Repository 'msstatstmt'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt

Changeset 0:fd3dc69b78ff (2021-01-24)
Next changeset 1:b79d4c961009 (2021-02-05)
Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 7c5032273bfe66383e072457aeea888917f7ebed"
added:
msstatstmt.xml
test-data/ComparisonResultMQ.tsv
test-data/ComparisonResultOMS.tsv
test-data/ProfilePlot.pdf
test-data/ProfilePlot_list.pdf
test-data/QCPlot.pdf
test-data/annotation.txt
test-data/comparison_matrix.txt
test-data/evidence.txt
test-data/input.msstatstmt.txt
test-data/input.oms.txt
test-data/proteinGroups.txt
test-data/proteinIDs.txt
b
diff -r 000000000000 -r fd3dc69b78ff msstatstmt.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/msstatstmt.xml Sun Jan 24 16:40:12 2021 +0000
[
b'@@ -0,0 +1,398 @@\n+<tool id="msstatstmt" name="MSstatsTMT" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">\n+    <description>protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling</description>\n+    <macros>\n+        <token name="@TOOL_VERSION@">1.8.0</token>\n+        <token name="@GALAXY_VERSION@">0</token>\n+        <xml name="input_options_shared">\n+            <param name="useUniquePeptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Use unique peptide" help="Yes (default) removes peptides that are assigned for more than one protein. We assume to use unique peptide for each protein." />\n+            <param name="rmPSM_withMissing_withinRun" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove PSM with missing value within run" help="Yes will remove PSM with any missing value within each run. Default is No." />\n+            <param name="rmPSM_withfewMea_withinRun" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove PSM with few measurements within run" help="Only for \'Remove PSM with missing value within run = No\'. Yes (default) will remove the features that have 1 or 2 measurements within each run." />\n+            <param name="rmProtein_with1Feature" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove proteins with one feature" help="Yes will remove the proteins which have only 1 peptide and charge. Default is No." />\n+        </xml>\n+    </macros>\n+    <requirements>\n+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-msstatstmt</requirement>\n+    </requirements>\n+    <command detect_errors="exit_code"><![CDATA[\n+        cat \'$msstatstmt_script\' > \'$out_r_script\' &&\n+        Rscript \'$msstatstmt_script\'\n+        && cat msstats*.log > \'$out_msstats_log\'\n+        && cat msstatstmt.log > \'$out_msstatstmt_log\'\n+    ]]></command>\n+    <configfiles>\n+        <configfile name="msstatstmt_script"><![CDATA[\n+library(MSstatsTMT, warn.conflicts = F, quietly = T, verbose = F)\n+\n+#if $input.input_src == \'MSstatsTMT\'\n+    input <- read.table("$input.msstatstmt_input", sep="\\t", header=TRUE)\n+\n+#elif $input.input_src == \'MaxQuant\'\n+    proteinGroups.mq <- read.table("$input.proteinGroups", sep="\\t", header=TRUE)\n+    evidence.mq <- read.table("$input.evidence", sep="\\t", header=TRUE)\n+    annotation.mq <- read.table("$input.annotation", sep="\\t", header=TRUE)\n+\n+    input <- MaxQtoMSstatsTMTFormat(evidence = evidence.mq,\n+                                    proteinGroups = proteinGroups.mq,\n+                                    annotation = annotation.mq,\n+                                    which.proteinid = "$input.proteinID",\n+                                    rmProt_Only.identified.by.site = $input.input_options.rmProt_Onlyidentifiedbysite,\n+                                    useUniquePeptide = $input.input_options.useUniquePeptide,\n+                                    rmPSM_withMissing_withinRun = $input.input_options.rmPSM_withMissing_withinRun,\n+                                    rmPSM_withfewMea_withinRun = $input.input_options.rmPSM_withfewMea_withinRun,\n+                                    rmProtein_with1Feature = $input.input_options.rmProtein_with1Feature,\n+                                    summaryforMultipleRows = $input.input_options.summaryforMultipleRows)\n+\n+#elif $input.input_src == \'OpenMS\'\n+    input.oms <- read.table("$input.oms_input", sep="\\t", header=TRUE)\n+\n+    input <- OpenMStoMSstatsTMTFormat(input.oms,\n+                                      useUniquePeptide = $input.input_options.useUniquePeptide,\n+                                      rmPSM_withMissing_withinRun = $input.input_options.rmPSM_withMissing_withinRun,\n+                                      rmPSM_withfewMea_withinRun = $input.input_options.rmPSM_withfewMea_withinRun,\n+                                      rmProtein_with1Feature = $input.in'..b'ed_outputs" value="msstats_log"/>\n+            <output name="out_group_comp">\n+                <assert_contents>\n+                    <has_n_lines n="51" />\n+                    <has_n_columns n="8" />\n+                    <has_text text="Long_LF-Short_HF" />\n+                    <has_text text="sp|O35226|PSMD4_MOUSE" />\n+                </assert_contents>\n+            </output>\n+        </test>\n+    </tests>\n+    <help><![CDATA[\n+MSstatsTMT is an R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It is applicable to isobaric labeling quantitative proteomics, including iTRAQ and TMT data. MSstatsTMT provides functionalities for two types of analysis: 1) Protein summarization based on peptide quantification data and visualization; 2) Model-based group comparison to detect significant changes in abundance.\n+\n+**Notes**\n+\n+- MSstatsTMT 11 column format: For TMT datasets an additional \'Channel\' column is required.\n+\n+    ::\n+\n+    #>            ProteinName                               PeptideSequence\n+    #> 1 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR\n+    #> 2 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR\n+    #> 3 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR\n+    #> 4 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR\n+    #> 5 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR\n+    #> 6 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR\n+    #>   PrecursorCharge                                             PSM Mixture\n+    #> 1               3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3       3\n+    #> 2               3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3       3\n+    #> 3               3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3       3\n+    #> 4               3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3       3\n+    #> 5               3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3       3\n+    #> 6               3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3       3\n+    #>   TechRepMixture   Run Channel BioReplicate Condition Intensity\n+    #> 1            3_3 3_3_3       1           21   Long_HF        NA\n+    #> 2            3_3 3_3_3       2           22      Norm  1068.580\n+    #> 3            3_3 3_3_3       3           23    Long_M  1508.330\n+    #> 4            3_3 3_3_3       4           24   Long_HF        NA\n+    #> 5            3_3 3_3_3       5           25   Long_LF  1580.951\n+    #> 6            3_3 3_3_3       6           26   Long_HF  1820.072\n+\n+    For more information please visit the `MSstatsConvert documentation <https://bioconductor.org/packages/devel/bioc/vignettes/MSstatsConvert/inst/doc/msstats_data_format.html>`_\n+\n+- Comparison matrix as tabular file\n+\n+    - 1st column: name of comparison\n+    - additionally one column for each condition that is present in the tabular file. Use 1 and -1 to indicate the conditions to compare and 0 for conditions that are not compared. Multiple groups can be combined by using 0.5.\n+    - first row contains the names of the groups, they must exactly match the condition name used in the annotation file\n+    - each additional row represents one comparison\n+    - Example for a two group comparison\n+\n+       ::\n+\n+               names     groupA  groupB\n+          groupA-groupB    1      -1\n+\n+\n+    - Example for an experiment with 5 groups and 4 different comparisons\n+\n+       ::\n+\n+          names    G1   G2   G3   G4   G5\n+          G2-G1    -1    1    0    0    0\n+          G4-G5     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+For additional help please visit the `MSstatsTMT documentation <https://msstats.org/msstatstmt/>`_\n+]]>\n+    </help>\n+    <citations>\n+        <citation type="doi">10.1074/mcp.ra120.002105</citation>\n+    </citations>\n+</tool>\n'
