| Previous changeset 10:24a09ca67621 (2017-08-01) Next changeset 12:bd06df00180a (2018-01-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c |
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modified:
deseq2.R deseq2.xml test-data/deseq2_out.tab |
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added:
test-data/sailfish/out_deseq2_sailfish.tab test-data/sailfish/sailfish_quant.sf1.tab test-data/sailfish/sailfish_quant.sf2.tab test-data/sailfish/sailfish_quant.sf3.tab test-data/sailfish/sailfish_quant.sf4.tab test-data/sailfish/sailfish_quant.sf5.tab test-data/sailfish/sailfish_quant.sf6.tab test-data/tx2gene.tab |
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removed:
test-data/deseq2_out_filtered.tab test-data/deseq2_tximport_out.tab test-data/deseq2_tximport_out_filtered.tab test-data/genes_sub.gtf test-data/sailfish_quant_result1.tab test-data/sailfish_quant_result2.tab test-data/sailfish_quant_result3.tab test-data/sailfish_quant_result4.tab |
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| diff -r 24a09ca67621 -r 25204a860b79 deseq2.R --- a/deseq2.R Tue Aug 01 17:20:46 2017 -0400 +++ b/deseq2.R Sun Jan 28 04:04:12 2018 -0500 |
| [ |
| @@ -55,6 +55,7 @@ "plots" , "p", 1, "character", "sample_table", "s", 1, "character", "tximport", "i", 0, "logical", + "txtype", "y", 1, "character", "tx2gene", "x", 1, "character", # a space-sep tx-to-gene map or GTF file (auto detect .gtf/.GTF) "fit_type", "t", 1, "integer", "many_contrasts", "m", 0, "logical", @@ -238,7 +239,7 @@ library("tximport") txiFiles <- as.character(sampleTable[,2]) names(txiFiles) <- as.character(sampleTable[,1]) - txi <- tximport(txiFiles, type="sailfish", tx2gene=tx2gene) + txi <- tximport(txiFiles, type=opt$txtype, tx2gene=tx2gene) dds <- DESeqDataSetFromTximport(txi, sampleTable[,3:ncol(sampleTable),drop=FALSE], designFormula) |
| b |
| diff -r 24a09ca67621 -r 25204a860b79 deseq2.xml --- a/deseq2.xml Tue Aug 01 17:20:46 2017 -0400 +++ b/deseq2.xml Sun Jan 28 04:04:12 2018 -0500 |
| [ |
| b'@@ -1,8 +1,8 @@\n-<tool id="deseq2" name="DESeq2" version="2.11.39">\n+<tool id="deseq2" name="DESeq2" version="2.11.40">\n <description>Determines differentially expressed features from count tables</description>\n <requirements>\n- <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>\n- <requirement type="package" version="1.20.0">r-getopt</requirement>\n+ <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>\n+ <requirement type="package" version="1.6.0">bioconductor-tximport</requirement>\n </requirements>\n <stdio>\n <regex match="Execution halted"\n@@ -18,68 +18,65 @@\n level="fatal"\n description="An undefined error occurred, please check your input carefully and contact your administrator." />\n </stdio>\n- <version_command>\n- <![CDATA[\n- echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\\$otherPkgs\\$DESeq2\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\n- ]]>\n- </version_command>\n- <command>\n- <![CDATA[\n- #if $tximport.tximport_selector == \'tximport\':\n- #if $tximport.mapping_format.mapping_format_selector == \'gtf\':\n- ln -s \'$tximport.mapping_format.gtf_file\' mapping.gtf &&\n- #else:\n- ln -s \'$tximport.mapping_format.tabular_file\' mapping.txt &&\n- #end if\n+ <version_command><![CDATA[\n+echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\\$otherPkgs\\$DESeq2\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\n+ ]]></version_command>\n+ <command><![CDATA[\n+#if $tximport.tximport_selector == \'tximport\':\n+ #if $tximport.mapping_format.mapping_format_selector == \'gtf\':\n+ ln -s \'$tximport.mapping_format.gtf_file\' mapping.gtf &&\n+ #else:\n+ ln -s \'$tximport.mapping_format.tabular_file\' mapping.txt &&\n+ #end if\n+#end if\n+\n+#import json\n+Rscript \'${__tool_directory__}/deseq2.R\'\n+ -o \'$deseq_out\'\n+ #if $pdf:\n+ -p \'$plots\'\n+ #end if\n+ #if $normCounts:\n+ -n \'$counts_out\'\n+ #end if\n+ #set $temp_factor_names = list()\n+ #for $factor in $rep_factorName:\n+ #set $temp_factor = list()\n+ #for $level in $factor.rep_factorLevel:\n+ #set $count_files = list()\n+ #for $file in $level.countsFile:\n+ $count_files.append(str($file))\n+ #end for\n+ $temp_factor.append( {str($level.factorLevel): $count_files} )\n+ #end for\n+ $temp_factor.reverse()\n+ $temp_factor_names.append([str($factor.factorName), $temp_factor])\n+ #end for\n+ -f \'#echo json.dumps(temp_factor_names)#\'\n+ -t $fit_type\n+ #if $outlier_replace_off:\n+ -a\n+ #end if\n+ #if $outlier_filter_off:\n+ -b\n+ #end if\n+ #if $auto_mean_filter_off:\n+ -c\n+ #end if\n+ #if $many_contrasts:\n+ -m\n+ #end if\n+ #if $tximport.tximport_selector == \'tximport\':\n+ -i\n+ -y $tximport.txtype\n+ #if $tximport.mapping_format.mapping_format_selector == \'gtf\':\n+ -x mapping.gtf\n+ #else:\n+ -x mapping.txt\n #end if\n \n- #import json\n- Rscript \'${__tool_directory__}/deseq2.R\'\n- -o \'$deseq_out\'\n- #if $pdf:\n- -p \'$plots\'\n- #end if\n- #if $normCounts:\n- -n \'$counts_out\'\n- #end if\n- #set $temp_factor_names = list()\n- #for $factor in $rep_factorName:\n- #set $temp_factor = list()\n- #for $level in $factor.rep_factorLevel:\n- #set $count_files = list()\n- #for $file in $level.countsFile:\n- $count_files.append(str($file))\n- #end for\n- $temp_factor.append( {str($level.factor'..b'enerated from **featureCounts** or **HTSeq-count** as input. Count tables must be generated for each sample individually. DESeq2 is capable of handling multiple factors that affect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Optionally, you can input one or more secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level.\n \n The following table gives some examples of factors and their levels:\n \n@@ -231,6 +239,50 @@\n \n *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor \'Treatment\' given in above table, DESeq2 computes fold changes of \'Treated\' samples against \'Untreated\', i.e. the values correspond to up or down regulations of genes in Treated samples.\n \n+DESeq2_ can also take transcript-level counts from quantification tools such as, **kallisto**, **Salmon** and **Sailfish**, and this Galaxy wrapper incorporates the Bioconductor tximport_ package to process the transcript counts for DESeq2. \n+\n+**Salmon or Sailfish Files**\n+\n+Salmon or Sailfish ``quant.sf`` files can be imported by setting type to *Salmon* or *Sailfish* respectively above. Note: for previous version of Salmon or Sailfish, in which the quant.sf files start with comment lines you will need to remove the comment lines before inputting here. An example of the format is shown below.\n+\n+Example:\n+\n+============ ========== =============== =========== ===========\n+Name Length EffectiveLength TPM NumReads\n+------------ ---------- --------------- ----------- -----------\n+NR_001526 164 20.4518 0 0\n+NR_001526_1 164 20.4518 0 0\n+NR_001526_2 164 20.4518 0 0\n+NM_130786 1764 1956.04 2.47415 109.165\n+NR_015380 2129 2139.53 1.77331 85.5821\n+NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05\n+NM_001198819 9527 7964.62 0 0\n+NM_001198820 9410 7855.78 0 0\n+NM_014576 9267 7714.88 0.0481114 8.37255\n+============ ========== =============== =========== ===========\n+\n+**kallisto Files**\n+\n+kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below.