| Next changeset 1:7c7a2a381dfe (2018-06-21) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ commit 3b9aec9beb72407e01f4a0c5b31c17ac3f92a851 |
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added:
rcas.xml readme.rst test-data/GSEA.data.tsv test-data/coverageprofilelist.data.tsv test-data/exonIntronBoundaryCoverage.fiveprime.data.tsv test-data/exonIntronBoundaryCoverage.threeprime.data.tsv test-data/getTargetedGenesTable.data.tsv test-data/goBP.data.tsv test-data/goCC.data.tsv test-data/goMF.data.tsv test-data/input.Homo_sapiens.GRCh37-chr1-f10k.75.gtf test-data/input.Homo_sapiens.GRCh37-chr1-f10k.75.gtf.granges.rds test-data/input.TIA1.bed test-data/input.msigdb_test.gmt test-data/motif_analysis_table.data.tsv test-data/output.TIA1.bed.RCAS.report.html test-data/query_gene_types.data.tsv test-data/summarizeQueryRegions.data.tsv test-data/transcriptBoundaryCoverage.fiveprime.data.tsv test-data/transcriptBoundaryCoverage.threeprime.data.tsv |
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| diff -r 000000000000 -r aa9579837a2e rcas.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rcas.xml Thu Apr 13 12:36:05 2017 -0400 |
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| b'@@ -0,0 +1,228 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<tool id="rcas" name="RNA Centric Annotation System" version="1.1.1">\n+ <requirements>\n+ <requirement type="package" version="1.1.1">bioconductor-rcas</requirement>\n+ </requirements>\n+ <stdio>\n+ <regex match="Execution halted" source="both" level="fatal" description="Execution halted." />\n+ <exit_code range="1:" />\n+ </stdio>\n+ <command><![CDATA[Rscript \'$script_file\'\n+\n+ &&\n+ mv *RCAS.report.html RCAS.report.html\n+\n+\n+ #if $run_anot == "TRUE":\n+ &&\n+ mv Figure*summarizeQueryRegions.data.tsv summarizeQueryRegions.data.tsv &&\n+ mv Figure*query_gene_types.data.tsv query_gene_types.data.tsv &&\n+ mv Figure*transcriptBoundaryCoverage.fiveprime.data.tsv transcriptBoundaryCoverage.fiveprime.data.tsv &&\n+ mv Figure*transcriptBoundaryCoverage.threeprime.data.tsv transcriptBoundaryCoverage.threeprime.data.tsv &&\n+ mv Figure*exonIntronBoundaryCoverage.fiveprime.data.tsv exonIntronBoundaryCoverage.fiveprime.data.tsv &&\n+ mv Figure*exonIntronBoundaryCoverage.threeprime.data.tsv exonIntronBoundaryCoverage.threeprime.data.tsv &&\n+ mv Figure*coverageprofilelist.data.tsv coverageprofilelist.data.tsv &&\n+ mv Table*getTargetedGenesTable.data.tsv getTargetedGenesTable.data.tsv\n+ #end if\n+\n+\n+ #if $run_GOrich == "TRUE":\n+ &&\n+ mv Table*goBP.data.tsv goBP.data.tsv &&\n+ mv Table*goMF.data.tsv goMF.data.tsv &&\n+ mv Table*goCC.data.tsv goCC.data.tsv\n+ #end if\n+\n+\n+ #if $choice.run_PATHrich == "TRUE":\n+ &&\n+ mv Table*GSEA.data.tsv GSEA.data.tsv\n+ #end if\n+\n+\n+ #if $run_motif == "TRUE":\n+ &&\n+ mv Table*motif_analysis_table.data.tsv motif_analysis_table.data.tsv\n+ #end if]]></command>\n+ <configfiles>\n+ <configfile name="script_file">library("RCAS")\n+\n+ runReport(queryFilePath = \'${input_BED}\',\n+\n+ gffFilePath = \'${input_GTF}\',\n+\n+ #if $choice.run_PATHrich == "TRUE":\n+ msigdbFilePath = \'${choice.input_human_msigdb_gmt}\',\n+ #end if\n+\n+ annotationSummary = ${run_anot},\n+\n+ goAnalysis = ${run_GOrich},\n+\n+ msigdbAnalysis = ${choice.run_PATHrich},\n+\n+ motifAnalysis = ${run_motif},\n+\n+ genomeVersion = \'${genomeVersion}\',\n+\n+ outDir = getwd(),\n+\n+ printProcessedTables = TRUE,\n+\n+ sampleN = \'${downsampling}\',\n+\n+ selfContained = TRUE)</configfile>\n+ </configfiles>\n+ <inputs>\n+ <param name="genomeVersion" type="select" label="Genome Version">\n+ <option value="hg19" selected="true">hg19</option>\n+ <option value="dm3">dm3</option>\n+ <option value="ce10">ce10</option>\n+ <option value="mm9">mm9</option>\n+ </param>\n+ <param name="input_BED" type="data" format="BED" label="Target regions in BED format" help="The coordinates should be in accord with Genome Version." />\n+ <param name="input_GTF" type="data" format="GTF" label="Reference annotation in ENSEMBL GTF format" />\n+ <param name="run_anot" label="Run annotation." type="boolean" falsevalue="FALSE" truevalue="TRUE" checked="True" help="Use this option if you want to run annotation." />\n+ <param name="run_GOrich" label="Run GO term enrichment" type="boolean" falsevalue="FALSE" truevalue="TRUE" checked="False" help="Use this option if you want to run GO term enrichment (supported genome versions: hg19, mm9, dm3)." />\n+ <conditional name="choice">\n+ <param name="run_PATHrich" type="select" label="Run gene set enrichment" help="Use this option if you want to run gene set enrichment.">\n+ <optio'..b' <filter>choice[\'run_PATHrich\'] == "TRUE"</filter>\n+ </data>\n+ <data name="motif" format="tsv" from_work_dir="motif_analysis_table.data.tsv" label="${tool.name} on ${on_string}: Motif">\n+ <filter>run_motif == True</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input_BED" value="input.TIA1.bed" />\n+ <param name="input_GTF" value="input.Homo_sapiens.GRCh37-chr1-f10k.75.gtf" />\n+ <param name="input_human_msigdb_gmt" value="input.msigdb_test.gmt" />\n+ <param name="run_anot" value="TRUE" />\n+ <param name="run_GOrich" value="TRUE" />\n+ <param name="run_PATHrich" value="TRUE" />\n+ <param name="run_motif" value="TRUE" />\n+ <param name="genomeVersion" value="hg19" />\n+ <output name="report" file="output.TIA1.bed.RCAS.report.html" ftype="html" compare="sim_size" />\n+ <output name="summarizeQueryRegions" file="summarizeQueryRegions.data.tsv" ftype="tsv" />\n+ <output