| Next changeset 1:4d72d204dcfa (2018-02-17) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe |
|
added:
mageck_count.xml mageck_macros.xml test-data/.Rapp.history test-data/demo/demo1/sample.txt test-data/demo/demo2/library.txt test-data/demo/demo2/test1.fastq test-data/demo/demo2/test2.fastq test-data/in.mageckQC.gmt test-data/in.mle.design_matrix.txt test-data/out.count.bam.txt test-data/out.count.fastq.txt test-data/out.count.log.txt test-data/out.count.unmapped.txt test-data/out.countsummary.pdf test-data/out.countsummary.txt test-data/out.mageckGSEA.txt test-data/out.mle.gene_summary.txt test-data/out.mle.log.txt test-data/out.mle.sgrna_summary.txt test-data/out.pathway.log.txt test-data/out.pathway.pathway_summary.txt test-data/out.test.R test-data/out.test.gene_summary.txt test-data/out.test.log.txt test-data/out.test.normalized.txt test-data/out.test.pdf test-data/out.test.sgrna_summary.txt test-data/test1.bam test-data/test1.fastq.gz |
| b |
| diff -r 000000000000 -r b80c0e046539 mageck_count.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mageck_count.xml Wed Feb 14 06:42:18 2018 -0500 |
| [ |
| b'@@ -0,0 +1,269 @@\n+<?xml version="1.0"?>\n+<tool id="mageck_count" name="MAGeCK count" version="@VERSION@" >\n+ <description>- collect sgRNA read counts from read mapping files</description>\n+ <macros>\n+ <import>mageck_macros.xml</import>\n+ </macros>\n+ <expand macro="requirements">\n+ <requirement type="package" version="9.22">ghostscript</requirement>\n+ </expand>\n+ <expand macro="version" />\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+#if str($reads.format_select) == "files":\n+\n+ #if $reads.sample.is_of_type(\'fastq.gz\', \'fastqsanger.gz\'):\n+ ln -s \'${reads.sample}\' \'input.gz\' && \n+ #set $infile = \'input.gz\'\n+ #elif $reads.sample.is_of_type(\'fastq\'):\n+ ln -s \'${reads.sample}\' \'input.fastq\' &&\n+ #set $infile = \'input.fastq\'\n+ #elif $reads.sample.is_of_type(\'bam\'):\n+ ln -s \'${reads.sample}\' \'input.bam\' && \n+ #set $infile = \'input.bam\'\n+ #end if\n+\n+#end if\n+\n+mageck count\n+\n+#if str($reads.format_select) == "files":\n+ --fastq $infile\n+ -l \'$reads.sgrna_library_file\'\n+#if $reads.sample_label:\n+ --sample-label \'$reads.sample_label\'\n+#end if\n+\n+#elif str($reads.format_select) == "table":\n+ -k \'$reads.counts\'\n+ #if \'$sgrna_library_file\':\n+ -l \'$sgrna_library_file\'\n+ #end if\n+\n+#end if\n+\n+-n output\n+\n+#if $out.pdfreportOpt:\n+ $out.pdfreportOpt\n+ --keep-tmp\n+#end if\n+\n+$out.unmappedOpt\n+\n+#if $adv.trim5:\n+ --trim-5 $adv.trim5\n+#end if\n+--norm-method $adv.norm_method\n+#if $adv.control_sgrna:\n+ --control-sgrna $adv.control_sgrna\n+#end if\n+--sgrna-len $adv.sgrna_len\n+$adv.count_n\n+$adv.reverse_complement\n+$adv.test_run\n+\n+#if $adv.gmt_file:\n+ --gmt-file \'$adv.gmt_file\'\n+#end if\n+\n+#if $out.pdfreportOpt:\n+ &&\n+ gs -dBATCH -dNOPAUSE -q -dPDFSETTINGS=/prepress -sDEVICE=pdfwrite -sOutputFile=merged.pdf *.pdf\n+#end if\n+ ]]></command>\n+ <inputs>\n+ <conditional name="reads">\n+ <param name="format_select" type="select" label="Reads Files or Count Table?" help="You can choose to input either separate files of reads (one per sample) or a single count table">\n+ <option value="files">Separate Reads files</option>\n+ <option value="table">Single Count table</option>\n+ </param>\n+ <when value="files">\n+ <param name="sample" argument="--fastq" type="data" format="fastq,fastq.gz,bam" multiple="false" label="Sample reads" help="The input reads must be in FASTQ, FASTQ.GZ or BAM format and all files must be in the same format." />\n+ <param name="sgrna_library_file" type="data" argument="--list-seq" format="txt,tabular,tsv,csv" label="sgRNA library file" help="A library file must be provided with three columns containing the sgRNA ID, sequence, and gene it is targeting, see Help below for more information." />\n+ <param name="sample_label" argument="--sample-label" type="text" optional="true" value="" label="Sample label" help="Optionally, you can specify a sample label to use in the output file header."/>\n+ </when>\n+ <when value="table">\n+ <param name="counts" argument="-k" type="data" format="tabular" optional="true" label="Counts Table" help="Alternatively, a tab-separated file of read counts can be used as input. See Help below for format" />\n+ <param name="sgrna_library_file" type="data" argument="--list-seq" format="txt,tabular,tsv,csv" optional="True" label="sgRNA library file" help="Optionally, a library file can be provided with three columns containing the sgRNA ID, sequence, and gene it is targeting, see Help below for more information." />\n+ </when>\n+ </conditional>\n+\n+ <section name="out" title="Output Options">\n+ <param name="countsummaryOpt" type="boolean" truevalue="True" falsevalue="" checked="false" optional="'..b't Summary** file containing statistics of the input file (the statistics of fastq file are also in the PDF report). An example count summary file is shown below.\n+\n+Example:\n+\n+ ========== ===== ===== ====== ========== =========== ========== ========= ======== ============ ======================= ========================== ============\n+ File Label Reads Mapped Percentage TotalsgRNAs Zerocounts GiniIndex NegSelQC NegSelQCPval NegSelQCPvalPermutation NegSelQCPvalPermutationFDR NegSelQCGene\n+ ========== ===== ===== ====== ========== =========== ========== ========= ======== ============ ======================= ========================== ============\n+ InputFile1 L1 2500 1453 0.5812 2550 1276 0.5267 0 1 1 1 0.0\n+ ========== ===== ===== ====== ========== =========== ========== ========= ======== ============ ======================= ========================== ============\n+\n+-----\n+\n+**More Information**\n+\n+**Overview of the MAGeCK algorithm**\n+\n+Briefly, read counts from different samples are first median-normalized to adjust for the effect of library sizes and read count distributions. Then the variance of read counts is estimated by sharing information across features, and a negative binomial (NB) model is used to test whether sgRNA abundance differs significantly between treatments and controls. This approach is similar to those used for differential RNA-Seq analysis. We rank sgRNAs based on P-values calculated from the NB model, and use a modified robust ranking aggregation (RRA) algorithm named \xce\xb1-RRA to identify positively or negatively selected genes. More specifically, \xce\xb1-RRA assumes that if a gene has no effect on selection, then sgRNAs targeting this gene should be uniformly distributed across the ranked list of all the sgRNAs. \xce\xb1-RRA ranks genes by comparing the skew in rankings to the uniform null model, and prioritizes genes whose sgRNA rankings are consistently higher than expected. \xce\xb1-RRA calculates the statistical significance of the skew by permutation, and a detailed description of the algorithm is presented in the Materials and methods section of the MAGeCK paper. Finally, MAGeCK reports positively and negatively selected pathways by applying \xce\xb1-RRA to the rankings of genes in a pathway.\n+\n+**MAGeCK FAQs**\n+\n+**The 5\' trim length option can only trim a fixed length of nucleotides before sgRNA, but what if the trimming length is different in different reads?**\n+MAGeCK enables automatically determining trimming length, even the length may be different within the same fastq files.\n+Alternatively, you can use **cutadapt** to trim the adaptor sequences of variable length before running MAGeCK.\n+\n+**How do I get the simple statistics of my input files?**\n+MAGeCK produces a **Count Summary** file containing the statistics of the input files, the statistics are also in the PDF report. The statistics can also be found in the log file for **MAGeCK** count.\n+\n+**How do I know the quality of my samples?**\n+For simple QC terms, you can just take a look at the sample statistics. Generally in a good negative selection sample:\n+\n+#. the mapped reads should be over 60 percent of the total number reads\n+#. the number of zero-count sgRNAs should be few (<5%, and prefered <1%). One exception is in positive selection experiments, where the number of zero-count sgRNAs may be much higher, but the percentage of mapped reads should be reasonably high.\n+\n+For more information on using MAGeCK, see the `MAGeCK website here`_.\n+\n+.. _MAGeCK: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0554-4\n+.. _`100% validation rate`: https://sourceforge.net/p/mageck/wiki/Home/\n+.. _`Prof. Xiaole Shirley Liu\'s lab`: http://liulab.dfci.harvard.edu/\n+.. _`MAGeCK website here`: https://sourceforge.net/p/mageck/wiki/QA/#using-mageck\n+\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |
| b |
| diff -r 000000000000 -r b80c0e046539 mageck_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mageck_macros.xml Wed Feb 14 06:42:18 2018 -0500 |
| b |
| @@ -0,0 +1,27 @@ +<?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="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> + </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 000000000000 -r b80c0e046539 test-data/demo/demo1/sample.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demo/demo1/sample.txt Wed Feb 14 06:42:18 2018 -0500 |
| 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 000000000000 -r b80c0e046539 test-data/demo/demo2/library.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demo/demo2/library.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| b'@@ -0,0 +1,2550 @@\n+s_10007\tTGTTCACAGTATAGTTTGCC\tCCNA1\n+s_10008\tTTCTCCCTAATTGCTTGCTG\tCCNA1\n+s_10027\tACATGTTGCTTCCCCTTGCA\tCCNC\n+s_10035\tAGAGACCAGCCCGCTGACCG\tCCND2\n+s_10164\tGCAGGCGGTACTCAAGGGCA\tCCS\n+s_10200\tTTAGAGAAGATCCATCATTC\tCCT7\n+s_10232\tAACACGACAGACTTCTGTTC\tCD164\n+s_10264\tGAGTCACAGGACGCCCTGAT\tCD1D\n+s_10340\tCACGGCTCTGTCACCATCAC\tCD276\n+s_1035\tACACTTGTCATCCGCCTTCA\tADAMTS14\n+s_10381\tTCTTTCAGCTCAACAGGCCA\tCD300LG\n+s_10387\tACCACAGCCGAGCTCGTCGC\tCD320\n+s_10401\tCCTCGAGTAGGCCGACGCCC\tCD37\n+s_10402\tCCTGGGCGTCGGCCTACTCG\tCD37\n+s_10405\tTCAGACCGTACCTTGCAACA\tCD38\n+s_10408\tCCGACACACAAGCTCTGTTG\tCD3D\n+s_10417\tCAGAGACTGACATGGAACAG\tCD3G\n+s_10425\tCTGCACCGCTCATGCTCGCC\tCD40\n+s_10434\tTGAAGCAATATGTGTCATAC\tCD44\n+s_10437\tGAGAAACATGTCCATATATA\tCD46\n+s_10448\tCATACCAGCTGAGCCGTCCG\tCD5\n+s_10461\tAATGGTCAGATTGATGTACC\tCD55\n+s_10481\tTTGAGCTGGTCAGGTGGGGC\tCD6\n+s_10518\tCATCTACATCCTCATCGCTG\tCD81\n+s_10541\tGGCGCGCCACGATGCGGCCG\tCD8B\n+s_10563\tTTTCTTTCACTGCATCCTCC\tCD99L2\n+s_10582\tTAAAGCTTCTACGCAGATTT\tCDC14B\n+s_10594\tTCTCTTCTGCTTCAAGTCTT\tCDC20B\n+s_10615\tTTGCTTTACTCTTTCATTGT\tCDC27\n+s_10616\tGCGCTCACCTCGTAGATGTT\tCDC34\n+s_1064\tACATGGCGAGAGGTGCTCAA\tADAMTS4\n+s_10657\tAGCTGTATGCACAAAGTTTG\tCDC42SE2\n+s_10658\tCAATGTCCAGATGCAGCTCG\tCDC42SE2\n+s_10660\tTCGTATCCACGAGCTGCATC\tCDC42SE2\n+s_10675\tCCAAGTAGATCTTTTCGATC\tCDC73\n+s_10731\tACTCACCACTGTCAATTGCC\tCDH13\n+s_10739\tGCTTTGTGTCTCCGTCCCCC\tCDH16\n+s_10770\tTGGACTACGAGGAGGTGCAC\tCDH23\n+s_10785\tTCTACAGCGAAGACACCCTC\tCDH3\n+s_1085\tGACGTAGCAGCATTAAACAG\tADAMTS9\n+s_10862\tGGTGAGAGTGACCAAGCTTC\tCDK17\n+s_10943\tGCATTTAAGTACAACTCCAT\tCDKL5\n+s_10946\tTTCATGAAGATTCCTAACAT\tCDKL5\n+s_1101\tTCCTGGCCGCTCGAATCTCC\tADAMTSL4\n+s_11025\tGGGCCCATCGTCTCGCACTC\tCDSN\n+s_11035\tCAACCCCACAGGTGAAGATC\tCDX1\n+s_11054\tCAAATTGTAGGATATGCAAT\tCEACAM1\n+s_11055\tCATGCCATTCAATGTTGCAG\tCEACAM1\n+s_11095\tCGAGTACGGCTACGTGAGCC\tCEBPB\n+s_1113\tGCTTGAGTGTATGCACAAAT\tADAR\n+s_11153\tAGCCTGTCCGTTTGCTAACG\tCELF4\n+s_1116\tAGCTGACGCTGTCTCACGCC\tADARB1\n+s_11211\tGAAGACGTTCTCATAACATT\tCENPK\n+s_11218\tTTCTTTCGCAATACATCCAG\tCENPL\n+s_11222\tCCAAGATGGTGGCCGTGTTC\tCENPM\n+s_1123\tCCTCAGCATGGCTATCATTG\tADAT1\n+s_11251\tTTTGTAGTCGTCAGCTCATC\tCEP104\n+s_1127\tGTCTACAACAATGAAGTTGT\tADAT2\n+s_11294\tAGTTACAACTTTTGCCCAGC\tCEP41\n+s_11296\tCCAGTCTTGATTTGATATGC\tCEP41\n+s_11317\tACAGCTGAGCCAAGAACTAA\tCEP63\n+s_1136\tTCCCATACACGCCCTCATCA\tADC\n+s_11386\tTGCCGGCAATGAAGGCAATC\tCERS2\n+s_11438\tTTTTTTTACATCAAACCCCA\tCETN3\n+s_11456\tCATCCTGGAGATACTCCTTT\tCFH\n+s_11513\tACGTGCCTGAGGGCTACTCC\tCGREF1\n+s_11527\tAGCCGCGCACGAAGCCCACA\tCHAC1\n+s_11585\tAGCCAGTCGGATGATGATTC\tCHD1\n+s_11598\tTTACACGCTTCTTGCGTTTT\tCHD3\n+s_1161\tACCTTAACTGCTCTCTGATC\tADCY10\n+s_11692\tTGAGATATGTGCCCCTCGTT\tCHL1\n+s_11714\tCTCATGGTGGCCTGAATCTC\tCHMP3\n+s_11744\tTTTCAGGTGCATACATTCAG\tCHN1\n+s_1177\tTGAGCAGCTTCACAAGCTCC\tADCY3\n+s_11788\tCGTGAACTGCATCTGCTCAG\tCHRDL1\n+s_1179\tCTCGTAGAAGAGGTCTTCGC\tADCY4\n+s_118\tTTACAAGTTGGTTTTGCAGT\tABCA12\n+s_1183\tCTGCACCCACTATCCGGCTG\tADCY5\n+s_11837\tTTCTAATGCTCTTCGTCCAG\tCHRNA9\n+s_11862\tTGGGGTCGTAGTTTTGCATC\tCHRNG\n+s_11877\tCCTGCAGAAGCTCTATGACC\tCHST13\n+s_11928\tACGTCTGTCTGTACCAGCAT\tCHUK\n+s_11984\tATGTCTTACCAACCCATCCA\tCINP\n+s_11988\tTACCTGTGATGGATCATTTG\tCIR1\n+s_12015\tTACCCTGGGGTAGCCTCAAA\tCITED1\n+s_12019\tCTGGGCAGGGCGGTAAATCT\tCIZ1\n+s_12021\tTCCTACAGGTGTGGACTTCC\tCIZ1\n+s_12049\tCCTTTCAGTAGTTGCCATCT\tCKLF-CMTM1\n+s_12057\tCCGGCAGAAAGTGTGTGCCG\tCKMT2\n+s_12069\tCTGTATCTGCTTGAAGCTAC\tCLCA1\n+s_12082\tGTCAAAGCAATCCTGTTTTT\tCLCC1\n+s_12089\tTCCCCTGTGCGATTGAGAGC\tCLCF1\n+s_1212\tGACCAGAGTGAACTCCGAGC\tADD1\n+s_12120\tGCTCCTGTCCCTCAAGTATG\tCLCN7\n+s_12121\tGGACGCCCACCTCATACTTG\tCLCN7\n+s_12138\tACATGTCCAGGGCGCAGATC\tCLDN10\n+s_12140\tTTAGGGCTGTGCTCAATGAC\tCLDN10\n+s_12160\tTCAGAACGAAGATGCCCGTC\tCLDN17\n+s_12177\tACGGGACTTCTACTCACCAC\tCLDN2\n+s_12187\tGCATCCCTGACATCATACCT\tCLDN25\n+s_12197\tGTCTCCAGGTCTTGCCGCCT\tCLDN7\n+s_12203\tCACACTAACTGAGCAGTTCA\tCLDND1\n+s_12209\tCGTGGTTGCATTCCTGCCAC\tCLDND2\n+s_1224\tTGAAGTCCGCGATCTGTCGC\tADD2\n+s_12262\tTGACAGGACCGCGCAGTTCT\tCLEC3B\n+s_12310\tGCACAGCTTCTGCACTGTCT\tCLIC1\n+s_1238\tCTTCAACCTCTTCAATGCAA\tADH4\n+s_12420\tGAACAGCACGATCTTGTGTA\tCLPTM1\n+s_12425\tCGCATTCATATGTCAGTTTT\tCLPX\n+s_12433\tCATCTGCCTATGGAATGTCC\tCLRN2\n+s_12463\tTCTCTTTCCAGCTGGTTCTG'..b's_7053\tTTCTCACCGGCAAGACCTAG\tC1QTNF7\n+s_7059\tAGAGCTCACGTAAGCATCTC\tC1QTNF9B\n+s_707\tCGTTTCAGTCCACCTGATCC\tACPL2\n+s_7088\tCTGAACACTCACCAGACTGC\tC1orf106\n+s_7105\tAGTACCAAAGCATCATTGTC\tC1orf111\n+s_7128\tCTGCCGTAACATCTCCTCGC\tC1orf122\n+s_714\tCGCTTCTCACCGTGGTCAGC\tACPT\n+s_7144\tATTTGACCTTACTCTTATAC\tC1orf130\n+s_7162\tCCACACTCACCTGTCGAGGA\tC1orf144\n+s_7217\tTACCCATGTGCCTGCTGAGC\tC1orf186\n+s_7234\tCCAACTTACCTTTGTTTCCC\tC1orf198\n+s_7252\tCACATTCCCTGTTGCCTTCG\tC1orf212\n+s_730\tTTGACTCAGCATCACGCCCT\tACSBG1\n+s_7306\tGTCCTGTGTCACTCCTGCTT\tC1orf49\n+s_7336\tCTTGTGCTGCCTGGAGGACG\tC1orf61\n+s_7341\tTCAGCCAAAGAAACAAGCCG\tC1orf63\n+s_7465\