b
diff -r 000000000000 -r fd3dc69b78ff test-data/ComparisonResultMQ.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ComparisonResultMQ.tsv Sun Jan 24 16:40:12 2021 +0000
b
@@ -0,0 +1,21 @@
+Protein Label log2FC SE DF pvalue adj.pvalue issue
+A0AVT1 0.5-0.125 0.0459140468602267 0.0474422843160846 116 0.335164005070896 0.822221311811471 NA
+A0AVT1 0.667-0.5 -0.0347134408375791 0.0474422843160846 116 0.465828334323653 0.667552545857577 NA
+A0AVT1 1-0.667 0.0100154092766274 0.0474422843160846 116 0.833174018550089 0.940152649394416 NA
+A0AVT1 0.125-1 -0.021216015299275 0.0474422843160846 116 0.655567209214914 0.819459011518642 NA
+A5YKK6 0.5-0.125 -0.016772256118999 0.0744507596642494 100 0.822221311811471 0.822221311811471 NA
+A5YKK6 0.667-0.5 -0.110319974743075 0.0744507596642494 100 0.14154201340981 0.667552545857577 NA
+A5YKK6 1-0.667 0.0139660644806773 0.0744507596642494 100 0.851579784295866 0.940152649394416 NA
+A5YKK6 0.125-1 0.113126166381397 0.0744507596642494 100 0.131798142053549 0.658990710267745 NA
+O00244 0.5-0.125 -0.0156508772815425 0.0682347886810856 53.000030119526 0.819465761023282 0.822221311811471 NA
+O00244 0.667-0.5 -0.0294718890720826 0.0682347886810856 53.0000301194669 0.667552545857577 0.667552545857577 NA
+O00244 1-0.667 0.0051472900119096 0.0682347886810856 53.0000301198214 0.940152649394416 0.940152649394416 NA
+O00244 0.125-1 0.0399754763417155 0.0682347886810856 53.0000301198805 0.560461721740615 0.819459011518642 NA
+O15155 0.5-0.125 -0.123990068983335 0.0866910179912548 74.0000185442367 0.156853424148432 0.78426712074216 NA
+O15155 0.667-0.5 0.0927485478396167 0.0866910179912548 74.0000185442794 0.288152948639375 0.667552545857577 NA
+O15155 1-0.667 0.0321620244158099 0.0866910179912548 74.0000185441883 0.711700472592962 0.940152649394416 NA
+O15155 0.125-1 -0.000920503272092004 0.0866910179912548 74.0000185442186 0.991556629278691 0.991556629278691 NA
+O43324 0.5-0.125 0.0152670632400447 0.0438758832843402 116 0.728500668584055 0.822221311811471 NA
+O43324 0.667-0.5 -0.0209367496923783 0.0438758832843402 116 0.634130851594821 0.667552545857577 NA
+O43324 1-0.667 -0.0214089494994808 0.0438758832843402 116 0.626510915565937 0.940152649394416 NA
+O43324 0.125-1 0.0270786359518144 0.0438758832843402 116 0.538335789287531 0.819459011518642 NA
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diff -r 000000000000 -r fd3dc69b78ff test-data/ComparisonResultOMS.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ComparisonResultOMS.tsv Sun Jan 24 16:40:12 2021 +0000
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@@ -0,0 +1,51 @@
+Protein Label log2FC SE DF pvalue adj.pvalue issue
+sp|O35226|PSMD4_MOUSE Long_LF-Long_M -0.383179803981914 0.527191298717049 14.9884328166668 0.478527616562928 0.59815952070366 NA
+sp|O35226|PSMD4_MOUSE Long_LF-Short_HF 0.0882369965045162 0.502911594582881 15.0390600722389 0.8630647434109 0.984104509620049 NA
+sp|O35226|PSMD4_MOUSE Long_LF-Short_LF -0.10216446137782 0.502911594582881 15.0390600722389 0.841743949160878 0.874883198184189 NA
+sp|O35226|PSMD4_MOUSE Long_LF-Long_HF -0.328462149546436 0.602733119385758 16.1398012678652 0.593235929314306 0.741544911642882 NA
+sp|O35226|PSMD4_MOUSE Long_M-Short_HF 0.47141680048643 0.502911594582881 15.0390600721863 0.363376299217604 0.363376299217604 NA
+sp|O35226|PSMD4_MOUSE Long_M-Short_LF 0.281015342604094 0.502911594582881 15.0390600721863 0.584538978297001 0.584538978297001 NA
+sp|O35226|PSMD4_MOUSE Long_M-Long_HF 0.0547176544354783 0.602733119385758 16.139801267835 0.928782510971178 0.928782510971178 NA
+sp|O35226|PSMD4_MOUSE Short_HF-Short_LF -0.190401457882336 0.471534232431088 14.9884328167143 0.692068471060088 0.86508558882511 NA
+sp|O35226|PSMD4_MOUSE Short_HF-Long_HF -0.416699146050952 0.588867012748811 16.3341661892905 0.489150498443171 0.489150498443171 NA
+sp|O35226|PSMD4_MOUSE Short_LF-Long_HF -0.226297688168616 0.588867012748811 16.3341661892905 0.705717957951678 0.705717957951678 NA
+sp|P26039|TLN1_MOUSE Long_LF-Long_M 0.206543141229644 0.241801846316277 16.7173721151932 0.405077902275477 0.59815952070366 NA
+sp|P26039|TLN1_MOUSE Long_LF-Short_HF -0.262104619746879 0.22797216369472 16.2181784416581 0.266930907348235 0.667327268370588 NA
+sp|P26039|TLN1_MOUSE Long_LF-Short_LF -0.0587517518880176 0.22797216369472 16.2181784423512 0.799868705720086 0.874883198184189 NA
+sp|P26039|TLN1_MOUSE Long_LF-Long_HF 0.0581034793274496 0.227986625060127 16.496580862692 0.801985214775151 0.801985214775151 NA
+sp|P26039|TLN1_MOUSE Long_M-Short_HF -0.468647760976522 0.241801846316277 16.7173721151896 0.0696826273738251 0.174206568434563 NA
+sp|P26039|TLN1_MOUSE Long_M-Short_LF -0.265294893117661 0.241801846316277 16.717372115579 0.288125143114041 0.360156428892551 NA
+sp|P26039|TLN1_MOUSE Long_M-Long_HF -0.148439661902194 0.24181450682934 17.4895460585841 0.547211637736597 0.912019396227662 NA
+sp|P26039|TLN1_MOUSE Short_HF-Short_LF 0.203352867858861 0.22797216369472 16.2181784423512 0.385432635130512 0.86508558882511 NA
+sp|P26039|TLN1_MOUSE Short_HF-Long_HF 0.320208099074328 0.227986625060127 16.496580862692 0.178717487753558 0.446793719383895 NA
+sp|P26039|TLN1_MOUSE Short_LF-Long_HF 0.116855231215467 0.227986625060127 16.4965808620176 0.615058343911905 0.705717957951678 NA
+sp|Q9CPV4|GLOD4_MOUSE Long_LF-Long_M 0.25555080905785 0.204994595200998 17.0421561513356 0.229399133800579 0.573497834501448 NA
+sp|Q9CPV4|GLOD4_MOUSE Long_LF-Short_HF 0.0231288211008092 0.192434256668014 17.0018627060465 0.905740932154957 0.984104509620049 NA
+sp|Q9CPV4|GLOD4_MOUSE Long_LF-Short_LF -0.0545169780702144 0.192434256668014 17.0018627060693 0.780366117700975 0.874883198184189 NA
+sp|Q9CPV4|GLOD4_MOUSE Long_LF-Long_HF 0.225590581428028 0.211122127897028 17.9298759357605 0.299456594038713 0.66452396194088 NA
+sp|Q9CPV4|GLOD4_MOUSE Long_M-Short_HF -0.232421987957041 0.204994595200998 17.0421561513669 0.272578223920862 0.363376299217604 NA
+sp|Q9CPV4|GLOD4_MOUSE Long_M-Short_LF -0.310067787128064 0.204994595200999 17.0421561513982 0.148712726058908 0.247854543431513 NA
+sp|Q9CPV4|GLOD4_MOUSE Long_M-Long_HF -0.0299602276298223 0.221510708762242 17.8353960172994 0.893925759406093 0.928782510971178 NA
+sp|Q9CPV4|GLOD4_MOUSE Short_HF-Short_LF -0.0776457991710236 0.192434256668014 17.0018627061181 0.6916151602086 0.86508558882511 NA
+sp|Q9CPV4|GLOD4_MOUSE Short_HF-Long_HF 0.202461760327219 0.211122127897028 17.9298759357841 0.350323213440776 0.484186002468373 NA
+sp|Q9CPV4|GLOD4_MOUSE Short_LF-Long_HF 0.280107559498242 0.211122127897028 17.9298759357841 0.201240018508565 0.503100046271412 NA
+sp|Q9D8N0|EF1G_MOUSE Long_LF-Long_M -0.0292530553989313 0.37228482848991 16.9779747499087 0.938287706052358 0.938287706052358 NA
+sp|Q9D8N0|EF1G_MOUSE Long_LF-Short_HF -0.419721682263011 0.349405159767641 16.9509262044737 0.246171857050291 0.667327268370588 NA
+sp|Q9D8N0|EF1G_MOUSE Long_LF-Short_LF -0.636875339688006 0.349405159767641 16.9509262044737 0.0860305527455646 0.430152763727823 NA
