| Next changeset 1:3e2606fa85bf (2020-07-25) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" |
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added:
msstats.xml test-data/MSstats ProfilePlot.pdf test-data/QC_plot.pdf test-data/comparison_matrix.csv test-data/condition_plot.pdf test-data/msstats_testfile.tsv test-data/msstats_testfile.txt test-data/profile_wsum_plot.pdf test-data/qq_plot.pdf test-data/residual_plot.pdf test-data/residualplot.pdf test-data/test_MQ_annotation.txt test-data/test_MQ_evidence.tabular test-data/test_MQ_group12_comparison_matrix.csv test-data/test_MQ_proteingroups.tabular test-data/test_swath_annotations.tabular test-data/test_swath_group12_comparison_matrix.csv test-data/test_swath_input_data.tabular test-data/volcanoplot.pdf |
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| diff -r 000000000000 -r 80b40b9ab835 msstats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msstats.xml Sat Jul 25 13:21:47 2020 -0400 |
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| b'@@ -0,0 +1,782 @@\n+<tool id="msstats" name="MSstats" version="@VERSION@.0" python_template_version="3.5">\n+ <description>statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry</description>\n+ <macros>\n+ <token name="@VERSION@">3.20.1</token>\n+ <xml name="useUniquePeptide">\n+ <param name="useUniquePeptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="remove peptides that are assigned for more than one proteins" help="We assume to use unique peptide for each protein"/>\n+ </xml>\n+ <xml name="summaryforMultipleRows">\n+ <param name="summaryforMultipleRows" type="select" label="Summary for MultipleRows" help="summaryforMultipleRows - when there are multiple measurements for certain feature and certain run, use highest or sum of all">\n+ <option value="max" selected="true">max</option>\n+ <option value="sum">sum</option>\n+ </param>\n+ </xml>\n+ <xml name="fewMeasurements">\n+ <param name="fewMeasurements" type="select" label="Remove the features that have 1 or 2 measurements across runs" help="(fewMeasurements)">\n+ <option value="remove" selected="true">remove</option>\n+ <option value="keep">keep</option>\n+ </param>\n+ </xml>\n+ <xml name="removeProtein_with1Peptide">\n+ <param name="removeProtein_with1Peptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove the proteins which have only 1 peptide and charge"/>\n+ </xml>\n+ \n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">bioconductor-msstats</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ cat \'$msstats_script\' > \'$r_script\' &&\n+ cat \'$msstats_script\' &&\n+ Rscript \'$msstats_script\'\n+ && cat msstats*.log > $log\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="msstats_script"><![CDATA[\n+library(\'MSstats\', warn.conflicts = F, quietly = T, verbose = F)\n+\n+#if $input.input_src == \'MSstats\'\n+\n+ #if $input.msstats_input.is_of_type(\'csv\')\n+raw <- read.csv("$input.msstats_input")\n+ #else\n+raw <- read.table("$input.msstats_input", sep="\\t", header=TRUE)\n+ #end if\n+\n+#elif $input.input_src == \'MaxQuant\'\n+\\# Read in MaxQuant files\n+mq_evidence <- read.table("$input.evidence", sep="\\t", header=TRUE)\n+\n+mq_proteinGroups <- read.table("$input.proteinGroups", sep="\\t", header=TRUE)\n+\n+\\# Read in annotation including condition and biological replicates per run.\n+\\# Users should make this annotation file. It is not the output from MaxQuant.\n+ #if $input.annotation.is_of_type(\'csv\')\n+annot <- read.csv("$input.annotation", header=TRUE)\n+ #else\n+annot <- read.table("$input.annotation", sep="\\t", header=TRUE)\n+ #end if\n+\n+raw <- MaxQtoMSstatsFormat(evidence=mq_evidence, \n+ proteinGroups=mq_proteinGroups,\n+ annotation=annot, \n+ proteinID="$input.proteinID",\n+ useUniquePeptide=$input.input_options.useUniquePeptide, \n+ summaryforMultipleRows=$input.input_options.summaryforMultipleRows, \n+ fewMeasurements="$input.input_options.fewMeasurements", \n+ removeMpeptides=$input.input_options.removeMpeptides,\n+ removeOxidationMpeptides=$input.input_options.removeOxidationMpeptides,\n+ removeProtein_with1Peptide=$input.input_options.removeProtein_with1Peptide)\n+\n+#elif $input.input_src == \'OpenMS\'\n+\n+ #if $input.evidence.is_of_type(\'csv\')\n+input <- read.csv("$input.evidence", header=TRUE)\n+ #else\n+input <- read.table("$input.evidence", sep="\\t", header=TRUE)\n+ #end if\n+ #if $input.annotation.is_of_type(\'csv\')\n+annot <- read.csv("$input.annotation", header=TRUE)\n+ #else\n+ann'..b' 0 0 0 1 -1\n+ G3-G5 0 0 -1 0 1\n+ G1+G2-G5 0.5 0.5 0 0 -1\n+\n+**Options**\n+\n+- data conversion from MaxQuant and OpenSWATH to MSstats format: \n+\n+ - MaxQuant input: + Contaminant, + Reverse, + Only.identified.by.site, proteins are automatically removed during conversion\n+ \n+- data processing options: \n+\n+ - MaxQuant input: Contaminants and reverse and only ID by site) from MaxQuant tool are automatically removed; \n+ - log transformation\n+ - normalization of MS runs\n+ - Feature selection\n+ - Missing value imputation: \n+ \n+ - MaxQuant input: All missing values are NA, usecensoredInt must be \'NA\'\n+ - OpenSWATH input: secensoredInt must be \'0\'\n+ - Summary method: TMP + censoredInt = NULL: It assumes that all intensities are missing at random, therefore no action with MBimpute = FALSE or error with MBimpute = TRUE\n+ - censoredInt=\'NA\'or\'0\'& MBimpute=TRUE: AFT model-based imputation usingcutoffCensoredvalue in the AFT model\n+ - censoredInt=\'NA\'or\'0\'&MBimpute=FALSE: censored intensities (hereNA\xe2\x80\x99s) will be replaced withthe value specified incutoffCensored.\n+ - Summarizing intensities per MS run\n+- group comparison: automatic detection of differentially abundant proteins between two conditions, conditions have to be specified with the \'comparison matrix\'\n+- quantification per sample or group\n+\n+ - sample: relative protein abundance in each biological replicate. If there are technical replicates for biological replicates,sample quantification will be the median among technical replicates. If there is no technical replicate for biological replicate (sample), sample quantification will be the same as run-level summarization.\n+ - group: relative protein abundance in each condition, summarized over the biological replicates (median among sample quantification). In presence of completely missing values in a condition, the estimates will be zero\n+\n+**Output options**\n+\n+- Different outputs available. Especially for studies with many proteins, it is suggested to select only the necessary pdf outputs as many of them generate one plot per protein.