tCATTCCAGTTGGGGTAGTCC\tC20orf26\n+s_747\tTCTTCCGACCAACACGCTTA\tACSL1\n+s_7498\tCTCCTGGGTCTTCTCAATCT\tC20orf96\n+s_7539\tCACTCGCCTTACCTCGCCCT\tC22orf25\n+s_7562\tTCATGGCAGGGTCCCACATC\tC22orf42\n+s_76\tCGTGGATCCACGAAGCGAGA\tAARS2\n+s_7626\tGTAGCTAATGCTGCCTACCT\tC2orf43\n+s_7629\tCAAGCAGTGCATCCGATCCA\tC2orf44\n+s_7674\tGGTGTGGTCCGAGACCACCA\tC2orf57\n+s_7681\tGGCCCACAGCATGTCCTCCA\tC2orf62\n+s_7692\tTAGATCACATCAAGCAGTGT\tC2orf63\n+s_77\tACCCACCTTGATATCCTCCT\tAARSD1\n+s_7715\tCCTTACCCGGGCATGAGTCC\tC2orf70\n+s_7793\tTACTTCTGTGCAGGCCATGC\tC3orf18\n+s_7794\tTCTTGCAGGTTTTGTACATC\tC3orf18\n+s_78\tAGGAAAAGGTGGCCTGGCCG\tAARSD1\n+s_7803\tCCAGACGGTGATGTAAAATC\tC3orf22\n+s_781\tCCGAGAGCGTTGCTTTGATC\tACSS1\n+s_782\tCGGGCATGTAGATGGCAACA\tACSS1\n+s_7822\tACTCAGCGTCTCCCGCCTCC\tC3orf27\n+s_7838\tCGTGAGAAGAGACACCTGTG\tC3orf35\n+s_786\tCACATGTTGACTCCCCTTCC\tACSS2\n+s_791\tGTTGCTTTAGTGTTTGTAAC\tACSS3\n+s_7927\tACCCATGGCTCCGATGGAGA\tC4orf19\n+s_7940\tTGTGCAAATTAATATGCTGC\tC4orf26\n+s_7970\tTCTGAAACATTATAGTGTCC\tC4orf37\n+s_8000\tCTGCGCACCGCGCTCATTTT\tC4orf52\n+s_804\tCGTACAGGGATAGCACAGCC\tACTB\n+s_8073\tTCTTCTAGAACTTTACACAC\tC5orf51\n+s_8141\tTGAGCCTCCAACATTCAAAA\tC6orf162\n+s_8148\tTCCATGTTAAAGCCATTACT\tC6orf165\n+s_82\tCTATGCCAAAGTGAACTCCA\tAARSD1\n+s_8227\tTATGAACAATATAAAGCCAT\tC7orf10\n+s_825\tTGCCAAGACCTCGTAACCTG\tACTL6A\n+s_8281\tCTGCACCTTCACTCAGTACC\tC7orf59\n+s_8318\tTTCTCCTGTGCAGTTACCCC\tC8A\n+s_8403\tAGGTTACCTGCAGGGTGGTC\tC9orf100\n+s_8419\tACCGGGAGGCGCAGTGATAT\tC9orf123\n+s_8470\tCCGCGGATCACGCCCCGATG\tC9orf24\n+s_8476\tGACCATAGTGCTTTTCCTCG\tC9orf3\n+s_8498\tGCTCCAGCAGACACCTATTC\tC9orf50\n+s_8514\tGGGCTCCATATTCGACTGTC\tC9orf71\n+s_8592\tGGTGCGTCCTCGGAGATCAG\tCA6\n+s_8699\tGTTTGAGCGCATCAGCATGT\tCACNA1G\n+s_8705\tCCGGGGTCCGGGCTGCTCCG\tCACNA1I\n+s_871\tCGAACCTGTTCAGGGGACAC\tACTR8\n+s_8738\tCCCGTCCGCGGTCCCGTTCT\tCACNB4\n+s_874\tTTGCTTGATCCACCATTTTA\tACTR8\n+s_8757\tCCAGCTGACATCCGAGTCCA\tCACNG5\n+s_8795\tCGCTGTGCAGAGTTACTATG\tCADPS\n+s_8797\tGCTGTTCCGCCAACGACTCC\tCADPS\n+s_8848\tGGCGCAGTACCGCGCCAATG\tCALHM2\n+s_8879\tGCCGCACAATCAGTGTGTAC\tCALR\n+s_8880\tTCTTCCGGTTTTGAAGCATC\tCALR\n+s_8907\tCTGCTGAAGCACCCCAACAT\tCAMK2A\n+s_8910\tACCTCTGGCTGACAGCTTCT\tCAMK2B\n+s_8917\tTTTTGCTGCGTACTCCTGCG\tCAMK2G\n+s_8918\tACCAACAACTTCTTCGGCGC\tCAMK2N1\n+s_893\tTGCCCACGATCTCCATGTGC\tACVR1B\n+s_8930\tTCTCACTCTGCAGCTTGTAC\tCAMKK1\n+s_8939\tCCTTGCGGCCGTCCCGCTTC\tCAMKV\n+s_8954\tCCCTTTACCTTTTGATGAGC\tCAMSAP1\n+s_9038\tTTTCGATGAAACTTTGATCA\tCAPN3\n+s_906\tTGCCACTTATGTTAATTGCG\tACVR2A\n+s_9064\tGGATGCCGTTTCTAAGTACC\tCAPRIN1\n+s_9077\tAAGACTCCGACTGCAGTGCC\tCAPSL\n+s_9109\tTCAAATAGTACTTCCTTCCT\tCARD17\n+s_9124\tTCCTTGTAGTCTAATGAGTT\tCARD8\n+s_9126\tTTACGTATCATTTGTCACAC\tCARD8\n+s_913\tCTCACTATAAAAGACAGTGA\tACY1\n+s_9161\tTGTTTCAATTTCTCTGCTTC\tCASC1\n+s_9171\tCAAGACTGCATCAGTTAAAG\tCASD1\n+s_9196\tGCACCTCAACTGTACCAAAG\tCASP10\n+s_9221\tTCCTGCAGCTCATCCGAATA\tCASP4\n+s_9223\tCGTCAACCACAGTGTAGCCC\tCASP5\n+s_9257\tCACTTGCAACACCGTTTCTA\tCASR\n+s_9285\tCGATAAGCTTGAGGATGCGC\tCATSPER3\n+s_9506\tTCTCCTACCTTCAATGCCCC\tCCDC120\n+s_9507\tCAGTTCAGGGCTGGACCAGC\tCCDC121\n+s_9517\tCACTGCCTGCGTATGACTTG\tCCDC125\n+s_952\tTTGATTCAGGGGTGAGCTTA\tADAM12\n+s_9584\tCATCACTTCCTCCTGAAAAA\tCCDC149\n+s_964\tTCATTTGACTTAATCTTCCG\tADAM18\n+s_9646\tTTCAGCTTTCAGTTCTTGAC\tCCDC170\n+s_9678\tCTCATAGACATCAGTCACCT\tCCDC28B\n+s_9710\tACACTTTTTGCGCTCCTCGT\tCCDC40\n+s_9725\tCTCCAACCGTCCGTCCAGCC\tCCDC43\n+s_9732\tCCTGCACCGCGTGCGAGAGC\tCCDC48\n+s_976\tTCCATTGAGAGAAATCGTTC\tADAM21\n+s_9763\tTACGACAATGATAAAGCTAA\tCCDC62\n+s_9791\tACTCACCTGTGTCCCCATTG\tCCDC69\n+s_9868\tCCTTCTCGCGCGCCTGTGCC\tCCDC89\n+s_991\tATCGCCCCTCTGAGCAGTCC\tADAM30\n+s_9925\tGCCTGCGCCTTGGACACAGT\tCCL1\n+s_9973\tATACTCACATCACAGCCCGC\tCCL26\n' |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/demo/demo2/test1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demo/demo2/test1.fastq Wed Feb 14 06:42:18 2018 -0500 |
| b |
| b'@@ -0,0 +1,10000 @@\n+@MISEQ:152:000000000-A8HE7:1:1101:14429:1925 1:N:0:ANATCG\n+CAGAAATACAGTGCGACCTGTTTTAGAGCT\n++\n+AAA?11DFF11@1FEGGC0FDFHFF0B1D1\n+@MISEQ:152:000000000-A8HE7:1:1101:12740:1966 1:N:0:ANATCA\n+CTCCACTTCACTGTCAGTTGGTTTTAGAGC\n++\n+1>AAACB1B@133BA33AB1BEHHAFFHHG\n+@MISEQ:152:000000000-A8HE7:1:1101:16950:1984 1:N:0:ANATCG\n+CCTACACGCACCTGGCGTCCGTTTTAGAGC\n++\n+>1>1>CF1?1ADGGGF0EEEGGHHGCEHFG\n+@MISEQ:152:000000000-A8HE7:1:1101:17242:1990 1:N:0:ANATCG\n+CGATCCACAATTTTAAAAGAAAAGGGGGGA\n++\n+>11AAAFFFAFFGF3FEGBFF110000AE#\n+@MISEQ:152:000000000-A8HE7:1:1101:14179:1995 1:N:0:ANATCG\n+ATCACATCTGTTTTAGAGCTAGAAATAGCA\n++\n+A3AABDFFFBDFGGFFFBGBGG4FEGHGBF\n+@MISEQ:152:000000000-A8HE7:1:1101:12622:2006 1:N:0:ANATCG\n+TGTTGCAAGGCTAGTCCGTTATCAACTTGA\n++\n+AAAA?FF5@3AFGAGGGGGGGGHEB4AAF4\n+@MISEQ:152:000000000-A8HE7:1:1101:16776:2010 1:N:0:ANATCG\n+GCAGACGTTGGCTAAGGCTAGTCCGATATC\n++\n+BBBBBF@A3AFFGGGF4GGBGGBBE22A2D\n+@MISEQ:152:000000000-A8HE7:1:1101:11913:2010 1:N:0:ANATCG\n+TATCATATCCCCATGTTTGCGTTTTAGAGC\n++\n+AA>>3@5BFDF@G4BEGGCGGGGGGEGFFH\n+@MISEQ:152:000000000-A8HE7:1:1101:13624:2011 1:N:0:ANATCG\n+CCAGAACGACCACGTCTGTTTAGAGCTAGC\n++\n+AA?1AFFA>ADDGGGGG0AB3331B1AGG1\n+@MISEQ:152:000000000-A8HE7:1:1101:17657:2029 1:N:0:ANATCG\n+TACCTTGGATCACTTACATCGTTTTAGAGC\n++\n+AA1AADF111B>111BGG3GA1BFFA0A11\n+@MISEQ:152:000000000-A8HE7:1:1101:16812:2029 1:N:0:ANATCG\n+CTTCAAGCTGTAATTCCGTAGTTTTAGAGC\n++\n+AAAAA13@1@1DG3FGGGGAEGGGBDBBDF\n+@MISEQ:152:000000000-A8HE7:1:1101:13595:2033 1:N:0:ANATCG\n+TCAGCATCTCCAGAGCTGCCGTTTTAGAGC\n++\n+1A1AAFFF11@1B1FG111BEFGHGHCABG\n+@MISEQ:152:000000000-A8HE7:1:1101:13444:2034 1:N:0:ANATCG\n+ACAGTTCTGTATGACATCATGTTTTAGAGC\n++\n+?A11AFF3D@@DBGG13B1BGGHHHGGGHH\n+@MISEQ:152:000000000-A8HE7:1:1101:12520:2041 1:N:0:ANCTCG\n+TGAAAGTACTAGAAAACGTGGCACCGAGTC\n++\n+A>1>AF@3BD3DFAGB11AAF00B00AA0A\n+@MISEQ:152:000000000-A8HE7:1:1101:13860:2049 1:N:0:ANATCG\n+CTCCGGCTGTGGAGGCTGTGGTTTTAGAGC\n++\n+BBBBB@BBBFFFGGGGGGFGGGGHGGHHHH\n+@MISEQ:152:000000000-A8HE7:1:1101:12559:2049 1:N:0:ANATCG\n+TGACATCGTAGACTCGCCCAGTTTTAGAGC\n++\n+A1AAA3F1>>AAF3F1ECE?CGHHHGFGFG\n+@MISEQ:152:000000000-A8HE7:1:1101:18030:2053 1:N:0:ANATCG\n+TCTCACCGTGCTGTCACATTTAGAGCTAGA\n++\n+AAAA?FFAC1AAFFFAFGGGGF311AFDG1\n+@MISEQ:152:000000000-A8HE7:1:1101:14400:2054 1:N:0:ANATCG\n+GGGCGATGCACCGTTAATCGTTTTAGAGCT\n++\n+A33AA?@AAFFFGGCEGGGGGGGGHCGBGG\n+@MISEQ:152:000000000-A8HE7:1:1101:17476:2054 1:N:0:ANATCG\n+CTGACGGGACCATGAAAATCGTTTTAGAGC\n++\n+1>>AA11A>>1AFGBGGFGGCFCFCHHFBA\n+@MISEQ:152:000000000-A8HE7:1:1101:11326:2062 1:N:0:ANATCG\n+CAGCTACTTCTTCCTTGCGCTTTTAGGGCT\n++\n+>>>>>@1FFFFFGFCG1E1E0EFH3010A0\n+@MISEQ:152:000000000-A8HE7:1:1101:15694:2064 1:N:0:ANATAG\n+TCCCCTGACGCCCGAGCAGCGTTTTAGAGC\n++\n+3>AAAFAFFAABGGGCGG4CAEEEFEBBEF\n+@MISEQ:152:000000000-A8HE7:1:1101:17231:2064 1:N:0:ANATCG\n+GTCCTCCCGATGACTGCCATGTTTTAGAGC\n++\n+A>>AAFFAA?D1GGEABGF1GGHGHBFE1D\n+@MISEQ:152:000000000-A8HE7:1:1101:11454:2072 1:N:0:ANATCG\n+CCTCTGACCTCAAGTTAAAATAAGGCTAGT\n++\n+1A1A11DDFFFFE1AFD3GD31BBGBCGEE\n+@MISEQ:152:000000000-A8HE7:1:1101:11841:2085 1:N:0:ANATCG\n+CGTCCCTCCTGACGCTCAGAGTTTTAGAGC\n++\n+AAAB@BFFBFFBF2AEFGGCGGGHHHHHHH\n+@MISEQ:152:000000000-A8HE7:1:1101:15365:2092 1:N:0:ANATCG\n+CCTACCAGGGCTGTTGATTAGTTTTAGAGC\n++\n+AAAAA>C1?1AFGFGFF3FFGGHH3FFF1A\n+@MISEQ:152:000000000-A8HE7:1:1101:18500:2095 1:N:0:ANATCG\n+CCCATGTGCCCAGATGCACTGTTTTAGAGC\n++\n+AAA??1BFF1F11A1F1F1FA3AF0A0BAA\n+@MISEQ:152:000000000-A8HE7:1:1101:11881:2096 1:N:0:ANATCG\n+GTACCTCTTAGTTGACATTTGTTTTAGAGC\n++\n+AA1>>FF1DDDBFGGFGCGGGGHHHHGHHH\n+@MISEQ:152:000000000-A8HE7:1:1101:14801:2113 1:N:0:ANATCG\n+GGCAGAGCGCACATTGTTCTGTTTTAGAGC\n++\n+>>AA33ACDADBGGGBFGGFGGHGHHHHHG\n+@MISEQ:152:000000000-A8HE7:1:1101:14238:2115 1:N:0:ANATCG\n+TCTCCAAAATAAGGCTAGTCCGTTATCAAC\n++\n+BBBBBFBF>FFFGGGFGCBGFEHHGAGFEF\n+@MISEQ:152:000000000-A8HE7:1:1101:15070:2115 1:N:0:ANATCG\n+TCCGCCGGGCGATCCGCCTGGTTTTAGAGC\n++\n+>1111111A>0>0FEFAE?A/FFCCEFC1F\n+@MISEQ:152:000000000-A8HE7:1:1101:17465:2116 1:N:0:ANATCG\n+CCATCCTGCCTTCAAGTACCGTTTTAGAGC\n++\n+AA3>AFFFFFFFGGCFFGGEEFGHGHHBGD\n+@MISEQ:152:000000000-A8HE7:1:1101:11476:2123 1:N:0:ANATCG\n+CGTGAAGACAGGT'..b'01:19674:3663 1:N:0:ANATAG\n+TGTACCCTGCCCACACTCCCGTTTTAGAGC\n++\n+A>A113@1BAFA1FE1B1FFGGHHG3A111\n+@MISEQ:152:000000000-A8HE7:1:1101:11709:3663 1:N:0:ANATCG\n+TGGCTCACCAGTACCCCTCTGTTTTAGAGC\n++\n+AAAA111111C@AEDAFFE1CFGHHHBFHH\n+@MISEQ:152:000000000-A8HE7:1:1101:14789:3664 1:N:0:ANATCG\n+AGTAGCAAAACATGTTACGTGTTTTAGAGC\n++\n+?AAAAFFFFFFAGB3BGGGAGFHHHBGFHG\n+@MISEQ:152:000000000-A8HE7:1:1101:10966:3664 1:N:0:ANATCG\n+GGGCTCCATATTCGACTGTCGTTTTAGAGC\n++\n+CCCCCCBFFFFFGGGGGGGGGFEFFHHGHH\n+@MISEQ:152:000000000-A8HE7:1:1101:20525:3665 1:N:0:ANATCG\n+CTCCTCGAAGGGCCGACACGTTTTAGAGCT\n++\n+>AA3AB33CA22AEE2EA2EBFGGHFBDFG\n+@MISEQ:152:000000000-A8HE7:1:1101:17351:3665 1:N:0:ANATCG\n+GAGCCCTACCCGCTCGTCTAGTTTTAGAGC\n++\n+BBBBBBFFCCFAE2EEEC4FFGFGFHHFHH\n+@MISEQ:152:000000000-A8HE7:1:1101:10622:3665 1:N:0:ANATCG\n+CGTATCGCCACCCTGGCATCGTTTTAGAGC\n++\n+AB>AAFBAABBFGCFCFFGGGFGGGHFFHH\n+@MISEQ:152:000000000-A8HE7:1:1101:11162:3666 1:N:0:ANATCG\n+TGTGTACAGCTCTCCTCCGTTTTAGAGCTA\n++\n+ABAAAFFFF4CFGGGBGCCGGGGGFEGHFH\n+@MISEQ:152:000000000-A8HE7:1:1101:19098:3666 1:N:0:ANATCG\n+ATCCACCCCTGCTTTCCGTTGTTTTAGAGC\n++\n+11AA@F1>DAAACDGFG11AEFGG0301A1\n+@MISEQ:152:000000000-A8HE7:1:1101:11814:3668 1:N:0:ANATCG\n+ACCCTCGTTCAGCGGCTTGAGTTTTAGAGC\n++\n+ABBABBBAAFF@F2EEG2EFEFGGHCFFFF\n+@MISEQ:152:000000000-A8HE7:1:1101:14609:3668 1:N:0:ANATCG\n+TTCTTACCTTGGGGGTAGTCCGTTATCGAT\n++\n+>3>A?5@CB5D44AAA2CFEFEGHFA5222\n+@MISEQ:152:000000000-A8HE7:1:1101:11790:3668 1:N:0:ANATCG\n+CTGCTGAAGCACCCCAACATGTTTTAGAGC\n++\n+>11>>1D1DFB1CAF1E1FGFEGDFFHFFH\n+@MISEQ:152:000000000-A8HE7:1:1101:13710:3668 1:N:0:ANATCG\n+TTACCCTGCCCACACTCCTGTTTTAGAGCT\n++\n+>>A3>CF4AFA4AEEGC44GGGFHGHHHHH\n+@MISEQ:152:000000000-A8HE7:1:1101:19043:3669 1:N:0:ANACCG\n+CTTATAGTCAGCCTCAAAAGTTTTAGAGCT\n++\n+BBABAFF5FFF44BGGGGGGB5FFFFFHHH\n+@MISEQ:152:000000000-A8HE7:1:1101:13832:3671 1:N:0:ANATCG\n+AAGAAGATGATGCAGAGTCCGTTATCAACT\n++\n+>>A11B1113BDGGE1FFGGFGHGG3F3FD\n+@MISEQ:152:000000000-A8HE7:1:1101:18171:3671 1:N:0:ANATAG\n+CATACCAGCTGAGCCGTCCGGCTTTAGAGC\n++\n+B@BBBFFFBFFFAGGGFGGGEGEGHHGHFH\n+@MISEQ:152:000000000-A8HE7:1:1101:13736:3671 1:N:0:ANATCG\n+CCCGGTCGGATGCGGCCCCCGTTTTAGAGC\n++\n+1>1AA>A1@1A0C0EE0EGGGGHHGHHHGH\n+@MISEQ:152:000000000-A8HE7:1:1101:17567:3671 1:N:0:ANATCG\n+GTCCAACGGAAAGTGGCCACGTTTTAGAGC\n++\n+?AAABFFABAADF55FFGGCGFGBAGHHFG\n+@MISEQ:152:000000000-A8HE7:1:1101:14881:3671 1:N:0:ANATCG\n+TCCGCAGCCCTCCACACGTAGTTTTAGAGC\n++\n+AAAA111>>1B>11B1A0B0EFHHGGCFHF\n+@MISEQ:152:000000000-A8HE7:1:1101:16313:3672 1:N:0:ANATCA\n+ACTGACCCTTTGCCGCAGCAGTTTAGAGCT\n++\n+1>1>AF1C1>@11FEGCAEAGFGBGBFHD1\n+@MISEQ:152:000000000-A8HE7:1:1101:15652:3672 1:N:0:ANATCT\n+CCCGATGATCTCGATGCCCGTTTTAGAGCT\n++\n+>A>A?AAD3DFFGF13A1CAEGGFFGGHGH\n+@MISEQ:152:000000000-A8HE7:1:1101:18193:3673 1:N:0:ANATCG\n+TTCGGAGCTGAGGAACATGCGTTTTAGAGC\n++\n+AA?AA3A@FCBF2C4AEDGBEEGGGHHHHH\n+@MISEQ:152:000000000-A8HE7:1:1101:17624:3673 1:N:0:ANATCG\n+CCATCATGCCACACAAGATCGTTTTAGAGC\n++\n+ABBBBF55DFFFGGCC4B4FCFGFFGFCFH\n+@MISEQ:152:000000000-A8HE7:1:1101:21520:3674 1:N:0:ANATCG\n+TTATCAACTTGAAAAAGTGGCACCGAGTCG\n++\n+AAAAABF1B@D1BEAFA11D111AEEC0B0\n+@MISEQ:152:000000000-A8HE7:1:1101:17841:3674 1:N:0:ANATAG\n+TCCATCTCGTTTGTTTTTCTGTTTTAGAGC\n++\n+BABBB5554AAAEGEGGGFBEGGHHGGBGG\n+@MISEQ:152:000000000-A8HE7:1:1101:21445:3674 1:N:0:ANATCG\n+TCTCCTATCAAGGCCATTCTGTTTTAGAGC\n++\n+B?ABBF45D55BEAGAFGFFGGHHHGH4GG\n+@MISEQ:152:000000000-A8HE7:1:1101:13569:3674 1:N:0:ANATCG\n+AGGATCCTGAGACGTTCCTCGTTTTAGAGC\n++\n+>AA1>CBFDF1D1E11BCFGGGGGGHHHHH\n+@MISEQ:152:000000000-A8HE7:1:1101:15838:3674 1:N:0:ANATCG\n+TTCCCTATCAGTAGAAATAGCAAGTCAAAA\n++\n+AA11111@B3BD333B31A11A11F13F3A\n+@MISEQ:152:000000000-A8HE7:1:1101:16429:3675 1:N:0:ANATCG\n+CTGGTCTCGCCGGTAGCTATGTTTTAGAGC\n++\n+AAA1AF3@1A111A001333GGHHGHHFHH\n+@MISEQ:152:000000000-A8HE7:1:1101:8184:3675 1:N:0:ANATCG\n+GACTCCTATCATCATGTCGGTTATCAACTT\n++\n+BABB@FFFFFFFGBGGDGGGEEDFFFGHHG\n+@MISEQ:152:000000000-A8HE7:1:1101:16716:3675 1:N:0:ANATCG\n+GCCCACATGCAACTTTGTTGGTTAGAGCTA\n++\n+>AA>1AAF11DFC113FB1BFAGH011FAF\n+@MISEQ:152:000000000-A8HE7:1:1101:10571:3675 1:N:0:ANATCG\n+TCTTCAATTGTGTAGCGAAGGTTTTAGGGC\n++\n+>1AAAFFFFF3BFGGGGGEECB11AFGGHG\n' |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/demo/demo2/test2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demo/demo2/test2.fastq Wed Feb 14 06:42:18 2018 -0500 |
| b |