name="query_gene_types" file="query_gene_types.data.tsv" ftype="tsv" />\n+ <output name="transcriptBoundaryCoverage.fiveprime" file="transcriptBoundaryCoverage.fiveprime.data.tsv" ftype="tsv" />\n+ <output name="transcriptBoundaryCoverage.threeprime" file="transcriptBoundaryCoverage.threeprime.data.tsv" ftype="tsv" />\n+ <output name="exonIntronBoundaryCoverage.fiveprime" file="exonIntronBoundaryCoverage.fiveprime.data.tsv" ftype="tsv" />\n+ <output name="exonIntronBoundaryCoverage.threeprime" file="exonIntronBoundaryCoverage.threeprime.data.tsv" ftype="tsv" />\n+ <output name="coverageprofilelist" file="coverageprofilelist.data.tsv" ftype="tsv" />\n+ <output name="getTargetedGenesTable" file="getTargetedGenesTable.data.tsv" ftype="tsv" />\n+ <output name="goCC" file="goCC.data.tsv" ftype="tsv" compare="sim_size"/>\n+ <output name="goBP" file="goBP.data.tsv" ftype="tsv" compare="sim_size"/>\n+ <output name="goMF" file="goMF.data.tsv" ftype="tsv" compare="sim_size"/>\n+ <output name="GSEA" file="GSEA.data.tsv" ftype="tsv" />\n+ <output name="motif" file="motif_analysis_table.data.tsv" ftype="tsv" compare="sim_size" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[.. class:: infomark\n+\n+**Purpose**\n+\n+RNA Centric Annotation System (RCAS) automatically generates\n+dynamic annotations for custom input files\n+that contain transcriptomic target regions.\n+RCAS automatically summarizes annotated features\n+that overlap with targets in the BED file,\n+and perform enrichment analysis of\n+Gene Ontology (GO) terms, gene set and motifs.\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Inputs**\n+\n+1. A target region file in BED format\n+2. A reference annotation file in GTF format\n+3. A Human Molecular Signatures Database (MSigDB) (only needed for gene set enrichment)\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Outputs**\n+\n+The outputs consist of a dynamic HTML file and\n+a dozen of tabular files.\n+The dynamic HTML file is composed of the interactive tables and figures,\n+which can be downloaded and viewed with a web browser.\n+\n+The tabular files correspond to the respective figures in the HTML file,\n+which are the results\n+of different RCAS analysis, as following:\n+\n+1. Annotation summary for query regions\n+\n+ * Query regions summary\n+ * Query gene types\n+ * Transcript boundary coverage (5\')\n+ * Transcript boundary coverage (3\')\n+ * Exon-intron boundary coverage (5\')\n+ * Exon-intron boundary coverage (3\')\n+ * Coverage profile list\n+ * Targeted genes\n+\n+2. GO term analysis results\n+\n+ * GO term enrichment (cellular compartments)\n+ * GO term enrichment (biological processes)\n+ * GO term enrichment (molecular functions)\n+\n+3. Gene set enrichment analysis results\n+\n+4. Motif analysis results]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/nar/gkx120</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r aa9579837a2e readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Thu Apr 13 12:36:05 2017 -0400 |
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| @@ -0,0 +1,16 @@ +Important notes +---------------- + +- the dependencies of the tool are handled by the conda dependency resolver + +- to install the dependencies, the galaxy administrator needs to configure to ensure the conda channels - bioconda, r, conda-forge, defaults + +- by default, the conda installation includes hg19 + +- to enable analysis for mm9, ce10, dm3, the administrator needs to separately install the relevant packages from the channel bioconda + - bioconductor-bsgenome.dmelanogaster.ucsc.dm3 + - bioconductor-bsgenome.celegans.ucsc.ce10 + - bioconductor-bsgenome.mmusculus.ucsc.mm9 + - bioconductor-org.mm.eg.db + - bioconductor-org.ce.eg.db + - bioconductor-org.dm.eg.db |
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| diff -r 000000000000 -r aa9579837a2e test-data/GSEA.data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSEA.data.tsv Thu Apr 13 12:36:05 2017 -0400 |
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| @@ -0,0 +1,11 @@ +treatment expectedInTreatment BH bonferroni foldEnrichment +KEGG GLYCOLYSIS GLUCONEOGENESIS 0 0 1 1 NA +KEGG CITRATE CYCLE TCA CYCLE 0 0 1 1 NA +KEGG PENTOSE PHOSPHATE PATHWAY 0 0 1 1 NA +KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS 0 0 1 1 NA +KEGG FRUCTOSE AND MANNOSE METABOLISM 0 0 1 1 NA +KEGG GALACTOSE METABOLISM 0 0 1 1 NA +KEGG ASCORBATE AND ALDARATE METABOLISM 0 0 1 1 NA +KEGG FATTY ACID METABOLISM 0 0 1 1 NA +KEGG STEROID BIOSYNTHESIS 0 0 1 1 NA +KEGG PRIMARY BILE ACID BIOSYNTHESIS 0 0 1 1 NA |
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| diff -r 000000000000 -r aa9579837a2e test-data/coverageprofilelist.data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverageprofilelist.data.tsv Thu Apr 13 12:36:05 2017 -0400 |
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|
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/exonIntronBoundaryCoverage.fiveprime.data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exonIntronBoundaryCoverage.fiveprime.data.tsv Thu Apr 13 12:36:05 2017 -0400 |
| b |
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|
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/exonIntronBoundaryCoverage.threeprime.data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exonIntronBoundaryCoverage.threeprime.data.tsv Thu Apr 13 12:36:05 2017 -0400 |
| b |
| b'@@ -0,0 +1,2001 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|
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/getTargetedGenesTable.data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/getTargetedGenesTable.data.tsv Thu Apr 13 12:36:05 2017 -0400 |