\n+\n+ - MSstats log - check log file for warnings and information on the analysis steps (txt)\n+ - r-script - can be used to re-run analysis outside Galaxy (txt)\n+ - processed_data - transformed, normalized, imputed intensities (tabular)\n+ - runlevel_data - summarized intensities per run (tabular)\n+ - qcplot - log2 intensity boxplot for all proteins and run on first page, followed by one boxplot per protein (pdf)\n+ - profile_plot - log2 intensity profiles one plot per protein and run (pdf)\n+ - profile_wsum_plot - log2 intensity profiles one plot per protein and run with run summarization (pdf)\n+ - condition_plot - log2 intensity range for each protein and condition (pdf)\n+ - quant_sample_matrix - relative protein abundance in each biological replicate (tabular)\n+ - quant_sample_long - relative protein abundance in each biological replicate, long format (tabular)\n+ - quant_group_matrix - relative protein abundance in each condition (tabular)\n+ - quant_group_long - relative protein abundance in each condition, long format (tabular)\n+ - comparison_result - summary of statistical results per protein and comparison (tabular)\n+ - model_qc - summary statistics per run (tabular)\n+ - qqplot - one QQplot per protein (pdf)\n+ - residualplot - one residual plot per protein (pdf)\n+ - volcanoplot - one volcano plot per comparison (pdf)\n+ - heatmap - needs at least 2 comparisons, one heatmap for all proteins and comparisons (pdf)\n+ - comparisonplot - log2 intensity range for each protein and comparison (pdf) \n+\n+For additional help please visit the `MSstats documentation <http://msstats.org/msstats-2/>`_\n+\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btu305</citation>\n+ </citations>\n+</tool>\n+\n' |
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| diff -r 000000000000 -r 80b40b9ab835 test-data/comparison_matrix.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/comparison_matrix.csv Sat Jul 25 13:21:47 2020 -0400 |
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| @@ -0,0 +1,7 @@ +name,C1,C2,C3,C4,C5,C6 +C2-C1,-1,1,0,0,0,0 +C3-C2,0,-1,1,0,0,0 +C4-C3,0,0,-1,1,0,0 +C5-C4,0,0,0,-1,1,0 +C6-C5,0,0,0,0,-1,1 +C1-C6,1,0,0,0,0,-1 |
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| diff -r 000000000000 -r 80b40b9ab835 test-data/condition_plot.pdf |
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| diff -r 000000000000 -r 80b40b9ab835 test-data/msstats_testfile.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/msstats_testfile.tsv Sat Jul 25 13:21:47 2020 -0400 |
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| b'@@ -0,0 +1,2071 @@\n+ProteinName\tPeptideSequence\tPrecursorCharge\tFragmentIon\tProductCharge\tIsotopeLabelType\tCondition\tBioReplicate\tRun\tIntensity\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC1\t1\t1\t2636791.5\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC1\t1\t2\t1992418.5\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC1\t1\t3\t1982146.38\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC2\t1\t4\t5019594\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC2\t1\t5\t4560467.5\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC2\t1\t6\t3627848.75\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC5\t1\t13\t145511.83\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC5\t1\t14\t291829.69\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC6\t1\t16\t786667.38\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC6\t1\t17\t705295.31\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC6\t1\t18\t453448.78\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC3\t1\t7\tNA\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC3\t1\t8\tNA\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC3\t1\t9\tNA\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC4\t1\t10\tNA\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC4\t1\t11\tNA\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC4\t1\t12\tNA\r\n+bovine\tS.PVDIDTK_5\tNA\t5\tNA\tL\tC5\t1\t15\tNA\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC1\t1\t1\t4986404\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC1\t1\t2\t4693992.5\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC1\t1\t3\t4339490\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC2\t1\t4\t11542069\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC2\t1\t5\t10575928\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC2\t1\t6\t4152980\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC4\t1\t10\t614860.19\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC4\t1\t11\t635362.62\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC4\t1\t12\t306664.91\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC5\t1\t13\t1184493.38\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC5\t1\t14\t978215.5\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC5\t1\t15\t894807.88\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC6\t1\t16\t2295039.5\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC6\t1\t17\t2020316.12\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC6\t1\t18\t1936865.88\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC3\t1\t7\tNA\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC3\t1\t8\tNA\r\n+bovine\tG.PLTGTYR_8\tNA\t8\tNA\tL\tC3\t1\t9\tNA\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC3\t1\t9\t77861.25\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC4\t1\t10\t1320352.38\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC4\t1\t11\t1079136.5\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC4\t1\t12\t1044234.25\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC5\t1\t13\t982332.94\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC5\t1\t14\t531641.88\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC5\t1\t15\t1007074.81\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC6\t1\t16\t1107556\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC6\t1\t17\t2447382.5\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC6\t1\t18\t1468012.75\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC1\t1\t1\tNA\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC1\t1\t2\tNA\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC1\t1\t3\tNA\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC2\t1\t4\tNA\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC2\t1\t5\tNA\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC2\t1\t6\tNA\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC3\t1\t7\tNA\r\n+rabbit\tK.KDGADFAK_16\tNA\t16\tNA\tL\tC3\t1\t8\tNA\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC1\t1\t1\t757400.06\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC1\t1\t2\t762311.94\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC1\t1\t3\t650693\