\n+s_5256\tBCOR\t2\t0\n+s_51731\tSLC35B3\t1\t1\n+s_12987\tCOL6A6\t1\t1\n+s_56745\tTJP3\t1\t0\n+s_19340\tFAM120AOS\t1\t0\n+'..b'54019\tSSPN\t0\t1\n+s_45566\tRAB11FIP1\t0\t1\n+s_59204\tTRPM3\t0\t1\n+s_59133\tTRMT61B\t0\t2\n+s_42162\tPKHD1L1\t0\t1\n+s_43834\tPRAMEF13\t0\t1\n+s_10402\tCD37\t0\t1\n+s_9109\tCARD17\t0\t1\n+s_60839\tUSP15\t0\t1\n+s_39972\tPABPC4\t0\t1\n+s_27236\tIL24\t0\t1\n+s_46265\tRASSF4\t0\t1\n+s_16554\tDNM2\t0\t1\n+s_35935\tNAALADL2\t0\t1\n+s_51276\tSLC22A5\t0\t1\n+s_42560\tPLEKHS1\t0\t1\n+s_57992\tTMUB1\t0\t1\n+s_49625\tSEC22A\t0\t1\n+s_13389\tCPO\t0\t1\n+s_2828\tAP3B2\t0\t1\n+s_13328\tCPED1\t0\t1\n+s_53048\tSON\t0\t1\n+s_10541\tCD8B\t0\t1\n+s_1971\tALDH8A1\t0\t1\n+s_19126\tF7\t0\t1\n+s_25027\tHECW2\t0\t1\n+s_47005\tRGL2\t0\t1\n+s_18920\tEVX2\t0\t1\n+s_54314\tSTAU2\t0\t1\n+s_52093\tSLC5A5\t0\t1\n+s_53993\tSSBP1\t0\t1\n+s_9285\tCATSPER3\t0\t1\n+s_31206\tLMAN2\t0\t1\n+s_35569\tMYD88\t0\t1\n+s_37035\tNINJ1\t0\t1\n+s_36342\tNCR3\t0\t1\n+s_42261\tPLA2G2E\t0\t1\n+s_14520\tCXorf61\t0\t1\n+s_51179\tSLC1A2\t0\t1\n+s_17762\tEIF2B4\t0\t1\n+s_55911\tTCP10L2\t0\t1\n+s_38429\tNUSAP1\t0\t1\n+s_39964\tPABPC1\t0\t1\n+s_20106\tFAM71B\t0\t1\n+s_43533\tPPP1R13B\t0\t1\n+s_41145\tPDP1\t0\t1\n+s_60396\tUCKL1\t0\t1\n+s_22715\tGGPS1\t0\t1\n+s_47777\tRNF44\t0\t1\n+s_48179\tRPL36\t0\t1\n+s_28436\tKAT8\t0\t1\n+s_35497\tMXRA7\t0\t1\n+s_51312\tSLC24A4\t0\t1\n+s_38336\tNUMB\t0\t1\n+s_59340\tTSHZ2\t0\t1\n+s_17942\tELF1\t0\t1\n+s_13309\tCPE\t0\t1\n+s_44319\tPRPF39\t0\t1\n+s_10943\tCDKL5\t0\t1\n+s_8000\tC4orf52\t0\t1\n+s_54801\tSUSD4\t0\t1\n+s_60603\tUMODL1\t0\t1\n+s_13512\tCRB1\t0\t1\n+s_11317\tCEP63\t0\t1\n+s_64878\tZPLD1\t0\t1\n+s_3670\tARPC1A\t0\t1\n+s_17214\tDYX1C1\t0\t1\n+s_41077\tPDIA2\t0\t1\n+s_61529\tVWA5A\t0\t1\n+s_7234\tC1orf198\t0\t1\n+s_25696\tHNF4A\t0\t1\n+s_59602\tTTC39A\t0\t1\n+s_10437\tCD46\t0\t1\n+s_38683\tOGG1\t0\t1\n+s_13026\tCOLEC12\t0\t1\n+s_56621\tTIFA\t0\t1\n+s_39865\tOXSM\t0\t1\n+s_16190\tDLX3\t0\t2\n+s_14995\tDAXX\t0\t1\n+s_8705\tCACNA1I\t0\t1\n+s_37286\tNMB\t0\t1\n+s_15700\tDERL1\t0\t1\n+s_55147\tTAAR8\t0\t1\n+s_77\tAARSD1\t0\t1\n+s_28834\tKCNQ4\t0\t1\n+s_18171\tEMR1\t0\t1\n+s_54403\tSTK3\t0\t1\n+s_60248\tUBE3A\t0\t1\n+s_41879\tPIGR\t0\t1\n+s_53691\tSPRR3\t0\t1\n+s_40457\tPCBD1\t0\t1\n+s_46821\tRERG\t0\t1\n+s_30162\tKRT8\t0\t1\n+s_18409\tEPHA10\t0\t1\n+s_42181\tPKM\t0\t1\n+s_53151\tSOX30\t0\t1\n+s_18106\tEMCN\t0\t1\n+s_32504\tMAN1A2\t0\t1\n+s_33723\tMFNG\t0\t1\n+s_14338\tCUTA\t0\t1\n+s_56207\tTEX9\t0\t1\n+s_6292\tC12orf23\t0\t1\n+s_36482\tNDUFAF3\t0\t1\n+s_30741\tLDLR\t0\t3\n+s_13035\tCOMMD1\t0\t1\n+s_14463\tCXXC4\t0\t1\n+s_37274\tNLRP7\t0\t1\n+s_51774\tSLC35F3\t0\t1\n+s_33625\tMETTL23\t0\t1\n+s_29554\tKIRREL3\t0\t1\n+s_3312\tARHGAP30\t0\t1\n+s_42554\tPLEKHO1\t0\t1\n+s_30215\tKRTAP12-3\t0\t1\n+s_38679\tOGG1\t0\t1\n+s_22810\tGIMAP8\t0\t1\n+s_47780\tRNF6\t0\t1\n+s_39737\tOTOA\t0\t1\n+s_47413\tRLBP1\t0\t1\n+s_2037\tALG9\t0\t1\n+s_39802\tOTUD7A\t0\t1\n+s_46298\tRAVER2\t0\t1\n+s_54380\tSTK17A\t0\t1\n+s_2226\tAMIGO2\t0\t1\n+s_31115\tLIN9\t0\t1\n+s_3051\tAPOF\t0\t1\n+s_5503\tBMF\t0\t1\n+s_19215\tFAIM\t0\t1\n+s_56492\tTHEM4\t0\t1\n+s_7128\tC1orf122\t0\t1\n+s_18445\tEPHA8\t0\t1\n+s_56014\tTEAD4\t0\t1\n+s_10425\tCD40\t0\t1\n+s_64479\tZNF688\t0\t1\n+s_45139\tPTPN22\t0\t1\n+s_32474\tMAMDC4\t0\t1\n+s_21927\tGAB1\t0\t1\n+s_38901\tOR10W1\t0\t1\n+s_58633\tTRA2B\t0\t1\n+s_19633\tFAM178A\t0\t1\n+s_35406\tMUC4\t0\t1\n+s_49881\t5-Sep\t0\t1\n+s_63487\tZNF223\t0\t1\n+s_19859\tFAM213B\t0\t1\n+s_44065\tPRKACB\t0\t1\n+s_26987\tIKBKG\t0\t1\n+s_18273\tENPP3\t0\t1\n+s_18362\tEPB41L1\t0\t1\n+s_786\tACSS2\t0\t1\n+s_44181\tPRLH\t0\t1\n+s_52989\tSNX8\t0\t1\n+s_45141\tPTPN22\t0\t1\n+s_4025\tASS1\t0\t1\n+s_44910\tPTCH1\t0\t1\n+s_13662\tCRK\t0\t1\n+s_12089\tCLCF1\t0\t1\n+s_43122\tPOLR3G\t0\t1\n+s_5268\tBDH1\t0\t1\n+s_54609\tSTXBP4\t0\t1\n+s_25732\tHNRNPCL1\t0\t1\n+s_32962\tMATN3\t0\t1\n+s_15113\tDCAF6\t0\t1\n+s_40597\tPCDHB2\t0\t1\n+s_43158\tPOMT1\t0\t1\n+s_29627\tKLF15\t0\t1\n+s_46321\tRBBP5\t0\t1\n+s_636\tACO1\t0\t1\n+s_22316\tGATAD2A\t0\t1\n+s_18782\tESYT1\t0\t1\n+s_17442\tEDNRB\t0\t1\n+s_49844\tSEPP1\t0\t1\n+s_37945\tNRL\t0\t1\n+s_1663\tAIF1L\t0\t1\n+s_12049\tCKLF-CMTM1\t0\t1\n+s_47791\tRNF8\t0\t1\n+s_49957\tSERPINA3\t0\t1\n+s_36386\tNDOR1\t0\t1\n+s_46355\tRBFOX3\t0\t1\n+s_38592\tOCM2\t0\t1\n+s_54679\tSULT1B1\t0\t1\n+s_62114\tWNT8A\t0\t1\n+s_64791\tZNF85\t0\t1\n+s_47594\tRNF145\t0\t1\n+s_38124\tNTM\t0\t1\n+s_12906\tCOL22A1\t0\t1\n+s_24644\tHAAO\t0\t1\n+s_28135\tITM2A\t0\t1\n+s_47786\tRNF7\t0\t1\n+s_15988\tDIO1\t0\t1\n+s_6200\tC11orf49\t0\t1\n+s_37801\tNR1H4\t0\t1\n+s_43430\tPPIL4\t0\t1\n+s_1661\tAIF1\t0\t1\n+s_22033\tGAD1\t0\t1\n+s_53153\tSOX30\t0\t1\n+s_14364\tCWF19L1\t0\t1\n+s_20616\tFBXO7\t0\t1\n+s_20861\tFGD1\t0\t1\n+s_20325\tFAS\t0\t1\n+s_64851\tZNRF3\t0\t1\n+s_13405\tCPS1\t0\t1\n+s_10657\tCDC42SE2\t0\t1\n+s_27332\tIL4I1\t0\t1\n+s_39620\tOSBP2\t0\t1\n+s_7970\tC4orf37\t0\t1\n+s_2376\tANGPTL6\t0\t1\n+s_9732\tCCDC48\t0\t1\n+s_38832\tOPTC\t0\t1\n+s_11928\tCHUK\t0\t1\n+s_52833\tSNRPB2\t0\t1\n' |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.countsummary.pdf |
| b |
| Binary file test-data/out.countsummary.pdf has changed |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.countsummary.txt --- a/test-data/out.countsummary.txt Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.countsummary.txt Wed Apr 04 11:03:59 2018 -0400 |
| b |
| @@ -1,2 +1,2 @@ File Label Reads Mapped Percentage TotalsgRNAs Zerocounts GiniIndex NegSelQC NegSelQCPval NegSelQCPvalPermutation NegSelQCPvalPermutationFDR NegSelQCGene -input.gz sample1 2500 1453 0.5812 2550 1276 0.5267 0 1 1 1 0.0 +input_0.gz test1_fastq_gz 2500 1453 0.5812 2550 1276 0.5267 0 1 1 1 0.0 |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.countsummary_multi.pdf |
| b |
| Binary file test-data/out.countsummary_multi.pdf has changed |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.mle.log.txt --- a/test-data/out.mle.log.txt Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.mle.log.txt Wed Apr 04 11:03:59 2018 -0400 |
| [ |
| b'@@ -1,749 +1,57 @@\n-INFO @ Mon, 12 Feb 2018 21:46:26: Parameters: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/bin/mageck mle -k /tmp/tmpRFR3vr/files/000/dataset_1.dat -d /tmp/tmpRFR3vr/files/000/dataset_2.dat -n output --norm-method median --genes-varmodeling 1000 --permutation-round 10 --adjust-method fdr --threads 1 \n-INFO @ Mon, 12 Feb 2018 21:46:27: Cannot parse design matrix as a string; try to parse it as a file name ... \n-INFO @ Mon, 12 Feb 2018 21:46:27: Design matrix: \n-INFO @ Mon, 12 Feb 2018 21:46:27: [[1. 0. 0.] \n-INFO @ Mon, 12 Feb 2018 21:46:27: [1. 0. 0.] \n-INFO @ Mon, 12 Feb 2018 21:46:27: [1. 1. 0.] \n-INFO @ Mon, 12 Feb 2018 21:46:27: [1. 0. 1.]] \n-INFO @ Mon, 12 Feb 2018 21:46:27: Beta labels:baseline,HL60,KBM7 \n-INFO @ Mon, 12 Feb 2018 21:46:27: Included samples:HL60.initial,KBM7.initial,HL60.final,KBM7.final \n-INFO @ Mon, 12 Feb 2018 21:46:27: Loaded samples:HL60.initial;KBM7.initial;HL60.final;KBM7.final \n-INFO @ Mon, 12 Feb 2018 21:46:27: Sample index: 0;1;2;3 \n-INFO @ Mon, 12 Feb 2018 21:46:27: Loaded 100 genes. \n-DEBUG @ Mon, 12 Feb 2018 21:46:27: Initial (total) size factor: 1.6654412961322171 2.025116092944715 0.720025234995028 0.6592307725342162 \n-DEBUG @ Mon, 12 Feb 2018 21:46:27: Median factor: 1.4705915949061357 1.773663484525946 0.6311218804203026 0.5731039100868989 \n-INFO @ Mon, 12 Feb 2018 21:46:27: Final size factor: 1.4705915949061357 1.773663484525946 0.6311218804203026 0.5731039100868989 \n-INFO @ Mon, 12 Feb 2018 21:46:27: size factor: 0.6799984465189518,0.5638048078028025,1.5844800046134337,1.744884273862957 \n-INFO @ Mon, 12 Feb 2018 21:46:27: Thread 0 started. \n-INFO @ Mon, 12 Feb 2018 21:46:27: Thread 0: total 100 instances. \n-INFO @ Mon, 12 Feb 2018 21:46:27: Thread 0: Calculating AAAS (1) ... \n-INFO @ Mon, 12 Feb 2018 21:46:27: Thread 0 completed. \n-INFO @ Mon, 12 Feb 2018 21:46:27: All threads completed. \n-INFO @ Mon, 12 Feb 2018 21:46:27: Modeling the mean and variance ... \n-INFO @ Mon, 12 Feb 2018 21:46:27: Linear regression: y=-0.902175602829449x+14.539230037913281 \n-INFO @ Mon, 12 Feb 2018 21:46:27: Run the algorithm for the second time ... \n-WARNING @ Mon, 12 Feb 2018 