+sp|Q9D8N0|EF1G_MOUSE Long_LF-Long_HF 0.382884624362653 0.385288574432951 17.6095913725243 0.333799379353359 0.66452396194088 NA
+sp|Q9D8N0|EF1G_MOUSE Long_M-Short_HF -0.39046862686408 0.37228482848991 16.9779747498993 0.308951927063802 0.363376299217604 NA
+sp|Q9D8N0|EF1G_MOUSE Long_M-Short_LF -0.607622284289075 0.37228482848991 16.9779747499225 0.12105691102517 0.247854543431513 NA
+sp|Q9D8N0|EF1G_MOUSE Long_M-Long_HF 0.412137679761584 0.404013790735018 17.5394873331272 0.321542705137548 0.80385676284387 NA
+sp|Q9D8N0|EF1G_MOUSE Short_HF-Short_LF -0.217153657424995 0.349405159767641 16.9509262044339 0.542542500525742 0.86508558882511 NA
+sp|Q9D8N0|EF1G_MOUSE Short_HF-Long_HF 0.802606306625664 0.385288574432951 17.6095913725336 0.052101547489607 0.260507737448035 NA
+sp|Q9D8N0|EF1G_MOUSE Short_LF-Long_HF 1.01975996405066 0.385288574432951 17.6095913725146 0.0166092362988973 0.0830461814944865 NA
+sp|Q9JJY4|DDX20_MOUSE Long_LF-Long_M 2.45995196155331 0.327239555031399 3 0.00487854786069601 0.0243927393034801 NA
+sp|Q9JJY4|DDX20_MOUSE Long_LF-Short_HF 0.00707677460370881 0.327239555031399 3 0.984104509620049 0.984104509620049 NA
+sp|Q9JJY4|DDX20_MOUSE Long_LF-Short_LF 0.0560594243497512 0.327239555031399 3 0.874883198184189 0.874883198184189 NA
+sp|Q9JJY4|DDX20_MOUSE Long_LF-Long_HF -0.253924754413934 0.258705583599809 3 0.398714377164528 0.66452396194088 NA
+sp|Q9JJY4|DDX20_MOUSE Long_M-Short_HF -2.4528751869496 0.327239555031399 3 0.00491917026136221 0.0245958513068111 NA
+sp|Q9JJY4|DDX20_MOUSE Long_M-Short_LF -2.40389253720356 0.327239555031399 3 0.00521294777747177 0.0260647388873589 NA
+sp|Q9JJY4|DDX20_MOUSE Long_M-Long_HF -2.71387671596724 0.258705583599809 3 0.00184965070893247 0.00924825354466235 NA
+sp|Q9JJY4|DDX20_MOUSE Short_HF-Short_LF 0.0489826497460424 0.327239555031399 3 0.890510434698273 0.890510434698273 NA
+sp|Q9JJY4|DDX20_MOUSE Short_HF-Long_HF -0.261001529017642 0.258705583599809 3 0.387348801974698 0.484186002468373 NA
+sp|Q9JJY4|DDX20_MOUSE Short_LF-Long_HF -0.309984178763685 0.258705583599809 3 0.316862696170734 0.52810449361789 NA
b
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diff -r 000000000000 -r fd3dc69b78ff test-data/ProfilePlot_list.pdf
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diff -r 000000000000 -r fd3dc69b78ff test-data/QCPlot.pdf
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diff -r 000000000000 -r fd3dc69b78ff test-data/annotation.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotation.txt Sun Jan 24 16:40:12 2021 +0000
b
b'@@ -0,0 +1,151 @@\n+Run\tChannel\tCondition\tMixture\tBioReplicate\tFraction\tTechRepMixture\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.0\tNorm\tMixture1\t1.X126\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.1\t0.667\tMixture1\t1.X127_N\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.2\t0.125\tMixture1\t1.X127_C\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.3\t0.5\tMixture1\t1.X128_N\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.4\t1\tMixture1\t1.X128_C\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.5\t0.125\tMixture1\t1.X129_N\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.6\t0.5\tMixture1\t1.X129_C\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.7\t1\tMixture1\t1.X130_N\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.8\t0.667\tMixture1\t1.X130_C\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.9\tNorm\tMixture1\t1.X131\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02\tchannel.0\tNorm\tMixture1\t2.X126\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02\tchannel.1\t0.667\tMixture1\t2.X127_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02\tchannel.2\t0.125\tMixture1\t2.X127_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02\tchannel.3\t0.5\tMixture1\t2.X128_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02\tchannel.4\t1\tMixture1\t2.X128_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02\tchannel.5\t0.125\tMixture1\t2.X129_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02\tchannel.6\t0.5\tMixture1\t2.X129_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02\tchannel.7\t1\tMixture1\t2.X130_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02\tchannel.8\t0.667\tMixture1\t2.X130_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02\tchannel.9\tNorm\tMixture1\t2.X131\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03\tchannel.0\tNorm\tMixture1\t3.X126\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03\tchannel.1\t0.667\tMixture1\t3.X127_N\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03\tchannel.2\t0.125\tMixture1\t3.X127_C\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03\tchannel.3\t0.5\tMixture1\t3.X128_N\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03\tchannel.4\t1\tMixture1\t3.X128_C\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03\tchannel.5\t0.125\tMixture1\t3.X129_N\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03\tchannel.6\t0.5\tMixture1\t3.X129_C\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03\tchannel.7\t1\tMixture1\t3.X130_N\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03\tchannel.8\t0.667\tMixture1\t3.X130_C\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03\tchannel.9\tNorm\tMixture1\t3.X131\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01\tchannel.0\tNorm\tMixture2\t4.X126\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01\tchannel.1\t0.5\tMixture2\t4.X127_N\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01\tchannel.2\t1\tMixture2\t4.X127_C\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01\tchannel.3\t0.667\tMixture2\t4.X128_N\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01\tchannel.4\t0.125\tMixture2\t4.X128_C\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01\tchannel.5\t1\tMixture2\t4.X129_N\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01\tchannel.6\t0.667\tMixture2\t4.X129_C\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01\tchannel.7\t0.125\tMixture2\t4.X130_N\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01\tchannel.8\t0.5\tMixture2\t4.X130_C\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01\tchannel.9\tNorm\tMixture2\t4.X131\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02\tchannel.0\tNorm\tMixture2\t5.X126\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02\tchannel.1\t0.5\tMixture2\t5.X127_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02\tchannel.2\t1\tMixture2\t5.X127_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02\tchannel.3\t0.667\tMixture2\t5.X128_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02\tchannel.4\t0.125\tMixture2\t5.X128_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02\tchannel.5\t1\tMixture2\t5.X129_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02\tchannel.6\t0.667\tMixture2\t5.X129_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02\tchannel.7\t0.125\tMixture2\t5.X130_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02\tchannel.8\t0.5\tMixture2\t5.X130_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02\tchannel.9\tNorm\tMixture2\t5.X131\t1\t2\n+16'..b'01\tchannel.9\tNorm\tMixture4\t10.X131\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02\tchannel.0\tNorm\tMixture4\t11.X126\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02\tchannel.1\t1\tMixture4\t11.X127_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02\tchannel.2\t0.5\tMixture4\t11.X127_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02\tchannel.3\t0.125\tMixture4\t11.X128_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02\tchannel.4\t0.667\tMixture4\t11.X128_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02\tchannel.5\t0.667\tMixture4\t11.X129_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