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC2\t1\t4\t2012540.75\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC2\t1\t5\t1717716.38\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC2\t1\t6\t1043808.69\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC5\t1\t15\t31156.11\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC6\t1\t16\t314525.84\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC6\t1\t17\t202212.78\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC3\t1\t7\tNA\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC3\t1\t8\tNA\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC3\t1\t9\tNA\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC4\t1\t10\tNA\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC4\t1\t11\tNA\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC4\t1\t12\tNA\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC5\t1\t13\tNA\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC5\t1\t14\tNA\r\n+bovine\tD.GPLTGTYR_23\tNA\t23\tNA\tL\tC6\t1\t18\tNA\r\n+bovine\tL.VYGEATSR_34\tNA\t34\tNA\tL\tC1\t1\t1\t760166.38\r\n+bovine\tL.VYGEATSR_34\tNA\t34\tNA\tL\tC1\t1\t2\t641802.75\r\n+bovine\tL.VYGEATSR_34\tNA\t34\tNA\tL\tC1\t1\t3\t410943.62\r\n+bovine\tL.VYGEATSR_34\tNA\t34\tNA\tL\tC2\t1\t4\t1457042\r\n+bovine\tL.VYGEATSR_34\tNA\t34\tNA\tL\tC2\t1\t5\t1425005.5\r\n+bovine\tL.VYGEATSR_34\tNA\t34\tNA\tL\tC2\t1\t6\t282299.16\r\n+bovine\tL.VYGEATSR_34\tNA\t34\tNA\tL\tC5\t1\t13\t49361.02\r\n+bovine\tL.VYGEATSR_34\tNA\t34\tNA\tL\tC6\t1\t16\t131189.78\r\n+bovine\tL.VYGEATSR_34\tNA\t34\tNA\tL\tC6\t1\t17\t4'..b'29\tNA\t229\tNA\tL\tC6\t1\t16\t398901.31\r\n+myg_horse\tR.LFTGHPETLEK_288\tNA\t288\tNA\tL\tC6\t1\t16\t28099974\r\n+cyc_horse\tK.TGPNLHGLFGRK_313\tNA\t313\tNA\tL\tC6\t1\t16\t2091031.25\r\n+rabbit\tK.GILAADESTGSIAK_337\tNA\t337\tNA\tL\tC6\t1\t16\t29458320\r\n+rabbit\tK.GILAADESTGSIAK_337\tNA\t337\tNA\tL\tC6\t1\t17\tNA\r\n+rabbit\tK.GILAADESTGSIAK_337\tNA\t337\tNA\tL\tC6\t1\t18\tNA\r\n+rabbit\t-.PHSHPALTPEQK_347\tNA\t347\tNA\tL\tC6\t1\t16\t60745488\r\n+rabbit\tK.ADDGRPFPQVIK_352\tNA\t352\tNA\tL\tC6\t1\t16\t201815664\r\n+chicken\tK.FESNFNTQATNR_437\tNA\t437\tNA\tL\tC6\t1\t16\t11950873\r\n+cyc_horse\tK.HKTGPNLHGLFGR_449\tNA\t449\tNA\tL\tC6\t1\t16\t1972952.12\r\n+yeast\tK.VVGLSTLPEIYEK_466\tNA\t466\tNA\tL\tC6\t1\t16\t1706257.12\r\n+cyc_horse\tK.TGQAPGFTYTDANK_484\tNA\t484\tNA\tL\tC6\t1\t16\t43382268\r\n+cyc_horse\tK.TGQAPGFTYTDANK_487\tNA\t487\tNA\tL\tC6\t1\t16\t250591.5\r\n+cyc_horse\tK.KTEREDLIAYLK_495\tNA\t495\tNA\tL\tC6\t1\t16\t9878534\r\n+cyc_horse\tR.KTGQAPGFTYTDANK_587\tNA\t587\tNA\tL\tC6\t1\t16\t207089.36\r\n+cyc_horse\tR.KTGQAPGFTYTDANK_592\tNA\t592\tNA\tL\tC6\t1\t16\t20085126\r\n+yeast\tR.VLGIDGGEGKEELFR_619\tNA\t619\tNA\tL\tC6\t1\t16\t755915.75\r\n+chicken\tN.TDGSTDYGILQINSR_632\tNA\t632\tNA\tL\tC6\t1\t16\t294854.19\r\n+chicken\tN.TDGSTDYGILQINSR_632\tNA\t632\tNA\tL\tC6\t1\t17\tNA\r\n+rabbit\tK.RLQSIGTENTEENR_648\tNA\t648\tNA\tL\tC6\t1\t16\t56317012\r\n+chicken\tR.NTDGSTDYGILQINSR_720\tNA\t720\tNA\tL\tC6\t1\t16\t4187614.75\r\n+chicken\tR.HGLDNYR_30\tNA\t30\tNA\tL\tC6\t1\t17\t864865.5\r\n+cyc_horse\tK.KTEREDLIAYLK_54\tNA\t54\tNA\tL\tC6\t1\t17\t2365524.75\r\n+cyc_horse\tG.PNLHGLFGR_65\tNA\t65\tNA\tL\tC6\t1\t17\t4145274.5\r\n+rabbit\tL.FHETLYQK_87\tNA\t87\tNA\tL\tC6\t1\t17\t4132209\r\n+rabbit\tK.KELSDIAHR_93\tNA\t93\tNA\tL\tC6\t1\t17\t4033437.75\r\n+rabbit\tR.LQSIGTENTEENRR_106\tNA\t106\tNA\tL\tC6\t1\t17\t3018036.75\r\n+bovine\tF.HWGSSDDQGSEHTVDR_229\tNA\t229\tNA\tL\tC6\t1\t17\t316840.91\r\n+myg_horse\tR.LFTGHPETLEK_288\tNA\t288\tNA\tL\tC6\t1\t17\t25877560\r\n+cyc_horse\tK.TGPNLHGLFGRK_313\tNA\t313\tNA\tL\tC6\t1\t17\t2023335.88\r\n+rabbit\t-.PHSHPALTPEQK_347\tNA\t347\tNA\tL\tC6\t1\t17\t46163236\r\n+rabbit\tK.ADDGRPFPQVIK_352\tNA\t352\tNA\tL\tC6\t1\t17\t173521376\r\n+chicken\tK.FESNFNTQATNR_437\tNA\t437\tNA\tL\tC6\t1\t17\t10224265\r\n+cyc_horse\tK.HKTGPNLHGLFGR_449\tNA\t449\tNA\tL\tC6\t1\t17\t1802600.88\r\n+yeast\tK.VVGLSTLPEIYEK_466\tNA\t466\tNA\tL\tC6\t1\t17\t1318484.25\r\n+cyc_horse\tK.TGQAPGFTYTDANK_484\tNA\t484\tNA\tL\tC6\t1\t17\t41364608\r\n+cyc_horse\tK.TGQAPGFTYTDANK_487\tNA\t487\tNA\tL\tC6\t1\t17\t222454.2\r\n+cyc_horse\tK.KTEREDLIAYLK_495\tNA\t495\tNA\tL\tC6\t1\t17\t9824986\r\n+cyc_horse\tR.KTGQAPGFTYTDANK_587\tNA\t587\tNA\tL\tC6\t1\t17\t168165.75\r\n+cyc_horse\tR.KTGQAPGFTYTDANK_592\tNA\t592\tNA\tL\tC6\t1\t17\t18743524\r\n+yeast\tR.VLGIDGGEGKEELFR_619\tNA\t619\tNA\tL\tC6\t1\t17\t620280.94\r\n+rabbit\tK.RLQSIGTENTEENR_648\tNA\t648\tNA\tL\tC6\t1\t17\t64790368\r\n+chicken\tR.NTDGSTDYGILQINSR_720\tNA\t720\tNA\tL\tC6\t1\t17\t4137431.25\r\n+chicken\tR.HGLDNYR_30\tNA\t30\tNA\tL\tC6\t1\t18\t635161.19\r\n+cyc_horse\tK.KTEREDLIAYLK_54\tNA\t54\tNA\tL\tC6\t1\t18\t1680103.12\r\n+cyc_horse\tG.PNLHGLFGR_65\tNA\t65\tNA\tL\tC6\t1\t18\t3964661.25\r\n+chicken\tK.RHGLDNYR_72\tNA\t72\tNA\tL\tC6\t1\t18\t50402.97\r\n+rabbit\tL.FHETLYQK_87\tNA\t87\tNA\tL\tC6\t1\t18\t3394803.5\r\n+rabbit\tK.KELSDIAHR_93\tNA\t93\tNA\tL\tC6\t1\t18\t3285149.25\r\n+rabbit\tR.LQSIGTENTEENRR_106\tNA\t106\tNA\tL\tC6\t1\t18\t1964464.75\r\n+bovine\tF.HWGSSDDQGSEHTVDR_229\tNA\t229\tNA\tL\tC6\t1\t18\t318532.91\r\n+myg_horse\tR.LFTGHPETLEK_288\tNA\t288\tNA\tL\tC6\t1\t18\t21277078\r\n+cyc_horse\tK.TGPNLHGLFGRK_313\tNA\t313\tNA\tL\tC6\t1\t18\t2059622.12\r\n+rabbit\t-.PHSHPALTPEQK_347\tNA\t347\tNA\tL\tC6\t1\t18\t48864024\r\n+rabbit\tK.ADDGRPFPQVIK_352\tNA\t352\tNA\tL\tC6\t1\t18\t169235648\r\n+chicken\tK.FESNFNTQATNR_437\tNA\t437\tNA\tL\tC6\t1\t18\t12272937\r\n+cyc_horse\tK.HKTGPNLHGLFGR_449\tNA\t449\tNA\tL\tC6\t1\t18\t1363316.38\r\n+yeast\tK.VVGLSTLPEIYEK_466\tNA\t466\tNA\tL\tC6\t1\t18\t502316.78\r\n+cyc_horse\tK.TGQAPGFTYTDANK_484\tNA\t484\tNA\tL\tC6\t1\t18\t36616228\r\n+cyc_horse\tK.TGQAPGFTYTDANK_487\tNA\t487\tNA\tL\tC6\t1\t18\t187206.12\r\n+cyc_horse\tK.KTEREDLIAYLK_495\tNA\t495\tNA\tL\tC6\t1\t18\t8853706\r\n+cyc_horse\tR.KTGQAPGFTYTDANK_587\tNA\t587\tNA\tL\tC6\t1\t18\t118278.85\r\n+cyc_horse\tR.KTGQAPGFTYTDANK_592\tNA\t592\tNA\tL\tC6\t1\t18\t21869690\r\n+yeast\tR.VLGIDGGEGKEELFR_619\tNA\t619\tNA\tL\tC6\t1\t18\t699193.69\r\n+chicken\tN.TDGSTDYGILQINSR_632\tNA\t632\tNA\tL\tC6\t1\t18\t94331.48\r\n+rabbit\tK.RLQSIGTENTEENR_648\tNA\t648\tNA\tL\tC6\t1\t18\t63117572\r\n+chicken\tR.NTDGSTDYGILQINSR_720\tNA\t720\tNA\tL\tC6\t1\t18\t4207624\r\n+bovine\tF.HWGSSDDQGSEHTVDR_229\tNA\t229\tNA\tL\tC3\t1\t9\tNA\r\n' |
| b |
| diff -r 000000000000 -r 80b40b9ab835 test-data/msstats_testfile.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/msstats_testfile.txt Sat Jul 25 13:21:47 2020 -0400 |
| b |