| b |
| @@ -0,0 +1,89 @@ +tx_name transcripts exons promoters fiveUTRs introns cds threeUTRs +1 ENST00000378609 5 4 0 1 1 1 3 +2 ENST00000327044 2 1 0 0 1 0 1 +3 ENST00000347370 2 2 0 0 0 0 2 +4 ENST00000378536 2 2 0 0 0 0 2 +5 ENST00000450390 2 2 0 0 0 0 2 +6 ENST00000477976 2 1 0 0 1 0 0 +7 ENST00000263741 1 1 0 0 0 0 1 +8 ENST00000291386 1 1 0 0 0 0 1 +9 ENST00000306256 1 1 0 0 0 1 0 +10 ENST00000308647 1 1 0 0 0 1 0 +11 ENST00000323275 1 0 0 0 1 0 0 +12 ENST00000360001 1 1 0 0 0 0 1 +13 ENST00000378512 1 1 0 0 0 1 0 +14 ENST00000378513 1 0 0 0 1 0 0 +15 ENST00000378518 1 0 0 0 1 0 0 +16 ENST00000378567 1 0 0 0 1 0 0 +17 ENST00000378726 1 1 0 0 0 0 0 +18 ENST00000400809 1 0 0 0 1 0 0 +19 ENST00000400920 1 0 1 1 1 0 0 +20 ENST00000400921 1 0 0 1 1 0 0 +21 ENST00000408952 1 0 0 1 1 0 0 +22 ENST00000411962 1 0 0 0 1 0 0 +23 ENST00000418865 1 1 0 0 0 0 0 +24 ENST00000419704 1 0 0 0 1 0 0 +25 ENST00000421495 1 0 0 1 1 0 0 +26 ENST00000429572 1 1 0 0 0 0 0 +27 ENST00000430786 1 0 0 0 1 0 1 +28 ENST00000434686 1 0 0 1 1 0 0 +29 ENST00000434694 1 0 0 0 1 0 0 +30 ENST00000435064 1 0 0 0 1 0 0 +31 ENST00000439272 1 0 0 1 1 0 0 +32 ENST00000443438 1 1 0 0 0 1 0 +33 ENST00000450926 1 0 0 0 1 0 0 +34 ENST00000458452 1 0 0 0 1 0 1 +35 ENST00000461106 1 0 0 0 1 0 0 +36 ENST00000461465 1 0 0 1 1 0 0 +37 ENST00000461893 1 1 0 0 0 0 0 +38 ENST00000465727 1 1 0 0 0 0 1 +39 ENST00000466651 1 0 0 0 1 0 0 +40 ENST00000468310 1 0 0 0 1 0 0 +41 ENST00000469113 1 1 0 0 1 0 0 +42 ENST00000470596 1 0 0 1 1 0 0 +43 ENST00000471354 1 1 0 0 0 0 0 +44 ENST00000471930 1 1 0 0 0 0 0 +45 ENST00000472194 1 1 0 0 0 0 0 +46 ENST00000472614 1 0 0 0 1 0 0 +47 ENST00000474481 1 1 0 0 0 0 0 +48 ENST00000478938 1 1 0 0 0 0 0 +49 ENST00000481140 1 0 0 0 1 0 0 +50 ENST00000481223 1 1 0 0 0 0 1 +51 ENST00000482365 1 1 0 0 0 0 0 +52 ENST00000482621 1 0 0 0 1 0 1 +53 ENST00000482686 1 0 1 1 1 0 0 +54 ENST00000483767 1 1 0 0 0 0 0 +55 ENST00000485748 1 1 0 0 0 0 0 +56 ENST00000486681 1 0 1 1 1 0 0 +57 ENST00000487214 1 0 0 0 1 0 0 +58 ENST00000488042 1 0 0 0 1 0 0 +59 ENST00000488340 1 0 0 0 1 0 0 +60 ENST00000488353 1 1 0 0 0 1 0 +61 ENST00000494748 1 1 0 0 0 0 0 +62 ENST00000495347 1 0 0 1 1 0 0 +63 ENST00000496007 1 1 0 0 0 0 0 +64 ENST00000496325 1 0 0 1 1 0 0 +65 ENST00000496353 1 1 0 0 0 0 0 +66 ENST00000498173 1 1 0 0 0 0 0 +67 ENST00000505849 1 1 0 0 1 0 0 +68 ENST00000525603 1 0 0 0 1 0 0 +69 ENST00000526113 1 0 0 0 1 0 0 +70 ENST00000526332 1 0 0 0 1 0 0 +71 ENST00000526797 1 0 0 0 1 0 1 +72 ENST00000526904 1 0 0 0 1 0 0 +73 ENST00000527098 1 0 0 0 1 0 1 +74 ENST00000527719 1 0 0 0 1 0 0 +75 ENST00000528879 1 0 0 0 1 0 0 +76 ENST00000530031 1 0 0 0 1 0 0 +77 ENST00000531377 1 0 0 0 1 0 0 +78 ENST00000532772 1 0 0 0 1 0 0 +79 ENST00000540437 1 0 0 0 1 0 0 +80 ENST00000545578 1 0 0 0 1 0 0 +81 ENST00000605895 1 1 0 0 0 1 0 +82 ENST00000378733 0 0 1 0 0 0 0 +83 ENST00000425828 0 0 1 0 0 0 0 +84 ENST00000444968 0 0 1 0 0 0 0 +85 ENST00000462432 0 0 1 0 0 0 0 +86 ENST00000480479 0 0 1 0 0 0 0 +87 ENST00000480646 0 0 1 0 0 0 0 +88 ENST00000492998 0 0 1 0 0 0 0 |
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/goBP.data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/goBP.data.tsv Thu Apr 13 12:36:05 2017 -0400 |
| b |
| @@ -0,0 +1,33 @@ +Term Significant Expected bonferroni bh foldEnrichment +GO:0006139 nucleobase-containing compound metabolic... 6 4.2 1 0.596363636363636 1.43 +GO:0006725 cellular aromatic compound metabolic pro... 6 4.2 1 0.596363636363636 1.43 +GO:0046483 heterocycle metabolic process 6 4.2 1 0.596363636363636 1.43 +GO:1901360 organic cyclic compound metabolic proces... 6 4.2 1 0.596363636363636 1.43 +GO:0019538 protein metabolic process 6 4.4 1 0.596363636363636 1.36 +GO:0050794 regulation of cellular process 8 6 1 0.596363636363636 1.33 +GO:0044260 cellular macromolecule metabolic process 7 5.4 1 0.596363636363636 1.3 +GO:0034641 cellular nitrogen compound metabolic pro... 6 4.6 1 0.596363636363636 1.3 +GO:0050789 regulation of biological process 8 6.2 1 0.596363636363636 1.29 +GO:0065007 biological regulation 8 6.2 1 0.596363636363636 1.29 +GO:0009059 macromolecule biosynthetic process 5 4 1 0.596363636363636 1.25 +GO:0031323 regulation of cellular metabolic process 5 4 1 0.596363636363636 1.25 +GO:0034645 cellular macromolecule biosynthetic proc... 5 4 1 0.596363636363636 1.25 +GO:0044710 single-organism metabolic process 5 4 1 0.596363636363636 1.25 +GO:0080090 regulation of primary metabolic process 5 4 1 0.596363636363636 1.25 +GO:0043170 macromolecule metabolic process 7 5.8 1 0.596363636363636 1.21 +GO:0006807 nitrogen compound metabolic process 6 5 1 0.596363636363636 1.2 +GO:0050896 response to stimulus 6 5 1 0.596363636363636 1.2 +GO:0044271 cellular nitrogen compound biosynthetic ... 5 4.2 1 0.596363636363636 1.19 +GO:0051716 cellular response to stimulus 5 4.2 1 0.596363636363636 1.19 +GO:0044237 cellular metabolic process 8 6.8 1 0.596363636363636 1.18 +GO:0019222 regulation of metabolic process 5 4.4 1 0.653913043478261 1.14 +GO:0009987 cellular process 10 9.2 1 0.596363636363636 1.09 +GO:0008152 metabolic process 8 7.6 1 0.687407407407407 1.05 +GO:0009058 biosynthetic process 5 4.8 1 0.687407407407407 1.04 +GO:0044249 cellular biosynthetic process 5 4.8 1 0.687407407407407 1.04 +GO:1901576 organic substance biosynthetic process 5 4.8 1 0.687407407407407 1.04 +GO:0044238 primary metabolic process 7 7 1 0.728275862068966 1 +GO:0071704 organic substance metabolic process 7 7 1 0.728275862068966 1 +GO:0008150 biological_process 10 10 1 1 1 +GO:0044699 single-organism process 8 8.2 1 0.774193548387097 0.98 +GO:0044763 single-organism cellular process 8 8.2 1 0.774193548387097 0.98 |
