| Previous changeset 0:aa9579837a2e (2017-04-13) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ commit 5c6486dead878a8c9521e1d6d50b3a537a2ec2b0 |
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modified:
rcas.xml readme.rst test-data/coverageprofilelist.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.granges.rds test-data/summarizeQueryRegions.data.tsv |
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added:
test-data/EIF4A3Sauliere20121a.bed test-data/EIF4A3Sauliere20121b.bed test-data/FMR1_Ascano2012a_hg19.bed test-data/FMR1_Ascano2012b_hg19.bed test-data/FUS_Nakaya2013c_hg19.bed test-data/FUS_Nakaya2013d_hg19.bed test-data/hg19.sample.gtf test-data/input.TIA1.bed.RCAS.report.html test-data/test2_multi_set_analysis_report.html |
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removed:
test-data/motif_analysis_table.data.tsv test-data/output.TIA1.bed.RCAS.report.html |
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| diff -r aa9579837a2e -r 7c7a2a381dfe rcas.xml --- a/rcas.xml Thu Apr 13 12:36:05 2017 -0400 +++ b/rcas.xml Thu Jun 21 15:07:13 2018 -0400 |
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| b'@@ -1,206 +1,246 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<tool id="rcas" name="RNA Centric Annotation System" version="1.1.1">\n+<tool id="rcas" name="RCAS" version="1.5.4">\n+ <description>- RNA Centric Annotation System</description>\n <requirements>\n- <requirement type="package" version="1.1.1">bioconductor-rcas</requirement>\n+ <requirement type="package" version="1.5.4">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 $choice.run_PATHrich == "TRUE":\n- &&\n- mv Table*GSEA.data.tsv GSEA.data.tsv\n- #end if\n-\n+ <command><![CDATA[\n+ cat \'$script_file\' &&\n+ #if $analysis_type.analysis_type_selector == \'single_set_analysis\':\n+ Rscript \'$script_file\' &&\n+ mv *RCAS.report.html RCAS.report.html\n+ #if $run_annot == "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+ #if $analysis_type.run_go == "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- #if $run_motif == "TRUE":\n- &&\n- mv Table*motif_analysis_table.data.tsv motif_analysis_table.data.tsv\n- #end if]]></command>\n+ #if $analysis_type.gsea_set.run_gsea == "TRUE":\n+ &&\n+ mv Table*GSEA.data.tsv GSEA.data.tsv\n+ #end if\n+ #else:\n+ Rscript \'$script_file\'\n+ #end if\n+ ]]></command>\n '..b'pe_selector" value="multi_set_analysis"/>\n+ <param name="multi_bed_file" value="EIF4A3Sauliere20121a.bed,EIF4A3Sauliere20121b.bed,FMR1_Ascano2012a_hg19.bed,FMR1_Ascano2012b_hg19.bed,FUS_Nakaya2013c_hg19.bed,FUS_Nakaya2013d_hg19.bed"/>\n+ <param name="input_gtf_file" value="hg19.sample.gtf"/>\n+ <param name="run_annot" value="TRUE"/>\n+ <param name="run_motif" value="TRUE"/>\n+ <param name="genome_version" value="hg19" />\n+ <output name="multi_report" file="test2_multi_set_analysis_report.html" ftype="html" compare="sim_size" delta="20000"/>\n </test>\n </tests>\n- <help><![CDATA[.. class:: infomark\n+ <help><![CDATA[\n \n-**Purpose**\n+**Introduction**\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+RCAS is an R/Bioconductor package designed as a generic reporting tool for the functional analysis of transcriptome-wide regions of interest detected by high-throughput experiments. Such transcriptomic regions could be, for instance, signal peaks detected by CLIP-Seq analysis for protein-RNA interaction sites, RNA modification sites (alias the epitranscriptome), CAGE-tag locations, or any other collection of query regions at the level of the transcriptome. RCAS produces in-depth annotation summaries and coverage profiles based on the distribution of the query regions with respect to transcript features (exons, introns, 5\xe2\x80\x99/3\xe2\x80\x99 UTR regions, exon-intron boundaries, promoter regions). Moreover, RCAS can carry out functional enrichment analyses of annotated gene sets, GO terms, and de novo motif discovery. RCAS is available in the Bioconductor repository, packaged in multiple environments including Conda, Galaxy, and Guix, and as a webservice at http://rcas.mdc-berlin.de/.