| b'@@ -0,0 +1,2071 @@\n+ProteinName,PeptideSequence,PrecursorCharge,FragmentIon,ProductCharge,IsotopeLabelType,Condition,BioReplicate,Run,Intensity\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C1,1,1,2636791.5\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C1,1,2,1992418.5\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C1,1,3,1982146.38\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C2,1,4,5019594\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C2,1,5,4560467.5\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C2,1,6,3627848.75\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C5,1,13,145511.83\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C5,1,14,291829.69\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C6,1,16,786667.38\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C6,1,17,705295.31\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C6,1,18,453448.78\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C3,1,7,NA\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C3,1,8,NA\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C3,1,9,NA\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C4,1,10,NA\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C4,1,11,NA\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C4,1,12,NA\r\n+bovine,S.PVDIDTK_5,NA,5,NA,L,C5,1,15,NA\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C1,1,1,4986404\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C1,1,2,4693992.5\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C1,1,3,4339490\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C2,1,4,11542069\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C2,1,5,10575928\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C2,1,6,4152980\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C4,1,10,614860.19\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C4,1,11,635362.62\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C4,1,12,306664.91\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C5,1,13,1184493.38\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C5,1,14,978215.5\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C5,1,15,894807.88\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C6,1,16,2295039.5\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C6,1,17,2020316.12\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C6,1,18,1936865.88\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C3,1,7,NA\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C3,1,8,NA\r\n+bovine,G.PLTGTYR_8,NA,8,NA,L,C3,1,9,NA\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C3,1,9,77861.25\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C4,1,10,1320352.38\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C4,1,11,1079136.5\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C4,1,12,1044234.25\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C5,1,13,982332.94\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C5,1,14,531641.88\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C5,1,15,1007074.81\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C6,1,16,1107556\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C6,1,17,2447382.5\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C6,1,18,1468012.75\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C1,1,1,NA\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C1,1,2,NA\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C1,1,3,NA\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C2,1,4,NA\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C2,1,5,NA\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C2,1,6,NA\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C3,1,7,NA\r\n+rabbit,K.KDGADFAK_16,NA,16,NA,L,C3,1,8,NA\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C1,1,1,757400.06\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C1,1,2,762311.94\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C1,1,3,650693\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C2,1,4,2012540.75\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C2,1,5,1717716.38\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C2,1,6,1043808.69\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C5,1,15,31156.11\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C6,1,16,314525.84\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C6,1,17,202212.78\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C3,1,7,NA\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C3,1,8,NA\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C3,1,9,NA\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C4,1,10,NA\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C4,1,11,NA\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C4,1,12,NA\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C5,1,13,NA\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C5,1,14,NA\r\n+bovine,D.GPLTGTYR_23,NA,23,NA,L,C6,1,18,NA\r\n+bovine,L.VYGEATSR_34,NA,34,NA,L,C1,1,1,760166.38\r\n+bovine,L.VYGEATSR_34,NA,34,NA,L,C1,1,2,641802.75\r\n+bovine,L.VYGEATSR_34,NA,34,NA,L,C1,1,3,410943.62\r\n+bovine,L.VYGEATSR_34,NA,34,NA,L,C2,1,4,1457042\r\n+bovine,L.VYGEATSR_34,NA,34,NA,L,C2,1,5,1425005.5\r\n+bovine,L.VYGEATSR_34,NA,34,NA,L,C2,1,6,282299.16\r\n+bovine,L.VYGEATSR_34,NA,34,NA,L,C5,1,13,49361.02\r\n+bovine,L.VYGEATSR_34,NA,34,NA,L,C6,1,16,131189.78\r\n+bovine,L.VYGEATSR_34,NA,34,NA,L,C6,1,17,4'..b'01.31\r\n+myg_horse,R.LFTGHPETLEK_288,NA,288,NA,L,C6,1,16,28099974\r\n+cyc_horse,K.TGPNLHGLFGRK_313,NA,313,NA,L,C6,1,16,2091031.25\r\n+rabbit,K.GILAADESTGSIAK_337,NA,337,NA,L,C6,1,16,29458320\r\n+rabbit,K.GILAADESTGSIAK_337,NA,337,NA,L,C6,1,17,NA\r\n+rabbit,K.GILAADESTGSIAK_337,NA,337,NA,L,C6,1,18,NA\r\n+rabbit,-.PHSHPALTPEQK_347,NA,347,NA,L,C6,1,16,60745488\r\n+rabbit,K.ADDGRPFPQVIK_352,NA,352,NA,L,C6,1,16,201815664\r\n+chicken,K.FESNFNTQATNR_437,NA,437,NA,L,C6,1,16,11950873\r\n+cyc_horse,K.HKTGPNLHGLFGR_449,NA,449,NA,L,C6,1,16,1972952.12\r\n+yeast,K.VVGLSTLPEIYEK_466,NA,466,NA,L,C6,1,16,1706257.12\r\n+cyc_horse,K.TGQAPGFTYTDANK_484,NA,484,NA,L,C6,1,16,43382268\r\n+cyc_horse,K.TGQAPGFTYTDANK_487,NA,487,NA,L,C6,1,16,250591.5\r\n+cyc_horse,K.KTEREDLIAYLK_495,NA,495,NA,L,C6,1,16,9878534\r\n+cyc_horse,R.KTGQAPGFTYTDANK_587,NA,587,NA,L,C6,1,16,207089.36\r\n+cyc_horse,R.KTGQAPGFTYTDANK_592,NA,592,NA,L,C6,1,16,20085126\r\n+yeast,R.VLGIDGGEGKEELFR_619,NA,619,NA,L,C6,1,16,755915.75\r\n+chicken,N.TDGSTDYGILQINSR_632,NA,632,NA,L,C6,1,16,294854.19\r\n+chicken,N.TDGSTDYGILQINSR_632,NA,632,NA,L,C6,1,17,NA\r\n+rabbit,K.RLQSIGTENTEENR_648,NA,648,NA,L,C6,1,16,56317012\r\n+chicken,R.NTDGSTDYGILQINSR_720,NA,720,NA,L,C6,1,16,4187614.75\r\n+chicken,R.HGLDNYR_30,NA,30,NA,L,C6,1,17,864865.5\r\n+cyc_horse,K.KTEREDLIAYLK_54,NA,54,NA,L,C6,1,17,2365524.75\r\n+cyc_horse,G.PNLHGLFGR_65,NA,65,NA,L,C6,1,17,4145274.5\r\n+rabbit,L.FHETLYQK_87,NA,87,NA,L,C6,1,17,4132209\r\n+rabbit,K.