| b'@@ -0,0 +1,10000 @@\n+@MISEQ:152:000000000-A8HE7:1:1101:12014:1936 1:N:0:GNCTAA\n+CACTACCTTAGAAATAGCACGTTAAAATAA\n++\n+>>11>FCFFFD1FDFGDFF1ABGHCF1AAB\n+@MISEQ:152:000000000-A8HE7:1:1101:13315:1937 1:N:0:GNCTAG\n+CCCATCGAGATCTCTCTGACGTTTTAGAGC\n++\n+1>11AFA11>>FFG31A3BB?FFHE3BA1A\n+@MISEQ:152:000000000-A8HE7:1:1101:17562:1953 1:N:0:GNCTAA\n+CACCAGCCACTTACTGTGCGTTTTAGAGCT\n++\n+AAAA11>A1CFFGGF3BA1AAEEE3011DF\n+@MISEQ:152:000000000-A8HE7:1:1101:14418:1961 1:N:0:GNCTAT\n+CGCTCAGCTGCCCAAACCCAGTTTTAGAGC\n++\n+AAA1A1>C11B1FFEGGF1FCGHHHGGFHG\n+@MISEQ:152:000000000-A8HE7:1:1101:19853:1969 1:N:0:GNCTAA\n+CCACGCAGCCGATCCAGTCCGTTTTAGAGC\n++\n+1AAA@ADD?A1>E0A1131BEGGFFFFFFG\n+@MISEQ:152:000000000-A8HE7:1:1101:13114:1978 1:N:0:GNCTAA\n+CGGGGGAGAACCCGACGCGTTTTAGAGCTA\n++\n+A@A?AD@?0CFAGG?EAEEAAEFGCGGHFH\n+@MISEQ:152:000000000-A8HE7:1:1101:19171:1980 1:N:0:GNCTAA\n+GAGTCCCTGAAGATGATCTTGTTTTAGAGC\n++\n+11>>AF1BFFFFFGGFFGGCGGHC13B1FF\n+@MISEQ:152:000000000-A8HE7:1:1101:13552:1987 1:N:0:GNCTAA\n+TCCTTATCATTTGCACCACCGTTTTAGAGC\n++\n+AAAAA3D1FBDBA3EDC11AEGGHGABAFF\n+@MISEQ:152:000000000-A8HE7:1:1101:14030:1991 1:N:0:GNCTAA\n+CCCAGTGCATCCTCGTCCCTGTTTTAGAGC\n++\n+AAAA1FFFF3DBBFAGFGGDFGGHGHHHHG\n+@MISEQ:152:000000000-A8HE7:1:1101:18336:1993 1:N:0:GNCTAA\n+CTAACATCACTTCTCTGTAGGTTTTAGAGC\n++\n+>>>>AF3B@D1BFGGGDAFGBGHG13ABFA\n+@MISEQ:152:000000000-A8HE7:1:1101:12130:2005 1:N:0:GNCTAA\n+GCCTGGTTTTAGAGCTAGAAATAGCAAGTT\n++\n+?AAAA?CDFAB>1F1FFF1B3G31BD1ABA\n+@MISEQ:152:000000000-A8HE7:1:1101:13467:2010 1:N:0:GNCTAA\n+CAACGTCCCCCACCTCCTCCGTTTTAGAGC\n++\n+A@AAAAAAABBBGGGGGFGGGGHHGGBG3F\n+@MISEQ:152:000000000-A8HE7:1:1101:14166:2013 1:N:0:GNCTAA\n+TCACCGTCCGCTGCGACTGGTTTTAGAGCT\n++\n+AA1AA1FAADDAGGGCEGGF1BEEFHHHGF\n+@MISEQ:152:000000000-A8HE7:1:1101:13401:2014 1:N:0:GNCTAA\n+TTTAGCAAGTTAAAATAAGGCTAGTCCGTT\n++\n+AAAA@DFF1BD33BGFGCGGGGFEE3D00F\n+@MISEQ:152:000000000-A8HE7:1:1101:13793:2029 1:N:0:GNCTAA\n+CTGCCAACATGATGAAGAAGGTTTTAGAGC\n++\n+A>AAAC@AA1CDGDEFGGGFGGHHGHHHHH\n+@MISEQ:152:000000000-A8HE7:1:1101:19424:2030 1:N:0:GNCTAA\n+TTACGTAGGACCTCTCAGCAGTTTTAGAGC\n++\n+1>AAACBF@1FAGFEGG3FFGGHGHGCEFF\n+@MISEQ:152:000000000-A8HE7:1:1101:13415:2031 1:N:0:GNCTAA\n+ACTCACCAAGACGCCCATCTGTTTTAGAGC\n++\n+1>AAAFFB1BFFEEG1E0FFGGHHGHGGGH\n+@MISEQ:152:000000000-A8HE7:1:1101:18009:2034 1:N:0:GNCTAA\n+ACTCTCTTACCTCTTCTCTAGTTTTAGAGC\n++\n+1AAA1B13@DFFGBFGGGGBFGHHFEGCFH\n+@MISEQ:152:000000000-A8HE7:1:1101:11975:2035 1:N:0:GNCTAA\n+ACCAGGCAGACAAACACTTGGTTTTAGAGC\n++\n+BBBBBB@BABF4GGGGGFGGGGHHEGGFGH\n+@MISEQ:152:000000000-A8HE7:1:1101:12052:2040 1:N:0:GNCTAA\n+CTTGATATCAATCCCACTCCGTTATCAACT\n++\n+1>A111BDFDFFFGBAG1F1EFGCHF33C3\n+@MISEQ:152:000000000-A8HE7:1:1101:17121:2041 1:N:0:GNCTAA\n+ACCTGCATTAGACTTGAATGGTTTTAGAGC\n++\n+1>A?A1B@D1@3G3BF1F3BGGHHCHB11A\n+@MISEQ:152:000000000-A8HE7:1:1101:14480:2041 1:N:0:GNCTAA\n+TTTCGCGATGCCTCAGTTCTGTTTTAGAGC\n++\n+AA1A?A?1A1AC3AC1FF3AEFGFHHHGHH\n+@MISEQ:152:000000000-A8HE7:1:1101:13535:2043 1:N:0:GNCTAA\n+CTTGATATCCATCCCACTCCGTTATCAACT\n++\n+AA>11BB3133@11A1B1BEGGHACD3FA3\n+@MISEQ:152:000000000-A8HE7:1:1101:12360:2045 1:N:0:GNCTAA\n+AACGCCAGCCCTCGAACCATGTTTTAGAGC\n++\n+AAAAADA?>AABGE0BA00AGGHHCGHHGG\n+@MISEQ:152:000000000-A8HE7:1:1101:18203:2050 1:N:0:GNCTAA\n+TCCTATACAGAAACTCTTTGGTTTTAGAGC\n++\n+A@AAA5DFF5FFCG5GFGFGCEGFDHHGHF\n+@MISEQ:152:000000000-A8HE7:1:1101:17008:2056 1:N:0:GNCTAA\n+TCGGACGCCTCACAAGGCTAGTCCGATATC\n++\n+1AAA>D?DD?AFAGF00F1FGF3D000A0D\n+@MISEQ:152:000000000-A8HE7:1:1101:16217:2059 1:N:0:GNCTAA\n+CCGACGTTCTCTTGCGGCATGTTTTAGAGC\n++\n+AAA>ADDAF@FFCGBE2EECEGFGHHGF3D\n+@MISEQ:152:000000000-A8HE7:1:1101:12782:2059 1:N:0:GNCTAA\n+TCCAAGGCCTCCCTCCACGTTTTAGAGCTA\n++\n+AAABAFAAACFBGGGGGGGGFGF5F4EGHC\n+@MISEQ:152:000000000-A8HE7:1:1101:13133:2059 1:N:0:GNCTAA\n+CCACGCCCCAACTGGAACAGTTTTAGAGCT\n++\n+AAAAAAADDAAABG1G11FBDGHHB01AB1\n+@MISEQ:152:000000000-A8HE7:1:1101:13454:2059 1:N:0:GNCTAA\n+CTGGGGAACTACCGGCTCAGTTTTAGAGCC\n++\n+B@?AADA@AFFFGCGEEEG4BGHHB433F2\n+@MISEQ:152:000000000-A8HE7:1:1101:12641:2062 1:N:0:GNCTAA\n+ATTGTGCATCTATAAGCTGCGTTTTAGAGC\n++\n+AAAAAFBFFFB@FFF3FF1FEGGGGHHHHH\n+@MISEQ:152:000000000-A8HE7:1:1101:17410:2064 1:N:0:GNCTAA\n+CTTACCCGTCGGA'..b'1101:16742:3186 1:N:0:GNCTAA\n+TTATATCTGCGTGATTTTCGGGTTTAGAGC\n++\n+ABBBBFFFFB3A??4BGGG?EE4AAFGGHG\n+@MISEQ:152:000000000-A8HE7:1:1101:12979:3187 1:N:0:GNCTAA\n+CTGGGTGGAGCGCTCTGTCCGTTTTAGAGC\n++\n+AABB3BA2AAFBGGGCFGGGGAFGFHGHHH\n+@MISEQ:152:000000000-A8HE7:1:1101:19431:3188 1:N:0:GNCTAA\n+GATAGCAGTTAACATAAGGCTAGTCCGTTA\n++\n+CC@BBFFFFFFFGFGGGGFGGGFF55?GFE\n+@MISEQ:152:000000000-A8HE7:1:1101:9502:3188 1:N:0:GNCTAA\n+TCGTCAACTGACTTGATGTGGTTTTAGAGC\n++\n+BBBBBBBFFFFFGGGGCGGGGBFGGGCGGF\n+@MISEQ:152:000000000-A8HE7:1:1101:11652:3189 1:N:0:GNCTAA\n+CAATCTACATCTTCTGCATTGTTTTAGAGC\n++\n+ABBBBFF5B5DFGGDBGDGFFGHHHGGHFF\n+@MISEQ:152:000000000-A8HE7:1:1101:16707:3189 1:N:0:ANCTAA\n+AGGCCAAGCGAGCAGTACAGGTTTTAGAGC\n++\n+AA?ABABBBBBBEECGEGGF4BBGFFFFGG\n+@MISEQ:152:000000000-A8HE7:1:1101:10583:3189 1:N:0:GNCCAA\n+ACAATGGCCAACCCTATTATGTTTTAGAGC\n++\n+AAA?AFBFFCBBECGFG5DFFGHHHHBGGH\n+@MISEQ:152:000000000-A8HE7:1:1101:19130:3189 1:N:0:GNCTAA\n+GTTTTACCGTTGCATCGTGGTTTAGAGCTA\n++\n+>>>AAFFFBAAA?GFGFAFEAFHHHAFGFG\n+@MISEQ:152:000000000-A8HE7:1:1101:18578:3189 1:N:0:GNCTAA\n+AGCTGTATGCACAAAGTTTGGTTTTAGAGC\n++\n+BABBBFFFBBFDGFGGGFFGCFHH2FCFFH\n+@MISEQ:152:000000000-A8HE7:1:1101:12107:3190 1:N:0:GNCTAA\n+TCACATTTATGTCACCCAGTGTTTTAGAGC\n++\n+BBBBBFFFFFFFGGGBG2AFGGHHC5AAGF\n+@MISEQ:152:000000000-A8HE7:1:1101:10057:3190 1:N:0:GNCTAA\n+GACCAGAACACGGGCTGGATGTTTTAGAGC\n++\n+B3AAAFFF4F42EEE?CE4DGBGGBGHFHG\n+@MISEQ:152:000000000-A8HE7:1:1101:19721:3190 1:N:0:GNCTAA\n+TGACAGGGAGGAGGAAACTTGTTTTAGAGC\n++\n+AAABBFAAAB@B2EEGGGGFGGHFHHHHHH\n+@MISEQ:152:000000000-A8HE7:1:1101:17999:3190 1:N:0:GNCTAA\n+TGTCCTGCAGTTAACTCAGTTTTAGAGCTA\n++\n+333AAFFFFBFBGDGGGGGGGGHHB4BGHF\n+@MISEQ:152:000000000-A8HE7:1:1101:9109:3191 1:N:0:GNCTAA\n+CTCAAGATCCCATCTGAGAGGTTTTAGAGC\n++\n+A3AA34DBFDFFFGGCBGGFAFFBFGF4GH\n+@MISEQ:152:000000000-A8HE7:1:1101:13192:3191 1:N:0:GNCTAA\n+TAGCACTTGCTGTAGACCCGTTTTAGAGCT\n++\n+CBCCCFFFFFFFGGFGGGGGGGHGGHHHHG\n+@MISEQ:152:000000000-A8HE7:1:1101:15114:3191 1:N:0:GNCTAA\n+GCTGTGACACTTGAACTTGTGTTTTAGAGC\n++\n+>AA?3BD5DCFFGFGFGGF5FGHFHGFFGG\n+@MISEQ:152:000000000-A8HE7:1:1101:18874:3191 1:N:0:GNCTAA\n+TCTGAAACATTATAGTGTCCGTTATCAACT\n++\n+1AA11@1DBDFFG3AG3GGG1AFFHGFHFE\n+@MISEQ:152:000000000-A8HE7:1:1101:16968:3191 1:N:0:GNCTAA\n+GATGGAGAAGACAGCGTACTGTTTTAGAGC\n++\n+AA@?AFFFFF11BA1EAE00BBFGHHHGGG\n+@MISEQ:152:000000000-A8HE7:1:1101:15434:3192 1:N:0:GNCCAA\n+TGTGGTTCCGGTCCGTCTTGGTTTTAGAGC\n++\n+1A1AA1>BB1AD?EE00FAFGFGHFHHBGH\n+@MISEQ:152:000000000-A8HE7:1:1101:17671:3192 1:N:0:GNATAA\n+TCAGCTCCTGCAGTTTCTTGGTTTTAGAGC\n++\n+A1AA111B1@CBABF33BFDFEA1A3B1B1\n+@MISEQ:152:000000000-A8HE7:1:1101:17035:3193 1:N:0:GNCTAA\n+CCTTTACCTAGAAGATCCATGTTTTAGAGC\n++\n+AAAAAFFFDFFFGGGGGBGCGGHHHGHGHH\n+@MISEQ:152:000000000-A8HE7:1:1101:18144:3193 1:N:0:GNCTAA\n+CCCGTTGTACCAGCCACGAGTTAGAGCTAT\n++\n+>AA>1CAAF3DB11A1F1AEEFHBDEA113\n+@MISEQ:152:000000000-A8HE7:1:1101:12031:3193 1:N:0:GNCTAA\n+CTCACAGCATTCCCGTTAGCGTTTTAGAGC\n++\n+BABBAFDAFFFFGGGGA2FGGGFGFCGGHF\n+@MISEQ:152:000000000-A8HE7:1:1101:19648:3194 1:N:0:GNCTAA\n+CCTGCACCGCGTGCGAGAGCGTTTTAGAGC\n++\n+AAAA@CFFD?D1EE0A0EE00AEEFFFGHH\n+@MISEQ:152:000000000-A8HE7:1:1101:18823:3194 1:N:0:GNCTAA\n+CCTGTTGCCCGCCGCCTGCAGTTTTAGAGC\n++\n+AAA?A11F1B>@EEAA0FGGFGHHDF0CGH\n+@MISEQ:152:000000000-A8HE7:1:1101:10505:3195 1:N:0:GNCTAA\n+TCAACCGCATCAGCCGTATCGTTTTAGAGC\n++\n+BB@BBFBDBBBFGGFGGGGFFGGFDFF3EB\n+@MISEQ:152:000000000-A8HE7:1:1101:16489:3195 1:N:0:GNCTAA\n+TCTTCGATTCTCAAAGTGTTTTAGAGCTAG\n++\n+ABABBBBFFFFFGBEG5BAAGGHHHDGGBE\n+@MISEQ:152:000000000-A8HE7:1:1101:19940:3195 1:N:0:GNATAA\n+ACGTCTGTCTGTACCAGCATGTTTTAGAGC\n++\n+BBBAAFBFFBFFGGBGGGGBGGHHB54445\n+@MISEQ:152:000000000-A8HE7:1:1101:20955:3195 1:N:0:GNCTAA\n+GTCCTTTGAAGAATTCTTTCGTTTTAGAGC\n++\n+A1>>A3@FD1111131A33GCBAAAFBBGF\n+@MISEQ:152:000000000-A8HE7:1:1101:9576:3196 1:N:0:GNCTAA\n+ACCTTTGAATCTCCCCAGCTGGTTTTAGAG\n++\n+BBBBBFBFFFFFDGFFG?FFFBBFGAGF44\n+@MISEQ:152:000000000-A8HE7:1:1101:11146:3196 1:N:0:GNCTAA\n+CGTCCTGTAGTTGTCCCCCCGTTTTAGAGC\n++\n+AA3>AAFFDDFFGFGGCGEG?AAABDG3AG\n+@MISEQ:152:000000000-A8HE7:1:1101:10918:3197 1:N:0:GNCTAA\n+ACCATTGGTTTACCATAAAAGTTTTAGAGC\n++\n+A1AAA11CDAFFFGG31F1FDFGGHB0FDF\n' |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/in.mageckQC.gmt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in.mageckQC.gmt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| @@ -0,0 +1,1 @@ +KEGG_RIBOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIBOSOME RPL35 RPL23 RPL3 RPL3L RPL31 RPL4 RPL5 RPL32 RPS10 RPL34 RPS11 RPS12 RPL36AL RPS13 RPL35A RPL37A RPS15 RPL37 RPL38 RPL14 RPS15A FAU RPSA RPS16 RPL27 RPS17 RPL26 RPL24 RPL29 RPL28 RPL27A UBA52 RPL30 RPL36 RPS20 RPS19 RPS18 RPS4X RSL24D1P11 RPS4Y1 RPS5 RPL22L1 RPL26L1 RPS6 RPLP2 RPL22 RPL23A RPL18 RPL18A RPL19 RPL21 RPS3A RPL10A RPS27L RPS3 RPS2 MRPL13 RPL17 RPL15 RPL36A RPL12 RPL13 RPL41 RPL10 RPL39 RPL11 RPL8 RPL9 RPL13A RPL7A RPS26 RPS27 RPS25 RPS29 RPLP1 RPS27A RPLP0 RPS28 RPS24 RPS9 RSL24D1 RPS23 RPS8 RPS21 RPS7 RPL10L RPL7 RPL6 |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/in.mle.design_matrix.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in.mle.design_matrix.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| @@ -0,0 +1,5 @@ +Samples baseline HL60 KBM7 +HL60.initial 1 0 0 +KBM7.initial 1 0 0 +HL60.final 1 1 0 +KBM7.final 1 0 1 \ No newline at end of file |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.count.bam.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.count.bam.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| b'@@ -0,0 +1,2551 @@\n+sgRNA\tGene\tsample1\n+s_10007\tCCNA1\t0\n+s_10008\tCCNA1\t0\n+s_10027\tCCNC\t0\n+s_10035\tCCND2\t0\n+s_10164\tCCS\t0\n+s_10200\tCCT7\t0\n+s_10232\tCD164\t0\n+s_10264\tCD1D\t0\n+s_10340\tCD276\t0\n+s_1035\tADAMTS14\t0\n+s_10381\tCD300LG\t0\n+s_10387\tCD320\t0\n+s_10401\tCD37\t0\n+s_10402\tCD37\t0\n+s_10405\tCD38\t0\n+s_10408\tCD3D\t0\n+s_10417\tCD3G\t0\n+s_10425\tCD40\t0\n+s_10434\tCD44\t0\n+s_10437\tCD46\t0\n+s_10448\tCD5\t0\n+s_10461\tCD55\t0\n+s_10481\tCD6\t0\n+s_10518\tCD81\t0\n+s_10541\tCD8B\t0\n+s_10563\tCD99L2\t0\n+s_10582\tCDC14B\t0\n+s_10594\tCDC20B\t0\n+s_10615\tCDC27\t0\n+s_10616\tCDC34\t0\n+s_1064\tADAMTS4\t0\n+s_10657\tCDC42SE2\t0\n+s_10658\tCDC42SE2\t0\n+s_10660\tCDC42SE2\t0\n+s_10675\tCDC73\t0\n+s_10731\tCDH13\t0\n+s_10739\tCDH16\t0\n+s_10770\tCDH23\t0\n+s_10785\tCDH3\t0\n+s_1085\tADAMTS9\t0\n+s_10862\tCDK17\t0\n+s_10943\tCDKL5\t0\n+s_10946\tCDKL5\t0\n+s_1101\tADAMTSL4\t0\n+s_11025\tCDSN\t0\n+s_11035\tCDX1\t0\n+s_11054\tCEACAM1\t0\n+s_11055\tCEACAM1\t0\n+s_11095\tCEBPB\t0\n+s_1113\tADAR\t0\n+s_11153\tCELF4\t0\n+s_1116\tADARB1\t0\n+s_11211\tCENPK\t0\n+s_11218\tCENPL\t0\n+s_11222\tCENPM\t0\n+s_1123\tADAT1\t0\n+s_11251\tCEP104\t0\n+s_1127\tADAT2\t0\n+s_11294\tCEP41\t0\n+s_11296\tCEP41\t0\n+s_11317\tCEP63\t0\n+s_1136\tADC\t0\n+s_11386\tCERS2\t0\n+s_11438\tCETN3\t0\n+s_11456\tCFH\t0\n+s_11513\tCGREF1\t0\n+s_11527\tCHAC1\t0\n+s_11585\tCHD1\t0\n+s_11598\tCHD3\t0\n+s_1161\tADCY10\t0\n+s_11692\tCHL1\t0\n+s_11714\tCHMP3\t0\n+s_11744\tCHN1\t0\n+s_1177\tADCY3\t0\n+s_11788\tCHRDL1\t0\n+s_1179\tADCY4\t0\n+s_118\tABCA12\t0\n+s_1183\tADCY5\t0\n+s_11837\tCHRNA9\t0\n+s_11862\tCHRNG\t0\n+s_11877\tCHST13\t0\n+s_11928\tCHUK\t0\n+s_11984\tCINP\t0\n+s_11988\tCIR1\t0\n+s_12015\tCITED1\t0\n+s_12019\tCIZ1\t0\n+s_12021\tCIZ1\t0\n+s_12049\tCKLF-CMTM1\t0\n+s_12057\tCKMT2\t0\n+s_12069\tCLCA1\t0\n+s_12082\tCLCC1\t0\n+s_12089\tCLCF1\t0\n+s_1212\tADD1\t0\n+s_12120\tCLCN7\t0\n+s_12121\tCLCN7\t0\n+s_12138\tCLDN10\t0\n+s_12140\tCLDN10\t0\n+s_12160\tCLDN17\t0\n+s_12177\tCLDN2\t0\n+s_12187\tCLDN25\t0\n+s_12197\tCLDN7\t0\n+s_12203\tCLDND1\t0\n+s_12209\tCLDND2\t0\n+s_1224\tADD2\t0\n+s_12262\tCLEC3B\t0\n+s_12310\tCLIC1\t0\n+s_1238\tADH4\t0\n+s_12420\tCLPTM1\t0\n+s_12425\tCLPX\t0\n+s_12433\tCLRN2\t0\n+s_12463\tCLTB\t0\n+s_12481\tCLUL1\t0\n+s_12522\tCMPK2\t0\n+s_12532\tCMTM1\t0\n+s_12576\tCNBP\t0\n+s_12578\tCNBP\t0\n+s_12589\tCNEP1R1\t0\n+s_12611\tCNGB1\t0\n+s_12624\tCNIH2\t0\n+s_12662\tCNNM3\t0\n+s_12666\tCNNM3\t0\n+s_12691\tCNOT4\t0\n+s_12695\tCNOT6\t0\n+s_12701\tCNOT7\t0\n+s_12703\tCNOT7\t0\n+s_12708\tCNP\t0\n+s_12738\tCNRIP1\t0\n+s_12764\tCNTN2\t0\n+s_12812\tCOASY\t0\n+s_12850\tCOG6\t0\n+s_12856\tCOG8\t0\n+s_12875\tCOL14A1\t0\n+s_12886\tCOL17A1\t0\n+s_12906\tCOL22A1\t0\n+s_12923\tCOL27A1\t0\n+s_1296\tADORA1\t0\n+s_12983\tCOL6A3\t0\n+s_12987\tCOL6A6\t0\n+s_13026\tCOLEC12\t0\n+s_13035\tCOMMD1\t0\n+s_13046\tCOMMD4\t0\n+s_13067\tCOMT\t0\n+s_13073\tCOPA\t0\n+s_13091\tCOPG1\t0\n+s_13123\tCOQ2\t0\n+s_13167\tCORO2A\t0\n+s_13190\tCOTL1\t0\n+s_13197\tCOX11\t0\n+s_13198\tCOX11\t0\n+s_13220\tCOX4I2\t0\n+s_13242\tCOX6C\t0\n+s_13244\tCOX6C\t0\n+s_13253\tCOX7A2L\t0\n+s_13287\tCPA5\t0\n+s_13290\tCPA6\t0\n+s_13309\tCPE\t0\n+s_13322\tCPEB3\t0\n+s_13328\tCPED1\t0\n+s_13338\tCPLX3\t0\n+s_13387\tCPO\t0\n+s_13389\tCPO\t0\n+s_13393\tCPOX\t0\n+s_13401\tCPPED1\t0\n+s_13405\tCPS1\t0\n+s_13427\tCPSF3L\t0\n+s_13428\tCPSF3L\t0\n+s_13486\tCR2\t0\n+s_1351\tADRA2A\t0\n+s_13512\tCRB1\t0\n+s_13554\tCREB3L3\t0\n+s_13557\tCREB3L4\t0\n+s_1357\tADRB1\t0\n+s_13572\tCREBL2\t0\n+s_13575\tCREBRF\t0\n+s_13579\tCREBZF\t0\n+s_13595\tCREM\t0\n+s_13602\tCRH\t0\n+s_1366\tADRBK2\t0\n+s_13662\tCRK\t0\n+s_13683\tCRMP1\t0\n+s_13686\tCRMP1\t0\n+s_13702\tCROT\t0\n+s_13718\tCRTAM\t0\n+s_13730\tCRTC2\t0\n+s_13755\tCRYBA1\t0\n+s_1376\tADSS\t0\n+s_13856\tCSF3\t0\n+s_13857\tCSF3\t0\n+s_13863\tCSF3R\t0\n+s_13874\tCSH2\t0\n+s_13879\tCSHL1\t0\n+s_1393\tAEN\t0\n+s_13930\tCSNK1G3\t0\n+s_13937\tCSNK2A1\t0\n+s_1394\tAEN\t0\n+s_13958\tCSPP1\t0\n+s_1396\tAES\t0\n+s_13985\tCSRP3\t0\n+s_13990\tCST11\t0\n+s_14021\tCSTA\t0\n+s_14052\tCT62\t0\n+s_14099\tCTCFL\t0\n+s_14107\tCTD-2616J11.4\t0\n+s_14153\tCTIF\t0\n+s_14157\tCTLA4\t0\n+s_14161\tCTLA4\t0\n+s_14163\tCTNNA1\t0\n+s_14187\tCTNND2\t0\n+s_14189\tCTNND2\t0\n+s_14209\tCTRL\t0\n+s_14226\tCTSC\t0\n+s_14264\tCTSS\t0\n+s_14266\tCTSW\t0\n+s_14274\tCTTN\t0\n+s_14282\tCTU1\t0\n+s_14286\tCTU2\t0\n+s_14338\tCUTA\t0\n+s_14364\tCWF19L1\t0\n+s_14369\tCWH43\t0\n+s_14370\tCWH43\t0\n+s_14418\tCXCL3\t0\n+s_14425\tCXCL6\t0\n+s_14439\tCXCR4\t0\n+s_14454\tCXXC1\t0\n+s_14463\tCXXC4\t0\n+s_14467\tCXXC5\t0\n+s_14485\tCXorf27\t0\n+s_14497\tCXorf40A\t0\n+s_1450\tAGA\t0\n+s_14520\tCXorf61\t0\n+s_14555\tCYB5B\t0\n+s_14576\tCYB5R4\t0\n+s_14586\tCYBA\t0\n+s_14670\tC'..b'\tZFC3H1\t0\n+s_62985\tZFHX3\t0\n+s_63034\tZFP64\t0\n+s_63079\tZFYVE1\t0\n+s_63097\tZFYVE21\t0\n+s_63104\tZFYVE27\t0\n+s_63107\tZFYVE27\t0\n+s_63114\tZFYVE28\t0\n+s_63149\tZIC2\t0\n+s_63192\tZMAT1\t0\n+s_63195\tZMAT2\t0\n+s_63208\tZMAT5\t0\n+s_63217\tZMIZ2\t0\n+s_63228\tZMYM3\t0\n+s_63232\tZMYM3\t0\n+s_63234\tZMYM3\t0\n+s_6326\tC12orf49\t0\n+s_63302\tZNF132\t0\n+s_63316\tZNF138\t0\n+s_63362\tZNF167\t0\n+s_63368\tZNF169\t0\n+s_6339\tC12orf53\t0\n+s_63396\tZNF182\t0\n+s_63398\tZNF184\t0\n+s_63435\tZNF200\t0\n+s_63487\tZNF223\t0\n+s_63489\tZNF224\t0\n+s_63517\tZNF233\t0\n+s_63594\tZNF276\t0\n+s_636\tACO1\t0\n+s_63600\tZNF28\t0\n+s_63612\tZNF280D\t0\n+s_63701\tZNF330\t0\n+s_63746\tZNF354B\t0\n+s_63755\tZNF362\t0\n+s_6376\tC12orf74\t0\n+s_63774\tZNF37A\t0\n+s_63785\tZNF384\t0\n+s_63798\tZNF385D\t0\n+s_63818\tZNF397\t0\n+s_63835\tZNF410\t0\n+s_63893\tZNF433\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_64012\tZNF496\t0\n+s_64039\tZNF506\t0\n+s_6409\tC14orf105\t0\n+s_64098\tZNF534\t0\n+s_64137\tZNF554\t0\n+s_64147\tZNF558\t0\n+s_64149\tZNF558\t0\n+s_64166\tZNF563\t0\n+s_64241\tZNF586\t0\n+s_6427\tC14orf133\t0\n+s_64297\tZNF611\t0\n+s_64356\tZNF639\t0\n+s_6438\tC14orf159\t0\n+s_64380\tZNF646\t0\n+s_64393\tZNF655\t0\n+s_64395\tZNF655\t0\n+s_64396\tZNF655\t0\n+s_64419\tZNF668\t0\n+s_64424\tZNF669\t0\n+s_64432\tZNF671\t0\n+s_64459\tZNF682\t0\n+s_64465\tZNF684\t0\n+s_64479\tZNF688\t0\n+s_64491\tZNF692\t0\n+s_6450\tC14orf176\t0\n+s_64581\tZNF746\t0\n+s_64601\tZNF75D\t0\n+s_64627\tZNF772\t0\n+s_64628\tZNF772\t0\n+s_64633\tZNF774\t0\n+s_64637\tZNF775\t0\n+s_64638\tZNF776\t0\n+s_64652\tZNF780A\t0\n+s_64662\tZNF783\t0\n+s_64791\tZNF85\t0\n+s_64839\tZNHIT6\t0\n+s_64851\tZNRF3\t0\n+s_64862\tZP2\t0\n+s_64868\tZP4\t0\n+s_64869\tZPBP\t0\n+s_64871\tZPBP\t0\n+s_64878\tZPLD1\t0\n+s_64898\tZSCAN10\t0\n+s_64923\tZSCAN22\t0\n+s_64930\tZSCAN30\t0\n+s_64995\tZYG11A\t0\n+s_64997\tZYG11A\t0\n+s_6525\tC15orf39\t0\n+s_6592\tC16orf13\t0\n+s_6618\tC16orf53\t0\n+s_6639\tC16orf62\t0\n+s_6674\tC16orf86\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_6827\tC17orf90\t0\n+s_6844\tC18orf1\t0\n+s_6849\tC18orf21\t0\n+s_6859\tC18orf32\t0\n+s_6862\tC18orf34\t0\n+s_6867\tC18orf54\t0\n+s_6906\tC19orf38\t0\n+s_691\tACP1\t0\n+s_6922\tC19orf44\t0\n+s_7045\tC1QTNF6\t0\n+s_7053\tC1QTNF7\t0\n+s_7059\tC1QTNF9B\t0\n+s_707\tACPL2\t0\n+s_7088\tC1orf106\t0\n+s_7105\tC1orf111\t0\n+s_7128\tC1orf122\t0\n+s_714\tACPT\t0\n+s_7144\tC1orf130\t0\n+s_7162\tC1orf144\t0\n+s_7217\tC1orf186\t0\n+s_7234\tC1orf198\t0\n+s_7252\tC1orf212\t0\n+s_730\tACSBG1\t0\n+s_7306\tC1orf49\t0\n+s_7336\tC1orf61\t0\n+s_7341\tC1orf63\t0\n+s_7465\tC20orf26\t0\n+s_747\tACSL1\t0\n+s_7498\tC20orf96\t0\n+s_7539\tC22orf25\t0\n+s_7562\tC22orf42\t0\n+s_76\tAARS2\t0\n+s_7626\tC2orf43\t0\n+s_7629\tC2orf44\t0\n+s_7674\tC2orf57\t0\n+s_7681\tC2orf62\t0\n+s_7692\tC2orf63\t0\n+s_77\tAARSD1\t0\n+s_7715\tC2orf70\t0\n+s_7793\tC3orf18\t0\n+s_7794\tC3orf18\t0\n+s_78\tAARSD1\t0\n+s_7803\tC3orf22\t0\n+s_781\tACSS1\t0\n+s_782\tACSS1\t0\n+s_7822\tC3orf27\t0\n+s_7838\tC3orf35\t0\n+s_786\tACSS2\t0\n+s_791\tACSS3\t0\n+s_7927\tC4orf19\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_8148\tC6orf165\t0\n+s_82\tAARSD1\t0\n+s_8227\tC7orf10\t0\n+s_825\tACTL6A\t0\n+s_8281\tC7orf59\t0\n+s_8318\tC8A\t0\n+s_8403\tC9orf100\t0\n+s_8419\tC9orf123\t0\n+s_8470\tC9orf24\t0\n+s_8476\tC9orf3\t0\n+s_8498\tC9orf50\t0\n+s_8514\tC9orf71\t0\n+s_8592\tCA6\t0\n+s_8699\tCACNA1G\t0\n+s_8705\tCACNA1I\t0\n+s_871\tACTR8\t0\n+s_8738\tCACNB4\t0\n+s_874\tACTR8\t0\n+s_8757\tCACNG5\t0\n+s_8795\tCADPS\t0\n+s_8797\tCADPS\t0\n+s_8848\tCALHM2\t0\n+s_8879\tCALR\t0\n+s_8880\tCALR\t0\n+s_8907\tCAMK2A\t0\n+s_8910\tCAMK2B\t0\n+s_8917\tCAMK2G\t0\n+s_8918\tCAMK2N1\t0\n+s_893\tACVR1B\t0\n+s_8930\tCAMKK1\t0\n+s_8939\tCAMKV\t0\n+s_8954\tCAMSAP1\t0\n+s_9038\tCAPN3\t0\n+s_906\tACVR2A\t0\n+s_9064\tCAPRIN1\t0\n+s_9077\tCAPSL\t0\n+s_9109\tCARD17\t0\n+s_9124\tCARD8\t0\n+s_9126\tCARD8\t0\n+s_913\tACY1\t0\n+s_9161\tCASC1\t0\n+s_9171\tCASD1\t0\n+s_9196\tCASP10\t0\n+s_9221\tCASP4\t0\n+s_9223\tCASP5\t0\n+s_9257\tCASR\t0\n+s_9285\tCATSPER3\t0\n+s_9506\tCCDC120\t0\n+s_9507\tCCDC121\t0\n+s_9517\tCCDC125\t0\n+s_952\tADAM12\t0\n+s_9584\tCCDC149\t0\n+s_964\tADAM18\t0\n+s_9646\tCCDC170\t0\n+s_9678\tCCDC28B\t0\n+s_9710\tCCDC40\t0\n+s_9725\tCCDC43\t0\n+s_9732\tCCDC48\t0\n+s_976\tADAM21\t0\n+s_9763\tCCDC62\t0\n+s_9791\tCCDC69\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 000000000000 -r b80c0e046539 test-data/out.count.fastq.