| Previous changeset 80:14defeb423a7 (2020-01-26) Next changeset 82:369fef559cfc (2020-02-23) |
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Commit message:
"planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 323de18b21453fa652ae3abb7e847704e13a65ed" |
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modified:
macros.xml minfi_analysis.xml |
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added:
README.md test-data/Differentially_Methylated_Positions.bed test-data/Differentially_Methylated_Regions.bed test-data/GSM1588704_8795207135_R01C02_Grn.idat test-data/GSM1588704_8795207135_R01C02_Red.idat test-data/GSM1588705_8795207119_R05C02_Grn.idat test-data/GSM1588705_8795207119_R05C02_Red.idat test-data/GSM1588706_8795207135_R02C02_Grn.idat test-data/GSM1588706_8795207135_R02C02_Red.idat test-data/GSM1588707_8795207119_R06C02_Grn.idat test-data/GSM1588707_8795207119_R06C02_Red.idat test-data/Quality_Control_Plot.png test-data/Quality_Control_Report.txt test-data/SNPInfo_Table.txt test-data/phenotypeTable.txt test-data/ucsc.gtf |
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| diff -r 14defeb423a7 -r 8ab24a5229bd README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue Feb 11 09:14:55 2020 -0500 |
| [ |
| @@ -0,0 +1,14 @@ +[](https://travis-ci.org/kpbioteam/ewas_galaxy) + + +# 🔬📚 Infinium Human Methylation BeadChip: a pipeline for population epigenetics integrated into Galaxy + +This repository contains Infinium Human Methylation BeadChip pipeline that can be installed and used inside the Galaxy. +The Tool is avaliable through [Galaxy Tool Shed](https://toolshed.g2.bx.psu.edu/view/kpbioteam/ewastools/53aaf097238c) and ready to use via [Docker](https://galaxyproject.org/use/ewas-galaxy/). + +Analysis pipline includes: + * raw intensity data loading + * .idat preprocessing + * optional normalisation of the data and quality control with additional sample check. + +This gives the user the opportunity to perform any of these preparation and data cleaning steps, including a recommended 'genetic variation annotation step'. Finally, the generated dataset can be used to hunt (find) differentially-methylated positions DMP and regions DMR with respect to a phenotype co-variate. |
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| diff -r 14defeb423a7 -r 8ab24a5229bd macros.xml --- a/macros.xml Sun Jan 26 16:58:09 2020 -0500 +++ b/macros.xml Tue Feb 11 09:14:55 2020 -0500 |
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| @@ -1,23 +1,24 @@ +<?xml version="1.0"?> <macros> - <token name="@VERSION@">@MINFI_VERSION@</token> - <xml name="requirements"> - <requirements> - <requirement type="package" version="3.6.2">r-base</requirement> - <requirement type="package" version="@VERSION@">bioconductor-minfi</requirement> - <requirement type="package" version="0.4.0">bioconductor-illuminahumanmethylation27kmanifest</requirement> - <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19</requirement> - <requirement type="package" version="0.4.0">bioconductor-illuminahumanmethylation450kmanifest</requirement> - <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement> - <requirement type="package" version="0.3.0">bioconductor-illuminahumanmethylationepicmanifest</requirement> - <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19</requirement> - <requirement type="package" version="1.46.0">bioconductor-rtracklayer</requirement> - <yield /> - </requirements> - </xml> - <token name="@MINFI_VERSION@">1.32.0</token> - <xml name="citations"> - <citations> - <citation type="doi">10.1093/bioinformatics/btu049</citation> - </citations> - </xml> + <token name="@VERSION@">@MINFI_VERSION@</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="3.6.2">r-base</requirement> + <requirement type="package" version="@VERSION@">bioconductor-minfi</requirement> + <requirement type="package" version="0.4.0">bioconductor-illuminahumanmethylation27kmanifest</requirement> + <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19</requirement> + <requirement type="package" version="0.4.0">bioconductor-illuminahumanmethylation450kmanifest</requirement> + <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement> + <requirement type="package" version="0.3.0">bioconductor-illuminahumanmethylationepicmanifest</requirement> + <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19</requirement> + <requirement type="package" version="1.46.0">bioconductor-rtracklayer</requirement> + <yield/> + </requirements> + </xml> + <token name="@MINFI_VERSION@">1.32.0</token> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btu049</citation> + </citations> + </xml> </macros> |