KELSDIAHR_93,NA,93,NA,L,C6,1,17,4033437.75\r\n+rabbit,R.LQSIGTENTEENRR_106,NA,106,NA,L,C6,1,17,3018036.75\r\n+bovine,F.HWGSSDDQGSEHTVDR_229,NA,229,NA,L,C6,1,17,316840.91\r\n+myg_horse,R.LFTGHPETLEK_288,NA,288,NA,L,C6,1,17,25877560\r\n+cyc_horse,K.TGPNLHGLFGRK_313,NA,313,NA,L,C6,1,17,2023335.88\r\n+rabbit,-.PHSHPALTPEQK_347,NA,347,NA,L,C6,1,17,46163236\r\n+rabbit,K.ADDGRPFPQVIK_352,NA,352,NA,L,C6,1,17,173521376\r\n+chicken,K.FESNFNTQATNR_437,NA,437,NA,L,C6,1,17,10224265\r\n+cyc_horse,K.HKTGPNLHGLFGR_449,NA,449,NA,L,C6,1,17,1802600.88\r\n+yeast,K.VVGLSTLPEIYEK_466,NA,466,NA,L,C6,1,17,1318484.25\r\n+cyc_horse,K.TGQAPGFTYTDANK_484,NA,484,NA,L,C6,1,17,41364608\r\n+cyc_horse,K.TGQAPGFTYTDANK_487,NA,487,NA,L,C6,1,17,222454.2\r\n+cyc_horse,K.KTEREDLIAYLK_495,NA,495,NA,L,C6,1,17,9824986\r\n+cyc_horse,R.KTGQAPGFTYTDANK_587,NA,587,NA,L,C6,1,17,168165.75\r\n+cyc_horse,R.KTGQAPGFTYTDANK_592,NA,592,NA,L,C6,1,17,18743524\r\n+yeast,R.VLGIDGGEGKEELFR_619,NA,619,NA,L,C6,1,17,620280.94\r\n+rabbit,K.RLQSIGTENTEENR_648,NA,648,NA,L,C6,1,17,64790368\r\n+chicken,R.NTDGSTDYGILQINSR_720,NA,720,NA,L,C6,1,17,4137431.25\r\n+chicken,R.HGLDNYR_30,NA,30,NA,L,C6,1,18,635161.19\r\n+cyc_horse,K.KTEREDLIAYLK_54,NA,54,NA,L,C6,1,18,1680103.12\r\n+cyc_horse,G.PNLHGLFGR_65,NA,65,NA,L,C6,1,18,3964661.25\r\n+chicken,K.RHGLDNYR_72,NA,72,NA,L,C6,1,18,50402.97\r\n+rabbit,L.FHETLYQK_87,NA,87,NA,L,C6,1,18,3394803.5\r\n+rabbit,K.KELSDIAHR_93,NA,93,NA,L,C6,1,18,3285149.25\r\n+rabbit,R.LQSIGTENTEENRR_106,NA,106,NA,L,C6,1,18,1964464.75\r\n+bovine,F.HWGSSDDQGSEHTVDR_229,NA,229,NA,L,C6,1,18,318532.91\r\n+myg_horse,R.LFTGHPETLEK_288,NA,288,NA,L,C6,1,18,21277078\r\n+cyc_horse,K.TGPNLHGLFGRK_313,NA,313,NA,L,C6,1,18,2059622.12\r\n+rabbit,-.PHSHPALTPEQK_347,NA,347,NA,L,C6,1,18,48864024\r\n+rabbit,K.ADDGRPFPQVIK_352,NA,352,NA,L,C6,1,18,169235648\r\n+chicken,K.FESNFNTQATNR_437,NA,437,NA,L,C6,1,18,12272937\r\n+cyc_horse,K.HKTGPNLHGLFGR_449,NA,449,NA,L,C6,1,18,1363316.38\r\n+yeast,K.VVGLSTLPEIYEK_466,NA,466,NA,L,C6,1,18,502316.78\r\n+cyc_horse,K.TGQAPGFTYTDANK_484,NA,484,NA,L,C6,1,18,36616228\r\n+cyc_horse,K.TGQAPGFTYTDANK_487,NA,487,NA,L,C6,1,18,187206.12\r\n+cyc_horse,K.KTEREDLIAYLK_495,NA,495,NA,L,C6,1,18,8853706\r\n+cyc_horse,R.KTGQAPGFTYTDANK_587,NA,587,NA,L,C6,1,18,118278.85\r\n+cyc_horse,R.KTGQAPGFTYTDANK_592,NA,592,NA,L,C6,1,18,21869690\r\n+yeast,R.VLGIDGGEGKEELFR_619,NA,619,NA,L,C6,1,18,699193.69\r\n+chicken,N.TDGSTDYGILQINSR_632,NA,632,NA,L,C6,1,18,94331.48\r\n+rabbit,K.RLQSIGTENTEENR_648,NA,648,NA,L,C6,1,18,63117572\r\n+chicken,R.NTDGSTDYGILQINSR_720,NA,720,NA,L,C6,1,18,4207624\r\n+bovine,F.HWGSSDDQGSEHTVDR_229,NA,229,NA,L,C3,1,9,NA\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 80b40b9ab835 test-data/profile_wsum_plot.pdf |
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| diff -r 000000000000 -r 80b40b9ab835 test-data/residualplot.pdf |
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| diff -r 000000000000 -r 80b40b9ab835 test-data/test_MQ_annotation.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MQ_annotation.txt Sat Jul 25 13:21:47 2020 -0400 |
| b |
| @@ -0,0 +1,5 @@ +Raw.file Condition BioReplicate Run IsotopeLabelType +qx017084.raw.thermo r1 1 1 L +qx017098.raw.thermo r1 2 2 L +qx017108.raw.thermo r2 3 3 L +qx017142.raw.thermo r2 4 4 L |
| b |
| diff -r 000000000000 -r 80b40b9ab835 test-data/test_MQ_evidence.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MQ_evidence.tabular Sat Jul 25 13:21:47 2020 -0400 |
| [ |
| b'@@ -0,0 +1,377 @@\n+Sequence\tLength\tModifications\tModified sequence\tMissed cleavages\tProteins\tLeading proteins\tLeading razor protein\tType\tRaw file\tExperiment\tMS/MS m/z\tCharge\tm/z\tMass\tResolution\tUncalibrated - Calibrated m/z [ppm]\tUncalibrated - Calibrated m/z [Da]\tMass error [ppm]\tMass error [Da]\tUncalibrated mass error [ppm]\tUncalibrated mass error [Da]\tMax intensity m/z 0\tRetention time\tRetention length\tCalibrated retention time\tCalibrated retention time start\tCalibrated retention time finish\tRetention time calibration\tMatch time difference\tMatch m/z difference\tMatch q-value\tMatch score\tNumber of data points\tNumber of scans\tNumber of isotopic peaks\tPIF\tFraction of total spectrum\tBase peak fraction\tPEP\tMS/MS count\tMS/MS scan number\tScore\tDelta score\tCombinatorics\tIntensity\tReporter PIF\tReporter fraction\tReverse\tPotential contaminant\tid\tProtein group IDs\tPeptide ID\tMod. peptide ID\tMS/MS IDs\tBest MS/MS\n+AGVNFSEFTGVWK\t13\tUnmodified\t_AGVNFSEFTGVWK_\t0\tsp|O75340|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1\tsp|O75340|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1\tsp|O75340|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1\tMULTI-MSMS\tqx017084.raw.thermo\tqx017084.raw.thermo.raw\t721.359252929688\t2\t721.359159\t1440.70376\t42360.4144635535\t-0.091576\t-6.6059E-05\t0.74813\t0.00053967\t0.65655\t0.00047361\t721.359648409678\t50.416\t0.47058\t50.416\t50.188\t50.658\t0\t\t\t\t\t64\t25\t3\t0\t0\t0\t3.9614E-06\t1\t23572\t125.97\t108.53\t1\t4473600\t\t\t\t\t403\t70\t91\t91\t465\t465\n+AGVNFSEFTGVWK\t13\tUnmodified\t_AGVNFSEFTGVWK_\t0\tsp|O75340|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1\tsp|O75340|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1\tsp|O75340|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1\tMULTI-MSMS\tqx017098.raw.thermo\tqx017098.raw.thermo.raw\t721.358459472656\t2\t721.359159\t1440.70376\t43136.0205663856\t0.40167\t0.00028975\t-0.40019\t-0.00028868\t0.0014836\t1.0702E-06\t721.360017373921\t50.783\t0.4347\t50.783\t50.534\t50.969\t0\t\t\t\t\t51\t20\t4\t0\t0\t0\t3.5477E-19\t1\t23915\t161.51\t133.74\t1\t4300800\t\t\t\t\t404\t70\t91\t91\t466\t466\n+AGVNFSEFTGVWK\t13\tUnmodified\t_AGVNFSEFTGVWK_\t0\tsp|O75340|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1\tsp|O75340|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1\tsp|O75340|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1\tMULTI-MSMS\tqx017108.raw.thermo\tqx017108.raw.thermo.raw\t721.360778808594\t2\t721.359159\t1440.70376\t42371.4225301907\t0.19861\t0.00014327\t0.55082\t0.00039734\t0.74943\t0.00054061\t721.359162635718\t51.233\t0.35978\t51.233\t51.013\t51.373\t7.1054E-15\t\t\t\t\t48\t17\t4\t0\t0\t0\t0.00074335\t1\t23907\t95.573\t82.482\t1\t5160600\t\t\t\t\t405\t70\t91\t91\t467\t467\n+AGVNFSEFTGVWK\t13\tUnmodified\t_AGVNFSEFTGVWK_\t0\tsp|O75340|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1\tsp|O75340|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1\tsp|O75340|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1\tMULTI-MSMS\tqx017142.raw.thermo\tqx017142.raw.thermo.raw\t721.860961914063\t2\t721.359159\t1440.70376\t41210.7333402874\t0.15402\t0.0001111\t1.2349\t0.00089081\t1.3889\t0.0010