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.count.fastq.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| b'@@ -0,0 +1,2551 @@\n+sgRNA\tGene\tsample1\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_23900\tG'..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 000000000000 -r b80c0e046539 test-data/out.count.log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.count.log.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| @@ -0,0 +1,46 @@ +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. |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.count.unmapped.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.count.unmapped.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| b'@@ -0,0 +1,935 @@\n+CAGAAATACAGTGCGACCTG\tCAGAAATACAGTGCGACCTG\t1\n+CGATCCACAATTTTAAAAGA\tCGATCCACAATTTTAAAAGA\t1\n+ATCACATCTGTTTTAGAGCT\tATCACATCTGTTTTAGAGCT\t1\n+TGTTGCAAGGCTAGTCCGTT\tTGTTGCAAGGCTAGTCCGTT\t1\n+CCAGAACGACCACGTCTGTT\tCCAGAACGACCACGTCTGTT\t1\n+TACCTTGGATCACTTACATC\tTACCTTGGATCACTTACATC\t1\n+CTTCAAGCTGTAATTCCGTA\tCTTCAAGCTGTAATTCCGTA\t1\n+TGAAAGTACTAGAAAACGTG\tTGAAAGTACTAGAAAACGTG\t1\n+TCTCACCGTGCTGTCACATT\tTCTCACCGTGCTGTCACATT\t1\n+GGGCGATGCACCGTTAATCG\tGGGCGATGCACCGTTAATCG\t1\n+CAGCTACTTCTTCCTTGCGC\tCAGCTACTTCTTCCTTGCGC\t1\n+CCTCTGACCTCAAGTTAAAA\tCCTCTGACCTCAAGTTAAAA\t1\n+TCTCCAAAATAAGGCTAGTC\tTCTCCAAAATAAGGCTAGTC\t5\n+TCCGCCGGGCGATCCGCCTG\tTCCGCCGGGCGATCCGCCTG\t1\n+CCCATCTCTTGTCTCTGTTT\tCCCATCTCTTGTCTCTGTTT\t1\n+CCCACCACTTATTTTTCCAC\tCCCACCACTTATTTTTCCAC\t1\n+TAAGCACGTTCGAGTCCATG\tTAAGCACGTTCGAGTCCATG\t1\n+ATTAGAGCTAGAAATAGCAA\tATTAGAGCTAGAAATAGCAA\t1\n+TACGCTGACCTCCGCAACCT\tTACGCTGACCTCCGCAACCT\t1\n+GACTCCTATCATCATGTCGG\tGACTCCTATCATCATGTCGG\t4\n+CTACACAGATCCTTCCGTGA\tCTACACAGATCCTTCCGTGA\t1\n+ATCTTTCATGTCGAGACACA\tATCTTTCATGTCGAGACACA\t1\n+CTTCACGATGCCAGCCGTTT\tCTTCACGATGCCAGCCGTTT\t1\n+ACCCGCGTCCTCGTCGTCGA\tACCCGCGTCCTCGTCGTCGA\t1\n+TCCGCGCTTCCAGCCGCTCC\tTCCGCGCTTCCAGCCGCTCC\t1\n+TGTTCTTACCTGTGTTCGCG\tTGTTCTTACCTGTGTTCGCG\t1\n+TAGCCAGAAAACTTTACTCT\tTAGCCAGAAAACTTTACTCT\t1\n+CTCAAAATAGCGAGTTAAAA\tCTCAAAATAGCGAGTTAAAA\t5\n+CTCCAACCGTCCGTTATCAA\tCTCCAACCGTCCGTTATCAA\t2\n+CCGCGCACCACCGAGTCGGT\tCCGCGCACCACCGAGTCGGT\t3\n+TTTTGGGAGTACCGTGGACT\tTTTTGGGAGTACCGTGGACT\t1\n+AGTCCTGTCCCATGCGATTG\tAGTCCTGTCCCATGCGATTG\t1\n+CGCTGCCATCAACTTGAAAA\tCGCTGCCATCAACTTGAAAA\t6\n+CCTGCGTCCCGTGCAGGTGA\tCCTGCGTCCCGTGCAGGTGA\t1\n+GGGTAGTGACCCGTCCGTTA\tGGGTAGTGACCCGTCCGTTA\t2\n+CTTCAGTCCAAATGTAGCCG\tCTTCAGTCCAAATGTAGCCG\t1\n+CATGCCTCTTCATAGTTAAG\tCATGCCTCTTCATAGTTAAG\t1\n+TTCAGCAAGTTAAAATAAGG\tTTCAGCAAGTTAAAATAAGG\t6\n+CACGCTGACCCAGCCTATCG\tCACGCTGACCCAGCCTATCG\t1\n+TGCCGTCTTGGCGGGCCCCC\tTGCCGTCTTGGCGGGCCCCC\t1\n+CACGGTAACGGAGCGATTTG\tCACGGTAACGGAGCGATTTG\t1\n+TCCTCTCATGTGAAGTTATT\tTCCTCTCATGTGAAGTTATT\t1\n+CCAGCTTGTTCCTCTCCCCC\tCCAGCTTGTTCCTCTCCCCC\t1\n+GCTGTACCTGGAAAATCATG\tGCTGTACCTGGAAAATCATG\t1\n+TGCTTGGGCCGCTCCTCACA\tTGCTTGGGCCGCTCCTCACA\t1\n+GGGCAAGTCCGTTATCAACT\tGGGCAAGTCCGTTATCAACT\t4\n+GATGACACACCTGACCAGCC\tGATGACACACCTGACCAGCC\t1\n+TCTACATCTCCGACCACGTT\tTCTACATCTCCGACCACGTT\t1\n+CTGTCCGTTCTCAACTTGAA\tCTGTCCGTTCTCAACTTGAA\t4\n+GCAGAAGCGAGTAACATCGG\tGCAGAAGCGAGTAACATCGG\t1\n+GTGTCAATGGTCCATCGTTT\tGTGTCAATGGTCCATCGTTT\t1\n+TTATCGGCAGGCTATCCGTT\tTTATCGGCAGGCTATCCGTT\t3\n+CTGGAGTCACCCTACGTTGG\tCTGGAGTCACCCTACGTTGG\t1\n+TGCGTCAGTCGCCTACCTGT\tTGCGTCAGTCGCCTACCTGT\t1\n+GCTCACTCTCGCTCCTGTTT\tGCTCACTCTCGCTCCTGTTT\t1\n+CCAGTATTCCCACAATTTTA\tCCAGTATTCCCACAATTTTA\t1\n+CACTGTCCTGCACCGCCGTT\tCACTGTCCTGCACCGCCGTT\t1\n+AGATCATTGCTTTAGAGCTA\tAGATCATTGCTTTAGAGCTA\t1\n+CGATGACGTTACCGCAGCCG\tCGATGACGTTACCGCAGCCG\t1\n+ACCTTAATATTTGCCTCATC\tACCTTAATATTTGCCTCATC\t1\n+GCTGCGAGCCCGTTATCAAC\tGCTGCGAGCCCGTTATCAAC\t4\n+TCCGGACGGTCTGCACGTGT\tTCCGGACGGTCTGCACGTGT\t2\n+CCCGTTTTAGTCTCAGCCCC\tCCCGTTTTAGTCTCAGCCCC\t1\n+GCTGTAGATCCGTCCGTCAG\tGCTGTAGATCCGTCCGTCAG\t1\n+TCGCTGTTCTCCTCCGTTTT\tTCGCTGTTCTCCTCCGTTTT\t1\n+TTGCCCTACAGATGCCTTCT\tTTGCCCTACAGATGCCTTCT\t1\n+CCACGGTGTTCATGCATGTG\tCCACGGTGTTCATGCATGTG\t1\n+GATGGCATCAATGAATCGCG\tGATGGCATCAATGAATCGCG\t1\n+CGGAGGCTCAAACATCGCGT\tCGGAGGCTCAAACATCGCGT\t2\n+ATTCCTTATCCCACCATCTC\tATTCCTTATCCCACCATCTC\t1\n+GGTTTACAACTTGGAAAAGT\tGGTTTACAACTTGGAAAAGT\t1\n+GTCAGACCTAGTACCGCTAG\tGTCAGACCTAGTACCGCTAG\t1\n+CGTACGACCTGACAGCCAAG\tCGTACGACCTGACAGCCAAG\t1\n+GGCACGTTATCAACTTGAAA\tGGCACGTTATCAACTTGAAA\t5\n+TCACGACGCCGCCCCACTGG\tTCACGACGCCGCCCCACTGG\t1\n+CTATAACCACCTAGTACGTT\tCTATAACCACCTAGTACGTT\t1\n+CAACAAGCCATCAACGCCAG\tCAACAAGCCATCAACGCCAG\t1\n+TGACCAGCCACGCCCCTACA\tTGACCAGCCACGCCCCTACA\t1\n+TTGCAGGTCATTTGATCTTG\tTTGCAGGTCATTTGATCTTG\t1\n+TCGAAACCACAGATGTCCCT\tTCGAAACCACAGATGTCCCT\t1\n+TCTGTACGCGTGTTCCTTTG\tTCTGTACGCGTGTTCCTTTG\t1\n+CAGACACAGCGAGTCCGTTA\tCAGACACAGCGAGTCCGTTA\t2\n+ACCTGCAACGCTGCGCGCCG\tACCTGCAACGCTGCGCGCCG\t1\n+GCTCGAGCAGCACACATCAT\tGCTCGAGCAGCACACATCAT\t1\n+ACGGGCTTGCCTTGACAAGT\tACGGGCTTGCCTTGACAAGT\t1\n+TTTTCCGATTCCCGAGACCG\tTTTTCCGATTCCCGAGACCG\t1\n+CCGAGCGCATATGCCCAAGT\tCCGAGCGCATATGCCCAAGT\t1\n+AACCTTCAAAGGCCATCGTT\tAACCTTCAAAGGCCATCGTT\t1\n+ATATCGCTCTATTCTCCATG'..b'GAATAAACGTTGATA\tTAAGCGAATAAACGTTGATA\t1\n+CGACTCTTGGCCAATCCCCT\tCGACTCTTGGCCAATCCCCT\t1\n+GCACTCAGTGCGAAGTCAAG\tGCACTCAGTGCGAAGTCAAG\t1\n+ACACTGCGTGTCTCCCAGTT\tACACTGCGTGTCTCCCAGTT\t1\n+CCGTCCCACCCGACTTATTG\tCCGTCCCACCCGACTTATTG\t1\n+TGTCACAGTTCTCGCAGCAC\tTGTCACAGTTCTCGCAGCAC\t1\n+CGCCAGCATCGAAAGGTACG\tCGCCAGCATCGAAAGGTACG\t1\n+GCAGCCGTATCAACTTGAAA\tGCAGCCGTATCAACTTGAAA\t1\n+CAATGGCGGCAGTCGCGCTC\tCAATGGCGGCAGTCGCGCTC\t1\n+TTTACATGACTTCCAAGCGT\tTTTACATGACTTCCAAGCGT\t1\n+GTGTCCGTTCTCAACTTGAA\tGTGTCCGTTCTCAACTTGAA\t1\n+CATTGGGCATTAACATTTGT\tCATTGGGCATTAACATTTGT\t1\n+ACCGAACATGCGATCCTCCG\tACCGAACATGCGATCCTCCG\t1\n+GTTGCACGTAAACTTGCGCG\tGTTGCACGTAAACTTGCGCG\t1\n+TGCAAACTTACCTGGGGCTG\tTGCAAACTTACCTGGGGCTG\t1\n+CGGCATTCATGTACCTCCAG\tCGGCATTCATGTACCTCCAG\t1\n+TCTGGCAGGCCACCGTTTAG\tTCTGGCAGGCCACCGTTTAG\t1\n+TCCGTTTTTTCGAGTTTAGA\tTCCGTTTTTTCGAGTTTAGA\t1\n+TGCGATGCTGACGTTCTCAG\tTGCGATGCTGACGTTCTCAG\t1\n+TCGCCAAGAGGGCGCAATCG\tTCGCCAAGAGGGCGCAATCG\t1\n+TAACAGAGTTTGCCATGCTC\tTAACAGAGTTTGCCATGCTC\t1\n+CAGCGCTAGCAGACCAGGTT\tCAGCGCTAGCAGACCAGGTT\t1\n+CGTCACATCATTCAACTCCT\tCGTCACATCATTCAACTCCT\t1\n+AACGAAACACCTTCCGATGT\tAACGAAACACCTTCCGATGT\t1\n+TCACCCGCTCATCAAATCCG\tTCACCCGCTCATCAAATCCG\t1\n+CTGACCGCCCTTAGCGTTAG\tCTGACCGCCCTTAGCGTTAG\t1\n+AACACCTGTCAGCCGACTGT\tAACACCTGTCAGCCGACTGT\t1\n+AATTCCTCTAGAGCTAGAAA\tAATTCCTCTAGAGCTAGAAA\t1\n+TCCGGCAGCAGGTCTCGTAC\tTCCGGCAGCAGGTCTCGTAC\t1\n+ACCGGCAGAAGCCCCTGACG\tACCGGCAGAAGCCCCTGACG\t1\n+GCGCCCTGCGCTCCTTCCGC\tGCGCCCTGCGCTCCTTCCGC\t1\n+AACTACTGACGTCGCACTAG\tAACTACTGACGTCGCACTAG\t1\n+GCCCTGAGAGACACCGCCTG\tGCCCTGAGAGACACCGCCTG\t1\n+TTCAAGCAAGTTAAAATAAG\tTTCAAGCAAGTTAAAATAAG\t1\n+TGGGCACTGACCGTGGGCAG\tTGGGCACTGACCGTGGGCAG\t1\n+TGAAGTCCTGCGCGATCTCA\tTGAAGTCCTGCGCGATCTCA\t1\n+TCGCGACTACAGAGCCCCGG\tTCGCGACTACAGAGCCCCGG\t1\n+CAGCGCCATCTCGTAGGTTA\tCAGCGCCATCTCGTAGGTTA\t1\n+ACCTCCAGGCTGGTCCGTTA\tACCTCCAGGCTGGTCCGTTA\t1\n+AGCGACTACGACTCTGTTGT\tAGCGACTACGACTCTGTTGT\t1\n+TGAAGATTGAAAGTTAAAAT\tTGAAGATTGAAAGTTAAAAT\t1\n+CTTGTCTCAAATCAGCTACT\tCTTGTCTCAAATCAGCTACT\t1\n+GCGTTTTCATCCTGTCGCGT\tGCGTTTTCATCCTGTCGCGT\t1\n+ACTTGAGACAAGCTCTCGCG\tACTTGAGACAAGCTCTCGCG\t1\n+TCCAAAACTCCTTTACCAAG\tTCCAAAACTCCTTTACCAAG\t1\n+TGACCTCGACTGCTCTGACG\tTGACCTCGACTGCTCTGACG\t1\n+TCTTGTTCCGATACACCGAT\tTCTTGTTCCGATACACCGAT\t1\n+ACGCTTGAGCGACGAGACCG\tACGCTTGAGCGACGAGACCG\t1\n+ACGCCCAGCGCTCGTACACT\tACGCCCAGCGCTCGTACACT\t1\n+TTGCGAATGTTACCATCTCG\tTTGCGAATGTTACCATCTCG\t1\n+ATAACGTGATCACAGACATG\tATAACGTGATCACAGACATG\t1\n+ACGAGATGTCCCGCGCCAGG\tACGAGATGTCCCGCGCCAGG\t1\n+AACTCGCGATGCCATCTCCG\tAACTCGCGATGCCATCTCCG\t1\n+TGTTCTCCTGCGCCTGCACG\tTGTTCTCCTGCGCCTGCACG\t1\n+ACTTACCAACTACCATATGT\tACTTACCAACTACCATATGT\t1\n+AACCACTGCGTCCTTATCGT\tAACCACTGCGTCCTTATCGT\t1\n+CTGTGACCCATGCCTCCAAG\tCTGTGACCCATGCCTCCAAG\t1\n+TAGCTTACTCGAAATTCACG\tTAGCTTACTCGAAATTCACG\t1\n+GTGACTCCAGCTATCCAGGT\tGTGACTCCAGCTATCCAGGT\t1\n+TACTCACTCGGCAAACTTGG\tTACTCACTCGGCAAACTTGG\t1\n+CTTCAAGTTAAAATACGGCT\tCTTCAAGTTAAAATACGGCT\t1\n+ACCCCATCCTTTCATTGAGG\tACCCCATCCTTTCATTGAGG\t1\n+ACACCATTTAGAGCGTGTCT\tACACCATTTAGAGCGTGTCT\t1\n+TAGGCTTACCTAGTTTGCAC\tTAGGCTTACCTAGTTTGCAC\t1\n+CTCCAGAACCTGCCCAAGAA\tCTCCAGAACCTGCCCAAGAA\t1\n+TTTTCCAGCACTCGAATGCG\tTTTTCCAGCACTCGAATGCG\t1\n+TCCCGCGAGACGAGCTGCGT\tTCCCGCGAGACGAGCTGCGT\t1\n+CTCGTCGCAGCCCACAAGCA\tCTCGTCGCAGCCCACAAGCA\t1\n+CCCCCCCACTCTCAACGGGT\tCCCCCCCACTCTCAACGGGT\t1\n+TCTCTCCGCGCAGCAACTCA\tTCTCTCCGCGCAGCAACTCA\t1\n+GCTTACATAGCAAATCTATG\tGCTTACATAGCAAATCTATG\t1\n+TCTGGTGATCTCTCCCGAGT\tTCTGGTGATCTCTCCCGAGT\t1\n+CCGTATCCCCACTCTCATCA\tCCGTATCCCCACTCTCATCA\t1\n+ACATTTGTTCTGCAAAGACA\tACATTTGTTCTGCAAAGACA\t1\n+ATCATGTTTCTAAAGCCGCG\tATCATGTTTCTAAAGCCGCG\t1\n+TTCCAAAATACGACTTTACC\tTTCCAAAATACGACTTTACC\t1\n+ATCAGTTTTAGAGCTAGAAA\tATCAGTTTTAGAGCTAGAAA\t1\n+CCGTTCTCAACTTGAAAAAG\tCCGTTCTCAACTTGAAAAAG\t1\n+CTGCATATCTTCGAGATGCT\tCTGCATATCTTCGAGATGCT\t1\n+ACTTCGACACGACCTCTACG\tACTTCGACACGACCTCTACG\t1\n+CTCCTCGAAGGGCCGACACG\tCTCCTCGAAGGGCCGACACG\t1\n+TGTGTACAGCTCTCCTCCGT\tTGTGTACAGCTCTCCTCCGT\t1\n+CTTATAGTCAGCCTCAAAAG\tCTTATAGTCAGCCTCAAAAG\t1\n+TCCGCAGCCCTCCACACGTA\tTCCGCAGCCCTCCACACGTA\t1\n+CCCGATGATCTCGATGCCCG\tCCCGATGATCTCGATGCCCG\t1\n+TCTCCTATCAAGGCCATTCT\tTCTCCTATCAAGGCCATTCT\t1\n+AGGATCCTGAGACGTTCCTC\tAGGATCCTGAGACGTTCCTC\t1\n+TTCCCTATCAGTAGAAATAG\tTTCCCTATCAGTAGAAATAG\t1\n+CTGGTCTCGCCGGTAGCTAT\tCTGGTCTCGCCGGTAGCTAT\t1\n' |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.countsummary.pdf |
| b |
| Binary file test-data/out.countsummary.pdf has changed |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.countsummary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.countsummary.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| @@ -0,0 +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 |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.mageckGSEA.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.mageckGSEA.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| @@ -0,0 +1,2 @@ +Pathway Size ES p p_permutation FDR Ranking Hits LFC +KEGG_RIBOSOME 88 1 0 0 0 1 0 0 |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.mle.gene_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.mle.gene_summary.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| b'@@ -0,0 +1,101 @@\n+Gene\tsgRNA\tHL60|beta\tHL60|z\tHL60|p-value\tHL60|fdr\tHL60|wald-p-value\tHL60|wald-fdr\tKBM7|beta\tKBM7|z\tKBM7|p-value\tKBM7|fdr\tKBM7|wald-p-value\tKBM7|wald-fdr\n+A1CF\t10\t0.21726\t2.3501\t0.09\t0.098901\t0.018771\t0.045548\t0.22205\t2.4019\t0.11\t0.13258\t0.016311\t0.044445\n+AAAS\t10\t0.20562\t2.038\t0.108\t0.11368\t0.041547\t0.048311\t0.22245\t2.2047\t0.11\t0.13258\t0.027472\t0.044445\n+AAK1\t10\t0.25639\t2.1126\t0.054\t0.07\t0.034633\t0.045548\t0.31519\t2.5972\t0.026\t0.092857\t0.0093995\t0.044445\n+AATF\t10\t0.26019\t2.137\t0.048\t0.07\t0.032596\t0.045548\t0.17209\t1.4898\t0.202\t0.20612\t0.13627\t0.14195\n+AATK\t10\t0.37034\t2.5201\t0.012\t0.07\t0.011733\t0.045548\t0.32484\t2.2105\t0.024\t0.088889\t0.027074\t0.044445\n+ABCB8\t10\t0.25311\t2.4583\t0.054\t0.07\t0.013958\t0.045548\t0.2626\t2.5505\t0.058\t0.10345\t0.010756\t0.044445\n+ABCC1\t10\t0.20905\t2.0722\t0.106\t0.11277\t0.038249\t0.045548\t0.2381\t2.3602\t0.086\t0.10886\t0.018265\t0.044445\n+ABCF1\t10\t0.26857\t2.0808\t0.046\t0.07\t0.037453\t0.045548\t0.2407\t1.8649\t0.082\t0.10886\t0.062201\t0.069889\n+ABHD14B\t10\t0.25291\t2.1394\t0.054\t0.07\t0.032402\t0.045548\t0.24531\t2.0751\t0.076\t0.10857\t0.037979\t0.049559\n+ABI1\t10\t0.28136\t2.2952\t0.038\t0.07\t0.021724\t0.045548\t0.23619\t1.9267\t0.086\t0.10886\t0.054023\t0.062096\n+ABL1\t10\t0.35653\t2.8826\t0.014\t0.07\t0.0039444\t0.045548\t0.19033\t1.5389\t0.172\t0.17938\t0.12383\t0.13174\n+ABL2\t10\t0.31786\t2.537\t0.026\t0.07\t0.011181\t0.045548\t0.28849\t2.3026\t0.044\t0.096154\t0.0213\t0.044445\n+ABLIM2\t10\t0.33199\t2.1246\t0.024\t0.07\t0.033624\t0.045548\t0.35781\t2.2898\t0.016\t0.088889\t0.022035\t0.044445\n+ABT1\t10\t0.64492\t1.2807\t0\t0\t0.20031\t0.20031\t0.56048\t1.113\t0\t0\t0.26572\t0.26572\n+ABTB1\t10\t0.25881\t2.2156\t0.048\t0.07\t0.026717\t0.045548\t0.27981\t2.3954\t0.048\t0.096154\t0.016601\t0.044445\n+ACAD11\t10\t0.2457\t2.1273\t0.056\t0.07\t0.033397\t0.045548\t0.26753\t2.3163\t0.052\t0.098113\t0.020539\t0.044445\n+ACAD9\t10\t0.28033\t2.3396\t0.038\t0.07\t0.019306\t0.045548\t0.23942\t1.9982\t0.084\t0.10886\t0.045699\t0.055059\n+ACAT2\t10\t0.33017\t1.9472\t0.024\t0.07\t0.051509\t0.056401\t0.34801\t2.0524\t0.016\t0.088889\t0.040129