\n+\n+Currently supported genome builds are hg19 and hg38 (human), mm9 and mm10 (mouse), dm3 (fly), and ce10 (worm). Modules for annotation summaries and motif analysis are supported for each of these genome builds. GO term and gene-set enrichment analyses are supported for hg19, hg38, mm9, mm10, and dm3. ce10 is currently not supportedfor GO/GSEA modules.\n+\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+1. One (single sample analysis) or several (multi sample analysis) genomic target region files in BED format\n+2. A genome reference annotation file in GTF format\n+3. A human Molecular Signatures Database (MSigDB) (only in single sample analysis for gene set enrichment analysis)\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+The outputs consist of a dynamic HTML file (both for single and multi sample analysis) and optionally a number (depending on selected options) of tabular files (single sample analysis only).\n+The dynamic HTML file is composed of 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+The tabular files contain the RCAS analysis results, corresponding to the \n+respective figures in the HTML file:\n \n 1. Annotation summary for query regions\n \n@@ -221,7 +261,9 @@\n \n 3. Gene set enrichment analysis results\n \n-4. Motif analysis results]]></help>\n+4. Motif analysis results (no table output in 1.5.4.)\n+\n+ ]]></help>\n <citations>\n <citation type="doi">10.1093/nar/gkx120</citation>\n </citations>\n' |
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| diff -r aa9579837a2e -r 7c7a2a381dfe readme.rst --- a/readme.rst Thu Apr 13 12:36:05 2017 -0400 +++ b/readme.rst Thu Jun 21 15:07:13 2018 -0400 |
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| @@ -3,14 +3,18 @@ - 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 +- to install the dependencies, the galaxy administrator needs to enable 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 +- to enable analysis for hg38, mm9, mm10, ce10, or dm3, the administrator needs to separately install the relevant packages from the bioconda channel + + - bioconductor-bsgenome.hsapiens.ucsc.hg38 + - bioconductor-bsgenome.mmusculus.ucsc.mm9 + - bioconductor-bsgenome.mmusculus.ucsc.mm10 + - bioconductor-bsgenome.celegans.ucsc.ce10 - 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 aa9579837a2e -r 7c7a2a381dfe test-data/EIF4A3Sauliere20121a.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EIF4A3Sauliere20121a.bed Thu Jun 21 15:07:13 2018 -0400 |
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| diff -r aa9579837a2e -r 7c7a2a381dfe test-data/EIF4A3Sauliere20121b.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EIF4A3Sauliere20121b.bed Thu Jun 21 15:07:13 2018 -0400 |
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| diff -r aa9579837a2e -r 7c7a2a381dfe test-data/FMR1_Ascano2012a_hg19.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FMR1_Ascano2012a_hg19.bed Thu Jun 21 15:07:13 2018 -0400 |
| b |
| @@ -0,0 +1,132 @@ +chr1 874707 874728 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 17 + +chr1 874707 874728 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 17 + +chr1 874707 874728 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 17 + +chr1 874707 874728 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 17 + +chr1 874707 874728 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 17 + +chr1 874707 874728 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 17 + +chr1 874707 874728 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 17 + +chr1 874707 874728 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 17 + +chr1 874707 874728 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 17 + +chr1 874707 874728 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 17 + +chr1 878223 878246 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 79 + +chr1 878223 878246 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 79 + +chr1 878223 878246 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 79 + +chr1 878223 878246 