019\t721.359927564114\t51.407\t0.32173\t51.407\t51.231\t51.553\t0\t\t\t\t\t70\t22\t4\t0\t0\t0\t0.00082495\t1\t23919\t94.309\t71.923\t1\t2277800\t\t\t\t\t406\t70\t91\t91\t468\t468\n+AVPIPPHPIYIPPSMMEHTLPPPPSGLPFNAQPR\t34\tUnmodified\t_AVPIPPHPIYIPPSMMEHTLPPPPSGLPFNAQPR_\t0\tsp|O15042|SR140_HUMANU2snRNP-associatedSURPmotif-containingproteinOS=HomosapiensOX=9606GN=U2SURPPE=1SV=2\tsp|O15042|SR140_HUMANU2snRNP-associatedSURPmotif-containingproteinOS=HomosapiensOX=9606GN=U2SURPPE=1SV=2\tsp|O15042|SR140_HUMANU2snRNP-associatedSURPmotif-containingproteinOS=HomosapiensOX=9606GN=U2SURPPE=1SV=2\tMULTI-MSMS\tqx017098.raw.thermo\tqx017098.raw.thermo.raw\t925.487121582031\t4\t924.736185\t3694.91564\t38120.1731614502\t0.25291\t0.00023387\t-0.25764\t-0.00023825\t-0.0047341\t-4.3778E-06\t924.986965011687\t50.527\t0.319'..b'tRNAhelicaseDDX3YOS=HomosapiensOX=9606GN=DDX3YPE=1SV=2\tsp|O00571|DDX3X_HUMANATP-dependentRNAhelicaseDDX3XOS=HomosapiensOX=9606GN=DDX3XPE=1SV=3\tsp|O00571|DDX3X_HUMANATP-dependentRNAhelicaseDDX3XOS=HomosapiensOX=9606GN=DDX3XPE=1SV=3\tMULTI-MSMS\tqx017098.raw.thermo\tqx017098.raw.thermo.raw\t363.873016357422\t3\t363.873224\t1088.59784\t59654.1364546842\t0.14442\t5.2549E-05\t-0.45644\t-0.00016609\t-0.31203\t-0.00011354\t363.873020249688\t11.826\t0.37473\t11.826\t11.596\t11.971\t0\t\t\t\t\t101\t35\t4\t0\t0\t0\t0.012071\t1\t3758\t72.325\t55.487\t1\t20486000\t\t\t\t\t9699\t36\t3411\t3411\t10561\t10561\n+YVLTGRYDSAPATDGSGTALGWTVAWK\t27\tUnmodified\t_YVLTGRYDSAPATDGSGTALGWTVAWK_\t1\tCON__Streptavidin\tCON__Streptavidin\tCON__Streptavidin\tMULTI-MSMS\tqx017084.raw.thermo\tqx017084.raw.thermo.raw\t949.139526367188\t3\t948.471479\t2842.39261\t36402.0105929257\t0.0033467\t3.1743E-06\t-0.26516\t-0.0002515\t-0.26182\t-0.00024833\t948.805464098878\t51.049\t1.4855\t51.049\t50.158\t51.644\t0\t\t\t\t\t145\t87\t3\t0\t0\t0\t4.7686E-06\t1\t23799\t68.657\t65.978\t1\t8369200\t\t\t\t+\t9722\t5\t3420\t3420\t10584\t10584\n+YVLTGRYDSAPATDGSGTALGWTVAWK\t27\tUnmodified\t_YVLTGRYDSAPATDGSGTALGWTVAWK_\t1\tCON__Streptavidin\tCON__Streptavidin\tCON__Streptavidin\tMULTI-MSMS\tqx017084.raw.thermo\tqx017084.raw.thermo.raw\t948.463439941406\t3\t948.471479\t2842.39261\t36496.1377452404\t0.21497\t0.00020389\t-0.22789\t-0.00021615\t-0.012928\t-1.2262E-05\t948.805710886511\t53.143\t0.75048\t53.143\t52.671\t53.421\t0\t\t\t\t\t109\t50\t4\t0\t0\t0\t0.00035493\t1\t24973\t45.611\t43.034\t1\t2875500\t\t\t\t+\t9723\t5\t3420\t3420\t10585\t10585\n+YVLTGRYDSAPATDGSGTALGWTVAWK\t27\tUnmodified\t_YVLTGRYDSAPATDGSGTALGWTVAWK_\t1\tCON__Streptavidin\tCON__Streptavidin\tCON__Streptavidin\tMULTI-MSMS\tqx017084.raw.thermo\tqx017084.raw.thermo.raw\t949.143249511719\t3\t948.471479\t2842.39261\t36512.9308557025\t0.18849\t0.00017878\t0.48869\t0.00046351\t0.67718\t0.00064228\t948.806493581645\t53.747\t0.4756\t53.747\t53.513\t53.988\t0\t\t\t\t\t28\t23\t2\t0\t0\t0\t0.012211\t1\t25466\t33.075\t30.395\t1\t2313800\t\t\t\t+\t9724\t5\t3420\t3420\t10586\t10586\n+YVLTGRYDSAPATDGSGTALGWTVAWK\t27\tUnmodified\t_YVLTGRYDSAPATDGSGTALGWTVAWK_\t1\tCON__Streptavidin\tCON__Streptavidin\tCON__Streptavidin\tMSMS\tqx017084.raw.thermo\tqx017084.raw.thermo.raw\t948.474914550781\t3\t948.471479\t2842.39261\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\t49.726\t1\t49.726\t49.226\t50.226\t0\t\t\t\t\t\t\t\t0\t0\t0\t0.00084764\t1\t23206\t42.321\t39.642\t1\t\t\t\t\t+\t9725\t5\t3420\t3420\t10587\t10587\n+YVLTGRYDSAPATDGSGTALGWTVAWK\t27\tUnmodified\t_YVLTGRYDSAPATDGSGTALGWTVAWK_\t1\tCON__Streptavidin\tCON__Streptavidin\tCON__Streptavidin\tMULTI-MSMS\tqx017098.raw.thermo\tqx017098.raw.thermo.raw\t948.471923828125\t3\t948.471479\t2842.39261\t37011.4098748445\t0.22811\t0.00021636\t-0.20984\t-0.00019903\t0.018268\t1.7327E-05\t948.80600297521\t52.146\t0.66429\t52.146\t51.911\t52.575\t-7.1054E-15\t\t\t\t\t66\t41\t2\t0\t0\t0\t0.00097659\t1\t24873\t42.791\t37.131\t1\t5299100\t\t\t\t+\t9726\t5\t3420\t3420\t10588\t10588\n+YVLTGRYDSAPATDGSGTALGWTVAWK\t27\tUnmodified\t_YVLTGRYDSAPATDGSGTALGWTVAWK_\t1\tCON__Streptavidin\tCON__Streptavidin\tCON__Streptavidin\tMSMS\tqx017098.raw.thermo\tqx017098.raw.thermo.raw\t948.472351074219\t3\t948.471479\t2842.39261\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\t54.064\t1\t54.064\t53.564\t54.564\t0\t\t\t\t\t\t\t\t0\t0\t0\t0.02741\t1\t25750\t30.337\t27.688\t1\t\t\t\t\t+\t9727\t5\t3420\t3420\t10589\t10589\n+YVLTGRYDSAPATDGSGTALGWTVAWK\t27\tUnmodified\t_YVLTGRYDSAPATDGSGTALGWTVAWK_\t1\tCON__Streptavidin\tCON__Streptavidin\tCON__Streptavidin\tMULTI-MSMS\tqx017108.raw.thermo\tqx017108.raw.thermo.raw\t948.807678222656\t3\t948.471479\t2842.39261\t36765.2824362004\t0.1315\t0.00012473\t0.76937\t0.00072972\t0.90087\t0.00085445\t949.141505946679\t51.181\t0.21534\t51.181\t51.05\t51.265\t0\t\t\t\t\t17\t10\t2\t0\t0\t0\t1.6442E-05\t2\t23954\t65.071\t58.039\t1\t2246000\t\t\t\t+\t9728\t5\t3420\t3420\t10590;10591\t10590\n+YVLTGRYDSAPATDGSGTALGWTVAWK\t27\tUnmodified\t_YVLTGRYDSAPATDGSGTALGWTVAWK_\t1\tCON__Streptavidin\tCON__Streptavidin\tCON__Streptavidin\tMULTI-SECPEP\tqx017142.raw.thermo\tqx017142.raw.thermo.raw\t948.362670898438\t3\t948.471479\t2842.39261\t38179.8384221645\t0.1593\t0.00015109\t0.69367\t0.00065793\t0.85297\t0.00080902\t948.806821786669\t51.148\t0.41207\t51.148\t50.942\t51.354\t0\t\t\t\t\t49\t25\t3\t0\t0\t0\t0.049949\t1\t23807\t28.404\t22.04\t1\t1796900\t\t\t\t+\t9729\t5\t3420\t3420\t10592\t10592\n' |
| b |
| diff -r 000000000000 -r 80b40b9ab835 test-data/test_MQ_group12_comparison_matrix.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MQ_group12_comparison_matrix.csv Sat Jul 25 13:21:47 2020 -0400 |
| b |
| @@ -0,0 +1,2 @@ +name,r1,r2 +r2-r1,-1,1 |
| b |
| diff -r 000000000000 -r 80b40b9ab835 test-data/test_MQ_proteingroups.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MQ_proteingroups.tabular Sat Jul 25 13:21:47 2020 -0400 |
| [ |
