| Next changeset 1:2c4e879a81cf (2023-05-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 |
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IsoformSwitchAnalyzeR.R isoformswitchanalyzer.xml macros.xml test-data/annotation_salmon.gtf.gz test-data/cpc2_result.txt test-data/iupred2a_result.txt.gz test-data/pfam_results.txt test-data/salmon_cond1_rep1.sf test-data/salmon_cond1_rep2.sf test-data/salmon_cond2_rep1.sf test-data/salmon_cond2_rep2.sf test-data/signalP_results.txt test-data/test01.RData test-data/test02_counts.tabular test-data/test02_samples_annotation.tabular test-data/test03_cancer_counts.tabular test-data/test03_health_counts.tabular test-data/test04.RData test-data/test04_summary.tabular test-data/test06_consequences_enrichment.tabular test-data/test06_consequences_summary.tabular test-data/test06_splicing_enrichment.tabular test-data/test06_splicing_summary.tabular test-data/test06_switching.tabular test-data/test08_single_gene.pdf test-data/transcriptome.fasta.gz |
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| diff -r 000000000000 -r f3fefb6d8254 IsoformSwitchAnalyzeR.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/IsoformSwitchAnalyzeR.R Tue Jan 24 18:37:14 2023 +0000 |
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| b'@@ -0,0 +1,924 @@\n+# Load the IsoformSwitchAnalyzeR library\n+library(IsoformSwitchAnalyzeR,\n+ quietly = TRUE,\n+ warn.conflicts = FALSE)\n+library(argparse, quietly = TRUE, warn.conflicts = FALSE)\n+library(dplyr, quietly = TRUE, warn.conflicts = FALSE)\n+\n+# setup R error handling to go to stderr\n+options(\n+ show.error.messages = FALSE,\n+ error = function() {\n+ cat(geterrmessage(), file = stderr())\n+ q("no", 1, FALSE)\n+ }\n+)\n+\n+# we need that to not crash galaxy with an UTF8 error on German LC settings.\n+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")\n+\n+################################################################################\n+### Input Processing\n+################################################################################\n+\n+\n+# Collect arguments from command line\n+parser <- ArgumentParser(description = "IsoformSwitcheR R script")\n+\n+parser$add_argument("--modeSelector")\n+parser$add_argument("--parentDir", required = FALSE, help = "Parent directory")\n+parser$add_argument("--readLength",\n+ required = FALSE,\n+ type = "integer",\n+ help = "Read length (required for stringtie)")\n+parser$add_argument("--annotation", required = FALSE, help = "Annotation")\n+parser$add_argument("--transcriptome", required = FALSE, help = "Transcriptome")\n+parser$add_argument(\n+ "--fixStringTieAnnotationProblem",\n+ action = "store_true",\n+ required = FALSE,\n+ help = "Fix StringTie annotation problem"\n+)\n+parser$add_argument("--countFiles", required = FALSE, help = "Count files")\n+parser$add_argument("--toolSource", required = FALSE, help = "Tool source")\n+parser$add_argument("--rObject", required = FALSE, help = "R object")\n+parser$add_argument("--IFcutoff",\n+ required = FALSE,\n+ type = "numeric",\n+ help = "IFcutoff")\n+parser$add_argument(\n+ "--geneExpressionCutoff",\n+ required = FALSE,\n+ type = "numeric",\n+ help = "Gene expression cutoff"\n+)\n+parser$add_argument(\n+ "--isoformExpressionCutoff",\n+ required = FALSE,\n+ type = "numeric",\n+ help = "Isoform expression cutoff"\n+)\n+parser$add_argument("--alpha",\n+ required = FALSE,\n+ type = "numeric",\n+ help = "")\n+parser$add_argument("--dIFcutoff",\n+ required = FALSE,\n+ type = "numeric",\n+ help = "dIF cutoff")\n+parser$add_argument(\n+ "--onlySigIsoforms",\n+ required = FALSE,\n+ action = "store_true",\n+ help = "Only significative isoforms"\n+)\n+parser$add_argument(\n+ "--filterForConsequences",\n+ required = FALSE,\n+ action = "store_true",\n+ help = "Filter for consequences"\n+)\n+parser$add_argument(\n+ "--removeSingleIsformGenes",\n+ required = FALSE,\n+ action = "store_true",\n+ help = "Remove single isoform genes"\n+)\n+parser$add_argument(\n+ "--keepIsoformInAllConditions",\n+ required = FALSE,\n+ action = "store_true",\n+ help = "Keep isoform in all conditions"\n+)\n+parser$add_argument(\n+ "--correctForConfoundingFactors",\n+ required = FALSE,\n+ action = "store_true",\n+ help = "Correct for confunding factors"\n+)\n+parser$add_argument(\n+ "--overwriteIFvalues",\n+ required = FALSE,\n+ action = "store_true",\n+ help = "Overwrite IF values"\n+)\n+parser$add_argument(\n+ "--reduceToSwitchingGenes",\n+ required = FALSE,\n+ action = "store_true",\n+ help = "Reduce to switching genes"\n+)\n+parser$add_argument(\n+ "--reduceFurtherToGenesWithConsequencePotential",\n+ required = FALSE,\n+ action = "store_true",\n+ help = "Reduce further to genes with consequence potential"\n+)\n+parser$add_argument(\n+ "--keepIsoformInAllConditions2",\n+ required = FALSE,\n+ action = "store_true",\n+ help = "Keep isoform in ll conditions"\n+)\n+parser$add_argument("--minORFlength",\n+ required = FALSE,\n+ type = "integer",\n+ help = "")\n+parser$add_argument("--orfMethod", required = FALSE, help = "ORF methods")\n+p'..b',\n+ alpha = args$alpha,\n+ dIFcutoff = args$dIFcutoff,\n+ countGenes = args$countGenes,\n+ analysisOppositeConsequence = args$analysisOppositeConsequence,\n+ plot = TRUE,\n+ localTheme = theme_bw(base_size = 12),\n+ minEventsForPlotting = 10,\n+ returnResult = TRUE\n+ )\n+ dev.off()\n+\n+ write.table(\n+ consequenceEnrichment,\n+ file = "consequencesEnrichment.tsv",\n+ quote = FALSE,\n+ sep = "\\t",\n+ col.names = TRUE,\n+ row.names = FALSE\n+ )\n+\n+\n+ outputFile <- file.path(getwd(), "splicingEnrichment.pdf")\n+ pdf(\n+ file = outputFile,\n+ onefile = FALSE,\n+ height = 6,\n+ width = 9\n+ )\n+ splicingEnrichment <- extractSplicingEnrichment(\n+ SwitchList,\n+ splicingToAnalyze = "all",\n+ alpha = args$alpha,\n+ dIFcutoff = args$dIFcutoff,\n+ onlySigIsoforms = args$onlySigIsoforms,\n+ countGenes = args$countGenes,\n+ plot = TRUE,\n+ minEventsForPlotting = 10,\n+ returnResult = TRUE\n+ )\n+ dev.off()\n+\n+ write.table(\n+ splicingEnrichment,\n+ file = "splicingEnrichment.tsv",\n+ quote = FALSE,\n+ sep = "\\t",\n+ col.names = TRUE,\n+ row.names = FALSE\n+ )\n+\n+\n+ outputFile <- file.path(getwd(), "splicingSummary.pdf")\n+ pdf(\n+ file = outputFile,\n+ onefile = FALSE,\n+ height = 6,\n+ width = 9\n+ )\n+ splicingSummary <- extractSplicingSummary(\n+ SwitchList,\n+ splicingToAnalyze = "all",\n+ asFractionTotal = args$asFractionTotal,\n+ alpha = args$alpha,\n+ dIFcutoff = args$dIFcutoff,\n+ onlySigIsoforms = args$onlySigIsoforms,\n+ plot = TRUE,\n+ plotGenes = args$plotGenes,\n+ localTheme = theme_bw(),\n+ returnResult = TRUE\n+ )\n+ dev.off()\n+\n+ write.table(\n+ splicingSummary,\n+ file = "splicingSummary.tsv",\n+ quote = FALSE,\n+ sep = "\\t",\n+ col.names = TRUE,\n+ row.names = FALSE\n+ )\n+\n+\n+ ### Volcano like plot:\n+ outputFile <- file.path(getwd(), "volcanoPlot.pdf")\n+ pdf(\n+ file = outputFile,\n+ onefile = FALSE,\n+ height = 6,\n+ width = 9\n+ )\n+ ggplot(data = SwitchList$isoformFeatures, aes(x = dIF, y = -log10(isoform_switch_q_value))) +\n+ geom_point(aes(color = abs(dIF) > 0.1 &\n+ isoform_switch_q_value < 0.05), # default cutoff\n+ size = 1) +\n+ geom_hline(yintercept = -log10(0.05), linetype = "dashed") + # default cutoff\n+ geom_vline(xintercept = c(-0.1, 0.1), linetype = "dashed") + # default cutoff\n+ facet_wrap(~ condition_2) +\n+ scale_color_manual("Signficant\\nIsoform Switch", values = c("black", "red")) +\n+ labs(x = "dIF", y = "-Log10 ( Isoform Switch Q Value )") +\n+ theme_bw()\n+ dev.off()\n+\n+\n+ ### Switch vs Gene changes:\n+ outputFile <- file.path(getwd(), "switchGene.pdf")\n+ pdf(\n+ file = outputFile,\n+ onefile = FALSE,\n+ height = 6,\n+ width = 9\n+ )\n+ ggplot(data = SwitchList$isoformFeatures,\n+ aes(x = gene_log2_fold_change, y = dIF)) +\n+ geom_point(aes(color = abs(dIF) > 0.1 &\n+ isoform_switch_q_value < 0.05),\n+ size = 1) +\n+ facet_wrap(~ condition_2) +\n+ geom_hline(yintercept = 0, linetype = "dashed") +\n+ geom_vline(xintercept = 0, linetype = "dashed") +\n+ scale_color_manual("Signficant\\nIsoform Switch", values = c("black", "red")) +\n+ labs(x = "Gene log2 fold change", y = "dIF") +\n+ theme_bw()\n+ dev.off()\n+\n+ outputFile <- file.path(getwd(), "splicingGenomewide.pdf")\n+ pdf(\n+ file = outputFile,\n+ onefile = FALSE,\n+ height = 6,\n+ width = 9\n+ )\n+ splicingGenomeWide <- extractSplicingGenomeWide(\n+ SwitchList,\n+ featureToExtract = "all",\n+ splicingToAnalyze = c("A3", "MES", "ATSS"),\n+ plot = TRUE,\n+ returnResult = TRUE\n+ )\n+ dev.off()\n+ }\n+ save(SwitchList, file = "SwitchList.Rda")\n+\n+}\n' |
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| diff -r 000000000000 -r f3fefb6d8254 isoformswitchanalyzer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/isoformswitchanalyzer.xml Tue Jan 24 18:37:14 2023 +0000 |
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| b'@@ -0,0 +1,1030 @@\n+<tool id="isoformswitchanalyzer" name="IsoformSwitchAnalyzeR" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@">\n+ <description>statistical identification of isoform switching</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro=\'xrefs\'/>\n+ <expand macro=\'requirements\'/>\n+ <stdio>\n+ <regex match="Execution halted"\n+ source="both"\n+ level="fatal"\n+ description="Execution halted." />\n+ <regex match="Error in"\n+ source="both"\n+ level="fatal"\n+ description="An undefined error occurred, please check your input carefully and contact your administrator." />\n+ <regex match="Fatal error"\n+ source="both"\n+ level="fatal"\n+ description="An undefined error occurred, please check your input carefully and contact your administrator." />\n+ </stdio>\n+ <command><![CDATA[\n+ #if $functionMode.selector == \'data_import\'\n+ #if $functionMode.transcriptome.is_of_type("fasta.gz"):\n+ ln -s \'${functionMode.transcriptome}\' \'./transcriptome.fasta.gz\' &&\n+ #set $transcriptome = \'./transcriptome.fasta.gz\' \n+ #else\n+ ln -s \'${functionMode.transcriptome}\' \'./transcriptome.fasta\'\n+ #set $transcriptome = \'./transcriptome.fasta\' \n+ #end if\n+ #if $functionMode.genomeAnnotation.is_of_type("gtf.gz"):\n+ ln -s \'${functionMode.genomeAnnotation}\' \'./annotation.gtf.gz\' &&\n+ #set $annotation = \'./annotation.gtf.gz\' \n+ #else\n+ ln -s \'${functionMode.genomeAnnotation}\' \'./annotation.gtf\' &&\n+ #set $annotation = \'./annotation.gtf\' \n+ #end if\n+ mkdir -p \'input_files\' &&\n+ #if $functionMode.countFiles != \'disabled\':\n+ mkdir -p "count_files/factor1/" &&\n+ mkdir -p "count_files/factor2/" &&\n+ #end if\n+ #if $functionMode.tool_source.selector == \'stringtie\'\n+ #set $filename = \'t_data.ctab\'\n+ #else\n+ #set $filename = \'quant.sf\'\n+ #end if\n+\n+ #for $index in range(len($functionMode.first_factor.trans_counts)):\n+ mkdir \'./input_files/${functionMode.first_factor.factorLevel}${index}/\' &&\n+ ln -s $functionMode.first_factor.trans_counts[$index] \'./input_files/${functionMode.first_factor.factorLevel}${index}/${filename}\' &&\n+ #end for\n+\n+ #for $index in range(len($functionMode.second_factor.trans_counts)):\n+ mkdir \'./input_files/${functionMode.second_factor.factorLevel}${index}/\' &&\n+ ln -s $functionMode.second_factor.trans_counts[$index] \'./input_files/${functionMode.second_factor.factorLevel}${index}/${filename}\' &&\n+ #end for\n+ \n+ Rscript \'${__tool_directory__}/IsoformSwitchAnalyzeR.R\'\n+ --modeSelector $functionMode.selector\n+ --parentDir \'./input_files\'\n+ --annotation $annotation\n+ --transcriptome $transcriptome\n+ --toolSource $functionMode.tool_source.selector\n+ #if $functionMode.tool_source.selector == \'stringtie\'\n+ --readLength $functionMode.tool_source.averageSize\n+ $functionMode.tool_source.fixStringTieAnnotationProblem\n+ #end if\n+ --countFiles $functionMode.countFiles\n+ #else if $functionMode.selector == \'first_step\'\n+ Rscript \'${__tool_directory__}/IsoformSwitchAnalyzeR.R\'\n+ --modeSelector $functionMode.selector\n+ --rObject $functionMode.robject\n+ '..b'_size value="1157" delta="50"/>\n+ <has_text text="A5 gain (paired with A5 loss)"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- Test 08: analyze single gene-->\n+ <test expect_num_outputs="2">\n+ <conditional name="functionMode">\n+ <param name="selector" value="second_step"/>\n+ <param name="robject" value="test04.RData"/>\n+ <conditional name="analysis_mode">\n+ <param name="selector" value="single"/>\n+ <param name="gene" value="NADK"/>\n+ </conditional>\n+ </conditional>\n+ <output name="single_gene" ftype="pdf" file="test08_single_gene.pdf" compare="sim_size"/>\n+ <output name="switchList" ftype="rdata">\n+ <assert_contents>\n+ <has_size value="531580" delta="300"/>\n+ </assert_contents>\n+ </output> \n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+.. class:: infomark\n+\n+**Purpose**\n+\n+IsoformSwitchAnalyzeR is an easy-to use-R package that enables statistical identification of isoform switching from RNA-seq derived quantification \n+of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR facilitates integration of many sources of (predicted) annotation such as Open \n+Reading Frame (ORF/CDS), protein domains (via Pfam), signal peptides (via SignalP), Intrinsically Disordered Regions (IDR, via NetSurfP-2 or IUPred2A), \n+coding potential (via CPAT or CPC2) and sensitivity to Non-sense Mediated Decay (NMD) and more. The combination of identified isoform switches and \n+their annotation enables IsoformSwitchAnalyzeR to predict potential functional consequences of the identified isoform switches \xe2\x80\x94 such as loss of \n+protein domains \xe2\x80\x94 thereby identifying isoform switches of particular interest. Lastly, IsoformSwitchAnalyzeR provides article-ready visualization \n+methods for isoform switches for individual genes as well as both summary statistics and visualization of the genome-wide changes/consequences of \n+isoform switches, their consequences and the associated alternative splicing.\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Differential isoform expression (DIE) and differential isoform usage (DIU)**\n+\n+Differential isoform expression (DIE) and differential isoform usage (DIU) are related but distinct concepts. DIE assesses the difference of \n+absolute expression in isoform level. In contrast, DIU assesses the difference of relative expression in isoform level. For example, if the \n+expression of two isoforms of one gene are 10 and 20 in control and 50 and 100 in case, then there is DIE but no DIU because the relative \n+expression of the first isoform is 1/3 in both case and control. \n+\n+-----\n+\n+.. class:: infomark\n+\n+**ORF identification methods (novel isoform analysis)**\n+\n+- **Longest**: Identifies the longest ORF in the transcript (after filtering via minORFlength). This approach is similar to what the CPAT tool uses in it is analysis of coding potential.\n+- **LongestAnnotated**: Identifies the longest ORF (after filtering via minORFlength) downstream of an annotated translation start site (which are supplied via the cds argument).\n+- **Longest.AnnotatedWhenPossible**: A merge between "longestAnnotated" and "longest". For all isoforms where CDS start positions from known isoform overlap, only these CDS starts are considered and the longest ORF is annotated (similar to "longestAnnotated"). All isoforms without any overlapping CDS start sites they will be analysed with the "longest" approach.\n+- **MostUpstream**: Identifies the most upstream ORF in the transcript (after filtering via minORFlength).\n+- **MostUpstreamAnnoated**: Identifies the ORF (after filtering via minORFlength) downstream of the most upstream overlapping annotated translation start site (supplied via the cds argument).\n+\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r f3fefb6d8254 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jan 24 18:37:14 2023 +0000 |