21:46:27: A1CF: beta value does not converge. Try to increase the value of alpha .. \n-WARNING @ Mon, 12 Feb 2018 21:46:27: A1CF: alpha: 0.01 \n-WARNING @ Mon, 12 Feb 2018 21:46:28: A1CF: reaches the maximum number of iterations. \n-WARNING @ Mon, 12 Feb 2018 21:46:28: A1CF: alpha: 0.03 \n-WARNING @ Mon, 12 Feb 2018 21:46:29: A1CF: reaches the maximum number of iterations. \n-WARNING @ Mon, 12 Feb 2018 21:46:29: A1CF: alpha: 0.09 \n-INFO @ Mon, 12 Feb 2018 21:46:29: Calculating AAAS (1) ... \n-WARNING @ Mon, 12 Feb 2018 21:46:29: AAAS: beta value does not converge. Try to increase the value of alpha .. \n-WARNING @ Mon, 12 Feb 2018 21:46:29: AAAS: alpha: 0.01 \n-WARNING @ Mon, 12 Feb 2018 21:46:30: AAAS: reaches the maximum number of iterations. \n-WARNING @ Mon, 12 Feb 2018 21:46:30: AAAS: alpha: 0.03 \n-WARNING @ Mon, 12 Feb 2018 21:46:31: AAAS: reaches the maximum number of iterations. \n-WARNING @ Mon, 12 Feb 2018 21:46:31: AAAS: alpha: 0.09 \n-WARNING @ Mon, 12 Feb 2018 21:46:31: AAK1: beta value does not converge. Try to increase the value of alpha .. \n-WARNING @ Mon, 12 Feb 2018 21:46:31: AAK1: alpha: 0.01 \n-WARNING @ Mon, 12 Feb 2018 21:46:31: AAK1: reaches the maximum number of iterations. \n-WARNING @ Mon, 12 Feb 2018 21:46:31: AAK1: alpha: 0.03 \n-WARNING @ Mon, 12 Feb 2018 21:46:32: AAK1: reaches the maximum number of iterations. \n-WARNING @ Mon, 12 Feb 2018 21:46:32: AAK1: alpha: 0.09 \n-WARNING @ Mon, 12 Feb 2018 21:46:32: AATF: beta value does not converge. Try to increase the value of alpha .. \n-WARNING @ Mon, 12 Feb 2018 21:46:32: AATF: alpha: 0.01 \n-WARNING @ Mon, 12 Feb 2018 21:46:33: AATF: reaches the maximum number of iterations. \n-WARNING @ Mon, 12 Feb 2018 21:46:33: AATF: alpha: 0.03 \n-WARNING @ Mon, 12 Feb 2018 21:46:33: '..b'ds 1 \n+INFO @ Sun, 25 Mar 2018 22:27:42: Cannot parse design matrix as a string; try to parse it as a file name ... \n+INFO @ Sun, 25 Mar 2018 22:27:42: Design matrix: \n+INFO @ Sun, 25 Mar 2018 22:27:42: [[1. 0. 0.] \n+INFO @ Sun, 25 Mar 2018 22:27:42: [1. 0. 0.] \n+INFO @ Sun, 25 Mar 2018 22:27:42: [1. 1. 0.] \n+INFO @ Sun, 25 Mar 2018 22:27:42: [1. 0. 1.]] \n+INFO @ Sun, 25 Mar 2018 22:27:42: Beta labels:baseline,HL60,KBM7 \n+INFO @ Sun, 25 Mar 2018 22:27:42: Included samples:HL60.initial,KBM7.initial,HL60.final,KBM7.final \n+INFO @ Sun, 25 Mar 2018 22:27:42: Loaded samples:HL60.initial;KBM7.initial;HL60.final;KBM7.final \n+INFO @ Sun, 25 Mar 2018 22:27:42: Sample index: 0;1;2;3 \n+INFO @ Sun, 25 Mar 2018 22:27:42: Loaded 100 genes. \n+DEBUG @ Sun, 25 Mar 2018 22:27:42: Initial (total) size factor: 1.6654412961322171 2.025116092944715 0.720025234995028 0.6592307725342162 \n+DEBUG @ Sun, 25 Mar 2018 22:27:42: Median factor: 1.4705915949061357 1.773663484525946 0.6311218804203026 0.5731039100868989 \n+INFO @ Sun, 25 Mar 2018 22:27:42: Final size factor: 1.4705915949061357 1.773663484525946 0.6311218804203026 0.5731039100868989 \n+INFO @ Sun, 25 Mar 2018 22:27:42: size factor: 0.6799984465189518,0.5638048078028025,1.5844800046134337,1.744884273862957 \n+INFO @ Sun, 25 Mar 2018 22:27:42: Thread 0 started. \n+INFO @ Sun, 25 Mar 2018 22:27:42: Thread 0: total 1 instances. \n+INFO @ Sun, 25 Mar 2018 22:27:42: Thread 0 completed. \n+INFO @ Sun, 25 Mar 2018 22:27:42: All threads completed. \n+INFO @ Sun, 25 Mar 2018 22:27:42: Modeling the mean and variance ... \n+INFO @ Sun, 25 Mar 2018 22:27:42: Run the algorithm for the second time ... \n+INFO @ Sun, 25 Mar 2018 22:27:42: Calculating AAAS (1) ... \n+INFO @ Sun, 25 Mar 2018 22:27:43: Permuting groups of gene with 9 sgRNAs per gene. Group progress: 1/2 \n+INFO @ Sun, 25 Mar 2018 22:27:43: Start permuting 2 rounds ... \n+INFO @ Sun, 25 Mar 2018 22:27:43: Collecting 999 sgRNAs from 100 genes. \n+INFO @ Sun, 25 Mar 2018 22:27:43: Permuting round 0 ... \n+INFO @ Sun, 25 Mar 2018 22:27:43: Thread 0 started. \n+INFO @ Sun, 25 Mar 2018 22:27:43: Thread 0: total 100 instances. \n+INFO @ Sun, 25 Mar 2018 22:27:43: Thread 0: Calculating AAAS (1) ... \n+INFO @ Sun, 25 Mar 2018 22:27:45: Thread 0 completed. \n+INFO @ Sun, 25 Mar 2018 22:27:45: All threads completed. \n+INFO @ Sun, 25 Mar 2018 22:27:45: Permuting round 1 ... \n+INFO @ Sun, 25 Mar 2018 22:27:45: Thread 0 started. \n+INFO @ Sun, 25 Mar 2018 22:27:45: Thread 0: total 100 instances. \n+INFO @ Sun, 25 Mar 2018 22:27:45: Thread 0: Calculating AAAS (1) ... \n+INFO @ Sun, 25 Mar 2018 22:27:46: Thread 0 completed. \n+INFO @ Sun, 25 Mar 2018 22:27:46: All threads completed. \n+INFO @ Sun, 25 Mar 2018 22:27:46: Assigning p values... \n+INFO @ Sun, 25 Mar 2018 22:27:46: Permuting groups of gene with 10 sgRNAs per gene. Group progress: 2/2 \n+INFO @ Sun, 25 Mar 2018 22:27:46: Start permuting 2 rounds ... \n+INFO @ Sun, 25 Mar 2018 22:27:46: Collecting 999 sgRNAs from 100 genes. \n+INFO @ Sun, 25 Mar 2018 22:27:46: Permuting round 0 ... \n+INFO @ Sun, 25 Mar 2018 22:27:47: Thread 0 started. \n+INFO @ Sun, 25 Mar 2018 22:27:47: Thread 0: total 100 instances. \n+INFO @ Sun, 25 Mar 2018 22:27:47: Thread 0: Calculating AAAS (1) ... \n+INFO @ Sun, 25 Mar 2018 22:27:48: Thread 0 completed. \n+INFO @ Sun, 25 Mar 2018 22:27:48: All threads completed. \n+INFO @ Sun, 25 Mar 2018 22:27:49: Permuting round 1 ... \n+INFO @ Sun, 25 Mar 2018 22:27:49: Thread 0 started. \n+INFO @ Sun, 25 Mar 2018 22:27:49: Thread 0: total 100 instances. \n+INFO @ Sun, 25 Mar 2018 22:27:49: Thread 0: Calculating AAAS (1) ... \n+INFO @ Sun, 25 Mar 2018 22:27:50: Thread 0 completed. \n+INFO @ Sun, 25 Mar 2018 22:27:50: All threads completed. \n+INFO @ Sun, 25 Mar 2018 22:27:50: Assigning p values... \n+INFO @ Sun, 25 Mar 2018 22:27:50: Writing gene results to output.gene_summary.txt \n+INFO @ Sun, 25 Mar 2018 22:27:50: Writing sgRNA results to output.sgrna_summary.txt \n' |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.normcounts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.normcounts.txt Wed Apr 04 11:03:59 2018 -0400 |
| b |
| b'@@ -0,0 +1,2551 @@\n+sgRNA\tGene\ttest1_fastq_gz\n+s_47512\tRNF111\t2.0\n+s_24835\tHCFC1R1\t2.0\n+s_14784\tCYP4B1\t8.0\n+s_51146\tSLC18A1\t2.0\n+s_58960\tTRIM5\t2.0\n+s_48256\tRPRD2\t2.0\n+s_30297\tKRTAP5-5\t2.0\n+s_14555\tCYB5B\t2.0\n+s_39959\tPAAF1\t2.0\n+s_45293\tPUF60\t2.0\n+s_49358\tSCN8A\t2.0\n+s_64995\tZYG11A\t2.0\n+s_4029\tASTE1\t2.0\n+s_45554\tR3HDML\t2.0\n+s_34264\tMMRN1\t2.0\n+s_37459\tNOL6\t2.0\n+s_23990\tGPX7\t2.0\n+s_20268\tFANCC\t2.0\n+s_14157\tCTLA4\t2.0\n+s_36773\tNEURL4\t36.0\n+s_18804\tETFB\t2.0\n+s_782\tACSS1\t2.0\n+s_18272\tENPP2\t2.0\n+s_46620\tRCN1\t2.0\n+s_55436\tTAS2R3\t2.0\n+s_57947\tTMPRSS2\t2.0\n+s_6438\tC14orf159\t2.0\n+s_33846\tMGST2\t2.0\n+s_16328\tDNAH6\t2.0\n+s_17875\tEIF4G1\t2.0\n+s_2305\tANAPC11\t2.0\n+s_2500\tANKRD2\t2.0\n+s_82\tAARSD1\t2.0\n+s_55329\tTAL1\t2.0\n+s_57926\tTMPRSS11E\t16.0\n+s_38414\tNUP98\t8.0\n+s_50044\tSERPINF1\t2.0\n+s_9257\tCASR\t2.0\n+s_63396\tZNF182\t2.0\n+s_56478\tTHBS3\t2.0\n+s_17191\tDYRK1A\t2.0\n+s_11988\tCIR1\t2.0\n+s_43313\tPPARD\t2.0\n+s_44681\tPSMA4\t2.0\n+s_10387\tCD320\t2.0\n+s_64869\tZPBP\t2.0\n+s_54385\tSTK17B\t2.0\n+s_25423\tHIST1H4D\t2.0\n+s_54172\tST8SIA4\t18.0\n+s_1161\tADCY10\t2.0\n+s_29184\tKIAA0913\t2.0\n+s_42977\tPOLD3\t2.0\n+s_49449\tSCUBE1\t2.0\n+s_24181\tGRM4\t2.0\n+s_52507\tSMARCA5\t2.0\n+s_28674\tKCNJ10\t2.0\n+s_61074\tVAMP2\t8.0\n+s_3954\tASIC2\t2.0\n+s_2385\tANK1\t2.0\n+s_18397\tEPDR1\t2.0\n+s_18377\tEPB41L4B\t2.0\n+s_34580\tMRAP2\t2.0\n+s_48676\tRUFY3\t20.0\n+s_691\tACP1\t2.0\n+s_30460\tLAMP2\t2.0\n+s_42637\tPLRG1\t2.0\n+s_12695\tCNOT6\t2.0\n+s_33316\tMECOM\t4.0\n+s_35081\tMSRB2\t2.0\n+s_58512\tTPD52L2\t2.0\n+s_19912\tFAM22F\t2.0\n+s_45517\tQSOX2\t2.0\n+s_56705\tTINAG\t2.0\n+s_10946\tCDKL5\t2.0\n+s_57473\tTMEM211\t4.0\n+s_57657\tTMEM44\t2.0\n+s_43200\tPOT1\t2.0\n+s_19436\tFAM135A\t2.0\n+s_184\tABCB9\t2.0\n+s_30171\tKRT84\t2.0\n+s_44758\tPSMC3IP\t2.0\n+s_48313\tRPS3\t2.0\n+s_58142\tTNFSF12\t12.0\n+s_59718\tTTLL6\t14.0\n+s_9725\tCCDC43\t2.0\n+s_5135\tBCKDHA\t2.0\n+s_36539\tNDUFC2\t2.0\n+s_27251\tIL27RA\t2.0\n+s_48939\tSAMD10\t2.0\n+s_27343\tIL5RA\t2.0\n+s_28386\tKANK2\t2.0\n+s_27610\tINSRR\t2.0\n+s_2769\tAOC3\t4.0\n+s_58632\tTRA2B\t24.0\n+s_6674\tC16orf86\t2.0\n+s_22902\tGJD4\t2.0\n+s_48278\tRPS15A\t2.0\n+s_61998\tWIPF2\t2.0\n+s_4937\tBAIAP3\t4.0\n+s_54471\tSTOML1\t4.0\n+s_19157\tFABP12\t2.0\n+s_5434\tBIN1\t4.0\n+s_42042\tPIP5K1A\t2.0\n+s_7794\tC3orf18\t2.0\n+s_54846\tSVIL\t2.0\n+s_62273\tXPA\t2.0\n+s_45859\tRACGAP1\t2.0\n+s_53626\tSPOCK3\t2.0\n+s_43295\tPPAP2C\t14.0\n+s_11788\tCHRDL1\t4.0\n+s_50636\tSHQ1\t2.0\n+s_16705\tDPF1\t2.0\n+s_39741\tOTOF\t2.0\n+s_27505\tINHBE\t2.0\n+s_707\tACPL2\t2.0\n+s_15418\tDDX3Y\t12.0\n+s_56018\tTEAD4\t2.0\n+s_44367\tPRR12\t2.0\n+s_25875\tHOXB5\t2.0\n+s_49360\tSCN9A\t2.0\n+s_16244\tDMPK\t2.0\n+s_3909\tASCC2\t2.0\n+s_55088\tSYT6\t2.0\n+s_54311\tSTAU1\t2.0\n+s_53890\tSRP72\t2.0\n+s_11035\tCDX1\t2.0\n+s_18178\tEMR3\t4.0\n+s_16084\tDLD\t2.0\n+s_47207\tRHOBTB1\t2.0\n+s_40267\tPARK2\t12.0\n+s_43104\tPOLR3B\t2.0\n+s_2200\tAMDHD2\t2.0\n+s_12738\tCNRIP1\t2.0\n+s_17842\tEIF4A3\t2.0\n+s_57950\tTMPRSS3\t2.0\n+s_62146\tWRN\t2.0\n+s_11055\tCEACAM1\t2.0\n+s_54580\tSTX2\t2.0\n+s_29277\tKIAA1407\t2.0\n+s_33428\tMEF2A\t2.0\n+s_59797\tTUBB\t2.0\n+s_18113\tEME1\t2.0\n+s_29839\tKLHL8\t2.0\n+s_18058\tELP2\t2.0\n+s_49497\tSDCBP2\t6.0\n+s_16874\tDRP2\t2.0\n+s_13572\tCREBL2\t2.0\n+s_20540\tFBXO30\t2.0\n+s_64380\tZNF646\t2.0\n+s_50366\tSH2B1\t2.0\n+s_2548\tANKRD33B\t2.0\n+s_41183\tPDXP\t2.0\n+s_16315\tDNAH12\t2.0\n+s_19996\tFAM49B\t2.0\n+s_30751\tLDLRAD3\t2.0\n+s_36960\tNGEF\t2.0\n+s_39015\tOR2A2\t2.0\n+s_26302\tHSPB2\t2.0\n+s_64297\tZNF611\t10.0\n+s_730\tACSBG1\t2.0\n+s_50271\tSFXN4\t2.0\n+s_8592\tCA6\t4.0\n+s_13683\tCRMP1\t2.0\n+s_51103\tSLC16A7\t2.0\n+s_63785\tZNF384\t2.0\n+s_16339\tDNAH9\t2.0\n+s_55936\tTCTEX1D1\t2.0\n+s_14497\tCXorf40A\t2.0\n+s_1123\tADAT1\t2.0\n+s_41304\tPERP\t2.0\n+s_18719\tESAM\t2.0\n+s_35118\tMSX2\t2.0\n+s_30128\tKRT6A\t2.0\n+s_402\tABTB1\t2.0\n+s_32578\tMAP1LC3A\t2.0\n+s_45063\tPTMA\t2.0\n+s_43551\tPPP1R14D\t2.0\n+s_2538\tANKRD32\t2.0\n+s_40384\tPAX1\t2.0\n+s_29076\tKIAA0101\t2.0\n+s_40482\tPCDH10\t2.0\n+s_2348\tANGPT2\t2.0\n+s_59756\tTTYH3\t2.0\n+s_34330\tMOB4\t2.0\n+s_49331\tSCN2B\t2.0\n+s_54905\tSYDE1\t2.0\n+s_39101\tOR2T1\t2.0\n+s_36623\tNEDD4L\t2.0\n+s_40500\tPCDH15\t4.0\n+s_10660\tCDC42SE2\t2.0\n+s_30867\tLGALS13\t2.0\n+s_24322\tGSTK1\t4.0\n+s_59167\tTRPC1\t2.0\n+s_57440\tTMEM201\t2.0\n+s_50539\tSHC1\t2.0\n+s_37087\tNIT1\t2.0\n+s_56345\tTGFB2\t2.0\n+s_55388\tTARM1\t2.0\n+s_1224\tADD2\t2.0\n+s_5256\tBCOR\t4.0\n+s_51731\tSLC35B3\t2.0\n+s_12987\tCOL6A6\t2.0\n+s_56745\tTJP3\t2.0\n+s_19340\tFAM120AOS\t2.0\n+s_53904'..b'A\t0\n+s_57422\tTMEM198\t0\n+s_57429\tTMEM2\t0\n+s_57475\tTMEM212\t0\n+s_57531\tTMEM231\t0\n+s_57568\tTMEM245\t0\n+s_57700\tTMEM54\t0\n+s_57873\tTMF1\t0\n+s_57992\tTMUB1\t0\n+s_58180\tTNIP1\t0\n+s_58211\tTNKS2\t0\n+s_58237\tTNNT1\t0\n+s_58256\tTNPO2\t0\n+s_58259\tTNPO3\t0\n+s_58309\tTOM1\t0\n+s_58485\tTP73\t0\n+s_58503\tTPD52\t0\n+s_58533\tTPI1\t0\n+s_5857\tBSPRY\t0\n+s_58612\tTPSG1\t0\n+s_58633\tTRA2B\t0\n+s_58655\tTRAF3\t0\n+s_58668\tTRAF3IP2\t0\n+s_58690\tTRAK1\t0\n+s_58809\tTRIB2\t0\n+s_58962\tTRIM50\t0\n+s_58968\tTRIM52\t0\n+s_59050\tTRIO\t0\n+s_59107\tTRMT1L\t0\n+s_59133\tTRMT61B\t0\n+s_59160\tTROVE2\t0\n+s_59173\tTRPC4\t0\n+s_59196\tTRPM1\t0\n+s_59204\tTRPM3\t0\n+s_59311\tTSEN54\t0\n+s_59332\tTSHB\t0\n+s_59340\tTSHZ2\t0\n+s_59360\tTSNARE1\t0\n+s_5952\tBTG4\t0\n+s_59539\tTTC21A\t0\n+s_59602\tTTC39A\t0\n+s_59654\tTTC9C\t0\n+s_59717\tTTLL6\t0\n+s_5974\tBTN3A1\t0\n+s_59748\tTTYH1\t0\n+s_59807\tTUBB2B\t0\n+s_59859\tTULP1\t0\n+s_59870\tTULP3\t0\n+s_59955\tTXNDC8\t0\n+s_59983\tTXNRD2\t0\n+s_600\tACE\t0\n+s_60169\tUBE2H\t0\n+s_60209\tUBE2Q2\t0\n+s_60237\tUBE2V2\t0\n+s_60248\tUBE3A\t0\n+s_60250\tUBE3B\t0\n+s_60373\tUBXN6\t0\n+s_60396\tUCKL1\t0\n+s_60423\tUEVLD\t0\n+s_60438\tUFSP1\t0\n+s_60449\tUGDH\t0\n+s_60517\tUGT2A1\t0\n+s_60542\tUGT3A1\t0\n+s_60603\tUMODL1\t0\n+s_60614\tUNC119\t0\n+s_60649\tUNC5B\t0\n+s_6068\tC10orf125\t0\n+s_6071\tC10orf128\t0\n+s_60753\tUQCRC2\t0\n+s_60780\tURM1\t0\n+s_60839\tUSP15\t0\n+s_60851\tUSP19\t0\n+s_60925\tUSP4\t0\n+s_6100\tC10orf53\t0\n+s_6106\tC10orf54\t0\n+s_61149\tVAV2\t0\n+s_61173\tVCAM1\t0\n+s_61178\tVCAN\t0\n+s_61221\tVEPH1\t0\n+s_61263\tVIL1\t0\n+s_61341\tVPS13C\t0\n+s_61344\tVPS13D\t0\n+s_61367\tVPS29\t0\n+s_61529\tVWA5A\t0\n+s_61531\tVWA5A\t0\n+s_61587\tWBP1\t0\n+s_61595\tWBP2\t0\n+s_61623\tWDFY1\t0\n+s_61640\tWDHD1\t0\n+s_61662\tWDR16\t0\n+s_61695\tWDR26\t0\n+s_61739\tWDR44\t0\n+s_6200\tC11orf49\t0\n+s_62019\tWISP1\t0\n+s_62098\tWNT5B\t0\n+s_62114\tWNT8A\t0\n+s_62171\tWTAP\t0\n+s_62249\tXKR3\t0\n+s_62257\tXKR6\t0\n+s_62275\tXPC\t0\n+s_62320\tXRCC4\t0\n+s_62361\tYAE1D1\t0\n+s_62550\tZBBX\t0\n+s_62559\tZBED6\t0\n+s_62567\tZBTB1\t0\n+s_62624\tZBTB37\t0\n+s_62657\tZBTB47\t0\n+s_62759\tZC3H7A\t0\n+s_62845\tZDHHC11\t0\n+s_62862\tZDHHC16\t0\n+s_62881\tZDHHC2\t0\n+s_6292\tC12orf23\t0\n+s_62975\tZFC3H1\t0\n+s_63034\tZFP64\t0\n+s_63104\tZFYVE27\t0\n+s_63107\tZFYVE27\t0\n+s_63114\tZFYVE28\t0\n+s_63217\tZMIZ2\t0\n+s_63228\tZMYM3\t0\n+s_63234\tZMYM3\t0\n+s_6326\tC12orf49\t0\n+s_63302\tZNF132\t0\n+s_63362\tZNF167\t0\n+s_63435\tZNF200\t0\n+s_63487\tZNF223\t0\n+s_63594\tZNF276\t0\n+s_636\tACO1\t0\n+s_63746\tZNF354B\t0\n+s_63755\tZNF362\t0\n+s_6376\tC12orf74\t0\n+s_63903\tZNF436\t0\n+s_63905\tZNF438\t0\n+s_63923\tZNF442\t0\n+s_63934\tZNF445\t0\n+s_63935\tZNF446\t0\n+s_63964\tZNF469\t0\n+s_63983\tZNF480\t0\n+s_6409\tC14orf105\t0\n+s_64137\tZNF554\t0\n+s_64241\tZNF586\t0\n+s_6427\tC14orf133\t0\n+s_64356\tZNF639\t0\n+s_64393\tZNF655\t0\n+s_64396\tZNF655\t0\n+s_64419\tZNF668\t0\n+s_64424\tZNF669\t0\n+s_64459\tZNF682\t0\n+s_64479\tZNF688\t0\n+s_64581\tZNF746\t0\n+s_64627\tZNF772\t0\n+s_64638\tZNF776\t0\n+s_64652\tZNF780A\t0\n+s_64791\tZNF85\t0\n+s_64851\tZNRF3\t0\n+s_64871\tZPBP\t0\n+s_64878\tZPLD1\t0\n+s_64898\tZSCAN10\t0\n+s_64930\tZSCAN30\t0\n+s_64997\tZYG11A\t0\n+s_6525\tC15orf39\t0\n+s_6592\tC16orf13\t0\n+s_6639\tC16orf62\t0\n+s_6707\tC17orf102\t0\n+s_6710\tC17orf104\t0\n+s_6728\tC17orf112\t0\n+s_6736\tC17orf39\t0\n+s_6794\tC17orf72\t0\n+s_6814\tC17orf80\t0\n+s_6849\tC18orf21\t0\n+s_6859\tC18orf32\t0\n+s_6862\tC18orf34\t0\n+s_6906\tC19orf38\t0\n+s_7053\tC1QTNF7\t0\n+s_7128\tC1orf122\t0\n+s_7144\tC1orf130\t0\n+s_7162\tC1orf144\t0\n+s_7234\tC1orf198\t0\n+s_7341\tC1orf63\t0\n+s_747\tACSL1\t0\n+s_76\tAARS2\t0\n+s_7674\tC2orf57\t0\n+s_7681\tC2orf62\t0\n+s_7692\tC2orf63\t0\n+s_77\tAARSD1\t0\n+s_78\tAARSD1\t0\n+s_781\tACSS1\t0\n+s_786\tACSS2\t0\n+s_7940\tC4orf26\t0\n+s_7970\tC4orf37\t0\n+s_8000\tC4orf52\t0\n+s_804\tACTB\t0\n+s_8073\tC5orf51\t0\n+s_8141\tC6orf162\t0\n+s_8227\tC7orf10\t0\n+s_8281\tC7orf59\t0\n+s_8318\tC8A\t0\n+s_8403\tC9orf100\t0\n+s_8470\tC9orf24\t0\n+s_8699\tCACNA1G\t0\n+s_8705\tCACNA1I\t0\n+s_871\tACTR8\t0\n+s_874\tACTR8\t0\n+s_8757\tCACNG5\t0\n+s_8797\tCADPS\t0\n+s_8879\tCALR\t0\n+s_8910\tCAMK2B\t0\n+s_893\tACVR1B\t0\n+s_8930\tCAMKK1\t0\n+s_8954\tCAMSAP1\t0\n+s_9064\tCAPRIN1\t0\n+s_9077\tCAPSL\t0\n+s_9109\tCARD17\t0\n+s_913\tACY1\t0\n+s_9171\tCASD1\t0\n+s_9196\tCASP10\t0\n+s_9285\tCATSPER3\t0\n+s_9506\tCCDC120\t0\n+s_9507\tCCDC121\t0\n+s_952\tADAM12\t0\n+s_9584\tCCDC149\t0\n+s_964\tADAM18\t0\n+s_9646\tCCDC170\t0\n+s_9710\tCCDC40\t0\n+s_9732\tCCDC48\t0\n+s_976\tADAM21\t0\n+s_9763\tCCDC62\t0\n+s_9868\tCCDC89\t0\n+s_991\tADAM30\t0\n+s_9925\tCCL1\t0\n+s_9973\tCCL26\t0\n' |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.test.R --- a/test-data/out.test.R Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.test.R Wed Apr 04 11:03:59 2018 -0400 |
| [ |