\n+\n+Example:\n+\n+============ ========== =============== =========== ===========\n+target_id length eff_length est_counts tpm \n+------------ ---------- --------------- ----------- -----------\n+NR_001526 164 20.4518 0 0 \n+NR_001526_1 164 20.4518 0 0 \n+NR_001526_2 164 20.4518 0 0 \n+NM_130786 1764 1956.04 109.165 2.47415 \n+NR_015380 2129 2139.53 85.5821 1.77331 \n+NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07\n+NM_001198819 9527 7964.62 0 0 \n+NM_001198820 9410 7855.78 0 0 \n+NM_014576 9267 7714.88 8.37255 0.0481114 \n+============ ========== =============== =========== ===========\n+\n+-----\n+\n **Output**\n \n DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF.\n@@ -249,8 +301,8 @@\n ====== ==========================================================\n \n .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html\n-]]>\n- </help>\n+.. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html\n+ ]]></help>\n <citations>\n <citation type="doi">10.1186/s13059-014-0550-8</citation>\n </citations>\n' |
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/deseq2_out.tab --- a/test-data/deseq2_out.tab Tue Aug 01 17:20:46 2017 -0400 +++ b/test-data/deseq2_out.tab Sun Jan 28 04:04:12 2018 -0500 |
| b |
| b'@@ -1,2834 +1,2836 @@\n-FBgn0003360\t1933.95040021558\t-2.83991687102949\t0.130961183226077\t-21.685180303594\t2.83145715225916e-104\t8.01868665519794e-101\n-FBgn0029167\t1648.81894046778\t-2.12372809661971\t0.112113641166475\t-18.9426377961111\t5.07877286348768e-80\t7.19154237469855e-77\n-FBgn0025111\t655.359768612902\t2.55894864737254\t0.138302392167512\t18.502562445002\t1.96886643746806e-76\t1.85860991696985e-73\n-FBgn0029896\t211.4755450268\t-2.07407256675321\t0.148479559524082\t-13.9687413769355\t2.41863176928996e-44\t1.71239129265729e-41\n-FBgn0000071\t151.249383869297\t2.06458183573632\t0.169507970356844\t12.1798510795098\t3.98007926509498e-34\t2.2543168957498e-31\n-FBgn0026562\t20055.4860668702\t-1.91086677288847\t0.162950135227575\t-11.72669645361\t9.3018616082061e-32\t4.39047867907328e-29\n-FBgn0023479\t1361.36610109448\t-1.42156038315625\t0.123506669852343\t-11.5099887710986\t1.17493699264726e-30\t4.7534593759672e-28\n-FBgn0027279\t1317.42349329018\t-1.15350641683542\t0.100486484478956\t-11.479219546953\t1.67788211203e-30\t5.9397026765862e-28\n-FBgn0003501\t116.651152955291\t1.78808517820052\t0.168523284263855\t10.6103152808305\t2.6684710536031e-26\t8.39678891533777e-24\n-FBgn0001226\t617.110611842554\t1.46001027487631\t0.147791323783547\t9.8788632343169\t5.14128115253018e-23\t1.45601082239655e-20\n-FBgn0001224\t272.471006012668\t1.31615145351197\t0.136612104703843\t9.6342227972054\t5.73241384383797e-22\t1.47583600052265e-19\n-FBgn0011260\t80.9068053807535\t1.71137695334904\t0.184209293173416\t9.29039422423677\t1.53717911159917e-20\t3.62774270337403e-18\n-FBgn0001137\t215.314997012827\t-1.28521041958388\t0.147255230704248\t-8.72777431020518\t2.59733309121308e-18\t5.65819024178112e-16\n-FBgn0003137\t2007.00068863624\t0.887637733050618\t0.105603853136098\t8.4053536560514\t4.26574175582113e-17\t8.62898618034675e-15\n-FBgn0002527\t17292.4505923723\t-0.735525851248499\t0.0925908703182105\t-7.94382695314009\t1.96037033074251e-15\t3.70117918444186e-13\n-FBgn0003748\t480.807341866837\t1.0077289575536\t0.131418781117298\t7.66807414424389\t1.74597956991682e-14\t3.09038383875277e-12\n-FBgn0001258\t671.110480695285\t0.892579602246089\t0.118082428269998\t7.55895365062437\t4.06324645426887e-14\t6.76889056381731e-12\n-FBgn0029002\t744.250236684945\t1.17587357213075\t0.158901984567632\t7.39999299146744\t1.3619168560445e-13\t2.14274918684335e-11\n-FBgn0001225\t193.977269091929\t1.18755187988066\t0.162298240188024\t7.31709646700343\t2.53393701950439e-13\t3.77689981012444e-11\n-FBgn0024288\t23.7733297010346\t-1.53124613304998\t0.214027995178113\t-7.15441983080616\t8.40275357027009e-13\t1.18982990555024e-10\n-FBgn0030237\t915.313685217584\t-0.849090147800569\t0.119257593849088\t-7.119799422375\t1.08084238487668e-12\t1.45759315903369e-10\n-FBgn0000116\t279.97574453728\t1.11564052545628\t0.158195330230593\t7.05229745928697\t1.75987475853307e-12\t2.16694144181116e-10\n-FBgn0002868\t45.7700929054867\t-1.5116382077707\t0.214235290118145\t-7.05597199666347\t1.71398343560758e-12\t2.16694144181116e-10\n-FBgn0016715\t64.2462306620967\t-1.41041403927465\t0.200700383800857\t-7.02746059855132\t2.10326174171527e-12\t2.48184885522401e-10\n-FBgn0000406\t120.154935949727\t-1.37736447095804\t0.199387971637467\t-6.90796169722013\t4.91666679704611e-12\t5.56960014769384e-10\n-FBgn0003502\t503.917225808725\t0.798463461494388\t0.120378797322169\t6.63292439579261\t3.29100401581098e-11\t3.58466283568334e-09\n-FBgn0024315\t31.3113542635758\t-1.3441403462269\t0.210263016185052\t-6.39266177483124\t1.63022599937328e-10\t1.70992593712042e-08\n-FBgn0029801\t670.98347311978\t-0.753327405425992\t0.124011322611833\t-6.07466632529979\t1.2424579800214e-09\t1.25665749979307e-07\n-FBgn0003076\t687.758986559078\t0.664168283408389\t0.110059206543036\t6.03464539014901\t1.59312139235705e-09\t1.45539347843715e-07\n-FBgn0004396\t1073.28279035238\t0.949255128802144\t0.157140716950303\t6.04079672808386\t1.53355079043847e-09\t1.45539347843715e-07\n-FBgn0027949\t652.544029710057\t0.643759137597885\t0.106651072172851\t6.03612438658411\t1.57859588675635e-09\t1.45539347843715e-07\n-FBgn0010591\t719.537870853329\t-0.675875965524672\t0.113603985922342\t-5.94940362380146\t2.69121248118555e-09\t2.3817230458'..b'+FBgn0004145\t7491.45125397969\t-0.00173132067848596\t0.130735346083461\t-0.0132429425580186\t0.989433969431458\t0.995023840801423\n+FBgn0013753\t257.142556697253\t0.00176669459661468\t0.147060504114112\t0.0120133859682937\t0.990414935368546\t0.995023840801423\n+FBgn0029508\t9.16870388329025\t0.00181163494877155\t0.148275321853417\t0.0122180476570639\t0.990251650951921\t0.995023840801423\n+FBgn0030594\t3.62961762362224\t-0.00200184429802549\t0.167413079084327\t-0.011957514364915\t0.990459511256463\t0.995023840801423\n+FBgn0017545\t12846.908740161\t0.00194663965106323\t0.176329464444646\t0.0110397865563434\t0.991191703673788\t0.99540655145695\n+FBgn0024230\t108.716502253845\t-0.00173422559968481\t0.178807465301691\t-0.00969884337188475\t0.992261563938755\t0.996127974566926\n+FBgn0012049\t1265.58497665408\t0.00101117762944179\t0.135745746875029\t0.00744905569949612\t0.994056568430144\t0.997576598771611\n+FBgn0001330\t194.903765892257\t-0.000816269237547889\t0.14376919601152\t-0.00567763651876083\t0.995469925818087\t0.99758195536367\n+FBgn0019968\t916.955935302438\t0.000652756303083771\t0.111176432369112\t0.00587135500909567\t0.995315363402696\t0.99758195536367\n+FBgn0026144\t5.67468986225991\t0.000953027816136364\t0.15634695816877\t0.0060955955094925\t0.995136448572679\t0.99758195536367\n+FBgn0029128\t2.36245282088433\t-0.000882240149496632\t0.13466626528014\t-0.00655130776561855\t0.994772850071998\t0.99758195536367\n+FBgn0029858\t84.7675753900815\t-0.000900927656668868\t0.189266326880986\t-0.00476010535796675\t0.996201999769985\t0.997962696128716\n+FBgn0020521\t2.3653829049525\t-0.000570950637375731\t0.141108882116086\t-0.00404617079246669\t0.996771631603193\t0.998180496100158\n+FBgn0026619\t134.661568577878\t-0.000562339849358497\t0.167804683312013\t-0.00335115706105111\t0.997326168524797\t0.998383031296106\n+FBgn0010504\t279.265073900721\t-0.000280958492894278\t0.124020050305149\t-0.00226542798686975\t0.998192451531772\t0.998897389703758\n+FBgn0011327\t221.75669985069\t-0.000210436168350216\t0.13552520454093\t-0.00155274562442488\t0.998761088737257\t0.999113634126857\n