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| @@ -0,0 +1,68 @@ +<macros> + <token name="@TOOL_VERSION@">1.20.0</token> + <token name="@SUFFIX_VERSION@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-isoformswitchanalyzer</requirement> + <requirement type="package" version="2.2.1">r-argparse</requirement> + <requirement type="package" version="1.0.10">r-dplyr</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btz247</citation> + <citation type="doi">10.1158/1541-7786.MCR-16-0459</citation> + </citations> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">IsoformSwitchAnalyzeR</xref> + <xref type="bioconductor">isoformswitchanalyzer</xref> + </xrefs> + </xml> + <xml name="macro_disordered_regions"> + <param argument="smoothingWindowSize" type="integer" min="1" value="5" label="Smoothing window size" help="An integer indicating how + large a sliding window should be used to calculate a smoothed (via mean) disordered probability score of a particular position in + a peptide. This has as a smoothing effect which prevents IDRs from not being detected (or from being split into sub-IDRs) by a + single residue with low probability. The trade off is worse accuracy of detecting the exact edges of the IDRs. To turn it off + smoothing simply set to 1." /> + <param argument="probabilityCutoff" type="float" min="0" value="0.5" label="Probability cutoff" help="Cutoff applied to the (smoothed) + disordered probability score for calling a residue as disordered. The default, 30 amino acids, is an accepted standard for long IDRs" /> + <param argument="minIdrSize" type="integer" min="0" value="30" label="Minimum IDR size" help="How long a stretch of disordered amino acid + constitute the region part of the Intrinsically Disordered Region (IDR) definition. The default, 30 amino acids, is an accepted + standard for long IDRs" /> + </xml> + <xml name="macro_alpha_difcutoff"> + <param argument="alpha" type="float" min="0" max="1" value="0.05" label="Alpha value" help="The cutoff which the FDR correct p-values must be smaller + than for calling significant switches." /> + <param argument="dIFcutoff" type="float" min="0" max="1" value="0.1" label="dIFcutoff" help="The cutoff which the changes in (absolute) isoform usage + must be larger than before an isoform is considered switching. This cutoff can remove cases where isoforms with (very) low dIF values are deemed + significant and thereby included in the downstream analysis. This cutoff is analogous to having a cutoff on log2 fold change in a normal differential + expression analysis of genes to ensure the genes have a certain effect size. Default is 0.1 (10%)" /> + </xml> + <xml name="macro_ifcutoff" token_value="" token_help=""> + <param argument="IFcutoff" type="float" min="0" max="1" value="@VALUE@" label="IFcutoff" help="@HELP@" /> + </xml> + <xml name="macro_onlysigisoforms1"> + <param argument="onlySigIsoforms" type="boolean" truevalue="--onlySigIsoforms" falsevalue="" checked="false" label="Only significantly differential + used isoforms" help="This parameter indicates whether both isoforms the pairs considered if reduceFurtherToGenesWithConsequenshould be significantly + differential used (as indicated by the alpha and dIFcutoff parameters). Default is disabled (aka only one of the isoforms in a pair should be + significantly differential used)" /> + </xml> + <xml name="macro_onlysigisoforms2"> + <param argument="onlySigIsoforms" type="boolean" truevalue="--onlySigIsoforms" falsevalue="" checked="false" label="Only significantly differential + used isoforms" help="This parameter indicates whether to only consider significant isoforms, meaning only analyzing genes where at least two isoforms + which both have significant usage changes in opposite direction (quite strict). Naturally this only works if the isoform switch test used have isoform + resolution (which the build in *isoformSwitchTestDEXSeq* has). If disabled all isoforms with an absolute dIF value larger than dIFcutoff in a gene with + significant switches (defined by alpha and dIFcutoff) are included in the pairwise comparison" /> + </xml> + <xml name="macro_keeisoforminall" token_checked=""> + <param argument="keepIsoformInAllConditions" type="boolean" truevalue="--keepIsoformInAllConditions" falsevalue="" checked="@CHECKED@" label="Keep isoforms in all conditions" + help="This parameter indicates whether an isoform should be kept in all comparisons even if it is only deemed significant (as defined by the + alpha and dIFcutoff parameters) in one comparison" /> + </xml> + <xml name="macro_onlyswitching"> + <param argument="onlySwitchingGenes" type="boolean" truevalue="--onlySwitchingGenes" falsevalue="" checked="true" label="Only switching genes" help="Only + analyze genes with isoform switches (as indicated by the alpha and dIFcutoff parameters)" /> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r f3fefb6d8254 test-data/annotation_salmon.gtf.gz |
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| Binary file test-data/annotation_salmon.gtf.gz has changed |
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| diff -r 000000000000 -r f3fefb6d8254 test-data/cpc2_result.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cpc2_result.txt Tue Jan 24 18:37:14 2023 +0000 |
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| b'@@ -0,0 +1,163 @@\n+#ID\tpeptide_length\tFickett_score\tpI\tORF_integrity\tcoding_probability\tlabel\n+TCONS_00000007\t390\t0.2582\t10.4859008789\t1\t0.95915\tcoding\n+TCONS_00000008\t390\t0.25739\t10.4859008789\t1\t0.957303\tcoding\n+TCONS_00000009\t390\t0.25739\t10.4859008789\t1\t0.957303\tcoding\n+TCONS_00000018\t25\t0.31765\t6.51007080078\t1\t0.00467786\tnoncoding\n+TCONS_00000019\t25\t0.26913\t6.51007080078\t1\t0.00858439\tnoncoding\n+TCONS_00000020\t92\t0.2912\t5.29876708984\t1\t0.189591\tnoncoding\n+TCONS_00000045\t803\t0.37445\t8.87176513672\t1\t1\tcoding\n+TCONS_00000046\t639\t0.40486\t8.06036376953\t1\t1\tcoding\n+TCONS_00000047\t639\t0.37861\t8.06036376953\t1\t1\tcoding\n+TCONS_00000048\t705\t0.37861\t8.63128662109\t1\t1\tcoding\n+TCONS_00000049\t428\t0.36298\t8.53863525391\t1\t0.999999\tcoding\n+TCONS_00000066\t635\t0.44536\t9.07708740234\t1\t1\tcoding\n+TCONS_00000067\t587\t0.43101\t9.26470947266\t1\t1\tcoding\n+TCONS_00000068\t508\t0.43101\t9.27154541016\t1\t1\tcoding\n+TCONS_00000173\t245\t0.28197\t7.08636474609\t1\t0.979227\tcoding\n+TCONS_00000174\t635\t0.46597\t6.21282958984\t1\t1\tcoding\n+TCONS_00000175\t196\t0.37128\t9.26434326172\t1\t0.958991\tcoding\n+TCONS_00000176\t293\t0.45712\t6.01593017578\t1\t0.999998\tcoding\n+TCONS_00000190\t240\t0.44582\t10.256652832\t1\t0.999427\tcoding\n+TCONS_00000191\t239\t0.46696\t10.256652832\t1\t0.999722\tcoding\n+TCONS_00000192\t176\t0.32021\t8.80865478516\t1\t0.733325\tcoding\n+TCONS_00000219\t393\t0.40691\t9.05352783203\t1\t1\tcoding\n+TCONS_00000220\t643\t0.41764\t9.43267822266\t1\t1\tcoding\n+TCONS_00000221\t1045\t0.46291\t6.78863525391\t1\t1\tcoding\n+TCONS_00000222\t1044\t0.45332\t6.78863525391\t1\t1\tcoding\n+TCONS_00000223\t1069\t0.44806\t6.76422119141\t1\t1\tcoding\n+TCONS_00000234\t1154\t0.39339\t8.66094970703\t1\t1\tcoding\n+TCONS_00000235\t1771\t0.41107\t5.38665771484\t1\t1\tcoding\n+TCONS_00000236\t1817\t0.41259\t5.41876220703\t1\t1\tcoding\n+TCONS_00000237\t1798\t0.43495\t5.29583740234\t1\t1\tcoding\n+TCONS_00000240\t1810\t0.43495\t5.38397216797\t1\t1\tcoding\n+TCONS_00000245\t139\t0.34852\t5.82745361328\t1\t0.76941\tcoding\n+TCONS_00000246\t165\t0.31325\t7.64581298828\t1\t0.703493\tcoding\n+TCONS_00000248\t123\t0.33613\t10.3421020508\t1\t0.264633\tnoncoding\n+TCONS_00000298\t758\t0.45593\t6.52203369141\t1\t1\tcoding\n+TCONS_00000299\t758\t0.46041\t6.52203369141\t1\t1\tcoding\n+TCONS_00000312\t667\t0.36679\t6.41033935547\t1\t1\tcoding\n+TCONS_00000313\t387\t0.30609\t6.46966552734\t1\t0.999993\tcoding\n+TCONS_00000339\t227\t0.33385\t9.29840087891\t1\t0.961376\tcoding\n+TCONS_00000340\t1683\t0.47452\t6.66705322266\t1\t1\tcoding\n+TCONS_00000341\t1719\t0.4579\t7.02398681641\t1\t1\tcoding\n+TCONS_00000342\t98\t0.3518\t4.85064697266\t1\t0.369301\tnoncoding\n+TCONS_00000343\t600\t0.45355\t4.98431396484\t-1\t0.998486\tcoding\n+TCONS_00000344\t1482\t0.47872\t6.41021728516\t1\t1\tcoding\n+TCONS_00000345\t116\t0.30429\t10.1972045898\t-1\t0.162618\tnoncoding\n+TCONS_00000356\t254\t0.40674\t5.39898681641\t1\t0.999957\tcoding\n+TCONS_00000357\t254\t0.42462\t5.39898681641\t1\t0.999972\tcoding\n+TCONS_00000358\t136\t0.30721\t10.6095581055\t1\t0.237752\tnoncoding\n+TCONS_00000359\t254\t0.40509\t5.39898681641\t1\t0.999955\tcoding\n+TCONS_00000360\t254\t0.38471\t5.39898681641\t1\t0.999917\tcoding\n+TCONS_00000411\t102\t0.3652\t10.3181762695\t1\t0.208176\tnoncoding\n+TCONS_00000412\t165\t0.30507\t8.96710205078\t1\t0.542238\tcoding\n+TCONS_00000413\t199\t0.32603\t9.98638916016\t1\t0.824741\tcoding\n+TCONS_00000414\t177\t0.30012\t12.1777954102\t1\t0.240739\tnoncoding\n+TCONS_00000415\t289\t0.28925\t6.91888427734\t1\t0.997798\tcoding\n+TCONS_00000417\t93\t0.29021\t5.77752685547\t1\t0.154229\tnoncoding\n+TCONS_00000418\t171\t0.34593\t9.22052001953\t1\t0.793203\tcoding\n+TCONS_00000493\t273\t0.31388\t5.44525146484\t1\t0.999661\tcoding\n+TCONS_00000494\t63\t0.38578\t5.38140869141\t-1\t0.0255393\tnoncoding\n+TCONS_00000507\t1240\t0.41886\t6.11456298828\t1\t1\tcoding\n+TCONS_00000508\t1240\t0.41886\t6.11456298828\t1\t1\tcoding\n+TCONS_00000509\t1128\t0.4155\t6.19488525391\t1\t1\tcoding\n+TCONS_00000558\t905\t0.35693\t11.8355102539\t1\t1\tcoding\n+TCONS_00000559\t917\t0.37177\t11.8427124023\t1\t1\tcoding\n+TCONS_00000560\t707\t0.41144\t12.0840454102\t-1\t0.590766\tcoding\n+TCONS_00000561\t799\t0.39573\t12.0907592773\t-1\t0.384218\tnoncoding\n+TCONS_00003865\t131\t0.33101\t4.31634521484\t1\t0.8266\tcoding\n+TCONS_00003866\t363\t0.47306\t4.75836181641\t1\t1\t'..b'999998\tcoding\n+TCONS_00003941\t406\t0.36022\t8.64654541016\t1\t0.999998\tcoding\n+TCONS_00003942\t255\t0.44417\t8.50299072266\t1\t0.999875\tcoding\n+TCONS_00003943\t237\t0.42944\t6.72222900391\t1\t0.999783\tcoding\n+TCONS_00003959\t247\t0.35124\t7.68707275391\t1\t0.997117\tcoding\n+TCONS_00003962\t267\t0.38203\t8.27752685547\t1\t0.99952\tcoding\n+TCONS_00004002\t1230\t0.41804\t6.02728271484\t1\t1\tcoding\n+TCONS_00004003\t1542\t0.39677\t5.94085693359\t1\t1\tcoding\n+TCONS_00004004\t461\t0.42883\t6.36956787109\t1\t1\tcoding\n+TCONS_00004005\t436\t0.45545\t6.78009033203\t1\t1\tcoding\n+TCONS_00004006\t261\t0.3185\t8.07342529297\t1\t0.992714\tcoding\n+TCONS_00004033\t330\t0.48037\t7.66522216797\t1\t1\tcoding\n+TCONS_00004034\t351\t0.46903\t8.57061767578\t1\t1\tcoding\n+TCONS_00004035\t381\t0.45317\t8.85467529297\t1\t1\tcoding\n+TCONS_00004036\t266\t0.47782\t7.69989013672\t1\t0.999977\tcoding\n+TCONS_00004037\t371\t0.47753\t6.83697509766\t1\t1\tcoding\n+TCONS_00004042\t235\t0.39553\t5.70355224609\t1\t0.999737\tcoding\n+TCONS_00004044\t193\t0.3727\t4.98150634766\t1\t0.996425\tcoding\n+TCONS_00004046\t418\t0.37805\t6.01275634766\t1\t1\tcoding\n+TCONS_00004049\t427\t0.38921\t6.00994873047\t1\t1\tcoding\n+TCONS_00004051\t182\t0.29544\t6.61358642578\t1\t0.869812\tcoding\n+TCONS_00004066\t540\t0.35446\t5.74041748047\t1\t1\tcoding\n+TCONS_00004067\t231\t0.37327\t4.52069091797\t1\t0.999796\tcoding\n+TCONS_00004068\t598\t0.42983\t5.16754150391\t1\t1\tcoding\n+TCONS_00004102\t336\t0.43537\t9.26934814453\t1\t0.999997\tcoding\n+TCONS_00004103\t271\t0.41692\t8.95745849609\t1\t0.999841\tcoding\n+TCONS_00004104\t239\t0.35865\t9.64447021484\t1\t0.988602\tcoding\n+TCONS_00004110\t982\t0.44298\t4.81036376953\t1\t1\tcoding\n+TCONS_00004111\t972\t0.44298\t4.82574462891\t1\t1\tcoding\n+TCONS_00004112\t963\t0.44298\t4.86297607422\t1\t1\tcoding\n+TCONS_00004208\t280\t0.43625\t8.52239990234\t1\t0.999963\tcoding\n+TCONS_00004209\t156\t0.44836\t6.21368408203\t1\t0.97777\tcoding\n+TCONS_00004210\t803\t0.45827\t7.30816650391\t1\t1\tcoding\n+TCONS_00004224\t1118\t0.46023\t4.64739990234\t1\t1\tcoding\n+TCONS_00004225\t421\t0.45899\t4.53948974