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| diff -r 14defeb423a7 -r 8ab24a5229bd minfi_analysis.xml --- a/minfi_analysis.xml Sun Jan 26 16:58:09 2020 -0500 +++ b/minfi_analysis.xml Tue Feb 11 09:14:55 2020 -0500 |
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| b'@@ -1,30 +1,31 @@\n-<tool id="minfi_analysis" name="Infinium Human Methylation BeadChip" version="2.1.0">\n- <description>Determines differentially methylated regions and positions from idat files</description>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n- <expand macro="requirements">\n- <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>\n- </expand>\n- <command detect_errors="exit_code"><![CDATA[\n+<?xml version=\'1.0\'?>\n+<tool id=\'minfi_analysis\' name=\'Infinium Human Methylation BeadChip\' version=\'2.1.0\'>\n+ <description>Determines differentially methylated regions and positions from Infinium Methylation Assays</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro=\'requirements\'>\n+ <requirement type=\'package\' version=\'0.6.0\'>bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>\n+ </expand>\n+ <command detect_errors=\'exit_code\'><![CDATA[\n #for $counter, $input in enumerate($files_red):\n- #set $redname = str( getattr( $input, \'element_identifier\', \'sample\' ) ).replace( "/", \'-\' ).replace( "\\t", "-" )\n+ #set $redname = str( getattr( $input, \'element_identifier\', \'sample\' ) ).replace( \'/\', \'-\' ).replace( \'\\t\', \'-\' )\n ln -s $input ./${redname} &&\n #end for\n #for $counter, $input in enumerate($files_grn):\n- #set $grnname = str( getattr( $input, \'element_identifier\', \'sample\' ) ).replace( "/", \'-\' ).replace( "\\t", "-" )\n+ #set $grnname = str( getattr( $input, \'element_identifier\', \'sample\' ) ).replace( \'/\', \'-\' ).replace( \'\\t\', \'-\' )\n ln -s $input ./${grnname} &&\n #end for\n Rscript \'$minfi_analysis_script\'\n ]]></command>\n- <configfiles>\n- <configfile name="minfi_analysis_script"><![CDATA[\n-\trequire("minfi", quietly = TRUE)\n-\trequire("IlluminaHumanMethylation27kanno.ilmn12.hg19", quietly = TRUE)\n-\trequire("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE)\n- require("IlluminaHumanMethylationEPICanno.ilm10b4.hg19", quietly = TRUE)\n+ <configfiles>\n+ <configfile name=\'minfi_analysis_script\'><![CDATA[\n+\trequire(\'minfi\', quietly = TRUE)\n+\trequire(\'IlluminaHumanMethylation27kanno.ilmn12.hg19\', quietly = TRUE)\n+\trequire(\'IlluminaHumanMethylation450kanno.ilmn12.hg19\', quietly = TRUE)\n+ require(\'IlluminaHumanMethylationEPICanno.ilm10b4.hg19\', quietly = TRUE)\n \toptions(warn = -1)\n-\tRGSet <- read.metharray(list.files(pattern="_Red.idat")) #load .IDAT files\n+\tRGSet <- read.metharray(list.files(pattern=\'_Red.idat\')) #load .IDAT files\n \n \tMSet <- preprocessRaw(RGSet) #create objects contains CpGs signals\n \n@@ -34,23 +35,23 @@\n plotQC(qc)\n \tdev.off()\n \n-\tRSet <- ratioConvert(MSet, what = "both", keepCN = TRUE) #store Beta values and/or M values\n+\tRSet <- ratioConvert(MSet, what = \'both\', keepCN = TRUE) #store Beta values and/or M values\n \tGRSet <- mapToGenome(RSet)\n \n \n-\tif (\'$optpp\' == "na" ) {\n+\tif (\'$optpp\' == \'na\' ) {\n \tGRSet <- mapToGenome(RSet) #mapping Ilumina methylation array data to the genome\n-\t} else if (\'$optpp\' == "ppfun" ) {\n+\t} else if (\'$optpp\' == \'ppfun\' ) {\n \tGRSet <- preprocessFunnorm(RGSet) #optional - implements the functional normalization algorithm\n-\t} else if (\'$optpp\' == "ppq" ) {\n+\t} else if (\'$optpp\' == \'ppq\' ) {\n \tGRSet <- preprocessQuantile(RGSet, fixOutliers = TRUE,\n removeBadSamples = TRUE, badSampleCutoff = 10.5,\n quantileNormalize = TRUE, stratified = TRUE,\n mergeManifest = FALSE, sex = NULL) #optional - implements stratified quantile normalization preprocessing\n-\t} else if (\'$optpp\' == "ppsnp" ) {\n+\t} else if (\'$optpp\' == \'ppsnp\' ) {\n \tsnps <- getSnpInfo(GRSet) #optional - retrieve the chromosome and the position of each SNP\n \twrite.table(snps, \'$table\')\n-\tGRSet <- dropLociWithSnps(GRSet, snps=c("SBE","CpG"), maf=0) #optional - drop the probes that contain either a SNP at the CpG interrogation or at the singl'..b'am>\n+ <param name=\'q_cutoff\' type=\'float\' value=\'1\' label=\'qCutoff Size\' help=\'DMPs with an FDR q-value greater than this will not be returned.