02\tchannel.6\t1\tMixture4\t11.X129_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02\tchannel.7\t0.5\tMixture4\t11.X130_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02\tchannel.8\t0.125\tMixture4\t11.X130_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02\tchannel.9\tNorm\tMixture4\t11.X131\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03\tchannel.0\tNorm\tMixture4\t12.X126\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03\tchannel.1\t1\tMixture4\t12.X127_N\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03\tchannel.2\t0.5\tMixture4\t12.X127_C\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03\tchannel.3\t0.125\tMixture4\t12.X128_N\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03\tchannel.4\t0.667\tMixture4\t12.X128_C\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03\tchannel.5\t0.667\tMixture4\t12.X129_N\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03\tchannel.6\t1\tMixture4\t12.X129_C\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03\tchannel.7\t0.5\tMixture4\t12.X130_N\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03\tchannel.8\t0.125\tMixture4\t12.X130_C\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03\tchannel.9\tNorm\tMixture4\t12.X131\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01\tchannel.0\tNorm\tMixture5\t13.X126\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01\tchannel.1\t0.667\tMixture5\t13.X127_N\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01\tchannel.2\t0.125\tMixture5\t13.X127_C\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01\tchannel.3\t0.5\tMixture5\t13.X128_N\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01\tchannel.4\t1\tMixture5\t13.X128_C\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01\tchannel.5\t0.125\tMixture5\t13.X129_N\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01\tchannel.6\t0.5\tMixture5\t13.X129_C\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01\tchannel.7\t1\tMixture5\t13.X130_N\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01\tchannel.8\t0.667\tMixture5\t13.X130_C\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01\tchannel.9\tNorm\tMixture5\t13.X131\t1\t1\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02\tchannel.0\tNorm\tMixture5\t14.X126\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02\tchannel.1\t0.667\tMixture5\t14.X127_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02\tchannel.2\t0.125\tMixture5\t14.X127_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02\tchannel.3\t0.5\tMixture5\t14.X128_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02\tchannel.4\t1\tMixture5\t14.X128_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02\tchannel.5\t0.125\tMixture5\t14.X129_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02\tchannel.6\t0.5\tMixture5\t14.X129_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02\tchannel.7\t1\tMixture5\t14.X130_N\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02\tchannel.8\t0.667\tMixture5\t14.X130_C\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02\tchannel.9\tNorm\tMixture5\t14.X131\t1\t2\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.0\tNorm\tMixture5\t15.X126\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.1\t0.667\tMixture5\t15.X127_N\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.2\t0.125\tMixture5\t15.X127_C\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.3\t0.5\tMixture5\t15.X128_N\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.4\t1\tMixture5\t15.X128_C\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.5\t0.125\tMixture5\t15.X129_N\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.6\t0.5\tMixture5\t15.X129_C\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.7\t1\tMixture5\t15.X130_N\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.8\t0.667\tMixture5\t15.X130_C\t1\t3\n+161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.9\tNorm\tMixture5\t15.X131\t1\t3\n'
b
diff -r 000000000000 -r fd3dc69b78ff test-data/comparison_matrix.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/comparison_matrix.txt Sun Jan 24 16:40:12 2021 +0000
b
@@ -0,0 +1,5 @@
+name 0.125 0.5 0.667 1
+0.5-0.125 -1 1 0 0
+0.667-0.5 0 -1 1 0
+1-0.667 0 0 -1 1
+0.125-1 1 0 0 -1
\ No newline at end of file
b
diff -r 000000000000 -r fd3dc69b78ff test-data/evidence.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evidence.txt Sun Jan 24 16:40:12 2021 +0000
[
b'@@ -0,0 +1,156 @@\n+Sequence\tLength\tModifications\tModified sequence\tArg10 Probabilities\tLys8 Probabilities\tLys8+TMT6 Probabilities\tOxidation (M) Probabilities\tArg10 Score Diffs\tLys8 Score Diffs\tLys8+TMT6 Score Diffs\tOxidation (M) Score Diffs\tArg10\tLys8\tLys8+TMT6\tOxidation (M)\tMissed cleavages\tProteins\tLeading proteins\tLeading razor protein\tGene names\tProtein names\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 intensity corrected 0\tReporter intensity corrected 1\tReporter intensity corrected 2\tReporter intensity corrected 3\tReporter intensity corrected 4\tReporter intensity corrected 5\tReporter intensity corrected 6\tReporter intensity corrected 7\tReporter intensity corrected 8\tReporter intensity corrected 9\tReporter intensity 0\tReporter intensity 1\tReporter intensity 2\tReporter intensity 3\tReporter intensity 4\tReporter intensity 5\tReporter intensity 6\tReporter intensity 7\tReporter intensity 8\tReporter intensity 9\tReporter intensity count 0\tReporter intensity count 1\tReporter intensity count 2\tReporter intensity count 3\tReporter intensity count 4\tReporter intensity count 5\tReporter intensity count 6\tReporter intensity count 7\tReporter intensity count 8\tReporter intensity count 9\tReporter PIF\tReporter fraction\tReverse\tPotential contaminant\tid\tProtein group IDs\tPeptide ID\tMod. peptide ID\tMS/MS IDs\tBest MS/MS\tAIF MS/MS IDs\tArg10 site IDs\tLys8 site IDs\tLys8+TMT6 site IDs\tOxidation (M) site IDs\n+AAANFSDR\t8\tArg10\t_AAANFSDR(ar)_\tAAANFSDR(1)\t\t\t\tAAANFSDR(66.96)\t\t\t\t1\t0\t0\t0\t0\tA5YKK6\tA5YKK6\tA5YKK6\tCNOT1\tCCR4-NOT transcription complex subunit 1\tMULTI-MSMS\t161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03\tM4R3\t545.79\t2\t431.208076\t860.401598\t85067.94\t0.79511\t0.00034286\t265720\t114.58\t265720\t114.58\t545.789495303649\t49.598\t0.42772\t49.598\t49.373\t49.801\t0\t\t\t\t\t16\t10\t2\t0.469855487346649\t0.000767308170907199\t0.023196829482913\t0.042982\t1\t20152\t66.962\t22.845\t1\t6851100\t2118.6\t2269.9\t1982.4\t1761.8\t2145.1\t2072.2\t2421.1\t2571\t1797.2\t2288.5\t1992.9\t2146.1\t2001.8\t1837.5\t2195.6\t2092.3\t2437.3\t2529.5\t1807.2\t2277\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t\t\t\t\t241\t18\t31\t31\t245\t245\t\t31\t\t\t\n+AAANFSDR\t8\tArg10\t_AAANFSDR(ar)_\tAAANFSDR(1)\t\t\t\tAAANFSDR(88.37)\t\t\t\t1\t0\t0\t0\t0\tA5YKK6\tA5YKK6\tA5YKK6\tCNOT1\tCCR4-NOT transcription complex subunit 1\tMULTI-MSMS\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01\tM5R1\t545.7897\t2\t431.208076\t860.401598\t83670.9\t0.66409\t0.00028636\t265720\t114.58\t265720\t114.58\t545.789482528973\t48.985\t0.62196\t48.985\t48.668\t49.29\t0\t\t\t\t\t30\t17\t3\t0.838059902191162\t0.00133275322150439\t0.0186835266649723\t0.0065304\t1\t20598\t88.37\t52.925\t1\t3845700\t440.95\t451.5\t731.09\t480.91\t781.02\t528.87\t494.97\t603.61\t434.65\t593.29\t416.59\t427.4\t716.2\t491.98\t795.16\t534.4\t513.05\t596.05\t434.54\t588.65\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t\t\t\t\t242\t18\t31\t31\t246\t246\t\t31\t\t\t\n+AIVQQWLEYR\t10\tArg10\t_AIVQQWLEYR(ar)_\tAIVQQWLEYR(1)\t\t\t\tAIVQQWLEYR(82.49)\t\t\t\t1\t0\t0\t0\t0\tO43324\tO43324\tO43324\tEEF1E1\tEukaryotic translation elongation factor 1 