609\t-1\t0.973057\tcoding\n+TCONS_00004226\t421\t0.44359\t4.57159423828\t-1\t0.96468\tcoding\n+TCONS_00004227\t675\t0.45899\t4.70831298828\t-1\t0.999734\tcoding\n+TCONS_00004228\t66\t0.33686\t6.80340576172\t1\t0.0354495\tnoncoding\n+TCONS_00004229\t58\t0.29129\t5.33721923828\t1\t0.0407299\tnoncoding\n+TCONS_00004230\t58\t0.31538\t5.33721923828\t1\t0.0352243\tnoncoding\n+TCONS_00004240\t290\t0.33959\t9.24139404297\t1\t0.997755\tcoding\n+TCONS_00004241\t690\t0.33757\t8.11077880859\t1\t1\tcoding\n+TCONS_00004265\t244\t0.27217\t10.4834594727\t1\t0.687188\tcoding\n+TCONS_00004266\t79\t0.43829\t4.32464599609\t1\t0.437694\tnoncoding\n+TCONS_00004267\t707\t0.47238\t6.42047119141\t1\t1\tcoding\n+TCONS_00004269\t848\t0.47412\t5.32684326172\t1\t1\tcoding\n+TCONS_00004270\t895\t0.47183\t5.22821044922\t1\t1\tcoding\n+TCONS_00004271\t893\t0.44107\t5.22821044922\t1\t1\tcoding\n+TCONS_00004310\t54\t0.37557\t9.51605224609\t1\t0.0330365\tnoncoding\n+TCONS_00004311\t79\t0.32206\t5.22454833984\t1\t0.1083\tnoncoding\n+TCONS_00004325\t213\t0.34713\t9.88677978516\t1\t0.941803\tcoding\n+TCONS_00004326\t402\t0.33446\t10.098449707\t1\t0.999891\tcoding\n+TCONS_00004327\t516\t0.35013\t9.76885986328\t1\t1\tcoding\n+TCONS_00004328\t554\t0.39012\t9.68572998047\t1\t1\tcoding\n+TCONS_00004329\t516\t0.38144\t9.76885986328\t1\t1\tcoding\n+TCONS_00004330\t554\t0.44952\t9.68572998047\t1\t1\tcoding\n+TCONS_00004332\t344\t0.41511\t9.41571044922\t1\t0.999995\tcoding\n+TCONS_00004333\t134\t0.44227\t4.53216552734\t1\t0.966241\tcoding\n+TCONS_00004375\t244\t0.43202\t9.56231689453\t1\t0.999455\tcoding\n+TCONS_00004376\t637\t0.47308\t8.22589111328\t1\t1\tcoding\n+TCONS_00004377\t634\t0.47308\t8.22589111328\t1\t1\tcoding\n+TCONS_00004378\t533\t0.47513\t9.19793701172\t1\t1\tcoding\n+TCONS_00004379\t536\t0.47513\t9.19793701172\t1\t1\tcoding\n+TCONS_00004380\t495\t0.46189\t9.26446533203\t1\t1\tcoding\n+TCONS_00004381\t596\t0.45922\t8.41583251953\t1\t1\tcoding\n+TCONS_00004382\t474\t0.47513\t9.34429931641\t1\t1\tcoding\n+TCONS_00004439\t288\t0.3259\t9.63568115234\t1\t0.993329\tcoding\n+TCONS_00004440\t243\t0.32342\t9.61492919922\t1\t0.961925\tcoding\n+TCONS_00004441\t335\t0.33728\t9.78558349609\t1\t0.999271\tcoding\n+TCONS_00004442\t335\t0.33728\t9.78558349609\t1\t0.999271\tcoding\n+TCONS_00004443\t115\t0.32346\t9.71331787109\t1\t0.190316\tnoncoding\n' |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/iupred2a_result.txt.gz |
| b |
| Binary file test-data/iupred2a_result.txt.gz has changed |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/pfam_results.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pfam_results.txt Tue Jan 24 18:37:14 2023 +0000 |
| b |
| b'@@ -0,0 +1,369 @@\n+# pfam_scan.pl, run at Mon Feb 4 16:16:14 2019\n+#\n+# Copyright (c) 2009 Genome Research Ltd\n+# Freely distributed under the GNU \n+# General Public License\n+#\n+# Authors: Jaina Mistry (jm14@sanger.ac.uk), John Tate (jt6@sanger.ac.uk), \n+# Rob Finn (rdf@sanger.ac.uk)\n+#\n+# This is free software; you can redistribute it and/or modify it under\n+# the terms of the GNU General Public License as published by the Free Software\n+# Foundation; either version 2 of the License, or (at your option) any later version.\n+# This program is distributed in the hope that it will be useful, but WITHOUT\n+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS\n+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more\n+# details.\n+#\n+# You should have received a copy of the GNU General Public License along with\n+# this program. If not, see <http://www.gnu.org/licenses/>. \n+# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =\n+# query sequence file: 01_intermediary_test_data_AA.fasta\n+# cpu number specified: 20\n+# searching against: /aura-internal/software/PfamScan/datafiles//Pfam-A.hmm, with cut off --cut_ga\n+# resolve clan overlaps: on\n+# predict active sites: on\n+# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =\n+#\n+# <seq id> <alignment start> <alignment end> <envelope start> <envelope end> <hmm acc> <hmm name> <type> <hmm start> <hmm end> <hmm length> <bit score> <E-value> <significance> <clan> <predicted_active_site_residues>\n+\n+TCONS_00000045 227 714 227 714 PF00858.19 ASC Family 1 439 439 277.4 1.7e-82 1 No_clan \n+TCONS_00000046 63 550 63 550 PF00858.19 ASC Family 1 439 439 278.4 8.4e-83 1 No_clan \n+TCONS_00000047 63 550 63 550 PF00858.19 ASC Family 1 439 439 278.4 8.4e-83 1 No_clan \n+TCONS_00000048 129 616 129 616 PF00858.19 ASC Family 1 439 439 277.9 1.2e-82 1 No_clan \n+TCONS_00000049 92 339 89 339 PF00858.19 ASC Family 199 439 439 182.9 8e-54 1 No_clan \n+TCONS_00000066 24 94 20 102 PF12037.3 DUF3523 Family 4 73 276 64.5 7.2e-18 1 No_clan \n+TCONS_00000066 141 334 131 334 PF12037.3 DUF3523 Family 72 276 276 241.7 7e-72 1 No_clan \n+TCONS_00000066 396 522 396 523 PF00004.24 AAA Family 1 131 132 70.7 1.3e-19 1 CL0023 \n+TCONS_00000067 24 286 20 286 PF12037.3 DUF3523 Family 4 276 276 326.1 1.2e-97 1 No_clan \n+TCONS_00000067 348 474 348 475 PF00004.24 AAA Family 1 131 132 70.8 1.1e-19 1 CL0023 \n+TCONS_00000068 1 207 1 207 PF12037.3 DUF3523 Family 59 276 276 251.4 7.7e-75 1 No_clan \n+TCONS_00000068 269 395 269 396 PF00004.24 AAA Family 1 131 132 71.2 8.8e-20 1 CL0023 \n+TCONS_00000173 25 63 25 63 PF00097.20 zf-C3HC4 Domain 1 41 41 23.9 2.3e-05 1 CL0229 \n+TCONS_00000174 25 63 25 63 PF00097.20 zf-C3HC4 Domain 1 41 41 22.1 8.4e-05 1 CL0229 \n+TCONS_00000174 95 144 93 145 PF00643.19 zf-B_box Domain 3 41 42 35.4 7.1e-09 1 No_clan \n+TCONS_00000190 3 86 3 88 PF05485.7 THAP Domain 1 83 85 71.5 4.6e-20 1 No_clan \n+TCONS_00000191 3 86 3 88 PF05485.7 THAP Domain 1 83 85 71.5 4.6e-20 1 No_clan \n+TCONS_00000192 3 86 3 88 PF05485.7 THAP Domain 1 83 85 72.5 2.3e-20 1 No_clan \n+TCONS_00000219 46 171 46 '..b' 70 56.4 1.6e-15 1 CL0221 \n+TCONS_00004380 28 92 28 96 PF00076.17 RRM_1 Domain 1 64 70 51.3 6.6e-14 1 CL0221 \n+TCONS_00004380 109 170 109 176 PF00076.17 RRM_1 Domain 1 59 70 36.3 3e-09 1 CL0221 \n+TCONS_00004380 204 265 204 266 PF00076.17 RRM_1 Domain 1 69 70 56.6 1.4e-15 1 CL0221 \n+TCONS_00004381 129 193 129 197 PF00076.17 RRM_1 Domain 1 64 70 50.9 8.6e-14 1 CL0221 \n+TCONS_00004381 210 271 210 277 PF00076.17 RRM_1 Domain 1 59 70 35.9 3.9e-09 1 CL0221 \n+TCONS_00004381 305 366 305 367 PF00076.17 RRM_1 Domain 1 69 70 56.2 1.8e-15 1 CL0221 \n+TCONS_00004382 88 149 88 155 PF00076.17 RRM_1 Domain 1 59 70 36.4 2.8e-09 1 CL0221 \n+TCONS_00004382 183 244 183 245 PF00076.17 RRM_1 Domain 1 69 70 56.7 1.3e-15 1 CL0221 \n+TCONS_00004439 20 27 19 71 PF07004.7 SHIPPO-rpt Repeat 2 9 37 4.8 59 1 No_clan \n+TCONS_00004439 140 159 140 171 PF07004.7 SHIPPO-rpt Repeat 1 20 37 11.2 0.54 1 No_clan \n+TCONS_00004439 178 210 178 213 PF07004.7 SHIPPO-rpt Repeat 1 34 37 14.6 0.047 1 No_clan \n+TCONS_00004439 220 235 219 246 PF07004.7 SHIPPO-rpt Repeat 2 17 37 12.4 0.22 1 No_clan \n+TCONS_00004439 259 269 259 276 PF07004.7 SHIPPO-rpt Repeat 1 11 37 9.2 2.3 1 No_clan \n+TCONS_00004440 95 114 95 126 PF07004.7 SHIPPO-rpt Repeat 1 20 37 11.5 0.43 1 No_clan \n+TCONS_00004440 133 165 133 168 PF07004.7 SHIPPO-rpt Repeat 1 34 37 14.9 0.036 1 No_clan \n+TCONS_00004440 175 191 174 202 PF07004.7 SHIPPO-rpt Repeat 2 18 37 12.8 0.17 1 No_clan \n+TCONS_00004440 214 224 214 231 PF07004.7 SHIPPO-rpt Repeat 1 11 37 9.5 1.8 1 No_clan \n+TCONS_00004441 67 74 66 93 PF07004.7 SHIPPO-rpt Repeat 2 9 37 4.3 83 1 No_clan \n+TCONS_00004441 187 206 187 218 PF07004.7 SHIPPO-rpt Repeat 1 20 37 10.9 0.66 1 No_clan \n+TCONS_00004441 225 257 225 260 PF07004.7 SHIPPO-rpt Repeat 1 34 37 14.3 0.058 1 No_clan \n+TCONS_00004441 267 282 266 293 PF07004.7 SHIPPO-rpt Repeat 2 17 37 12.2 0.27 1 No_clan \n+TCONS_00004441 306 316 306 323 PF07004.7 SHIPPO-rpt Repeat 1 11 37 9.0 2.7 1 No_clan \n+TCONS_00004442 67 74 66 93 PF07004.7 SHIPPO-rpt Repeat 2 9 37 4.3 83 1 No_clan \n+TCONS_00004442 187 206 187 218 PF07004.7 SHIPPO-rpt Repeat 1 20 37 10.9 0.66 1 No_clan \n+TCONS_00004442 225 257 225 260 PF07004.7 SHIPPO-rpt Repeat 1 34 37 14.3 0.058 1 No_clan \n+TCONS_00004442 267 282 266 293 PF07004.7 SHIPPO-rpt Repeat 2 17 37 12.2 0.27 1 No_clan \n+TCONS_00004442 306 316 306 323 PF07004.7 SHIPPO-rpt Repeat 1 11 37 9.0 2.7 1 No_clan \n+TCONS_00004443 15 25 15 52 PF07004.7 SHIPPO-rpt Repeat 1 11 37 4.0 1.1e+02 1 No_clan \n+TCONS_00004443 55 74 55 86 PF07004.7 SHIPPO-rpt Repeat 1 20 37 13.1 0.13 1 No_clan \n+TCONS_00004443 93 105 93 113 PF07004.7 SHIPPO-rpt Repeat 1 13 37 13.6 0.094 1 No_clan \n' |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/salmon_cond1_rep1.sf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/salmon_cond1_rep1.sf Tue Jan 24 18:37:14 2023 +0000 |
| b |
| b'@@ -0,0 +1,1093 @@\n+Name\tLength\tEffectiveLength\tTPM\tNumReads\n+TCONS_00000001\t1652\t1652\t11.1815\t11.6729\n+TCONS_00000002\t1488\t1488\t0\t0\n+TCONS_00000003\t1595\t1595\t0\t0\n+TCONS_00000006\t78\t78\t28475.5\t0.324245\n+TCONS_00000007\t2750\t2750\t32.5198\t59.1913\n+TCONS_00000008\t4369\t4369\t10.0237\t29.7173\n+TCONS_00000009\t4272\t4272\t15.3493\t44.4535\n+TCONS_00000010\t937\t937\t0\t0\n+TCONS_00000012\t1584\t1584\t47709\t47512.3\n+TCONS_00000013\t694\t694\t2748.13\t1007.75\n+TCONS_00000015\t1023\t1023\t16380.9\t9816.85\n+TCONS_00000016\t510\t510\t0\t0\n+TCONS_00000017\t854\t854\t0\t0\n+TCONS_00000018\t701\t701\t57.6706\t21.4335\n+TCONS_00000019\t517\t517\t48.5659\t11.7325\n+TCONS_00000020\t1543\t1543\t196.837\t190.32\n+TCONS_00000021\t2682\t2682\t59.2833\t105.056\n+TCONS_00000022\t3043\t3043\t0.47982\t0.972736\n+TCONS_00000023\t490\t490\t4.37202\t0.972736\n+TCONS_00000024\t2554\t2554\t0\t0\n+TCONS_00000025\t2121\t2121\t36.5397\t50.2604\n+TCONS_00000026\t2560\t2560\t144.607\t243.785\n+TCONS_00000027\t955\t955\t51.7022\t28.4991\n+TCONS_00000028\t2003\t2003\t112.974\t145.972\n+TCONS_00000029\t1149\t1149\t56.5546\t38.9299\n+TCONS_00000030\t2398\t2398\t11.0247\t17.3234\n+TCONS_00000031\t2554\t2554\t16.5029\t27.7514\n+TCONS_00000032\t2293\t2293\t45.2628\t67.7627\n+TCONS_00000033\t662\t662\t2821.38\t970.791\n+TCONS_00000034\t7319\t7319\t1948.03\t9837.85\n+TCONS_00000035\t673\t673\t9.4226\t3.31544\n+TCONS_00000036\t971\t971\t106.506\t59.9124\n+TCONS_00000037\t1616\t1616\t0\t0\n+TCONS_00000041\t2259\t2259\t0\t0\n+TCONS_00000042\t2278\t2278\t0\t0\n+TCONS_00000043\t2111\t2111\t0\t0\n+TCONS_00000044\t2790\t2790\t1006.18\t1859.87\n+TCONS_00000045\t3054\t3054\t8.45822\t17.2131\n+TCONS_00000046\t2960\t2960\t21.2277\t41.7893\n+TCONS_00000047\t2590\t2590\t12.0013\t20.4869\n+TCONS_00000048\t2684\t2684\t4.21879\t7.48206\n+TCONS_00000049\t2530\t2530\t11.4481\t19.0569\n+TCONS_00000050\t1239\t1239\t847.508\t637.313\n+TCONS_00000051\t1181\t1181\t139.312\t99.0486\n+TCONS_00000052\t1932\t1932\t14.4788\t17.981\n+TCONS_00000053\t2192\t2192\t845.357\t1205.22\n+TCONS_00000054\t2558\t2558\t2.88743\t4.86368\n+TCONS_00000055\t1747\t1747\t272.665\t302.96\n+TCONS_00000056\t1594\t1594\t55.4717\t55.6352\n+TCONS_00000057\t1741\t1741\t175.51\t194.266\n+TCONS_00000058\t491\t491\t0\t0\n+TCONS_00000059\t2141\t2141\t38.7529\t53.8526\n+TCONS_00000060\t2536\t2536\t309.875\t517.144\n+TCONS_00000061\t3859\t3859\t18.4899\t48.1504\n+TCONS_00000062\t2432\t2432\t462.516\t737.879\n+TCONS_00000063\t1939\t1939\t32.3298\t40.3101\n+TCONS_00000064\t2667\t2667\t192.737\t339.504\n+TCONS_00000065\t1170\t1170\t406.751\t286.03\n+TCONS_00000066\t2611\t2611\t41.1192\t70.8031\n+TCONS_00000067\t2467\t2467\t1092.68\t1770.26\n+TCONS_00000068\t2329\t2329\t1496.94\t2279.16\n+TCONS_00000069\t2616\t2616\t12.7511\t22.0012\n+TCONS_00000070\t1048\t1048\t0\t0\n+TCONS_00000071\t3243\t3243\t23.23\t50.3786\n+TCONS_00000072\t3201\t3201\t230.473\t492.98\n+TCONS_00000073\t3231\t3231\t0\t0\n+TCONS_00000074\t3026\t3026\t71.9881\t145.076\n+TCONS_00000076\t2930\t2930\t39.4169\t76.761\n+TCONS_00000077\t2890\t2890\t14.8124\t28.427\n+TCONS_00000078\t3311\t3311\t50.6086\t112.187\n+TCONS_00000079\t2590\t2590\t35.4331\t60.4861\n+TCONS_00000080\t2308\t2308\t32.0146\t48.2684\n+TCONS_00000081\t585\t585\t0\t0\n+TCONS_00000082\t1239\t1239\t2.05912\t1.54843\n+TCONS_00000083\t1306\t1306\t0\t0\n+TCONS_00000084\t905\t905\t36.2798\t18.7156\n+TCONS_00000085\t850\t850\t0.00268498\t0.0012807\n+TCONS_00000086\t906\t906\t68.4177\t35.3429\n+TCONS_00000087\t848\t848\t0\t0\n+TCONS_00000088\t1808\t1808\t45.8269\t52.8948\n+TCONS_00000089\t921\t921\t18.4517\t9.72736\n+TCONS_00000090\t1101\t1101\t0\t0\n+TCONS_00000091\t1925\t1925\t0.786404\t0.972736\n+TCONS_00000092\t2324\t2324\t0\t0\n+TCONS_00000093\t2112\t2112\t26.7569\t36.634\n+TCONS_00000094\t2032\t2032\t0\t0\n+TCONS_00000095\t2009\t2009\t4.54047\t5.88592\n+TCONS_00000096\t1745\t1745\t10.9251\t12.1235\n+TCONS_00000097\t1212\t1212\t0\t0\n+TCONS_00000098\t1849\t1849\t0\t0\n+TCONS_00000099\t1859\t1859\t0\t0\n+TCONS_00000100\t2089\t2089\t6.18632\t8.36934\n+TCONS_00000101\t1943\t1943\t86.4024\t107.974\n+TCONS_00000102\t5706\t5706\t1751.24\t6847.09\n+TCONS_00000103\t3093\t3093\t3557.39\t7337.62\n+TCONS_00000104\t3203\t3203\t170.625\t365.207\n+TCONS_00000105\t4834\t4834\t1.54004\t5.0719900000000004\n+TCONS_00000106\t3951\t3951\t0\t0\n+TCONS_00000107\t3939\t3939\t0.667472\t1.77595\n+TCONS_00000108\t4854\t4854\t0\t0\n+TCONS_00000109\t5564\t5564\t2.54328\t9.68858\n+TCONS_00000110\t'..b'13\n+TCONS_00004330\t1860\t1860\t817.941\t974.161\n+TCONS_00004331\t2544\t2544\t19.2164\t32.1786\n+TCONS_00004332\t2537\t2537\t228.027\t380.711\n+TCONS_00004333\t927\t927\t285.674\t151.813\n+TCONS_00004334\t5160\t5160\t351.787\t1239.65\n+TCONS_00004335\t4949\t4949\t53.2798\t179.804\n+TCONS_00004336\t5786\t5786\t517.716\t2053.48\n+TCONS_00004337\t5850\t5850\t199.863\t801.782\n+TCONS_00004338\t6175\t6175\t385.109\t1633.41\n+TCONS_00004340\t6283\t6283\t292.991\t1265.07\n+TCONS_00004342\t1915\t1915\t0\t0\n+TCONS_00004343\t2088\t2088\t28.2445\t38.1914\n+TCONS_00004344\t5241\t5241\t101.151\t362.236\n+TCONS_00004345\t5087\t5087\t980.268\t3403.75\n+TCONS_00004346\t5096\t5096\t1001.05\t3482.3\n+TCONS_00004347\t5000\t5000\t14.401\t49.1184\n+TCONS_00004348\t5136\t5136\t4096.6\