\t0.049805\n+ACBD6\t10\t0.26005\t2.4829\t0.048\t0.07\t0.013031\t0.045548\t0.22982\t2.1942\t0.094\t0.1175\t0.028219\t0.044707\n+ACD\t10\t0.29956\t2.263\t0.028\t0.07\t0.023633\t0.045548\t0.30306\t2.2895\t0.036\t0.096154\t0.022052\t0.044445\n+ACHE\t10\t0.26039\t1.9394\t0.048\t0.07\t0.052453\t0.056401\t0.27459\t2.0451\t0.05\t0.096154\t0.04084\t0.049805\n+ACIN1\t10\t0.24992\t1.6773\t0.054\t0.07\t0.093484\t0.097379\t0.16332\t1.1553\t0.222\t0.22424\t0.24796\t0.25047\n+ACLY\t10\t0.64139\t1.3277\t0\t0\t0.18428\t0.18614\t0.56404\t1.1676\t0\t0\t0.24298\t0.24794\n+ACO2\t10\t0.26736\t2.3551\t0.048\t0.07\t0.018518\t0.045548\t0.24404\t2.1496\t0.078\t0.10886\t0.031586\t0.045123\n+ACP1\t10\t0.30066\t2.0818\t0.028\t0.07\t0.037363\t0.045548\t0.32268\t2.2343\t0.024\t0.088889\t0.025465\t0.044445\n+ACRC\t10\t0.316\t2.1738\t0.026\t0.07\t0.029722\t0.045548\t0.32721\t2.2508\t0.024\t0.088889\t0.024396\t0.044445\n+ACSL6\t10\t0.30715\t2.5085\t0.028\t0.07\t0.012125\t0.045548\t0.27154\t2.2176\t0.05\t0.096154\t0.026579\t0.044445\n+ACSS2\t10\t0.27125\t2.396\t0.044\t0.07\t0.016573\t0.045548\t0.31578\t2.7894\t0.024\t0.088889\t0.0052812\t0.044445\n+ACTL6A\t10\t0.23154\t2.2408\t0.072\t0.085714\t0.025038\t0.045548\t0.20097\t1.945\t0.138\t0.14681\t0.051771\t0.060199\n+ACTL6B\t10\t0.30195\t2.3158\t0.028\t0.07\t0.020569\t0.045548\t0.29791\t2.2849\t0.036\t0.096154\t0.02232\t0.044445\n+ACTL7A\t10\t0.22531\t2.1897\t0.078\t0.089655\t0.028544\t0.045548\t0.2423\t2.3549\t0.082\t0.10886\t0.018527\t0.044445\n+ACTN1\t10\t0.30451\t2.4532\t0.028\t0.07\t0.014161\t0.045548\t0.27462\t2.2124\t0.05\t0.096154\t0.026942\t0.044445\n+ACTN4\t10\t0.3039\t2.2464\t0.028\t0.07\t0.024679\t0.045548\t0.33156\t2.4509\t0.022\t0.088889\t0.01425\t0.044445\n+ACTR1A\t10\t0.28127\t2.1093\t0.038\t0.07\t0.034915\t0.045548\t0.30952\t2.3212\t0.028\t0.093333\t0.020274\t0.044445\n+ACTR3\t10\t0.28223\t2.1469\t0.038\t0.07\t0.031799\t0.045548\t0.25252\t1.9209\t0.068\t0.10462\t0.054741\t0.062206\n+ACTR5\t10\t0.2754\t2.7989\t0.04\t0.07\t0.0051271\t0.045548\t0.20514\t2.0849\t0.136\t0.14624\t0.037074\t0.049433\n+ACTR8\t10\t0.23674\t1.6117\t0.06\t0.074074\t0.10703\t0.10922\t0.21097\t1.4362\t0.122\t0.13407\t0.15095\t0.15562\n+ACTRT3\t10\t0.2132\t1.984\t0.096\t0.10435\t0.047252\t0.053696\t0.25182\t2.3435\t0.068\t0.10462\t0.019105\t0.044445\n+ACVR1B\t10\t0.28652\t2.2884\t0.034\t0.'..b'028\t0.07\t0.037665\t0.045548\t0.3371\t2.2368\t0.02\t0.088889\t0.025302\t0.044445\n+ADH7\t10\t0.23185\t2.1764\t0.072\t0.085714\t0.029529\t0.045548\t0.25313\t2.3761\t0.068\t0.10462\t0.017497\t0.044445\n+ADI1\t10\t0.26344\t2.2066\t0.048\t0.07\t0.027345\t0.045548\t0.2966\t2.4843\t0.038\t0.096154\t0.012981\t0.044445\n+ADIRF\t10\t0.23157\t2.1952\t0.072\t0.085714\t0.028148\t0.045548\t0.21758\t2.0626\t0.118\t0.13258\t0.039152\t0.049559\n+ADK\t10\t0.25823\t2.3541\t0.05\t0.07\t0.018569\t0.045548\t0.25466\t2.3215\t0.066\t0.10462\t0.020258\t0.044445\n+ADNP2\t10\t0.19944\t2.0931\t0.12\t0.12245\t0.036336\t0.045548\t0.25778\t2.7054\t0.06\t0.10345\t0.0068216\t0.044445\n+ADNP\t10\t0.33596\t1.9412\t0.024\t0.07\t0.052236\t0.056401\t0.44376\t2.5641\t0\t0\t0.010346\t0.044445\n+ADPRHL2\t10\t0.26332\t2.3044\t0.048\t0.07\t0.021202\t0.045548\t0.27219\t2.382\t0.05\t0.096154\t0.017218\t0.044445\n+ADRA1A\t10\t0.26321\t2.4075\t0.048\t0.07\t0.016062\t0.045548\t0.24245\t2.2176\t0.08\t0.10886\t0.026583\t0.044445\n+ADRA1B\t10\t0.26869\t2.4689\t0.046\t0.07\t0.013554\t0.045548\t0.24756\t2.2747\t0.076\t0.10857\t0.022923\t0.044445\n+ADRB1\t10\t0.26113\t2.1522\t0.048\t0.07\t0.031385\t0.045548\t0.25076\t2.0666\t0.068\t0.10462\t0.038768\t0.049559\n+ADRB2\t10\t0.3434\t2.0721\t0.018\t0.07\t0.038261\t0.045548\t0.32418\t1.9561\t0.024\t0.088889\t0.050457\t0.059361\n+ADRB3\t10\t0.27356\t2.3431\t0.042\t0.07\t0.019123\t0.045548\t0.26345\t2.1408\t0.056\t0.10345\t0.032287\t0.045408\n+ADRBK1\t10\t0.39621\t2.5298\t0.006\t0.07\t0.011414\t0.045548\t0.38361\t2.4493\t0.004\t0.057143\t0.014314\t0.044445\n+ADRBK2\t10\t0.311\t2.4196\t0.028\t0.07\t0.015537\t0.045548\t0.30224\t2.3515\t0.036\t0.096154\t0.018698\t0.044445\n+ADRM1\t10\t0.19795\t2.0633\t0.12\t0.12245\t0.039089\t0.045987\t0.21217\t2.2114\t0.122\t0.13407\t0.027005\t0.044445\n+AEBP1\t10\t0.30109\t2.094\t0.028\t0.07\t0.036256\t0.045548\t0.31995\t2.2252\t0.024\t0.088889\t0.026067\t0.044445\n+AEBP2\t10\t0.25078\t2.3902\t0.054\t0.07\t0.016839\t0.045548\t0.25977\t2.4758\t0.06\t0.10345\t0.013293\t0.044445\n+AEN\t10\t0.31767\t2.5501\t0.026\t0.07\t0.010771\t0.045548\t0.21703\t1.7422\t0.118\t0.13258\t0.081467\t0.089524\n+AES\t10\t0.27613\t2.5026\t0.04\t0.07\t0.01233\t0.045548\t0.28435\t2.5771\t0.048\t0.096154\t0.0099638\t0.044445\n+AFAP1L2\t10\t0.27787\t2.5825\t0.038\t0.07\t0.0098091\t0.045548\t0.25248\t2.3465\t0.068\t0.10462\t0.018949\t0.044445\n+AFF1\t10\t0.24186\t2.0236\t0.056\t0.07\t0.043007\t0.049434\t0.28577\t2.391\t0.044\t0.096154\t0.0168\t0.044445\n+AFF2\t10\t0.22079\t1.9621\t0.086\t0.095556\t0.049749\t0.055889\t0.28962\t2.5737\t0.044\t0.096154\t0.010061\t0.044445\n+AFF3\t10\t0.22476\t2.1578\t0.078\t0.089655\t0.030942\t0.045548\t0.21756\t2.0887\t0.118\t0.13258\t0.03673\t0.049433\n+AFF4\t10\t0.31149\t2.1142\t0.028\t0.07\t0.034496\t0.045548\t0.3627\t2.4618\t0.012\t0.088889\t0.013825\t0.044445\n+AFMID\t10\t0.22778\t2.1955\t0.078\t0.089655\t0.02813\t0.045548\t0.22159\t2.1358\t0.112\t0.13258\t0.032694\t0.045408\n+AFTPH\t10\t0.25053\t2.1997\t0.054\t0.07\t0.027828\t0.045548\t0.24929\t2.1888\t0.072\t0.10746\t0.028613\t0.044707\n+AGAP2\t10\t0.3135\t2.4258\t0.028\t0.07\t0.015274\t0.045548\t0.27805\t2.1516\t0.048\t0.096154\t0.031432\t0.045123\n+AGAP3\t10\t0.27682\t2.4409\t0.04\t0.07\t0.01465\t0.045548\t0.31626\t2.7887\t0.024\t0.088889\t0.0052921\t0.044445\n+AGBL5\t10\t0.18851\t1.7706\t0.146\t0.14747\t0.076634\t0.080668\t0.25487\t2.3938\t0.066\t0.10462\t0.016673\t0.044445\n+AGFG1\t10\t0.26133\t2.2912\t0.048\t0.07\t0.021954\t0.045548\t0.24813\t2.0639\t0.074\t0.10857\t0.039025\t0.049559\n+AGL\t10\t0.65242\t1.6625\t0\t0\t0.096417\t0.099399\t0.60099\t1.5314\t0\t0\t0.12566\t0.13228\n+AGPAT3\t10\t0.20246\t2.1377\t0.112\t0.11667\t0.03254\t0.045548\t0.18609\t1.9649\t0.174\t0.17938\t0.049424\t0.058838\n+AGPAT5\t10\t0.32784\t1.8786\t0.024\t0.07\t0.060303\t0.064152\t0.31917\t1.8289\t0.024\t0.088889\t0.067418\t0.074909\n+AGTPBP1\t10\t0.25153\t2.1735\t0.054\t0.07\t0.029741\t0.045548\t0.29805\t2.5755\t0.036\t0.096154\t0.01001\t0.044445\n+AHCTF1\t10\t0.24987\t2.2694\t0.054\t0.07\t0.023245\t0.045548\t0.18875\t1.7143\t0.174\t0.17938\t0.086471\t0.09399\n+AHCY\t10\t0.25511\t1.9574\t0.054\t0.07\t0.0503\t0.055889\t0.20591\t1.5799\t0.136\t0.14624\t0.11413\t0.12272\n+AHNAK2\t10\t0.27116\t2.5067\t0.044\t0.07\t0.012185\t0.045548\t0.27693\t2.5601\t0.048\t0.096154\t0.010466\t0.044445\n+AHNAK\t10\t0.22102\t2.4775\t0.084\t0.094382\t0.01323\t0.045548\t0.21459\t2.4055\t0.118\t0.13258\t0.016151\t0.044445\n+AHRR\t9\t0.19687\t2.5399\t0.15\t0.15\t0.011087\t0.045548\t0.18565\t2.2584\t0.226\t0.226\t0.023923\t0.044445\n' |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.mle.log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.mle.log.txt Wed Feb 14 06:42:18 2018 -0500 |
| [ |
| b'@@ -0,0 +1,749 @@\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: A'..b'1:49:12: Collecting 999 sgRNAs from 100 genes. \n+INFO @ Mon, 12 Feb 2018 21:49:12: Permuting round 0 ... \n+INFO @ Mon, 12 Feb 2018 21:49:12: Thread 0 started. \n+INFO @ Mon, 12 Feb 2018 21:49:12: Thread 0: total 100 instances. \n+INFO @ Mon, 12 Feb 2018 21:49:12: Thread 0: Calculating AAAS (1) ... \n+INFO @ Mon, 12 Feb 2018 21:49:13: Thread 0 completed. \n+INFO @ Mon, 12 Feb 2018 21:49:13: All threads completed. \n+INFO @ Mon, 12 Feb 2018 21:49:13: Permuting round 1 ... \n+INFO @ Mon, 12 Feb 2018 21:49:13: Thread 0 started. \n+INFO @ Mon, 12 Feb 2018 21:49:13: Thread 0: total 100 instances. \n+INFO @ Mon, 12 Feb 2018 21:49:13: Thread 0: Calculating AAAS (1) ... \n+INFO @ Mon, 12 Feb 2018 21:49:14: Thread 0 completed. \n+INFO @ Mon, 12 Feb 2018 21:49:14: All threads completed. \n+INFO @ Mon, 12 Feb 2018 21:49:14: Permuting round 2 ... \n+INFO @ Mon, 12 Feb 2018 21:49:14: Thread 0 started. \n+INFO @ Mon, 12 Feb 2018 21:49:14: Thread 0: total 100 instances. \n+INFO @ Mon, 12 Feb 2018 21:49:14: Thread 0: Calculating AAAS (1) ... \n+INFO @ Mon, 12 Feb 2018 21:49:15: Thread 0 completed. \n+INFO @ Mon, 12 Feb 2018 21:49:15: All threads completed. \n+INFO @ Mon, 12 Feb 2018 21:49:15: Permuting round 3 ... \n+INFO @ Mon, 12 Feb 2018 21:49:15: Thread 0 started. \n+INFO @ Mon, 12 Feb 2018 21:49:15: Thread 0: total 100 instances. \n+INFO @ Mon, 12 Feb 2018 21:49:15: Thread 0: Calculating AAAS (1) ... \n+INFO @ Mon, 12 Feb 2018 21:49:16: Thread 0 completed. \n+INFO @ Mon, 12 Feb 2018 21:49:16: All threads completed. \n+INFO @ Mon, 12 Feb 2018 21:49:16: Permuting round 4 ... \n+INFO @ Mon, 12 Feb 2018 21:49:16: Thread 0 started. \n+INFO @ Mon, 12 Feb 2018 21:49:16: Thread 0: total 100 instances. \n+INFO @ Mon, 12 Feb 2018 21:49:16: Thread 0: Calculating AAAS (1) ... \n+INFO @ Mon, 12 Feb 2018 21:49:16: Thread 0 completed. \n+INFO @ Mon, 12 Feb 2018 21:49:16: All threads completed. \n+INFO @ Mon, 12 Feb 2018 21:49:17: Permuting round 5 ... \n+INFO @ Mon, 12 Feb 2018 21:49:17: Thread 0 started. \n+INFO @ Mon, 12 Feb 2018 21:49:17: Thread 0: total 100 instances. \n+INFO @ Mon, 12 Feb 2018 21:49:17: Thread 0: Calculating AAAS (1) ... \n+INFO @ Mon, 12 Feb 2018 21:49:17: Thread 0 completed. \n+INFO @ Mon, 12 Feb 2018 21:49:17: All threads completed. \n+INFO @ Mon, 12 Feb 2018 21:49:18: Permuting round 6 ... \n+INFO @ Mon, 12 Feb 2018 21:49:18: Thread 0 started. \n+INFO @ Mon, 12 Feb 2018 21:49:18: Thread 0: total 100 instances. \n+INFO @ Mon, 12 Feb 2018 21:49:18: Thread 0: Calculating AAAS (1) ... \n+INFO @ Mon, 12 Feb 2018 21:49:19: Thread 0 completed. \n+INFO @ Mon, 12 Feb 2018 21:49:19: All threads completed. \n+INFO @ Mon, 12 Feb 2018 21:49:19: Permuting round 7 ... \n+INFO @ Mon, 12 Feb 2018 21:49:19: Thread 0 started. \n+INFO @ Mon, 12 Feb 2018 21:49:19: Thread 0: total 100 instances. \n+INFO @ Mon, 12 Feb 2018 21:49:19: Thread 0: Calculating AAAS (1) ... \n+INFO @ Mon, 12 Feb 2018 21:49:20: Thread 0 completed. \n+INFO @ Mon, 12 Feb 2018 21:49:20: All threads completed. \n+INFO @ Mon, 12 Feb 2018 21:49:20: Permuting round 8 ... \n+INFO @ Mon, 12 Feb 2018 21:49:20: Thread 0 started. \n+INFO @ Mon, 12 Feb 2018 21:49:20: Thread 0: total 100 instances. \n+INFO @ Mon, 12 Feb 2018 21:49:20: Thread 0: Calculating AAAS (1) ... \n+INFO @ Mon, 12 Feb 2018 21:49:21: Thread 0 completed. \n+INFO @ Mon, 12 Feb 2018 21:49:21: All threads completed. \n+INFO @ Mon, 12 Feb 2018 21:49:21: Permuting round 9 ... \n+INFO @ Mon, 12 Feb 2018 21:49:21: Thread 0 started. \n+INFO @ Mon, 12 Feb 2018 21:49:21: Thread 0: total 100 instances. \n+INFO @ Mon, 12 Feb 2018 21:49:21: Thread 0: Calculating AAAS (1) ... \n+INFO @ Mon, 12 Feb 2018 21:49:21: Thread 0 completed. \n+INFO @ Mon, 12 Feb 2018 21:49:21: All threads completed. \n+INFO @ Mon, 12 Feb 2018 21:49:22: Assigning p values... \n+INFO @ Mon, 12 Feb 2018 21:49:22: Writing gene results to output.gene_summary.txt \n+INFO @ Mon, 12 Feb 2018 21:49:22: Writing sgRNA results to output.sgrna_summary.txt \n' |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.mle.sgrna_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.mle.sgrna_summary.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| b'@@ -0,0 +1,1000 @@\n+Gene\tsgRNA\teff\n+A1CF\tA1CF_m52595977\t1\n+A1CF\tA1CF_m52596017\t1\n+A1CF\tA1CF_m52596056\t1\n+A1CF\tA1CF_m52603842\t1\n+A1CF\tA1CF_m52603847\t1\n+A1CF\tA1CF_p52595870\t1\n+A1CF\tA1CF_p52595881\t1\n+A1CF\tA1CF_p52596023\t1\n+A1CF\tA1CF_p52601638\t1\n+A1CF\tA1CF_p52603829\t1\n+AAAS\tAAAS_m53714382\t1\n+AAAS\tAAAS_m53715169\t1\n+AAAS\tAAAS_m53715176\t1\n+AAAS\tAAAS_m53715212\t1\n+AAAS\tAAAS_m53715238\t1\n+AAAS\tAAAS_p53714367\t1\n+AAAS\tAAAS_p53714374\t1\n+AAAS\tAAAS_p53714391\t1\n+AAAS\tAAAS_p53714405\t1\n+AAAS\tAAAS_p53714441\t1\n+AAK1\tAAK1_m69870049\t1\n+AAK1\tAAK1_m69870056\t1\n+AAK1\tAAK1_m69870103\t1\n+AAK1\tAAK1_m69870119\t1\n+AAK1\tAAK1_m69870125\t1\n+AAK1\tAAK1_m69870131\t1\n+AAK1\tAAK1_m69870137\t1\n+AAK1\tAAK1_p69870063\t1\n+AAK1\tAAK1_p69870070\t1\n+AAK1\tAAK1_p69870105\t1\n+AATF\tAATF_m35306444\t1\n+AATF\tAATF_m35306475\t1\n+AATF\tAATF_m35306482\t1\n+AATF\tAATF_m35306509\t1\n+AATF\tAATF_m35307516\t1\n+AATF\tAATF_m35307525\t1\n+AATF\tAATF_p35306410\t1\n+AATF\tAATF_p35306466\t1\n+AATF\tAATF_p35307505\t1\n+AATF\tAATF_p35307527\t1\n+AATK\tAATK_m79102275\t1\n+AATK\tAATK_m79102281\t1\n+AATK\tAATK_m79102298\t1\n+AATK\tAATK_m79102320\t1\n+AATK\tAATK_m79102325\t1\n+AATK\tAATK_p79102286\t1\n+AATK\tAATK_p79102311\t1\n+AATK\tAATK_p79104850\t1\n+AATK\tAATK_p79104858\t1\n+AATK\tAATK_p79104864\t1\n+ABCB8\tABCB8_m150725643\t1\n+ABCB8\tABCB8_m150725669\t1\n+ABCB8\tABCB8_m150730720\t1\n+ABCB8\tABCB8_p150725600\t1\n+ABCB8\tABCB8_p150725605\t1\n+ABCB8\tABCB8_p150725612\t1\n+ABCB8\tABCB8_p150725675\t1\n+ABCB8\tABCB8_p150730680\t1\n+ABCB8\tABCB8_p150730705\t1\n+ABCB8\tABCB8_p150730712\t1\n+ABCC1\tABCC1_m16043636\t1\n+ABCC1\tABCC1_m16043645\t1\n+ABCC1\tABCC1_m16101705\t1\n+ABCC1\tABCC1_m16101777\t1\n+ABCC1\tABCC1_m16101788\t1\n+ABCC1\tABCC1_m16101799\t1\n+ABCC1\tABCC1_p16043597\t1\n+ABCC1\tABCC1_p16101667\t1\n+ABCC1\tABCC1_p16101710\t1\n+ABCC1\tABCC1_p16101721\t1\n+ABCF1\tABCF1_m30539291\t1\n+ABCF1\tABCF1_p30539251\t1\n+ABCF1\tABCF1_p30539272\t1\n+ABCF1\tABCF1_p30545181\t1\n+ABCF1\tABCF1_p30545587\t1\n+ABCF1\tABCF1_p30545605\t1\n+ABCF1\tABCF1_p30545610\t1\n+ABCF1\tABCF1_p30545638\t1\n+ABCF1\tABCF1_p30545878\t1\n+ABCF1\tABCF1_p30545888\t1\n+ABHD14B\tABHD14B_m52004073\t1\n+ABHD14B\tABHD14B_m52004106\t1\n+ABHD14B\tABHD14B_m52004113\t1\n+ABHD14B\tABHD14B_m52004122\t1\n+ABHD14B\tABHD14B_p52004005\t1\n+ABHD14B\tABHD14B_p52004011\t1\n+ABHD14B\tABHD14B_p52004019\t1\n+ABHD14B\tABHD14B_p52004061\t1\n+ABHD14B\tABHD14B_p52004076\t1\n+ABHD14B\tABHD14B_p52004124\t1\n+ABI1\tABI1_m27149710\t1\n+ABI1\tABI1_m27149743\t1\n+ABI1\tABI1_m27149751\t1\n+ABI1\tABI1_m27149764\t1\n+ABI1\tABI1_p27112164\t1\n+ABI1\tABI1_p27112174\t1\n+ABI1\tABI1_p27112180\t1\n+ABI1\tABI1_p27149695\t1\n+ABI1\tABI1_p27149701\t1\n+ABI1\tABI1_p27149733\t1\n+ABL1\tABL1_m133729449\t1\n+ABL1\tABL1_m133729456\t1\n+ABL1\tABL1_m133729467\t1\n+ABL1\tABL1_m133729488\t1\n+ABL1\tABL1_m133729532\t1\n+ABL1\tABL1_m133729594\t1\n+ABL1\tABL1_p133729441\t1\n+ABL1\tABL1_p133729469\t1\n+ABL1\tABL1_p133729492\t1\n+ABL1\tABL1_p133729502\t1\n+ABL2\tABL2_m179100447\t1\n+ABL2\tABL2_m179100544\t1\n+ABL2\tABL2_m179100554\t1\n+ABL2\tABL2_m179100597\t1\n+ABL2\