FBgn0010602\t788.37057626526\t-0.000120355421911384\t0.117913033701391\t-0.00102071347105002\t0.999185588621862\t0.999185588621862\n FBgn0000003\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0000014\t0.774548298118524\t0.00827091884508803\t0.0792234901769868\t0.104399829225027\t0.916852058201328\tNA\n@@ -3362,7 +3364,6 @@\n FBgn0013467\t0.105352514349918\t0.00872518825807776\t0.0476319012243461\t0.183179508560495\t0.85465717212165\tNA\n FBgn0013672\t32.2343447251885\t-0.026574633997878\t0.0789974708191096\t-0.336398541906857\tNA\tNA\n FBgn0013673\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0013680\t9.65311858025122\t0.100945622860549\t0.0898103513940739\t1.12398650371175\tNA\tNA\n FBgn0013681\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0013682\t49.1512095932707\t0.0416127054476129\t0.0878441008281923\t0.47371087022679\tNA\tNA\n FBgn0013683\t1.06135572369289\t0.0507762622659519\t0.0809158097805592\t0.627519670181332\t0.530318646477612\tNA\n@@ -3694,7 +3695,7 @@\n FBgn0028867\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0028868\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0028870\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0028871\t1.30688716654013\t-0.0827799575015634\t0.0749279765878027\t-1.10479371352781\tNA\tNA\n+FBgn0028871\t1.30688716654013\t-0.0827799575015634\t0.0749279765878027\t-1.10479371352781\t0.269248985130732\tNA\n FBgn0028872\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0028873\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0028875\t0.306412078433015\t-0.00818803272986435\t0.0526497593393943\t-0.15551890137013\t0.876412254086124\tNA\n@@ -3862,7 +3863,6 @@\n FBgn0030050\t1.58908631955764\t-0.0847523877989257\t0.10392226572933\t-0.815536374271002\t0.414765352454612\tNA\n FBgn0030058\t0.100529782041548\t-0.0122785059273882\t0.0476319012243461\t-0.257779043283545\t0.796577439055695\tNA\n FBgn0030074\t0.080862070626247\t0.00872518825807775\t0.0476319012243461\t0.183179508560495\t0.85465717212165\tNA\n-FBgn0030078\t24.2253301322966\t0.473125173225922\t0.199979801311173\t2.36586480296442\tNA\tNA\n FBgn0030080\t0.325102132866858\t-0.0260146539807918\t0.0534896275034751\t-0.486349507277867\t0.626719383754575\tNA\n FBgn0030094\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030097\t0.100529782041548\t-0.0122785059273882\t0.0476319012243461\t-0.257779043283545\t0.796577439055695\tNA\n' |
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/deseq2_out_filtered.tab --- a/test-data/deseq2_out_filtered.tab Tue Aug 01 17:20:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,11362 +0,0 @@\n-<<<<<<< 32814b042e5c76fbb4786cff0edf98023718d3b2\n-<<<<<<< c2d5ab40b214e429d8a9d0c5b2b35adfc46a87e6\n-FBgn0003360\t1933.95040021558\t-2.83931225259512\t0.131427106250417\t-21.6037036316175\t1.65776764506556e-103\t4.8042106354e-100\n-FBgn0029167\t1648.81894046778\t-2.12846961402501\t0.111026270383108\t-19.1708647573273\t6.48222732792777e-82\t9.39274739816734e-79\n-FBgn0025111\t655.359768612902\t2.56442932254547\t0.137667337786547\t18.6277250928003\t1.91492266642432e-77\t1.84981529576589e-74\n-FBgn0029896\t211.4755450268\t-2.08777266242928\t0.146415559688566\t-14.259226730206\t3.92782602934154e-46\t2.84570995825794e-43\n-FBgn0000071\t151.249383869297\t2.07788820686474\t0.168180792411128\t12.3550863155956\t4.57265091805509e-35\t2.65030847210473e-32\n-FBgn0027279\t1317.42349329018\t-1.15789518800581\t0.0979487486398482\t-11.8214393147923\t3.02457627375306e-32\t1.46087034022273e-29\n-FBgn0023479\t1361.36610109448\t-1.42278093472624\t0.123382435239163\t-11.5314706827462\t9.15659861926778e-31\t3.79083182837686e-28\n-FBgn0026562\t20055.4860668702\t-1.89651458906925\t0.165538620287047\t-11.4566291888905\t2.17828498754631e-30\t7.89083736738651e-28\n-FBgn0003501\t116.651152955291\t1.80587013415947\t0.166034666709106\t10.8764643550215\t1.4923989382969e-27\t4.80552458131602e-25\n-FBgn0001224\t272.471006012668\t1.32281610420226\t0.134495231954035\t9.83541263867513\t7.92420868827822e-23\t2.29643567786303e-20\n-FBgn0001226\t617.110611842554\t1.45833378003199\t0.148670311493448\t9.80917955563887\t1.02800965013455e-22\t2.70833815099084e-20\n-FBgn0011260\t80.9068053807535\t1.72804169137515\t0.182772479814818\t9.45460549162528\t3.24242333829425e-21\t7.83045236198062e-19\n-FBgn0001137\t215.314997012827\t-1.29233946143563\t0.145480311328745\t-8.88326021323463\t6.49288454986043e-19\t1.4474138019612e-16\n-FBgn0003137\t2007.00068863624\t0.88961461517836\t0.104287926638967\t8.53037013822416\t1.45880207669652e-17\t3.01972029876181e-15\n-FBgn0002527\t17292.4505923723\t-0.73741537684446\t0.0906423933125779\t-8.13543585837923\t4.10458911152738e-16\t7.9300661634709e-14\n-FBgn0003748\t480.807341866837\t1.01051140923348\t0.130425339228426\t7.74781507344736\t9.34871517251503e-15\t1.69328603562178e-12\n-FBgn0001258\t671.110480695285\t0.895361035906691\t0.116548074382586\t7.68233229634957\t1.56217979166483e-14\t2.66305708014393e-12\n-FBgn0001225\t193.977269091929\t1.19104458118686\t0.161805985086091\t7.36094267806688\t1.82615977838543e-13\t2.94011724320054e-11\n-FBgn0024288\t23.7733297010346\t-1.57498520895134\t0.214878970749195\t-7.32963864942211\t2.30774118216246e-13\t3.51991260310884e-11\n-FBgn0029002\t744.250236684945\t1.17108784869134\t0.160714198398625\t7.28677279518668\t3.1746761716241e-13\t4.60010577268332e-11\n-FBgn0030237\t915.313685217584\t-0.850733962006436\t0.118429991807523\t-7.18343342781852\t6.79821458130211e-13\t9.38153612219691e-11\n-FBgn0002868\t45.7700929054867\t-1.52440216488712\t0.214738495601196\t-7.09887698812132\t1.25774693967815e-12\t1.59658579154825e-10\n-FBgn0016715\t64.2462306620967\t-1.42223206792763\t0.200375069888307\t-7.09784939174522\t1.26713158059385e-12\t1.59658579154825e-10\n-FBgn0000116\t279.97574453728\t1.11632215948692\t0.158425268315346\t7.04636432910989\t1.83653016084046e-12\t2.21761016921486e-10\n-FBgn0000406\t120.154935949727\t-1.37174695998837\t0.200388894764987\t-6.84542405205206\t7.62496639944616e-12\t8.83886105023799e-10\n-FBgn0003502\t503.917225808725\t0.801327660473763\t0.118268610139101\t6.77548894445694\t1.23986224053237e-11\t1.38196952810108e-09\n-FBgn0024315\t31.3113542635758\t-1.3763209973179\t0.20963230775834\t-6.56540497996374\t5.18916350280528e-11\t5.56970215967767e-09\n-FBgn0027949\t652.544029710057\t0.646429666729111\t0.103801654132743\t6.22754687418032\t4.73795011529377e-10\t4.90377836932905e-08\n-FBgn0003076\t687.758986559078\t0.667050302734252\t0.107718459531582\t6.19253473949538\t5.92042952512063e-10\t5.91634647027572e-08\n-FBgn0029801\t670.98347311978\t-0.754988069284397\t0.123107613719941\t-6.13274879165415\t8.63734806999727e-10\t8.34367823561736e-08\n-FBgn0010591\t719.537870853329\t-0.678169968761112\t0.111477787189876\t-6.08345380596773\t1.17620817098387e-09\t1.09956492887459e-07\n-FBgn00'..b'834\t0.341683203371434\tNA\n-FBgn0030618\t0.205882296391466\t0.00423405052771355\t0.0447574735163511\t0.0945998555116551\t0.924632664607429\tNA\n-FBgn0030619\t0.080862070626247\t0.0230872191457161\t0.0399975247953908\t0.577216196847676\t0.563793416904323\tNA\n-=======\n-=======\n->>>>>>> add