t14366.4\n+TCONS_00004349\t2198\t2198\t14.286\t20.4281\n+TCONS_00004350\t2326\t2326\t0.63978\t0.972736\n+TCONS_00004351\t2057\t2057\t431.919\t574.563\n+TCONS_00004352\t3348\t3348\t1.65232e-4\t3.70601e-4\n+TCONS_00004353\t3300\t3300\t1.75827\t3.88399\n+TCONS_00004354\t3333\t3333\t0.00295076\t0.006587\n+TCONS_00004355\t3494\t3494\t0\t0\n+TCONS_00004356\t3639\t3639\t41.4875\t101.588\n+TCONS_00004357\t4462\t4462\t953.215\t2888.66\n+TCONS_00004359\t4264\t4264\t33.9993\t98.2736\n+TCONS_00004360\t4498\t4498\t0\t0\n+TCONS_00004361\t2089\t2089\t0.944197\t1.27738\n+TCONS_00004362\t2126\t2126\t193.146\t266.355\n+TCONS_00004363\t2411\t2411\t184.813\t292.099\n+TCONS_00004364\t3586\t3586\t634.332\t1529.48\n+TCONS_00004365\t14287\t14287\t1616.25\t16123.9\n+TCONS_00004366\t14290\t14290\t283.723\t2831.04\n+TCONS_00004367\t846\t846\t0\t0\n+TCONS_00004368\t3903\t3903\t0\t0\n+TCONS_00004369\t3883\t3883\t0\t0\n+TCONS_00004370\t510\t510\t0\t0\n+TCONS_00004371\t8653\t8653\t317.993\t1905.8\n+TCONS_00004372\t8587\t8587\t402.536\t2393.7\n+TCONS_00004373\t3921\t3921\t0\t0\n+TCONS_00004374\t2834\t2834\t0\t0\n+TCONS_00004375\t1637\t1637\t0\t0\n+TCONS_00004376\t2740\t2740\t381.392\t691.499\n+TCONS_00004377\t2731\t2731\t1507.46\t2723.58\n+TCONS_00004378\t2565\t2565\t3090.62\t5221.23\n+TCONS_00004379\t2574\t2574\t716.981\t1215.82\n+TCONS_00004380\t2451\t2451\t0\t0\n+TCONS_00004381\t2617\t2617\t0\t0\n+TCONS_00004382\t2388\t2388\t105.248\t164.634\n+TCONS_00004383\t4314\t4314\t215.254\t629.791\n+TCONS_00004384\t4492\t4492\t131.698\t401.896\n+TCONS_00004385\t1586\t1586\t462.44\t461.188\n+TCONS_00004386\t540\t540\t28.0658\t7.23642\n+TCONS_00004387\t738\t738\t132.236\t52.605\n+TCONS_00004388\t646\t646\t11.3049\t3.76195\n+TCONS_00004389\t2552\t2552\t132.768\t223.075\n+TCONS_00004390\t2791\t2791\t42.753\t79.0566\n+TCONS_00004391\t4088\t4088\t56.5353\t156.379\n+TCONS_00004392\t4129\t4129\t655.899\t1833.26\n+TCONS_00004394\t1768\t1768\t0\t0\n+TCONS_00004395\t697\t697\t0\t0\n+TCONS_00004396\t2041\t2041\t0\t0\n+TCONS_00004397\t5192\t5192\t88.3184\t313.221\n+TCONS_00004398\t1287\t1287\t1188.4\t933.981\n+TCONS_00004399\t1547\t1547\t498.386\t483.295\n+TCONS_00004400\t1074\t1074\t76.6189\t48.6791\n+TCONS_00004401\t1607\t1607\t23.1245\t23.4052\n+TCONS_00004402\t1631\t1631\t93.0909\t95.8001\n+TCONS_00004403\t1553\t1553\t60.8488\t59.2645\n+TCONS_00004404\t1566\t1566\t502.092\t493.633\n+TCONS_00004405\t1676\t1676\t191.708\t203.386\n+TCONS_00004406\t1824\t1824\t95.2429\t111.01\n+TCONS_00004408\t1244\t1244\t5.60264\t4.23291\n+TCONS_00004409\t934\t934\t0\t0\n+TCONS_00004410\t1607\t1607\t1433.78\t1451.18\n+TCONS_00004412\t1394\t1394\t52.7327\t45.4323\n+TCONS_00004413\t2160\t2160\t0\t0\n+TCONS_00004414\t1411\t1411\t6.2186\t5.43243\n+TCONS_00004415\t2054\t2054\t41.6408\t55.3047\n+TCONS_00004416\t2077\t2077\t154.003\t207.041\n+TCONS_00004418\t953\t953\t3.81388\t2.09688\n+TCONS_00004419\t1774\t1774\t0\t0\n+TCONS_00004420\t2239\t2239\t110.069\t160.582\n+TCONS_00004421\t1842\t1842\t1279.56\t1507.67\n+TCONS_00004422\t2924\t2924\t1046.74\t2033.98\n+TCONS_00004423\t2686\t2686\t0\t0\n+TCONS_00004424\t4859\t4859\t0\t0\n+TCONS_00004425\t5799\t5799\t0\t0\n+TCONS_00004426\t3940\t3940\t0\t0\n+TCONS_00004427\t5094\t5094\t0\t0\n+TCONS_00004428\t2703\t2703\t0\t0\n+TCONS_00004429\t2798\t2798\t5.44027e-4\t0.00100868\n+TCONS_00004431\t2725\t2725\t4.8564\t8.75362\n+TCONS_00004432\t4461\t4461\t0\t0\n+TCONS_00004433\t4548\t4548\t0\t0\n+TCONS_00004434\t4417\t4417\t0\t0\n+TCONS_00004435\t4424\t4424\t0\t0\n+TCONS_00004436\t686\t686\t0\t0\n+TCONS_00004439\t2497\t2497\t88.8612\t145.849\n+TCONS_00004440\t2827\t2827\t12.5506\t23.5274\n+TCONS_00004441\t2683\t2683\t156.143\t276.811\n+TCONS_00004442\t2803\t2803\t0\t0\n+TCONS_00004443\t1653\t1653\t16.116\t16.8357\n' |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/salmon_cond1_rep2.sf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/salmon_cond1_rep2.sf Tue Jan 24 18:37:14 2023 +0000 |
| b |
| b'@@ -0,0 +1,1093 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5241\t5241\t155.001\t555.081\n+TCONS_00004345\t5087\t5087\t986.331\t3424.81\n+TCONS_00004346\t5096\t5096\t1772\t6164.14\n+TCONS_00004347\t5000\t5000\t17.8227\t60.7891\n+TCONS_00004348\t5136\t5136\t3578.95\t12551\n+TCONS_00004349\t2198\t2198\t272.719\t389.97\n+TCONS_00004350\t2326\t2326\t0.448641\t0.682124\n+TCONS_00004351\t2057\t2057\t611.143\t812.978\n+TCONS_00004352\t3348\t3348\t0\t0\n+TCONS_00004353\t3300\t3300\t2.46707\t5.44969\n+TCONS_00004354\t3333\t3333\t0.00326853\t0.00729636\n+TCONS_00004355\t3494\t3494\t0\t0\n+TCONS_00004356\t3639\t3639\t56.5689\t138.516\n+TCONS_00004357\t4462\t4462\t1140.54\t3456.33\n+TCONS_00004359\t4264\t4264\t56.0565\t162.029\n+TCONS_00004360\t4498\t4498\t0\t0\n+TCONS_00004361\t2089\t2089\t2.14287\t2.89905\n+TCONS_00004362\t2126\t2126\t190.394\t262.56\n+TCONS_00004363\t2411\t2411\t176.613\t279.139\n+TCONS_00004364\t3586\t3586\t185.294\t446.773\n+TCONS_00004365\t14287\t14287\t5743.53\t57297.8\n+TCONS_00004366\t14290\t14290\t1240.5\t12377.9\n+TCONS_00004367\t846\t846\t322.826\t153.071\n+TCONS_00004368\t3903\t3903\t0.0101707\t0.0280627\n+TCONS_00004369\t3883\t3883\t1.48074\t4.06468\n+TCONS_00004370\t510\t510\t0\t0\n+TCONS_00004371\t8653\t8653\t478.317\t2866.65\n+TCONS_00004372\t8587\t8587\t568.553\t3380.92\n+TCONS_00004373\t3921\t3921\t0\t0\n+TCONS_00004374\t2834\t2834\t0\t0\n+TCONS_00004375\t1637\t1637\t0.283549\t0.293004\n+TCONS_00004376\t2740\t2740\t289.799\t525.433\n+TCONS_00004377\t2731\t2731\t1179.9\t2131.75\n+TCONS_00004378\t2565\t2565\t2277.44\t3847.46\n+TCONS_00004379\t2574\t2574\t509.044\t863.207\n+TCONS_00004380\t2451\t2451\t0\t0\n+TCONS_00004381\t2617\t2617\t0\t0\n+TCONS_00004382\t2388\t2388\t89.2775\t139.653\n+TCONS_00004383\t4314\t4314\t313.143\t916.196\n+TCONS_00004384\t4492\t4492\t110.131\t336.081\n+TCONS_00004385\t1586\t1586\t567.04\t565.504\n+TCONS_00004386\t540\t540\t217.637\t56.115\n+TCONS_00004387\t738\t738\t168.593\t67.0681\n+TCONS_00004388\t646\t646\t13.0752\t4.35108\n+TCONS_00004389\t2552\t2552\t59.8523\t100.563\n+TCONS_00004390\t2791\t2791\t41.4315\t76.613\n+TCONS_00004391\t4088\t4088\t91.3879\t252.783\n+TCONS_00004392\t4129\t4129\t498.976\t1394.65\n+TCONS_00004394\t1768\t1768\t0\t0\n+TCONS_00004395\t697\t697\t0.195125\t0.0719674\n+TCONS_00004396\t2041\t2041\t0\t0\n+TCONS_00004397\t5192\t5192\t29.62\t105.047\n+TCONS_00004398\t1287\t1287\t1229.48\t966.267\n+TCONS_00004399\t1547\t1547\t71.3578\t69.1972\n+TCONS_00004400\t1074\t1074\t142.83\t90.7456\n+TCONS_00004401\t1607\t1607\t0\t0\n+TCONS_00004402\t1631\t1631\t192.089\t197.679\n+TCONS_00004403\t1553\t1553\t0\t0\n+TCONS_00004404\t1566\t1566\t193.265\t190.009\n+TCONS_00004405\t1676\t1676\t121.508\t128.91\n+TCONS_00004406\t1824\t1824\t29.0902\t33.9059\n+TCONS_00004408\t1244\t1244\t3.57145\t2.6983\n+TCONS_00004409\t934\t934\t0\t0\n+TCONS_00004410\t1607\t1607\t1594.15\t1613.5\n+TCONS_00004412\t1394\t1394\t327.298\t281.987\n+TCONS_00004413\t2160\t2160\t0\t0\n+TCONS_00004414\t1411\t1411\t5.04991\t4.41149\n+TCONS_00004415\t2054\t2054\t37.355\t49.6126\n+TCONS_00004416\t2077\t2077\t124.816\t167.802\n+TCONS_00004418\t953\t953\t0\t0\n+TCONS_00004419\t1774\t1774\t0\t0\n+TCONS_00004420\t2239\t2239\t205.454\t299.74\n+TCONS_00004421\t1842\t1842\t1284.91\t1513.96\n+TCONS_00004422\t2924\t2924\t962.225\t1869.77\n+TCONS_00004423\t2686\t2686\t0\t0\n+TCONS_00004424\t4859\t4859\t0\t0\n+TCONS_00004425\t5799\t5799\t0\t0\n+TCONS_00004426\t3940\t3940\t0\t0\n+TCONS_00004427\t5094\t5094\t0\t0\n+TCONS_00004428\t2703\t2703\t2.28441\t4.08209\n+TCONS_00004429\t2798\t2798\t0\t0\n+TCONS_00004431\t2725\t2725\t0.00591119\t0.0106549\n+TCONS_00004432\t4461\t4461\t0.00134022\t0.00422657\n+TCONS_00004433\t4548\t4548\t0\t0\n+TCONS_00004434\t4417\t4417\t0.147425\t0.460339\n+TCONS_00004435\t4424\t4424\t0.0695635\t0.217558\n+TCONS_00004436\t686\t686\t0\t0\n+TCONS_00004439\t2497\t2497\t40.3414\t66.2127\n+TCONS_00004440\t2827\t2827\t12.8311\t24.0531\n+TCONS_00004441\t2683\t2683\t241.43\t428.007\n+TCONS_00004442\t2803\t2803\t6.05059\t11.2398\n+TCONS_00004443\t1653\t1653\t14.842\t15.5048\n' |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/salmon_cond2_rep1.sf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/salmon_cond2_rep1.sf Tue Jan 24 18:37:14 2023 +0000 |
| b |
| b'@@ -0,0 +1,1093 @@\n+Name\tLength\tEffectiveLength\tTPM\tNumReads\n+TCONS_00000001\t1652\t1652\t0\t0\n+TCONS_00000002\t1488\t1488\t0\t0\n+TCONS_00000003\t1595\t1595\t0\t0\n+TCONS_00000006\t78\t78\t1377990\t4.67384\n+TCONS_00000007\t2750\t2750\t329.487\t589.154\n+TCONS_00000008\t4369\t4369\t358.067\t1050.07\n+TCONS_00000009\t4272\t4272\t0.00971677\t0.0278293\n+TCONS_00000010\t937\t937\t0\t0\n+TCONS_00000012\t1584\t1584\t88354.2\t85156.6\n+TCONS_00000013\t694\t694\t6801.86\t2276.16\n+TCONS_00000015\t1023\t1023\t31724.9\t17994.9\n+TCONS_00000016\t510\t510\t0\t0\n+TCONS_00000017\t854\t854\t0\t0\n+TCONS_00000018\t701\t701\t86.5869\t29.4037\n+TCONS_00000019\t517\t517\t0\t0\n+TCONS_00000020\t1543\t1543\t121.215\t113.315\n+TCONS_00000021\t2682\t2682\t27.6282\t48.0737\n+TCONS_00000022\t3043\t3043\t23.7597\t47.4061\n+TCONS_00000023\t490\t490\t0\t0\n+TCONS_00000024\t2554\t2554\t0\t0\n+TCONS_00000025\t2121\t2121\t8.21721\t11.0393\n+TCONS_00000026\t2560\t2560\t167.146\t276.421\n+TCONS_00000027\t955\t955\t158.746\t82.4125\n+TCONS_00000028\t2003\t2003\t234.098\t294.967\n+TCONS_00000029\t1149\t1149\t184.96\t121.388\n+TCONS_00000030\t2398\t2398\t9.52126\t14.6556\n+TCONS_00000031\t2554\t2554\t12.1632\t20.0637\n+TCONS_00000032\t2293\t2293\t4.25187e-4\t6.2291e-4\n+TCONS_00000033\t662\t662\t1003.63\t313.147\n+TCONS_00000034\t7319\t7319\t1882.49\t9446.49\n+TCONS_00000035\t673\t673\t4.17578\t1.33538\n+TCONS_00000036\t971\t971\t27.6915\t14.6892\n+TCONS_00000037\t1616\t1616\t2.03063\t2.00307\n+TCONS_00000041\t2259\t2259\t5.07399\t7.31156\n+TCONS_00000042\t2278\t2278\t0.00524265\t0.00762502\n+TCONS_00000043\t2111\t2111\t9.51204\t12.7115\n+TCONS_00000044\t2790\t2790\t291.136\t528.811\n+TCONS_00000045\t3054\t3054\t2.05334\t4.11285\n+TCONS_00000046\t2960\t2960\t5.612\t10.8679\n+TCONS_00000047\t2590\t2590\t21.0208\t35.2095\n+TCONS_00000048\t2684\t2684\t6.52646\t11.3654\n+TCONS_00000049\t2530\t2530\t29.7772\t48.6133\n+TCONS_00000050\t1239\t1239\t644.637\t464.085\n+TCONS_00000051\t1181\t1181\t137.01\t93.0183\n+TCONS_00000052\t1932\t1932\t15.435\t18.6737\n+TCONS_00000053\t2192\t2192\t201.703\t281.098\n+TCONS_00000054\t2558\t2558\t3.23266\t5.34153\n+TCONS_00000055\t1747\t1747\t0\t0\n+TCONS_00000056\t1594\t1594\t83.5124\t81.0804\n+TCONS_00000057\t1741\t1741\t475.434\t510.996\n+TCONS_00000058\t491\t491\t55.8942\t10.6831\n+TCONS_00000059\t2141\t2141\t41.0204\t55.6882\n+TCONS_00000060\t2536\t2536\t494.032\t808.638\n+TCONS_00000061\t3859\t3859\t77.4015\t199.083\n+TCONS_00000062\t2432\t2432\t478.775\t748.464\n+TCONS_00000063\t1939\t1939\t119.152\t144.742\n+TCONS_00000064\t2667\t2667\t106.773\t184.656\n+TCONS_00000065\t1170\t1170\t264.323\t177.397\n+TCONS_00000066\t2611\t2611\t55.8615\t94.3965\n+TCONS_00000067\t2467\t2467\t1032.87\t1640.23\n+TCONS_00000068\t2329\t2329\t317.113\t472.649\n+TCONS_00000069\t2616\t2616\t29.3079\t49.6291\n+TCONS_00000070\t1048\t1048\t6.84937\t4.00615\n+TCONS_00000071\t3243\t3243\t0.00599657\t0.0128123\n+TCONS_00000072\t3201\t3201\t99.9908\t210.673\n+TCONS_00000073\t3231\t3231\t0\t0\n+TCONS_00000074\t3026\t3026\t102.016\t202.32\n+TCONS_00000076\t2930\t2930\t47.3159\t90.6262\n+TCONS_00000077\t2890\t2890\t25.253\t47.6541\n+TCONS_00000078\t3311\t3311\t0\t0\n+TCONS_00000079\t2590\t2590\t109.105\t182.749\n+TCONS_00000080\t2308\t2308\t0\t0\n+TCONS_00000081\t585\t585\t224.576\t57.8466\n+TCONS_00000082\t1239\t1239\t36.4726\t26.2572\n+TCONS_00000083\t1306\t1306\t17.9878\t13.8017\n+TCONS_00000084\t905\t905\t0\t0\n+TCONS_00000085\t850\t850\t8.25962\t3.67487\n+TCONS_00000086\t906\t906\t51.4446\t24.9253\n+TCONS_00000087\t848\t848\t16.8154\t7.4577\n+TCONS_00000088\t1808\t1808\t89.9153\t100.9\n+TCONS_00000089\t921\t921\t2.69713\t1.33538\n+TCONS_00000090\t1101\t1101\t24.6753\t15.3569\n+TCONS_00000091\t1925\t1925\t42.116\t50.7445\n+TCONS_00000092\t2324\t2324\t863.746\t1284.34\n+TCONS_00000093\t2112\t2112\t0\t0\n+TCONS_00000094\t2032\t2032\t0\t0\n+TCONS_00000095\t2009\t2009\t39.3944\t49.8046\n+TCONS_00000096\t1745\t1745\t0\t0\n+TCONS_00000097\t1212\t1212\t4.2835\t3.002\n+TCONS_00000098\t1849\t1849\t8.06605\t9.28521\n+TCONS_00000099\t1859\t1859\t18.5776\t21.5169\n+TCONS_00000100\t2089\t2089\t57.7278\t76.2475\n+TCONS_00000101\t1943\t1943\t109.674\t133.539\n+TCONS_00000102\t5706\t5706\t778.44\t3018.63\n+TCONS_00000103\t3093\t3093\t780.296\t1584.45\n+TCONS_00000104\t3203\t3203\t22.6022\t47.653\n+TCONS_00000105\t4834\t4834\t0\t0\n+TCONS_00000106\t3951\t3951\t0\t0\n+TCONS_00000107\t3939\t3939\t3.13321e-5\t8.23607e-5\n+TCONS_00000108\t4854\t4854\t0.299922\t0.'