| b'@@ -10,7 +10,7 @@\n # outputfile=\'__OUTPUT_FILE__\'\n targetgenelist=c("ACIN1","ACTR8","AHCY","ACLY","AATF","AGBL5","AHCTF1","ABT1","ADIRF","ABCF1")\n # samplelabel=sub(\'.\\\\w+.\\\\w+$\',\'\',colnames(gstable)[startindex]);\n-samplelabel=\'HL60.final,KBM7.final_vs_HL60.initial,KBM7.initial neg.\'\n+samplelabel=\'HL60_final,KBM7_final_vs_HL60_initial,KBM7_initial neg.\'\n \n \n # You need to write some codes in front of this code:\n@@ -116,7 +116,7 @@\n # Do not modify the variables beginning with "__"\n targetmat=list(c(561.4907165816957,824.0396348113272,428.37415340969943,579.047491896501),c(3424.79939695118,3818.2871009576584,1992.3498917052,690.0506672205338),c(846.6456878299913,985.6508562937211,335.0024675413113,415.97581680707134),c(2432.636481525409,2122.257249136931,1067.465489792653,155.6333179800872),c(1308.1851773762019,2186.1913587343615,1482.5909580453515,997.3120339679854),c(405.68439208520414,268.16807081144486,170.34023773287015,109.85881269182627),c(640.8637498157573,559.4234589775174,711.6436598617687,632.2603542941043),c(946.5969148654764,470.6260845366416,663.0651476194316,457.74505288260946),c(246.9383256170808,177.59474888175154,28.39003962214503,0.0),c(568.8400715107754,612.7018836420428,564.0154538266146,270.64176251684285))\n targetgene="ACIN1"\n-collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final")\n+collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")\n \n # set up color using RColorBrewer\n #library(RColorBrewer)\n@@ -151,7 +151,7 @@\n # Do not modify the variables beginning with "__"\n targetmat=list(c(2484.0819660289676,2349.578527705573,2172.7843657481662,910.9126552363929),c(992.1629154257711,1005.1862786707138,743.8190381001997,200.26346063614164),c(1267.0287897733551,1156.1418152202027,251.09412821363824,42.34141739164138),c(1500.738276518092,1315.977089213779,800.5991173444897,1476.2277955464156),c(1925.5309914189038,2054.7712445618654,194.94493873872918,235.16652091844063),c(351.29916561001374,781.4168950797068,227.75120674654121,624.2498158686586),c(1719.74905340467,1006.9622261595313,356.45271970026533,222.0063506480656),c(903.9706562768137,1445.6212558974576,1482.5909580453515,1055.1023468944147),c(651.152846716469,1081.552020689867,576.0023594448536,1072.2677863775127),c(285.1549712482957,408.46792242802854,99.0496937928171,44.630142656054424))\n targetgene="ACTR8"\n-collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final")\n+collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")\n \n # set up color using RColorBrewer\n #library(RColorBrewer)\n@@ -186,7 +186,7 @@\n # Do not modify the variables beginning with "__"\n targetmat=list(c(301.3235520922712,657.1005708624807,228.38209651592223,137.32351586478285),c(1142.0897559789987,1099.311495578042,112.92926871919911,100.70391163417409),c(789.3207193831689,671.3081507730209,723.6305654800077,588.7745742702564),c(392.45555321286054,412.0198174056636,334.37157777193033,213.99581222261992),c(2009.3136376104133,2235.917888421252,2437.1271791188055,1937.9781176417478),c(1071.5359486598327,406.69197493921104,645.4002340767636,349.602784139093),c(61.7345814042702,218.44154112455442,614.4866353770946,452.5954210376801),c(651.152846716469,879.0940069646701,237.21455328725622,18.88198343140764),c(1625.6773103124485,1410.1023061211074,2146.286995434164,1986.613529510525),c(1053.8974968300413,882.6459019423052,106.6203710253891,105.85354347910344))\n targetgene="AHCY"\n-collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final")\n+collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")\n \n # set up color using RColorBrewer\n #library(RColorBrewer)\n@@ -221,7 +221,7 @@\n # Do not modify the variables beginning with "__"\n targetmat=list(c(1268.498660759171,1411.8782536099247,1136.2324746551822,603.6512884889412),c(327.78122983695846,454.642557137284,51.73296108924205,24.031615276336996),c(132.28838872343613,241.5288584791821,123.02350502929512,65.80085135187511),c(495.34652221997754,586.0626713097802,279.4841678357833,243.749240'..b'748304,1296.4784760779562,1222.1792911965672),c(1193.5352404825571,1355.0479339677643,1622.0175970785526,1905.9359639399652),c(868.6937526172306,701.4992580829187,720.4761166331027,603.6512884889412),c(798.1399452980647,768.9852626579842,1478.8056194290655,1756.0244591209105),c(1168.5474337236858,907.5091667857504,879.4603385171149,977.8578692204745),c(809.8989131845924,687.2916781723785,678.8373918539567,865.7103312642352),c(1246.4505959719315,753.0017352586266,1301.5255942330043,1264.5207085882087),c(826.0674940285679,797.4004224790644,977.8791425405509,2066.7189137649816))\n targetgene="ADCK1"\n-collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final")\n+collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")\n \n # set up color using RColorBrewer\n #library(RColorBrewer)\n@@ -822,7 +822,7 @@\n # Do not modify the variables beginning with "__"\n targetmat=list(c(1863.7964100146337,1585.9211075140413,1761.4442361117538,1464.211987908247),c(742.2848478370584,598.4943037315028,943.8110949939769,820.5080072920774),c(1568.3523418656262,2083.1864043829455,1810.6536381234716,1887.6261618246608),c(1018.6205931704583,513.248824268262,679.4682816233377,824.5132765048003),c(1140.6198849931827,1191.6607649965529,880.0912282864958,977.8578692204745),c(135.22813069506805,118.98848175077354,351.40560154521734,399.95473995618005),c(665.8515565746286,701.4992580829187,986.7115993118849,746.6966175147567),c(418.9132309575478,300.1351256101601,376.6411923204574,645.4205245644794),c(561.4907165816957,543.4399315781598,881.9838975946388,580.7640358448108),c(442.4311667306031,229.0972260574595,395.5678854018874,651.142337725512))\n targetgene="ADARB2"\n-collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final")\n+collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")\n \n # set up color using RColorBrewer\n #library(RColorBrewer)\n@@ -857,7 +857,7 @@\n # Do not modify the variables beginning with "__"\n targetmat=list(c(734.9354929079785,358.74139274113816,541.9343118982795,378.7840312603593),c(595.2977492554626,591.3905137762326,1061.787481868224,887.4532212761591),c(1655.0747300287676,943.0281165621008,1069.358159100796,2038.1098479598186),c(626.1650399575977,884.4218494311227,517.3296108924205,858.2719741548927),c(680.5502664327881,747.673892792174,533.1018551269456,1016.194017399393),c(662.9118146029966,777.8650001020718,864.9498738213518,787.3214909580882),c(880.4527205037583,621.5816210861304,671.8976043907657,1040.7978139918332),c(94.07174309222125,447.5387671820139,711.6436598617687,927.5059134033875),c(399.80490814194036,806.280159923152,1147.58849050404,1059.1076161071376),c(698.1887182625796,531.0082991564371,504.0809257354195,347.8862401907832))\n targetgene="ACSS2"\n-collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final")\n+collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")\n \n # set up color using RColorBrewer\n #library(RColorBrewer)\n@@ -892,7 +892,7 @@\n # Do not modify the variables beginning with "__"\n targetmat=list(c(408.62413405683606,523.9045092011671,483.89245311522745,701.494293542599),c(1805.0015705819953,1434.9655709645526,1712.2348341000356,2152.546111180471),c(3017.64513388016,2642.609863360463,1834.6274493599499,3573.2723190648703),c(1649.1952460855039,783.1928425685244,773.4708572611067,1332.0381038883936),c(959.82575373782,1397.6706736993847,1429.5962174173474,2811.126806015325),c(495.34652221997754,301.9110730989776,336.89513684945433,555.015876620164),c(1491.9190506031964,1331.9606166131366,2087.614246881731,1983.1804416139055),c(429.2023278582595,889.7496918975753,567.8007924429005,1132.9190058844583),c(427.7324568724435,573.6310388880576,655.4944703868597,899.4690289143276),c(690.8393633334998,767.2093151691668,1040.33722970927,993.3067647552625))\n targetgene="ADNP"\n-collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final")\n+collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")\n \n # set up color using RColorBrewer\n #library(RColorBrewer)\n' |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.test.log.txt --- a/test-data/out.test.log.txt Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.test.log.txt Wed Apr 04 11:03:59 2018 -0400 |
| b |