\'/>\n+ <param name=\'variance_shrinkage\' type=\'boolean\' truevalue=\'TRUE\' falsevalue=\'FALSE\' label=\'Variance Shrinkage\' help=\'Enable variance shrinkage is recommended when sample sizes are small.\'/>\n+ <param type=\'data\' name=\'ucsc_genome\' format=\'gtf\' label=\'Genome Table\' help=\'Reference Sequence e.g. wgEncodeHaibMethyl450Gm12878SitesRep1.\'/>\n+ </inputs>\n+ <outputs>\n+ <data name=\'qctab\' format=\'txt\' label=\'Quality Control Report\'/>\n+ <data name=\'qcpng\' format=\'png\' label=\'Quality Control Plot\'/>\n+ <data name=\'table\' format=\'txt\' label=\'SNPInfo Table\'/>\n+ <data name=\'dmr\' format=\'bed\' label=\'Differentially Methylated Regions\'/>\n+ <data name=\'dmp\' format=\'bed\' label=\'Differentially Methylated Positions\'/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name=\'files_red\' value=\'GSM1588707_8795207119_R06C02_Red.idat,GSM1588706_8795207135_R02C02_Red.idat,GSM1588705_8795207119_R05C02_Red.idat,GSM1588704_8795207135_R01C02_Red.idat\' ftype=\'idat\'/>\n+ <param name=\'files_grn\' value=\'GSM1588707_8795207119_R06C02_Grn.idat,GSM1588706_8795207135_R02C02_Grn.idat,GSM1588705_8795207119_R05C02_Grn.idat,GSM1588704_8795207135_R01C02_Grn.idat\' ftype=\'idat\'/>\n+ <param name=\'optpp\' value=\'ppsnp\'/>\n+ <param name=\'grset\' value=\'GRSet_without_SNPs.rdata\'/>\n+ <param name=\'phenotype_table\' value=\'phenotypeTable.txt\'/>\n+ <param name=\'maxgap_size\' value=\'250\'/>\n+ <param name=\'cutoff_size\' value=\'0.1\'/>\n+ <param name=\'number_of_resamples\' value=\'0\'/>\n+ <param name=\'null_method\' value=\'permutation\'/>\n+ <param name=\'grset\' value=\'GRSet_without_SNPs.rdata\'/>\n+ <param name=\'phenotype\' value=\'categorical\'/>\n+ <param name=\'q_cutoff\' value=\'1\'/>\n+ <param name=\'variance_shrinkage\' value=\'FALSE\'/>\n+ <param name=\'ucsc_genome\' value=\'ucsc.gtf\'/>\n+ <output name=\'qctab\' file=\'Quality_Control_Report.txt\'/>\n+ <output name=\'qcpng\' file=\'Quality_Control_Plot.png\' compare=\'sim_size\'/>\n+ <output name=\'table\' file=\'SNPInfo_Table.txt\'/>\n+ <output name=\'dmr\' file=\'Differentially_Methylated_Regions.bed\'/>\n+ <output name=\'dmp\' file=\'Differentially_Methylated_Positions.bed\'/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n \n .. class:: infomark\n \t\n@@ -167,7 +162,7 @@\n \n *(optional) Preprocessing Methods*: by this step probes can be stratified by region via quantile normalization or by extended implementation of functional normalisation recommended for cases where global changes are expected such as in cancer-normal comparisons. In addition unwanted probes containing either a SNP at the CpG interrogation or at the single nucleotide extension can be removed (recommended). \n \n-*Phenotype Table*: table of compared probes and their characteristics, may be categorical (e.g. cancer vs. normal) or continuous (e.g. blood pressure). \n+*Phenotype Table*: table of compared samples and their characteristics, may be categorical (e.g. cancer vs. normal) or continuous (e.g. blood pressure). \n \n ========== ============== ===============\n Accession Sensitivity Treatment\n@@ -177,6 +172,8 @@\n GSM1588705 sensitive MAPKi\n ---------- -------------- ---------------\n GSM1588706 resistant BRAFi\n+---------- -------------- ---------------\n+GSM1588707 resistant BRAFi\n ========== ============== =============== \n \n *Note*: phenotype covariate table must include the following information:\n@@ -194,7 +191,7 @@\n \n *Differentially Methylated Positions*: single genomic position that has a different methylated level in two different groups of samples (or conditions) save as multiple track lines in a single BED file.\n ]]></help>\n- <citations>\n- <citation type="doi">10.18129/B9.bioc.illuminaio</citation>\n-</citations>\n-</tool>\t\n+ <citations>\n+ <citation type=\'doi\'>10.18129/B9.bioc.illuminaio</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 14defeb423a7 -r 8ab24a5229bd test-data/Differentially_Methylated_Positions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Differentially_Methylated_Positions.bed Tue Feb 11 09:14:55 2020 -0500 |