| b'@@ -0,0 +1,6 @@\n+Protein IDs\tMajority protein IDs\tPeptide counts (all)\tPeptide counts (razor+unique)\tPeptide counts (unique)\tFasta headers\tNumber of proteins\tPeptides\tRazor + unique peptides\tUnique peptides\tPeptides qx017084.raw.thermo.raw\tPeptides qx017098.raw.thermo.raw\tPeptides qx017108.raw.thermo.raw\tPeptides qx017142.raw.thermo.raw\tRazor + unique peptides qx017084.raw.thermo.raw\tRazor + unique peptides qx017098.raw.thermo.raw\tRazor + unique peptides qx017108.raw.thermo.raw\tRazor + unique peptides qx017142.raw.thermo.raw\tUnique peptides qx017084.raw.thermo.raw\tUnique peptides qx017098.raw.thermo.raw\tUnique peptides qx017108.raw.thermo.raw\tUnique peptides qx017142.raw.thermo.raw\tSequence coverage [%]\tUnique + razor sequence coverage [%]\tUnique sequence coverage [%]\tMol. weight [kDa]\tSequence length\tSequence lengths\tQ-value\tScore\tSequence coverage qx017084.raw.thermo.raw [%]\tSequence coverage qx017098.raw.thermo.raw [%]\tSequence coverage qx017108.raw.thermo.raw [%]\tSequence coverage qx017142.raw.thermo.raw [%]\tIntensity\tIntensity qx017084.raw.thermo.raw\tIntensity qx017098.raw.thermo.raw\tIntensity qx017108.raw.thermo.raw\tIntensity qx017142.raw.thermo.raw\tLFQ intensity qx017084.raw.thermo.raw\tLFQ intensity qx017098.raw.thermo.raw\tLFQ intensity qx017108.raw.thermo.raw\tLFQ intensity qx017142.raw.thermo.raw\tMS/MS count qx017084.raw.thermo.raw\tMS/MS count qx017098.raw.thermo.raw\tMS/MS count qx017108.raw.thermo.raw\tMS/MS count qx017142.raw.thermo.raw\tMS/MS count\tOnly identified by site\tReverse\tPotential contaminant\tid\tPeptide IDs\tPeptide is razor\tMod. peptide IDs\tEvidence IDs\tMS/MS IDs\tBest MS/MS\n+CON__P00761;sp|Q9BYE2|TMPSD_HUMANTransmembraneproteaseserine13OS=HomosapiensOX=9606GN=TMPRSS13PE=2SV=5\tCON__P00761\t12;1\t12;1\t11;0\t\t2\t12\t12\t11\t11\t9\t6\t7\t11\t9\t6\t7\t11\t8\t6\t6\t55.8\t55.8\t52.4\t24.409\t231\t231;586\t0\t323.31\t52.4\t42.4\t25.1\t28.6\t315290000000\t69471000000\t104380000000\t85482000000\t55957000000\t81547000000\t90521000000\t73698000000\t69308000000\t52\t55\t24\t17\t148\t\t\t+\t0\t191;1309;1310;1734;1735;1950;1951;2169;2550;2725;2741;3032\tTrue;True;True;True;True;True;True;True;True;True;True;True\t191;1309;1310;1734;1735;1950;1951;2169;2550;2725;2741;3032\t642;3773;3774;3775;3776;3777;3778;3779;3780;3781;3782;3783;3784;3785;3786;3787;3788;3789;3790;3791;4894;4895;4896;4897;4898;4899;4900;4901;4902;4903;4904;4905;4906;4907;4908;4909;4910;4911;4912;4913;4914;4915;4916;4917;4918;4919;4920;4921;4922;4923;4924;4925;4926;4927;4928;4929;4930;4931;4932;4933;4934;4935;4936;4937;4938;4939;4940;4941;4942;4943;4944;4945;4946;4947;4948;4949;5510;5511;5512;5513;5514;5515;5516;5517;5518;5519;5520;6324;6325;7230;7231;7232;7233;7234;7235;7236;7237;7238;7239;7240;7241;7242;7243;7244;7664;7665;7666;7667;7698;8571;8572;8573;8574;8575;8576;8577;8578;8579;8580;8581;8582;8583;8584;8585;8586;8587;8588;8589;8590;8591;8592;8593;8594;8595;8596;8597;8598;8599;8600\t711;4091;4092;4093;4094;4095;4096;4097;4098;4099;4100;4101;4102;4103;4104;4105;4106;4107;4108;4109;4110;4111;4112;4113;5259;5260;5261;5262;5263;5264;5265;5266;5267;5268;5269;5270;5271;5272;5273;5274;5275;5276;5277;5278;5279;5280;5281;5282;5283;5284;5285;5286;5287;5288;5289;5290;5291;5292;5293;5294;5295;5296;5297;5298;5299;5300;5301;5302;5303;5304;5305;5306;5307;5308;5309;5310;5311;5312;5313;5314;5315;5316;5317;5318;5319;5320;5321;5322;5323;5324;5325;5326;5327;5920;5921;5922;5923;5924;5925;5926;5927;5928;5929;5930;5931;5932;6876;6877;7873;7874;7875;7876;7877;7878;7879;7880;7881;7882;7883;7884;7885;7886;7887;7888;7889;7890;7891;8330;8331;8332;8333;8334;8335;8336;8337;8338;8370;9324;9325;9326;9327;9328;9329;9330;9331;9332;9333;9334;9335;9336;9337;9338;9339;9340;9341;9342;9343;9344;9345;9346;9347;9348;9349;9350;9351;9352;9353\t711;4096;4113;5280;5325;5928;5932;6877;7873;8336;8370;9326\n+CON__Streptavidin\tCON__Streptavidin\t5\t5\t5\t\t1\t5\t5\t5\t5\t5\t4\t4\t5\t5\t4\t4\t5\t5\t4\t4\t38.1\t38.1\t38.1\t16.622\t160\t160\t0\t323.31\t38.1\t38.1\t35.6\t35.6\t83940000000\t21814000000\t18233000000\t23239000000\t20655000000\t18280000000\t17665000000\t23044000000\t21752000000\t105\t89\t'..b';10333;10334;10335;10336;10337;10584;10585;10586;10587;10588;10589;10590;10591;10592\t6366;8397;10253;10336;10584\n+sp|O00571|DDX3X_HUMANATP-dependentRNAhelicaseDDX3XOS=HomosapiensOX=9606GN=DDX3XPE=1SV=3;sp|O15523|DDX3Y_HUMANATP-dependentRNAhelicaseDDX3YOS=HomosapiensOX=9606GN=DDX3YPE=1SV=2;sp|Q9NQI0|DDX4_HUMANProbableATP-dependentRNAhelicaseDDX4OS=HomosapiensOX=9606GN=DDX4PE=1SV=2\tsp|O00571|DDX3X_HUMANATP-dependentRNAhelicaseDDX3XOS=HomosapiensOX=9606GN=DDX3XPE=1SV=3;sp|O15523|DDX3Y_HUMANATP-dependentRNAhelicaseDDX3YOS=HomosapiensOX=9606GN=DDX3YPE=1SV=2\t16;12;1\t15;11;1\t15;11;1\tsp|O00571|DDX3X_HUMAN ATP-dependent RNA helicase DDX3X OS=Homo sapiens OX=9606 GN=DDX3X PE=1 SV=3;sp|O15523|DDX3Y_HUMAN ATP-dependent RNA helicase DDX3Y OS=Homo sapiens OX=9606 GN=DDX3Y PE=1 SV=2\t3\t16\t15\t15\t6\t8\t10\t7\t5\t7\t9\t7\t5\t7\t9\t7\t30.5\t28.9\t28.9\t73.243\t662\t662;660;724\t0\t139.71\t11.9\t14.5\t18.1\t15.1\t208140000\t33627000\t77909000\t43548000\t53059000\t49987000\t73419000\t39452000\t45285000\t6\t8\t9\t8\t31\t\t\t\t36\t385;414;596;1187;1194;1700;2068;2417;2446;2586;2687;2780;3109;3116;3383;3411\tTrue;True;True;True;True;True;False;True;True;True;True;True;True;True;True;True\t385;414;596;1187;1194;1700;2068;2417;2446;2586;2687;2780;3109;3116;3383;3411\t1147;1148;1149;1223;1696;1697;1698;3414;3426;3427;3428;3429;3430;3431;3432;4797;5819;5820;5821;6878;6879;6880;6961;7317;7318;7566;7567;7568;7818;8813;8814;8825;9597;9699\t1242;1243;1244;1322;1809;1810;1811;3708;3720;3721;3722;3723;3724;3725;3726;5158;6242;6243;6244;7470;7471;7472;7559;7970;7971;8231;8232;8233;8494;9578;9579;9591;10441;10561\t1243;1322;1809;3708;3722;5158;6243;7471;7559;7970;8233;8494;9578;9591;10441;10561\n+sp|O15042|SR140_HUMANU2snRNP-associatedSURPmotif-containingproteinOS=HomosapiensOX=9606GN=U2SURPPE=1SV=2\tsp|O15042|SR140_HUMANU2snRNP-associatedSURPmotif-containingproteinOS=HomosapiensOX=9606GN=U2SURPPE=1SV=2\t23\t23\t23\tsp|O15042|SR140_HUMAN U2 snRNP-associated SURP motif-containing protein OS=Homo sapiens OX=9606 GN=U2SURP PE=1 SV=2\t1\t23\t23\t23\t13\t11\t15\t11\t13\t11\t15\t11\t13\t11\t15\t11\t30.5\t30.5\t30.5\t118.29\t1029\t1029\t0\t194.25\t20.7\t16.5\t18.9\t14.7\t407370000\t88901000\t117120000\t131340000\t70007000\t105870000\t128020000\t98409000\t75078000\t15\t13\t14\t11\t53\t\t\t\t41\t255;575;738;739;771;796;918;919;1594;1595;1920;1999;2002;2147;2164;2207;2356;2652;2679;2717;2875;3030;3403\tTrue;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True\t255;575;738;739;771;796;918;919;1594;1595;1920;1999;2002;2147;2164;2207;2356;2652;2679;2717;2875;3030;3403\t805;806;1640;2051;2052;2053;2054;2123;2124;2125;2192;2193;2194;2650;2651;2652;4536;4537;4538;5444;5647;5648;5649;5652;5653;5654;5655;6263;6311;6411;6412;6413;6414;6715;7488;7541;7542;7647;8150;8151;8152;8153;8154;8563;8564;8565;8566;9677;9678;9679;9680;9681;9682\t880;881;1753;2180;2181;2182;2183;2252;2253;2254;2327;2328;2329;2884;2885;2886;4883;4884;4885;5854;6062;6063;6064;6065;6068;6069;6070;6071;6809;6861;6965;6966;6967;6968;6969;7287;8147;8206;8207;8312;8313;8881;8882;8883;8884;8885;9315;9316;9317;9318;9319;10539;10540;10541;10542;10543;10544\t880;1753;2181;2183;2254;2327;2885;2886;4883;4885;5854;6063;6068;6809;6861;6965;7287;8147;8206;8312;8883;9316;10544\n+sp|O75340|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1\tsp|O75340|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1\t7\t7\t7\tsp|O75340|PDCD6_HUMAN Programmed cell death protein 6 OS=Homo sapiens OX=9606 GN=PDCD6 PE=1 SV=1\t1\t7\t7\t7\t7\t5\t4\t4\t7\t5\t4\t4\t7\t5\t4\t4\t35.1\t35.1\t35.1\t21.868\t191\t191\t0\t75.309\t35.1\t30.9\t24.1\t26.2\t147020000\t47158000\t52195000\t27422000\t20248000\t39231000\t45817000\t39568000\t22407000\t8\t5\t4\t4\t21\t\t\t\t70\t91;405;1929;2307;2626;3003;3365\tTrue;True;True;True;True;True;True\t91;405;1929;2307;2626;3003;3365\t403;404;405;406;1203;1204;5463;5464;5465;5466;5467;6619;6620;7429;8486;8487;8488;9558;9559;9560;9561\t465;466;467;468;1301;1302;5873;5874;5875;5876;5877;7186;7187;8084;9234;9235;9236;10401;10402;10403;10404;10405\t466;1302;5874;7187;8084;9234;10403\n' |