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 79 + +chr1 878223 878246 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 79 + +chr1 878223 878246 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 79 + +chr1 878223 878246 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 79 + +chr1 878223 878246 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 79 + +chr1 878223 878246 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 79 + +chr1 878223 878246 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 79 + +chr1 878223 878246 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 79 + +chr1 878223 878246 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 79 + +chr1 878223 878246 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 79 + +chr1 878223 878246 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 79 + +chr1 878702 878714 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 878702 878714 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 878702 878714 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 878702 878714 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 878702 878714 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 878702 878714 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 878702 878714 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 878702 878714 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 878702 878714 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 878702 878714 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 879477 879499 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 879477 879499 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 879477 879499 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 879477 879499 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 879477 879499 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 879477 879499 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 879477 879499 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 879477 879499 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 879477 879499 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 879477 879499 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 + +chr1 879532 879556 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 + +chr1 879532 879556 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 + +chr1 879532 879556 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 + +chr1 879532 879556 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 + +chr1 879532 879556 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 + +chr1 879532 879556 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 + +chr1 879532 879556 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 + +chr1 879532 879556 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 + +chr1 879532 879556 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 + +chr1 879532 879556 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 + +chr1 879532 879556 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 + +chr1 879532 879556 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 + +chr1 879532 879556 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 + +chr1 879795 879824 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 53 + +chr1 879795 879824 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 53 + +chr1 879795 879824 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 53 + +chr1 879795 879824 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 53 + +chr1 879795 879824 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 53 + +chr1 879795 879824 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 53 + +chr1 879795 879824 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 53 + +chr1 880004 880024 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 1 - 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+chr1 887894 887908 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 - +chr1 887894 887908 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 - +chr1 887894 887908 