tABL2_p179095768\t1\n+ABL2\tABL2_p179100489\t1\n+ABL2\tABL2_p179100503\t1\n+ABL2\tABL2_p179100524\t1\n+ABL2\tABL2_p179100556\t1\n+ABL2\tABL2_p179100578\t1\n+ABLIM2\tABLIM2_m8108265\t1\n+ABLIM2\tABLIM2_m8108274\t1\n+ABLIM2\tABLIM2_m8108279\t1\n+ABLIM2\tABLIM2_m8108294\t1\n+ABLIM2\tABLIM2_m8108316\t1\n+ABLIM2\tABLIM2_m8160405\t1\n+ABLIM2\tABLIM2_p8108286\t1\n+ABLIM2\tABLIM2_p8108299\t1\n+ABLIM2\tABLIM2_p8108320\t1\n+ABLIM2\tABLIM2_p8108331\t1\n+ABT1\tABT1_m26597238\t1\n+ABT1\tABT1_m26597359\t1\n+ABT1\tABT1_m26597388\t1\n+ABT1\tABT1_p26597221\t1\n+ABT1\tABT1_p26597240\t1\n+ABT1\tABT1_p26597266\t1\n+ABT1\tABT1_p26597293\t1\n+ABT1\tABT1_p26597300\t1\n+ABT1\tABT1_p26597313\t1\n+ABT1\tABT1_p26597361\t1\n+ABTB1\tABTB1_m127395233\t1\n+ABTB1\tABTB1_m127395403\t1\n+ABTB1\tABTB1_m127395808\t1\n+ABTB1\tABTB1_m127395813\t1\n+ABTB1\tABTB1_m127395855\t1\n+ABTB1\tABTB1_m127395860\t1\n+ABTB1\tABTB1_p127395220\t1\n+ABTB1\tABTB1_p127395242\t1\n+ABTB1\tABTB1_p127395252\t1\n+ABTB1\tABTB1_p127395834\t1\n+ACAD11\tACAD11_m132378487\t1\n+ACAD11\tACAD11_m132378519\t1\n+ACAD11\tACAD11_m132378564\t1\n+ACAD11\tACAD11_m132378578\t1\n+ACAD11\tACAD11_p132378460\t1\n+ACAD11\tACAD11_p132378489\t1\n+ACAD11\tACAD11_p132378501\t1\n+ACAD11\tACAD11_p132378525\t1\n+ACAD11\tACAD11_p132378547\t1\n+ACAD11\tACAD11_p132378566\t1\n+ACAD9\tACAD9_m128598565\t'..b'AFF4_m132272826\t1\n+AFF4\tAFF4_m132272833\t1\n+AFF4\tAFF4_m132272841\t1\n+AFF4\tAFF4_m132272866\t1\n+AFF4\tAFF4_p132272747\t1\n+AFF4\tAFF4_p132272762\t1\n+AFF4\tAFF4_p132272771\t1\n+AFF4\tAFF4_p132272844\t1\n+AFF4\tAFF4_p132272853\t1\n+AFMID\tAFMID_m76183481\t1\n+AFMID\tAFMID_m76183493\t1\n+AFMID\tAFMID_m76187074\t1\n+AFMID\tAFMID_m76187079\t1\n+AFMID\tAFMID_p76183445\t1\n+AFMID\tAFMID_p76183450\t1\n+AFMID\tAFMID_p76183465\t1\n+AFMID\tAFMID_p76183473\t1\n+AFMID\tAFMID_p76187060\t1\n+AFMID\tAFMID_p76187082\t1\n+AFTPH\tAFTPH_m64778617\t1\n+AFTPH\tAFTPH_m64778646\t1\n+AFTPH\tAFTPH_m64778724\t1\n+AFTPH\tAFTPH_m64778773\t1\n+AFTPH\tAFTPH_m64778841\t1\n+AFTPH\tAFTPH_m64778905\t1\n+AFTPH\tAFTPH_p64778649\t1\n+AFTPH\tAFTPH_p64778713\t1\n+AFTPH\tAFTPH_p64778754\t1\n+AFTPH\tAFTPH_p64778890\t1\n+AGAP2\tAGAP2_m58128438\t1\n+AGAP2\tAGAP2_m58128444\t1\n+AGAP2\tAGAP2_m58128454\t1\n+AGAP2\tAGAP2_m58129187\t1\n+AGAP2\tAGAP2_m58129192\t1\n+AGAP2\tAGAP2_p58128423\t1\n+AGAP2\tAGAP2_p58129143\t1\n+AGAP2\tAGAP2_p58129148\t1\n+AGAP2\tAGAP2_p58129153\t1\n+AGAP2\tAGAP2_p58129171\t1\n+AGAP3\tAGAP3_m150784003\t1\n+AGAP3\tAGAP3_p150783818\t1\n+AGAP3\tAGAP3_p150783825\t1\n+AGAP3\tAGAP3_p150783857\t1\n+AGAP3\tAGAP3_p150783866\t1\n+AGAP3\tAGAP3_p150783903\t1\n+AGAP3\tAGAP3_p150783915\t1\n+AGAP3\tAGAP3_p150783972\t1\n+AGAP3\tAGAP3_p150784007\t1\n+AGAP3\tAGAP3_p150784015\t1\n+AGBL5\tAGBL5_m27275887\t1\n+AGBL5\tAGBL5_m27275950\t1\n+AGBL5\tAGBL5_m27275975\t1\n+AGBL5\tAGBL5_m27276001\t1\n+AGBL5\tAGBL5_m27276006\t1\n+AGBL5\tAGBL5_p27275820\t1\n+AGBL5\tAGBL5_p27275854\t1\n+AGBL5\tAGBL5_p27275870\t1\n+AGBL5\tAGBL5_p27275876\t1\n+AGBL5\tAGBL5_p27275898\t1\n+AGFG1\tAGFG1_m228337138\t1\n+AGFG1\tAGFG1_m228337178\t1\n+AGFG1\tAGFG1_m228337201\t1\n+AGFG1\tAGFG1_m228337208\t1\n+AGFG1\tAGFG1_m228337217\t1\n+AGFG1\tAGFG1_m228337248\t1\n+AGFG1\tAGFG1_m228337276\t1\n+AGFG1\tAGFG1_p228337142\t1\n+AGFG1\tAGFG1_p228337168\t1\n+AGFG1\tAGFG1_p228337221\t1\n+AGL\tAGL_m100327112\t1\n+AGL\tAGL_m100327128\t1\n+AGL\tAGL_m100327135\t1\n+AGL\tAGL_m100327186\t1\n+AGL\tAGL_m100327263\t1\n+AGL\tAGL_p100327060\t1\n+AGL\tAGL_p100327074\t1\n+AGL\tAGL_p100327114\t1\n+AGL\tAGL_p100327219\t1\n+AGL\tAGL_p100327246\t1\n+AGPAT3\tAGPAT3_m45379563\t1\n+AGPAT3\tAGPAT3_m45379570\t1\n+AGPAT3\tAGPAT3_m45379578\t1\n+AGPAT3\tAGPAT3_m45379590\t1\n+AGPAT3\tAGPAT3_m45379606\t1\n+AGPAT3\tAGPAT3_p45379552\t1\n+AGPAT3\tAGPAT3_p45379592\t1\n+AGPAT3\tAGPAT3_p45379613\t1\n+AGPAT3\tAGPAT3_p45379618\t1\n+AGPAT3\tAGPAT3_p45379648\t1\n+AGPAT5\tAGPAT5_m6566202\t1\n+AGPAT5\tAGPAT5_m6566212\t1\n+AGPAT5\tAGPAT5_m6566223\t1\n+AGPAT5\tAGPAT5_m6566233\t1\n+AGPAT5\tAGPAT5_m6566240\t1\n+AGPAT5\tAGPAT5_m6566254\t1\n+AGPAT5\tAGPAT5_m6566307\t1\n+AGPAT5\tAGPAT5_p6566182\t1\n+AGPAT5\tAGPAT5_p6566257\t1\n+AGPAT5\tAGPAT5_p6566262\t1\n+AGTPBP1\tAGTPBP1_m88296213\t1\n+AGTPBP1\tAGTPBP1_m88296222\t1\n+AGTPBP1\tAGTPBP1_m88307605\t1\n+AGTPBP1\tAGTPBP1_m88307687\t1\n+AGTPBP1\tAGTPBP1_m88307696\t1\n+AGTPBP1\tAGTPBP1_p88296203\t1\n+AGTPBP1\tAGTPBP1_p88307644\t1\n+AGTPBP1\tAGTPBP1_p88307675\t1\n+AGTPBP1\tAGTPBP1_p88307700\t1\n+AGTPBP1\tAGTPBP1_p88307705\t1\n+AHCTF1\tAHCTF1_m247067252\t1\n+AHCTF1\tAHCTF1_m247068844\t1\n+AHCTF1\tAHCTF1_m247068867\t1\n+AHCTF1\tAHCTF1_m247068886\t1\n+AHCTF1\tAHCTF1_m247068945\t1\n+AHCTF1\tAHCTF1_m247070906\t1\n+AHCTF1\tAHCTF1_m247070995\t1\n+AHCTF1\tAHCTF1_m247094617\t1\n+AHCTF1\tAHCTF1_p247076572\t1\n+AHCTF1\tAHCTF1_p247079429\t1\n+AHCY\tAHCY_m32883210\t1\n+AHCY\tAHCY_m32883247\t1\n+AHCY\tAHCY_m32883267\t1\n+AHCY\tAHCY_m32883301\t1\n+AHCY\tAHCY_m32883330\t1\n+AHCY\tAHCY_p32883227\t1\n+AHCY\tAHCY_p32883238\t1\n+AHCY\tAHCY_p32883253\t1\n+AHCY\tAHCY_p32883304\t1\n+AHCY\tAHCY_p32883309\t1\n+AHNAK2\tAHNAK2_m105423801\t1\n+AHNAK2\tAHNAK2_m105423809\t1\n+AHNAK2\tAHNAK2_m105423822\t1\n+AHNAK2\tAHNAK2_m105423829\t1\n+AHNAK2\tAHNAK2_m105423836\t1\n+AHNAK2\tAHNAK2_m105444536\t1\n+AHNAK2\tAHNAK2_m105444541\t1\n+AHNAK2\tAHNAK2_m105444555\t1\n+AHNAK2\tAHNAK2_p105423957\t1\n+AHNAK2\tAHNAK2_p105423983\t1\n+AHNAK\tAHNAK_m62303488\t1\n+AHNAK\tAHNAK_m62303507\t1\n+AHNAK\tAHNAK_m62303523\t1\n+AHNAK\tAHNAK_m62303528\t1\n+AHNAK\tAHNAK_m62303548\t1\n+AHNAK\tAHNAK_m62303560\t1\n+AHNAK\tAHNAK_p62303470\t1\n+AHNAK\tAHNAK_p62303477\t1\n+AHNAK\tAHNAK_p62303510\t1\n+AHNAK\tAHNAK_p62303551\t1\n+AHRR\tAHRR_m344006\t1\n+AHRR\tAHRR_m344069\t1\n+AHRR\tAHRR_m353878\t1\n+AHRR\tAHRR_m353892\t1\n+AHRR\tAHRR_m353898\t1\n+AHRR\tAHRR_p344008\t1\n+AHRR\tAHRR_p344030\t1\n+AHRR\tAHRR_p344036\t1\n+AHRR\tAHRR_p344042\t1\n' |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.pathway.log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.pathway.log.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| @@ -0,0 +1,30 @@ +INFO @ Mon, 12 Feb 2018 04:19:29: Parameters: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/bin/mageck pathway --gene-ranking /tmp/tmpd9LSrs/files/000/dataset_19.dat --gmt-file /tmp/tmpd9LSrs/files/000/dataset_20.dat -n sample1 --method gsea --sort-criteria neg --ranking-column 2 --ranking-column-2 8 --pathway-alpha 0.25 --permutation 1000 +INFO @ Mon, 12 Feb 2018 04:19:29: Welcome to MAGeCK v0.5.7. Command: pathway +INFO @ Mon, 12 Feb 2018 04:19:29: GSEA command for negative selection: mageckGSEA -s -c 2 -p 1000 -g "/tmp/tmpd9LSrs/files/000/dataset_20.dat" -r "/tmp/tmpd9LSrs/files/000/dataset_19.dat" -o sample1.pathway.low.txt +INFO @ Mon, 12 Feb 2018 04:19:29: Running command: mageckGSEA -s -c 2 -p 1000 -g "/tmp/tmpd9LSrs/files/000/dataset_20.dat" -r "/tmp/tmpd9LSrs/files/000/dataset_19.dat" -o sample1.pathway.low.txt +INFO @ Mon, 12 Feb 2018 04:19:29: Command message: +INFO @ Mon, 12 Feb 2018 04:19:29: GMT file: /tmp/tmpd9LSrs/files/000/dataset_20.dat +INFO @ Mon, 12 Feb 2018 04:19:29: Rank file: /tmp/tmpd9LSrs/files/000/dataset_19.dat +INFO @ Mon, 12 Feb 2018 04:19:29: Output file: sample1.pathway.low.txt +INFO @ Mon, 12 Feb 2018 04:19:29: pathway size:1 +INFO @ Mon, 12 Feb 2018 04:19:29: rank size:101 +INFO @ Mon, 12 Feb 2018 04:19:29: Permutations:1000 +INFO @ Mon, 12 Feb 2018 04:19:29: . +INFO @ Mon, 12 Feb 2018 04:19:29: +INFO @ Mon, 12 Feb 2018 04:19:29: End command message. +INFO @ Mon, 12 Feb 2018 04:19:29: GSEA command for positive selection: mageckGSEA -s -c 8 -p 1000 -g "/tmp/tmpd9LSrs/files/000/dataset_20.dat" -r "/tmp/tmpd9LSrs/files/000/dataset_19.dat" -o sample1.pathway.high.txt +INFO @ Mon, 12 Feb 2018 04:19:29: Running command: mageckGSEA -s -c 8 -p 1000 -g "/tmp/tmpd9LSrs/files/000/dataset_20.dat" -r "/tmp/tmpd9LSrs/files/000/dataset_19.dat" -o sample1.pathway.high.txt +INFO @ Mon, 12 Feb 2018 04:19:29: Command message: +INFO @ Mon, 12 Feb 2018 04:19:29: GMT file: /tmp/tmpd9LSrs/files/000/dataset_20.dat +INFO @ Mon, 12 Feb 2018 04:19:29: Rank file: /tmp/tmpd9LSrs/files/000/dataset_19.dat +INFO @ Mon, 12 Feb 2018 04:19:29: Output file: sample1.pathway.high.txt +INFO @ Mon, 12 Feb 2018 04:19:29: pathway size:1 +INFO @ Mon, 12 Feb 2018 04:19:29: rank size:101 +INFO @ Mon, 12 Feb 2018 04:19:29: Permutations:1000 +INFO @ Mon, 12 Feb 2018 04:19:29: . +INFO @ Mon, 12 Feb 2018 04:19:29: +INFO @ Mon, 12 Feb 2018 04:19:29: End command message. +INFO @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.low.tmp +INFO @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.high.tmp +INFO @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.low.txt +INFO @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.high.txt |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.pathway.pathway_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.pathway.pathway_summary.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| @@ -0,0 +1,2 @@ +id num neg|score neg|rra neg|p-value neg|fdr neg|rank neg|goodgene neg|lfc pos|score pos|rra pos|p-value pos|fdr pos|rank pos|goodgene pos|lfc +KEGG_RIBOSOME 88 1 0 0 0 1 0 0 1 0 0 0 1 0 0 |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.test.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.test.R Wed Feb 14 06:42:18 2018 -0500 |
| [ |
| b'@@ -0,0 +1,930 @@\n+pdf(file=\'output.pdf\',width=4.5,height=4.5);\n+gstable=read.table(\'output.gene_summary.txt\',header=T)\n+# \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=20)\n+ # text(tx+50,ty,targetgene,col=colors[i])\n+ }\n+ legend(\'topright\',tglist,pch=20,pt.cex = 2,cex=1,col=colors)\n+ }\n+}\n+\n+\n+\n+plotrandvalues<-function(val,targetgenelist, ...){\n+ # choose the one with the best distance distribution\n+ \n+ mindiffvalue=0;\n+ randval=val;\n+ for(i in 1:20){\n+ randval0=sample(val)\n+ vindex=sort(which(names(randval0) %in% targetgenelist))\n+ if(max(vindex)>0.9*length(val)){\n+ # print(\'pass...\')\n+ next;\n+ }\n+ mindiffind=min(diff(vindex));\n+ if (mindiffind > mindiffvalue){\n+ mindiffvalue=mindiffind;\n+ randval=randval0;\n+ # print(paste(\'Diff: \',mindiffvalue))\n+ }\n+ }\n+ plot(randval,log=\'y\',ylim=c(max(randval),min(randval)),pch=20,col=\'grey\', ...)\n+ \n+ if(length(targetgenelist)>0){\n+ for(i in 1:length(targetgenelist)){\n+ targetgene=targetgenelist[i];\n+ tx=which(names(randval)==targetgene);ty=randval[targetgene];\n+ points(tx,ty,col=colors[(i %% length(colors)) ],cex=2,pch=20)\n+ text(tx+50,ty,targetgene,col=colors[i])\n+ }\n+ }\n+ \n+}\n+\n+\n+\n+\n+# set.seed(1235)\n+\n+\n+\n+pvec=gstable[,startindex]\n+names(pvec)=gstable[,\'id\']\n+pvec=sort(pvec);\n+\n+plotrankedvalues(pvec,targetgenelist,xlab=\'Genes\',ylab=\'RRA score\',main=paste(\'Distribution of RRA scores in \\\\n\',samplelabel))\n+\n+# plotrandvalues(pvec,targetgenelist,xlab=\'Genes\',ylab=\'RRA score\',main=paste(\'Distribution of RRA scores in \\\\n\',samplelabel))\n+\n+\n+pvec=gstable[,startindex+1]\n+names(pvec)=gstable[,\'id\']\n+pvec=sort(pvec);\n+\n+plotrankedvalues(pvec,targetgenelist,xlab=\'Genes\',ylab=\'p value\',main=paste(\'Distribution of p values in \\\\n\',samplelabel))\n+\n+# plotrandvalues(pvec,targetgenelist,xlab=\'Genes\',ylab=\'p value\',main=paste(\'Distribution of p values in \\\\n\',samplelabel))\n+\n+\n+\n+# you need to write after this code:\n+# dev.off()\n+\n+\n+\n+\n+\n+\n+# parameters\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(946.5969148654764,470.6260845366416,663.0651476194316,45'..b'2554626,591.3905137762326,1061.787481868224,887.4532212761591),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+\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+dev.off()\n+Sweave("output_summary.Rnw");\n+library(tools);\n+\n+texi2dvi("output_summary.tex",pdf=TRUE);\n+\n' |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.test.gene_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.test.gene_summary.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| b'@@ -0,0 +1,101 @@\n+id\tnum\tneg|score\tneg|p-value\tneg|fdr\tneg|rank\tneg|goodsgrna\tneg|lfc\tpos|score\tpos|p-value\tpos|fdr\tpos|rank\tpos|goodsgrna\tpos|lfc\n+ACIN1\t10\t5.4294e-05\t0.00039421\t0.03518\t1\t9\t-0.8802\t0.98898\t0.98938\t0.994616\t98\t0\t-0.8802\n+ACTR8\t10\t0.00010064\t0.00070359\t0.03518\t2\t8\t-0.8638\t0.99479\t0.99462\t0.994616\t100\t0\t-0.8638\n+AHCY\t10\t0.00022009\t0.0015619\t0.051023\t3\t6\t-0.56069\t0.12721\t0.33167\t0.925081\t32\t2\t-0.56069\n+ACLY\t10\t0.00028907\t0.0020409\t0.051023\t4\t7\t-0.80032\t0.99461\t0.99442\t0.994616\t99\t0\t-0.80032\n+AATF\t10\t0.0015332\t0.0091467\t0.161427\t5\t8\t-0.70265\t0.9788\t0.98038\t0.994616\t96\t1\t-0.70265\n+AGBL5\t10\t0.0016215\t0.0096856\t0.161427\t6\t8\t-0.35789\t0.95384\t0.96824\t0.994616\t94\t1\t-0.35789\n+AHCTF1\t10\t0.0024367\t0.013897\t0.161843\t7\t5\t-0.23527\t0.73207\t0.88328\t0.994616\t85\t2\t-0.23527\n+ABT1\t10\t0.002511\t0.014316\t0.161843\t8\t7\t-0.58957\t0.81143\t0.91158\t0.994616\t87\t1\t-0.58957\n+ADIRF\t10\t0.0025672\t0.014566\t0.161843\t9\t7\t-0.38313\t0.51897\t0.75574\t0.994616\t71\t2\t-0.38313\n+ABCF1\t10\t0.0056079\t0.028159\t0.281587\t10\t5\t-0.082059\t0.2082\t0.46003\t0.925081\t49\t4\t-0.082059\n+ACTL6A\t10\t0.0081355\t0.038738\t0.352159\t11\t6\t-0.34362\t0.62569\t0.81868\t0.994616\t77\t2\t-0.34362\n+ACHE\t10\t0.011853\t0.053428\t0.433786\t12\t5\t-0.12062\t0.84881\t0.92691\t0.994616\t89\t2\t-0.12062\n+ADRB1\t10\t0.012576\t0.056392\t0.433786\t13\t3\t0.11433\t0.21006\t0.46255\t0.925081\t50\t5\t0.11433\n+ACTR3\t10\t0.014694\t0.064815\t0.462967\t14\t5\t-0.33481\t0.7562\t0.89168\t0.994616\t86\t1\t-0.33481\n+ACAD9\t10\t0.017938\t0.07741\t0.516068\t15\t5\t-0.31684\t0.014914\t0.066023\t0.551771\t11\t3\t-0.31684\n+ACTR1A\t10\t0.034608\t0.12629\t0.761624\t16\t5\t-0.022985\t0.10323\t0.29124\t0.925081\t29\t4\t-0.022985\n+ACP1\t10\t0.035849\t0.12948\t0.761624\t17\t6\t-0.18317\t0.98651\t0.98676\t0.994616\t97\t0\t-0.18317\n+ACTRT3\t10\t0.048507\t0.16474\t0.915197\t18\t5\t-0.42641\t0.17889\t0.41551\t0.925081\t41\t3\t-0.42641\n+AGPAT5\t10\t0.067777\t0.21474\t0.999686\t19\t5\t-0.18272\t0.83413\t0.92091\t0.994616\t88\t2\t-0.18272\n+AGPAT3\t10\t0.076532\t0.23376\t0.999686\t20\t5\t-0.26457\t0.48565\t0.73713\t0.994616\t68\t3\t-0.26457\n+ACO2\t10\t0.078341\t0.23737\t0.999686\t21\t3\t0.16994\t0.4585\t0.7169\t0.994616\t64\t4\t0.16994\n+AGL\t10\t0.10162\t0.28017\t0.999686\t22\t5\t-0.089501\t0.17049\t0.4023\t0.925081\t40\t4\t-0.089501\n+ABL1\t10\t0.10476\t0.28603\t0.999686\t23\t5\t-0.21329\t0.69153\t0.85923\t0.994616\t81\t2\t-0.21329\n+ACTL7A\t10\t0