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/goCC.data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/goCC.data.tsv Thu Apr 13 12:36:05 2017 -0400 |
| b |
| @@ -0,0 +1,18 @@ +Term Significant Expected bonferroni bh foldEnrichment +GO:0044446 intracellular organelle part 10 3.97 0.001054 0.000935 2.52 +GO:0044422 organelle part 10 4.15 0.00187 0.000935 2.41 +GO:0043231 intracellular membrane-bounded organelle 11 6.13 0.01156 0.00385333333333333 1.79 +GO:0043227 membrane-bounded organelle 11 6.49 0.02448 0.00612 1.69 +GO:0043229 intracellular organelle 11 6.85 0.04896 0.009792 1.61 +GO:0005737 cytoplasm 10 6.31 0.21097 0.0234411111111111 1.58 +GO:0043226 organelle 11 7.21 0.09401 0.0156683333333333 1.53 +GO:0005622 intracellular 11 7.57 0.17408 0.02176 1.45 +GO:0044424 intracellular part 11 7.57 0.17408 0.02176 1.45 +GO:0044444 cytoplasmic part 6 4.33 1 0.2988175 1.39 +GO:0005623 cell 11 9.2 1 0.176042727272727 1.2 +GO:0044464 cell part 11 9.2 1 0.176042727272727 1.2 +GO:0005575 cellular_component 11 11 1 1 1 +GO:0016020 membrane 6 6.31 1 0.927794615384615 0.95 +GO:0044425 membrane part 4 5.23 1 1 0.76 +GO:0016021 integral component of membrane 2 4.33 1 1 0.46 +GO:0031224 intrinsic component of membrane 2 4.33 1 1 0.46 |
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/goMF.data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/goMF.data.tsv Thu Apr 13 12:36:05 2017 -0400 |
| b |
| @@ -0,0 +1,5 @@ +Term Significant Expected bonferroni bh foldEnrichment +GO:0005515 protein binding 10 7.13 0.164 0.164 1.4 +GO:0005488 binding 11 9.78 0.944 0.472 1.12 +GO:0003674 molecular_function 11 11 1 1 1 +GO:0043167 ion binding 5 5.09 1 0.872 0.98 |
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/input.Homo_sapiens.GRCh37-chr1-f10k.75.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.Homo_sapiens.GRCh37-chr1-f10k.75.gtf Thu Apr 13 12:36:05 2017 -0400 |
| b |
| b'@@ -0,0 +1,10000 @@\n+#!genome-build GRCh37.p13\n+#!genome-version GRCh37\n+#!genome-date 2009-02\n+#!genome-build-accession NCBI:GCA_000001405.14\n+#!genebuild-last-updated 2013-09\n+1\tpseudogene\tgene\t11869\t14412\t.\t+\t.\tgene_id "ENSG00000223972"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene";\n+1\tprocessed_transcript\ttranscript\t11869\t14409\t.\t+\t.\tgene_id "ENSG00000223972"; transcript_id "ENST00000456328"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana";\n+1\tprocessed_transcript\texon\t11869\t12227\t.\t+\t.\tgene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "1"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana"; exon_id "ENSE00002234944";\n+1\tprocessed_transcript\texon\t12613\t12721\t.\t+\t.\tgene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "2"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana"; exon_id "ENSE00003582793";\n+1\tprocessed_transcript\texon\t13221\t14409\t.\t+\t.\tgene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "3"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana"; exon_id "ENSE00002312635";\n+1\ttranscribed_unprocessed_pseudogene\ttranscript\t11872\t14412\t.\t+\t.\tgene_id "ENSG00000223972"; transcript_id "ENST00000515242"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene"; transcript_name "DDX11L1-201"; transcript_source "ensembl";\n+1\ttranscribed_unprocessed_pseudogene\texon\t11872\t12227\t.\t+\t.\tgene_id "ENSG00000223972"; transcript_id "ENST00000515242"; exon_number "1"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene"; transcript_name "DDX11L1-201"; transcript_source "ensembl"; exon_id "ENSE00002234632";\n+1\ttranscribed_unprocessed_pseudogene\texon\t12613\t12721\t.\t+\t.\tgene_id "ENSG00000223972"; transcript_id "ENST00000515242"; exon_number "2"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene"; transcript_name "DDX11L1-201"; transcript_source "ensembl"; exon_id "ENSE00003608237";\n+1\ttranscribed_unprocessed_pseudogene\texon\t13225\t14412\t.\t+\t.\tgene_id "ENSG00000223972"; transcript_id "ENST00000515242"; exon_number "3"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene"; transcript_name "DDX11L1-201"; transcript_source "ensembl"; exon_id "ENSE00002306041";\n+1\ttranscribed_unprocessed_pseudogene\ttranscript\t11874\t14409\t.\t+\t.\tgene_id "ENSG00000223972"; transcript_id "ENST00000518655"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene"; transcript_name "DDX11L1-202"; transcript_source "ensembl";\n+1\ttranscribed_unprocessed_pseudogene\texon\t11874\t12227\t.\t+\t.\tgene_id "ENSG00000223972"; transcript_id "ENST00000518655"; exon_number "1"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene"; transcript_name "DDX11L1-202"; transcript_source "ensembl"; exon_id "ENSE00002269724";\n+1\ttranscribed_unprocessed_pseudogene\texon\t12595\t12721\t.\t+\t.\tgene_id "ENSG00000223972"; transcript_id "ENST00000518655"; exon_number "2"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene"; transcript_name "DDX11L1-202"; transcript_source "ensembl"; exon_id "ENSE00002270865";\n+1\ttranscribed_unprocessed_pseudogene\texon\t13403\t13655\t.\t+\t.\tgene_id "ENSG00000223972"; transcript_id "ENST00000518655"; exon_number "3"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene"; transcript_name "DDX11L1-202"; transcript_source "ensembl"; exon_id "ENSE00002216795";\n+1\ttranscribed_unprocessed_pseudogene\texon\t13661\t14409\t.\t+\t.