new deseq2\n-FBgn0030443\t0.080862070626247\t0.023087219145506\t0.0399975247950268\t0.577216196847677\t0.563793416904322\tNA\n-FBgn0030449\t0.631222387582343\t-0.069918508729723\t0.0690250631909992\t-1.01294378443742\t0.311087013088738\tNA\n-FBgn0030462\t0.0923751652987496\t-0.0204895043497049\t0.040273193485586\t-0.5087628413932\t0.610918468289381\tNA\n-FBgn0030477\t0.661041167025807\t-0.00819847469940316\t0.0850498198112658\t-0.0963961442551719\t0.923205954303339\tNA\n-FBgn0030491\t1.23119801662681\t0.0641480244241913\t0.107889436871621\t0.594571871762773\t0.552129686837968\tNA\n-FBgn0030492\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030493\t0.105352514349918\t0.0254741503089926\t0.040583050041178\t0.627704183967076\t0.530197743974527\tNA\n-FBgn0030494\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030495\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030509\t0.105352514349918\t0.0254741503089926\t0.040583050041178\t0.627704183967076\t0.530197743974527\tNA\n-FBgn0030536\t1.19456732550319\t-0.0654391021551412\t0.0865521046423288\t-0.756065983901423\t0.449609635388738\tNA\n-FBgn0030537\t0.0923751652987496\t-0.0204895043497049\t0.040273193485586\t-0.5087628413932\t0.610918468289381\tNA\n-FBgn0030538\t0.080862070626247\t0.023087219145506\t0.0399975247950268\t0.577216196847677\t0.563793416904322\tNA\n-FBgn0030539\t0.181391852667795\t0.000922878063793952\t0.0431227546273171\t0.0214011853317305\t0.982925628025152\tNA\n-FBgn0030540\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030541\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030542\t0.24813606918961\t0.0328712249934809\t0.0428867883451263\t0.766465064461196\t0.443399631338737\tNA\n-FBgn0030543\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030544\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030551\t0.700889780748892\t0.0020840503361408\t0.0848780550075907\t0.0245534648025856\t0.980411137804398\tNA\n-FBgn0030558\t0.100529782041548\t-0.0209903901433803\t0.0404598159836309\t-0.518795986414583\t0.603903017085169\tNA\n-FBgn0030563\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030566\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030569\t0.953050839550445\t0.0285435775734393\t0.0975885126788574\t0.292489113625187\t0.76991268222557\tNA\n-FBgn0030570\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030577\t0.269423611141796\t-0.026592624307814\t0.0432208120592152\t-0.615273592531775\t0.538374054087345\tNA\n-FBgn0030578\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030595\t0.90385617240921\t0.0140835782037349\t0.0874061821492121\t0.161127941496091\t0.87199263363864\tNA\n-FBgn0030608\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030614\t0.210705028699836\t0.0343775297986814\t0.043774172333087\t0.785338202104552\t0.432255303094243\tNA\n-FBgn0030617\t0.267076655602412\t0.0501740190928278\t0.0527678364612048\t0.950844727729477\t0.341683203385323\tNA\n-FBgn0030618\t0.205882296391466\t0.00423405052709174\t0.0447574735119474\t0.09459985550707\t0.924632664611071\tNA\n-FBgn0030619\t0.080862070626247\t0.023087219145506\t0.0399975247950268\t0.577216196847677\t0.563793416904322\tNA\n-<<<<<<< 32814b042e5c76fbb4786cff0edf98023718d3b2\n->>>>>>> add new deseq2\n-=======\n->>>>>>> add new deseq2\n-FBgn0030620\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030621\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030622\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030623\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030624\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030640\t0\tNA\tNA\tNA\tNA\tNA\n-<<<<<<< 32814b042e5c76fbb4786cff0edf98023718d3b2\n-<<<<<<< c2d5ab40b214e429d8a9d0c5b2b35adfc46a87e6\n-FBgn0030663\t1.2590203447849\t0.0316273222798865\t0.104066953284795\t0.303913214345129\t0.761194010092697\tNA\n-FBgn0030688\t0.827337508607711\t0.0122149676539822\t0.0936309991990391\t0.130458584854102\t0.896203618553293\tNA\n-=======\n-FBgn0030663\t1.2590203447849\t0.0316273222752506\t0.104066953276194\t0.303913214325699\t0.7611940101075\tNA\n-FBgn0030688\t0.827337508607711\t0.0122149676551879\t0.0936309992070552\t0.13045858485581\t0.896203618551941\tNA\n->>>>>>> add new deseq2\n-=======\n-FBgn0030663\t1.2590203447849\t0.0316273222752506\t0.104066953276194\t0.303913214325699\t0.7611940101075\tNA\n-FBgn0030688\t0.827337508607711\t0.0122149676551879\t0.0936309992070552\t0.13045858485581\t0.896203618551941\tNA\n->>>>>>> add new deseq2\n' |
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/deseq2_tximport_out.tab --- a/test-data/deseq2_tximport_out.tab Tue Aug 01 17:20:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -WASH7P 9900.55558083217 -4.23770405949884 0.206202398724737 -20.5511870167709 7.51041665825148e-94 3.00416666330059e-93 -DDX11L1 537.947385623122 0.311741386141816 0.207236860051557 1.50427576476627 0.132510376563798 0.265020753127596 -MIR6859-1 1535.69554043224 0.215149819624812 0.188163354844762 1.14342040618012 0.252864083997862 0.33715211199715 -MIR6859-2 80.7433269754715 -0.177756825325613 0.275440631693817 -0.645354406256263 0.5186975427612 0.5186975427612 |
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/genes_sub.gtf --- a/test-data/genes_sub.gtf Tue Aug 01 17:20:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,15 +0,0 @@ -chr1 unknown exon 11874 12227 . + . gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NM_001168316"; tss_id "TSS16107"; -chr1 unknown exon 12613 12721 . + . gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NM_174914"; tss_id "TSS16107"; -chr1 unknown exon 13221 14409 . + . gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NR_031764"; tss_id "TSS16107"; -chr1 unknown exon 14362 14829 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_004503"; tss_id "TSS8151"; -chr1 unknown exon 14970 15038 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_006897"; tss_id "TSS8151"; -chr1 unknown exon 15796 15947 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_014212"; tss_id "TSS8151"; -chr1 unknown exon 16607 16765 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_014620"; tss_id "TSS8151"; -chr1 unknown exon 16858 17055 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_017409"; tss_id "TSS8151"; -chr1 unknown exon 17233 17368 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_017410"; tss_id "TSS8151"; -chr1 unknown exon 17369 17436 . - . gene_id "MIR6859-2"; gene_name "MIR6859-2"; transcript_id "NM_018953"; tss_id "TSS24460"; -chr1 unknown exon 17369 17436 . - . gene_id "MIR6859-1"; gene_name "MIR6859-1"; transcript_id "NM_022658"; tss_id "TSS24460"; -chr1 unknown exon 17606 17742 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_153633"; tss_id "TSS8151"; -chr1 unknown exon 17915 18061 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_153693"; tss_id "TSS8151"; -chr1 unknown exon 18268 18366 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_173860"; tss_id "TSS8151"; -chr1 unknown exon 24738 24891 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NR_003084"; tss_id "TSS8151"; |