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| b'@@ -0,0 +1,464888 @@\n+chr\tstart\tend\tnames\tpval\tqval\n+chr16\t53468112\t53468112\tcg00000029\t0.273485175006601\t0.239609190206712\n+chr3\t37459206\t37459206\tcg00000108\t0.623243998636913\t0.39258989981719\n+chr3\t171916037\t171916037\tcg00000109\t0.232539543925332\t0.216244969633372\n+chr1\t91194675\t91194675\tcg00000165\t0.248020671814953\t0.225232373436069\n+chr8\t42263295\t42263295\tcg00000236\t0.230215862279736\t0.214851543324713\n+chr14\t69341139\t69341139\tcg00000289\t0.268327315390556\t0.236767279985355\n+chr16\t28890100\t28890100\tcg00000292\t0.0058372332805385\t0.0220344081686113\n+chr8\t41167803\t41167803\tcg00000321\t0.462489859333497\t0.330321758498426\n+chr1\t230560793\t230560793\tcg00000363\t0.0385403800900197\t0.0665130564433204\n+chr15\t23034447\t23034447\tcg00000622\t0.18160031067637\t0.184482262176172\n+chr9\t139997925\t139997925\tcg00000658\t0.631469535337436\t0.395501230069459\n+chr19\t54695678\t54695678\tcg00000714\t0.900754608784968\t0.47905542242334\n+chr6\t25282780\t25282780\tcg00000721\t0.0455820567003055\t0.0741735576910669\n+chr3\t128902377\t128902377\tcg00000734\t0.960672634519289\t0.494732871296244\n+chr12\t124086477\t124086477\tcg00000769\t0.899624518031061\t0.478732527820523\n+chr4\t154609858\t154609858\tcg00000884\t0.906826256415091\t0.480736216615489\n+chr15\t59785307\t59785307\tcg00000905\t0.709841485040243\t0.422009978640979\n+chr11\t2720463\t2720463\tcg00000924\t0.933364876748635\t0.487711474670278\n+chr8\t49890609\t49890609\tcg00000948\t0.978493984862554\t0.499333411033056\n+chr1\t5937253\t5937253\tcg00000957\t0.0592699234314915\t0.0881400020336562\n+chr8\t87081553\t87081553\tcg00001099\t0.269277956580276\t0.237308413102509\n+chr3\t15106711\t15106711\tcg00001245\t0.728616646274826\t0.428116835020146\n+chr14\t60389786\t60389786\tcg00001249\t0.160188380275175\t0.169981775579059\n+chr16\t3463964\t3463964\tcg00001261\t0.0602365606021472\t0.0890826668240909\n+chr20\t48959005\t48959005\tcg00001269\t0.0185995917225724\t0.0419275290139671\n+chr1\t166958440\t166958440\tcg00001349\t0.00210678338535948\t0.0145319619679991\n+chr1\t214170377\t214170377\tcg00001364\t0.281669878488749\t0.244056526948174\n+chr1\t43831042\t43831042\tcg00001446\t0.00813133824320487\t0.0261085946594264\n+chr19\t54746946\t54746946\tcg00001510\t0.871735099155927\t0.470986350866867\n+chr1\t51034866\t51034866\tcg00001534\t0.941336640837796\t0.489841381999452\n+chr10\t80828703\t80828703\tcg00001582\t0.495135464109364\t0.343901384447645\n+chr1\t200011787\t200011787\tcg00001583\t0.000186463642048131\t0.00907721359047842\n+chr2\t11484705\t11484705\tcg00001594\t0.847778025682725\t0.464401674520496\n+chr16\t89761661\t89761661\tcg00001687\t0.70875697089707\t0.421649727009037\n+chr2\t105460264\t105460264\tcg00001747\t0.300585127007446\t0.254220166025132\n+chr2\t103414042\t103414042\tcg00001791\t0.00741837801699207\t0.0248538270071218\n+chr12\t11905390\t11905390\tcg00001793\t0.778442060769949\t0.443806097170459\n+chr14\t101154025\t101154025\tcg00001809\t0.0100420599352783\t0.0292462908122588\n+chr16\t47008491\t47008491\tcg00001854\t0.490463407920156\t0.341969954541432\n+chr10\t69990589\t69990589\tcg00001874\t0.0259219428577307\t0.0515649861220453\n+chr18\t60055085\t60055085\tcg00001930\t0.643274774132072\t0.399594721762803\n+chr1\t20960011\t20960011\tcg00002028\t0.322334023696921\t0.265507774104347\n+chr19\t39798482\t39798482\tcg00002033\t0.00538940317056318\t0.0212042423412914\n+chr21\t30390417\t30390417\tcg00002080\t0.00218210824223853\t0.014697261364833\n+chr17\t79670411\t79670411\tcg00002116\t0.29221122878682\t0.249772316213451\n+chr2\t238249537\t238249537\tcg00002145\t0.00274012547425348\t0.0159175767587452\n+chr8\t19555033\t19555033\tcg00002190\t0.358060059556713\t0.283070409602944\n+chr8\t144120399\t144120399\tcg00002224\t0.707474789933135\t0.421226361675999\n+chr18\t67873061\t67873061\tcg00002236\t0.0882303094313435\t0.114641108069523\n+chr16\t30366435\t30366435\tcg00002406\t0.929549023034964\t0.486698299957923\n+chr3\t57743543\t57743543\tcg00002426\t0.151242152548759\t0.163736565345604\n+chr10\t28961565\t28961565\tcg00002449\t0.744754807347051\t0.433313520653788\n+chr8\t120428418\t120428418\tcg00002464\t0.524129700744645\t0.355542290873176\n+chr2\t218988877\t218988877\tcg00002473\t0.0863486733476217\t0.112974531628471\n+chr4\t2264510\t2264510\tcg000'..b'+chr19\t21666099\t21666099\tcg27663389\t0.110740163126761\t0.133250041564222\n+chr15\t80444408\t80444408\tcg27663476\t0.00888627086723007\t0.0273738880202672\n+chr14\t102360737\t102360737\tcg27663587\t0.269411540397791\t0.237379183218323\n+chr17\t15523510\t15523510\tcg27663733\t0.0294158194660536\t0.0558947504810295\n+chr16\t71929910\t71929910\tcg27663791\t0.839424788037992\t0.462081226590046\n+chr12\t49504641\t49504641\tcg27663799\t0.549789377111119\t0.365563581892934\n+chr11\t60162624\t60162624\tcg27663936\t0.0174377170555988\t0.040304458138289\n+chr12\t103696381\t103696381\tcg27663938\t0.189554529176272\t0.189650769488219\n+chr16\t57405979\t57405979\tcg27664018\t0.0149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|