\tgene_id "ENSG00000223972"; transcript_id "ENST00000518655"; exon_number "4"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene"; tr'..b'2591"; transcript_id "ENST00000294599"; gene_name "MEGF6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "MEGF6-001"; transcript_source "ensembl_havana";\n+1\tprotein_coding\texon\t3447644\t3448012\t.\t-\t.\tgene_id "ENSG00000162591"; transcript_id "ENST00000294599"; exon_number "1"; gene_name "MEGF6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "MEGF6-001"; transcript_source "ensembl_havana"; exon_id "ENSE00001206859";\n+1\tprotein_coding\tCDS\t3447644\t3447809\t.\t-\t0\tgene_id "ENSG00000162591"; transcript_id "ENST00000294599"; exon_number "1"; gene_name "MEGF6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "MEGF6-001"; transcript_source "ensembl_havana"; protein_id "ENSP00000294599";\n+1\tprotein_coding\tstart_codon\t3447807\t3447809\t.\t-\t0\tgene_id "ENSG00000162591"; transcript_id "ENST00000294599"; exon_number "1"; gene_name "MEGF6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "MEGF6-001"; transcript_source "ensembl_havana";\n+1\tprotein_coding\texon\t3440688\t3440810\t.\t-\t.\tgene_id "ENSG00000162591"; transcript_id "ENST00000294599"; exon_number "2"; gene_name "MEGF6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "MEGF6-001"; transcript_source "ensembl_havana"; exon_id "ENSE00001123278";\n+1\tprotein_coding\tCDS\t3440688\t3440810\t.\t-\t2\tgene_id "ENSG00000162591"; transcript_id "ENST00000294599"; exon_number "2"; gene_name "MEGF6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "MEGF6-001"; transcript_source "ensembl_havana"; protein_id "ENSP00000294599";\n+1\tprotein_coding\texon\t3431966\t3432091\t.\t-\t.\tgene_id "ENSG00000162591"; transcript_id "ENST00000294599"; exon_number "3"; gene_name "MEGF6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "MEGF6-001"; transcript_source "ensembl_havana"; exon_id "ENSE00001123265";\n+1\tprotein_coding\tCDS\t3431966\t3432091\t.\t-\t2\tgene_id "ENSG00000162591"; transcript_id "ENST00000294599"; exon_number "3"; gene_name "MEGF6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "MEGF6-001"; transcript_source "ensembl_havana"; protein_id "ENSP00000294599";\n+1\tprotein_coding\texon\t3431114\t3431236\t.\t-\t.\tgene_id "ENSG00000162591"; transcript_id "ENST00000294599"; exon_number "4"; gene_name "MEGF6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "MEGF6-001"; transcript_source "ensembl_havana"; exon_id "ENSE00001123261";\n+1\tprotein_coding\tCDS\t3431114\t3431236\t.\t-\t2\tgene_id "ENSG00000162591"; transcript_id "ENST00000294599"; exon_number "4"; gene_name "MEGF6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "MEGF6-001"; transcript_source "ensembl_havana"; protein_id "ENSP00000294599";\n+1\tprotein_coding\texon\t3428570\t3428692\t.\t-\t.\tgene_id "ENSG00000162591"; transcript_id "ENST00000294599"; exon_number "5"; gene_name "MEGF6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "MEGF6-001"; transcript_source "ensembl_havana"; exon_id "ENSE00001123255";\n+1\tprotein_coding\tCDS\t3428570\t3428692\t.\t-\t2\tgene_id "ENSG00000162591"; transcript_id "ENST00000294599"; exon_number "5"; gene_name "MEGF6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "MEGF6-001"; transcript_source "ensembl_havana"; protein_id "ENSP00000294599";\n+1\tprotein_coding\texon\t3428114\t3428251\t.\t-\t.\tgene_id "ENSG00000162591"; transcript_id "ENST00000294599"; exon_number "6"; gene_name "MEGF6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "MEGF6-001"; transcript_source "ensembl_havana"; exon_id "ENSE00001123248";\n+1\tprotein_coding\tCDS\t3428114\t3428251\t.\t-\t2\tgene_id "ENSG00000162591"; transcript_id "ENST00000294599"; exon_number "6"; gene_name "MEGF6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "MEGF6-001"; transcript_source "ensembl_havana"; protein_id "ENSP00000294599";\n' |
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/input.Homo_sapiens.GRCh37-chr1-f10k.75.gtf.granges.rds |
| b |
| Binary file test-data/input.Homo_sapiens.GRCh37-chr1-f10k.75.gtf.granges.rds has changed |
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/input.TIA1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.TIA1.bed Thu Apr 13 12:36:05 2017 -0400 |
| b |
| b'@@ -0,0 +1,10000 @@\n+chr3\t123210549\t123210564\tiCLIP#TIA1_wang2010a_hg19*TIA1\t11\t-\n+chr9\t74606829\t74606830\tiCLIP#TIA1_wang2010a_hg19*TIA1\t2\t+\n+chr10\t105371321\t105371323\tiCLIP#TIA1_wang2010a_hg19*TIA1\t6\t-\n+chr14\t70444693\t70444719\tiCLIP#TIA1_wang2010a_hg19*TIA1\t8\t+\n+chr12\t26225727\t26225732\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t+\n+chr5\t58267147\t58267171\tiCLIP#TIA1_wang2010a_hg19*TIA1\t9\t-\n+chr17\t26994880\t26994892\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chrX\t153701919\t153701943\tiCLIP#TIA1_wang2010a_hg19*TIA1\t5\t+\n+chr5\t59893057\t59893094\tiCLIP#TIA1_wang2010a_hg19*TIA1\t9\t-\n+chr4\t125729716\t125729718\tiCLIP#TIA1_wang2010a_hg19*TIA1\t2\t+\n+chrX\t64290727\t64290728\tiCLIP#TIA1_wang2010a_hg19*TIA1\t2\t-\n+chr6\t160201930\t160201933\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t-\n+chr11\t70281364\t70281384\tiCLIP#TIA1_wang2010a_hg19*TIA1\t19\t+\n+chr12\t51142324\t51142330\tiCLIP#TIA1_wang2010a_hg19*TIA1\t6\t+\n+chr16\t28837178\t28837188\tiCLIP#TIA1_wang2010a_hg19*TIA1\t5\t+\n+chr1\t54497807\t54497828\tiCLIP#TIA1_wang2010a_hg19*TIA1\t21\t-\n+chr9\t125890477\t125890485\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t-\n+chr20\t2442487\t2442497\tiCLIP#TIA1_wang2010a_hg19*TIA1\t18\t-\n+chr10\t111896002\t111896003\tiCLIP#TIA1_