..b'49\n+TCONS_00004335\t4949\t4949\t0\t0\n+TCONS_00004336\t5786\t5786\t254.426\t1001\n+TCONS_00004337\t5850\t5850\t0\t0\n+TCONS_00004338\t6175\t6175\t293.607\t1235.89\n+TCONS_00004340\t6283\t6283\t137.933\t591.14\n+TCONS_00004342\t1915\t1915\t0\t0\n+TCONS_00004343\t2088\t2088\t41.5518\t54.8527\n+TCONS_00004344\t5241\t5241\t8.24683\t29.2686\n+TCONS_00004345\t5087\t5087\t0\t0\n+TCONS_00004346\t5096\t5096\t93.5654\t322.479\n+TCONS_00004347\t5000\t5000\t3.57736\t12.0868\n+TCONS_00004348\t5136\t5136\t425.45\t1478.37\n+TCONS_00004349\t2198\t2198\t29.1022\t40.6809\n+TCONS_00004350\t2326\t2326\t0.44885\t0.668048\n+TCONS_00004351\t2057\t2057\t56.9186\t73.8911\n+TCONS_00004352\t3348\t3348\t15.3114\t33.8511\n+TCONS_00004353\t3300\t3300\t36.2405\t78.8922\n+TCONS_00004354\t3333\t3333\t96.0602\t211.355\n+TCONS_00004355\t3494\t3494\t23.2555\t53.8145\n+TCONS_00004356\t3639\t3639\t54.1566\t130.873\n+TCONS_00004357\t4462\t4462\t520.674\t1561.17\n+TCONS_00004359\t4264\t4264\t40.118\t114.673\n+TCONS_00004360\t4498\t4498\t2.51869\t7.61607\n+TCONS_00004361\t2089\t2089\t4.58538\t6.05642\n+TCONS_00004362\t2126\t2126\t188.206\t253.508\n+TCONS_00004363\t2411\t2411\t58.1801\t90.0886\n+TCONS_00004364\t3586\t3586\t176.834\t420.704\n+TCONS_00004365\t14287\t14287\t730.281\t7261.91\n+TCONS_00004366\t14290\t14290\t118.195\t1175.58\n+TCONS_00004367\t846\t846\t0\t0\n+TCONS_00004368\t3903\t3903\t64.1217\t166.921\n+TCONS_00004369\t3883\t3883\t7.083e-4\t0.00183383\n+TCONS_00004370\t510\t510\t0\t0\n+TCONS_00004371\t8653\t8653\t107.246\t639.306\n+TCONS_00004372\t8587\t8587\t350.665\t2074\n+TCONS_00004373\t3921\t3921\t1.34987\t3.53115\n+TCONS_00004374\t2834\t2834\t116.373\t214.996\n+TCONS_00004375\t1637\t1637\t5.74673\t5.75407\n+TCONS_00004376\t2740\t2740\t223.501\t398.062\n+TCONS_00004377\t2731\t2731\t1127.58\t2001.07\n+TCONS_00004378\t2565\t2565\t1305.74\t2164.03\n+TCONS_00004379\t2574\t2574\t231.398\t384.971\n+TCONS_00004380\t2451\t2451\t6.58024\t10.3752\n+TCONS_00004381\t2617\t2617\t9.29533\t15.747\n+TCONS_00004382\t2388\t2388\t106.963\t163.887\n+TCONS_00004383\t4314\t4314\t15.9207\t46.0705\n+TCONS_00004384\t4492\t4492\t0\t0\n+TCONS_00004385\t1586\t1586\t1.82702\t1.76348\n+TCONS_00004386\t540\t540\t1.06121\t0.239589\n+TCONS_00004387\t738\t738\t0\t0\n+TCONS_00004388\t646\t646\t0\t0\n+TCONS_00004389\t2552\t2552\t31.6687\t52.1938\n+TCONS_00004390\t2791\t2791\t78.0578\t141.837\n+TCONS_00004391\t4088\t4088\t77.2774\t211.274\n+TCONS_00004392\t4129\t4129\t543.731\t1502.3\n+TCONS_00004394\t1768\t1768\t0\t0\n+TCONS_00004395\t697\t697\t13.8243\t4.65544\n+TCONS_00004396\t2041\t2041\t1.55748\t2.00429\n+TCONS_00004397\t5192\t5192\t87.9633\t309.141\n+TCONS_00004398\t1287\t1287\t3618.98\t2728.17\n+TCONS_00004399\t1547\t1547\t170.21\t159.598\n+TCONS_00004400\t1074\t1074\t58.2416\t35.1355\n+TCONS_00004401\t1607\t1607\t31.5673\t30.9381\n+TCONS_00004402\t1631\t1631\t4.37347\t4.3605\n+TCONS_00004403\t1553\t1553\t25.0089\t23.5557\n+TCONS_00004404\t1566\t1566\t410.122\t390.06\n+TCONS_00004405\t1676\t1676\t37.3476\t38.4249\n+TCONS_00004406\t1824\t1824\t33.4016\t37.8598\n+TCONS_00004408\t1244\t1244\t6.57668\t4.75791\n+TCONS_00004409\t934\t934\t13.6156\t6.86636\n+TCONS_00004410\t1607\t1607\t277.546\t272.014\n+TCONS_00004412\t1394\t1394\t26.0146\t21.5789\n+TCONS_00004413\t2160\t2160\t11.2444\t15.4161\n+TCONS_00004414\t1411\t1411\t7.51267\t6.3219900000000004\n+TCONS_00004415\t2054\t2054\t8.6179\t11.1694\n+TCONS_00004416\t2077\t2077\t130.669\t171.48\n+TCONS_00004418\t953\t953\t13.1216\t6.79351\n+TCONS_00004419\t1774\t1774\t0\t0\n+TCONS_00004420\t2239\t2239\t370.852\t529.151\n+TCONS_00004421\t1842\t1842\t492.533\t564.54\n+TCONS_00004422\t2924\t2924\t866.093\t1655.19\n+TCONS_00004423\t2686\t2686\t0.431717\t0.752418\n+TCONS_00004424\t4859\t4859\t0.217532\t0.713293\n+TCONS_00004425\t5799\t5799\t0.883374\t3.48362\n+TCONS_00004426\t3940\t3940\t0\t0\n+TCONS_00004427\t5094\t5094\t1.08287\t3.73065\n+TCONS_00004428\t2703\t2703\t2.26131\t3.96831\n+TCONS_00004429\t2798\t2798\t3.68503\t6.71422\n+TCONS_00004431\t2725\t2725\t2.96653e-4\t5.25201e-4\n+TCONS_00004432\t4461\t4461\t0\t0\n+TCONS_00004433\t4548\t4548\t39.3861\t120.489\n+TCONS_00004434\t4417\t4417\t29.2748\t86.8454\n+TCONS_00004435\t4424\t4424\t15.5536\t46.2177\n+TCONS_00004436\t686\t686\t140.56\t46.2416\n+TCONS_00004439\t2497\t2497\t6.58664\t10.5995\n+TCONS_00004440\t2827\t2827\t7.43093\t13.6917\n+TCONS_00004441\t2683\t2683\t122.443\t213.14\n+TCONS_00004442\t2803\t2803\t1.3733\t2.50705\n+TCONS_00004443\t1653\t1653\t5.04101\t5.10446\n' |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/salmon_cond2_rep2.sf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/salmon_cond2_rep2.sf Tue Jan 24 18:37:14 2023 +0000 |
| b |
| b'@@ -0,0 +1,1093 @@\n+Name\tLength\tEffectiveLength\tTPM\tNumReads\n+TCONS_00000001\t1652\t1652\t0\t0\n+TCONS_00000002\t1488\t1488\t0.621918\t0.654207\n+TCONS_00000003\t1595\t1595\t0\t0\n+TCONS_00000006\t78\t78\t835811\t2.8349\n+TCONS_00000007\t2750\t2750\t400.032\t715.295\n+TCONS_00000008\t4369\t4369\t321.749\t943.567\n+TCONS_00000009\t4272\t4272\t0.202507\t0.579991\n+TCONS_00000010\t937\t937\t0\t0\n+TCONS_00000012\t1584\t1584\t100259\t96630.9\n+TCONS_00000013\t694\t694\t7026.17\t2351.22\n+TCONS_00000015\t1023\t1023\t33690.7\t19110\n+TCONS_00000016\t510\t510\t0\t0\n+TCONS_00000017\t854\t854\t0\t0\n+TCONS_00000018\t701\t701\t92.5542\t31.4301\n+TCONS_00000019\t517\t517\t0\t0\n+TCONS_00000020\t1543\t1543\t82.8399\t77.4408\n+TCONS_00000021\t2682\t2682\t29.7021\t51.6823\n+TCONS_00000022\t3043\t3043\t32.1328\t64.1123\n+TCONS_00000023\t490\t490\t0\t0\n+TCONS_00000024\t2554\t2554\t4.23036\t6.97813\n+TCONS_00000025\t2121\t2121\t0\t0\n+TCONS_00000026\t2560\t2560\t200.885\t332.22\n+TCONS_00000027\t955\t955\t157.065\t81.5396\n+TCONS_00000028\t2003\t2003\t232.477\t292.924\n+TCONS_00000029\t1149\t1149\t188.186\t123.505\n+TCONS_00000030\t2398\t2398\t17.3996\t26.7824\n+TCONS_00000031\t2554\t2554\t7.16309\t11.8158\n+TCONS_00000032\t2293\t2293\t0\t0\n+TCONS_00000033\t662\t662\t1123.84\t350.655\n+TCONS_00000034\t7319\t7319\t1849.52\t9281.01\n+TCONS_00000035\t673\t673\t2.45178\t0.784059\n+TCONS_00000036\t971\t971\t33.0539\t17.5337\n+TCONS_00000037\t1616\t1616\t1.32641\t1.30841\n+TCONS_00000041\t2259\t2259\t13.599\t19.596\n+TCONS_00000042\t2278\t2278\t0.00559733\t0.00814088\n+TCONS_00000043\t2111\t2111\t5.89099\t7.8725\n+TCONS_00000044\t2790\t2790\t267.968\t486.73\n+TCONS_00000045\t3054\t3054\t2.64622\t5.30039\n+TCONS_00000046\t2960\t2960\t18.508\t35.8418\n+TCONS_00000047\t2590\t2590\t33.1576\t55.5385\n+TCONS_00000048\t2684\t2684\t3.56635\t6.21057\n+TCONS_00000049\t2530\t2530\t28.7413\t46.9221\n+TCONS_00000050\t1239\t1239\t730.129\t525.632\n+TCONS_00000051\t1181\t1181\t90.0279\t61.1212\n+TCONS_00000052\t1932\t1932\t14.5404\t17.5913\n+TCONS_00000053\t2192\t2192\t178.383\t248.599\n+TCONS_00000054\t2558\t2558\t1.97961\t3.27103\n+TCONS_00000055\t1747\t1747\t213.471\t230.344\n+TCONS_00000056\t1594\t1594\t104.682\t101.633\n+TCONS_00000057\t1741\t1741\t254.603\t273.647\n+TCONS_00000058\t491\t491\t78.7253\t15.0468\n+TCONS_00000059\t2141\t2141\t91.5793\t124.325\n+TCONS_00000060\t2536\t2536\t447.23\t732.031\n+TCONS_00000061\t3859\t3859\t62.2307\t160.063\n+TCONS_00000062\t2432\t2432\t345.07\t539.444\n+TCONS_00000063\t1939\t1939\t107.648\t130.768\n+TCONS_00000064\t2667\t2667\t175.108\t302.835\n+TCONS_00000065\t1170\t1170\t413.658\t277.622\n+TCONS_00000066\t2611\t2611\t55.8828\t94.4326\n+TCONS_00000067\t2467\t2467\t566.011\t898.843\n+TCONS_00000068\t2329\t2329\t786.459\t1172.2\n+TCONS_00000069\t2616\t2616\t23.0799\t39.0827\n+TCONS_00000070\t1048\t1048\t15.6591\t9.15889\n+TCONS_00000071\t3243\t3243\t0.0178632\t0.0381668\n+TCONS_00000072\t3201\t3201\t73.0075\t153.821\n+TCONS_00000073\t3231\t3231\t9.6167\t20.4656\n+TCONS_00000074\t3026\t3026\t102.204\t202.691\n+TCONS_00000076\t2930\t2930\t24.7046\t47.3178\n+TCONS_00000077\t2890\t2890\t30.1741\t56.9405\n+TCONS_00000078\t3311\t3311\t8.60342\t18.7958\n+TCONS_00000079\t2590\t2590\t94.6701\t158.571\n+TCONS_00000080\t2308\t2308\t0\t0\n+TCONS_00000081\t585\t585\t246.925\t63.6034\n+TCONS_00000082\t1239\t1239\t34.402\t24.7666\n+TCONS_00000083\t1306\t1306\t30.076\t23.0767\n+TCONS_00000084\t905\t905\t0\t0\n+TCONS_00000085\t850\t850\t12.3046\t5.47456\n+TCONS_00000086\t906\t906\t106.944\t51.8153\n+TCONS_00000087\t848\t848\t20.3516\t9.02603\n+TCONS_00000088\t1808\t1808\t69.8784\t78.4149\n+TCONS_00000089\t921\t921\t3.96399\t1.96262\n+TCONS_00000090\t1101\t1101\t31.5351\t19.6262\n+TCONS_00000091\t1925\t1925\t42.8944\t51.6823\n+TCONS_00000092\t2324\t2324\t828.909\t1232.54\n+TCONS_00000093\t2112\t2112\t0\t0\n+TCONS_00000094\t2032\t2032\t0\t0\n+TCONS_00000095\t2009\t2009\t68.5732\t86.694\n+TCONS_00000096\t1745\t1745\t18.6306\t20.0769\n+TCONS_00000097\t1212\t1212\t1.75108\t1.22721\n+TCONS_00000098\t1849\t1849\t22.152\t25.5002\n+TCONS_00000099\t1859\t1859\t16.8841\t19.5555\n+TCONS_00000100\t2089\t2089\t54.3286\t71.7578\n+TCONS_00000101\t1943\t1943\t113.906\t138.692\n+TCONS_00000102\t5706\t5706\t709.915\t2752.9\n+TCONS_00000103\t3093\t3093\t777.628\t1579.03\n+TCONS_00000104\t3203\t3203\t43.3036\t91.2986\n+TCONS_00000105\t4834\t4834\t1.93379\t6.30677\n+TCONS_00000106\t3951\t3951\t1.64288e-4\t4.33247e-4\n+TCONS_00000107\t3'..b'839\t10.3942\n+TCONS_00004332\t2537\t2537\t23.7927\t38.961\n+TCONS_00004333\t927\t927\t80.959\t40.4272\n+TCONS_00004334\t5160\t5160\t0\t0\n+TCONS_00004335\t4949\t4949\t0\t0\n+TCONS_00004336\t5786\t5786\t242.063\t952.36\n+TCONS_00004337\t5850\t5850\t0\t0\n+TCONS_00004338\t6175\t6175\t229.585\t966.402\n+TCONS_00004340\t6283\t6283\t166.823\t714.951\n+TCONS_00004342\t1915\t1915\t27.176\t32.5516\n+TCONS_00004343\t2088\t2088\t28.4611\t37.5716\n+TCONS_00004344\t5241\t5241\t4.2945\t15.2415\n+TCONS_00004345\t5087\t5087\t40.8351\t140.481\n+TCONS_00004346\t5096\t5096\t103.166\t355.568\n+TCONS_00004347\t5000\t5000\t5.52684\t18.6735\n+TCONS_00004348\t5136\t5136\t426.931\t1483.52\n+TCONS_00004349\t2198\t2198\t3.16078\t4.41835\n+TCONS_00004350\t2326\t2326\t1.31865\t1.96262\n+TCONS_00004351\t2057\t2057\t64.756\t84.0656\n+TCONS_00004352\t3348\t3348\t31.623\t69.9135\n+TCONS_00004353\t3300\t3300\t136.687\t297.555\n+TCONS_00004354\t3333\t3333\t0.00274081\t0.00603043\n+TCONS_00004355\t3494\t3494\t22.4161\t51.872\n+TCONS_00004356\t3639\t3639\t45.8456\t110.789\n+TCONS_00004357\t4462\t4462\t518.87\t1555.76\n+TCONS_00004359\t4264\t4264\t6.11996\t17.4933\n+TCONS_00004360\t4498\t4498\t0\t0\n+TCONS_00004361\t2089\t2089\t4.52441\t5.97589\n+TCONS_00004362\t2126\t2126\t169.394\t228.168\n+TCONS_00004363\t2411\t2411\t32.92\t50.9748\n+TCONS_00004364\t3586\t3586\t197.217\t469.197\n+TCONS_00004365\t14287\t14287\t755.99\t7517.56\n+TCONS_00004366\t14290\t14290\t131.468\t1307.6\n+TCONS_00004367\t846\t846\t0\t0\n+TCONS_00004368\t3903\t3903\t84.6913\t220.468\n+TCONS_00004369\t3883\t3883\t0\t0\n+TCONS_00004370\t510\t510\t1.81454\t0.654207\n+TCONS_00004371\t8653\t8653\t185.251\t1104.3\n+TCONS_00004372\t8587\t8587\t224.966\t1330.55\n+TCONS_00004373\t3921\t3921\t5.29009\t13.8384\n+TCONS_00004374\t2834\t2834\t164.66\t304.206\n+TCONS_00004375\t1637\t1637\t0\t0\n+TCONS_00004376\t2740\t2740\t177.331\t315.831\n+TCONS_00004377\t2731\t2731\t1258.05\t2232.61\n+TCONS_00004378\t2565\t2565\t1419.55\t2352.63\n+TCONS_00004379\t2574\t2574\t174.874\t290.933\n+TCONS_00004380\t2451\t2451\t0\t0\n+TCONS_00004381\t2617\t2617\t0\t0\n+TCONS_00004382\t2388\t2388\t76.283\t116.88\n+TCONS_00004383\t4314\t4314\t21.2511\t61.4952\n+TCONS_00004384\t4492\t4492\t0\t0\n+TCONS_00004385\t1586\t1586\t0.92831\t0.896026\n+TCONS_00004386\t540\t540\t10.5196\t2.37501\n+TCONS_00004387\t738\t738\t0\t0\n+TCONS_00004388\t646\t646\t0\t0\n+TCONS_00004389\t2552\t2552\t10.2353\t16.869\n+TCONS_00004390\t2791\t2791\t109.526\t199.017\n+TCONS_00004391\t4088\t4088\t43.8011\t119.751\n+TCONS_00004392\t4129\t4129\t577.809\t1596.46\n+TCONS_00004394\t1768\t1768\t61.9915\t67.8115\n+TCONS_00004395\t697\t697\t0\t0\n+TCONS_00004396\t2041\t2041\t1.5251\t1.96262\n+TCONS_00004397\t5192\t5192\t104.243\t366.356\n+TCONS_00004398\t1287\t1287\t2646.35\t1994.95\n+TCONS_00004399\t1547\t1547\t94.5968\t88.699\n+TCONS_00004400\t1074\t1074\t104.54\t63.0659\n+TCONS_00004401\t1607\t1607\t50.0332\t49.036\n+TCONS_00004402\t1631\t1631\t18.2766\t18.2224\n+TCONS_00004403\t1553\t1553\t9.36654\t8.82229\n+TCONS_00004404\t1566\t1566\t387.15\t368.212\n+TCONS_00004405\t1676\t1676\t52.3524\t53.8627\n+TCONS_00004406\t1824\t1824\t72.2985\t81.9484\n+TCONS_00004408\t1244\t1244\t14.7138\t10.6447\n+TCONS_00004409\t934\t934\t0\t0\n+TCONS_00004410\t1607\t1607\t296.235\t290.331\n+TCONS_00004412\t1394\t1394\t79.1313\t65.6388\n+TCONS_00004413\t2160\t2160\t14.3916\t19.7309\n+TCONS_00004414\t1411\t1411\t12.799\t10.7705\n+TCONS_00004415\t2054\t2054\t6.18476\t8.01588\n+TCONS_00004416\t2077\t2077\t118.072\t154.949\n+TCONS_00004418\t953\t953\t7.77114\t4.02338\n+TCONS_00004419\t1774\t1774\t0\t0\n+TCONS_00004420\t2239\t2239\t199.968\t285.325\n+TCONS_00004421\t1842\t1842\t600.875\t688.722\n+TCONS_00004422\t2924\t2924\t683.304\t1305.86\n+TCONS_00004423\t2686\t2686\t2.26253\t3.94325\n+TCONS_00004424\t4859\t4859\t2.96008\t9.70615\n+TCONS_00004425\t5799\t5799\t0\t0\n+TCONS_00004426\t3940\t3940\t0\t0\n+TCONS_00004427\t5094\t5094\t0.215708\t0.743146\n+TCONS_00004428\t2703\t2703\t0\t0\n+TCONS_00004429\t2798\t2798\t8.25825\t15.0468\n+TCONS_00004431\t2725\t2725\t0\t0\n+TCONS_00004432\t4461\t4461\t0\t0\n+TCONS_00004433\t4548\t4548\t48.5196\t148.429\n+TCONS_00004434\t4417\t4417\t20.4325\t60.614\n+TCONS_00004435\t4424\t4424\t11.1145\t33.0269\n+TCONS_00004436\t686\t686\t127.227\t41.8554\n+TCONS_00004439\t2497\t2497\t7.99159\t12.8604\n+TCONS_00004440\t2827\t2827\t14.0584\t25.903\n+TCONS_00004441\t2683\t2683\t143.47\t249.742\n+TCONS_00004442\t2803\t2803\t0\t0\n+TCONS_00004443\t1653\t1653\t0\t0\n' |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/signalP_results.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/signalP_results.txt Tue Jan 24 18:37:14 2023 +0000 |
| b |