| b |
| diff -r 14defeb423a7 -r 8ab24a5229bd test-data/Differentially_Methylated_Regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Differentially_Methylated_Regions.bed Tue Feb 11 09:14:55 2020 -0500 |
| b |
| b'@@ -0,0 +1,355737 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| diff -r 14defeb423a7 -r 8ab24a5229bd test-data/Quality_Control_Report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Quality_Control_Report.txt Tue Feb 11 09:14:55 2020 -0500 |
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| @@ -0,0 +1,5 @@ +"mMed" "uMed" +"GSM1588704_8795207135_R01C02" 11.7368246990989 11.616548843779 +"GSM1588705_8795207119_R05C02" 11.9095181142966 11.7879025593914 +"GSM1588706_8795207135_R02C02" 11.8372337003391 12.0977029635247 +"GSM1588707_8795207119_R06C02" 11.871135184243 12.0701209444768 |
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| diff -r 14defeb423a7 -r 8ab24a5229bd test-data/SNPInfo_Table.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SNPInfo_Table.txt Tue Feb 11 09:14:55 2020 -0500 |
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| b'@@ -0,0 +1,485513 @@\n+"Probe_rs" "Probe_maf" "CpG_rs" "CpG_maf" "SBE_rs" "SBE_maf"\n+"cg13869341" NA NA NA NA NA NA\n+"cg14008030" NA NA NA NA NA NA\n+"cg12045430" NA NA NA NA NA NA\n+"cg20826792" NA NA NA NA NA NA\n+"cg00381604" NA NA NA NA NA NA\n+"cg20253340" NA NA NA NA NA NA\n+"cg21870274" NA NA NA NA NA NA\n+"cg03130891" "rs77418980" 0.305556 NA NA NA NA\n+"cg24335620" "rs147502335" 0.0128 NA NA NA NA\n+"cg16162899" NA NA NA NA NA NA\n+"cg17149495" NA NA NA NA NA NA\n+"cg22802167" NA NA NA NA NA NA\n+"cg24669183" "rs6680725" 0.1081 NA NA NA NA\n+"cg17308840" NA NA NA NA NA NA\n+"cg17866181" NA NA NA NA NA NA\n+"cg24159721" NA NA NA NA NA NA\n+"cg15174812" NA NA NA NA NA NA\n+"cg08477687" NA NA NA NA NA NA\n+"cg00034556" NA NA NA NA NA NA\n+"cg00645010" NA NA NA NA NA NA\n+"cg15394630" NA NA NA NA NA NA\n+"cg05001044" NA NA NA NA NA NA\n+"cg03344490" NA NA NA NA NA NA\n+"cg17501828" NA NA NA NA NA NA\n+"cg23917638" NA NA NA NA NA NA\n+"cg18024856" NA NA NA NA NA NA\n+"cg18761878" NA NA NA NA NA NA\n+"cg27534567" NA NA NA NA NA NA\n+"cg08858441" NA NA NA NA NA NA\n+"cg03348902" NA NA NA NA NA NA\n+"cg01070250" NA NA NA NA NA NA\n+"cg21996134" NA NA NA NA NA NA\n+"cg07264491" NA NA NA NA NA NA\n+"cg15560884" NA NA NA NA NA NA\n+"cg10037654" NA NA NA NA NA NA\n+"cg14057946" "rs74512038" 0.076823 NA NA NA NA\n+"cg11422233" "rs74512038" 0.076823 NA NA NA NA\n+"cg16047670" "rs114983708" 0.115264 NA NA NA NA\n+"cg18263059" NA NA NA NA NA NA\n+"cg01014490" NA NA NA NA NA NA\n+"cg04231937" NA NA NA NA NA NA\n+"cg04496485" "rs149887893" 0.0261 NA NA NA NA\n+"cg17505339" NA NA NA NA NA NA\n+"cg09989996" NA NA NA NA NA NA\n+"cg11954957" "rs115498424" 0.029514 NA NA NA NA\n+"cg01068023" NA NA NA NA NA NA\n+"cg08167039" "rs3115849" 0.276256 NA NA NA NA\n+"cg20677962" "rs75333668" 0.0687 NA NA NA NA\n+"cg06402284" NA NA "rs71507462" 0.274931 NA NA\n+"cg24699430" "rs139039741" 0.0211 NA NA NA NA\n+"cg01551879" "rs142969342" 0.0485 NA NA NA NA\n+"cg22394869" NA NA NA NA NA NA\n+"cg02550592" NA NA NA NA NA NA\n+"cg03213877" NA NA "rs191770232" 0.0206 NA NA\n+"cg23803172" "rs191770232" 0.0206 NA NA NA NA\n+"cg19411932" "rs191770232" 0.0206 NA NA NA NA\n+"cg20788133" NA NA "rs2519025" 0.092322 NA NA\n+"cg08939496" NA NA NA NA NA NA\n+"cg16736630" NA NA NA NA NA NA\n+"cg01793617" NA NA NA NA NA NA\n+"cg09139287" NA NA "rs2905055" 0.336368 "rs2905055" 0.336368\n+"cg05662829" "rs2905055" 0.336368 NA NA NA NA\n+"cg22714517" NA NA NA NA NA NA\n+"cg00168193" NA NA "rs149504348" 0.0389 NA NA\n+"cg14280098" "rs74877941" 0.0545 NA NA NA NA\n+"cg15903280" "rs115634970" 0.030382 NA NA NA NA\n+"cg04352959" NA NA NA NA NA NA\n+"cg08258224" NA NA NA NA NA NA\n+"cg12285627" NA NA NA NA NA NA\n+"cg05898754" "rs112221884" 