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/sailfish/out_deseq2_sailfish.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/out_deseq2_sailfish.tab Sun Jan 28 04:04:12 2018 -0500 |
| b |
| @@ -0,0 +1,4 @@ +MIR6859-2 1.1858265336986 -1.58325519934585 1.29566733255222 -1.22196119294536 0.221722302676964 0.886889210707858 +DDX11L1 1.91972630671259 -0.204757212641591 1.31524142129485 -0.155680325548148 0.876285006005361 0.999999999763967 +MIR6859-1 0.294068009390125 -0.712896459907293 1.28824575367762 -0.55338545294805 0.579999497913718 0.999999999763967 +WASH7P 114.545909292233 -3.75034560711482e-10 1.2677635335979 -2.95823748492859e-10 0.999999999763967 0.999999999763967 |
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/sailfish/sailfish_quant.sf1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf1.tab Sun Jan 28 04:04:12 2018 -0500 |
| b |
| b'@@ -0,0 +1,48010 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|
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/sailfish/sailfish_quant.sf2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf2.tab Sun Jan 28 04:04:12 2018 -0500 |
| b |
| b'@@ -0,0 +1,48010 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0\t0\n+NM_175056\t3619\t2901.7\t0.0120886\t1\n+NM_003904\t1777\t1618.26\t36.1995\t1670.02\n+NM_017580\t4941\t4162.29\t7.74774\t919.344\n+NM_005455\t3144\t2524.11\t20.7689\t1494.48\n+NM_203350\t3069\t2445.95\t18.7678\t1308.67\n+NR_038420\t1674\t1697\t0.479102\t23.1782\n+NR_046217\t783\t487.114\t0.504078\t7\n+NM_001286568\t6818\t5867.68\t0.147893\t24.7392\n+NM_001286569\t6947\t5995.23\t0.107643\t18.3976\n+NM_032143\t6729\t5778.72\t0.831907\t137.049\n+NM_005089\t1509\t1367.2\t25.924\t1010.42\n+NM_182572\t2054\t1861.64\t0\t0\n+NM_001282415\t2272\t2079.64\t0\t0\n+NM_001282416\t2467\t2274.64\t0\t0\n+NM_032805\t2463\t2270.64\t0\t0\n+NM_001163391\t3517\t3037.04\t0.449737\t38.9386\n+NR_028077\t4342\t3745.35\t2.73673\t292.21\n+NR_024063\t4054\t3548.75\t0.298582\t30.2072\n+NM_025231\t1273\t1020.06\t5.22696\t152\n+NR_103455\t2186\t1928.5\t0\t0\n+NR_103456\t1989\t1738.01\t2.58406\t128.034\n+NM_001145542\t2573\t2921.74\t0.300257\t25.0095\n+NM_001145543\t2684\t3054.46\t1.05725\t92.0625\n+NM_001145544\t2218\t2503.33\t0.797698\t56.9281\n+NM_023926\t2928\t3259.54\t0\t0\n+NR_027135\t1778\t1585.64\t0\t0\n+NM_001007072\t934\t814.861\t1.55796\t36.1919\n+NM_017894\t988\t873.337\t0.669511\t16.669\n+NM_181877\t3747\t3771.5\t0.86685\t93.2028\n+NM_145238\t4216\t4070.6\t0.508421\t59\n+NM_145914\t1987\t1825.88\t4.51172\t234.847\n+NM_181846\t4643\t4619.94\t1.40277\t184.754\n+NM_001012455\t3160\t2967.64\t0\t0\n+NM_145115\t4349\t4341.49\t2.61839\t324.073\n+NM_001023560\t2834\t2429.12\t1.63144\t112.977\n+NM_001111039\t2831\t2426.13\t0.496342\t34.3293\n+NM_001287421\t2321\t1870\t1.66341\t88.6771\n+NM_001287422\t2231\t1801.51\t1.27983\t65.729\n+NM_152736\t2430\t1998.5\t0.900199\t51.2877\n+NM_152455\t5607\t5142.62\t3.68895\t540.826\n+NM_001112734\t4142\t3652.25\t1.26743\t131.964\n+NM_001166012\t4346\t3932.27\t0.104591\t11.7249\n+NM_001288711\t3439\t2904.9\t2.6135\t216.434\n+NM_001135216\t3047\t2598.01\t0\t0\n+NM_001243241\t2972\t2546.73\t0.0791284\t5.74493\n+NM_001243242\t2669\t2188.23\t0\t0\n+NM_001243243\t2571\t2103.54\t0.320025\t19.1914\n+NM_001243244\t2560\t2103.35\t0.484696\t29.0637\n+NM_030899\t3036\t2597.44\t0\t0\n+NM_001284527\t3173\t2987.72\t0.838473\t71.4167\n+NM_001284528\t2788\t2573.24\t0.69945\t51.3106\n+NM_001284529\t2235\t2002.76\t2.38473\t136.157\n+NM_017810\t3071\t2879.12\t0.683688\t56.1161\n+NM_152677\t2245\t1829.1\t0.154704\t8.06694\n+NM_024303\t1920\t1779.87\t1.41898\t72\n+NM_001080456\t1625\t1432.64\t0\t0\n+NM_001199479\t1833\t1601.81\t0.288092\t13.1556\n+NM_001199480\t1644\t1417.26\t2.7675\t111.817\n+NM_006299\t1680\t1455.87\t1.90561\t79.091\n+NM_080603\t2786\t2674.07\t5.46085\t416.297\n+NM_182521\t2446\t2253.64\t0\t0\n+NM_080752\t2815\t2707.78\t2.00793\t155\n+NR_037628\t2970\t2824.77\t0\t0\n+NM_023072\t4339\t5121.28\t4.39227\t641.265\n+NM_020883\t5834\t5831.9\t0.0481183\t8\n+NM_020928\t5502\t5124.83\t0.434865\t63.5337\n+NM_001042697\t2005\t1702.96\t2.28558\t110.961\n+NM_001042698\t1875\t1591.79\t2.90435\t131.797\n+NM_001242487\t6047\t6756.59\t0.277103\t53.3751\n+NM_001242488\t5955\t6646.48\t1.40329\t265.895\n+NM_015037\t6062\t6774.22\t3.15006\t608.343\n+NR_038357\t1458\t1378.13\t0.728304\t28.6137\n+NM_145062\t2211\t1705.96\t10.8425\t527.314\n+NM_004724\t2946\t2456.99\t7.58089\t531\n+NM_001287821\t3285\t2639.77\t0.30007\t22.5819\n+NM_001287822\t3189\t2563.11\t0\t0\n+NM_001287823\t3138\t2505.64\t3.3153\t236.817\n+NM_017975\t3190\t2553.11\t5.79904\t422.081\n+NM_001005413\t1519\t1291.81\t2.65649\t97.8311\n+NM_007057\t1660\t1439.67\t33.0427\t1356.15\n+NM_032997\t1851\t1637.22\t4.54806\t212.278\n+NM_007156\t5202\t4903.32\t0.487978\t68.212\n+NM_007157\t5640\t5323.04\t1.57834\t239.513\n+NM_001040653\t4813\t4827.93\t2.28264\t314.173\n+NM_025112\t3404\t3712.11\t2.15481\t228.035\n+NR_104249\t3584\t3853.87\t1.22491e-06\t0.000134577\n+NM_001004339\t4271\t3931.98\t0.320884\t35.969\n+NM_024646\t8140\t6846.49\t2.51144\t490.186\n+NM_001010972\t2305\t2569.37\t13.355\t978.228\n+NM_003461\t2308\t2573.55\t20.8903\t1532.67\n+NM_015113\t11394\t11827\t3.01682\t1017.18\n+NM_015534\t4322\t3486.88\t5.81461\t578\n' |
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/sailfish/sailfish_quant.sf3.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf3.tab Sun Jan 28 04:04:12 2018 -0500 |
| b |
| b'@@ -0,0 +1,48010 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3\t990.073\n+NM_005455\t3144\t2586.54\t15.2987\t1324.74\n+NM_203350\t3069\t2511.83\t24.5249\t2062.3\n+NR_038420\t1674\t1679.47\t0.680923\t38.2847\n+NR_046217\t783\t496.155\t0.722452\t12\n+NM_001286568\t6818\t5969.5\t0.277171\t55.3913\n+NM_001286569\t6947\t6094.96\t0.198665\t40.5366\n+NM_032143\t6729\t5878.58\t1.53745\t302.572\n+NM_005089\t1509\t1380.91\t15.1793\t701.731\n+NM_182572\t2054\t1857.44\t0\t0\n+NM_001282415\t2272\t2075.44\t0\t0\n+NM_001282416\t2467\t2270.44\t0\t0\n+NM_032805\t2463\t2266.44\t0\t0\n+NM_001163391\t3517\t3070.79\t1.35718\t139.521\n+NR_028077\t4342\t3792.93\t2.20246\t279.665\n+NR_024063\t4054\t3564.05\t0.530158\t63.2565\n+NM_025231\t1273\t1022.72\t4.54311\t155.548\n+NR_103455\t2186\t1927.05\t0.260494\t16.8053\n+NR_103456\t1989\t1723.63\t1.27646\t73.6557\n+NM_001145542\t2573\t2836.41\t8.65518e-09\t8.21865e-07\n+NM_001145543\t2684\t2968.48\t2.41517\t240.015\n+NM_001145544\t2218\t2430.23\t0.319467\t25.9913\n+NM_023926\t2928\t3284.71\t0.359906\t39.5768\n+NR_027135\t1778\t1581.44\t0\t0\n+NM_001007072\t934\t798.284\t1.03386\t27.6295\n+NM_017894\t988\t854.192\t0.259518\t7.42127\n+NM_181877\t3747\t3704.46\t1.20982\t150.038\n+NM_145238\t4216\t4029.25\t1.12685\t152\n+NM_145914\t1987\t1820.79\t2.84167\t173.216\n+NM_181846\t4643\t4560.75\t1.79455\t273.998\n+NM_001012455\t3160\t2600.1\t0.183892\t16.0069\n+NM_145115\t4349\t4269.64\t4.