wang2010a_hg19*TIA1\t2\t+\n+chr15\t59172129\t59172143\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t-\n+chr5\t133532839\t133532876\tiCLIP#TIA1_wang2010a_hg19*TIA1\t11\t-\n+chr12\t108916047\t108916065\tiCLIP#TIA1_wang2010a_hg19*TIA1\t6\t-\n+chr1\t162496453\t162496459\tiCLIP#TIA1_wang2010a_hg19*TIA1\t5\t+\n+chr2\t228393436\t228393442\tiCLIP#TIA1_wang2010a_hg19*TIA1\t6\t+\n+chr12\t53709455\t53709471\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t-\n+chr19\t45981888\t45981912\tiCLIP#TIA1_wang2010a_hg19*TIA1\t219\t-\n+chrX\t73062433\t73062444\tiCLIP#TIA1_wang2010a_hg19*TIA1\t12\t-\n+chr5\t58976554\t58976560\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t-\n+chr6\t42048526\t42048557\tiCLIP#TIA1_wang2010a_hg19*TIA1\t6\t+\n+chr18\t29444569\t29444578\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t-\n+chr6\t26123920\t26123956\tiCLIP#TIA1_wang2010a_hg19*TIA1\t10\t-\n+chr2\t51481241\t51481243\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chr12\t8800548\t8800566\tiCLIP#TIA1_wang2010a_hg19*TIA1\t7\t-\n+chr5\t131915366\t131915372\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t+\n+chr8\t41367097\t41367098\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t+\n+chr18\t3458203\t3458240\tiCLIP#TIA1_wang2010a_hg19*TIA1\t16\t+\n+chr14\t75283721\t75283725\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chr11\t118362654\t118362661\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chr7\t156626416\t156626437\tiCLIP#TIA1_wang2010a_hg19*TIA1\t8\t-\n+chr19\t9718393\t9718406\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t-\n+chr1\t183596159\t183596189\tiCLIP#TIA1_wang2010a_hg19*TIA1\t16\t-\n+chr10\t1086937\t1086969\tiCLIP#TIA1_wang2010a_hg19*TIA1\t12\t-\n+chr19\t1425974\t1425987\tiCLIP#TIA1_wang2010a_hg19*TIA1\t18\t+\n+chr11\t43414160\t43414162\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t+\n+chr1\t179068618\t179068642\tiCLIP#TIA1_wang2010a_hg19*TIA1\t9\t-\n+chr20\t10670183\t10670184\tiCLIP#TIA1_wang2010a_hg19*TIA1\t2\t+\n+chr6\t31508721\t31508769\tiCLIP#TIA1_wang2010a_hg19*TIA1\t11\t-\n+chr9\t126695525\t126695526\tiCLIP#TIA1_wang2010a_hg19*TIA1\t2\t-\n+chr13\t92828659\t92828678\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chr3\t194125684\t194125715\tiCLIP#TIA1_wang2010a_hg19*TIA1\t12\t-\n+chr20\t5945250\t5945253\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chr13\t92254399\t92254406\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t+\n+chr17\t58826333\t58826346\tiCLIP#TIA1_wang2010a_hg19*TIA1\t39\t-\n+chr3\t12113444\t12113455\tiCLIP#TIA1_wang2010a_hg19*TIA1\t9\t+\n+chr1\t42110396\t42110401\tiCLIP#TIA1_wang2010a_hg19*TIA1\t6\t-\n+chr7\t139050909\t139050923\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chr16\t67864219\t67864226\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t-\n+chr3\t42661573\t42661601\tiCLIP#TIA1_wang2010a_hg19*TIA1\t5\t+\n+chr11\t65268022\t65268138\tiCLIP#TIA1_wang2010a_hg19*TIA1\t37\t+\n+chr14\t62193139\t62193147\tiCLIP#TIA1_wang2010a_hg19*TIA1\t5\t+\n+chr6\t2785906\t2785942\tiCLIP#TIA1_wang2010a_hg19*TIA1\t18\t+\n+chr1\t76260367\t76260402\tiCLIP#TIA1_wang2010a_hg19*TIA1\t18\t+\n+chr2\t176042905\t176042909\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t-\n+chr11\t33730140\t33730160\tiCLIP#TIA1_wang2010a_hg19*TIA1\t27\t-\n+chr6\t138412412\t138412446\tiCLIP#TIA1_wang2010a_hg19*TIA1\t19\t-\n+chr8\t98863891\t98863907\tiCLIP#TIA1_wang2010a_hg19*TIA1\t15\t+\n+chr7\t'..b'251873\t26251898\tiCLIP#TIA1_wang2010a_hg19*TIA1\t31\t+\n+chr2\t219460137\t219460153\tiCLIP#TIA1_wang2010a_hg19*TIA1\t10\t+\n+chr2\t44036932\t44036941\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chr11\t8122551\t8122569\tiCLIP#TIA1_wang2010a_hg19*TIA1\t11\t+\n+chr5\t135276550\t135276562\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t+\n+chr6\t54531124\t54531125\tiCLIP#TIA1_wang2010a_hg19*TIA1\t2\t-\n+chr1\t101460524\t101460530\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t-\n+chr5\t180670854\t180670861\tiCLIP#TIA1_wang2010a_hg19*TIA1\t8\t-\n+chr2\t242035099\t242035127\tiCLIP#TIA1_wang2010a_hg19*TIA1\t5\t-\n+chr12\t97313945\t97313964\tiCLIP#TIA1_wang2010a_hg19*TIA1\t6\t+\n+chr8\t62569607\t62569633\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t-\n+chr17\t61176725\t61176738\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chr1\t43166973\t43166993\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chr3\t46963268\t46963270\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t-\n+chr5\t14399325\t14399339\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chr6\t99852179\t99852203\tiCLIP#TIA1_wang2010a_hg19*TIA1\t6\t-\n+chr16\t57181675\t57181688\tiCLIP#TIA1_wang2010a_hg19*TIA1\t14\t+\n+chr1\t40759048\t40759078\tiCLIP#TIA1_wang2010a_hg19*TIA1\t16\t+\n+chr17\t4071101\t4071105\tiCLIP#TIA1_wang2010a_hg19*TIA1\t5\t-\n+chr10\t75879886\t75879889\tiCLIP#TIA1_wang2010a_hg19*TIA1\t11\t+\n+chr1\t94982891\t94982892\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chrX\t153671428\t153671432\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chr3\t98515988\t98516014\tiCLIP#TIA1_wang2010a_hg19*TIA1\t9\t-\n+chr22\t50181580\t50181595\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t-\n+chr21\t33043413\t33043429\tiCLIP#TIA1_wang2010a_hg19*TIA1\t12\t-\n+chr17\t34174122\t34174157\tiCLIP#TIA1_wang2010a_hg19*TIA1\t14\t+\n+chr9\t101471384\t101471389\tiCLIP#TIA1_wang2010a_hg19*TIA1\t6\t-\n+chr15\t57756140\t57756141\tiCLIP#TIA1_wang2010a_hg19*TIA1\t2\t+\n+chr9\t77602130\t77602135\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t-\n+chr4\t7584319\t7584340\tiCLIP#TIA1_wang2010a