0.014639 NA NA NA NA\n+"cg03128332" NA NA NA NA NA NA\n+"cg15994267" NA NA NA NA NA NA\n+"cg16619049" "rs72631880" 0.136322 NA NA NA NA\n+"cg23100540" "rs72631880" 0.136322 NA NA NA NA\n+"cg20275697" NA NA NA NA NA NA\n+"cg05475702" 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0.13129 NA NA NA NA\n+"cg01782097" NA NA NA NA NA NA\n+"cg20825023" NA NA NA NA NA NA\n+"cg12549180" NA NA NA NA NA NA\n+"cg11851804" N'..b' NA NA NA NA NA\n+"cg25667057" NA NA NA NA NA NA\n+"cg23834181" NA NA NA NA NA NA\n+"cg03672679" NA NA NA NA NA NA\n+"cg04792227" NA NA NA NA NA NA\n+"cg00679624" NA NA NA NA NA NA\n+"cg20764275" NA NA NA NA NA NA\n+"cg14742615" NA NA NA NA NA NA\n+"cg01882666" NA NA NA NA NA NA\n+"cg03905640" NA NA NA NA NA NA\n+"cg01209756" NA NA NA NA NA NA\n+"cg17115812" NA NA NA NA NA NA\n+"cg14151065" NA NA NA NA NA NA\n+"cg25012987" NA NA NA NA NA NA\n+"cg16292375" NA NA NA NA NA NA\n+"cg16894943" NA NA NA NA NA NA\n+"cg06060201" NA NA NA NA NA NA\n+"cg04170994" NA NA NA NA NA NA\n+"cg09408193" NA NA NA NA NA NA\n+"cg10252249" NA NA NA NA NA NA\n+"cg23308414" NA NA NA NA NA NA\n+"cg26046487" NA NA NA NA NA NA\n+"cg10646950" NA NA NA NA NA NA\n+"cg00479827" NA NA NA NA NA NA\n+"cg10691859" NA NA NA NA NA NA\n+"cg15281205" NA NA NA NA NA NA\n+"cg05230942" NA NA NA NA NA NA\n+"cg13765957" NA NA NA NA NA NA\n+"cg26251715" NA NA NA NA NA NA\n+"cg03244189" NA NA NA NA NA NA\n+"cg13845521" NA NA NA NA NA NA\n+"cg10811597" NA NA NA NA NA NA\n+"cg11816202" NA NA NA NA NA NA\n+"cg00212031" NA NA NA NA NA NA\n+"cg15345074" NA NA NA NA NA NA\n+"cg11684211" NA NA NA NA NA NA\n+"cg06628792" NA NA NA NA NA NA\n+"cg00121626" NA NA NA NA NA NA\n+"cg15027426" NA NA NA NA NA NA\n+"cg00876332" NA NA NA NA NA NA\n+"cg15794778" NA NA NA NA NA NA\n+"cg09228985" NA NA NA NA NA NA\n+"cg06065495" NA NA NA NA NA NA\n+"cg03533500" NA NA NA NA NA NA\n+"cg06231362" NA NA NA NA NA NA\n+"cg25756647" NA NA NA NA NA NA\n+"cg06502680" NA NA NA NA NA NA\n+"cg20864678" NA NA NA NA NA NA\n+"cg14492024" NA NA NA NA NA NA\n+"cg05725925" NA NA NA NA NA NA\n+"cg05621349" NA NA NA NA NA NA\n+"cg10076560" NA NA NA NA NA NA\n+"cg15682993" NA NA NA NA NA NA\n+"cg07731488" NA NA NA NA NA NA\n+"cg05672930" NA NA NA NA NA NA\n+"cg17660627" NA NA NA NA NA NA\n+"cg14931215" NA NA NA NA NA NA\n+"cg00308367" NA NA NA NA NA NA\n+"cg27509967" NA NA NA NA NA NA\n+"cg15329860" NA NA NA NA NA NA\n+"cg25815185" NA NA NA NA NA NA\n+"cg27049643" NA NA NA NA NA NA\n+"cg26517491" NA NA NA NA NA NA\n+"cg15662272" NA NA NA NA NA NA\n+"cg02522936" NA NA NA NA NA NA\n+"cg10799208" NA NA NA NA NA NA\n+"cg26928789" NA NA NA NA NA NA\n+"cg09081202" NA NA NA NA NA NA\n+"cg01988452" NA NA NA NA NA NA\n+"cg13308744" NA NA NA NA NA NA\n+"cg10172760" NA NA NA NA NA NA\n+"cg10620659" NA NA NA NA NA NA\n+"cg15422579" NA NA NA NA NA NA\n+"cg15059553" NA NA NA NA NA NA\n+"cg01644972" NA NA NA NA NA NA\n+"cg02233190" NA NA NA NA NA NA\n+"cg26983535" NA NA NA NA NA NA\n+"cg11225091" NA NA NA NA NA NA\n+"cg03750315" NA NA NA NA NA NA\n+"cg02884332" NA NA NA NA NA NA\n+"cg08715207" NA NA NA NA NA NA\n+"cg08820785" NA NA NA NA NA NA\n+"cg10593480" NA NA NA NA NA NA\n+"cg00063477" "rs9341314" 0.036364 NA NA NA NA\n+"cg01900066" NA NA NA NA NA NA\n+"cg07747963" NA NA NA NA NA NA\n+"cg10841270" NA NA NA NA NA NA\n+"cg01943289" NA NA NA NA NA NA\n+"cg17741448" NA NA NA NA NA NA\n+"cg02012379" NA NA NA NA NA NA\n+"cg00676506" NA NA NA NA NA NA\n+"cg06322277" NA NA NA NA NA NA\n+"cg26058907" NA NA NA NA NA NA\n+"cg02050847" NA NA NA NA NA NA\n+"cg14029254" NA NA NA NA NA NA\n+"cg02352633" NA NA NA NA NA NA\n+"cg03416979" NA NA NA NA NA NA\n+"cg05051262" NA NA NA NA NA NA\n+"cg25427172" NA NA NA NA NA NA\n+"cg10666546" NA NA NA NA NA NA\n+"cg25640065" NA NA NA NA NA NA\n+"cg16552926" NA NA NA NA NA NA\n+"cg25918849" NA NA NA NA NA NA\n+"cg11021362" NA NA NA NA NA NA\n+"cg14467015" NA NA NA NA NA NA\n+"cg15516537" NA NA NA NA NA NA\n+"cg05999368" NA NA NA NA NA NA\n+"cg15462332" NA NA NA NA NA NA\n+"cg26497631" NA NA NA NA NA NA\n+"cg06865724" NA NA NA NA NA NA\n+"cg25914522" NA NA NA NA NA NA\n+"cg13808036" NA NA NA NA NA NA\n+"cg10267609" NA NA NA NA NA NA\n+"cg00335297" NA NA NA NA NA NA\n+"cg03827298" NA NA NA NA NA NA\n+"cg26983430" NA NA NA NA NA NA\n+"cg22051787" NA NA NA NA NA NA\n+"cg01757887" NA NA NA NA NA NA\n+"cg00061679" NA NA NA NA NA NA\n+"cg03930849" NA NA NA NA NA NA\n+"cg17939569" NA NA NA NA NA NA\n+"cg13365400" NA NA NA NA NA NA\n+"cg21106100" NA NA NA NA NA NA\n+"cg08265308" NA NA NA NA NA NA\n+"cg14273923" NA NA NA NA NA NA\n' |