.10642\t0.28885\t0.999686\t24\t3\t-0.049861\t0.37001\t0.63545\t0.994616\t60\t4\t-0.049861\n+ADRM1\t10\t0.11044\t0.29611\t0.999686\t25\t5\t-0.21536\t0.92156\t0.95934\t0.994616\t93\t1\t-0.21536\n+AAAS\t10\t0.13331\t0.33635\t0.999686\t26\t5\t-0.29594\t0.8856\t0.94423\t0.994616\t92\t2\t-0.29594\n+ACVR1B\t10\t0.15016\t0.36584\t0.999686\t27\t5\t-0.13523\t0.46763\t0.72484\t0.994616\t66\t3\t-0.13523\n+ACBD6\t10\t0.15512\t0.37399\t0.999686\t28\t5\t-0.10807\t0.10027\t0.28586\t0.925081\t28\t4\t-0.10807\n+AFF3\t10\t0.15611\t0.37585\t0.999686\t29\t5\t-0.23592\t0.48266\t0.73528\t0.994616\t67\t3\t-0.23592\n+AAK1\t10\t0.16107\t0.38447\t0.999686\t30\t3\t0.067339\t0.020241\t0.085684\t0.648311\t13\t3\t0.067339\n+ABI1\t10\t0.16609\t0.39238\t0.999686\t31\t4\t-0.23736\t0.51898\t0.75574\t0.994616\t72\t2\t-0.23736\n+ADPRHL2\t10\t0.17117\t0.40059\t0.999686\t32\t3\t-0.0055285\t0.44948\t0.70813\t0.994616\t63\t3\t-0.0055285\n+AEN\t10\t0.1767\t0.40971\t0.999686\t33\t4\t-0.16395\t0.57302\t0.78776\t0.994616\t75\t1\t-0.16395\n+ACRC\t10\t0.17897\t0.4133\t0.999686\t34\t2\t0.11912\t0.00017229\t0.0012026\t0.120259\t1\t4\t0.11912\n+ADAM10\t10\t0.18631\t0.42512\t0.999686\t35\t5\t-0.1958\t0.68077\t0.85283\t0.994616\t80\t2\t-0.1958\n+ADH5\t10\t0.18633\t0.42515\t0.999686\t36\t4\t0.031022\t0.1918\t0.43499\t0.925081\t44\t4\t0.031022\n+AFMID\t10\t0.19212\t0.434\t0.999686\t37\t5\t-0.26972\t0.87179\t0.93752\t0.994616\t90\t1\t-0.26972\n+ABCC1\t10\t0.21094\t0.45995\t0.999686\t38\t4\t-0.15482\t0.034488\t0.12876\t0.757397\t17\t2\t-0.15482\n+ADAP1\t10\t0.21183\t0.46089\t0.999686\t39\t2\t0.096871\t0.25461\t0.51972\t0.944937\t55\t2\t0.096871\n+ACSL6\t10\t0.22008\t0.4703\t0.999686\t40\t3\t0.051392\t0.20601\t0.45666\t0.925081\t48\t5\t0.051392\n+ABTB1\t10\t0.22588\t0.47636\t0.999686\t41\t4\t-0.083354\t0.25131\t0.51632\t0.944937\t54\t3\t-0.083354\n+ACVR2B\t10\t0.23534\t0.48652\t0.999686\t42\t4\t0.055993\t0.19801\t0.4447\t0.925081\t46\t5\t0.055993\n+ACTR5\t10\t0.23574\t0.48692\t0.999686\t43\t1\t0.25177\t0.13602\t0.34662\t0.925081\t35\t5\t0.25177\n+ACTL6B\t10\t0.24356\t0.4953\t0.999'..b'842\t0.65928\t0.999686\t55\t2\t0.17169\t0.12854\t0.33421\t0.925081\t33\t5\t0.17169\n+ACAT2\t10\t0.40932\t0.6698\t0.999686\t56\t4\t0.14699\t0.15687\t0.38081\t0.925081\t39\t5\t0.14699\n+ADK\t10\t0.40951\t0.67\t0.999686\t57\t2\t0.26565\t0.0059541\t0.030474\t0.507901\t6\t5\t0.26565\n+ACAD11\t10\t0.42024\t0.68005\t0.999686\t58\t4\t-0.14423\t0.95975\t0.97042\t0.994616\t95\t1\t-0.14423\n+AGAP2\t10\t0.46176\t0.70849\t0.999686\t59\t2\t-0.056853\t0.29633\t0.56235\t0.986579\t57\t3\t-0.056853\n+AFF1\t10\t0.47065\t0.71388\t0.999686\t60\t3\t0.053306\t0.57765\t0.79016\t0.994616\t76\t2\t0.053306\n+AEBP2\t10\t0.48698\t0.72413\t0.999686\t61\t2\t0.012265\t0.52118\t0.75696\t0.994616\t73\t3\t0.012265\n+ABCB8\t10\t0.50647\t0.73644\t0.999686\t62\t3\t0.33882\t0.046462\t0.16162\t0.808109\t20\t6\t0.33882\n+ADRB3\t10\t0.51898\t0.7441\t0.999686\t63\t2\t0.19518\t0.038271\t0.13897\t0.772039\t18\t4\t0.19518\n+ADAR\t10\t0.52118\t0.74547\t0.999686\t64\t3\t-0.16099\t0.48698\t0.7378\t0.994616\t69\t3\t-0.16099\n+ACD\t10\t0.52413\t0.74766\t0.999686\t65\t3\t-0.029641\t0.19552\t0.44071\t0.925081\t45\t2\t-0.029641\n+AHNAK\t10\t0.5343\t0.75419\t0.999686\t66\t1\t0.37532\t0.061763\t0.20069\t0.850611\t23\t6\t0.37532\n+AFTPH\t10\t0.54301\t0.75984\t0.999686\t67\t2\t-0.077488\t0.37895\t0.64371\t0.994616\t61\t4\t-0.077488\n+AHNAK2\t10\t0.54917\t0.76409\t0.999686\t68\t2\t0.33608\t0.025649\t0.10417\t0.651042\t16\t6\t0.33608\n+ADRA1B\t10\t0.56639\t0.77483\t0.999686\t69\t2\t0.01884\t0.11831\t0.31693\t0.925081\t30\t3\t0.01884\n+ADCK4\t10\t0.57302\t0.77943\t0.999686\t70\t1\t0.33858\t0.0026444\t0.014995\t0.499834\t3\t8\t0.33858\n+ADCK5\t10\t0.58588\t0.78762\t0.999686\t71\t2\t0.046549\t0.025048\t0.10262\t0.651042\t15\t4\t0.046549\n+ADH7\t10\t0.58676\t0.78818\t0.999686\t72\t3\t-0.090919\t0.87513\t0.93916\t0.994616\t91\t2\t-0.090919\n+ADRBK1\t10\t0.59228\t0.7922\t0.999686\t73\t3\t0.36204\t0.0048237\t0.025634\t0.507901\t5\t7\t0.36204\n+ADRA1A\t10\t0.59776\t0.79555\t0.999686\t74\t3\t-0.066085\t0.051892\t0.17533\t0.832539\t21\t3\t-0.066085\n+AHRR\t9\t0.60697\t0.79866\t0.999686\t75\t2\t-0.049891\t0.0044955\t0.023119\t0.507901\t4\t3\t-0.049891\n+AFF2\t10\t0.62328\t0.81222\t0.999686\t76\t2\t0.2294\t0.24493\t0.5098\t0.944937\t53\t4\t0.2294\n+AATK\t10\t0.63527\t0.82015\t0.999686\t77\t2\t0.27488\t0.054954\t0.18316\t0.832539\t22\t6\t0.27488\n+AFF4\t10\t0.6797\t0.85053\t0.999686\t78\t2\t0.30669\t0.071064\t0.22367\t0.894671\t25\t6\t0.30669\n+A1CF\t10\t0.69378\t0.85821\t0.999686\t79\t2\t0.0064333\t0.14158\t0.35569\t0.925081\t37\t4\t0.0064333\n+ADD1\t10\t0.74472\t0.87754\t0.999686\t80\t2\t0.11567\t0.34577\t0.61089\t0.994616\t58\t4\t0.11567\n+ADAD1\t10\t0.75052\t0.87973\t0.999686\t81\t2\t-0.0043567\t0.50142\t0.74596\t0.994616\t70\t2\t-0.0043567\n+ACTN4\t10\t0.80918\t0.90438\t0.999686\t82\t2\t0.2223\t0.021612\t0.090763\t0.648311\t14\t7\t0.2223\n+ADARB1\t10\t0.81584\t0.90757\t0.999686\t83\t1\t0.11123\t0.13975\t0.3527\t0.925081\t36\t4\t0.11123\n+ACSS2\t10\t0.82229\t0.91034\t0.999686\t84\t1\t0.19323\t0.013868\t0.061861\t0.551771\t9\t4\t0.19323\n+ADRB2\t10\t0.83749\t0.91809\t0.999686\t85\t2\t-0.009076\t0.70203\t0.86569\t0.994616\t82\t3\t-0.009076\n+AFAP1L2\t10\t0.85952\t0.92884\t0.999686\t86\t2\t0.23074\t0.21621\t0.47179\t0.925081\t51\t5\t0.23074\n+ACTN1\t10\t0.86536\t0.93211\t0.999686\t87\t2\t0.12145\t0.28536\t0.55189\t0.98552\t56\t3\t0.12145\n+ADARB2\t10\t0.87336\t0.93654\t0.999686\t88\t1\t0.36865\t0.0098559\t0.046302\t0.551771\t8\t6\t0.36865\n+ADCK2\t10\t0.88046\t0.94066\t0.999686\t89\t2\t-0.0071793\t0.3792\t0.64399\t0.994616\t62\t4\t-0.0071793\n+ABL2\t10\t0.92156\t0.95311\t0.999686\t90\t1\t0.15642\t0.53574\t0.76569\t0.994616\t74\t3\t0.15642\n+ADRBK2\t10\t0.9506\t0.96302\t0.999686\t91\t1\t0.2293\t0.2\t0.44756\t0.925081\t47\t5\t0.2293\n+ADCK1\t10\t0.96245\t0.96866\t0.999686\t92\t1\t0.31253\t0.0081355\t0.039596\t0.551771\t7\t6\t0.31253\n+ADNP2\t10\t0.96448\t0.96988\t0.999686\t93\t1\t0.11441\t0.14636\t0.36385\t0.925081\t38\t5\t0.11441\n+AGTPBP1\t10\t0.97247\t0.97465\t0.999686\t94\t1\t0.018825\t0.17891\t0.41555\t0.925081\t42\t4\t0.018825\n+ACVR1\t10\t0.97475\t0.97633\t0.999686\t95\t1\t0.22596\t0.09861\t0.28311\t0.925081\t27\t5\t0.22596\n+ADCK3\t10\t0.9877\t0.98797\t0.999686\t96\t0\t0.34147\t0.014963\t0.066213\t0.551771\t12\t6\t0.34147\n+AGAP3\t10\t0.99117\t0.99131\t0.999686\t97\t0\t0.36057\t0.0012992\t0.0079691\t0.398453\t2\t8\t0.36057\n+ADNP\t10\t0.99212\t0.99227\t0.999686\t98\t0\t0.35587\t0.014351\t0.063787\t0.551771\t10\t7\t0.35587\n+AES\t10\t0.9959\t0.99575\t0.999686\t99\t0\t0.21432\t0.24171\t0.50676\t0.944937\t52\t4\t0.21432\n+ACVR1C\t10\t0.99964\t0.99969\t0.999686\t100\t0\t0.29763\t0.042729\t0.15142\t0.796959\t19\t6\t0.29763\n' |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.test.log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.test.log.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| b'@@ -0,0 +1,112 @@\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 201'..b'nt: 100 \n+INFO @ Mon, 12 Feb 2018 03:40:03: Saving to output file... \n+INFO @ Mon, 12 Feb 2018 03:40:03: RRA completed. \n+INFO @ Mon, 12 Feb 2018 03:40:03: \n+INFO @ Mon, 12 Feb 2018 03:40:03: End command message. \n+DEBUG @ Mon, 12 Feb 2018 03:40:03: Sorting the merged items by negative selection... \n+INFO @ Mon, 12 Feb 2018 03:40:03: Loading top 10 genes from output.gene.low.txt: ACIN1,ACTR8,AHCY,ACLY,AATF,AGBL5,AHCTF1,ABT1,ADIRF,ABCF1 \n+DEBUG @ Mon, 12 Feb 2018 03:40:03: Column index:3 \n+INFO @ Mon, 12 Feb 2018 03:40:03: Loading top 10 genes from output.gene.high.txt: ACRC,AGAP3,ADCK4,AHRR,ADRBK1,ADK,ADCK1,ADARB2,ACSS2,ADNP \n+DEBUG @ Mon, 12 Feb 2018 03:40:03: Column index:9 \n+INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.plow.txt \n+INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.phigh.txt \n+INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.gene.low.txt \n+INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.gene.high.txt \n+INFO @ Mon, 12 Feb 2018 03:40:03: Running command: cd ./; Rscript output.R \n+INFO @ Mon, 12 Feb 2018 03:40:04: Command message: \n+INFO @ Mon, 12 Feb 2018 03:40:04: null device \n+INFO @ Mon, 12 Feb 2018 03:40:04: 1 \n+INFO @ Mon, 12 Feb 2018 03:40:04: Writing to file output_summary.tex \n+INFO @ Mon, 12 Feb 2018 03:40:04: Processing code chunks with options ... \n+INFO @ Mon, 12 Feb 2018 03:40:04: 1 : keep.source term verbatim (label = funcdef, output_summary.Rnw:27) \n+INFO @ Mon, 12 Feb 2018 03:40:04: 2 : keep.source term tex (label = tab1, output_summary.Rnw:37) \n+INFO @ Mon, 12 Feb 2018 03:40:04: 3 : keep.source term verbatim (output_summary.Rnw:77) \n+INFO @ Mon, 12 Feb 2018 03:40:04: 4 : keep.source term verbatim pdf (output_summary.Rnw:83) \n+INFO @ Mon, 12 Feb 2018 03:40:04: 5 : keep.source term verbatim pdf (output_summary.Rnw:201) \n+INFO @ Mon, 12 Feb 2018 03:40:04: 6 : keep.source term verbatim pdf (output_summary.Rnw:345) \n+INFO @ Mon, 12 Feb 2018 03:40:04: 7 : keep.source term verbatim pdf (output_summary.Rnw:489) \n+INFO @ Mon, 12 Feb 2018 03:40:04: 8 : keep.source term verbatim (output_summary.Rnw:567) \n+INFO @ Mon, 12 Feb 2018 03:40:04: 9 : keep.source term verbatim pdf (output_summary.Rnw:573) \n+INFO @ Mon, 12 Feb 2018 03:40:04: 10 : keep.source term verbatim pdf (output_summary.Rnw:691) \n+INFO @ Mon, 12 Feb 2018 03:40:04: 11 : keep.source term verbatim pdf (output_summary.Rnw:835) \n+INFO @ Mon, 12 Feb 2018 03:40:04: 12 : keep.source term verbatim pdf (output_summary.Rnw:979) \n+INFO @ Mon, 12 Feb 2018 03:40:04: \n+INFO @ Mon, 12 Feb 2018 03:40:04: You can now run (pdf)latex on \xe2\x80\x98output_summary.tex\xe2\x80\x99 \n+INFO @ Mon, 12 Feb 2018 03:40:04: Error in texi2dvi("output_summary.tex", pdf = TRUE) : \n+INFO @ Mon, 12 Feb 2018 03:40:04: pdflatex is not available \n+INFO @ Mon, 12 Feb 2018 03:40:04: Execution halted \n+INFO @ Mon, 12 Feb 2018 03:40:04: \n+INFO @ Mon, 12 Feb 2018 03:40:04: End command message. \n+INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary-*.pdf \n+INFO @ Mon, 12 Feb 2018 03:40:04: Command message: \n+INFO @ Mon, 12 Feb 2018 03:40:04: \n+INFO @ Mon, 12 Feb 2018 03:40:04: End command message. \n+INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.aux \n+INFO @ Mon, 12 Feb 2018 03:40:04: Command message: \n+INFO @ Mon, 12 Feb 2018 03:40:04: \n+INFO @ Mon, 12 Feb 2018 03:40:04: End command message. \n+INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.tex \n+INFO @ Mon, 12 Feb 2018 03:40:04: Command message: \n+INFO @ Mon, 12 Feb 2018 03:40:04: \n+INFO @ Mon, 12 Feb 2018 03:40:04: End command message. \n+INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.toc \n+INFO @ Mon, 12 Feb 2018 03:40:04: Command message: \n+INFO @ Mon, 12 Feb 2018 03:40:04: \n+INFO @ Mon, 12 Feb 2018 03:40:04: End command message. \n' |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.test.normalized.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.test.normalized.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| b'@@ -0,0 +1,1000 @@\n+sgRNA\tGene\tHL60.initial\tKBM7.initial\tHL60.final\tKBM7.final\n+A1CF_m52595977\tA1CF\t313.08251997879887\t486.6096119359992\t557.0756663634236\t100.13173031807082\n+A1CF_m52596017\tA1CF\t432.1420698298914\t731.6903653928164\t980.402701618075\t1081.994868751268\n+A1CF_m52596056\tA1CF\t618.8156850285179\t653.5486758848457\t357.0836094696463\t434.28561892237576\n+A1CF_m52603842\tA1CF\t402.7446501135722\t431.55523978265626\t198.0993875856342\t489.21502526828885\n+A1CF_m52603847\tA1CF\t0.0\t88.79737444087577\t91.47901656024509\t152.20023008346766\n+A1CF_p52595870\tA1CF\t915.7296241633413\t1035.3773859806115\t948.227323379644\t639.1265300873434\n+A1CF_p52595881\tA1CF\t714.3572991065552\t671.3081507730209\t1119.829340651276\t906.90738602367\n+A1CF_p52596023\tA1CF\t286.6248422341116\t761.8814727027142\t493.9866894253235\t442.86833866392465\n+A1CF_p52601638\tA1CF\t1093.584013447072\t815.1598973672396\t777.8870856467737\t1377.2404278605513\n+A1CF_p52603829\tA1CF\t111.71019492201273\t252.1845434120872\t209.4554034344922\t269.4973998846363\n+AAAS_m53714382\tAAAS\t1034.7891740144337\t1191.6607649965529\t504.0809257354195\t815.9305567632514\n+AAAS_m53715169\tAAAS\t956.8860117661881\t1113.5190754885823\t502.81914619665747\t966.9864242145125\n+AAAS_m53715176\tAAAS\t801.0796872696966\t158.05932650475887\t247.30878959735224\t379.92839389256585\n+AAAS_m53715212\tAAAS\t373.3472303972531\t603.8221461979552\t270.6517110644493\t424.5585365486203\n+AAAS_m53715238\tAAAS\t47.03587154611063\t239.7529109903646\t265.6045929094013\t44.05796133995116\n+AAAS_p53714367\tAAAS\t474.7683284185541\t582.510776332145\t411.34012963641237\t268.35303725242983\n+AAAS_p53714374\tAAAS\t430.6721988440754\t463.52229458137157\t540.0416425901366\t553.8715139879574\n+AAAS_p53714391\tAAAS\t415.9734889859159\t708.6030480381887\t601.8688399894746\t537.8504371370661\n+AAAS_p53714405\tAAAS\t1644.785633128056\t1520.2110504277932\t1395.5281698707734\t1553.4722732203559\n+AAAS_p53714441\tAAAS\t401.2747791277563\t580.7348288433276\t689.5625179334337\t474.33831104960404\n+AAK1_m69870049\tAAK1\t535.0330388370083\t825.8155823001447\t437.2066101810334\t1147.7957201031431\n+AAK1_m69870056\tAAK1\t933.3680759931327\t1255.5948745939834\t1409.4077447971554\t2011.2173261029654\n+AAK1_m69870103\tAAK1\t712.8874281207392\t802.728264945517\t576.6332492142345\t359.9020478289517\n+AAK1_m69870119\tAAK1\t595.2977492554626\t488.3855594248168\t508.4971541210865\t478.91576157843014\n+AAK1_m69870125\tAAK1\t402.7446501135722\t621.5816210861304\t1149.481159812183\t1202.1529451329532\n+AAK1_m69870131\tAAK1\t1108.2827233052317\t1355.0479339677643\t890.1854645965918\t1508.8421305643014\n+AAK1_m69870137\tAAK1\t1330.2332421634412\t522.1285617123496\t323.0155619230723\t456.6006902504029\n+AAK1_p69870063\tAAK1\t485.05742531926586\t296.5832306325251\t229.64387605468423\t651.7145190416153\n+AAK1_p69870070\tAAK1\t1456.6421469436134\t1275.1302969709761\t1129.292687191991\t962.4089736856864\n+AAK1_p69870105\tAAK1\t279.27548730503185\t289.479440677255\t581.6803673692825\t639.6987114034467\n+AATF_m35306444\tAATF\t659.9720726313648\t809.832054900787\t880.7221180558769\t802.1982051767731\n+AATF_m35306475\tAATF\t724.6463960072668\t1086.8798631563195\t695.2405258578626\t307.26136674745163\n+AATF_m35306482\tAATF\t836.3565909292796\t1289.3378768815162\t468.75109865008346\t177.94838930811443\n+AATF_m35306509\tAATF\t367.46774645398926\t571.85509139924\t300.30353022535627\t116.72498848506541\n+AATF_m35307516\tAATF\t518