_hg19*TIA1\t8\t+\n+chr5\t1479603\t1479622\tiCLIP#TIA1_wang2010a_hg19*TIA1\t9\t-\n+chr9\t12972574\t12972589\tiCLIP#TIA1_wang2010a_hg19*TIA1\t23\t-\n+chr10\t3163335\t3163351\tiCLIP#TIA1_wang2010a_hg19*TIA1\t5\t+\n+chr3\t138352021\t138352027\tiCLIP#TIA1_wang2010a_hg19*TIA1\t6\t+\n+chr4\t122589510\t122589521\tiCLIP#TIA1_wang2010a_hg19*TIA1\t12\t-\n+chr12\t46752494\t46752584\tiCLIP#TIA1_wang2010a_hg19*TIA1\t69\t-\n+chr3\t185635101\t185635121\tiCLIP#TIA1_wang2010a_hg19*TIA1\t16\t-\n+chr19\t57808594\t57808617\tiCLIP#TIA1_wang2010a_hg19*TIA1\t8\t+\n+chr5\t37327735\t37327751\tiCLIP#TIA1_wang2010a_hg19*TIA1\t28\t-\n+chr2\t69351782\t69351796\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chr19\t10265555\t10265565\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t-\n+chr14\t75601363\t75601383\tiCLIP#TIA1_wang2010a_hg19*TIA1\t11\t-\n+chr5\t34687090\t34687098\tiCLIP#TIA1_wang2010a_hg19*TIA1\t5\t+\n+chr15\t59956068\t59956086\tiCLIP#TIA1_wang2010a_hg19*TIA1\t6\t-\n+chr3\t50325571\t50325576\tiCLIP#TIA1_wang2010a_hg19*TIA1\t5\t-\n+chrM\t679\t715\tiCLIP#TIA1_wang2010a_hg19*TIA1\t12\t+\n+chr5\t98191904\t98191912\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t-\n+chr6\t149731577\t149731641\tiCLIP#TIA1_wang2010a_hg19*TIA1\t19\t+\n+chr19\t37835024\t37835039\tiCLIP#TIA1_wang2010a_hg19*TIA1\t5\t+\n+chr1\t22051802\t22051814\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t-\n+chr1\t174881027\t174881028\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chr17\t27528586\t27528594\tiCLIP#TIA1_wang2010a_hg19*TIA1\t2\t-\n+chr9\t86553535\t86553546\tiCLIP#TIA1_wang2010a_hg19*TIA1\t5\t-\n+chr19\t36616772\t36616810\tiCLIP#TIA1_wang2010a_hg19*TIA1\t28\t+\n+chr13\t66361692\t66361700\tiCLIP#TIA1_wang2010a_hg19*TIA1\t5\t-\n+chr13\t92237996\t92237997\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t+\n+chr6\t7480721\t7480724\tiCLIP#TIA1_wang2010a_hg19*TIA1\t2\t-\n+chr6\t30692268\t30692319\tiCLIP#TIA1_wang2010a_hg19*TIA1\t252\t+\n+chr1\t243449723\t243449731\tiCLIP#TIA1_wang2010a_hg19*TIA1\t5\t+\n+chr18\t57018617\t57018630\tiCLIP#TIA1_wang2010a_hg19*TIA1\t6\t-\n+chr11\t3383709\t3383750\tiCLIP#TIA1_wang2010a_hg19*TIA1\t7\t-\n+chr6\t144635086\t144635089\tiCLIP#TIA1_wang2010a_hg19*TIA1\t4\t+\n+chr4\t144475129\t144475143\tiCLIP#TIA1_wang2010a_hg19*TIA1\t5\t+\n+chr2\t17963500\t17963515\tiCLIP#TIA1_wang2010a_hg19*TIA1\t3\t+\n+chr11\t57093506\t57093540\tiCLIP#TIA1_wang2010a_hg19*TIA1\t30\t-\n+chr13\t100037791\t100037808\tiCLIP#TIA1_wang2010a_hg19*TIA1\t9\t+\n+chr13\t22067304\t22067334\tiCLIP#TIA1_wang2010a_hg19*TIA1\t7\t-\n' |
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/input.msigdb_test.gmt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.msigdb_test.gmt Thu Apr 13 12:36:05 2017 -0400 |
| b |
| @@ -0,0 +1,10 @@ +KEGG_GLYCOLYSIS_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOLYSIS_GLUCONEOGENESIS 55902 2645 5232 5230 5162 5160 5161 55276 7167 84532 2203 125 3099 126 3098 3101 127 5224 128 5223 124 230 501 92483 5313 160287 2023 5315 5214 669 5106 5105 219 217 218 10327 8789 5213 5211 3948 2597 2027 2026 441531 131 130 3945 220 221 222 223 224 130589 226 1738 1737 229 57818 3939 2538 5236 2821 +KEGG_CITRATE_CYCLE_TCA_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CITRATE_CYCLE_TCA_CYCLE 3420 1743 5106 1431 5162 5105 5160 642502 5161 283398 2271 6392 4967 6390 3419 6391 3418 3417 48 47 4191 1738 4190 1737 55753 5091 6389 8802 8803 8801 3421 50 +KEGG_PENTOSE_PHOSPHATE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PENTOSE_PHOSPHATE_PATHWAY 6120 22934 55276 25796 5634 8789 5213 5211 6888 7086 2203 84076 5226 64080 226 230 229 9563 729020 221823 5631 51071 2539 5236 8277 5214 2821 +KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 54575 54576 6120 54577 54578 54490 54579 51084 7358 10941 2990 54600 51181 729020 27294 10720 7360 9942 7365 231 7364 7363 79799 54657 7367 54658 54659 7366 +KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 4351 5373 5372 8789 5213 2762 5210 5211 9107 7167 29085 5209 197258 5208 8776 5207 57016 8790 3795 2203 8898 3099 3101 3098 226 230 229 9108 7264 231 6652 29926 5214 29925 +KEGG_GALACTOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GALACTOSE_METABOLISM 2645 2584 2720 2582 2683 55276 3906 5213 5211 8972 3099 3098 3101 2592 57818 2717 2595 3938 2585 2538 7360 5236 231 8704 2548 5214 +KEGG_ASCORBATE_AND_ALDARATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 54575 54576 54577 54578 219 54490 217 54579 55586 7358 10941 223 224 54600 501 10720 7365 7364 7363 79799 54657 54658 7367 54659 7366 +KEGG_FATTY_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FATTY_ACID_METABOLISM 1374 126129 35 219 36 33 217 34 1579 39 37 38 10449 3033 3032 3030 284541 131 130 23305 125 126 127 1892 128 223 224 51703 124 1962 2639 501 8310 2180 30 1376 1375 51 10455 1632 2181 2182 +KEGG_STEROID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STEROID_BIOSYNTHESIS 6646 4047 6713 10682 1595 1717 1594 1718 51478 6307 2222 6309 3988 1056 7108 50814 8435 +KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS 10858 10998 570 9420 1109 3295 6342 6718 8309 80270 1593 23600 1581 1582 51302 9023 |
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/motif_analysis_table.data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_analysis_table.data.tsv Thu Apr 13 12:36:05 2017 -0400 |
| b |
| @@ -0,0 +1,5 @@ +patterns scores fgHits bgHits fgSeq bgSeq ratio fgFrac bgFrac +1 ATTTTT 26 1719 412 1623 393 4.2 0.1624 0.0393 +2 TTTTTA 27.9 1864 404 1746 391 4.6 0.1747 0.0391 +3 TTTTCT 22.2 1280 296 1200 282 4.3 0.1201 0.0282 +4 TTTATT 22.3 1402 341 1280 314 4.1 0.1281 0.0314 |