epsilon-1\tMSMS\t161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01\tM2R1\t772.9348\t2\t658.355271\t1314.69599\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\t165.8\t1\t165.8\t165.3\t166.3\t0\t\t\t\t\t\t\t\tNaN\tNaN\tNaN\t0.012752\t1\t84632\t82.494\t27.033\t1\t\t751.04\t750.39\t738.84\t961.03\t809.28\t779.15\t1117.5\t999.37\t735.79\t918.49\t706.71\t710.95\t743.62\t972.83\t830.35\t797.05\t1116.3\t982.92\t743.38\t913.02\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t\t\t\t\t10484\t278\t1422\t1488\t10799\t10799\t\t812\t\t\t\n+AIVQQWLEYR\t10\tArg10\t_AIVQQWLEYR(ar)_\tAIVQQWLEYR(1)\t\t\t\tAIVQQWLEYR(91.7)\t\t\t\t1\t0\t0\t0\t0\tO43324\tO43324\tO43324\tEEF1E1\tEukaryotic'..b'\t9\tArg10\t_VVQTDETAR(ar)_\tVVQTDETAR(1)\t\t\t\tVVQTDETAR(71.22)\t\t\t\t1\t0\t0\t0\t0\tA0AVT1\tA0AVT1\tA0AVT1\tUBA6\tUbiquitin-like modifier-activating enzyme 6\tMULTI-MSMS\t161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03\tM4R3\t629.3482\t2\t514.765955\t1027.51736\t80355.71\t0.76825\t0.00039547\t222590\t114.58\t222590\t114.58\t629.347299563552\t49.034\t0.39581\t49.034\t48.836\t49.232\t0\t\t\t\t\t15\t9\t2\t0.555457711219788\t0.000340121041517705\t0.00503637827932835\t0.023708\t1\t19859\t71.221\t35.68\t1\t2320400\t656.22\t426.69\t391.4\t703.87\t318.77\t484.46\t425.44\t600.62\t267.88\t527.32\t616.05\t404.87\t409.98\t705.1\t332.89\t498.68\t425.22\t590.82\t271.16\t524.89\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t\t\t\t\t239740\t2\t33385\t34914\t247812\t247812\t\t2\t\t\t\n+VVQTDETAR\t9\tArg10\t_VVQTDETAR(ar)_\tVVQTDETAR(1)\t\t\t\tVVQTDETAR(88.13)\t\t\t\t1\t0\t0\t0\t0\tA0AVT1\tA0AVT1\tA0AVT1\tUBA6\tUbiquitin-like modifier-activating enzyme 6\tMULTI-MSMS\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01\tM5R1\t629.3483\t2\t514.765955\t1027.51736\t77340.94\t0.63815\t0.0003285\t222590\t114.58\t222590\t114.58\t629.347609716872\t48.355\t0.77984\t48.355\t47.957\t48.737\t-3.8147E-06\t\t\t\t\t26\t17\t2\t0.763215363025665\t0.0010706753237173\t0.0152358114719391\t0.0041991\t1\t20306\t88.134\t45.846\t1\t2038900\t303.8\t443.95\t408.45\t449.94\t278.11\t429.97\t556.52\t421.7\t344.24\t562.8\t286.48\t420.16\t402.93\t461.06\t296.75\t435.78\t550.57\t420.66\t348.74\t554.41\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t\t\t\t\t239741\t2\t33385\t34914\t247813\t247813\t\t2\t\t\t\n+WFCHIQHYPGIR\t12\tArg10\t_WFCHIQHYPGIR(ar)_\tWFCHIQHYPGIR(1)\t\t\t\tWFCHIQHYPGIR(41.69)\t\t\t\t1\t0\t0\t0\t0\tO43324\tO43324\tO43324\tEEF1E1\tEukaryotic translation elongation factor 1 epsilon-1\tMULTI-MSMS\t161117_SILAC_HeLa_UPS1_TMT10_Mixture2_03\tM2R3\t463.9934\t4\t406.702378\t1622.7804\t99411.17\t-0.51547\t-0.00020964\t140870\t57.291\t140870\t57.291\t464.244160409096\t107.8\t0.32216\t107.8\t107.61\t107.94\t0\t\t\t\t\t12\t7\t3\t0.777727544307709\t0.000821783323772252\t0.00363787729293108\t0.05337\t1\t50762\t41.689\t15.572\t1\t19265000\t3197.9\t3278.4\t3190.8\t2844.5\t3241.2\t2992.2\t2581.9\t3546.1\t2944.3\t2811.8\t3009.4\t3100.9\t3207\t2942.8\t3315.8\t3027.6\t2653.3\t3487.2\t2922.1\t2807.9\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t\t\t\t\t241630\t278\t33650\t35184\t249776\t249776\t\t\t\t\t\n+YDIDLPNK\t8\tLys8+TMT6\t_YDIDLPNK(ly)_\t\t\tYDIDLPNK(1)\t\t\t\tYDIDLPNK(52.72)\t\t0\t0\t1\t0\t0\tO00244\tO00244\tO00244\tATOX1\tCopper transport protein ATOX1\tMULTI-MSMS\t161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01\tM2R1\t482.2839\t3\t405.561841\t1213.66369\t88227.38\t0.35916\t0.00014566\t188350\t76.388\t188350\t76.388\t482.283895543023\t136.92\t0.63774\t136.92\t136.54\t137.17\t0\t\t\t\t\t25\t13\t3\t0.970517039299011\t0.00145375053398311\t0.0485036820173264\t0.038787\t1\t68038\t52.716\t8.3985\t1\t17244000\t3547.7\t4102.7\t3784.9\t3368.4\t3751.5\t4021\t3586.1\t3752.2\t3783.1\t3497.1\t3340\t3879.8\t3787.7\t3500.4\t3850.8\t4040.4\t3650.5\t3724\t3762.1\t3474.9\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t\t\t\t\t245202\t104\t34099\t35654\t253494\t253494\t\t\t\t\t\n+YDIDLPNK\t8\tLys8+TMT6\t_YDIDLPNK(ly)_\t\t\tYDIDLPNK(1)\t\t\t\tYDIDLPNK(54.61)\t\t0\t0\t1\t0\t0\tO00244\tO00244\tO00244\tATOX1\tCopper transport protein ATOX1\tMULTI-MSMS\t161117_SILAC_HeLa_UPS1_TMT10_Mixture3_02\tM3R2\t481.9497\t3\t405.561841\t1213.66369\t89530.23\t0.29417\t0.0001193\t188350\t76.388\t188350\t76.388\t481.949431561221\t135.35\t0.66937\t135.35\t134.87\t135.54\t0\t\t\t\t\t27\t13\t3\t0.966034054756165\t0.0010257251560688\t0.029427682980895\t0.034658\t1\t65957\t54.611\t11.982\t1\t10499000\t3065.6\t3112.5\t3116.7\t3502.4\t3432.9\t3080.7\t3612.8\t3030.7\t3101.8\t2974.9\t2885.2\t2947\t3130.3\t3568.1\t3507.1\t3128.5\t3652.8\t3005.4\t3103.3\t2951.7\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t\t\t\t\t245203\t104\t34099\t35654\t253495\t253495\t\t\t\t\t\n+YVLGDTAMQK\t10\tLys8+TMT6\t_YVLGDTAMQK(ly)_\t\t\tYVLGDTAMQK(1)\t\t\t\tYVLGDTAMQK(103.08)\t\t0\t0\t1\t0\t0\tA0AVT1\tA0AVT1\tA0AVT1\tUBA6\tUbiquitin-like modifier-activating enzyme 6\tMULTI-MSMS\t161117_SILAC_HeLa_UPS1_TMT10_Mixture4_01\tM4R1\t796.4564\t2\t681.87264\t1361.73073\t70254.26\t1.2993\t0.00088592\t168040\t114.58\t168040\t114.58\t796.453252543538\t128.03\t0.7942\t128.03\t127.85\t128.64\t0\t\t\t\t\t33\t18\t3\t0.592841506004334\t0.000338472134899348\t0.00606613606214523\t0.00098021\t1\t64067\t103.08\t41.603\t1\t17979000\t1565.1\t1676.8\t1441.3\t1433.1\t1462.8\t1363.3\t1579.2\t1601.7\t1317.4\t1303.5\t1472.1\t1585.9\t1456.4\t1483.1\t1501.7\t1383.8\t1594.6\t1576\t1319.3\t1300.6\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t\t\t\t\t252395\t2\t35093\t36681\t260943\t260943\t\t\t\t15\t\n'
b
diff -r 000000000000 -r fd3dc69b78ff test-data/input.msstatstmt.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.msstatstmt.txt Sun Jan 24 16:40:12 2021 +0000
b
b'@@ -0,0 +1,1521 @@\n+ProteinName\tPeptideSequence\tCharge\tPSM\tMixture\tTechRepMixture\tRun\tChannel\tBioReplicate\tCondition\tIntensity\n+A0AVT1\tNLVLAGIK(ly)\t2\tNLVLAGIK(ly)_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.0\t1.X126\tNorm\t1694.5\n+A0AVT1\tLFCDFGDEFEVLDTTGEEPK(ly)\t3\tLFCDFGDEFEVLDTTGEEPK(ly)_3\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.0\t1.X126\tNorm\t275.11\n+A0AVT1\tSYTAADATLK(ly)\t2\tSYTAADATLK(ly)_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.0\t1.X126\tNorm\t2252.2\n+O43324\tFIVDLTVQEK(ly)\t3\tFIVDLTVQEK(ly)_3\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.0\t1.X126\tNorm\t3631.9\n+O43324\tEYLLGSTAEEK(ly)\t2\tEYLLGSTAEEK(ly)_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.0\t1.X126\tNorm\t1375.2\n+A5YKK6\tDFALDSEESR(ar)\t2\tDFALDSEESR(ar)_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.0\t1.X126\tNorm\t757.83\n+O00244\tTVSYLGLE\t2\tTVSYLGLE_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.0\t1.X126\tNorm\t3244.7\n+O15155\tLLAEMDSQFDSTTGFLGK(ly)\t3\tLLAEMDSQFDSTTGFLGK(ly)_3\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.0\t1.X126\tNorm\t921.34\n+A0AVT1\tEDFTLLDFINAVK(ly)\t3\tEDFTLLDFINAVK(ly)_3\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.0\t1.X126\tNorm\t1122.1\n+A0AVT1\tNLVLAGIK(ly)\t2\tNLVLAGIK(ly)_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.1\t1.X127_N\t0.667\t1730.8\n+A0AVT1\tLFCDFGDEFEVLDTTGEEPK(ly)\t3\tLFCDFGDEFEVLDTTGEEPK(ly)_3\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.1\t1.X127_N\t0.667\t550.91\n+A0AVT1\tSYTAADATLK(ly)\t2\tSYTAADATLK(ly)_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.1\t1.X127_N\t0.667\t1718.6\n+O43324\tFIVDLTVQEK(ly)\t3\tFIVDLTVQEK(ly)_3\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.1\t1.X127_N\t0.667\t3925.5\n+O43324\tEYLLGSTAEEK(ly)\t2\tEYLLGSTAEEK(ly)_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.1\t1.X127_N\t0.667\t1345\n+A5YKK6\tDFALDSEESR(ar)\t2\tDFALDSEESR(ar)_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.1\t1.X127_N\t0.667\t679.27\n+O00244\tTVSYLGLE\t2\tTVSYLGLE_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.1\t1.X127_N\t0.667\t3160.4\n+O15155\tLLAEMDSQFDSTTGFLGK(ly)\t3\tLLAEMDSQFDSTTGFLGK(ly)_3\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.1\t1.X127_N\t0.667\t913.06\n+A0AVT1\tEDFTLLDFINAVK(ly)\t3\tEDFTLLDFINAVK(ly)_3\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.1\t1.X127_N\t0.667\t1004.7\n+A0AVT1\tNLVLAGIK(ly)\t2\tNLVLAGIK(ly)_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.2\t1.X127_C\t0.125\t2209\n+A0AVT1\tLFCDFGDEFEVLDTTGEEPK(ly)\t3\tLFCDFGDEFEVLDTTGEEPK(ly)_3\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.2\t1.X127_C\t0.125\t478.71\n+A0AVT1\tSYTAADATLK(ly)\t2\tSYTAADATLK(ly)_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.2\t1.X127_C\t0.125\t1639.5\n+O43324\tFIVDLTVQEK(ly)\t3\tFIVDLTVQEK(ly)_3\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.2\t1.X127_C\t0.125\t3585.8\n+O43324\tEYLLGSTAEEK(ly)\t2\tEYLLGSTAEEK(ly)_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.2\t1.X127_C\t0.125\t1468.2\n+A5YKK6\tDFALDSEESR(ar)\t2\tDFALDSEESR(ar)_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.2\t1.X127_C\t0.125\t1108.8\n+O00244\tTVSYLGLE\t2\tTVSYLGLE_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.2\t1.X127_C\t0.125\t3614.2\n+O15155\tLLAEMDSQFDSTTGFLGK(ly)\t3\tLLAEMDSQFDSTTGFLGK(ly)_3\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.2\t1.X127_C\t0.125\t1021.7\n+A0AVT1\tEDFTLLDFINAVK(ly)\t3\tEDFTLLDFINAVK(ly)_3\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.2\t1.X127_C\t0.125\t1169.5\n+A0AVT1\tNLVLAGIK(ly)\t2\tNLVLAGIK(ly)_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.3\t1.X128_N\t0.5\t1997.7\n+A0AVT1\tLFCDFGDEFEVLDTTGEEPK(ly)\t3\tLFCDFGDEFEVLDTTGEEPK(ly)_3\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.3\t1.X128_N\t0.5\t291.36\n+A0AVT1\tSYTAADATLK(ly)\t2\tSYTAADATLK(ly)_2\tMixture1\t1\t161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01\tchannel.3\t1.X128_N\t0.5\t1902.7\n+O43324\tFIVDLTVQEK(ly)\t3\tFIVD'..b'_N\t1\t263.39\n+A5YKK6\tDFALDSEESR(ar)\t2\tDFALDSEESR(ar)_2\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.7\t15.X130_N\t1\t1172.6\n+A0AVT1\tSYTAADATLK(ly)\t2\tSYTAADATLK(ly)_2\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.7\t15.X130_N\t1\t1304.4\n+A0AVT1\tNWSQCVELAR(ar)\t2\tNWSQCVELAR(ar)_2\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.7\t15.X130_N\t1\t159.63\n+A0AVT1\tK(ly)PNVGCQQDSEELLK(ly)\t3\tK(ly)PNVGCQQDSEELLK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.7\t15.X130_N\t1\t1051.1\n+O43324\tFIVDLTVQEK(ly)\t3\tFIVDLTVQEK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.7\t15.X130_N\t1\t3776.1\n+A5YKK6\tVDMLSEINIAPR(ar)\t3\tVDMLSEINIAPR(ar)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.7\t15.X130_N\t1\t931.89\n+O15155\tLLAEMDSQFDSTTGFLGK(ly)\t3\tLLAEMDSQFDSTTGFLGK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.7\t15.X130_N\t1\t806.34\n+O43324\tEYLLGSTAEEK(ly)\t3\tEYLLGSTAEEK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.7\t15.X130_N\t1\t2437.1\n+A0AVT1\tEDFTLLDFINAVK(ly)\t3\tEDFTLLDFINAVK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.8\t15.X130_C\t0.667\t1600.8\n+A0AVT1\tLFCDFGDEFEVLDTTGEEPK(ly)\t3\tLFCDFGDEFEVLDTTGEEPK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.8\t15.X130_C\t0.667\t738.76\n+A0AVT1\tCLIVDFSNPEAPLEIHTAMLALDQFQEK(ly)\t3\tCLIVDFSNPEAPLEIHTAMLALDQFQEK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.8\t15.X130_C\t0.667\t304.55\n+A5YKK6\tDFALDSEESR(ar)\t2\tDFALDSEESR(ar)_2\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.8\t15.X130_C\t0.667\t1238\n+A0AVT1\tSYTAADATLK(ly)\t2\tSYTAADATLK(ly)_2\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.8\t15.X130_C\t0.667\t1322.5\n+A0AVT1\tNWSQCVELAR(ar)\t2\tNWSQCVELAR(ar)_2\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.8\t15.X130_C\t0.667\t196.06\n+A0AVT1\tK(ly)PNVGCQQDSEELLK(ly)\t3\tK(ly)PNVGCQQDSEELLK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.8\t15.X130_C\t0.667\t854.31\n+O43324\tFIVDLTVQEK(ly)\t3\tFIVDLTVQEK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.8\t15.X130_C\t0.667\t3694.3\n+A5YKK6\tVDMLSEINIAPR(ar)\t3\tVDMLSEINIAPR(ar)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.8\t15.X130_C\t0.667\t1237.6\n+O15155\tLLAEMDSQFDSTTGFLGK(ly)\t3\tLLAEMDSQFDSTTGFLGK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.8\t15.X130_C\t0.667\t706.66\n+O43324\tEYLLGSTAEEK(ly)\t3\tEYLLGSTAEEK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.8\t15.X130_C\t0.667\t2321.1\n+A0AVT1\tEDFTLLDFINAVK(ly)\t3\tEDFTLLDFINAVK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.9\t15.X131\tNorm\t2181.9\n+A0AVT1\tLFCDFGDEFEVLDTTGEEPK(ly)\t3\tLFCDFGDEFEVLDTTGEEPK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.9\t15.X131\tNorm\t828.83\n+A0AVT1\tCLIVDFSNPEAPLEIHTAMLALDQFQEK(ly)\t3\tCLIVDFSNPEAPLEIHTAMLALDQFQEK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.9\t15.X131\tNorm\t197.58\n+A5YKK6\tDFALDSEESR(ar)\t2\tDFALDSEESR(ar)_2\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.9\t15.X131\tNorm\t1026.5\n+A0AVT1\tSYTAADATLK(ly)\t2\tSYTAADATLK(ly)_2\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.9\t15.X131\tNorm\t1442.4\n+A0AVT1\tNWSQCVELAR(ar)\t2\tNWSQCVELAR(ar)_2\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.9\t15.X131\tNorm\t250.01\n+A0AVT1\tK(ly)PNVGCQQDSEELLK(ly)\t3\tK(ly)PNVGCQQDSEELLK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.9\t15.X131\tNorm\t891.25\n+O43324\tFIVDLTVQEK(ly)\t3\tFIVDLTVQEK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.9\t15.X131\tNorm\t4249.6\n+A5YKK6\tVDMLSEINIAPR(ar)\t3\tVDMLSEINIAPR(ar)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.9\t15.X131\tNorm\t1259.1\n+O15155\tLLAEMDSQFDSTTGFLGK(ly)\t3\tLLAEMDSQFDSTTGFLGK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.9\t15.X131\tNorm\t812.69\n+O43324\tEYLLGSTAEEK(ly)\t3\tEYLLGSTAEEK(ly)_3\tMixture5\t3\t161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03\tchannel.9\t15.X131\tNorm\t2421.1\n'
b
diff -r 000000000000 -r fd3dc69b78ff test-data/input.oms.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.oms.txt Sun Jan 24 16:40:12 2021 +0000
b
b'@@ -0,0 +1,881 @@\n+RetentionTime\tProteinName\tPeptideSequence\tCharge\tChannel\tCondition\tBioReplicate\tRun\tMixture\tTechRepMixture\tFraction\tIntensity\tReference\n+4204.751215312020577\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)AAAASAAEAGIATPGTEDSDDALLK(TMT6plex)\t4\t6\tLong_HF\t16\t2_2_2\t2\t2_2\t2\t0.0\t"PAMI-176_Mouse_K-T_TMT_40ug_20pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=18336"\n+4204.751215312020577\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)AAAASAAEAGIATPGTEDSDDALLK(TMT6plex)\t4\t5\tLong_LF\t15\t2_2_2\t2\t2_2\t2\t0.0\t"PAMI-176_Mouse_K-T_TMT_40ug_20pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=18336"\n+4204.751215312020577\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)AAAASAAEAGIATPGTEDSDDALLK(TMT6plex)\t4\t9\tLong_LF\t19\t2_2_2\t2\t2_2\t2\t0.0\t"PAMI-176_Mouse_K-T_TMT_40ug_20pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=18336"\n+4204.751215312020577\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)AAAASAAEAGIATPGTEDSDDALLK(TMT6plex)\t4\t8\tLong_M\t18\t2_2_2\t2\t2_2\t2\t0.0\t"PAMI-176_Mouse_K-T_TMT_40ug_20pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=18336"\n+4204.751215312020577\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)AAAASAAEAGIATPGTEDSDDALLK(TMT6plex)\t4\t2\tNorm\t12\t2_2_2\t2\t2_2\t2\t0.0\t"PAMI-176_Mouse_K-T_TMT_40ug_20pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=18336"\n+4204.751215312020577\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)AAAASAAEAGIATPGTEDSDDALLK(TMT6plex)\t4\t7\tNorm\t17\t2_2_2\t2\t2_2\t2\t0.0\t"PAMI-176_Mouse_K-T_TMT_40ug_20pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=18336"\n+4204.751215312020577\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)AAAASAAEAGIATPGTEDSDDALLK(TMT6plex)\t4\t3\tShort_HF\t13\t2_2_2\t2\t2_2\t2\t0.0\t"PAMI-176_Mouse_K-T_TMT_40ug_20pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=18336"\n+4204.751215312020577\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)AAAASAAEAGIATPGTEDSDDALLK(TMT6plex)\t4\t10\tShort_HF\t20\t2_2_2\t2\t2_2\t2\t0.0\t"PAMI-176_Mouse_K-T_TMT_40ug_20pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=18336"\n+4204.751215312020577\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)AAAASAAEAGIATPGTEDSDDALLK(TMT6plex)\t4\t1\tShort_LF\t11\t2_2_2\t2\t2_2\t2\t0.0\t"PAMI-176_Mouse_K-T_TMT_40ug_20pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=18336"\n+4204.751215312020577\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)AAAASAAEAGIATPGTEDSDDALLK(TMT6plex)\t4\t4\tShort_LF\t14\t2_2_2\t2\t2_2\t2\t0.0\t"PAMI-176_Mouse_K-T_TMT_40ug_20pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=18336"\n+3585.997421872019913\tsp|P26039|TLN1_MOUSE\t.