06134\t580.519\n+NM_001023560\t2834\t2459.99\t1.47759\t121.686\n+NM_001111039\t2831\t2456.95\t0.56469\t46.4474\n+NM_001287421\t2321\t1904.36\t1.12051\t71.4367\n+NM_001287422\t2231\t1846.17\t0\t0\n+NM_152736\t2430\t2030.91\t1.15386\t78.4508\n+NM_152455\t5607\t5146.53\t5.04724\t869.608\n+NM_001112734\t4142\t3656.8\t1.87405\t229.423\n+NM_001166012\t4346\t3931.62\t0.441123\t58.0611\n+NM_001288711\t3439\t2903.49\t1.03245\t100.356\n+NM_001135216\t3047\t2609.46\t0.198972\t17.3819\n+NM_001243241\t2972\t2565.54\t0\t0\n+NM_001243242\t2669\t2221.94\t0\t0\n+NM_001243243\t2571\t2118.21\t9.66746e-06\t0.000685544\n+NM_001243244\t2560\t2119.16\t0.184038\t13.0564\n+NM_030899\t3036\t2610.4\t0.39548\t34.561\n+NM_001284527\t3173\t2985.02\t2.15079\t214.932\n+NM_001284528\t2788\t2579.97\t1.07109\t92.5116\n+NM_001284529\t2235\t2007.8\t1.52666\t102.617\n+NM_017810\t3071\t2875.9\t0.657894\t63.3409\n+NM_152677\t2245\t1851.74\t0.0812734\t5.03829\n+NM_024303\t1920\t1783.88\t2.3277\t139.011\n+NM_001080456\t1625\t1524.26\t0.0395208\t2.01669\n+NM_001199479\t1833\t1606.63\t0.353717\t19.0251\n+NM_001199480\t1644\t1424.22\t1.69304\t80.7233\n+NM_006299\t1680\t1464.07\t2.35142\t115.252\n+NM_080603\t2786\t2622.66\t6.07938\t533.773\n+NM_182521\t2446\t2249.44\t0\t0\n+NM_080752\t2815\t2676.53\t2.54292\t227.856\n+NR_037628\t2970\t2836.96\t0.517441\t49.1439\n+NM_023072\t4339\t4956.94\t4.84886\t804.651\n+NM_020883\t5834\t5782.39\t0.0568238\t11\n+NM_020928\t5502\t5163.86\t1.10789\t191.525\n+NM_001042697\t2005\t1724.86\t2.69474\t155.606\n+NM_001042698\t1875\t1611.49\t1.94565\t104.966\n+NM_001242487\t6047\t6519.97\t0.35095\t76.6031\n+NM_001242488\t5955\t6418.17\t2.56883\t551.952\n+NM_015037\t6062\t6536.77\t4.29068\t938.953\n+NR_038357\t1458\t1331.71\t1.41279\t62.9859\n+NM_145062\t2211\t1755.44\t9.69387\t569.69\n+NM_004724\t2946\t2505.37\t13.413\t1125\n+NM_001287821\t3285\t2697.29\t4.03351\t364.222\n+NM_001287822\t3189\t2616.34\t0.303983\t26.6255\n+NM_001287823\t3138\t2564.22\t0\t0\n+NM_017975\t3190\t2609.85\t16.6842\t1457.72\n+NM_001005413\t1519\t1286.43\t3.13859\t135.169\n+NM_007057\t1660\t1434.78\t67.8606\t3259.56\n+NM_032997\t1851\t1628.11\t10.7727\t587.168\n+NM_007156\t5202\t4918.95\t0.996459\t164.092\n+NM_007157\t5640\t5355.34\t1.98545\t355.96\n+NM_001040653\t4813\t4812.52\t2.55748\t412.04\n+NM_025112\t3404\t3660.33\t2.01529\t246.952\n+NR_104249\t3584\t3807.28\t0.525715\t67.0071\n+NM_001004339\t4271\t3969.41\t1.11649\t148.366\n+NM_024646\t8140\t6971.44\t3.82374\t892.412\n+NM_001010972\t2305\t2451.71\t29.5375\t2424.36\n+NM_003461\t2308\t2458.79\t29.538\t2431.41\n+NM_015113\t11394\t11785\t8.43254\t3326.92\n+NM_015534\t4322\t3573.57\t10.0651\t1204.14\n' |
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/sailfish/sailfish_quant.sf4.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf4.tab Sun Jan 28 04:04:12 2018 -0500 |
| b |
| b'@@ -0,0 +1,48010 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3904\t1777\t1586.79\t33.5806\t1357.26\n+NM_017580\t4941\t4262.49\t5.94646\t645.622\n+NM_005455\t3144\t2587.51\t28.769\t1896.11\n+NM_203350\t3069\t2511.01\t23.154\t1480.92\n+NR_038420\t1674\t1649.11\t1.22787\t51.5775\n+NR_046217\t783\t476.496\t0.494351\t6\n+NM_001286568\t6818\t6035.33\t0\t0\n+NM_001286569\t6947\t6116.3\t0.190218\t29.6344\n+NM_032143\t6729\t5903.41\t0.982022\t147.666\n+NM_005089\t1509\t1351.37\t26.0217\t895.708\n+NM_182572\t2054\t1835.38\t0\t0\n+NM_001282415\t2272\t2624.18\t0.0299213\t2\n+NM_001282416\t2467\t2767\t0\t0\n+NM_032805\t2463\t2759.31\t0\t0\n+NM_001163391\t3517\t3059.13\t0.561113\t43.7225\n+NR_028077\t4342\t3792.51\t1.95155\t188.522\n+NR_024063\t4054\t3553.18\t0.291129\t26.3488\n+NM_025231\t1273\t1004.35\t6.25421\t159.998\n+NR_103455\t2186\t1908.32\t0.060533\t2.94239\n+NR_103456\t1989\t1705.18\t2.28416\t99.2094\n+NM_001145542\t2573\t2791.58\t3.27047e-06\t0.00023255\n+NM_001145543\t2684\t2925.29\t0.765026\t57.0036\n+NM_001145544\t2218\t2383.64\t0.312873\t18.9962\n+NM_023926\t2928\t3136.75\t0\t0\n+NR_027135\t1778\t1559.38\t0\t0\n+NM_001007072\t934\t772.48\t0.41627\t8.19068\n+NM_017894\t988\t829.503\t0.958921\t20.2609\n+NM_181877\t3747\t3688.74\t0.642054\t60.3263\n+NM_145238\t4216\t4011.8\t0.812235\t83\n+NM_145914\t1987\t1796.51\t3.24996\t148.718\n+NM_181846\t4643\t4559.56\t1.45827\t169.363\n+NM_001012455\t3160\t2606.03\t0.0903888\t6\n+NM_145115\t4349\t4257.03\t2.87548\t311.799\n+NM_001023560\t2834\t2444.8\t1.42074\t88.474\n+NM_001111039\t2831\t2446.36\t0\t0\n+NM_001287421\t2321\t1894.02\t1.45489\t70.1896\n+NM_001287422\t2231\t1823.77\t0.713248\t33.1335\n+NM_152736\t2430\t2021.34\t1.13046\t58.2038\n+NM_152455\t5607\t5148.58\t4.44569\t583.021\n+NM_001112734\t4142\t3654.09\t1.94779\t181.292\n+NM_001166012\t4346\t3919.47\t0.240972\t24.0575\n+NM_001288711\t3439\t2907.7\t2.8835\t213.564\n+NM_001135216\t3047\t2605.77\t0.357514\t23.7294\n+NM_001243241\t2972\t2558.09\t0\t0\n+NM_001243242\t2669\t2204.23\t0.121168\t6.80299\n+NM_001243243\t2571\t2116.67\t0.231246\t12.4677\n+NM_001243244\t2560\t2126.92\t0\t0\n+NM_030899\t3036\t2604.41\t0\t0\n+NM_001284527\t3173\t2969.67\t0.422704\t31.9743\n+NM_001284528\t2788\t2563.5\t0.919011\t60.0083\n+NM_001284529\t2235\t1989.75\t2.33298\t118.241\n+NM_017810\t3071\t2860.19\t0.68333\t49.7832\n+NM_152677\t2245\t1851.24\t0.237545\t11.2012\n+NM_024303\t1920\t1756.55\t2.16797\t97\n+NM_001080456\t1625\t1502.88\t0.078368\t3\n+NM_001199479\t1833\t1588.58\t0.901778\t36.4894\n+NM_001199480\t1644\t1404.64\t0.689358\t24.6642\n+NM_006299\t1680\t1446.54\t2.27561\t83.8464\n+NM_080603\t2786\t2616.76\t6.41425\t427.531\n+NM_182521\t2446\t2227.38\t0\t0\n+NM_080752\t2815\t2651.55\t1.43668\t97.0324\n+NR_037628\t2970\t2813.89\t0.180924\t12.9676\n+NM_023072\t4339\t4880.25\t3.09359\t384.558\n+NM_020883\t5834\t5773.13\t0.0816043\t12\n+NM_020928\t5502\t5160.27\t1.54941\t203.655\n+NM_001042697\t2005\t1709.23\t4.35824\t189.744\n+NM_001042698\t1875\t1595.14\t0.602229\t24.4691\n+NM_001242487\t6047\t6475.41\t1.80413\t297.573\n+NM_001242488\t5955\t6371.8\t1.57548\t255.701\n+NM_015037\t6062\t6492.51\t2.49775\t413.066\n+NR_038357\t1458\t1307.56\t1.67779\t55.8802\n+NM_145062\t2211\t1737.58\t9.77827\t432.778\n+NM_004724\t2946\t2495.21\t9.37699\t595.975\n+NM_001287821\t3285\t2707.12\t1.21001\t83.4361\n+NM_001287822\t3189\t2627.5\t0\t0\n+NM_001287823\t3138\t2570.45\t1.64238\t107.532\n+NM_017975\t3190\t2619.14\t14.0891\t939.938\n+NM_001005413\t1519\t1268.79\t6.41606\t207.356\n+NM_007057\t1660\t1416.86\t71.1103\t2566.35\n+NM_032997\t1851\t1608.73\t8.23163\t337.308\n+NM_007156\t5202\t4913.47\t0.572489\t71.6495\n+NM_007157\t5640\t5351.13\t1.48101\t201.865\n+NM_001040653\t4813\t4801.38\t1.63099\t199.468\n+NM_025112\t3404\t3618.48\t2.50126\t230.538\n+NR_104249\t3584\t3680.74\t0\t0\n+NM_001004339\t4271\t3964.14\t0.842213\t85.0408\n+NM_024646\t8140\t7035.62\t3.99149\t715.31\n+NM_001010972\t2305\t2405.21\t14.6404\t896.938\n+NM_003461\t2308\t2411.67\t16.6115\t1020.43\n+NM_015113\t11394\t11743.8\t4.45862\t1333.72\n+NM_015534\t4322\t3595.14\t7.57282\t693.475\n' |
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/sailfish/sailfish_quant.sf5.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf5.tab Sun Jan 28 04:04:12 2018 -0500 |
| b |