.8644579930328\t632.2373060190355\t627.7353205340956\t308.9779106957614\n+AATF_m35307525\tAATF\t405.68439208520414\t259.28833336735727\t324.27734146183434\t166.5047629860492\n+AATF_p35306410\tAATF\t2096.0360257735547\t1960.6460276545372\t1573.4390848362154\t629.9716290296913\n+AATF_p35306466\tAATF\t277.8056163192159\t435.1071347602913\t182.32714335110919\t0.0\n+AATF_p35307505\tAATF\t995.1026573974029\t477.7298744919117\t728.0467938656747\t275.21921304566894\n+AATF_p35307527\tAATF\t2185.6981559083283\t1482.9161531626255\t1741.8866532609427\t1862.4501839161173\n+AATK_m79102275\tAATK\t912.7898821917094\t772.5371576356192\t2881.904466532411\t634.5490795585174\n+AATK_m79102281\tAATK\t683.49000840442\t816.9358448560571\t1095.224639645417\t1516.85266898'..b'+AHCTF1_m247094617\tAHCTF1\t845.1758168441753\t660.6524658401157\t541.3034221288985\t640.8430740356532\n+AHCTF1_p247076572\tAHCTF1\t551.2016196809839\t740.570102836904\t1103.42620664737\t622.5332719203489\n+AHCTF1_p247079429\tAHCTF1\t601.1772331987264\t900.4053768304803\t735.6174710982467\t754.1349746240991\n+AHCY_m32883210\tAHCY\t301.3235520922712\t657.1005708624807\t228.38209651592223\t137.32351586478285\n+AHCY_m32883247\tAHCY\t1142.0897559789987\t1099.311495578042\t112.92926871919911\t100.70391163417409\n+AHCY_m32883267\tAHCY\t789.3207193831689\t671.3081507730209\t723.6305654800077\t588.7745742702564\n+AHCY_m32883301\tAHCY\t392.45555321286054\t412.0198174056636\t334.37157777193033\t213.99581222261992\n+AHCY_m32883330\tAHCY\t2009.3136376104133\t2235.917888421252\t2437.1271791188055\t1937.9781176417478\n+AHCY_p32883227\tAHCY\t1071.5359486598327\t406.69197493921104\t645.4002340767636\t349.602784139093\n+AHCY_p32883238\tAHCY\t61.7345814042702\t218.44154112455442\t614.4866353770946\t452.5954210376801\n+AHCY_p32883253\tAHCY\t651.152846716469\t879.0940069646701\t237.21455328725622\t18.88198343140764\n+AHCY_p32883304\tAHCY\t1625.6773103124485\t1410.1023061211074\t2146.286995434164\t1986.613529510525\n+AHCY_p32883309\tAHCY\t1053.8974968300413\t882.6459019423052\t106.6203710253891\t105.85354347910344\n+AHNAK2_m105423801\tAHNAK2\t1215.5833052697965\t1655.1830595779245\t1491.4234148166854\t1543.7451908466005\n+AHNAK2_m105423809\tAHNAK2\t404.2145210993882\t470.6260845366416\t489.5704610396565\t643.1317993000663\n+AHNAK2_m105423822\tAHNAK2\t316.0222619504308\t735.2422603704514\t709.7509905536257\t664.8746893119902\n+AHNAK2_m105423829\tAHNAK2\t737.8752348796105\t879.0940069646701\t561.4918947490905\t402.81564653669636\n+AHNAK2_m105423836\tAHNAK2\t293.97419716319143\t816.9358448560571\t1369.0307995567714\t1079.1339621707518\n+AHNAK2_m105444536\tAHNAK2\t382.16645631214885\t454.642557137284\t707.8583212454827\t608.8009203338706\n+AHNAK2_m105444541\tAHNAK2\t761.3931706526657\t664.2043608177509\t846.6540705093029\t909.1961112880831\n+AHNAK2_m105444555\tAHNAK2\t504.1657481348733\t277.0478082555324\t162.13867073091717\t738.1138977732078\n+AHNAK2_p105423957\tAHNAK2\t676.1406534753403\t552.3196690222474\t313.5522153823573\t654.0032443060283\n+AHNAK2_p105423983\tAHNAK2\t363.0581334965414\t388.9325000510359\t977.24825277117\t556.1602392523705\n+AHNAK_m62303488\tAHNAK\t399.80490814194036\t504.3690868241744\t781.0415344936788\t643.1317993000663\n+AHNAK_m62303507\tAHNAK\t116.11980787946061\t236.20101601272955\t292.7328529927843\t19.4541647475109\n+AHNAK_m62303523\tAHNAK\t179.32426026954676\t298.3591781213426\t150.15176511267813\t305.5448227991418\n+AHNAK_m62303528\tAHNAK\t266.04664843268824\t797.4004224790644\t677.5756123151947\t839.3899907234851\n+AHNAK_m62303548\tAHNAK\t868.6937526172306\t980.3230138272686\t721.1070064024836\t327.859894127169\n+AHNAK_m62303560\tAHNAK\t704.0682022058435\t959.0116439614584\t1027.71943432165\t1504.8368613515786\n+AHNAK_p62303470\tAHNAK\t379.22671434051693\t731.6903653928164\t881.3530078252578\t997.3120339679854\n+AHNAK_p62303477\tAHNAK\t655.5624596739169\t500.8171918465394\t554.5521072858995\t475.4826736818106\n+AHNAK_p62303510\tAHNAK\t473.2984574327382\t451.09066215964896\t598.0835013731886\t493.2202944810117\n+AHNAK_p62303551\tAHNAK\t51.4454845035585\t40.846792242802856\t117.34549710486611\t31.4699723856794\n+AHRR_m344006\tAHRR\t345.4196816667499\t163.38716897121142\t474.42910657451245\t481.2044868428432\n+AHRR_m344069\tAHRR\t415.9734889859159\t372.9489726516783\t212.6098522813972\t349.03060282298975\n+AHRR_m353878\tAHRR\t1.469870985815957\t83.46953197442323\t0.0\t62.9399447713588\n+AHRR_m353892\tAHRR\t351.29916561001374\t150.9555365494888\t288.9475143764983\t416.54799812317464\n+AHRR_m353898\tAHRR\t561.4907165816957\t170.49095892648148\t199.3611671243962\t411.97054759434855\n+AHRR_p344008\tAHRR\t251.34793857452865\t221.99343610218943\t1564.6066280648815\t1502.5481360871656\n+AHRR_p344030\tAHRR\t736.4053638937945\t893.3015868752103\t1114.782222496228\t459.46159683091923\n+AHRR_p344036\tAHRR\t338.07032673767014\t607.3740411755903\t378.5338616286004\t65.22867003577186\n+AHRR_p344042\tAHRR\t1230.2820151279561\t525.6804566899846\t837.1907239685878\t945.2435342025885\n' |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.test.pdf |
| b |
| Binary file test-data/out.test.pdf has changed |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/out.test.sgrna_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.test.sgrna_summary.txt Wed Feb 14 06:42:18 2018 -0500 |
| b |
| b'@@ -0,0 +1,1000 @@\n+sgrna\tGene\tcontrol_count\ttreatment_count\tcontrol_mean\ttreat_mean\tLFC\tcontrol_var\tadj_var\tscore\tp.low\tp.high\tp.twosided\tFDR\thigh_in_treatment\n+AHRR_p344008\tAHRR\t251.35/221.99\t1564.6/1502.5\t236.67\t1533.6\t2.6908\t1178.2\t5085.6\t18.186\t1\t3.3319e-74\t6.6638e-74\t6.6571e-71\tTrue\n+ACAD9_m128598565\tACAD9\t739.35/925.27\t2528/2050.7\t832.31\t2289.3\t1.4586\t65590\t35597\t7.7226\t1\t5.7002e-15\t1.14e-14\t5.6945e-12\tTrue\n+ACTR8_m53916081\tACTR8\t1925.5/2054.8\t194.94/235.17\t1990.2\t215.06\t-3.2041\t4580.2\t54357\t7.6137\t1.3311e-14\t1\t2.6622e-14\t7.8608e-12\tFalse\n+ACRC_m70814198\tACRC\t76.433/90.573\t447.3/357.04\t83.503\t402.17\t2.2543\t2086.7\t1760.4\t7.5952\t1\t1.5737e-14\t3.1475e-14\t7.8608e-12\tTrue\n+ABCC1_p16101710\tABCC1\t52.915/26.639\t203.78/224.3\t39.777\t214.04\t2.3987\t277.85\t700.66\t6.5833\t1\t2.465e-11\t4.93e-11\t9.8502e-09\tTrue\n+ACTR8_m53916067\tACTR8\t1267/1156.1\t251.09/42.341\t1211.6\t146.72\t-3.0372\t13968\t31286\t6.021\t8.6646e-10\t1\t1.7329e-09\t2.3419e-07\tFalse\n+AAK1_m69870125\tAAK1\t402.74/621.58\t1149.5/1202.2\t512.16\t1175.8\t1.1974\t12666\t12223\t6.0027\t1\t9.7009e-10\t1.9402e-09\t2.3419e-07\tTrue\n+ADCK1_p78285331\tADCK1\t798.14/768.99\t1478.8/1756\t783.56\t1617.4\t1.0446\t19425\t19317\t5.9996\t1\t9.8882e-10\t1.9776e-09\t2.3419e-07\tTrue\n+AHCY_m32883247\tAHCY\t1142.1/1099.3\t112.93/100.7\t1120.7\t106.82\t-3.379\t494.86\t28685\t5.9891\t1.0549e-09\t1\t2.1098e-09\t2.3419e-07\tFalse\n+AHCTF1_m247070995\tAHCTF1\t1437.5/1095.8\t320.49/161.36\t1266.6\t240.92\t-2.3895\t35534\t33759\t5.5826\t1.1847e-08\t1\t2.3695e-08\t2.3671e-06\tFalse\n+AHCY_p32883309\tAHCY\t1053.9/882.65\t106.62/105.85\t968.27\t106.24\t-3.1761\t7331.9\t24378\t5.524\t1.6565e-08\t1\t3.3129e-08\t3.0087e-06\tFalse\n+ADCY1_p45614315\tADCY1\t2.9397/72.814\t210.72/187.1\t37.877\t198.91\t2.3624\t1360\t895.72\t5.3806\t1\t4.1374e-08\t8.2747e-08\t6.6138e-06\tTrue\n+ACTN4_p39138476\tACTN4\t449.78/475.95\t1056.7/977.86\t462.87\t1017.3\t1.1344\t1726.9\t10724\t5.3539\t1\t4.3033e-08\t8.6065e-08\t6.6138e-06\tTrue\n+ADAM12_m128076658\tADAM12\t768.74/767.21\t1432.1/1562.6\t767.98\t1497.4\t0.96239\t4258.6\t18836\t5.3145\t1\t5.3464e-08\t1.0693e-07\t7.63e-06\tTrue\n+ABT1_m26597388\tABT1\t1743.3/1980.2\t837.19/281.51\t1861.7\t559.35\t-1.733\t91226\t64053\t5.1459\t1.3309e-07\t1\t2.6618e-07\t1.7727e-05\tFalse\n+ACRC_p70814182\tACRC\t682.02/822.26\t1572.2/1333.8\t752.14\t1453\t0.949\t19128\t18646\t5.1324\t1\t1.4307e-07\t2.8614e-07\t1.7866e-05\tTrue\n+ACBD6_p180471256\tACBD6\t107.3/285.93\t553.29/687.76\t196.61\t620.53\t1.6531\t12498\t6924.5\t5.0942\t1\t1.7666e-07\t3.5333e-07\t2.0382e-05\tTrue\n+ACRC_p70811990\tACRC\t495.35/605.6\t1159.6/1617.6\t550.47\t1388.6\t1.3333\t55476\t27162\t5.0853\t1\t1.8362e-07\t3.6724e-07\t2.0382e-05\tTrue\n+ADRA1B_m159344001\tADRA1B\t329.25/309.01\t881.98/676.32\t319.13\t779.15\t1.2851\t10677\t8286.5\t5.0535\t1\t2.1699e-07\t4.3398e-07\t2.2818e-05\tTrue\n+AHCY_p32883238\tAHCY\t61.735/218.44\t614.49/452.6\t140.09\t533.54\t1.9217\t12691\t6123\t5.0282\t1\t2.5699e-07\t5.1398e-07\t2.5673e-05\tTrue\n+ACTR5_m37377141\tACTR5\t865.75/935.92\t1595.5/1695.4\t900.84\t1645.4\t0.86841\t3723.6\t22496\t4.9645\t1\t3.4447e-07\t6.8893e-07\t3.2774e-05\tTrue\n+ADARB2_m1779330\tADARB2\t135.23/118.99\t351.41/399.95\t127.11\t375.68\t1.556\t655.19\t2547.9\t4.9245\t1\t4.2536e-07\t8.5071e-07\t3.863e-05\tTrue\n+ADRB1_m115804012\tADRB1\t2166.6/1942.9\t1093.3/705.5\t2054.7\t899.42\t-1.191\t50114\t56324\t4.8681\t5.6346e-07\t1\t1.1269e-06\t4.8948e-05\tFalse\n+AHCTF1_m247070906\tAHCTF1\t1078.9/1609\t348.88/193.97\t1343.9\t271.43\t-2.3036\t76257\t48827\t4.8539\t6.0526e-07\t1\t1.2105e-06\t5.0388e-05\tFalse\n+ACIN1_m23538803\tACIN1\t2432.6/2122.3\t1067.5/155.63\t2277.4\t611.55\t-1.8952\t2.3194e+05\t1.1942e+05\t4.8207\t7.1537e-07\t1\t1.4307e-06\t5.7173e-05\tFalse\n+ACIN1_m23538698\tACIN1\t3424.8/3818.3\t1992.3/690.05\t3621.5\t1341.2\t-1.4324\t4.627e+05\t2.2481e+05\t4.8094\t7.5677e-07\t1\t1.5135e-06\t5.8155e-05\tFalse\n+ABCF1_p30545878\tABCF1\t2012.3/1989.1\t1064.3/432\t2000.7\t748.15\t-1.4179\t1.0009e+05\t69814\t4.7403\t1.0669e-06\t1\t2.1338e-06\t7.8951e-05\tFalse\n+ABCF1_p30539251\tABCF1\t1127.4/1198.8\t371.59/370.2\t1163.1\t370.9\t-1.6462\t1274\t29895\t4.5817\t2.3062e-06\t1\t4.6124e-06\t0.00016456\tFalse\n+ACTR1A_m104250365\tACTR1A\t402.74/161.61\t711.64/716.37\t282.18\t714.01\t1.3362\t14542\t8970.1\t4.5595\t1\t2.5679e-06\t5.1359e-06\t0.00017692\tTrue\n+ADRBK1_m6703'..b'PH_m64778724\tAFTPH\t49.976/127.87\t105.99/66.945\t88.922\t86.467\t-0.039928\t1897.9\t1774.5\t0.081538\t0.46751\t0.53249\t0.93501\t0.96456\tFalse\n+ADCK3_m227149144\tADCK3\t263.11/168.72\t189.27/231.73\t215.91\t210.5\t-0.036444\t2678.3\t4592\t0.080811\t0.4678\t0.5322\t0.93559\t0.96456\tFalse\n+ABCF1_p30545888\tABCF1\t264.58/353.41\t442.25/191.68\t309\t316.97\t0.036632\t17670\t10451\t0.077983\t0.53049\t0.46951\t0.93902\t0.9661\tTrue\n+ADD3_p111860411\tADD3\t593.83/834.7\t523.01/932.66\t714.26\t727.83\t0.027114\t56457\t30403\t0.077825\t0.53101\t0.46899\t0.93799\t0.96603\tTrue\n+ADARB2_m1779272\tADARB2\t1018.6/513.25\t679.47/824.51\t765.93\t751.99\t-0.026472\t69110\t35557\t0.07398\t0.47051\t0.52949\t0.94103\t0.96717\tFalse\n+ADRA1B_m159343921\tADRA1B\t67.614/245.08\t196.21/110.43\t156.35\t153.32\t-0.028039\t9713\t5375.9\t0.063038\t0.47487\t0.52513\t0.94974\t0.97432\tFalse\n+ACTR3_p114688931\tACTR3\t721.71/768.99\t584.83/888.6\t745.35\t736.72\t-0.016779\t23627\t20022\t0.060988\t0.47568\t0.52432\t0.95137\t0.97432\tFalse\n+AAAS_p53714391\tAAAS\t415.97/708.6\t601.87/537.85\t562.29\t569.86\t0.019263\t22433\t16355\t0.059205\t0.5236\t0.4764\t0.95279\t0.97432\tTrue\n+ADARB1_m46595715\tADARB1\t749.63/378.28\t472.54/673.46\t563.96\t573\t0.022906\t44569\t23763\t0.058653\t0.52333\t0.47667\t0.95335\t0.97432\tTrue\n+ADI1_p3523171\tADI1\t636.45/156.28\t564.02/250.04\t396.37\t407.03\t0.038194\t82286\t33445\t0.058293\t0.51593\t0.48407\t0.96814\t0.97895\tTrue\n+AGPAT3_m45379570\tAGPAT3\t127.88/230.87\t191.16/160.78\t179.38\t175.97\t-0.027492\t2882.6\t3736.7\t0.057892\t0.47692\t0.52308\t0.95383\t0.97432\tFalse\n+AHRR_p344042\tAHRR\t1230.3/525.68\t837.19/945.24\t877.98\t891.22\t0.021562\t1.2703e+05\t56920\t0.055478\t0.52207\t0.47793\t0.95587\t0.9754\tTrue\n+AEN_m89169500\tAEN\t679.08/568.3\t741.3/492.65\t623.69\t616.97\t-0.015604\t18524\t16137\t0.052901\t0.47891\t0.52109\t0.95781\t0.976\tFalse\n+ADCK4_m41220523\tADCK4\t565.9/776.09\t878.2/445.73\t670.99\t661.96\t-0.01952\t57802\t30074\t0.052147\t0.47921\t0.52079\t0.95841\t0.976\tFalse\n+AEBP2_p19615544\tAEBP2\t745.22/751.23\t736.25/773.59\t748.23\t754.92\t0.012832\t357.59\t18298\t0.049483\t0.51973\t0.48027\t0.96053\t0.97716\tTrue\n+AEBP1_p44144359\tAEBP1\t770.21/880.87\t577.9/1056.8\t825.54\t817.36\t-0.014356\t60403\t33744\t0.044558\t0.48223\t0.51777\t0.96446\t0.97895\tFalse\n+AHCTF1_p247079429\tAHCTF1\t601.18/900.41\t735.62/754.13\t750.79\t744.88\t-0.011396\t22470\t19735\t0.042105\t0.48321\t0.51679\t0.96641\t0.97895\tFalse\n+ADNP2_p77875499\tADNP2\t745.22/614.48\t453.61/920.64\t679.85\t687.12\t0.015331\t58803\t30566\t0.041603\t0.51657\t0.48343\t0.96686\t0.97895\tTrue\n+ACTR5_m37377171\tACTR5\t438.02/443.99\t482/391.94\t441\t436.97\t-0.013222\t2036.4\t10162\t0.040007\t0.48404\t0.51596\t0.96809\t0.97895\tFalse\n+ABTB1_m127395860\tABTB1\t945.13/1102.9\t885.77/1174.7\t1024\t1030.2\t0.0087472\t27089\t26326\t0.038419\t0.51532\t0.48468\t0.96935\t0.97895\tTrue\n+ACTL6B_m100253168\tACTL6B\t751.1/939.48\t471.91/1238.2\t845.29\t855.05\t0.016548\t1.5567e+05\t65863\t0.038041\t0.51493\t0.48507\t0.97013\t0.97895\tTrue\n+AEBP2_m19615572\tAEBP2\t1023/468.85\t729.31/774.73\t745.94\t752.02\t0.011697\t77295\t37922\t0.031226\t0.51242\t0.48758\t0.97515\t0.98302\tTrue\n+AFF1_p87967890\tAFF1\t824.6/1007\t526.79/1316.6\t915.78\t921.69\t0.0092723\t1.6426e+05\t70028\t0.022338\t0.50878\t0.49122\t0.98244\t0.98938\tTrue\n+ACHE_p100491656\tACHE\t2626.7/1706.7\t1749.5/2570.2\t2166.7\t2159.8\t-0.0045493\t3.8001e+05\t1.665e+05\t0.016725\t0.49333\t0.50667\t0.98666\t0.9925\tFalse\n+ACHE_m100491816\tACHE\t295.44/420.9\t380.43/338.73\t358.17\t359.58\t0.005641\t4369.4\t8062.6\t0.015671\t0.50624\t0.49376\t0.98753\t0.9925\tTrue\n+ACHE_m100491779\tACHE\t280.75/525.68\t298.41/505.24\t403.21\t401.82\t-0.0049676\t25692\t14696\t0.012018\t0.49521\t0.50479\t0.99041\t0.99439\tFalse\n+AGAP2_m58128444\tAGAP2\t2459.1/1609\t1964.6/2109.6\t2034.1\t2037.1\t0.0021679\t1.8592e+05\t99102\t0.0097214\t0.50388\t0.49612\t0.99224\t0.99523\tTrue\n+ADRB2_p148206450\tADRB2\t608.53/877.32\t955.17/533.27\t742.92\t744.22\t0.0025145\t62561\t32956\t0.0071485\t0.50284\t0.49716\t0.99432\t0.99631\tTrue\n+ACVRL1_m52306881\tACVRL1\t1665.4/1102.9\t1593/1178.1\t1384.1\t1385.6\t0.0015047\t1.2213e+05\t64899\t0.0056737\t0.50226\t0.49774\t0.99547\t0.99647\tTrue\n+ACAD11_m132378564\tACAD11\t989.22/1545.1\t1045.4/1487.1\t1267.1\t1266.2\t-0.0010322\t1.2602e+05\t63931\t0.0035873\t0.49857\t0.50143\t0.99714\t0.99714\tFalse\n' |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/test1.bam |
| b |
| Binary file test-data/test1.bam has changed |
| b |
| diff -r 000000000000 -r b80c0e046539 test-data/test1.fastq.gz |
| b |
| Binary file test-data/test1.fastq.gz has changed |