| b'@@ -1,112 +1,109 @@\n-INFO @ Mon, 12 Feb 2018 03:40:01: Parameters: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/bin/mageck test -k /tmp/tmp0xS0Jl/files/000/dataset_21.dat -t HL60.final,KBM7.final -c HL60.initial,KBM7.initial -n output --normcounts-to-file --pdf-report --norm-method median --gene-test-fdr-threshold 0.25 --adjust-method fdr --sort-criteria neg --remove-zero none --gene-lfc-method median \n-INFO @ Mon, 12 Feb 2018 03:40:01: Welcome to MAGeCK v0.5.7. Command: test \n-INFO @ Mon, 12 Feb 2018 03:40:01: Loading count table from /tmp/tmp0xS0Jl/files/000/dataset_21.dat \n-INFO @ Mon, 12 Feb 2018 03:40:01: Processing 1 lines.. \n-DEBUG @ Mon, 12 Feb 2018 03:40:01: Parsing error in line 1 (usually the header line). Skip this line. \n-INFO @ Mon, 12 Feb 2018 03:40:01: Loaded 999 records. \n-INFO @ Mon, 12 Feb 2018 03:40:01: Loading R template file: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/lib/python3.6/site-packages/mageck/plot_template.RTemplate. \n-INFO @ Mon, 12 Feb 2018 03:40:01: Loading R template file: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/lib/python3.6/site-packages/mageck/plot_template_indvgene.RTemplate. \n-INFO @ Mon, 12 Feb 2018 03:40:01: Loading Rnw template file: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/lib/python3.6/site-packages/mageck/plot_template.Rnw. \n-DEBUG @ Mon, 12 Feb 2018 03:40:01: Setting up the visualization module... \n-DEBUG @ Mon, 12 Feb 2018 03:40:01: Given sample labels: HL60.final,KBM7.final \n-DEBUG @ Mon, 12 Feb 2018 03:40:01: Converted index: 2 3 \n-INFO @ Mon, 12 Feb 2018 03:40:01: Treatment samples:HL60.final,KBM7.final \n-INFO @ Mon, 12 Feb 2018 03:40:01: Treatment sample index:2,3 \n-DEBUG @ Mon, 12 Feb 2018 03:40:01: Given sample labels: HL60.initial,KBM7.initial \n-DEBUG @ Mon, 12 Feb 2018 03:40:01: Converted index: 0 1 \n-INFO @ Mon, 12 Feb 2018 03:40:01: Control samples:HL60.initial,KBM7.initial \n-INFO @ Mon, 12 Feb 2018 03:40:01: Control sample index:0,1 \n-DEBUG @ Mon, 12 Feb 2018 03:40:01: Initial (total) size factor: 1.6666455325878438 2.027372749328462 0.7198064117880387 0.6589869375844738 \n-DEBUG @ Mon, 12 Feb 2018 03:40:01: Median factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618 \n-INFO @ Mon, 12 Feb 2018 03:40:01: Final size factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618 \n-INFO @ Mon, 12 Feb 2018 03:40:01: Writing normalized read counts to output.normalized.txt \n-DEBUG @ Mon, 12 Feb 2018 03:40:01: Adjusted model: 1.1175084644498339\t3.4299551007579927 \n-INFO @ Mon, 12 Feb 2018 03:40:01: Raw variance calculation: 0.5 for control, 0.5 for treatment \n-INFO @ Mon, 12 Feb 2018 03:40:01: Adjusted variance calculation: 0.3333333333333333 for raw variance, 0.6666666666666667 for modeling \n-INFO @ Mon, 12 Feb 2018 03:40:01: Use qnorm to reversely calculate sgRNA scores ... \n-DEBUG @ Mon, 12 Feb 2018 03:40:01: lower test FDR cutoff: 0.3283283283283283 \n-DEBUG @ Mon, 12 Feb 2018 03:40:01: higher test FDR cutoff: 0.34534534534534533 \n-INFO @ Mon, 12 Feb 2018 03:40:01: Running command: RRA -i output.plow.txt -o output.gene.low.txt -p 0.3283283283283283 --skip-gene NA --skip-gene na \n-INFO @ Mon, 12 Feb 2018 03:40:02: Command message: \n-INFO @ Mon, 12 Feb 2018 03:40:02: Welcome to RRA v 0.5.7. \n-INFO @ Mon, 12 Feb 2018 03:40:02: Skipping gene NA for permutation ... \n-INFO @ Mon, 12 Feb 2018 03:40:02: Skipping gene na for permutation ... \n-INFO @ Mon, 12 Feb 2018 03:40:02: Reading input file... \n-INFO @ Mon, 12 Feb 2018 03:40:02: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0 \n-INFO @ Mon, 12 Feb 2018 03:40:02: Computing lo-values for each group... \n-INFO @ Mon, 12 Feb 2018 03:40:02: Computing false discovery rate... \n-INFO @ Mon, 12 Feb 2'..b'+INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 9 sgRNAs... \n+INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 10 sgRNAs... \n+INFO @ Mon, 26 Mar 2018 08:37:53: Number of genes under FDR adjustment: 100 \n+INFO @ Mon, 26 Mar 2018 08:37:53: Saving to output file... \n+INFO @ Mon, 26 Mar 2018 08:37:53: RRA completed. \n+INFO @ Mon, 26 Mar 2018 08:37:53: \n+INFO @ Mon, 26 Mar 2018 08:37:53: End command message. \n+DEBUG @ Mon, 26 Mar 2018 08:37:53: Sorting the merged items by negative selection... \n+INFO @ Mon, 26 Mar 2018 08:37:53: Loading top 10 genes from output.gene.low.txt: ACIN1,ACTR8,AHCY,ACLY,AATF,AGBL5,AHCTF1,ABT1,ADIRF,ABCF1 \n+DEBUG @ Mon, 26 Mar 2018 08:37:53: Column index:3 \n+INFO @ Mon, 26 Mar 2018 08:37:53: Loading top 10 genes from output.gene.high.txt: ACRC,AGAP3,ADCK4,AHRR,ADRBK1,ADK,ADCK1,ADARB2,ACSS2,ADNP \n+DEBUG @ Mon, 26 Mar 2018 08:37:53: Column index:9 \n+INFO @ Mon, 26 Mar 2018 08:37:53: Running command: rm output.plow.txt \n+INFO @ Mon, 26 Mar 2018 08:37:53: Running command: rm output.phigh.txt \n+INFO @ Mon, 26 Mar 2018 08:37:54: Running command: rm output.gene.low.txt \n+INFO @ Mon, 26 Mar 2018 08:37:54: Running command: rm output.gene.high.txt \n+INFO @ Mon, 26 Mar 2018 08:37:54: Running command: cd ./; Rscript output.R \n+INFO @ Mon, 26 Mar 2018 08:37:59: Command message: \n+INFO @ Mon, 26 Mar 2018 08:37:59: null device \n+INFO @ Mon, 26 Mar 2018 08:37:59: 1 \n+INFO @ Mon, 26 Mar 2018 08:37:59: Writing to file output_summary.tex \n+INFO @ Mon, 26 Mar 2018 08:37:59: Processing code chunks with options ... \n+INFO @ Mon, 26 Mar 2018 08:37:59: 1 : keep.source term verbatim (label = funcdef, output_summary.Rnw:27) \n+INFO @ Mon, 26 Mar 2018 08:37:59: 2 : keep.source term tex (label = tab1, output_summary.Rnw:37) \n+INFO @ Mon, 26 Mar 2018 08:37:59: 3 : keep.source term verbatim (output_summary.Rnw:77) \n+INFO @ Mon, 26 Mar 2018 08:37:59: 4 : keep.source term verbatim pdf (output_summary.Rnw:83) \n+INFO @ Mon, 26 Mar 2018 08:37:59: 5 : keep.source term verbatim pdf (output_summary.Rnw:201) \n+INFO @ Mon, 26 Mar 2018 08:37:59: 6 : keep.source term verbatim pdf (output_summary.Rnw:345) \n+INFO @ Mon, 26 Mar 2018 08:37:59: 7 : keep.source term verbatim pdf (output_summary.Rnw:489) \n+INFO @ Mon, 26 Mar 2018 08:37:59: 8 : keep.source term verbatim (output_summary.Rnw:567) \n+INFO @ Mon, 26 Mar 2018 08:37:59: 9 : keep.source term verbatim pdf (output_summary.Rnw:573) \n+INFO @ Mon, 26 Mar 2018 08:37:59: 10 : keep.source term verbatim pdf (output_summary.Rnw:691) \n+INFO @ Mon, 26 Mar 2018 08:37:59: 11 : keep.source term verbatim pdf (output_summary.Rnw:835) \n+INFO @ Mon, 26 Mar 2018 08:37:59: 12 : keep.source term verbatim pdf (output_summary.Rnw:979) \n+INFO @ Mon, 26 Mar 2018 08:37:59: \n+INFO @ Mon, 26 Mar 2018 08:37:59: You can now run (pdf)latex on \xe2\x80\x98output_summary.tex\xe2\x80\x99 \n+INFO @ Mon, 26 Mar 2018 08:37:59: \n+INFO @ Mon, 26 Mar 2018 08:37:59: End command message. \n+INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary-*.pdf \n+INFO @ Mon, 26 Mar 2018 08:37:59: Command message: \n+INFO @ Mon, 26 Mar 2018 08:37:59: \n+INFO @ Mon, 26 Mar 2018 08:37:59: End command message. \n+INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary.aux \n+INFO @ Mon, 26 Mar 2018 08:37:59: Command message: \n+INFO @ Mon, 26 Mar 2018 08:37:59: \n+INFO @ Mon, 26 Mar 2018 08:37:59: End command message. \n+INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary.tex \n+INFO @ Mon, 26 Mar 2018 08:37:59: Command message: \n+INFO @ Mon, 26 Mar 2018 08:37:59: \n+INFO @ Mon, 26 Mar 2018 08:37:59: End command message. \n+INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary.toc \n+INFO @ Mon, 26 Mar 2018 08:37:59: Command message: \n+INFO @ Mon, 26 Mar 2018 08:37:59: \n+INFO @ Mon, 26 Mar 2018 08:37:59: End command message. \n' |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.test.normalized.txt --- a/test-data/out.test.normalized.txt Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.test.normalized.txt Wed Apr 04 11:03:59 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -sgRNA Gene HL60.initial KBM7.initial HL60.final KBM7.final +sgRNA Gene HL60_initial KBM7_initial HL60_final KBM7_final A1CF_m52595977 A1CF 313.08251997879887 486.6096119359992 557.0756663634236 100.13173031807082 A1CF_m52596017 A1CF 432.1420698298914 731.6903653928164 980.402701618075 1081.994868751268 A1CF_m52596056 A1CF 618.8156850285179 653.5486758848457 357.0836094696463 434.28561892237576 |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.test.pdf |
| b |
| Binary file test-data/out.test.pdf has changed |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.test.plots.pdf |
| b |
| Binary file test-data/out.test.plots.pdf has changed |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.test.report.pdf |
| b |
| Binary file test-data/out.test.report.pdf has changed |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/output.count_normalized.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.count_normalized.txt Wed Apr 04 11:03:59 2018 -0400 |
| b |