(TMT6plex)AAAFEDQENETVVVK(TMT6plex)\t2\t1\tLong_HF\t21\t3_3_3\t3\t3_3\t3\t1225.909546\t"PAMI-194_Mouse_U-Dd_TMT_40ug_22pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=15691"\n+3585.997421872019913\tsp|P26039|TLN1_MOUSE\t.(TMT6plex)AAAFEDQENETVVVK(TMT6plex)\t2\t4\tLong_HF\t24\t3_3_3\t3\t3_3\t3\t4350.732422\t"PAMI-194_Mouse_U-Dd_TMT_40ug_22pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=15691"\n+3585.997421872019913\tsp|P26039|TLN1_MOUSE\t.(TMT6plex)AAAFEDQENETVVVK(TMT6plex)\t2\t6\tLong_HF\t26\t3_3_3\t3\t3_3\t3\t4376.366699\t"PAMI-194_Mouse_U-Dd_TMT_40ug_22pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=15691"\n+3585.997421872019913\tsp|P26039|TLN1_MOUSE\t.(TMT6plex)AAAFEDQENETVVVK(TMT6plex)\t2\t8\tLong_HF\t28\t3_3_3\t3\t3_3\t3\t1454.959229\t"PAMI-194_Mouse_U-Dd_TMT_40ug_22pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=15691"\n+3585.997421872019913\tsp|P26039|TLN1_MOUSE\t.(TMT6plex)AAAFEDQENETVVVK(TMT6plex)\t2\t5\tLong_LF\t25\t3_3_3\t3\t3_3\t3\t2574.306641\t"PAMI-194_Mouse_U-Dd_TMT_40ug_22pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=15691"\n+3585.997421872019913\tsp|P26039|TLN1_MOUSE\t.(TMT6plex)AAAFEDQENETVVVK(TMT6plex)\t2\t3\tLong_M\t23\t3_3_3\t3\t3_3\t3\t1226.756104\t"PAMI-194_Mouse_U-Dd_TMT_40ug_22pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=15691"\n+3585.997421872019913\tsp|P26039|TLN'..b'E\t.(TMT6plex)VNVDIINFGEEEVNTEK(TMT6plex)\t3\t6\tLong_HF\t26\t3_3_6\t3\t3_3\t6\t0.0\t"PAMI-194_Mouse_U-Dd_TMT_40ug_28pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=24999"\n+5284.115870047979115\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VNVDIINFGEEEVNTEK(TMT6plex)\t3\t8\tLong_HF\t28\t3_3_6\t3\t3_3\t6\t0.0\t"PAMI-194_Mouse_U-Dd_TMT_40ug_28pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=24999"\n+5284.115870047979115\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VNVDIINFGEEEVNTEK(TMT6plex)\t3\t5\tLong_LF\t25\t3_3_6\t3\t3_3\t6\t0.0\t"PAMI-194_Mouse_U-Dd_TMT_40ug_28pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=24999"\n+5284.115870047979115\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VNVDIINFGEEEVNTEK(TMT6plex)\t3\t3\tLong_M\t23\t3_3_6\t3\t3_3\t6\t0.0\t"PAMI-194_Mouse_U-Dd_TMT_40ug_28pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=24999"\n+5284.115870047979115\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VNVDIINFGEEEVNTEK(TMT6plex)\t3\t2\tNorm\t22\t3_3_6\t3\t3_3\t6\t0.0\t"PAMI-194_Mouse_U-Dd_TMT_40ug_28pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=24999"\n+5284.115870047979115\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VNVDIINFGEEEVNTEK(TMT6plex)\t3\t9\tNorm\t29\t3_3_6\t3\t3_3\t6\t0.0\t"PAMI-194_Mouse_U-Dd_TMT_40ug_28pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=24999"\n+5284.115870047979115\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VNVDIINFGEEEVNTEK(TMT6plex)\t3\t7\tShort_HF\t27\t3_3_6\t3\t3_3\t6\t0.0\t"PAMI-194_Mouse_U-Dd_TMT_40ug_28pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=24999"\n+5284.115870047979115\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VNVDIINFGEEEVNTEK(TMT6plex)\t3\t10\tShort_LF\t30\t3_3_6\t3\t3_3\t6\t0.0\t"PAMI-194_Mouse_U-Dd_TMT_40ug_28pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=24999"\n+1623.401629680000042\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VSMEEQR\t2\t1\tLong_HF\t21\t3_3_2\t3\t3_3\t2\t5879.450195\t"PAMI-194_Mouse_U-Dd_TMT_40ug_20pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=2837"\n+1623.401629680000042\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VSMEEQR\t2\t4\tLong_HF\t24\t3_3_2\t3\t3_3\t2\t10037.72168\t"PAMI-194_Mouse_U-Dd_TMT_40ug_20pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=2837"\n+1623.401629680000042\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VSMEEQR\t2\t6\tLong_HF\t26\t3_3_2\t3\t3_3\t2\t3962.939697\t"PAMI-194_Mouse_U-Dd_TMT_40ug_20pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=2837"\n+1623.401629680000042\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VSMEEQR\t2\t8\tLong_HF\t28\t3_3_2\t3\t3_3\t2\t6245.194824\t"PAMI-194_Mouse_U-Dd_TMT_40ug_20pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=2837"\n+1623.401629680000042\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VSMEEQR\t2\t5\tLong_LF\t25\t3_3_2\t3\t3_3\t2\t12550.473633\t"PAMI-194_Mouse_U-Dd_TMT_40ug_20pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=2837"\n+1623.401629680000042\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VSMEEQR\t2\t3\tLong_M\t23\t3_3_2\t3\t3_3\t2\t31381.376953\t"PAMI-194_Mouse_U-Dd_TMT_40ug_20pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=2837"\n+1623.401629680000042\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VSMEEQR\t2\t2\tNorm\t22\t3_3_2\t3\t3_3\t2\t23872.552734\t"PAMI-194_Mouse_U-Dd_TMT_40ug_20pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=2837"\n+1623.401629680000042\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VSMEEQR\t2\t9\tNorm\t29\t3_3_2\t3\t3_3\t2\t25046.664063\t"PAMI-194_Mouse_U-Dd_TMT_40ug_20pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=2837"\n+1623.401629680000042\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VSMEEQR\t2\t7\tShort_HF\t27\t3_3_2\t3\t3_3\t2\t2045.723267\t"PAMI-194_Mouse_U-Dd_TMT_40ug_20pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=2837"\n+1623.401629680000042\tsp|O35226|PSMD4_MOUSE\t.(TMT6plex)VSMEEQR\t2\t10\tShort_LF\t30\t3_3_2\t3\t3_3\t2\t838.542725\t"PAMI-194_Mouse_U-Dd_TMT_40ug_20pctACN_25cm_120min_20160426_OT.mzML_controllerType=0 controllerNumber=1 scan=2837"\n'
b
diff -r 000000000000 -r fd3dc69b78ff test-data/proteinGroups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/proteinGroups.txt Sun Jan 24 16:40:12 2021 +0000
[
b'@@ -0,0 +1,6 @@\n+Protein IDs\tMajority protein IDs\tPeptide counts (all)\tPeptide counts (razor+unique)\tPeptide counts (unique)\tProtein names\tGene names\tFasta headers\tNumber of proteins\tPeptides\tRazor + unique peptides\tUnique peptides\tPeptides M1R1\tPeptides M1R2\tPeptides M1R3\tPeptides M2R1\tPeptides M2R2\tPeptides M2R3\tPeptides M3R1\tPeptides M3R2\tPeptides M3R3\tPeptides M4R1\tPeptides M4R2\tPeptides M4R3\tPeptides M5R1\tPeptides M5R2\tPeptides M5R3\tRazor + unique peptides M1R1\tRazor + unique peptides M1R2\tRazor + unique peptides M1R3\tRazor + unique peptides M2R1\tRazor + unique peptides M2R2\tRazor + unique peptides M2R3\tRazor + unique peptides M3R1\tRazor + unique peptides M3R2\tRazor + unique peptides M3R3\tRazor + unique peptides M4R1\tRazor + unique peptides M4R2\tRazor + unique peptides M4R3\tRazor + unique peptides M5R1\tRazor + unique peptides M5R2\tRazor + unique peptides M5R3\tUnique peptides M1R1\tUnique peptides M1R2\tUnique peptides M1R3\tUnique peptides M2R1\tUnique peptides M2R2\tUnique peptides M2R3\tUnique peptides M3R1\tUnique peptides M3R2\tUnique peptides M3R3\tUnique peptides M4R1\tUnique peptides M4R2\tUnique peptides M4R3\tUnique