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 43 - +chr1 889389 889406 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 53 - +chr1 889389 889406 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 53 - +chr1 889389 889406 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 53 - +chr1 889389 889406 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 53 - +chr1 889389 889406 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 53 - +chr1 889389 889406 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 53 - +chr1 891331 891358 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 31 - +chr1 891331 891358 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 31 - +chr1 891331 891358 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 31 - +chr1 891331 891358 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 31 - +chr1 891331 891358 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 31 - +chr1 891331 891358 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 31 - +chr1 891331 891358 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 31 - +chr1 891331 891358 PARCLIP#FMR1_Ascano2012a_hg19*FMR1 31 - 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| b |
| diff -r aa9579837a2e -r 7c7a2a381dfe test-data/FMR1_Ascano2012b_hg19.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FMR1_Ascano2012b_hg19.bed Thu Jun 21 15:07:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,401 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|
| b |
| diff -r aa9579837a2e -r 7c7a2a381dfe test-data/FUS_Nakaya2013c_hg19.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FUS_Nakaya2013c_hg19.bed Thu Jun 21 15:07:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,607 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|
| b |
| diff -r aa9579837a2e -r 7c7a2a381dfe test-data/FUS_Nakaya2013d_hg19.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FUS_Nakaya2013d_hg19.bed Thu Jun 21 15:07:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,524 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|
| b |
| diff -r aa9579837a2e -r 7c7a2a381dfe test-data/coverageprofilelist.data.tsv --- a/test-data/coverageprofilelist.data.tsv Thu Apr 13 12:36:05 2017 -0400 +++ b/test-data/coverageprofilelist.data.tsv Thu Jun 21 15:07:13 2018 -0400 |
| b |
| b'@@ -1,81 +1,81 @@\n bins\tmeanCoverage\tstandardError\tfeature\n-1\t1\t0.00372208436724566\t0.00214627525259149\ttranscripts\n+1\t1\t0.000126097409127828\t7.44798767352236e-05\ttranscripts\n 2\t2\t0\t0\ttranscripts\n 3\t3\t0\t0\ttranscripts\n 4\t4\t0\t0\ttranscripts\n 5\t5\t0\t0\ttranscripts\n 6\t6\t0\t0\ttranscripts\n 7\t7\t0\t0\ttranscripts\n-8\t8\t0.00124069478908189\t0.00124069478908189\ttranscripts\n-9\t9\t0.00248138957816377\t0.00175351724056266\ttranscripts\n-10\t10\t0.00372208436724566\t0.00214627525259149\ttranscripts\n-11\t11\t0.00124069478908189\t0.00124069478908189\ttranscripts\n+8\t8\t0.000485489265292912\t0.000485489265292912\ttranscripts\n+9\t9\t0.00178946363809887\t0.00135601594568615\ttranscripts\n+10\t10\t0.00242200589595131\t0.00152313919586472\ttranscripts\n+11\t11\t0.000381752242794426\t0.000381752242794426\ttranscripts\n 12\t12\t0\t0\ttranscripts\n 13\t13\t0\t0\ttranscripts\n 14\t14\t0\t0\ttranscripts\n 15\t15\t0\t0\ttranscripts\n 16\t16\t0\t0\ttranscripts\n 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38\t38\t0\t0\ttranscripts\n 39\t39\t0\t0\ttranscripts\n-40\t40\t0.00372208436724566\t0.00214627525259149\ttranscripts\n-41\t41\t0.00248138957816377\t0.00175351724056266\ttranscripts\n+40\t40\t9.30935139886934e-05\t5.36809232465321e-05\ttranscripts\n+41\t41\t0.0004856612873552\t0.000468491016439218\ttranscripts\n 42\t42\t0\t0\ttranscripts\n 43\t43\t0\t0\ttranscripts\n-44\t44\t0.00124069478908189\t0.00124069478908189\ttranscripts\n+44\t44\t3.26047040007688e-05\t3.26047040007688e-05\ttranscripts\n 45\t45\t0\t0\ttranscripts\n-46\t46\t0.011166253101737\t0.00370354335845504\ttranscripts\n-47\t47\t0.00372208436724566\t0.00214627525259149\ttranscripts\n-48\t48\t0.00124069478908189\t0.00124069478908189\ttranscripts\n+46\t46\t0.00152118069266176\t0.000535479114029691\ttranscripts\n+47\t47\t0.000578570123300056\t0.000333624664000674\ttranscripts\n+48\t48\t0.000200112062755143\t0.000200112062755143\ttranscripts\n 