| b'@@ -0,0 +1,2551 @@\n+sgRNA\tGene\ttest1_fastq_gz\n+s_47512\tRNF111\t2.0\n+s_24835\tHCFC1R1\t2.0\n+s_14784\tCYP4B1\t8.0\n+s_51146\tSLC18A1\t2.0\n+s_58960\tTRIM5\t2.0\n+s_48256\tRPRD2\t2.0\n+s_30297\tKRTAP5-5\t2.0\n+s_14555\tCYB5B\t2.0\n+s_39959\tPAAF1\t2.0\n+s_45293\tPUF60\t2.0\n+s_49358\tSCN8A\t2.0\n+s_64995\tZYG11A\t2.0\n+s_4029\tASTE1\t2.0\n+s_45554\tR3HDML\t2.0\n+s_34264\tMMRN1\t2.0\n+s_37459\tNOL6\t2.0\n+s_23990\tGPX7\t2.0\n+s_20268\tFANCC\t2.0\n+s_14157\tCTLA4\t2.0\n+s_36773\tNEURL4\t36.0\n+s_18804\tETFB\t2.0\n+s_782\tACSS1\t2.0\n+s_18272\tENPP2\t2.0\n+s_46620\tRCN1\t2.0\n+s_55436\tTAS2R3\t2.0\n+s_57947\tTMPRSS2\t2.0\n+s_6438\tC14orf159\t2.0\n+s_33846\tMGST2\t2.0\n+s_16328\tDNAH6\t2.0\n+s_17875\tEIF4G1\t2.0\n+s_2305\tANAPC11\t2.0\n+s_2500\tANKRD2\t2.0\n+s_82\tAARSD1\t2.0\n+s_55329\tTAL1\t2.0\n+s_57926\tTMPRSS11E\t16.0\n+s_38414\tNUP98\t8.0\n+s_50044\tSERPINF1\t2.0\n+s_9257\tCASR\t2.0\n+s_63396\tZNF182\t2.0\n+s_56478\tTHBS3\t2.0\n+s_17191\tDYRK1A\t2.0\n+s_11988\tCIR1\t2.0\n+s_43313\tPPARD\t2.0\n+s_44681\tPSMA4\t2.0\n+s_10387\tCD320\t2.0\n+s_64869\tZPBP\t2.0\n+s_54385\tSTK17B\t2.0\n+s_25423\tHIST1H4D\t2.0\n+s_54172\tST8SIA4\t18.0\n+s_1161\tADCY10\t2.0\n+s_29184\tKIAA0913\t2.0\n+s_42977\tPOLD3\t2.0\n+s_49449\tSCUBE1\t2.0\n+s_24181\tGRM4\t2.0\n+s_52507\tSMARCA5\t2.0\n+s_28674\tKCNJ10\t2.0\n+s_61074\tVAMP2\t8.0\n+s_3954\tASIC2\t2.0\n+s_2385\tANK1\t2.0\n+s_18397\tEPDR1\t2.0\n+s_18377\tEPB41L4B\t2.0\n+s_34580\tMRAP2\t2.0\n+s_48676\tRUFY3\t20.0\n+s_691\tACP1\t2.0\n+s_30460\tLAMP2\t2.0\n+s_42637\tPLRG1\t2.0\n+s_12695\tCNOT6\t2.0\n+s_33316\tMECOM\t4.0\n+s_35081\tMSRB2\t2.0\n+s_58512\tTPD52L2\t2.0\n+s_19912\tFAM22F\t2.0\n+s_45517\tQSOX2\t2.0\n+s_56705\tTINAG\t2.0\n+s_10946\tCDKL5\t2.0\n+s_57473\tTMEM211\t4.0\n+s_57657\tTMEM44\t2.0\n+s_43200\tPOT1\t2.0\n+s_19436\tFAM135A\t2.0\n+s_184\tABCB9\t2.0\n+s_30171\tKRT84\t2.0\n+s_44758\tPSMC3IP\t2.0\n+s_48313\tRPS3\t2.0\n+s_58142\tTNFSF12\t12.0\n+s_59718\tTTLL6\t14.0\n+s_9725\tCCDC43\t2.0\n+s_5135\tBCKDHA\t2.0\n+s_36539\tNDUFC2\t2.0\n+s_27251\tIL27RA\t2.0\n+s_48939\tSAMD10\t2.0\n+s_27343\tIL5RA\t2.0\n+s_28386\tKANK2\t2.0\n+s_27610\tINSRR\t2.0\n+s_2769\tAOC3\t4.0\n+s_58632\tTRA2B\t24.0\n+s_6674\tC16orf86\t2.0\n+s_22902\tGJD4\t2.0\n+s_48278\tRPS15A\t2.0\n+s_61998\tWIPF2\t2.0\n+s_4937\tBAIAP3\t4.0\n+s_54471\tSTOML1\t4.0\n+s_19157\tFABP12\t2.0\n+s_5434\tBIN1\t4.0\n+s_42042\tPIP5K1A\t2.0\n+s_7794\tC3orf18\t2.0\n+s_54846\tSVIL\t2.0\n+s_62273\tXPA\t2.0\n+s_45859\tRACGAP1\t2.0\n+s_53626\tSPOCK3\t2.0\n+s_43295\tPPAP2C\t14.0\n+s_11788\tCHRDL1\t4.0\n+s_50636\tSHQ1\t2.0\n+s_16705\tDPF1\t2.0\n+s_39741\tOTOF\t2.0\n+s_27505\tINHBE\t2.0\n+s_707\tACPL2\t2.0\n+s_15418\tDDX3Y\t12.0\n+s_56018\tTEAD4\t2.0\n+s_44367\tPRR12\t2.0\n+s_25875\tHOXB5\t2.0\n+s_49360\tSCN9A\t2.0\n+s_16244\tDMPK\t2.0\n+s_3909\tASCC2\t2.0\n+s_55088\tSYT6\t2.0\n+s_54311\tSTAU1\t2.0\n+s_53890\tSRP72\t2.0\n+s_11035\tCDX1\t2.0\n+s_18178\tEMR3\t4.0\n+s_16084\tDLD\t2.0\n+s_47207\tRHOBTB1\t2.0\n+s_40267\tPARK2\t12.0\n+s_43104\tPOLR3B\t2.0\n+s_2200\tAMDHD2\t2.0\n+s_12738\tCNRIP1\t2.0\n+s_17842\tEIF4A3\t2.0\n+s_57950\tTMPRSS3\t2.0\n+s_62146\tWRN\t2.0\n+s_11055\tCEACAM1\t2.0\n+s_54580\tSTX2\t2.0\n+s_29277\tKIAA1407\t2.0\n+s_33428\tMEF2A\t2.0\n+s_59797\tTUBB\t2.0\n+s_18113\tEME1\t2.0\n+s_29839\tKLHL8\t2.0\n+s_18058\tELP2\t2.0\n+s_49497\tSDCBP2\t6.0\n+s_16874\tDRP2\t2.0\n+s_13572\tCREBL2\t2.0\n+s_20540\tFBXO30\t2.0\n+s_64380\tZNF646\t2.0\n+s_50366\tSH2B1\t2.0\n+s_2548\tANKRD33B\t2.0\n+s_41183\tPDXP\t2.0\n+s_16315\tDNAH12\t2.0\n+s_19996\tFAM49B\t2.0\n+s_30751\tLDLRAD3\t2.0\n+s_36960\tNGEF\t2.0\n+s_39015\tOR2A2\t2.0\n+s_26302\tHSPB2\t2.0\n+s_64297\tZNF611\t10.0\n+s_730\tACSBG1\t2.0\n+s_50271\tSFXN4\t2.0\n+s_8592\tCA6\t4.0\n+s_13683\tCRMP1\t2.0\n+s_51103\tSLC16A7\t2.0\n+s_63785\tZNF384\t2.0\n+s_16339\tDNAH9\t2.0\n+s_55936\tTCTEX1D1\t2.0\n+s_14497\tCXorf40A\t2.0\n+s_1123\tADAT1\t2.0\n+s_41304\tPERP\t2.0\n+s_18719\tESAM\t2.0\n+s_35118\tMSX2\t2.0\n+s_30128\tKRT6A\t2.0\n+s_402\tABTB1\t2.0\n+s_32578\tMAP1LC3A\t2.0\n+s_45063\tPTMA\t2.0\n+s_43551\tPPP1R14D\t2.0\n+s_2538\tANKRD32\t2.0\n+s_40384\tPAX1\t2.0\n+s_29076\tKIAA0101\t2.0\n+s_40482\tPCDH10\t2.0\n+s_2348\tANGPT2\t2.0\n+s_59756\tTTYH3\t2.0\n+s_34330\tMOB4\t2.0\n+s_49331\tSCN2B\t2.0\n+s_54905\tSYDE1\t2.0\n+s_39101\tOR2T1\t2.0\n+s_36623\tNEDD4L\t2.0\n+s_40500\tPCDH15\t4.0\n+s_10660\tCDC42SE2\t2.0\n+s_30867\tLGALS13\t2.0\n+s_24322\tGSTK1\t4.0\n+s_59167\tTRPC1\t2.0\n+s_57440\tTMEM201\t2.0\n+s_50539\tSHC1\t2.0\n+s_37087\tNIT1\t2.0\n+s_56345\tTGFB2\t2.0\n+s_55388\tTARM1\t2.0\n+s_1224\tADD2\t2.0\n+s_5256\tBCOR\t4.0\n+s_51731\tSLC35B3\t2.0\n+s_12987\tCOL6A6\t2.0\n+s_56745\tTJP3\t2.0\n+s_19340\tFAM120AOS\t2.0\n+s_53904'..b'A\t0\n+s_57422\tTMEM198\t0\n+s_57429\tTMEM2\t0\n+s_57475\tTMEM212\t0\n+s_57531\tTMEM231\t0\n+s_57568\tTMEM245\t0\n+s_57700\tTMEM54\t0\n+s_57873\tTMF1\t0\n+s_57992\tTMUB1\t0\n+s_58180\tTNIP1\t0\n+s_58211\tTNKS2\t0\n+s_58237\tTNNT1\t0\n+s_58256\tTNPO2\t0\n+s_58259\tTNPO3\t0\n+s_58309\tTOM1\t0\n+s_58485\tTP73\t0\n+s_58503\tTPD52\t0\n+s_58533\tTPI1\t0\n+s_5857\tBSPRY\t0\n+s_58612\tTPSG1\t0\n+s_58633\tTRA2B\t0\n+s_58655\tTRAF3\t0\n+s_58668\tTRAF3IP2\t0\n+s_58690\tTRAK1\t0\n+s_58809\tTRIB2\t0\n+s_58962\tTRIM50\t0\n+s_58968\tTRIM52\t0\n+s_59050\tTRIO\t0\n+s_59107\tTRMT1L\t0\n+s_59133\tTRMT61B\t0\n+s_59160\tTROVE2\t0\n+s_59173\tTRPC4\t0\n+s_59196\tTRPM1\t0\n+s_59204\tTRPM3\t0\n+s_59311\tTSEN54\t0\n+s_59332\tTSHB\t0\n+s_59340\tTSHZ2\t0\n+s_59360\tTSNARE1\t0\n+s_5952\tBTG4\t0\n+s_59539\tTTC21A\t0\n+s_59602\tTTC39A\t0\n+s_59654\tTTC9C\t0\n+s_59717\tTTLL6\t0\n+s_5974\tBTN3A1\t0\n+s_59748\tTTYH1\t0\n+s_59807\tTUBB2B\t0\n+s_59859\tTULP1\t0\n+s_59870\tTULP3\t0\n+s_59955\tTXNDC8\t0\n+s_59983\tTXNRD2\t0\n+s_600\tACE\t0\n+s_60169\tUBE2H\t0\n+s_60209\tUBE2Q2\t0\n+s_60237\tUBE2V2\t0\n+s_60248\tUBE3A\t0\n+s_60250\tUBE3B\t0\n+s_60373\tUBXN6\t0\n+s_60396\tUCKL1\t0\n+s_60423\tUEVLD\t0\n+s_60438\tUFSP1\t0\n+s_60449\tUGDH\t0\n+s_60517\tUGT2A1\t0\n+s_60542\tUGT3A1\t0\n+s_60603\tUMODL1\t0\n+s_60614\tUNC119\t0\n+s_60649\tUNC5B\t0\n+s_6068\tC10orf125\t0\n+s_6071\tC10orf128\t0\n+s_60753\tUQCRC2\t0\n+s_60780\tURM1\t0\n+s_60839\tUSP15\t0\n+s_60851\tUSP19\t0\n+s_60925\tUSP4\t0\n+s_6100\tC10orf53\t0\n+s_6106\tC10orf54\t0\n+s_61149\tVAV2\t0\n+s_61173\tVCAM1\t0\n+s_61178\tVCAN\t0\n+s_61221\tVEPH1\t0\n+s_61263\tVIL1\t0\n+s_61341\tVPS13C\t0\n+s_61344\tVPS13D\t0\n+s_61367\tVPS29\t0\n+s_61529\tVWA5A\t0\n+s_61531\tVWA5A\t0\n+s_61587\tWBP1\t0\n+s_61595\tWBP2\t0\n+s_61623\tWDFY1\t0\n+s_61640\tWDHD1\t0\n+s_61662\tWDR16\t0\n+s_61695\tWDR26\t0\n+s_61739\tWDR44\t0\n+s_6200\tC11orf49\t0\n+s_62019\tWISP1\t0\n+s_62098\tWNT5B\t0\n+s_62114\tWNT8A\t0\n+s_62171\tWTAP\t0\n+s_62249\tXKR3\t0\n+s_62257\tXKR6\t0\n+s_62275\tXPC\t0\n+s_62320\tXRCC4\t0\n+s_62361\tYAE1D1\t0\n+s_62550\tZBBX\t0\n+s_62559\tZBED6\t0\n+s_62567\tZBTB1\t0\n+s_62624\tZBTB37\t0\n+s_62657\tZBTB47\t0\n+s_62759\tZC3H7A\t0\n+s_62845\tZDHHC11\t0\n+s_62862\tZDHHC16\t0\n+s_62881\tZDHHC2\t0\n+s_6292\tC12orf23\t0\n+s_62975\tZFC3H1\t0\n+s_63034\tZFP64\t0\n+s_63104\tZFYVE27\t0\n+s_63107\tZFYVE27\t0\n+s_63114\tZFYVE28\t0\n+s_63217\tZMIZ2\t0\n+s_63228\tZMYM3\t0\n+s_63234\tZMYM3\t0\n+s_6326\tC12orf49\t0\n+s_63302\tZNF132\t0\n+s_63362\tZNF167\t0\n+s_63435\tZNF200\t0\n+s_63487\tZNF223\t0\n+s_63594\tZNF276\t0\n+s_636\tACO1\t0\n+s_63746\tZNF354B\t0\n+s_63755\tZNF362\t0\n+s_6376\tC12orf74\t0\n+s_63903\tZNF436\t0\n+s_63905\tZNF438\t0\n+s_63923\tZNF442\t0\n+s_63934\tZNF445\t0\n+s_63935\tZNF446\t0\n+s_63964\tZNF469\t0\n+s_63983\tZNF480\t0\n+s_6409\tC14orf105\t0\n+s_64137\tZNF554\t0\n+s_64241\tZNF586\t0\n+s_6427\tC14orf133\t0\n+s_64356\tZNF639\t0\n+s_64393\tZNF655\t0\n+s_64396\tZNF655\t0\n+s_64419\tZNF668\t0\n+s_64424\tZNF669\t0\n+s_64459\tZNF682\t0\n+s_64479\tZNF688\t0\n+s_64581\tZNF746\t0\n+s_64627\tZNF772\t0\n+s_64638\tZNF776\t0\n+s_64652\tZNF780A\t0\n+s_64791\tZNF85\t0\n+s_64851\tZNRF3\t0\n+s_64871\tZPBP\t0\n+s_64878\tZPLD1\t0\n+s_64898\tZSCAN10\t0\n+s_64930\tZSCAN30\t0\n+s_64997\tZYG11A\t0\n+s_6525\tC15orf39\t0\n+s_6592\tC16orf13\t0\n+s_6639\tC16orf62\t0\n+s_6707\tC17orf102\t0\n+s_6710\tC17orf104\t0\n+s_6728\tC17orf112\t0\n+s_6736\tC17orf39\t0\n+s_6794\tC17orf72\t0\n+s_6814\tC17orf80\t0\n+s_6849\tC18orf21\t0\n+s_6859\tC18orf32\t0\n+s_6862\tC18orf34\t0\n+s_6906\tC19orf38\t0\n+s_7053\tC1QTNF7\t0\n+s_7128\tC1orf122\t0\n+s_7144\tC1orf130\t0\n+s_7162\tC1orf144\t0\n+s_7234\tC1orf198\t0\n+s_7341\tC1orf63\t0\n+s_747\tACSL1\t0\n+s_76\tAARS2\t0\n+s_7674\tC2orf57\t0\n+s_7681\tC2orf62\t0\n+s_7692\tC2orf63\t0\n+s_77\tAARSD1\t0\n+s_78\tAARSD1\t0\n+s_781\tACSS1\t0\n+s_786\tACSS2\t0\n+s_7940\tC4orf26\t0\n+s_7970\tC4orf37\t0\n+s_8000\tC4orf52\t0\n+s_804\tACTB\t0\n+s_8073\tC5orf51\t0\n+s_8141\tC6orf162\t0\n+s_8227\tC7orf10\t0\n+s_8281\tC7orf59\t0\n+s_8318\tC8A\t0\n+s_8403\tC9orf100\t0\n+s_8470\tC9orf24\t0\n+s_8699\tCACNA1G\t0\n+s_8705\tCACNA1I\t0\n+s_871\tACTR8\t0\n+s_874\tACTR8\t0\n+s_8757\tCACNG5\t0\n+s_8797\tCADPS\t0\n+s_8879\tCALR\t0\n+s_8910\tCAMK2B\t0\n+s_893\tACVR1B\t0\n+s_8930\tCAMKK1\t0\n+s_8954\tCAMSAP1\t0\n+s_9064\tCAPRIN1\t0\n+s_9077\tCAPSL\t0\n+s_9109\tCARD17\t0\n+s_913\tACY1\t0\n+s_9171\tCASD1\t0\n+s_9196\tCASP10\t0\n+s_9285\tCATSPER3\t0\n+s_9506\tCCDC120\t0\n+s_9507\tCCDC121\t0\n+s_952\tADAM12\t0\n+s_9584\tCCDC149\t0\n+s_964\tADAM18\t0\n+s_9646\tCCDC170\t0\n+s_9710\tCCDC40\t0\n+s_9732\tCCDC48\t0\n+s_976\tADAM21\t0\n+s_9763\tCCDC62\t0\n+s_9868\tCCDC89\t0\n+s_991\tADAM30\t0\n+s_9925\tCCL1\t0\n+s_9973\tCCL26\t0\n' |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/output_countsummary.Rnw --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_countsummary.Rnw Wed Apr 04 11:03:59 2018 -0400 |