| b"@@ -0,0 +1,3905 @@\n+# SignalP-4.1 euk predictions\n+>TCONS_00000007 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 39 0.130\n+ max. Y 39 0.122\n+ max. S 38 0.314\n+ mean S 1-38 0.114\n+ D 1-38 0.118 0.450 NO\n+Name=TCONS_00000007\tSP='NO' D=0.118 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00000008 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 39 0.130\n+ max. Y 39 0.122\n+ max. S 38 0.314\n+ mean S 1-38 0.114\n+ D 1-38 0.118 0.450 NO\n+Name=TCONS_00000008\tSP='NO' D=0.118 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00000009 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 39 0.130\n+ max. Y 39 0.122\n+ max. S 38 0.314\n+ mean S 1-38 0.114\n+ D 1-38 0.118 0.450 NO\n+Name=TCONS_00000009\tSP='NO' D=0.118 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00000020 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 27 0.186\n+ max. Y 27 0.254\n+ max. S 18 0.608\n+ mean S 1-26 0.355\n+ D 1-26 0.308 0.450 NO\n+Name=TCONS_00000020\tSP='NO' D=0.308 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00000023 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 34 0.110\n+ max. Y 12 0.110\n+ max. S 11 0.122\n+ mean S 1-11 0.112\n+ D 1-11 0.111 0.450 NO\n+Name=TCONS_00000023\tSP='NO' D=0.111 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00000024 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 34 0.110\n+ max. Y 12 0.110\n+ max. S 11 0.122\n+ mean S 1-11 0.112\n+ D 1-11 0.111 0.450 NO\n+Name=TCONS_00000024\tSP='NO' D=0.111 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00000025 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 60 0.110\n+ max. Y 13 0.117\n+ max. S 2 0.175\n+ mean S 1-12 0.125\n+ D 1-12 0.122 0.450 NO\n+Name=TCONS_00000025\tSP='NO' D=0.122 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00000026 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 49 0.112\n+ max. Y 46 0.112\n+ max. S 37 0.123\n+ mean S 1-45 0.105\n+ D 1-45 0.108 0.450 NO\n+Name=TCONS_00000026\tSP='NO' D=0.108 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00000027 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 35 0.154\n+ max. Y 35 0.119\n+ max. S 54 0.119\n+ mean S 1-34 0.095\n+ D 1-34 0.106 0.450 NO\n+Name=TCONS_00000027\tSP='NO' D=0.106 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00000028 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 21 0.345\n+ max. Y 21 0.301\n+ max. S 1 0.362\n+ mean S 1-20 0.252\n+ D 1-20 0.274 0.450 NO\n+Name=TCONS_00000028\tSP='NO' D=0.274 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00000029 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 21 0.345\n+ max. Y 21 0.301\n+ max. S 1 0.362\n+ mean S 1-20 0.252\n+ D 1-20 0.274 0.450 NO\n+Name=TCONS_00000029\tSP='NO' D=0.274 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00000030 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 42 0.111\n+ max. Y 15 0.115\n+ max. S 4 0.155\n+ mean S 1-14 0.118\n+ D 1-14 0.116 0.450 NO\n+Name=TCONS_00000030\tSP='NO' D=0.116 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00000031 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 42 0.111\n+ max. Y 15 0.115\n+ max. S 4 0.155\n+ mean S 1-14 0.118\n+ D 1-14 0.116 0.450 NO\n+Name=TCONS_00000031\tSP='NO' D=0.116 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00000032 \n+# Measure Positi"..b"on Value Cutoff signal peptide?\n+ max. C 24 0.161\n+ max. Y 24 0.123\n+ max. S 1 0.119\n+ mean S 1-23 0.094\n+ D 1-23 0.107 0.450 NO\n+Name=TCONS_00004422\tSP='NO' D=0.107 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00004428 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 41 0.117\n+ max. Y 41 0.109\n+ max. S 40 0.147\n+ mean S 1-40 0.098\n+ D 1-40 0.103 0.450 NO\n+Name=TCONS_00004428\tSP='NO' D=0.103 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00004429 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 20 0.127\n+ max. Y 16 0.290\n+ max. S 14 0.785\n+ mean S 1-15 0.705\n+ D 1-15 0.514 0.450 YES\n+Name=TCONS_00004429\tSP='YES' Cleavage site between pos. 15 and 16: LAA-HA D=0.514 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00004431 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 20 0.127\n+ max. Y 16 0.290\n+ max. S 14 0.785\n+ mean S 1-15 0.705\n+ D 1-15 0.514 0.450 YES\n+Name=TCONS_00004431\tSP='YES' Cleavage site between pos. 15 and 16: LAA-HA D=0.514 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00004433 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 21 0.176\n+ max. Y 21 0.296\n+ max. S 1 0.671\n+ mean S 1-20 0.479\n+ D 1-20 0.395 0.450 NO\n+Name=TCONS_00004433\tSP='NO' D=0.395 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00004434 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 31 0.111\n+ max. Y 11 0.151\n+ max. S 2 0.264\n+ mean S 1-10 0.177\n+ D 1-10 0.165 0.450 NO\n+Name=TCONS_00004434\tSP='NO' D=0.165 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00004435 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 51 0.109\n+ max. Y 67 0.103\n+ max. S 65 0.104\n+ mean S 1-66 0.094\n+ D 1-66 0.098 0.450 NO\n+Name=TCONS_00004435\tSP='NO' D=0.098 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00004436 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 21 0.176\n+ max. Y 21 0.296\n+ max. S 1 0.671\n+ mean S 1-20 0.479\n+ D 1-20 0.395 0.450 NO\n+Name=TCONS_00004436\tSP='NO' D=0.395 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00004439 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 67 0.199\n+ max. Y 67 0.142\n+ max. S 54 0.116\n+ mean S 1-66 0.096\n+ D 1-66 0.117 0.450 NO\n+Name=TCONS_00004439\tSP='NO' D=0.117 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00004440 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 22 0.590\n+ max. Y 22 0.271\n+ max. S 18 0.161\n+ mean S 1-21 0.124\n+ D 1-21 0.192 0.450 NO\n+Name=TCONS_00004440\tSP='NO' D=0.192 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00004441 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 42 0.125\n+ max. Y 42 0.110\n+ max. S 8 0.133\n+ mean S 1-41 0.101\n+ D 1-41 0.105 0.450 NO\n+Name=TCONS_00004441\tSP='NO' D=0.105 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00004442 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 42 0.125\n+ max. Y 42 0.110\n+ max. S 8 0.133\n+ mean S 1-41 0.101\n+ D 1-41 0.105 0.450 NO\n+Name=TCONS_00004442\tSP='NO' D=0.105 D-cutoff=0.450 Networks=SignalP-noTM\n+>TCONS_00004443 \n+# Measure Position Value Cutoff signal peptide?\n+ max. C 65 0.107\n+ max. Y 12 0.119\n+ max. S 1 0.138\n+ mean S 1-11 0.130\n+ D 1-11 0.125 0.450 NO\n+Name=TCONS_00004443\tSP='NO' D=0.125 D-cutoff=0.450 Networks=SignalP-noTM\n\\ No newline at end of file\n" |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/test01.RData |
| b |
| Binary file test-data/test01.RData has changed |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/test02_counts.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test02_counts.tabular Tue Jan 24 18:37:14 2023 +0000 |
| b |
| b'@@ -0,0 +1,355 @@\n+gene_names\tcancer0\tcancer1\thealth0\thealth1\n+AADACL3\t1.33294716142329\t1.60935135697703\t0\t0\n+AADACL4\t0.16565689184278\t0.245447543814652\t0\t0\n+ACAP3\t66.9545762637869\t99.4728681831285\t1393.95324090613\t1183.58827790662\n+ACOT7\t455.514031889104\t625.643253171647\t7395.10823740127\t2889.86502433136\n+ACTL8\t2.25786678564214\t2.8385206089638\t6.29646468356414\t9.65386190076367\n+AGMAT\t14.1868697001226\t20.8082199337387\t56.2113078807145\t41.8419006164206\n+AGRN\t223.424831149421\t331.946548429751\t2144.12485688125\t3783.10646304681\n+AGTRAP\t187.400533886563\t314.973593315019\t1943.78534029914\t2390.03265356525\n+AJAP1\t8.63047529957261\t13.8464275492248\t2.78718070452411\t0\n+AKR7A2\t83.7117317539189\t130.289924823431\t3829.83857542184\t3540.61290523654\n+AKR7A3\t1.86761600752251\t3.58107135446447\t19.1848890894377\t15.2519579815619\n+AKR7L\t1.63323529019925\t1.78518588259504\t12.0382831872031\t11.9429611381668\n+ALDH4A1\t80.0692491307954\t115.615849240505\t588.92974612004\t641.316225550933\n+ALPL\t598.739713486774\t931.026396105693\t12.5179727486086\t145.603586056744\n+ANGPTL7\t0.111187468282468\t0.164742599508691\t11.7533214949055\t12.3890347339164\n+APITD1\t27.9435627190935\t40.1067500091512\t802.720467188703\t663.18564778364\n+ARHGEF10L\t80.3813346280653\t125.687632167421\t575.337403596391\t982.752730025466\n+ARHGEF16\t44.2754028984311\t66.8497008399258\t8.93761413278206\t2.14380019716824\n+ARHGEF19\t115.733727841445\t189.932215231752\t192.61472131494\t216.922297485954\n+ASAP3\t88.368604104536\t144.185270660234\t977.339687032257\t832.468754427446\n+ATAD3A\t170.332210340393\t256.909438164756\t2909.59238880021\t1787.85567999184\n+ATAD3B\t115.009269719842\t186.922563175749\t1204.49289913673\t580.698972738788\n+ATAD3C\t9.18645892844685\t11.1689876678097\t20.3511517744843\t14.9657017546822\n+ATP13A2\t173.079288123976\t259.826155166127\t778.918736405516\t778.83424421371\n+AURKAIP1\t431.089374951588\t734.107961651523\t9367.79479097331\t6368.53564372911\n+B3GALT6\t34.5537089926203\t48.0941285791035\t1107.4652590036\t1344.53791709811\n+C1orf126\t0.748005384270891\t2.19315673139357\t0\t2.02937495588995\n+C1orf127\t0.219649529265469\t1.31728558966594\t0.73417113252224\t0\n+C1orf128\t157.021218105179\t205.564314627884\t2055.87258399552\t1840.70695418312\n+C1orf130\t0.270304535188066\t0.445000989755816\t0\t0.293709236838892\n+C1orf144\t169.905131358614\t236.936379177537\t6169.84439356059\t6172.79967616817\n+C1orf151\t81.934540083501\t106.83864564802\t2316.80019551674\t1742.26068228731\n+C1orf158\t0.306319741118665\t0\t0\t0\n+C1orf159\t25.4472609092091\t27.0936925692478\t255.003897423656\t260.387760636754\n+C1orf167\t0.852445327466635\t1.62734609336196\t4.28017084616318\t20.8037404760945\n+C1orf170\t1.12825925747856\t4.0128035997215\t42.2830759803238\t44.6208842491559\n+C1orf174\t65.3123327213875\t103.529715471474\t1150.25066664382\t1553.57631620601\n+C1orf187\t38.4882619397459\t66.6560127067159\t22.7498270005338\t2.90670998197146\n+C1orf200\t0.140010077377323\t0\t0\t0\n+C1orf201\t16.9572193953188\t29.7070533850009\t301.219367711266\t379.623514344136\n+C1orf211\t14.6209036697657\t26.998386277083\t1.41183164282385\t8.65855898698444\n+C1orf213\t0.518508587606857\t1.88619698952573\t76.5600381962453\t156.763728464001\n+C1orf222\t0.381237303744296\t0.529475492302115\t0\t0\n+C1orf70\t7.51184976845881\t19.8485556995299\t239.879629899723\t290.034472160915\n+C1orf86\t225.001393970245\t375.819392770559\t3491.25500640192\t2865.04772849532\n+C1orf89\t5.10917443855593\t12.0376749429161\t202.484599015937\t212.283237977287\n+C1orf93\t100.534745697611\t160.074553609957\t1576.8889615254\t1358.37868843451\n+CAD\t1.78359239559776\t5.00082342629287\t0\t13.4392425305562\n+CALML6\t2.92860771428337\t5.65982936080012\t0\t2.10905502038753\n+CAMK2N1\t14.2906082102419\t26.1322888570167\t8126.76185609601\t16305.1258047596\n+CAMTA1\t200.588720737929\t253.543060947236\t3055.15380157953\t4100.09091814611\n+CAPZB\t619.112320909139\t991.572432852428\t20316.4731362545\t24041.0162369706\n+CASP9\t51.1870965570691\t80.3510692413285\t340.999216471908\t304.57891159937\n+CASZ1\t13.6330268070182\t19.042062635585\t8.81866733613576\t9.75816312925625\n+CCDC27\t0.0573867205178809\t1.02033468450467\t0.75773394235314\t0\n+CC'..b'32\t11.9362517122089\t2.28760719149588\n+XLOC_000129\t18.772462633958\t29.3468930311443\t353.587071781866\t758.240294777622\n+XLOC_000138\t38.8700741575041\t51.7940496915431\t202.53853151081\t344.095867778729\n+XLOC_000148\t1.57031994775796\t2.0703046333356\t2.54033057482786\t0.518381268897529\n+XLOC_000158\t1.63670091555161\t4.29047267335988\t0\t0\n+XLOC_000173\t1.06214651959231\t1.12407426258865\t0.669622554351972\t7.18675196052498\n+XLOC_000174\t529.705405954172\t9418.1343848515\t3679.99023128108\t22568.9992411476\n+XLOC_000179\t53.0677442654029\t80.9418864284067\t485.640103066908\t724.628699874925\n+XLOC_000187\t1.0725849356793\t1.29123388065767\t26.360772631746\t15.4131952005694\n+XLOC_000188\t485.665022302667\t730.200923926726\t2500.18608736872\t2893.71714995025\n+XLOC_000190\t0.114539036581279\t0.169708372845532\t0\t0\n+XLOC_001217\t130.676612377691\t209.33874703643\t2027.34232722767\t1140.52321249461\n+XLOC_001218\t1.11065103222938\t4.57113901513204\t9.52791266360871\t0\n+XLOC_001219\t0.28644580395248\t0.462998956729158\t11.3705108476242\t19.898838698614\n+XLOC_001220\t76.2580000478759\t118.977904648644\t17.6627820045462\t27.9729729298378\n+XLOC_001222\t126.034325977775\t193.513860913044\t87.3738347178654\t163.72394213182\n+XLOC_001223\t163547.84518143\t150008.962644156\t31341.9338316771\t0\n+XLOC_001225\t163547.84518143\t150008.962644156\t31341.9338316771\t0\n+XLOC_001227\t28.4239434935344\t44.1599898071085\t42.4480653881083\t73.0480407662068\n+XLOC_001228\t2.96779776535697\t2.72934466849826\t37.1746781190191\t53.9434758606289\n+XLOC_001230\t1.04098840207296\t0\t9.44420723023971\t7.24002040593887\n+XLOC_001235\t0.643193954521966\t1.20378544200498\t0\t0\n+XLOC_001241\t4.11476546544828\t7.20519927331771\t27.1926538485809\t19.1088966517602\n+XLOC_001249\t9.59909351607688\t12.2964666116257\t170.271058414378\t55.3105894310116\n+XLOC_001255\t43.8864481692447\t57.2375911584504\t656.756902666893\t1708.04361756199\n+XLOC_001261\t0.90538512843992\t1.62893626076707\t0\t0\n+XLOC_001262\t2.57484095100331\t8.57724811776433\t32.879450200818\t28.7871005595427\n+XLOC_001265\t102.124501928649\t178.840887319719\t260.853867089462\t140.036931233652\n+XLOC_001269\t0.11275216952578\t0.222119105968671\t10.1892351170661\t27.5651269941468\n+XLOC_001271\t0\t0\t0.739963735624112\t0\n+XLOC_001272\t0\t0\t3.40547383237821\t18.2746745328208\n+XLOC_001279\t0\t0.196093126802293\t0\t0\n+XLOC_001300\t29.1309548025757\t32.8750060677505\t61.2454109786738\t99.1536701126289\n+XLOC_001302\t26.859308595584\t46.1638520055266\t48.8092380588883\t91.298890695025\n+XLOC_001321\t304.286653369147\t352.220285459156\t2808.34205445117\t1561.66669448542\n+XLOC_001325\t38.3463137232589\t44.5659670836712\t223.97284590171\t244.287622687443\n+XLOC_001335\t0.500183500127258\t0.594266737589076\t5.3417274447352\t0.450899882954414\n+XLOC_001338\t1730.03542846583\t3865.41697747869\t28354.734013617\t17953.5236839171\n+XLOC_001339\t7.23103916627791\t10.251015971773\t43.8346808379212\t47.6814554489967\n+XLOC_001349\t23.8440839846515\t29.2782663595089\t51.1774249153872\t102.986302873693\n+XLOC_001350\t1.4752288850076\t2.1408032514761\t0.816249598627034\t1.00664968225117\n+XLOC_001351\t21.2015565220575\t33.3290832161605\t1407.51704323402\t2617.27714122475\n+XLOC_001353\t83.4951990071602\t149.319321757687\t624.002928066391\t695.456434884007\n+XLOC_001356\t50.2094341503045\t115.190039740662\t230.807964129475\t606.651426727153\n+XLOC_001372\t1.91582617937623\t2.83861034753068\t14.2153949190097\t24.2174693160748\n+XLOC_001379\t0.0910349755442975\t0.134883347719491\t0\t5.64750205253292\n+XLOC_001388\t0.0532721212125523\t0.236667522431167\t0.70418227693387\t0.539833038602494\n+XLOC_001389\t6.75542956098647\t11.622221273691\t475.397331693707\t735.365654745429\n+XLOC_001394\t0\t0.325668438290865\t0\t0\n+XLOC_001401\t0.184850759376464\t0.27372057669569\t0\t0\n+XLOC_001404\t6.91245087404029\t18.7625395631549\t84.3316006411086\t171.862029782374\n+ZBTB17\t39.465672732615\t62.8537160424089\t792.615674949323\t724.307200079801\n+ZBTB40\t36.5722648528181\t24.6063437546859\t225.002031996727\t308.369466259324\n+ZBTB48\t38.6672531811893\t60.54808278606\t285.548786027533\t290.958457686854\n+ZNF436\t1.88956101189413\t3.81408651722365\t381.877284921004\t509.309870434116\n' |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/test02_samples_annotation.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test02_samples_annotation.tabular Tue Jan 24 18:37:14 2023 +0000 |