peptides M5R1\tUnique peptides M5R2\tUnique peptides M5R3\tSequence coverage [%]\tUnique + razor sequence coverage [%]\tUnique sequence coverage [%]\tMol. weight [kDa]\tSequence length\tSequence lengths\tQ-value\tScore\tReporter intensity corrected 0\tReporter intensity corrected 1\tReporter intensity corrected 2\tReporter intensity corrected 3\tReporter intensity corrected 4\tReporter intensity corrected 5\tReporter intensity corrected 6\tReporter intensity corrected 7\tReporter intensity corrected 8\tReporter intensity corrected 9\tReporter intensity 0\tReporter intensity 1\tReporter intensity 2\tReporter intensity 3\tReporter intensity 4\tReporter intensity 5\tReporter intensity 6\tReporter intensity 7\tReporter intensity 8\tReporter intensity 9\tReporter intensity count 0\tReporter intensity count 1\tReporter intensity count 2\tReporter intensity count 3\tReporter intensity count 4\tReporter intensity count 5\tReporter intensity count 6\tReporter intensity count 7\tReporter intensity count 8\tReporter intensity count 9\tReporter intensity corrected 0 M1R1\tReporter intensity corrected 1 M1R1\tReporter intensity corrected 2 M1R1\tReporter intensity corrected 3 M1R1\tReporter intensity corrected 4 M1R1\tReporter intensity corrected 5 M1R1\tReporter intensity corrected 6 M1R1\tReporter intensity corrected 7 M1R1\tReporter intensity corrected 8 M1R1\tReporter intensity corrected 9 M1R1\tReporter intensity corrected 0 M1R2\tReporter intensity corrected 1 M1R2\tReporter intensity corrected 2 M1R2\tReporter intensity corrected 3 M1R2\tReporter intensity corrected 4 M1R2\tReporter intensity corrected 5 M1R2\tReporter intensity corrected 6 M1R2\tReporter intensity corrected 7 M1R2\tReporter intensity corrected 8 M1R2\tReporter intensity corrected 9 M1R2\tReporter intensity corrected 0 M1R3\tReporter intensity corrected 1 M1R3\tReporter intensity corrected 2 M1R3\tReporter intensity corrected 3 M1R3\tReporter intensity corrected 4 M1R3\tReporter intensity corrected 5 M1R3\tReporter intensity corrected 6 M1R3\tReporter intensity corrected 7 M1R3\tReporter intensity corrected 8 M1R3\tReporter intensity corrected 9 M1R3\tReporter intensity corrected 0 M2R1\tReporter intensity corrected 1 M2R1\tReporter intensity corrected 2 M2R1\tReporter intensity corrected 3 M2R1\tReporter intensity corrected 4 M2R1\tReporter intensity corrected 5 M2R1\tReporter intensity corrected 6 M2R1\tReporter intensity corrected 7 M2R1\tReporter intensity corrected 8 M2R1\tReporter intensity corrected 9 M2R1\tReporter intensity corrected 0 M2R2\tReporter intensity corrected 1 M2R2\tReporter intensity corrected 2 M2R2\tReporter intensity corrected 3 M2R2\tReporter intensity corrected 4 M2R2\tReporter intensity corrected 5 M2R2\tReporter intensity corrected 6 M2R2\tReporter intensity corrected 7 M2R2\tReporter intensity corrected 8 M2R2\tReporter intensity corrected 9 M2R2\tReporter intensity corrected 0 M2R3\tReporter intensity corrected'..b'40544000\t21324000\t27736000\t231.39\t203.91\t178.98\t143.71\t0\t158.4\t0\t203.33\t0\t134.28\t168.18\t295.1\t0\t119.73\t99.696\t152.38\t11\t\t\t\t219\t18343\tTrue\t19194\t134080;134081;134082;134083;134084;134085;134086;134087;134088;134089;134090\t138646;138647;138648;138649;138650;138651;138652;138653;138654;138655;138656\t138648\t\t\t630\t\t\t\t80\t\n+O43324\tO43324\t5\t5\t5\tEukaryotic translation elongation factor 1 epsilon-1\tEEF1E1\t\t1\t5\t5\t5\t2\t1\t3\t3\t3\t4\t3\t2\t2\t1\t2\t4\t3\t2\t2\t2\t1\t3\t3\t3\t4\t3\t2\t2\t1\t2\t4\t3\t2\t2\t2\t1\t3\t3\t3\t4\t3\t2\t2\t1\t2\t4\t3\t2\t2\t29.3\t29.3\t29.3\t19.81\t174\t174\t0\t16.389\t90263\t85727\t86482\t86777\t90154\t86324\t88553\t89666\t86808\t87389\t84922\t81133\t87167\t88949\t92303\t87361\t89941\t88763\t86500\t86726\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t5007.1\t5270.5\t5054\t5346.4\t5313\t5201.4\t5222.7\t5254.8\t4649.2\t5170.8\t1291.1\t1420.6\t1324.3\t1310.6\t1400.6\t1146\t977.47\t1582.5\t1161.1\t1347.9\t6295.8\t5702.4\t5923.4\t5931.1\t6827.1\t5536.8\t6978.2\t6905.7\t5980.4\t6010.6\t8146.7\t7385.3\t8029.6\t8086.5\t8159.1\t8147.6\t8248.7\t8109.7\t7985.6\t8237\t6117.9\t5734.2\t5718.9\t6359.5\t6320.8\t6264.5\t6182.1\t6119.7\t6091.8\t6309.8\t13124\t12996\t11564\t11677\t12483\t11191\t11685\t12637\t12141\t11842\t5976.1\t6393.7\t6443.5\t5998.4\t6545.3\t7089\t6961.4\t6893.2\t6851.7\t6149.2\t5971.6\t5915.9\t5995.9\t5906.2\t5905.3\t5527.8\t5727.1\t5557.9\t5702.7\t5394.2\t5013.5\t5139.6\t5626.3\t5141.4\t5260.1\t5135.4\t5196.5\t5146.6\t5111.2\t5603.2\t2245.4\t2059.5\t2007.7\t2358.8\t1998.6\t2252.9\t1926.8\t2459\t2028.2\t2210.1\t1352.7\t1365.3\t1422.5\t1223\t1676.8\t1705.4\t1208.2\t1536.9\t1523.5\t1314.9\t9755.5\t8424.7\t7408.9\t8050.7\t8662.8\t8796.7\t9101.8\t8817.6\t8329.6\t8272.2\t5511.7\t4804.4\t5569.1\t5500.1\t5129.8\t5156.2\t5534.4\t5321.9\t5732.7\t5531.2\t7611.1\t6704.2\t7497.4\t7678\t8039.7\t6790\t7167.7\t7110.5\t7504.5\t7325.9\t6842.8\t6411.4\t6896.9\t6209.6\t6432.3\t6382.9\t6434.2\t6213.1\t6015.4\t6670.7\t4712.2\t4988.1\t5077\t5478.8\t5437.1\t5265.6\t5297.1\t5206.9\t4646.1\t5130.2\t1215.2\t1344\t1329.1\t1349.4\t1427.9\t1170.3\t1012.2\t1552.1\t1151.2\t1342.9\t5922.7\t5397.4\t5981.3\t6068.4\t6955.8\t5630.7\t7063.2\t6791.1\t5983.6\t5984.5\t7665.9\t6991.8\t8076.8\t8256.1\t8368.6\t8237.7\t8366.9\t8043.6\t7960.1\t8165.4\t5755\t5429\t5775.8\t6487.8\t6450.5\t6336.9\t6280.6\t6074.8\t6069.2\t6252.5\t12342\t12293\t11726\t12047\t12749\t11354\t11903\t12473\t12078\t11765\t5626.5\t6049.2\t6445.2\t6182.2\t6717.7\t7128.5\t7049.2\t6827.9\t6826.5\t6117.9\t5619.8\t5598.5\t6022.9\t6056.2\t6064.9\t5602.8\t5821.3\t5506.8\t5679.9\t5353.9\t4721.4\t4863.9\t5612\t5273.7\t5420.6\t5195.3\t5277\t5109.7\t5092.6\t5544.7\t2111.8\t1950.1\t2032.7\t2402.1\t2051.2\t2284.3\t1960.6\t2427.8\t2017\t2198.4\t1273.4\t1291.5\t1426.4\t1265.7\t1700.1\t1705.7\t1250.3\t1525.1\t1508.4\t1309.9\t9167.4\t7971.4\t7603.5\t8283.8\t8822.7\t8870.7\t9211.2\t8732.6\t8316.8\t8218.1\t5187.1\t4549.3\t5589.9\t5600.7\t5297\t5229\t5605.7\t5274.9\t5703.5\t5479.9\t7161.9\t6348.3\t7544.2\t7815.5\t8209.3\t6901.5\t7317.2\t7043.7\t7464.3\t7259.5\t6439.8\t6066.7\t6924.2\t6381.9\t6630.5\t6448.3\t6525.8\t6172.6\t6002.3\t6603.3\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t3\t3\t3\t3\t3\t3\t3\t3\t3\t3\t3\t3\t3\t3\t3\t3\t3\t3\t3\t3\t4\t4\t4\t4\t4\t4\t4\t4\t4\t4\t4\t4\t4\t4\t4\t4\t4\t4\t4\t4\t3\t3\t3\t3\t3\t3\t3\t3\t3\t3\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t4\t4\t4\t4\t4\t4\t4\t4\t4\t4\t3\t3\t3\t3\t3\t3\t3\t3\t3\t3\t4\t4\t4\t4\t4\t4\t4\t4\t4\t4\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t12.1\t6.3\t16.7\t17.8\t16.7\t23.6\t17.8\t12.1\t12.1\t6.3\t12.1\t22.4\t17.8\t12.1\t12.1\t906040000\t17358000\t19418000\t72255000\t27156000\t143730000\t70897000\t64233000\t17994000\t33973000\t14303000\t56500000\t127600000\t164880000\t45516000\t30235000\t225.19\t209.41\t208.5\t164.76\t118.7\t158.12\t152.05\t198.16\t298.54\t141.91\t181.98\t255.5\t133.09\t119.53\t106.03\t293.58\t40\t\t\t\t278\t1422;8957;9654;21644;33650\tTrue;True;True;True;True\t1488;9375;10095;22684;35184\t10484;10485;10486;10487;10488;10489;65782;65783;65784;65785;65786;65787;65788;65789;65790;65791;65792;65793;65794;65795;65796;65797;71304;71305;71306;71307;71308;71309;71310;71311;71312;71313;71314;71315;157377;157378;157379;157380;241630\t10799;10800;10801;10802;10803;10804;68075;68076;68077;68078;68079;68080;68081;68082;68083;68084;68085;68086;68087;68088;68089;68090;68091;73788;73789;73790;73791;73792;73793;73794;73795;73796;73797;73798;73799;162666;162667;162668;162669;249776\t10802;68083;73791;162666;249776\t812\t\t799;800;801\t\t78\t\t68;96;136\t\n'
b
diff -r 000000000000 -r fd3dc69b78ff test-data/proteinIDs.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/proteinIDs.txt Sun Jan 24 16:40:12 2021 +0000
b
@@ -0,0 +1,2 @@
+A0AVT1
+O00244