| [ |
| @@ -0,0 +1,237 @@ +% This is a template file for Sweave used in MAGeCK +% Author: Wei Li, Shirley Liu lab +% Do not modify lines beginning with "#__". +\documentclass{article} + +\usepackage{amsmath} +\usepackage{amscd} +\usepackage[tableposition=top]{caption} +\usepackage{ifthen} +\usepackage{fullpage} +\usepackage[utf8]{inputenc} +% \usepackage{longtable} + +\begin{document} +\setkeys{Gin}{width=0.9\textwidth} + +\title{MAGeCK Count Report} +\author{Wei Li} + +\maketitle + + +\tableofcontents + +\section{Summary} + +%Function definition +<<label=funcdef,include=FALSE,echo=FALSE>>= +genreporttable<-function(filelist,labellist,reads,mappedreads){ + xtb=data.frame(Label=labellist,Reads=reads,MappedReads=mappedreads,MappedPercentage=mappedreads/reads); + colnames(xtb)=c("Label","Reads","Mapped","Percentage"); + return (xtb); +} +genreporttable2<-function(filelist,labellist,sgrnas,zerocounts,gini){ + xtb=data.frame(Label=labellist,TotalsgRNAs=sgrnas,ZeroCounts=zerocounts,GiniIndex=gini); + colnames(xtb)=c("Label","TotalsgRNA","ZeroCounts","GiniIndex"); + return (xtb); +} +genreporttable3<-function(filelist,labellist){ + xtb=data.frame(File=filelist,Label=labellist); + colnames(xtb)=c("File","Label"); + return (xtb); +} + + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F"); + + + +genboxplot<-function(filename,...){ + #slmed=read.table(filename,header=T) + slmed=read.table(filename,header=T) + slmat=as.matrix(slmed[,c(-1,-2)]) + slmat_log=log2(slmat+1) + + boxplot(slmat_log,pch='.',las=2,ylab='log2(read counts)',cex.axis=0.8,...) +} + + +genhistplot<-function(filename,isfile=T,...){ + if(isfile){ + slmed=read.table(filename,header=T) + }else{ + slmed=filename; + } + tabsmat=as.matrix(log2(slmed[,c(-1,-2)]+1)) + colnames(tabsmat)=colnames(slmed)[c(-1,-2)] + samplecol=colors[((1:ncol(tabsmat)) %% length(colors)) ] + if(ncol(tabsmat)>=1){ + histlist=lapply(1:ncol(tabsmat),function(X){ return (hist(tabsmat[,X],plot=F,breaks=40)) }) + xrange=range(unlist(lapply(histlist,function(X){X$mids}))) + yrange=range(unlist(lapply(histlist,function(X){X$counts}))) + hst1=histlist[[1]] + plot(hst1$mids,hst1$counts,type='b',pch=20,xlim=c(0,xrange[2]*1.2),ylim=c(0,yrange[2]*1.2),xlab='log2(counts)',ylab='Frequency',main='Distribution of read counts',col = samplecol[1], ... ) + } + if(ncol(tabsmat)>=2){ + for(i in 2:ncol(tabsmat)){ + hstn=histlist[[i]] + lines(hstn$mids,hstn$counts,type='b',pch=20,col=samplecol[i]) + } + } + legend('topright',colnames(tabsmat),pch=20,lwd=1,col=samplecol) +} + + + +genclustering<-function(filename,...){ + #slmed=read.table(filename,header=T) + slmed=read.table(filename,header=T) + slmat=as.matrix(slmed[,c(-1,-2)]) + slmat_log=log2(slmat+1) + + result=tryCatch({ + library(gplots); + heatmap.2(cor(slmat_log),trace = 'none',density.info = 'none',cexRow = 0.8,cexCol = 0.8,offsetRow = -0.2,offsetCol = -0.2) + }, error=function(e){ + heatmap(cor(slmat_log),scale='none',cexRow = 0.8,cexCol = 0.8,cex.axis=0.8,...) + }); +} + +ctfit_tx=0; + + +panel.plot<-function(x,y,textnames=names(x),...){ + par(new=TRUE) + m<-cbind(x,y) + plot(m,pch=20,xlim = range(x)*1.1,ylim=range(y)*1.1,...) + text(x,y,textnames,...) +} + + +genpcaplot<-function(filename,...){ + #slmed=read.table(filename,header=T) + slmed=read.table(filename,header=T) + slmat=as.matrix(slmed[,c(-1,-2)]) + slmat_log=log2(slmat+1) + ctfit_tx<<-prcomp(t(slmat_log),center=TRUE) + + # par(mfrow=c(2,1)); + samplecol=colors[((1:ncol(slmat)) %% length(colors)) ] + # first 2 PCA + #plot(ctfit_tx$x[,1],ctfit_tx$x[,2],xlab='PC1',ylab='PC2',main='First 2 PCs',col=samplecol,xlim=1.1*range(ctfit_tx$x[,1]),ylim=1.1*range(ctfit_tx$x[,2])); + #text(ctfit_tx$x[,1],ctfit_tx$x[,2],rownames(ctfit_tx$x),col=samplecol); + # par(mfrow=c(1,1)); + if(length(samplecol)>2){ + pairs(ctfit_tx$x[,1:3],panel=panel.plot,textnames=rownames(ctfit_tx$x),main='First 3 principle components',col=samplecol) + }else{ + if(length(samplecol)>1){ + pairs(ctfit_tx$x[,1:2],panel=panel.plot,textnames=rownames(ctfit_tx$x),main='First 2 principle components',col=samplecol) + } + } + + +} + +genpcavar<-function(){ + # % variance + varpca=ctfit_tx$sdev^2 + varpca=varpca/sum(varpca)*100; + if(length(varpca)>10){ + varpca=varpca[1:10]; + } + plot(varpca,type='b',lwd=2,pch=20,xlab='PCs',ylab='% Variance explained'); +} + +@ + +%__FILE_SUMMARY__ + +The statistics of comparisons are listed in Table 1 and Table 2. +The corresponding fastq files in each row are listed in Table 3. + +<<label=tab1,echo=FALSE,results=tex>>= +library(xtable) +filelist=c("input_0.gz"); +labellist=c("test1_fastq_gz"); +reads=c(2500); +mappedreads=c(1453); +totalsgrnas=c(2550); +zerocounts=c(1276); +giniindex=c(0.5266899931488773); + +cptable=genreporttable(filelist,labellist,reads,mappedreads); +print(xtable(cptable, caption = "Summary of comparisons", label = "tab:one", + digits = c(0, 0, 0, 0,2), + align=c('c', 'c','c', 'c', 'c'), + table.placement = "tbp", + caption.placement = "top")) +@ + +<<label=tab2,echo=FALSE,results=tex>>= +library(xtable) +cptable=genreporttable2(filelist,labellist,totalsgrnas,zerocounts,giniindex); +print(xtable(cptable, caption = "Summary of comparisons", label = "tab:two", + digits = c(0, 0,0, 0,2), + align=c('c', 'c','c', 'c', 'c'), + table.placement = "tbp", + caption.placement = "top")) +@ + + + + + +<<label=tab3,echo=FALSE,results=tex>>= +library(xtable) +cptable=genreporttable3(filelist,labellist); +print(xtable(cptable, caption = "Summary of samples", label = "tab:three", + digits = c(0,0, 0), + align=c('c', 'p{9cm}', 'c'), + table.placement = "tbp", + caption.placement = "top")) +@ + + + + +The meanings of the columns are as follows. + +\begin{itemize} +\item \textbf{Row}: The row number in the table; +\item \textbf{File}: The filename of fastq file; +\item \textbf{Label}: Assigned label; +\item \textbf{Reads}: The total read count in the fastq file; +\item \textbf{Mapped}: Reads that can be mapped to gRNA library; +\item \textbf{Percentage}: The percentage of mapped reads; +\item \textbf{TotalsgRNAs}: The number of sgRNAs in the library; +\item \textbf{ZeroCounts}: The number of sgRNA with 0 read counts; +\item \textbf{GiniIndex}: The Gini Index of the read count distribution. Gini index can be used to measure the evenness of the read counts, and a smaller value means a more even distribution of the read counts. +\end{itemize} + + + +\newpage\section{Normalized read count distribution of all samples} +The following figure shows the distribution of median-normalized read counts in all samples. + + +<<fig=TRUE,echo=FALSE,width=4.5,height=4.5>>= +genboxplot("output.count_normalized.txt"); +@ + +The following figure shows the histogram of median-normalized read counts in all samples. + + +<<fig=TRUE,echo=FALSE,width=4.5,height=4.5>>= +genhistplot("output.count_normalized.txt"); +@ + +%__INDIVIDUAL_PAGE__ + + + +\end{document} + |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/output_summary.Rnw --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_summary.Rnw Wed Apr 04 11:03:59 2018 -0400 |