| b'@@ -0,0 +1,48010 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|
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/sailfish/sailfish_quant.sf6.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf6.tab Sun Jan 28 04:04:12 2018 -0500 |
| b |
| b'@@ -0,0 +1,48010 @@\n+Name\tLength\tEffectiveLength\tTPM\tNumReads\n+NR_001526\t164\t22.1354\t0\t0\n+NR_001526_1\t164\t22.1354\t0\t0\n+NR_001526_2\t164\t22.1354\t0\t0\n+NM_130786\t1764\t1951.04\t1.72605\t76.754\n+NR_015380\t2129\t2090.86\t2.21019\t105.326\n+NM_001198818\t9360\t7850.48\t4.02523e-07\t7.20223e-05\n+NM_001198819\t9527\t8019.07\t0\t0\n+NM_001198820\t9410\t7906.86\t1.13363e-10\t2.04294e-08\n+NM_014576\t9267\t7765.55\t0.130097\t23.026\n+NM_138932\t9291\t7781.28\t0.0115766\t2.0531\n+NM_138933\t9362\t7860.09\t1.06213e-07\t1.90277e-05\n+NM_000014\t4653\t4353.29\t0.0806291\t8\n+NR_026971\t2187\t1977.9\t0\t0\n+NM_001282424\t3789\t3537.28\t0.0197795\t1.59465\n+NM_144670\t5192\t4938.32\t0.0313162\t3.52475\n+NR_040112\t1201\t893.893\t0.0490834\t1\n+NM_001080438\t1023\t813.897\t0\t0\n+NM_017436\t2091\t2322.35\t7.12302\t377.027\n+NM_016161\t1771\t1561.9\t0\t0\n+NR_037584\t631\t422.671\t0\t0\n+NM_001173466\t1737\t1698.82\t0.304164\t11.777\n+NM_015665\t1836\t1801.26\t26.9596\t1106.81\n+NM_023928\t3321\t3450.01\t11.848\t931.631\n+NR_024035\t2171\t1982.93\t0.331897\t15\n+NM_001086\t1606\t1396.9\t0\t0\n+NM_207365\t1498\t1288.9\t0\t0\n+NR_110202\t772\t563.34\t0\t0\n+NR_110203\t712\t503.448\t0\t0\n+NM_001103170\t4049\t3696.23\t0\t0\n+NR_111984\t3832\t3491.47\t0.0376992\t3\n+NM_001013630\t1574\t1364.9\t0\t0\n+NR_026915\t1289\t1079.9\t0\t0\n+NM_001286682\t2119\t1709.38\t5.42481e-06\t0.000211351\n+NM_001286683\t2192\t1806.27\t0\t0\n+NM_016228\t2325\t1972.45\t0\t0\n+NM_182662\t2107\t1695.06\t0.0809907\t3.12896\n+NM_153698\t1224\t959.854\t9.00683\t197.041\n+NM_001271885\t3083\t2601.6\t1.57724e-08\t9.35233e-07\n+NM_001271886\t3344\t2917.57\t0.838302\t55.7445\n+NM_024666\t3199\t2733.58\t15.1825\t945.926\n+NM_014911\t21265\t19353.3\t4.48726\t1979.32\n+NM_024684\t503\t289.867\t11.3854\t75.2191\n+NM_001087\t1792\t1740.99\t33.9247\t1346.15\n+NM_001088\t1025\t940.88\t0\t0\n+NM_001166579\t1912\t1893.01\t0.490668\t21.17\n+NR_110548\t1081\t1044.57\t0.507601\t12.0848\n+NM_001271874\t2486\t2441.12\t10.5446\t586.68\n+NM_015511\t2765\t2760.33\t0.581185\t36.5642\n+NM_001025357\t1784\t1605.31\t0.529928\t19.3891\n+NM_001605\t3344\t3337.67\t70.0835\t5331.39\n+NM_020745\t4782\t5010.76\t6.41083\t732.147\n+NM_001261434\t1362\t1194.87\t17.6867\t481.67\n+NM_001286668\t3329\t2758.87\t1.89295\t119.029\n+NM_001286669\t3480\t2896.55\t0\t0\n+NM_001286670\t3004\t2480.99\t0.162095\t9.16589\n+NM_001286671\t3182\t2624.84\t0.106857\t6.39272\n+NM_001286672\t2979\t2429.27\t0.440558\t24.3927\n+NM_181806\t3601\t2995.65\t4.1966\t286.529\n+NM_015423\t2861\t2330.4\t23.4228\t1244.08\n+NM_005763\t5869\t4991.21\t1.96713\t223.779\n+NM_012138\t2140\t2061.14\t50.6596\t2379.85\n+NM_001080395\t5309\t5099.9\t0\t0\n+NM_004920\t5087\t4877.9\t0\t0\n+NR_027255\t1577\t1367.9\t0\t0\n+NM_000663\t5585\t5517.3\t0.102347\t12.8702\n+NM_001127448\t4907\t4777.05\t0\t0\n+NM_020686\t4813\t4697.46\t1.16882\t125.138\n+NM_005502\t10500\t9848.62\t0.147014\t33\n+NM_080282\t6331\t5282.48\t0.843718\t101.582\n+NR_002451\t1895\t1564.87\t2.05756\t73.3855\n+NM_015657\t8084\t7222.09\t0.230732\t37.9797\n+NM_173076\t9099\t8182.91\t0.0913208\t17.0317\n+NR_103740\t9179\t8248.63\t7.11705e-06\t0.00133802\n+NM_152701\t17184\t15415.5\t0.0811349\t28.5067\n+NR_003574\t4188\t4132.99\t0.0424634\t4\n+NM_001606\t8154\t9779.76\t0.254616\t56.7537\n+NM_212533\t8146\t9757.68\t0.136022\t30.2507\n+NM_001089\t6623\t7531.19\t0.716575\t123\n+NM_000350\t7323\t7454.27\t0.0176578\t3\n+NM_018672\t9249\t7477.14\t3.7888\t645.681\n+NM_172232\t8177\t6520.1\t4.72323\t701.897\n+NM_080284\t5296\t4470.23\t6.13171\t624.728\n+NM_019112\t6816\t8157.2\t3.63608\t676.014\n+NM_001288985\t6003\t5321.92\t0.0247693\t3.00444\n+NM_001288986\t5827\t5617.9\t0\t0\n+NM_007168\t5722\t5512.9\t0\t0\n+NM_080283\t6300\t5502.68\t0.843663\t105.809\n+NM_000927\t4715\t4249.77\t0.671145\t65.0073\n+NM_012089\t3856\t3600.72\t11.1214\t912.702\n+NM_003742\t4775\t4324.24\t0.0101463\t1\n+NM_000443\t3967\t3614.56\t0.69653\t57.382\n+NM_018849\t3988\t3634.51\t1.07451\t89.0093\n+NM_018850\t3826\t3491.99\t0.863064\t68.6905\n+NM_001163941\t5400\t4754.32\t0\t0\n+NM_001163942\t2246\t1854.32\t1.07385\t45.3847\n+NM_001163993\t1724\t1514.9\t0\t0\n+NM_178559\t4374\t3810.27\t0.305224\t26.5066\n+NM_005689\t3017\t3217.69\t8.59608\t630.413\n+NM_001271696\t2525\t2126.22\t7.19403\t348.626\n+NM_001271697\t2405\t2008.19\t0.00654825\t0.299717\n+NM_001271698\t2447\t2056.55\t0.265784\t12.458\n+NM_001271699\t2408\t2012.15\t0.458386\t21.0219\n+NM_004299\t2528\t2130.17\t9.15954\t444.702\n+NM_001282291\t4733\t5152.45'..b'.9\t0\t0\n+NM_001290104\t2722\t2460.87\t0.0741016\t4.15621\n+NM_003460\t2749\t2481.23\t3.78651e-06\t0.000214134\n+NM_001110354\t1299\t1165.68\t0.0765189\t2.03296\n+NM_007155\t1476\t1402.12\t0.185569\t5.93022\n+NM_021186\t2474\t2264.9\t0\t0\n+NM_001159878\t1221\t1011.9\t0\t0\n+NM_007009\t1224\t1014.9\t0\t0\n+NM_198844\t2190\t1674.3\t0\t0\n+NM_199321\t2256\t1720.21\t0.652172\t25.5696\n+NM_175056\t3619\t3409.9\t0\t0\n+NM_003904\t1777\t1614.49\t38.2466\t1407.37\n+NM_017580\t4941\t4249.07\t8.27505\t801.391\n+NM_005455\t3144\t2601.25\t37.6961\t2234.9\n+NM_203350\t3069\t2524.35\t29.0409\t1670.86\n+NR_038420\t1674\t1718.64\t1.74675\t68.4217\n+NR_046217\t783\t478.438\t0.275115\t3\n+NM_001286568\t6818\t6023.12\t0\t0\n+NM_001286569\t6947\t6115.47\t0.310243\t43.2427\n+NM_032143\t6729\t5896.85\t1.9202\t258.076\n+NM_005089\t1509\t1392.27\t29.1011\t923.451\n+NM_182572\t2054\t1844.9\t0\t0\n+NM_001282415\t2272\t2764.92\t0.0317371\t2\n+NM_001282416\t2467\t2882.03\t0\t0\n+NM_032805\t2463\t2879.24\t0\t0\n+NM_001163391\t3517\t3061.64\t1.39809\t97.5595\n+NR_028077\t4342\t3792.65\t3.03813\t262.621\n+NR_024063\t4054\t3563.81\t0.33496\t27.2075\n+NM_025231\t1273\t1011.3\t5.93849\t136.878\n+NR_103455\t2186\t1949.79\t0.256785\t11.4114\n+NR_103456\t1989\t1746.34\t1.50916\t60.0683\n+NM_001145542\t2573\t2925.32\t0.607793\t40.5237\n+NM_001145543\t2684\t3061.81\t0.321495\t22.4353\n+NM_001145544\t2218\t2508.47\t0.000715707\t0.0409189\n+NM_023926\t2928\t3263.78\t0\t0\n+NR_027135\t1778\t1568.9\t0\t0\n+NM_001007072\t934\t793.697\t0.884641\t16.003\n+NM_017894\t988\t851.733\t0.173968\t3.37717\n+NM_181877\t3747\t3761.13\t1.39712\t119.765\n+NM_145238\t4216\t4049.53\t1.30016\t120\n+NM_145914\t1987\t1829.85\t3.59818\t150.065\n+NM_181846\t4643\t4614.92\t2.12437\t223.447\n+NM_001012455\t3160\t2591.19\t0.169711\t10.0228\n+NM_145115\t4349\t4324.99\t2.9843\t294.176\n+NM_001023560\t2834\t2453.15\t0.91839\t51.3489\n+NM_001111039\t2831\t2450.21\t1.25012\t69.8126\n+NM_001287421\t2321\t1892.42\t3.11434\t134.327\n+NM_001287422\t2231\t1824.33\t0.258433\t10.7456\n+NM_152736\t2430\t2023.61\t0.681184\t31.4174\n+NM_152455\t5607\t5168.46\t6.56299\t773.113\n+NM_001112734\t4142\t3660.55\t2.40556\t200.698\n+NM_001166012\t4346\t3948.33\t0.152463\t13.7201\n+NM_001288711\t3439\t2904.95\t3.20569\t212.246\n+NM_001135216\t3047\t2621.84\t0.218534\t13.0589\n+NM_001243241\t2972\t2571.23\t0.229082\t13.4249\n+NM_001243242\t2669\t2213.04\t0.172721\t8