49\t49\t0\t0\ttranscripts\n-50\t50\t0.00124069478908189\t0.00124069478908189\ttranscripts\n-51\t51\t0.00124069478908189\t0.00124069478908189\ttranscripts\n+50\t50\t3.20869342003936e-05\t3.20869342003936e-05\ttranscripts\n+51\t51\t0.000171130315735433\t0.000171130315735433\ttranscripts\n 52\t52\t0\t0\ttranscripts\n 53\t53\t0\t0\ttranscripts\n 54\t54\t0\t0\ttranscripts\n-55\t55\t0.00248138957816377\t0.00175351724056266\ttranscripts\n-56\t56\t0.00124069478908189\t0.00124069478908189\ttranscripts\n-57\t57\t0.00248138957816377\t0.00175351724056266\ttranscripts\n-58\t58\t0.00124069478908189\t0.00124069478908189\ttranscripts\n+55\t55\t0.000413266175861921\t0.000293552278020561\ttranscripts\n+56\t56\t9.12275580207269e-06\t9.12275580207269e-06\ttranscripts\n+57\t57\t0.000243604299283799\t0.000220299849202671\ttranscripts\n+58\t58\t0.000243273488055272\t0.000243273488055272\t'..b'925925926\t0.00653204102054547\tthreeUTRs\n+625\t25\t0.00462962962962963\t0.00326602051027274\tthreeUTRs\n 626\t26\t0.00925925925925926\t0.00653204102054547\tthreeUTRs\n 627\t27\t0.00925925925925926\t0.00653204102054547\tthreeUTRs\n 628\t28\t0.00925925925925926\t0.00653204102054547\tthreeUTRs\n 629\t29\t0.00925925925925926\t0.00653204102054547\tthreeUTRs\n-630\t30\t0.0138888888888889\t0.00798137006782874\tthreeUTRs\n+630\t30\t0.0099400871459695\t0.00656296007905232\tthreeUTRs\n 631\t31\t0.00925925925925926\t0.00653204102054547\tthreeUTRs\n 632\t32\t0.00925925925925926\t0.00653204102054547\tthreeUTRs\n-633\t33\t0.00925925925925926\t0.00653204102054547\tthreeUTRs\n+633\t33\t0\t0\tthreeUTRs\n 634\t34\t0\t0\tthreeUTRs\n 635\t35\t0\t0\tthreeUTRs\n 636\t36\t0\t0\tthreeUTRs\n-637\t37\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n-638\t38\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n-639\t39\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n+637\t37\t0.000672043010752688\t0.000672043010752688\tthreeUTRs\n+638\t38\t0.00083485124468731\t0.00083485124468731\tthreeUTRs\n+639\t39\t0.000798212005108557\t0.000798212005108557\tthreeUTRs\n 640\t40\t0\t0\tthreeUTRs\n 641\t41\t0\t0\tthreeUTRs\n 642\t42\t0\t0\tthreeUTRs\n@@ -645,8 +645,8 @@\n 644\t44\t0\t0\tthreeUTRs\n 645\t45\t0\t0\tthreeUTRs\n 646\t46\t0\t0\tthreeUTRs\n-647\t47\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n-648\t48\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n+647\t47\t0.00303497942386831\t0.00303497942386831\tthreeUTRs\n+648\t48\t0.00169753086419753\t0.00169753086419753\tthreeUTRs\n 649\t49\t0\t0\tthreeUTRs\n 650\t50\t0\t0\tthreeUTRs\n 651\t51\t0\t0\tthreeUTRs\n@@ -654,20 +654,20 @@\n 653\t53\t0\t0\tthreeUTRs\n 654\t54\t0\t0\tthreeUTRs\n 655\t55\t0\t0\tthreeUTRs\n-656\t56\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n+656\t56\t0.00115740740740741\t0.00115740740740741\tthreeUTRs\n 657\t57\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n 658\t58\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n 659\t59\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n 660\t60\t0\t0\tthreeUTRs\n 661\t61\t0\t0\tthreeUTRs\n-662\t62\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n+662\t62\t0.000462962962962963\t0.000462962962962963\tthreeUTRs\n 663\t63\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n 664\t64\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n-665\t65\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n+665\t65\t0.00208333333333333\t0.00208333333333333\tthreeUTRs\n 666\t66\t0\t0\tthreeUTRs\n 667\t67\t0\t0\tthreeUTRs\n 668\t68\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n-669\t69\t0\t0\tthreeUTRs\n+669\t69\t0.000220458553791887\t0.000220458553791887\tthreeUTRs\n 670\t70\t0\t0\tthreeUTRs\n 671\t71\t0\t0\tthreeUTRs\n 672\t72\t0\t0\tthreeUTRs\n@@ -679,9 +679,9 @@\n 678\t78\t0\t0\tthreeUTRs\n 679\t79\t0\t0\tthreeUTRs\n 680\t80\t0\t0\tthreeUTRs\n-681\t81\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n+681\t81\t0.00154320987654321\t0.00154320987654321\tthreeUTRs\n 