| [ |
| b'@@ -0,0 +1,1063 @@\n+% This is a template file for Sweave used in MAGeCK\n+% Author: Wei Li, Shirley Liu lab\n+% Do not modify lines beginning with "#__".\n+\\documentclass{article}\n+\n+\\usepackage{amsmath}\n+\\usepackage{amscd}\n+\\usepackage[tableposition=top]{caption}\n+\\usepackage{ifthen}\n+\\usepackage{fullpage}\n+\\usepackage[utf8]{inputenc}\n+\n+\\begin{document}\n+\\setkeys{Gin}{width=0.9\\textwidth}\n+\n+\\title{MAGeCK Comparison Report}\n+\\author{Wei Li}\n+\n+\\maketitle\n+\n+\n+\\tableofcontents\n+\n+\\section{Summary}\n+\n+%Function definition\n+<<label=funcdef,include=FALSE,echo=FALSE>>=\n+genreporttable<-function(comparisons,ngenes,direction,fdr1,fdr5,fdr25){\n+ xtb=data.frame(Comparison=comparisons,Genes=ngenes,Selection=direction,FDR1=fdr1,FDR5=fdr5,FDR25=fdr25);\n+ colnames(xtb)=c("Comparison","Genes","Selection","FDR1%","FDR5%","FDR25%");\n+ return (xtb);\n+}\n+@\n+\n+The statistics of comparisons is as indicated in the following table. \n+\n+<<label=tab1,echo=FALSE,results=tex>>=\n+library(xtable)\n+comparisons=c("HL60_final,KBM7_final_vs_HL60_initial,KBM7_initial neg.","HL60_final,KBM7_final_vs_HL60_initial,KBM7_initial pos.");\n+ngenes=c(100,100);\n+direction=c("negative","positive");\n+fdr1=c(0,0);\n+fdr5=c(2,0);\n+fdr25=c(9,1);\n+\n+cptable=genreporttable(comparisons,ngenes,direction,fdr1,fdr5,fdr25);\n+print(xtable(cptable, caption = "Summary of comparisons", label = "tab:one",\n+ digits = c(0, 0, 0, 0, 0, 0, 0),\n+ table.placement = "tbp",\n+ caption.placement = "top"))\n+@\n+\n+The meanings of the columns are as follows.\n+\n+\\begin{itemize}\n+\\item \\textbf{Comparison}: The label for comparisons;\n+\\item \\textbf{Genes}: The number of genes in the library;\n+\\item \\textbf{Selection}: The direction of selection, either positive selection or negative selection;\n+\\item \\textbf{FDR1\\%}: The number of genes with FDR $<$ 1\\%;\n+\\item \\textbf{FDR5\\%}: The number of genes with FDR $<$ 5\\%;\n+\\item \\textbf{FDR25\\%}: The number of genes with FDR $<$ 25\\%;\n+\\end{itemize}\n+\n+The following figures show:\n+\n+\\begin{itemize}\n+\\item Individual sgRNA read counts of selected genes in selected samples; \n+\\item The distribution of RRA scores and p values of all genes; and\n+\\item The RRA scores and p values of selected genes.\n+\\end{itemize}\n+\n+\n+\\newpage\\section{Comparison results of HL60 final,KBM7 final vs HL60 initial,KBM7 initial neg.}\n+\n+The following figure shows the distribution of RRA score in the comparison HL60 final,KBM7 final vs HL60 initial,KBM7 initial neg., and the RRA scores of 10 genes.\n+\n+<<echo=FALSE>>=\n+gstable=read.table(\'output.gene_summary.txt\',header=T)\n+@\n+%\n+\n+\n+<<fig=TRUE,echo=FALSE,width=4.5,height=4.5>>=# \n+#\n+# parameters\n+# Do not modify the variables beginning with "__"\n+\n+# gstablename=\'__GENE_SUMMARY_FILE__\'\n+startindex=3\n+# outputfile=\'__OUTPUT_FILE__\'\n+targetgenelist=c("ACIN1","ACTR8","AHCY","ACLY","AATF","AGBL5","AHCTF1","ABT1","ADIRF","ABCF1")\n+# samplelabel=sub(\'.\\w+.\\w+$\',\'\',colnames(gstable)[startindex]);\n+samplelabel=\'HL60_final,KBM7_final_vs_HL60_initial,KBM7_initial neg.\'\n+\n+\n+# You need to write some codes in front of this code:\n+# gstable=read.table(gstablename,header=T)\n+# pdf(file=outputfile,width=6,height=6)\n+\n+\n+# set up color using RColorBrewer\n+#library(RColorBrewer)\n+#colors <- brewer.pal(length(targetgenelist), "Set1")\n+\n+colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",\n+ "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", \n+ "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",\n+ "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")\n+\n+######\n+# function definition\n+\n+plotrankedvalues<-function(val, tglist, ...){\n+ \n+ plot(val,log=\'y\',ylim=c(max(val),min(val)),type=\'l\',lwd=2, ...)\n+ if(length(tglist)>0){\n+ for(i in 1:length(tglist)){\n+ targetgene=tglist[i];\n+ tx=which(names(val)==targetgene);ty=val[targetgene];\n+ points(tx,ty,col=colors[(i %% length(colors)) ],cex=2,pch=2'..b'840312603593),c(595.2977492554626,591.3905137762326,1061.787481868224,887.4532212761591),c(1655.0747300287676,943.0281165621008,1069.358159100796,2038.1098479598186),c(626.1650399575977,884.4218494311227,517.3296108924205,858.2719741548927),c(680.5502664327881,747.673892792174,533.1018551269456,1016.194017399393),c(662.9118146029966,777.8650001020718,864.9498738213518,787.3214909580882),c(880.4527205037583,621.5816210861304,671.8976043907657,1040.7978139918332),c(94.07174309222125,447.5387671820139,711.6436598617687,927.5059134033875),c(399.80490814194036,806.280159923152,1147.58849050404,1059.1076161071376),c(698.1887182625796,531.0082991564371,504.0809257354195,347.8862401907832))\n+targetgene="ACSS2"\n+collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")\n+\n+# set up color using RColorBrewer\n+#library(RColorBrewer)\n+#colors <- brewer.pal(length(targetgenelist), "Set1")\n+\n+colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",\n+ "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", \n+ "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",\n+ "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")\n+\n+\n+## code\n+\n+targetmatvec=unlist(targetmat)+1\n+yrange=range(targetmatvec[targetmatvec>0]);\n+# yrange[1]=1; # set the minimum value to 1\n+for(i in 1:length(targetmat)){\n+ vali=targetmat[[i]]+1;\n+ if(i==1){\n+ plot(1:length(vali),vali,type=\'b\',las=1,pch=20,main=paste(\'sgRNAs in\',targetgene),ylab=\'Read counts\',xlab=\'Samples\',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt=\'n\',log=\'y\')\n+ axis(1,at=1:length(vali),labels=(collabel),las=2)\n+ # lines(0:100,rep(1,101),col=\'black\');\n+ }else{\n+ lines(1:length(vali),vali,type=\'b\',pch=20,col=colors[(i %% length(colors))])\n+ }\n+}\n+\n+\n+\n+# parameters\n+# Do not modify the variables beginning with "__"\n+targetmat=list(c(408.62413405683606,523.9045092011671,483.89245311522745,701.494293542599),c(1805.0015705819953,1434.9655709645526,1712.2348341000356,2152.546111180471),c(3017.64513388016,2642.609863360463,1834.6274493599499,3573.2723190648703),c(1649.1952460855039,783.1928425685244,773.4708572611067,1332.0381038883936),c(959.82575373782,1397.6706736993847,1429.5962174173474,2811.126806015325),c(495.34652221997754,301.9110730989776,336.89513684945433,555.015876620164),c(1491.9190506031964,1331.9606166131366,2087.614246881731,1983.1804416139055),c(429.2023278582595,889.7496918975753,567.8007924429005,1132.9190058844583),c(427.7324568724435,573.6310388880576,655.4944703868597,899.4690289143276),c(690.8393633334998,767.2093151691668,1040.33722970927,993.3067647552625))\n+targetgene="ADNP"\n+collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final")\n+\n+# set up color using RColorBrewer\n+#library(RColorBrewer)\n+#colors <- brewer.pal(length(targetgenelist), "Set1")\n+\n+colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF",\n+ "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", \n+ "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5",\n+ "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F")\n+\n+\n+## code\n+\n+targetmatvec=unlist(targetmat)+1\n+yrange=range(targetmatvec[targetmatvec>0]);\n+# yrange[1]=1; # set the minimum value to 1\n+for(i in 1:length(targetmat)){\n+ vali=targetmat[[i]]+1;\n+ if(i==1){\n+ plot(1:length(vali),vali,type=\'b\',las=1,pch=20,main=paste(\'sgRNAs in\',targetgene),ylab=\'Read counts\',xlab=\'Samples\',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt=\'n\',log=\'y\')\n+ axis(1,at=1:length(vali),labels=(collabel),las=2)\n+ # lines(0:100,rep(1,101),col=\'black\');\n+ }else{\n+ lines(1:length(vali),vali,type=\'b\',pch=20,col=colors[(i %% length(colors))])\n+ }\n+}\n+\n+\n+\n+par(mfrow=c(1,1));\n+@\n+%__INDIVIDUAL_PAGE__\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\\end{document}\n+\n' |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/test1.fastq.gz |
| b |
| Binary file test-data/test1.fastq.gz has changed |
| b |
| diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/test2.fastq.gz |
| b |
| Binary file test-data/test2.fastq.gz has changed |