.71193\n+NM_001243243\t2571\t2123.59\t0.208158\t10.075\n+NM_001243244\t2560\t2124.39\t0.265306\t12.8458\n+NM_030899\t3036\t2622.61\t0.282454\t16.8835\n+NM_001284527\t3173\t2999.13\t2.18109\t149.09\n+NM_001284528\t2788\t2592.07\t1.74602\t103.152\n+NM_001284529\t2235\t2015.1\t1.64447\t75.527\n+NM_017810\t3071\t2888.85\t0.258001\t16.9874\n+NM_152677\t2245\t1846.87\t0.235102\t9.89631\n+NM_024303\t1920\t1780.81\t1.92175\t78\n+NM_001080456\t1625\t1535.16\t0.0571607\t2\n+NM_001199479\t1833\t1605.17\t0.805722\t29.4772\n+NM_001199480\t1644\t1417.23\t2.59792\t83.9166\n+NM_006299\t1680\t1461.18\t2.19082\t72.961\n+NM_080603\t2786\t2651.31\t6.3134\t381.509\n+NM_182521\t2446\t2236.9\t0\t0\n+NM_080752\t2815\t2676.51\t1.83575\t111.986\n+NR_037628\t2970\t2839.99\t0.247409\t16.0144\n+NM_023072\t4339\t5093.59\t3.40274\t395.032\n+NM_020883\t5834\t5849.29\t0.135017\t18\n+NM_020928\t5502\t5233.87\t1.36579\t162.925\n+NM_001042697\t2005\t1721.2\t1.87818\t73.6799\n+NM_001042698\t1875\t1607.97\t1.23118\t45.121\n+NM_001242487\t6047\t6662.57\t0.0200948\t3.05145\n+NM_001242488\t5955\t6556.99\t3.30569\t494.022\n+NM_015037\t6062\t6679.97\t4.52148\t688.392\n+NR_038357\t1458\t1339.38\t1.9272\t58.8314\n+NM_145062\t2211\t1737.12\t13.4495\t532.499\n+NM_004724\t2946\t2494.53\t13.3577\t759.455\n+NM_001287821\t3285\t2687.7\t1.8008\t110.313\n+NM_001287822\t3189\t2630.03\t0\t0\n+NM_001287823\t3138\t2548.43\t5.88846e-10\t3.42022e-08\n+NM_017975\t3190\t2598.65\t18.1589\t1075.52\n+NM_001005413\t1519\t1284.41\t2.54879\t74.6136\n+NM_007057\t1660\t1431.67\t60.7454\t1982.14\n+NM_032997\t1851\t1624.67\t9.26582\t343.108\n+NM_007156\t5202\t4983.73\t0.7901\t89.7463\n+NM_007157\t5640\t5419.81\t2.19666\t271.349\n+NM_001040653\t4813\t4894.84\t2.98293\t332.784\n+NM_025112\t3404\t3743.16\t2.36646\t201.891\n+NR_104249\t3584\t3771.86\t0\t0\n+NM_001004339\t4271\t3988.53\t1.93742\t176.124\n+NM_024646\t8140\t7020.91\t5.71983\t915.285\n+NM_001010972\t2305\t2514.21\t9.63348\t552.032\n+NM_003461\t2308\t2517.66\t19.9571\t1145.18\n+NM_015113\t11394\t11923\t5.51517\t1498.73\n+NM_015534\t4322\t3563.7\t11.4566\t930.548\n' |
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/sailfish_quant_result1.tab --- a/test-data/sailfish_quant_result1.tab Tue Aug 01 17:20:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,32 +0,0 @@ -# sailfish (quasi-mapping-based) v0.7.6 -# [ program ] => sailfish -# [ command ] => quant -# [ index ] => { ./index_dir } -# [ mates1 ] => { ./mate1.fastq } -# [ mates2 ] => { ./mate2.fastq } -# [ libType ] => { IU } -# [ output ] => { ./ } -# [ biasCorrect ] => { } -# [ threads ] => { 1 } -# [ fldMean ] => { 200 } -# [ fldSD ] => { 80 } -# [ maxReadOcc ] => { 200 } -# [ maxFragLen ] => { 1000 } -# [ txpAggregationKey ] => { gene_id } -# [ mapping rate ] => { 100% } -# Name Length TPM NumReads -NM_001168316 2283 12398.5 159.361 -NM_174914 2385 111257 1500.04 -NR_031764 1853 10254.5 104.595 -NM_004503 1681 36198.8 330.806 -NM_006897 1541 80244.3 664 -NM_014212 2037 4852.08 55 -NM_014620 2300 45132.7 584.838 -NM_017409 1959 4330.19 47 -NM_017410 2396 3099.5 42 -NM_018953 1612 26168.3 228 -NM_022658 2288 378838 4881 -NM_153633 1666 40578.4 367.074 -NM_153693 2072 6430.57 74.2815 -NM_173860 849 240218 962 -NR_003084 1640 0 0 |
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/sailfish_quant_result2.tab --- a/test-data/sailfish_quant_result2.tab Tue Aug 01 17:20:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,32 +0,0 @@ -# sailfish (quasi-mapping-based) v0.7.6 -# [ program ] => sailfish -# [ command ] => quant -# [ index ] => { ./index_dir } -# [ mates1 ] => { ./mate1.fastq } -# [ mates2 ] => { ./mate2.fastq } -# [ libType ] => { IU } -# [ output ] => { ./ } -# [ biasCorrect ] => { } -# [ threads ] => { 1 } -# [ fldMean ] => { 200 } -# [ fldSD ] => { 80 } -# [ maxReadOcc ] => { 200 } -# [ maxFragLen ] => { 1000 } -# [ txpAggregationKey ] => { gene_id } -# [ mapping rate ] => { 100% } -# Name Length TPM NumReads -NM_001168316 2283 1239.5 159.361 -NM_174914 2385 11125 1505.04 -NR_031764 1853 1025.5 100.595 -NM_004503 1681 3619.8 320.806 -NM_006897 1541 8224.3 660 -NM_014212 2037 485.08 60 -NM_014620 2300 4513.7 580.838 -NM_017409 1959 433.19 45 -NM_017410 2396 3219.5 40 -NM_018953 1612 2616.3 220 -NM_022658 2288 37883 4880 -NM_153633 1666 4057.4 360.074 -NM_153693 2072 643.57 70.2815 -NM_173860 849 2521 960 -NR_003084 1640 1000 10 |
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/sailfish_quant_result3.tab --- a/test-data/sailfish_quant_result3.tab Tue Aug 01 17:20:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,32 +0,0 @@ -# sailfish (quasi-mapping-based) v0.7.6 -# [ program ] => sailfish -# [ command ] => quant -# [ index ] => { ./index_dir } -# [ mates1 ] => { ./mate1.fastq } -# [ mates2 ] => { ./mate2.fastq } -# [ libType ] => { IU } -# [ output ] => { ./ } -# [ biasCorrect ] => { } -# [ threads ] => { 1 } -# [ fldMean ] => { 200 } -# [ fldSD ] => { 80 } -# [ maxReadOcc ] => { 200 } -# [ maxFragLen ] => { 1000 } -# [ txpAggregationKey ] => { gene_id } -# [ mapping rate ] => { 100% } -# Name Length TPM NumReads -NM_001168316 2283 12398.5 15.361 -NM_174914 2385 121257 150.04 -NR_031764 1853 14254.5 10.595 -NM_004503 1681 30198.8 30.806 -NM_006897 1541 70244.3 64 -NM_014212 2037 4452.08 555 -NM_014620 2300 42132.7 54.838 -NM_017409 1959 4230.19 475 -NM_017410 2396 3199.5 423 -NM_018953 1612 29168.3 28 -NM_022658 2288 318838 481 -NM_153633 1666 41578.4 3367.074 -NM_153693 2072 6430.57 742.2815 -NM_173860 849 240218 92 -NR_003084 1640 0 90 |
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/sailfish_quant_result4.tab --- a/test-data/sailfish_quant_result4.tab Tue Aug 01 17:20:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,32 +0,0 @@ -# sailfish (quasi-mapping-based) v0.7.6 -# [ program ] => sailfish -# [ command ] => quant -# [ index ] => { ./index_dir } -# [ mates1 ] => { ./mate1.fastq } -# [ mates2 ] => { ./mate2.fastq } -# [ libType ] => { IU } -# [ output ] => { ./ } -# [ biasCorrect ] => { } -# [ threads ] => { 1 } -# [ fldMean ] => { 200 } -# [ fldSD ] => { 80 } -# [ maxReadOcc ] => { 200 } -# [ maxFragLen ] => { 1000 } -# [ txpAggregationKey ] => { gene_id } -# [ mapping rate ] => { 100% } -# Name Length TPM NumReads -NM_001168316 2283 12398.5 15.361 -NM_174914 2385 111260 120.04 -NR_031764 1853 10300.5 12.595 -NM_004503 1681 36250.8 32.806 -NM_006897 1541 80900.3 75 -NM_014212 2037 4900.08 540 -NM_014620 2300 45300.7 51.838 -NM_017409 1959 4400.19 470 -NM_017410 2396 3500.5 420 -NM_018953 1612 26568.3 30 -NM_022658 2288 378938 480 -NM_153633 1666 40878.4 3350.074 -NM_153693 2072 6830.57 740.2815 -NM_173860 849 240818 90 -NR_003084 1640 20 95 |
| b |
| diff -r 24a09ca67621 -r 25204a860b79 test-data/tx2gene.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tx2gene.tab Sun Jan 28 04:04:12 2018 -0500 |
| b |
| @@ -0,0 +1,16 @@ +TXNAME GENEID +NM_001168316 DDX11L1 +NM_174914 DDX11L1 +NR_031764 DDX11L1 +NM_004503 WASH7P +NM_006897 WASH7P +NM_014212 WASH7P +NM_014620 WASH7P +NM_017409 WASH7P +NM_017410 WASH7P +NM_018953 MIR6859-2 +NM_022658 MIR6859-1 +NM_153633 WASH7P +NM_153693 WASH7P +NM_173860 WASH7P +NR_003084 WASH7P \ No newline at end of file |