682\t82\t0\t0\tthreeUTRs\n-683\t83\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n+683\t83\t0.00185185185185185\t0.00185185185185185\tthreeUTRs\n 684\t84\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n 685\t85\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n 686\t86\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n@@ -690,12 +690,12 @@\n 689\t89\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n 690\t90\t0\t0\tthreeUTRs\n 691\t91\t0\t0\tthreeUTRs\n-692\t92\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n+692\t92\t0.00106837606837607\t0.00106837606837607\tthreeUTRs\n 693\t93\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n-694\t94\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n-695\t95\t0.0138888888888889\t0.00798137006782874\tthreeUTRs\n+694\t94\t0.00178062678062678\t0.00178062678062678\tthreeUTRs\n+695\t95\t0.0100961538461538\t0.0064528653708784\tthreeUTRs\n 696\t96\t0.00925925925925926\t0.00653204102054547\tthreeUTRs\n-697\t97\t0.00925925925925926\t0.00653204102054547\tthreeUTRs\n+697\t97\t0.00528846153846154\t0.00381457857454658\tthreeUTRs\n 698\t98\t0\t0\tthreeUTRs\n-699\t99\t0.00462962962962963\t0.00462962962962963\tthreeUTRs\n-700\t100\t0.0138888888888889\t0.00798137006782874\tthreeUTRs\n+699\t99\t0.0085978835978836\t0.00608355257726876\tthreeUTRs\n+700\t100\t0.00798105980743552\t0.00518483909147582\tthreeUTRs\n' |
| b |
| diff -r aa9579837a2e -r 7c7a2a381dfe test-data/goBP.data.tsv --- a/test-data/goBP.data.tsv Thu Apr 13 12:36:05 2017 -0400 +++ b/test-data/goBP.data.tsv Thu Jun 21 15:07:13 2018 -0400 |
| b |
| @@ -1,33 +1,39 @@ 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 +GO:0010467 gene expression 6 4.15 1 0.686923076923077 1.45 +GO:0006139 nucleobase-containing compound metabolic... 6 4.36 1 0.686923076923077 1.38 +GO:0006464 cellular protein modification process 6 4.36 1 0.686923076923077 1.38 +GO:0006725 cellular aromatic compound metabolic pro... 6 4.36 1 0.686923076923077 1.38 +GO:0036211 protein modification process 6 4.36 1 0.686923076923077 1.38 +GO:0046483 heterocycle metabolic process 6 4.36 1 0.686923076923077 1.38 +GO:1901360 organic cyclic compound metabolic proces... 6 4.36 1 0.686923076923077 1.38 +GO:0009059 macromolecule biosynthetic process 6 4.57 1 0.686923076923077 1.31 +GO:0034645 cellular macromolecule biosynthetic proc... 6 4.57 1 0.686923076923077 1.31 +GO:0043412 macromolecule modification 6 4.57 1 0.686923076923077 1.31 +GO:0044271 cellular nitrogen compound biosynthetic ... 6 4.77 1 0.686923076923077 1.26 +GO:0050896 response to stimulus 7 5.6 1 0.686923076923077 1.25 +GO:0050789 regulation of biological process 8 6.43 1 0.686923076923077 1.24 +GO:0065007 biological regulation 8 6.64 1 0.686923076923077 1.2 +GO:0034641 cellular nitrogen compound metabolic pro... 6 4.98 1 0.686923076923077 1.2 +GO:0051171 regulation of nitrogen compound metaboli... 5 4.15 1 0.686923076923077 1.2 +GO:0060255 regulation of macromolecule metabolic pr... 5 4.15 1 0.686923076923077 1.2 +GO:0044267 cellular protein metabolic process 6 5.19 1 0.686923076923077 1.16 +GO:0019222 regulation of metabolic process 5 4.36 1 0.686923076923077 1.15 +GO:0031323 regulation of cellular metabolic process 5 4.36 1 0.686923076923077 1.15 +GO:0080090 regulation of primary metabolic process 5 4.36 1 0.686923076923077 1.15 +GO:0050794 regulation of cellular process 7 6.23 1 0.686923076923077 1.12 +GO:0009058 biosynthetic process 6 5.4 1 0.686923076923077 1.11 +GO:0044249 cellular biosynthetic process 6 5.4 1 0.686923076923077 1.11 +GO:1901576 organic substance biosynthetic process 6 5.4 1 0.686923076923077 1.11 +GO:0009987 cellular process 11 9.96 1 0.686923076923077 1.1 +GO:0051716 cellular response to stimulus 5 4.57 1 0.707586206896552 1.09 +GO:0019538 protein metabolic process 6 5.6 1 0.707586206896552 1.07 +GO:0044260 cellular macromolecule metabolic process 7 6.64 1 0.707586206896552 1.05 +GO:0008150 biological_process 11 11 1 1 1 +GO:0043170 macromolecule metabolic process 7 7.06 1 0.836 0.99 +GO:1901564 organonitrogen compound metabolic proces... 6 6.43 1 0.87875 0.93 +GO:0032501 multicellular organismal process 4 4.36 1 0.87875 0.92 +GO:0006807 nitrogen compound metabolic process 7 7.68 1 0.932727272727273 0.91 +GO:0044237 cellular metabolic process 7 7.89 1 0.944864864864865 0.89 +GO:0008152 metabolic process 7 8.3 1 0.944864864864865 0.84 +GO:0044238 primary metabolic process 7 8.3 1 0.944864864864865 0.84 +GO:0071704 organic substance metabolic process 7 8.3 1 0.944864864864865 0.84 |