| b |
| diff -r 000000000000 -r 80b40b9ab835 test-data/test_swath_annotations.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_swath_annotations.tabular Sat Jul 25 13:21:47 2020 -0400 |
| b |
| @@ -0,0 +1,7 @@ +Filename Condition BioReplicate Run +in/TN125_mzML.mzML PC 93 in/TN125_mzML.mzML +in/TN126_mzML.mzML PC 94 in/TN126_mzML.mzML +in/TN127_mzML.mzML PC 95 in/TN127_mzML.mzML +in/TN128_mzML.mzML NPT 96 in/TN128_mzML.mzML +in/TN130_mzML.mzML NPT 97 in/TN130_mzML.mzML +in/TN132_mzML.mzML NPT 98 in/TN132_mzML.mzML |
| b |
| diff -r 000000000000 -r 80b40b9ab835 test-data/test_swath_group12_comparison_matrix.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_swath_group12_comparison_matrix.csv Sat Jul 25 13:21:47 2020 -0400 |
| b |
| @@ -0,0 +1,2 @@ +name,PC,NPT +NPT-PC,-1,1 |
| b |
| diff -r 000000000000 -r 80b40b9ab835 test-data/test_swath_input_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_swath_input_data.tabular Sat Jul 25 13:21:47 2020 -0400 |
| b |
| b'@@ -0,0 +1,101 @@\n+transition_group_id\tdecoy\trun_id\tfilename\tRT\tassay_rt\tdelta_rt\tiRT\tassay_iRT\tdelta_iRT\tid\tSequence\tFullPeptideName\tCharge\tmz\tIntensity\taggr_prec_Peak_Area\taggr_prec_Peak_Apex\tleftWidth\trightWidth\tpeak_group_rank\td_score\tm_score\taggr_Peak_Area\taggr_Peak_Apex\taggr_Fragment_Annotation\tProteinName\tm_score_peptide_experiment_wide\tm_score_peptide_global\tm_score_protein_experiment_wide\tm_score_protein_global\n+423\t0\t889071906042625605\tin/TN132_mzML.mzML\t5325.36\t5256.1179999999995\t69.242\t87.5431\t85.695654711\t1.8474452889999924\t1199218353298834649\tEIQSAFVSVLSENDELSQDVASK\tEIQSAFVSVLSENDELSQDVASK\t3\t832.4098\t23611.4\t364266.96875\t207563.7433682576\t5313.80810546875\t5333.849609375\t1\t2.8488500118255615\t0.009549725240522767\t0.0;3650.41;15201.5;0.0;4759.49;0.0\t0.0;3650.40747070312;7830.064453125;0.0;4759.48828125;0.0\t2538_y5_1;2539_y6_1;2540_y7_1;2541_y8_1;2542_y9_1;2543_y10_1\tQ5VYK3\t0.010408140884894468\t0.004167302113155219\t0.029706742629890506\t0.0004961143538950242\n+423\t0\t889071906042625605\tin/TN132_mzML.mzML\t5531.26\t5256.119000000001\t275.141\t93.269\t85.695654711\t7.573345289000002\t166706006410866516\tEIQSAFVSVLSENDELSQDVASK\tEIQSAFVSVLSENDELSQDVASK\t3\t832.4098\t21865.2\t236665.203125\t105140.4669526378\t5519.318359375\t5539.3671875\t2\t2.147339344024658\t0.036084000113324396\t2457.96;4095.13;7608.16;3518.53;4185.38;0.0\t2457.95703125;4095.13232421875;4873.98291015625;3518.53173828125;4185.380859375;0.0\t2538_y5_1;2539_y6_1;2540_y7_1;2541_y8_1;2542_y9_1;2543_y10_1\tQ5VYK3\t0.010408140884894468\t0.004167302113155219\t0.029706742629890506\t0.0004961143538950242\n+423\t0\t8738649111538528865\tin/TN128_mzML.mzML\t5335.45\t5267.61\t67.84\t87.4991\t85.695654711\t1.8034452889999955\t7184217712898338784\tEIQSAFVSVLSENDELSQDVASK\tEIQSAFVSVLSENDELSQDVASK\t3\t832.4098\t26634.7\t1025486.91015625\t554554.6715574464\t5321.2060546875\t5344.38916015625\t1\t3.003274440765381\t0.006938147807218546\t4465.53;0.0;6649.41;0.0;12675.1;2844.65\t4465.5263671875;0.0;6649.41015625;0.0;12675.0732421875;2829.1318359375\t2538_y5_1;2539_y6_1;2540_y7_1;2541_y8_1;2542_y9_1;2543_y10_1\tQ5VYK3\t0.007560168394463801\t0.004167302113155219\t0.0002576814152464623\t0.0004961143538950242\n+423\t0\t6278018466564674875\tin/TN127_mzML.mzML\t5317.69\t5201.161\t116.529\t88.1981\t85.695654711\t2.5024452889999935\t3423825581230557422\tEIQSAFVSVLSENDELSQDVASK\tEIQSAFVSVLSENDELSQDVASK\t3\t832.4098\t23346.2\t1484628.984375\t766641.0067096321\t5306.8408203125\t5329.921875\t1\t2.8805348873138428\t0.008959381635195364\t5437.71;0.0;17908.5;0.0;0.0;0.0\t5437.7099609375;0.0;17908.533203125;0.0;0.0;0.0\t2538_y5_1;2539_y6_1;2540_y7_1;2541_y8_1;2542_y9_1;2543_y10_1\tQ5VYK3\t0.00976473336891002\t0.004167302113155219\t0.00025800869963037295\t0.0004961143538950242\n+423\t0\t6278018466564674875\tin/TN127_mzML.mzML\t5131.22\t5201.155900000001\t-69.9359\t83.169\t85.695654711\t-2.526654711000006\t5942430694474115402\tEIQSAFVSVLSENDELSQDVASK\tEIQSAFVSVLSENDELSQDVASK\t3\t832.4098\t49459.8\t2093831.78125\t1003472.651304493\t5117.96435546875\t5144.05126953125\t2\t1.9592739343643188\t0.04862233078106762\t21719.8;0.0;4043.16;0.0;0.0;23696.8\t12108.626953125;0.0;4043.16259765625;0.0;0.0;23696.845703125\t2538_y5_1;2539_y6_1;2540_y7_1;2541_y8_1;2542_y9_1;2543_y10_1\tQ5VYK3\t0.00976473336891002\t0.004167302113155219\t0.00025800869963037295\t0.0004961143538950242\n+583\t0\t8738649111538528865\tin/TN128_mzML.mzML\t4839.97\t4802.6683\t37.3017\t73.8146\t72.833617323\t0.9809826770000001\t5943572014998216907\tELCSLASDLSQPDLVYK\tELC(UniMod:4)SLASDLSQPDLVYK\t2\t969.4799\t87558.6\t1826041.265625\t982217.416477133\t4836.904296875\t4859.30126953125\t1\t2.8217031955718994\t0.010088960422569853\t0.0;47552.0;0.0;0.0;21552.4;18454.2\t0.0;27760.08203125;0.0;0.0;21552.359375;18454.181640625\t3498_y6_1;3499_y8_1;3500_y9_1;3501_y10_1;3502_y11_1;3503_y12_1\tQ5VYK3\t0.01099721002526272\t0.003567781048869137\t0.0002576814152464623\t0.0004961143538950242\n+1537\t0\t8738649111538528865\tin/TN128_mzML.mzML\t4739.91\t4684.5367\t55.3733\t71.051\t69.565626532\t1.485373468000006\t3326198795867607659\tESSCLALNDLLR\tESSC(UniMod:4)LALNDLLR\t2\t695.8534\t78808.9\t1919526.8125\t635285.0960365'..b'\t1816.0326\t10.2574\t-9.42051\t-9.7889872355\t0.36847723550000033\t5308418974512910443\tAVPKEDIYSGGGGGGSR\tAVPKEDIYSGGGGGGSR\t3\t536.2655\t60332.5\t977138.03125\t504446.9051237924\t1818.917236328125\t1836.8218994140625\t1\t3.2051098346710205\t0.004465363142085978\t16637.5;0.0;0.0;43695.0;0.0;0.0\t16637.490234375;0.0;0.0;22508.033203125;0.0;0.0\t143688_y6_1;143689_y7_1;143690_y8_1;143691_y9_1;143693_b7_1;143692_y15_1\tQ13151\t0.0048635935323205854\t1.0999586661030975e-05\t2.200662970582778e-05\t8.543987090694456e-05\n+23948\t0\t7092145264621035912\tin/TN125_mzML.mzML\t1802.73\t1753.2397\t49.4903\t-7.73879\t-9.7889872355\t2.0501972355000007\t4937472284676581432\tAVPKEDIYSGGGGGGSR\tAVPKEDIYSGGGGGGSR\t3\t536.2655\t51740.8\t15512950.1875\t6230396.048348952\t1790.9522705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