| b |
| @@ -0,0 +1,5 @@ +sampleID condition +cancer0 cancer +cancer1 cancer +health0 health +health1 health |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/test03_cancer_counts.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test03_cancer_counts.tabular Tue Jan 24 18:37:14 2023 +0000 |
| b |
| b'@@ -0,0 +1,355 @@\n+Geneid\tcancer0\n+AADACL3\t1.33294716142329\n+AADACL4\t0.16565689184278\n+ACAP3\t66.9545762637869\n+ACOT7\t455.514031889104\n+ACTL8\t2.25786678564214\n+AGMAT\t14.1868697001226\n+AGRN\t223.424831149421\n+AGTRAP\t187.400533886563\n+AJAP1\t8.63047529957261\n+AKR7A2\t83.7117317539189\n+AKR7A3\t1.86761600752251\n+AKR7L\t1.63323529019925\n+ALDH4A1\t80.0692491307954\n+ALPL\t598.739713486774\n+ANGPTL7\t0.111187468282468\n+APITD1\t27.9435627190935\n+ARHGEF10L\t80.3813346280653\n+ARHGEF16\t44.2754028984311\n+ARHGEF19\t115.733727841445\n+ASAP3\t88.368604104536\n+ATAD3A\t170.332210340393\n+ATAD3B\t115.009269719842\n+ATAD3C\t9.18645892844685\n+ATP13A2\t173.079288123976\n+AURKAIP1\t431.089374951588\n+B3GALT6\t34.5537089926203\n+C1orf126\t0.748005384270891\n+C1orf127\t0.219649529265469\n+C1orf128\t157.021218105179\n+C1orf130\t0.270304535188066\n+C1orf144\t169.905131358614\n+C1orf151\t81.934540083501\n+C1orf158\t0.306319741118665\n+C1orf159\t25.4472609092091\n+C1orf167\t0.852445327466635\n+C1orf170\t1.12825925747856\n+C1orf174\t65.3123327213875\n+C1orf187\t38.4882619397459\n+C1orf200\t0.140010077377323\n+C1orf201\t16.9572193953188\n+C1orf211\t14.6209036697657\n+C1orf213\t0.518508587606857\n+C1orf222\t0.381237303744296\n+C1orf70\t7.51184976845881\n+C1orf86\t225.001393970245\n+C1orf89\t5.10917443855593\n+C1orf93\t100.534745697611\n+CAD\t1.78359239559776\n+CALML6\t2.92860771428337\n+CAMK2N1\t14.2906082102419\n+CAMTA1\t200.588720737929\n+CAPZB\t619.112320909139\n+CASP9\t51.1870965570691\n+CASZ1\t13.6330268070182\n+CCDC27\t0.0573867205178809\n+CCNL2\t154.506479643163\n+CDA\t13.5485774691298\n+CDC2L1\t290.944540530384\n+CDC2L2\t170.977132360159\n+CDC42\t203.801007690173\n+CELA2B\t0.159866211673547\n+CHD5\t3.05969618009437\n+CLCN6\t47.6704636085561\n+CLCNKA\t2.63522828591018\n+CLCNKB\t5.15929663864343\n+CLSTN1\t202.476075380806\n+CORT\t2.88722197591461\n+CPSF3L\t295.347158226512\n+CROCC\t78.3541158913447\n+CTNNBIP1\t77.4633730300185\n+CTRC\t0\n+Cort\t1.39537707894365\n+DDI2\t32.8160456278053\n+DDOST\t604.449663575025\n+DFFA\t130.006170003179\n+DFFB\t13.2342440141516\n+DHRS3\t87.0464324268709\n+DNAJC11\t170.344114526107\n+DNAJC16\t19.7622965555186\n+DVL1\t134.516467764835\n+DVL1L1\t3.31326839123532\n+E2F2\t10.4399946081232\n+ECE1\t66.4571391530656\n+EFHD2\t53.7957629609978\n+EIF4G3\t88.0324265767771\n+ENO1\t6558.87666660173\n+EPHA2\t77.3221844026497\n+EPHA8\t7.41680618002836\n+EPHB2\t32.3112950981041\n+ERRFI1\t61.8103776457282\n+ESPN\t19.6610267100338\n+ESPNP\t0.129073180931436\n+EXOSC10\t173.284597941512\n+FAM131C\t2.24876951909219\n+FAM132A\t3.84947896587315\n+FAM41C\t0.302278489637574\n+FAM43B\t5.46152884081911\n+FBLIM1\t111.14573835528\n+FBXO2\t154.152795959943\n+FBXO42\t32.5697215584544\n+FBXO44\t66.872920433567\n+FBXO6\t3.50735527954742\n+FHAD1\t0.921397741797418\n+FUCA1\t17.0659023558552\n+GABRD\t4.99857114177978\n+GALE\t66.7029801712116\n+GLTPD1\t23.9392818646217\n+GNB1\t552.837447538731\n+GPR153\t29.2904210431041\n+GPR157\t6.9246933142833\n+GRHL3\t3.17376836133494\n+H6PD\t9.73184391540445\n+HES2\t0.860500532694876\n+HES3\t187.003719783718\n+HES4\t3.26807877298495\n+HES5\t0.413503700004359\n+HMGCL\t39.2773527873122\n+HNRNPR\t358.051830999552\n+HP1BP3\t139.453393502231\n+HSPB7\t0.394310461505414\n+HSPG2\t121.689737329714\n+HTR1D\t13.8118225729494\n+HTR6\t2.35343259159145\n+ICMT\t166.884696441074\n+ID3\t449.723045510507\n+IFFO2\t11.1211442814015\n+IGSF21\t48.2382101870424\n+IL22RA1\t0.705781326914609\n+IL28RA\t26.6775412932847\n+ISG15\t119.116629191387\n+KCNAB2\t14.472866871752\n+KIAA0090\t75.0221900923905\n+KIAA0495\t53.1784425108188\n+KIAA0562\t23.4536077035124\n+KIAA1751\t0.124854649064705\n+KIAA2013\t87.6070922762549\n+KIF17\t15.2331384334259\n+KIF1B\t78.4463774846293\n+KLHDC7A\t29.4976583180273\n+KLHL17\t88.4149865150737\n+KLHL21\t45.7081683780084\n+LDLRAD2\t3.59538453721335\n+LRRC38\t0.997683514322432\n+LRRC47\t167.727959048214\n+LUZP1\t54.5077436444742\n+LYPLA2\t339.908534559412\n+LZIC\t24.5909618538249\n+MAD2L2\t797.802503952905\n+MASP2\t6.94294362970907\n+MEGF6\t24.9133362230742\n+MFAP2\t570.353630763356\n+MFN2\t109.138239264186\n+MIB2\t72.1921445934075\n+MIIP\t152.156382122545\n+MMEL1\t1.35218731641887\n+MMP23B\t7.44397573330445\n+MORN1\t12.1189773398316\n+MRPL20\t575.672594221529\n+MRTO4\t115.820605846853\n+MST1\t11.436606389674'..b'KHN1\t2.5736879406531\n+PLOD1\t109.603259722424\n+PNRC2\t143.027070406672\n+PQLC2\t38.0703573702872\n+PRAMEF12\t0\n+PRAMEF17\t0\n+PRDM16\t0.611027729076883\n+PRDM2\t18.6581906890874\n+PRKCZ\t117.712024291513\n+PTCHD2\t9.26750946108815\n+PUSL1\t94.6023146270327\n+Pex14\t13.4164623711511\n+RAP1GAP\t20.2795577553702\n+RBP7\t27.4187934555505\n+RCAN3\t17.5062860157843\n+RCC2\t609.224891778857\n+RER1\t95.2926149754708\n+RERE\t124.283460004597\n+RNF186\t0\n+RNF207\t8.17889719501219\n+RPL11\t9264.50338715238\n+RPL22\t548.222657612127\n+RSC1A1\t35.1225700307662\n+SAMD11\t0.975266140467855\n+SCNN1D\t7.71336638783454\n+SDF4\t227.240662691068\n+SDHB\t197.976221969527\n+SFRS13A\t205.264479559859\n+SH2D5\t32.9533496689486\n+SKI\t92.3897739483106\n+SLC25A33\t24.6601200693325\n+SLC25A34\t1.29825648901777\n+SLC2A5\t0.260483267812907\n+SLC2A7\t0.0850275751047418\n+SLC35E2\t148.195682693737\n+SLC45A1\t4.67322725382105\n+SNORA59B\t70.9971332886744\n+SPATA21\t0\n+SPEN\t44.739917755163\n+SPSB1\t9.36693255552896\n+SRM\t630.872113478932\n+SRRM1\t206.293153123351\n+SSU72\t421.885125021761\n+TARDBP\t338.973195508834\n+TAS1R1\t0.104532874176939\n+TAS1R3\t0.383670837382131\n+TCEA3\t0.342791887378255\n+TCEB3\t66.3457181111293\n+THAP3\t26.4479436136909\n+TMCO4\t7.28461701024201\n+TMEM201\t46.7212584959948\n+TMEM51\t27.3222662946233\n+TMEM52\t34.5935874213324\n+TMEM82\t3.19694443891178\n+TNFRSF14\t0.233903600408319\n+TNFRSF18\t4.12474694120627\n+TNFRSF1B\t3.51012702902294\n+TNFRSF25\t36.1105818392679\n+TNFRSF4\t0.075773999356543\n+TNFRSF8\t49.9796942851226\n+TNFRSF9\t0\n+TP73\t8.46926746361882\n+TPRG1L\t58.8362301900852\n+TTLL10\t1.73177686366537\n+UBE2J2\t92.7379743475829\n+UBE4B\t143.430326774727\n+UBIAD1\t38.0149429703894\n+UBR4\t303.552035743086\n+UBXN10\t1.79331869688632\n+USP48\t103.071349941227\n+UTS2\t0\n+VAMP3\t57.7621237024533\n+VPS13D\t20.9475855266294\n+VWA1\t63.5031219959163\n+VWA5B1\t2.22741438314528\n+WDR8\t77.6406065347677\n+WNT4\t7.61041931023364\n+XLOC_000001\t0\n+XLOC_000004\t163547.84518143\n+XLOC_000005\t81.6040495959105\n+XLOC_000008\t10486.3888872409\n+XLOC_000009\t807.284193808201\n+XLOC_000011\t3765.29512811875\n+XLOC_000012\t24.6631346886458\n+XLOC_000013\t3.27907501233071\n+XLOC_000014\t2.81993899604295\n+XLOC_000020\t3.78219361228549\n+XLOC_000021\t0.241006945522658\n+XLOC_000031\t66.3390004948641\n+XLOC_000032\t6.63384782773452\n+XLOC_000037\t0.812922956153769\n+XLOC_000040\t8.10149269013884\n+XLOC_000041\t10.6716692892124\n+XLOC_000042\t0.320111031048259\n+XLOC_000046\t13.0167464005023\n+XLOC_000058\t7.94858977433594\n+XLOC_000060\t3.70976322927918\n+XLOC_000064\t1.80705064391604\n+XLOC_000099\t26.9427447128\n+XLOC_000129\t18.772462633958\n+XLOC_000138\t38.8700741575041\n+XLOC_000148\t1.57031994775796\n+XLOC_000158\t1.63670091555161\n+XLOC_000173\t1.06214651959231\n+XLOC_000174\t529.705405954172\n+XLOC_000179\t53.0677442654029\n+XLOC_000187\t1.0725849356793\n+XLOC_000188\t485.665022302667\n+XLOC_000190\t0.114539036581279\n+XLOC_001217\t130.676612377691\n+XLOC_001218\t1.11065103222938\n+XLOC_001219\t0.28644580395248\n+XLOC_001220\t76.2580000478759\n+XLOC_001222\t126.034325977775\n+XLOC_001223\t163547.84518143\n+XLOC_001225\t163547.84518143\n+XLOC_001227\t28.4239434935344\n+XLOC_001228\t2.96779776535697\n+XLOC_001230\t1.04098840207296\n+XLOC_001235\t0.643193954521966\n+XLOC_001241\t4.11476546544828\n+XLOC_001249\t9.59909351607688\n+XLOC_001255\t43.8864481692447\n+XLOC_001261\t0.90538512843992\n+XLOC_001262\t2.57484095100331\n+XLOC_001265\t102.124501928649\n+XLOC_001269\t0.11275216952578\n+XLOC_001271\t0\n+XLOC_001272\t0\n+XLOC_001279\t0\n+XLOC_001300\t29.1309548025757\n+XLOC_001302\t26.859308595584\n+XLOC_001321\t304.286653369147\n+XLOC_001325\t38.3463137232589\n+XLOC_001335\t0.500183500127258\n+XLOC_001338\t1730.03542846583\n+XLOC_001339\t7.23103916627791\n+XLOC_001349\t23.8440839846515\n+XLOC_001350\t1.4752288850076\n+XLOC_001351\t21.2015565220575\n+XLOC_001353\t83.4951990071602\n+XLOC_001356\t50.2094341503045\n+XLOC_001372\t1.91582617937623\n+XLOC_001379\t0.0910349755442975\n+XLOC_001388\t0.0532721212125523\n+XLOC_001389\t6.75542956098647\n+XLOC_001394\t0\n+XLOC_001401\t0.184850759376464\n+XLOC_001404\t6.91245087404029\n+ZBTB17\t39.465672732615\n+ZBTB40\t36.5722648528181\n+ZBTB48\t38.6672531811893\n+ZNF436\t1.88956101189413\n' |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/test03_health_counts.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test03_health_counts.tabular Tue Jan 24 18:37:14 2023 +0000 |
| b |
| b'@@ -0,0 +1,355 @@\n+Geneid\thealth0\n+AADACL3\t0\n+AADACL4\t0\n+ACAP3\t1393.95324090613\n+ACOT7\t7395.10823740127\n+ACTL8\t6.29646468356414\n+AGMAT\t56.2113078807145\n+AGRN\t2144.12485688125\n+AGTRAP\t1943.78534029914\n+AJAP1\t2.78718070452411\n+AKR7A2\t3829.83857542184\n+AKR7A3\t19.1848890894377\n+AKR7L\t12.0382831872031\n+ALDH4A1\t588.92974612004\n+ALPL\t12.5179727486086\n+ANGPTL7\t11.7533214949055\n+APITD1\t802.720467188703\n+ARHGEF10L\t575.337403596391\n+ARHGEF16\t8.93761413278206\n+ARHGEF19\t192.61472131494\n+ASAP3\t977.339687032257\n+ATAD3A\t2909.59238880021\n+ATAD3B\t1204.49289913673\n+ATAD3C\t20.3511517744843\n+ATP13A2\t778.918736405516\n+AURKAIP1\t9367.79479097331\n+B3GALT6\t1107.4652590036\n+C1orf126\t0\n+C1orf127\t0.73417113252224\n+C1orf128\t2055.87258399552\n+C1orf130\t0\n+C1orf144\t6169.84439356059\n+C1orf151\t2316.80019551674\n+C1orf158\t0\n+C1orf159\t255.003897423656\n+C1orf167\t4.28017084616318\n+C1orf170\t42.2830759803238\n+C1orf174\t1150.25066664382\n+C1orf187\t22.7498270005338\n+C1orf200\t0\n+C1orf201\t301.219367711266\n+C1orf211\t1.41183164282385\n+C1orf213\t76.5600381962453\n+C1orf222\t0\n+C1orf70\t239.879629899723\n+C1orf86\t3491.25500640192\n+C1orf89\t202.484599015937\n+C1orf93\t1576.8889615254\n+CAD\t0\n+CALML6\t0\n+CAMK2N1\t8126.76185609601\n+CAMTA1\t3055.15380157953\n+CAPZB\t20316.4731362545\n+CASP9\t340.999216471908\n+CASZ1\t8.81866733613576\n+CCDC27\t0.75773394235314\n+CCNL2\t1152.06879708577\n+CDA\t176.302023749904\n+CDC2L1\t3112.41609597224\n+CDC2L2\t2067.4280282674\n+CDC42\t11564.694795414\n+CELA2B\t0\n+CHD5\t5.15789578430315\n+CLCN6\t574.076737032054\n+CLCNKA\t0.678927560712282\n+CLCNKB\t2.32675789513133\n+CLSTN1\t5093.23897792429\n+CORT\t8.23077012212674\n+CPSF3L\t3790.65155484617\n+CROCC\t165.209683502876\n+CTNNBIP1\t541.243734816617\n+CTRC\t2.62147985845083\n+Cort\t5.2816642560574\n+DDI2\t254.874844668067\n+DDOST\t13665.5007422144\n+DFFA\t1325.04655393129\n+DFFB\t127.460095995143\n+DHRS3\t1019.4715318943\n+DNAJC11\t2130.43084610145\n+DNAJC16\t344.527403240069\n+DVL1\t2152.3813715147\n+DVL1L1\t59.8262158993051\n+E2F2\t97.2088092893749\n+ECE1\t6832.6483396322\n+EFHD2\t2778.28294353325\n+EIF4G3\t2013.10224443396\n+ENO1\t93534.3399845077\n+EPHA2\t1390.10455203221\n+EPHA8\t0\n+EPHB2\t1707.12636087386\n+ERRFI1\t2062.3064004349\n+ESPN\t0.451453505296478\n+ESPNP\t0\n+EXOSC10\t1944.55712530741\n+FAM131C\t58.9032768191879\n+FAM132A\t128.448491513426\n+FAM41C\t4.95347952144023\n+FAM43B\t2.51816321877196\n+FBLIM1\t1673.86297734934\n+FBXO2\t53.5029060412522\n+FBXO42\t573.623814141438\n+FBXO44\t440.70354833884\n+FBXO6\t375.388875588851\n+FHAD1\t3.92992882180617\n+FUCA1\t173.703225947981\n+GABRD\t0.865565912204043\n+GALE\t1069.52511368286\n+GLTPD1\t930.45330751506\n+GNB1\t17713.2729458483\n+GPR153\t1159.24045408154\n+GPR157\t130.905914635676\n+GRHL3\t0.648123796243081\n+H6PD\t1098.37928461226\n+HES2\t2.59604614402101\n+HES3\t0\n+HES4\t11.5504692743939\n+HES5\t0\n+HMGCL\t1688.82684523087\n+HNRNPR\t6385.71855992608\n+HP1BP3\t4186.94412612279\n+HSPB7\t948.162427438671\n+HSPG2\t2789.41615140344\n+HTR1D\t0\n+HTR6\t0\n+ICMT\t2794.81710553285\n+ID3\t1856.58321013501\n+IFFO2\t254.481027389179\n+IGSF21\t0\n+IL22RA1\t5.34585936395826\n+IL28RA\t0\n+ISG15\t3105.38902825296\n+KCNAB2\t98.0568372347768\n+KIAA0090\t2619.54097689511\n+KIAA0495\t301.178753240637\n+KIAA0562\t552.955561310365\n+KIAA1751\t0\n+KIAA2013\t2235.34892030079\n+KIF17\t62.825982814168\n+KIF1B\t958.82950446031\n+KLHDC7A\t0\n+KLHL17\t402.664189240798\n+KLHL21\t1140.79410997292\n+LDLRAD2\t76.1340375265393\n+LRRC38\t0\n+LRRC47\t1609.60980616476\n+LUZP1\t793.059726494864\n+LYPLA2\t1769.12671671444\n+LZIC\t1005.55759760837\n+MAD2L2\t3002.54966649886\n+MASP2\t17.3641720890563\n+MEGF6\t107.890965396316\n+MFAP2\t4072.22816859979\n+MFN2\t3384.37411958815\n+MIB2\t548.104608562341\n+MIIP\t749.357895700436\n+MMEL1\t1.9457853553284\n+MMP23B\t42.2011921224724\n+MORN1\t117.104726780606\n+MRPL20\t10475.7619523782\n+MRTO4\t2266.6396732955\n+MST1\t18.1752386648597\n+MSTP9\t3.65209942678968\n+MTHFR\t582.652443982103\n+MTOR\t941.518274269282\n+MUL1\t1786.27725008401\n+MXRA8\t16870.3622806594\n+MYOM3\t0\n+NADK\t1436.260234407\n+NBL1\t15872.8448293203\n+NBPF1\t1706.92782325294\n+NBPF3\t363.760809561629\n+NECAP2\t3701.