| b |
| diff -r aa9579837a2e -r 7c7a2a381dfe test-data/goCC.data.tsv --- a/test-data/goCC.data.tsv Thu Apr 13 12:36:05 2017 -0400 +++ b/test-data/goCC.data.tsv Thu Jun 21 15:07:13 2018 -0400 |
| b |
| @@ -1,18 +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:0044422 organelle part 11 4.71 0.000357 0.0001785 2.34 +GO:0044446 intracellular organelle part 11 4.71 0.000357 0.0001785 2.34 +GO:0043231 intracellular membrane-bounded organelle 11 5.94 0.00782 0.00260666666666667 1.85 +GO:0044444 cytoplasmic part 9 5.06 0.17493 0.02499 1.78 +GO:0043227 membrane-bounded organelle 11 6.29 0.01666 0.004165 1.75 +GO:0043226 organelle 11 6.98 0.06375 0.010625 1.58 +GO:0043229 intracellular organelle 11 6.98 0.06375 0.010625 1.58 +GO:0005737 cytoplasm 10 6.63 0.35955 0.035955 1.51 +GO:0005622 intracellular 11 7.86 0.28016 0.0311288888888889 1.4 +GO:0044424 intracellular part 11 7.86 0.28016 0.0311288888888889 1.4 +GO:0005623 cell 11 9.25 1 0.175355 1.19 +GO:0044464 cell part 11 9.25 1 0.175355 1.19 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 +GO:0016020 membrane 6 6.11 1 0.863364615384615 0.98 +GO:0044425 membrane part 4 5.06 1 1 0.79 +GO:0016021 integral component of membrane 2 4.19 1 1 0.48 +GO:0031224 intrinsic component of membrane 2 4.19 1 1 0.48 |
| b |
| diff -r aa9579837a2e -r 7c7a2a381dfe test-data/goMF.data.tsv --- a/test-data/goMF.data.tsv Thu Apr 13 12:36:05 2017 -0400 +++ b/test-data/goMF.data.tsv Thu Jun 21 15:07:13 2018 -0400 |
| b |
| @@ -1,5 +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:0005515 protein binding 10 7.33 0.216 0.216 1.36 +GO:0005488 binding 11 10.19 1 0.78 1.08 GO:0003674 molecular_function 11 11 1 1 1 GO:0043167 ion binding 5 5.09 1 0.872 0.98 |
| b |
| diff -r aa9579837a2e -r 7c7a2a381dfe test-data/hg19.sample.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19.sample.gtf Thu Jun 21 15:07:13 2018 -0400 |
| b |
| b'@@ -0,0 +1,1000 @@\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"; transcript_name "DDX11L1-202"; transcript_source "ensembl"; exon_id "ENSE00002303382";\n+1\ttranscribed_unprocessed_pseudogene\ttranscript\t12010\t13670\t.\t+\t.\tgene_i'..b'56"; protein_id "ENSP00000368717";\n+1\tprotein_coding\texon\t906259\t906386\t.\t+\t.\tgene_id "ENSG00000187583"; transcript_id "ENST00000379407"; exon_number "6"; gene_name "PLEKHN1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "PLEKHN1-004"; transcript_source "ensembl_havana"; tag "CCDS"; ccds_id "CCDS53256"; exon_id "ENSE00001374990";\n+1\tprotein_coding\tCDS\t906259\t906386\t.\t+\t2\tgene_id "ENSG00000187583"; transcript_id "ENST00000379407"; exon_number "6"; gene_name "PLEKHN1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "PLEKHN1-004"; transcript_source "ensembl_havana"; tag "CCDS"; ccds_id "CCDS53256"; protein_id "ENSP00000368717";\n+1\tprotein_coding\texon\t906457\t906588\t.\t+\t.\tgene_id "ENSG00000187583"; transcript_id "ENST00000379407"; exon_number "7"; gene_name "PLEKHN1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "PLEKHN1-004"; transcript_source "ensembl_havana"; tag "CCDS"; ccds_id "CCDS53256"; exon_id "ENSE00003549084";\n+1\tprotein_coding\tCDS\t906457\t906588\t.\t+\t0\tgene_id "ENSG00000187583"; transcript_id "ENST00000379407"; exon_number "7"; gene_name "PLEKHN1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "PLEKHN1-004"; transcript_source "ensembl_havana"; tag "CCDS"; ccds_id "CCDS53256"; protein_id "ENSP00000368717";\n+1\tprotein_coding\texon\t906704\t906784\t.\t+\t.