| b |
| diff -r 14defeb423a7 -r 8ab24a5229bd test-data/phenotypeTable.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phenotypeTable.txt Tue Feb 11 09:14:55 2020 -0500 |
| b |
| @@ -0,0 +1,5 @@ +Accession Sensitivity Treatment +GSM1588704 sensitive MAPKi +GSM1588705 sensitive MAPKi +GSM1588706 resistant BRAFi +GSM1588707 resistant BRAFi \ No newline at end of file |
| b |
| diff -r 14defeb423a7 -r 8ab24a5229bd test-data/ucsc.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ucsc.gtf Tue Feb 11 09:14:55 2020 -0500 |
| b |
| b'@@ -0,0 +1,482421 @@\n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t15865\t15865\t824.000000\t+\t0\tgene_id "cg13869341"; transcript_id "cg13869341"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t18827\t18827\t565.000000\t+\t0\tgene_id "cg14008030"; transcript_id "cg14008030"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t29407\t29407\t115.000000\t+\t0\tgene_id "cg12045430"; transcript_id "cg12045430"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t29425\t29425\t244.000000\t+\t0\tgene_id "cg20826792"; transcript_id "cg20826792"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t29435\t29435\t55.000000\t+\t0\tgene_id "cg00381604"; transcript_id "cg00381604"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t68849\t68849\t212.000000\t+\t0\tgene_id "cg20253340"; transcript_id "cg20253340"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t69592\t69592\t88.000000\t-\t0\tgene_id "cg21870274"; transcript_id "cg21870274"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t91551\t91551\t307.000000\t-\t0\tgene_id "cg03130891"; transcript_id "cg03130891"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t135253\t135253\t582.000000\t-\t0\tgene_id "cg24335620"; transcript_id "cg24335620"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t449076\t449076\t795.000000\t+\t0\tgene_id "cg16162899"; transcript_id "cg16162899"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t530959\t530959\t561.000000\t+\t0\tgene_id "cg17149495"; transcript_id "cg17149495"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t533950\t533950\t886.000000\t+\t0\tgene_id "cg22802167"; transcript_id "cg22802167"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t534243\t534243\t474.000000\t-\t0\tgene_id "cg24669183"; transcript_id "cg24669183"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t542759\t542759\t37.000000\t-\t0\tgene_id "cg17308840"; transcript_id "cg17308840"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t546985\t546985\t840.000000\t-\t0\tgene_id "cg17866181"; transcript_id "cg17866181"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t565171\t565171\t174.000000\t-\t0\tgene_id "cg24159721"; transcript_id "cg24159721"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t566173\t566173\t170.000000\t-\t0\tgene_id "cg15174812"; transcript_id "cg15174812"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t566570\t566570\t272.000000\t+\t0\tgene_id "cg08477687"; transcript_id "cg08477687"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t566732\t566732\t216.000000\t-\t0\tgene_id "cg00034556"; transcript_id "cg00034556"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t567113\t567113\t90.000000\t+\t0\tgene_id "cg00645010"; transcript_id "cg00645010"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t567207\t567207\t150.000000\t-\t0\tgene_id "cg15394630"; transcript_id "cg15394630"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t567312\t567312\t147.000000\t+\t0\tgene_id "cg05001044"; transcript_id "cg05001044"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t567349\t567349\t103.000000\t-\t0\tgene_id "cg03344490"; transcript_id "cg03344490"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t567359\t567359\t198.000000\t-\t0\tgene_id "cg17501828"; transcript_id "cg17501828"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t567502\t567502\t303.000000\t-\t0\tgene_id "cg23917638"; transcript_id "cg23917638"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t567747\t567747\t59.000000\t+\t0\tgene_id "cg18024856"; transcript_id "cg18024856"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t568476\t568476\t386.000000\t-\t0\tgene_id "cg18761878"; transcript_id "cg18761878"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t568536\t568536\t110.000000\t+\t0\tgene_id "cg27534567"; transcript_id "cg27534567"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t569428\t569428\t397.000000\t-\t0\tgene_id "cg08858441"; transcript_id "cg08858441"; \n+chr1\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t569604\t569604\t203.000000\t-\t0\tgene_id "cg03348902"; transcript_id "cg03348902"; \n+chr1\thg1'..b'991"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51169029\t51169029\t662.000000\t-\t0\tgene_id "cg12502079"; transcript_id "cg12502079"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51169500\t51169500\t917.000000\t+\t0\tgene_id "cg06422471"; transcript_id "cg06422471"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51170003\t51170003\t791.000000\t+\t0\tgene_id "cg19324023"; transcript_id "cg19324023"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51171263\t51171263\t830.000000\t+\t0\tgene_id "cg09635994"; transcript_id "cg09635994"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51173065\t51173065\t131.000000\t+\t0\tgene_id "cg19004771"; transcript_id "cg19004771"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51173647\t51173647\t198.000000\t-\t0\tgene_id "cg20569369"; transcript_id "cg20569369"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51175365\t51175365\t286.000000\t-\t0\tgene_id "cg26034629"; transcript_id "cg26034629"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51175515\t51175515\t564.000000\t+\t0\tgene_id "cg25232725"; transcript_id "cg25232725"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51176408\t51176408\t117.000000\t-\t0\tgene_id "cg05615487"; transcript_id "cg05615487"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51176544\t51176544\t159.000000\t-\t0\tgene_id "cg00080682"; transcript_id "cg00080682"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51176712\t51176712\t704.000000\t-\t0\tgene_id "cg22122449"; transcript_id "cg22122449"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51177983\t51177983\t727.000000\t-\t0\tgene_id "cg08423507"; transcript_id "cg08423507"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51194097\t51194097\t291.000000\t-\t0\tgene_id "cg12121634"; transcript_id "cg12121634"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51195438\t51195438\t285.000000\t-\t0\tgene_id "cg04757410"; transcript_id "cg04757410"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51206645\t51206645\t842.000000\t+\t0\tgene_id "cg09456760"; transcript_id "cg09456760"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51213830\t51213830\t220.000000\t-\t0\tgene_id "cg16023925"; transcript_id "cg16023925"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51221675\t51221675\t23.000000\t+\t0\tgene_id "cg11295469"; transcript_id "cg11295469"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51221681\t51221681\t93.000000\t+\t0\tgene_id "cg06701842"; transcript_id "cg06701842"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51221737\t51221737\t40.000000\t-\t0\tgene_id "cg09007244"; transcript_id "cg09007244"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51221774\t51221774\t73.000000\t-\t0\tgene_id "cg27124406"; transcript_id "cg27124406"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51222011\t51222011\t17.000000\t+\t0\tgene_id "cg19565306"; transcript_id "cg19565306"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51222043\t51222043\t15.000000\t+\t0\tgene_id "cg22012975"; transcript_id "cg22012975"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51222051\t51222051\t19.000000\t+\t0\tgene_id "cg10353737"; transcript_id "cg10353737"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51222076\t51222076\t28.000000\t+\t0\tgene_id "cg22531257"; transcript_id "cg22531257"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51222252\t51222252\t63.000000\t-\t0\tgene_id "cg22662321"; transcript_id "cg22662321"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51222519\t51222519\t26.000000\t+\t0\tgene_id "cg06996138"; transcript_id "cg06996138"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51222729\t51222729\t132.000000\t+\t0\tgene_id "cg16817496"; transcript_id "cg16817496"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51223343\t51223343\t362.000000\t+\t0\tgene_id "cg07660283"; transcript_id "cg07660283"; \n+chr22\thg19_wgEncodeHaibMethyl450Gm12878SitesRep1\tCDS\t51225561\t51225561\t634.000000\t+\t0\tgene_id "cg09226288"; transcript_id "cg09226288"; \n' |