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/output.TIA1.bed.RCAS.report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.TIA1.bed.RCAS.report.html Thu Apr 13 12:36:05 2017 -0400 |
| [ |
| b'@@ -0,0 +1,530 @@\n+<!DOCTYPE html>\n+\n+<html xmlns="http://www.w3.org/1999/xhtml">\n+\n+<head>\n+\n+<meta charset="utf-8">\n+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />\n+<meta name="generator" content="pandoc" />\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="author" content="Bora Uyar, Dilmurat Yusuf, Ricardo Wurmus, Altuna Akalin" />\n+\n+<meta name="date" content="2017-04-07" />\n+\n+<title>The RNA Centric Analysis System Report</title>\n+\n+<script src="data:application/x-javascript;base64,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'..b'{\n+ function captureSVG (that, selector) {\n+ var container = document.querySelector(selector).parentNode,\n+ height = container.offsetHeight,\n+ width = container.offsetWidth,\n+ svgs = container.querySelectorAll(\'svg.main-svg\'),\n+ prefix = \'data:image/svg+xml;base64,\',\n+ data = \'\',\n+ draglayers = [];\n+\n+ for (var i = 0; i < svgs.length; i++) {\n+ // Remove drag layer because it looks like a black box\n+ // when rendered in Inkscape. This won\'t remove the\n+ // element from the DOM because we use querySelectorAll,\n+ // which returns a static node list.\n+ draglayers = svgs[i].getElementsByClassName(\'draglayer\');\n+ while (draglayers.length > 0) {\n+ draglayers[0].parentNode.removeChild(draglayers[0]);\n+ }\n+ // Some plots may contain non UTF-8 characters that cause\n+ // btoa to fail in Firefox, so we remove them with a call\n+ // to "replace".\n+ data = data + svgs[i].innerHTML.replace(/[\\u0100-\\uFFFF]/g,\'\');\n+ }\n+ data = prefix + btoa(\'<?xml version="1.0" standalone="yes"?>\'+\n+ \'<svg xmlns="http://www.w3.org/2000/svg" version="1.1" width="\' + width +\'" \' +\n+ \'height="\' + height + \'"\' + \'>\' +\n+ data + \'</svg>\');\n+\n+ // override link target\n+ that.href = data;\n+ return true;\n+ }\n+\n+ function generateModebarButton (selector) {\n+ var el = document.createElement(\'div\'),\n+ button = \'<a href=# download="rcas.svg" onClick=\\\'RCAS.captureSVG(this, "\'+\n+ selector + \'")\\\' \' +\n+ \'data-gravity="n" data-toggle="false" data-title="Download plot as a SVG" class="modebar-btn" rel="tooltip">\' +\n+ \'<svg viewBox="0 0 1000 1000" width="1em" height="1em">\'+\n+ \'<path transform="matrix(1 0 0 -1 0 850)" d="m500 450c-83 0-150-67-150-150 0-83 67-150 150-150 83 0 150 67 150 150 0 83-67 150-150 150z m400 150h-120c-16 0-34 13-39 29l-31 93c-6 15-23 28-40 28h-340c-16 0-34-13-39-28l-31-94c-6-15-23-28-40-28h-120c-55 0-100-45-100-100v-450c0-55 45-100 100-100h800c55 0 100 45 100 100v450c0 55-45 100-100 100z m-400-550c-138 0-250 112-250 250 0 138 112 250 250 250 138 0 250-112 250-250 0-138-112-250-250-250z m365 380c-19 0-35 16-35 35 0 19 16 35 35 35 19 0 35-16 35-35 0-19-16-35-35-35z"></path>\'+\n+ \'</svg>\'+\n+ \'</a>\';\n+\n+ el.innerHTML = button;\n+ el.className = \'modebar-group\';\n+ return el;\n+ }\n+\n+ function injectLink (pathToWidget) {\n+ var widget = document.getElementById(pathToWidget),\n+ button = generateModebarButton(\'#\' + pathToWidget + \' .main-svg\'),\n+ bar = widget.getElementsByClassName(\'modebar\')[0];\n+ // insert at the very beginning\n+ bar.insertBefore(button, bar.firstChild.nextSibling);\n+ }\n+\n+ // inject links in every widget\n+ function init () {\n+ var nodes = document.getElementsByClassName(\'js-plotly-plot\');\n+ for (var i = 0; i < nodes.length; i++) {\n+ injectLink(nodes[i].id);\n+ }\n+ }\n+\n+ return {\n+ captureSVG: captureSVG,\n+ init: init\n+ };\n+})();\n+\n+window.onload = RCAS.init;\n+</script>\n+\n+\n+</div>\n+</div>\n+\n+</div>\n+\n+<script>\n+\n+// add bootstrap table styles to pandoc tables\n+$(document).ready(function () {\n+ $(\'tr.header\').parent(\'thead\').parent(\'table\').addClass(\'table table-condensed\');\n+});\n+\n+</script>\n+\n+<!-- dynamically load mathjax for compatibility with self-contained -->\n+<script>\n+ (function () {\n+ var script = document.createElement("script");\n+ script.type = "text/javascript";\n+ script.src = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";\n+ document.getElementsByTagName("head")[0].appendChild(script);\n+ })();\n+</script>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/query_gene_types.data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/query_gene_types.data.tsv Thu Apr 13 12:36:05 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +feature count percent +1 protein_coding 18 0.2 |
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/summarizeQueryRegions.data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarizeQueryRegions.data.tsv Thu Apr 13 12:36:05 2017 -0400 |
| b |
| @@ -0,0 +1,8 @@ +count percent +transcripts 18 0.2 +exons 15 0.2 +promoters 4 0 +fiveUTRs 4 0 +introns 6 0.1 +cds 3 0 +threeUTRs 12 0.1 |
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/transcriptBoundaryCoverage.fiveprime.data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcriptBoundaryCoverage.fiveprime.data.tsv Thu Apr 13 12:36:05 2017 -0400 |
| b |
| b'@@ -0,0 +1,2001 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|
| b |
| diff -r 000000000000 -r aa9579837a2e test-data/transcriptBoundaryCoverage.threeprime.data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcriptBoundaryCoverage.threeprime.data.tsv Thu Apr 13 12:36:05 2017 -0400 |
| b |
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|