\tgene_id "ENSG00000187583"; transcript_id "ENST00000379407"; exon_number "8"; gene_name "PLEKHN1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "PLEKHN1-004"; transcript_source "ensembl_havana"; tag "CCDS"; ccds_id "CCDS53256"; exon_id "ENSE00001380204";\n+1\tprotein_coding\tCDS\t906704\t906784\t.\t+\t0\tgene_id "ENSG00000187583"; transcript_id "ENST00000379407"; exon_number "8"; gene_name "PLEKHN1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "PLEKHN1-004"; transcript_source "ensembl_havana"; tag "CCDS"; ccds_id "CCDS53256"; protein_id "ENSP00000368717";\n+1\tprotein_coding\texon\t907455\t907530\t.\t+\t.\tgene_id "ENSG00000187583"; transcript_id "ENST00000379407"; exon_number "9"; gene_name "PLEKHN1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "PLEKHN1-004"; transcript_source "ensembl_havana"; tag "CCDS"; ccds_id "CCDS53256"; exon_id "ENSE00001375540";\n+1\tprotein_coding\tCDS\t907455\t907530\t.\t+\t0\tgene_id "ENSG00000187583"; transcript_id "ENST00000379407"; exon_number "9"; gene_name "PLEKHN1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "PLEKHN1-004"; transcript_source "ensembl_havana"; tag "CCDS"; ccds_id "CCDS53256"; protein_id "ENSP00000368717";\n+1\tprotein_coding\texon\t907668\t907804\t.\t+\t.\tgene_id "ENSG00000187583"; transcript_id "ENST00000379407"; exon_number "10"; gene_name "PLEKHN1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "PLEKHN1-004"; transcript_source "ensembl_havana"; tag "CCDS"; ccds_id "CCDS53256"; exon_id "ENSE00001365628";\n+1\tprotein_coding\tCDS\t907668\t907804\t.\t+\t2\tgene_id "ENSG00000187583"; transcript_id "ENST00000379407"; exon_number "10"; gene_name "PLEKHN1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "PLEKHN1-004"; transcript_source "ensembl_havana"; tag "CCDS"; ccds_id "CCDS53256"; protein_id "ENSP00000368717";\n+1\tprotein_coding\texon\t908241\t908390\t.\t+\t.\tgene_id "ENSG00000187583"; transcript_id "ENST00000379407"; exon_number "11"; gene_name "PLEKHN1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "PLEKHN1-004"; transcript_source "ensembl_havana"; tag "CCDS"; ccds_id "CCDS53256"; exon_id "ENSE00001386720";\n+1\tprotein_coding\tCDS\t908241\t908390\t.\t+\t0\tgene_id "ENSG00000187583"; transcript_id "ENST00000379407"; exon_number "11"; gene_name "PLEKHN1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "PLEKHN1-004"; transcript_source "ensembl_havana"; tag "CCDS"; ccds_id "CCDS53256"; protein_id "ENSP00000368717";\n' |
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| diff -r aa9579837a2e -r 7c7a2a381dfe test-data/input.Homo_sapiens.GRCh37-chr1-f10k.75.gtf.granges.rds |
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| Binary file test-data/input.Homo_sapiens.GRCh37-chr1-f10k.75.gtf.granges.rds has changed |
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| diff -r aa9579837a2e -r 7c7a2a381dfe test-data/input.TIA1.bed.RCAS.report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.TIA1.bed.RCAS.report.html Thu Jun 21 15:07:13 2018 -0400 |
| [ |
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| diff -r aa9579837a2e -r 7c7a2a381dfe test-data/motif_analysis_table.data.tsv --- a/test-data/motif_analysis_table.data.tsv Thu Apr 13 12:36:05 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,5 +0,0 @@ -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 aa9579837a2e -r 7c7a2a381dfe test-data/output.TIA1.bed.RCAS.report.html --- a/test-data/output.TIA1.bed.RCAS.report.html Thu Apr 13 12:36:05 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
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| b |
| diff -r aa9579837a2e -r 7c7a2a381dfe test-data/summarizeQueryRegions.data.tsv --- a/test-data/summarizeQueryRegions.data.tsv Thu Apr 13 12:36:05 2017 -0400 +++ b/test-data/summarizeQueryRegions.data.tsv Thu Jun 21 15:07:13 2018 -0400 |
| b |
| @@ -6,3 +6,4 @@ introns 6 0.1 cds 3 0 threeUTRs 12 0.1 +NoFeatures 9977 99.8 |
| b |
| diff -r aa9579837a2e -r 7c7a2a381dfe test-data/test2_multi_set_analysis_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2_multi_set_analysis_report.html Thu Jun 21 15:07:13 2018 -0400 |
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