02434454676\n+NIPAL3\t1308.81945494026\n+NMNAT1\t314.687302277864\n+NOC2L\t3237.14842462\n+NOL9\t399.0'..b'\t183.485391801705\n+PINK1\t2692.36077455866\n+PLA2G2A\t22.9259041929206\n+PLA2G2F\t0\n+PLA2G5\t277.115482877212\n+PLCH2\t5.22902173840885\n+PLEKHG5\t107.045403068473\n+PLEKHM2\t2597.10278065526\n+PLEKHN1\t80.117711730481\n+PLOD1\t7647.61830726864\n+PNRC2\t2011.01065422974\n+PQLC2\t714.709789866736\n+PRAMEF12\t0\n+PRAMEF17\t0\n+PRDM16\t7.62453585986095\n+PRDM2\t394.131386140751\n+PRKCZ\t53.2817718056418\n+PTCHD2\t1.20260777463017\n+PUSL1\t1102.09270198373\n+Pex14\t583.441949667253\n+RAP1GAP\t1.93869267311573\n+RBP7\t22.1452327263775\n+RCAN3\t305.126521225719\n+RCC2\t1398.04583673645\n+RER1\t4103.2887729276\n+RERE\t1692.02943382284\n+RNF186\t0\n+RNF207\t54.0689440848903\n+RPL11\t120354.990597382\n+RPL22\t9672.8039620794\n+RSC1A1\t304.983855853392\n+SAMD11\t45.0300230436727\n+SCNN1D\t63.1275559900522\n+SDF4\t11192.2468917904\n+SDHB\t5863.32070994542\n+SFRS13A\t2681.6216041\n+SH2D5\t461.673162743305\n+SKI\t1927.52535349287\n+SLC25A33\t384.468466133855\n+SLC25A34\t13.5765083834194\n+SLC2A5\t16.3041560887102\n+SLC2A7\t0\n+SLC35E2\t2067.76811117078\n+SLC45A1\t209.893713081992\n+SNORA59B\t0\n+SPATA21\t0\n+SPEN\t370.216859396859\n+SPSB1\t1069.35809905486\n+SRM\t13885.6472427043\n+SRRM1\t1880.1932053956\n+SSU72\t7183.53255691694\n+TARDBP\t3389.02992475779\n+TAS1R1\t2.07586161450828\n+TAS1R3\t3.17808783001526\n+TCEA3\t697.871844834797\n+TCEB3\t1421.63855158543\n+THAP3\t610.415901745808\n+TMCO4\t686.596981615835\n+TMEM201\t483.629851870259\n+TMEM51\t615.525571093196\n+TMEM52\t23.2189296396117\n+TMEM82\t0\n+TNFRSF14\t757.172163875933\n+TNFRSF18\t22.6557540136091\n+TNFRSF1B\t1111.85800567783\n+TNFRSF25\t36.5881699419189\n+TNFRSF4\t6.79357920008104\n+TNFRSF8\t17.6154690266992\n+TNFRSF9\t1.77370767678915\n+TP73\t9.64068706122226\n+TPRG1L\t3064.62673856174\n+TTLL10\t0\n+UBE2J2\t2709.58020944209\n+UBE4B\t1536.28340626825\n+UBIAD1\t437.664397219596\n+UBR4\t2252.79227409763\n+UBXN10\t1.0834421848588\n+USP48\t1549.29896497382\n+UTS2\t0\n+VAMP3\t6927.79406589322\n+VPS13D\t348.297196578629\n+VWA1\t383.721886311972\n+VWA5B1\t0\n+WDR8\t661.677527392987\n+WNT4\t0\n+XLOC_000001\t12.3070651310389\n+XLOC_000004\t31341.9338316771\n+XLOC_000005\t63.7204722280739\n+XLOC_000008\t52511.5387324361\n+XLOC_000009\t3024.76545173384\n+XLOC_000011\t18029.8531686299\n+XLOC_000012\t333.581836425517\n+XLOC_000013\t65.2509443529865\n+XLOC_000014\t0.528120197752992\n+XLOC_000020\t127.598339288124\n+XLOC_000021\t0\n+XLOC_000031\t554.345368683344\n+XLOC_000032\t0\n+XLOC_000037\t0\n+XLOC_000040\t75.3048419278165\n+XLOC_000041\t50.4399805977379\n+XLOC_000042\t20.3091064417467\n+XLOC_000046\t95.0999386735299\n+XLOC_000058\t57.347962726739\n+XLOC_000060\t4.47183702697288\n+XLOC_000064\t0.340359169837346\n+XLOC_000099\t11.9362517122089\n+XLOC_000129\t353.587071781866\n+XLOC_000138\t202.53853151081\n+XLOC_000148\t2.54033057482786\n+XLOC_000158\t0\n+XLOC_000173\t0.669622554351972\n+XLOC_000174\t3679.99023128108\n+XLOC_000179\t485.640103066908\n+XLOC_000187\t26.360772631746\n+XLOC_000188\t2500.18608736872\n+XLOC_000190\t0\n+XLOC_001217\t2027.34232722767\n+XLOC_001218\t9.52791266360871\n+XLOC_001219\t11.3705108476242\n+XLOC_001220\t17.6627820045462\n+XLOC_001222\t87.3738347178654\n+XLOC_001223\t31341.9338316771\n+XLOC_001225\t31341.9338316771\n+XLOC_001227\t42.4480653881083\n+XLOC_001228\t37.1746781190191\n+XLOC_001230\t9.44420723023971\n+XLOC_001235\t0\n+XLOC_001241\t27.1926538485809\n+XLOC_001249\t170.271058414378\n+XLOC_001255\t656.756902666893\n+XLOC_001261\t0\n+XLOC_001262\t32.879450200818\n+XLOC_001265\t260.853867089462\n+XLOC_001269\t10.1892351170661\n+XLOC_001271\t0.739963735624112\n+XLOC_001272\t3.40547383237821\n+XLOC_001279\t0\n+XLOC_001300\t61.2454109786738\n+XLOC_001302\t48.8092380588883\n+XLOC_001321\t2808.34205445117\n+XLOC_001325\t223.97284590171\n+XLOC_001335\t5.3417274447352\n+XLOC_001338\t28354.734013617\n+XLOC_001339\t43.8346808379212\n+XLOC_001349\t51.1774249153872\n+XLOC_001350\t0.816249598627034\n+XLOC_001351\t1407.51704323402\n+XLOC_001353\t624.002928066391\n+XLOC_001356\t230.807964129475\n+XLOC_001372\t14.2153949190097\n+XLOC_001379\t0\n+XLOC_001388\t0.70418227693387\n+XLOC_001389\t475.397331693707\n+XLOC_001394\t0\n+XLOC_001401\t0\n+XLOC_001404\t84.3316006411086\n+ZBTB17\t792.615674949323\n+ZBTB40\t225.002031996727\n+ZBTB48\t285.548786027533\n+ZNF436\t381.877284921004\n' |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/test04.RData |
| b |
| Binary file test-data/test04.RData has changed |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/test04_summary.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test04_summary.tabular Tue Jan 24 18:37:14 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Comparison nrIsoforms nrSwitches nrGenes +cancer vs health 91 70 54 |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/test06_consequences_enrichment.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test06_consequences_enrichment.tabular Tue Jan 24 18:37:14 2023 +0000 |
| b |
| @@ -0,0 +1,6 @@ +condition_1 condition_2 conseqPair feature propOfRelevantEvents propCiLo propCiHi propPval nUp nDown propQval Significant +cancer health NMD_status NMD insensitive (paired with NMD sensitive) 0.333333333333333 0.00840375865961264 0.905700675949754 1 1 2 1 FALSE +cancer health intron_retention Intron retention gain (paired with Intron retention loss) 0.25 0.0548606445279928 0.571858461878189 0.14599609375 3 9 0.72998046875 FALSE +cancer health isoform_length Length gain (paired with Length loss) 0.423076923076923 0.233521983127443 0.630819619076033 0.557197093963623 11 15 0.928661823272706 FALSE +cancer health tss Tss more downstream (paired with Tss more upstream) 0.575757575757576 0.392153016187885 0.745238177265304 0.486850241664797 19 14 0.928661823272706 FALSE +cancer health tts Tts more downstream (paired with Tts more upstream) 0.5 0.210944638239297 0.789055361760703 1 6 6 1 FALSE |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/test06_consequences_summary.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test06_consequences_summary.tabular Tue Jan 24 18:37:14 2023 +0000 |
| b |
| @@ -0,0 +1,19 @@ +Comparison featureCompared switchConsequence nrGenesWithConsequences nrIsoWithConsequences +cancer vs health Intron +retention Intron retention gain 3 5 +cancer vs health Intron +retention Intron retention loss 9 11 +cancer vs health Isoform seq +similarity Length gain 11 17 +cancer vs health Isoform seq +similarity Length loss 15 26 +cancer vs health NMD +status NMD insensitive 1 3 +cancer vs health NMD +status NMD sensitive 2 2 +cancer vs health Tss Tss more downstream 19 30 +cancer vs health Tss Tss more upstream 14 29 +cancer vs health Tts Tts more downstream 6 13 +cancer vs health Tts Tts more upstream 6 8 +cancer vs health ORF +genomic Any consequence 0 0 |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/test06_splicing_enrichment.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test06_splicing_enrichment.tabular Tue Jan 24 18:37:14 2023 +0000 |
| b |
| @@ -0,0 +1,22 @@ +condition_1 condition_2 AStype nUp nDown propUp propUpCiLo propUpCiHi propUpPval propUpQval Significant Comparison +cancer health A3 gain (paired with A3 loss) 15 8 0.652173913043478 0.427343963036494 0.83623640162505 0.210039615631104 0.367569327354431 FALSE cancer +vs +health +cancer health A5 gain (paired with A5 loss) 9 6 0.6 0.322869766206282 0.836635676140487 0.60723876953125 0.60723876953125 FALSE cancer +vs +health +cancer health ATSS gain (paired with ATSS loss) 19 13 0.59375 0.406449246576476 0.763015899448257 0.377085587475449 0.495082259178162 FALSE cancer +vs +health +cancer health ATTS gain (paired with ATTS loss) 4 11 0.266666666666667 0.0778715462910436 0.551003241036971 0.11846923828125 0.340657552083334 FALSE cancer +vs +health +cancer health ES (paired with EI) 10 15 0.4 0.211254806465142 0.61334650374316 0.42435622215271 0.495082259178162 FALSE cancer +vs +health +cancer health IR gain (paired with IR loss) 3 9 0.25 0.0548606445279928 0.571858461878189 0.14599609375 0.340657552083334 FALSE cancer +vs +health +cancer health MES (paired with MEI) 2 8 0.2 0.0252107263268334 0.556095462307641 0.109375 0.340657552083334 FALSE cancer +vs +health |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/test06_splicing_summary.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test06_splicing_summary.tabular Tue Jan 24 18:37:14 2023 +0000 |
| b |
| @@ -0,0 +1,17 @@ +Comparison AStype splicingResult nrGenesWithConsequences nrIsoWithConsequences +cancer vs health A3 A3 in isoform used less 16 19 +cancer vs health A3 A3 in isoform used more 23 30 +cancer vs health A5 A5 in isoform used less 11 13 +cancer vs health A5 A5 in isoform used more 14 16 +cancer vs health ATSS ATSS in isoform used less 20 26 +cancer vs health ATSS ATSS in isoform used more 26 34 +cancer vs health ATTS ATTS in isoform used less 14 14 +cancer vs health ATTS ATTS in isoform used more 6 6 +cancer vs health ES ES in isoform used less 28 32 +cancer vs health ES ES in isoform used more 21 25 +cancer vs health IR IR in isoform used less 10 10 +cancer vs health IR IR in isoform used more 3 4 +cancer vs health MEE MEE in isoform used less 0 0 +cancer vs health MEE MEE in isoform used more 0 0 +cancer vs health MES MES in isoform used less 9 10 +cancer vs health MES MES in isoform used more 3 5 |
| b |
| diff -r 000000000000 -r f3fefb6d8254 test-data/test06_switching.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test06_switching.tabular Tue Jan 24 18:37:14 2023 +0000 |
| b |
| @@ -0,0 +1,55 @@ +gene_ref gene_id gene_name condition_1 condition_2 gene_switch_q_value switchConsequencesGene Rank +geneComp_00000066 CLSTN1 CLSTN1 cancer health 2.63840734749711e-51 FALSE 1 +geneComp_00000167 NADK NADK cancer health 5.98021460938895e-40 TRUE 2 +geneComp_00000210 PRKCZ PRKCZ cancer health 4.18324640310234e-37 TRUE 3 +geneComp_00000222 RPL11 RPL11 cancer health 2.39911661782576e-29 TRUE 4 +geneComp_00000227 SDF4 SDF4 cancer health 2.62564234344567e-28 TRUE 5 +geneComp_00000243 SRRM1 SRRM1 cancer health 7.11497254534458e-22 TRUE 6 +geneComp_00000017 ARHGEF10L ARHGEF10L cancer health 7.07643322536192e-20 TRUE 7 +geneComp_00000080 DVL1 DVL1 cancer health 2.7041623161036e-19 TRUE 8 +geneComp_00000138 KIF1B KIF1B cancer health 8.83353225639552e-16 TRUE 9 +geneComp_00000058 CDC2L1 CDC2L1 cancer health 5.02785283461027e-13 NA 10 +geneComp_00000019 ARHGEF19 ARHGEF19 cancer health 3.43190474162283e-12 TRUE 11 +geneComp_00000254 TMEM52 TMEM52 cancer health 9.43836095793092e-12 TRUE 12 +geneComp_00000101 FBXO44 FBXO44 cancer health 1.25146337218935e-11 TRUE 13 +geneComp_00000189 PER3 PER3 cancer health 2.618343550887e-11 TRUE 14 +geneComp_00000219 RERE RERE cancer health 9.86048379542823e-11 TRUE 15 +geneComp_00000003 ACAP3 ACAP3 cancer health 3.66320856918666e-08 TRUE 16 +geneComp_00000281 XLOC_000005 NA cancer health 6.83756168564135e-08 TRUE 17 +geneComp_00000301 XLOC_000129 NA cancer health 1.89169990108601e-07 TRUE 18 +geneComp_00000085 EIF4G3 EIF4G3 cancer health 9.53210349628728e-07 TRUE 19 +geneComp_00000277 WDR8 WDR8 cancer health 2.4050379356366e-06 TRUE 20 +geneComp_00000200 PLEKHG5 PLEKHG5 cancer health 2.65200395744161e-06 TRUE 21 +geneComp_00000165 MXRA8 MXRA8 cancer health 4.09018221463055e-06 TRUE 22 +geneComp_00000194 PIK3CD PIK3CD cancer health 4.26262542329329e-06 TRUE 23 +geneComp_00000118 HNRNPR HNRNPR cancer health 4.43094440336388e-06 NA 24 +geneComp_00000323 XLOC_001249 NA cancer health 5.97869364244676e-06 TRUE 25 +geneComp_00000342 XLOC_001353 NA cancer health 1.47897331984417e-05 TRUE 26 +geneComp_00000153 MIB2 MIB2 cancer health 1.85010676533132e-05 TRUE 27 +geneComp_00000004 ACOT7 ACOT7 cancer health 2.22089528793497e-05 TRUE 28 +geneComp_00000119 HP1BP3 HP1BP3 cancer health 3.95360727622295e-05 TRUE 29 +geneComp_00000352 ZBTB40 ZBTB40 cancer health 7.08120622533635e-05 FALSE 30 +geneComp_00000069 CROCC CROCC cancer health 0.00035468174423336 NA 31 +geneComp_00000142 LDLRAD2 LDLRAD2 cancer health 0.000443465792700213 TRUE 32 +geneComp_00000053 CASP9 CASP9 cancer health 0.0004985861544369 TRUE 33 +geneComp_00000077 DHRS3 DHRS3 cancer health 0.00050532341155672 TRUE 34 +geneComp_00000261 TNFRSF8 TNFRSF8 cancer health 0.00069495698171926 TRUE 35 +geneComp_00000267 UBE4B UBE4B cancer health 0.00069495698171926 TRUE 36 +geneComp_00000285 XLOC_000012 NA cancer health 0.00069495698171926 TRUE 37 +geneComp_00000083 ECE1 ECE1 cancer health 0.000730501167981291 TRUE 38 +geneComp_00000172 NIPAL3 NIPAL3 cancer health 0.000884959331769316 TRUE 39 +geneComp_00000252 TMEM201 TMEM201 cancer health 0.00130127619274632 TRUE 40 +geneComp_00000106 GALE GALE cancer health 0.00190711749673494 TRUE 41 +geneComp_00000056 CCNL2 CCNL2 cancer health 0.00213211505312704 TRUE 42 +geneComp_00000156 MMP23B MMP23B cancer health 0.00220763192701029 TRUE 43 +geneComp_00000223 RPL22 RPL22 cancer health 0.00414604315547501 TRUE 44 +geneComp_00000140 KLHL17 KLHL17 cancer health 0.0043156399415831 NA 45 +geneComp_00000131 KCNAB2 KCNAB2 cancer health 0.00450582195570915 TRUE 46 +geneComp_00000169 NBPF1 NBPF1 cancer health 0.00603768129678154 NA 47 +geneComp_00000132 KIAA0090 KIAA0090 cancer health 0.00637311306884828 NA 48 +geneComp_00000216 RCAN3 RCAN3 cancer health 0.00655117020038015 TRUE 49 +geneComp_00000160 MST1 MST1 cancer health 0.00970833700285509 TRUE 50 +geneComp_00000137 KIF17 KIF17 cancer health 0.020741914385789 TRUE 51 +geneComp_00000229 SFRS13A SFRS13A cancer health 0.035326111600384 TRUE 52 +geneComp_00000257 TNFRSF18 TNFRSF18 cancer health 0.0453089266879188 TRUE 53 +geneComp_00000256 TNFRSF14 TNFRSF14 cancer health 0.0490680824638558 TRUE 54 |
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| diff -r 000000000000 -r f3fefb6d8254 test-data/transcriptome.fasta.gz |
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