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

Changeset 11:d72c96ad9a16 (2021-06-15)
Previous changeset 10:f522c08e900c (2021-03-12) Next changeset 12:0839f84def5e (2021-06-20)
Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
modified:
macros.xml
maxquant.xml
added:
test-data/07/combined/txt/report_v1.0.9_combined.pdf
test-data/07/config.yml
test-data/07/mqpar.xml
test-data/ptxqc.fasta
test-data/ptxqc.mzXML
b
diff -r f522c08e900c -r d72c96ad9a16 macros.xml
--- a/macros.xml Fri Mar 12 08:41:06 2021 +0000
+++ b/macros.xml Tue Jun 15 07:55:59 2021 +0000
[
b'@@ -1,8 +1,32 @@\n <?xml version="1.0" ?>\n <macros>\n     <token name="@VERSION@">1.6.10.43</token>\n+    <token name="@VERSION_PTXQC@">1.0.9</token>\n     <token name="@SUBSTITUTION_RX@">[^\\w\\-\\s\\.]</token>\n-    <token name="@TMT10PLEX@"><![CDATA[- [TMT10plex-Lys126C,TMT10plex-Nter126C,0,0,0,0,True]\n+    <token name="@TMT2PLEX@">\n+                    - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]\n+                    - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]\n+    </token>\n+    <token name="@TMT6PLEX@">\n+                    - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True]\n+                    - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True]\n+                    - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True]\n+                    - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True]\n+                    - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True]\n+                    - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True]\n+    </token>\n+    <token name="@TMT8PLEX@">\n+                    - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True]\n+                    - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True]\n+                    - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True]\n+                    - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True]\n+                    - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True]\n+                    - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True]\n+                    - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True]\n+                    - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True]\n+    </token>\n+    <token name="@TMT10PLEX@">\n+                    - [TMT10plex-Lys126C,TMT10plex-Nter126C,0,0,0,0,True]\n                     - [TMT10plex-Lys127N,TMT10plex-Nter127N,0,0,0,0,True]\n                     - [TMT10plex-Lys127C,TMT10plex-Nter127C,0,0,0,0,True]\n                     - [TMT10plex-Lys128N,TMT10plex-Nter128N,0,0,0,0,True]\n@@ -12,18 +36,41 @@\n                     - [TMT10plex-Lys130N,TMT10plex-Nter130N,0,0,0,0,True]\n                     - [TMT10plex-Lys130C,TMT10plex-Nter130C,0,0,0,0,True]\n                     - [TMT10plex-Lys131N,TMT10plex-Nter131N,0,0,0,0,True]\n-    ]]></token>\n-\n+    </token>\n+    <token name="@TMT11PLEX@">\n+                    @TMT10PLEX@\n+                    - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True]\n+    </token>\n+    <token name="@ITRAQ4PLEX@">\n+                    - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False]\n+                    - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False]\n+                    - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False]\n+                    - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False]\n+    </token>\n+    <token name="@ITRAQ8PLEX@">\n+                    - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False]\n+                    @ITRAQ4PLEX@\n+                    - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False]\n+                    - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False]\n+                    - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False]\n+    </token>\n+    <token name="@IODOTMT6PLEX@">\n+                    - [iodoTMT6plex-Cys126,\'\',0,0,0,0,True]\n+                    - [iodoTMT6plex-Cys127,\'\',0,0,0,0,True]\n+                    - [iodoTMT6plex-Cys128,\'\',0,0,0,0,True]\n+                    - [iodoTMT6plex-Cys129,\'\',0,0,0,0,True]\n+                    - [iodoTMT6plex-Cys130,\'\',0,0,0,0,True]\n+                    - [iodoTMT6plex-Cys131,\'\',0,0,0,0,True]\n+    </token>\n     <xml name="requirements">\n         <requirements>\n             <requirement type="package" version="@VERSION@">maxquant</requirement>\n             <requirement type="package" version="3.7">python</requirement>\n             <requirement type="package" version="5.1.2">pyyaml</requirement>\n-            <requirement type="package" version="0.92.6">r-ptxqc</requirement>\n+            <requirement type="package" version="@VERSION_PTXQC@">r-ptxqc</requirement>\n             <requirement type="packa'..b'ion>\n     </xml>\n-\n     <xml name="ptxqc-opts">\n         <conditional name="qc">\n-            <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)"\n-                   type="boolean" checked="false"/>\n+            <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)" type="boolean" checked="false"/>\n             <when value="true">\n-                <param name="parameters" type="boolean" checked="true"\n-\t               label="use parameters.txt?" truevalue="yes" falsevalue="no" />\n-                <param name="summary" type="boolean" checked="true"\n-\t               label="use summary.txt?" truevalue="yes" falsevalue="no" />\n-                <param name="proteingroups" type="boolean" checked="true"\n-\t               label="use proteinGroups.txt?" truevalue="yes" falsevalue="no" />\n-                <param name="evidence" type="boolean" checked="true"\n-\t               label="use evidence.txt?" truevalue="yes" falsevalue="no" />\n-                <param name="msms" type="boolean" checked="true"\n-\t               label="use msms.txt?" truevalue="yes" falsevalue="no" />\n-                <param name="msmsscans" type="boolean" checked="true"\n-\t               label="use msmsScans.txt?" truevalue="yes" falsevalue="no" />\n+                <param name="parameters" type="boolean" checked="true" label="use parameters.txt?" truevalue="yes" falsevalue="no"/>\n+                <param name="summary" type="boolean" checked="true" label="use summary.txt?" truevalue="yes" falsevalue="no"/>\n+                <param name="proteingroups" type="boolean" checked="true" label="use proteinGroups.txt?" truevalue="yes" falsevalue="no"/>\n+                <param name="evidence" type="boolean" checked="true" label="use evidence.txt?" truevalue="yes" falsevalue="no"/>\n+                <param name="msms" type="boolean" checked="true" label="use msms.txt?" truevalue="yes" falsevalue="no"/>\n+                <param name="msmsscans" type="boolean" checked="true" label="use msmsScans.txt?" truevalue="yes" falsevalue="no"/>\n             </when>\n             <when value="false"/>\n         </conditional>\n     </xml>\n-    \n     <xml name="outputs">\n         <outputs>\n             <expand macro="output_from_wdir" name="proteinGroups" label="MaxQuant Protein Groups"/>\n@@ -183,7 +221,6 @@\n             </data>\n         </outputs>\n     </xml>\n-    \n     <xml name="modification">\n         <expand macro="mod_option" value="Acetyl (K)"/>\n         <expand macro="mod_option" value="Acetyl (Protein N-term)"/>\n@@ -601,7 +638,6 @@\n         <expand macro="mod_option" value="Cysteinyl"/>\n         <expand macro="mod_option" value="Cysteinyl - carbamidomethyl"/>\n     </xml>\n-\n     <xml name="label">\n         <expand macro="mod_option" value="Arg6"/>\n         <expand macro="mod_option" value="Arg10"/>\n@@ -638,7 +674,6 @@\n         <expand macro="mod_option" value="Leu7"/>\n         <expand macro="mod_option" value="Ile7"/>\n     </xml>\n-\n     <xml name="proteases">\n         <expand macro="mod_option" value="Trypsin"/>\n         <expand macro="mod_option" value="Trypsin/P"/>\n@@ -654,7 +689,6 @@\n         <expand macro="mod_option" value="Chymotrypsin+"/>\n         <expand macro="mod_option" value="Chymotrypsin"/>\n     </xml>\n-\n     <xml name="iso_labels">\n         <expand macro="mod_option" value="iTRAQ4plex-Nter114"/>\n         <expand macro="mod_option" value="iTRAQ4plex-Nter115"/>\n@@ -741,8 +775,7 @@\n         <expand macro="mod_option" value="iodoTMT6plex-Cys130"/>\n         <expand macro="mod_option" value="iodoTMT6plex-Cys131"/>\n     </xml>\n-\n-    <xml name="citations">        \n+    <xml name="citations">\n         <citations>\n             <citation type="bibtex">\n                 @article{cox2008maxquant,\n@@ -773,4 +806,4 @@\n             <citation type="doi">10.1021/acs.jproteome.5b00780</citation>\n         </citations>\n     </xml>\n-</macros>\n+</macros>\n\\ No newline at end of file\n'
b
diff -r f522c08e900c -r d72c96ad9a16 maxquant.xml
--- a/maxquant.xml Fri Mar 12 08:41:06 2021 +0000
+++ b/maxquant.xml Tue Jun 15 07:55:59 2021 +0000
[
b'@@ -1,4 +1,4 @@\n-<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy4">\n+<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy5">\n     <macros>\n         <xml name="output" token_format="tabular" token_label="default description" token_name="default">\n             <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">\n@@ -63,7 +63,7 @@\n               >> \'$log\' 2>&1\n           #end if\n         &&\n-        cp ./combined/txt/report_v0.92.6_combined.pdf \'$ptxqc_report\'\n+        cp \'./combined/txt/report_v@VERSION_PTXQC@_combined.pdf\' \'$ptxqc_report\'\n       #end if\n     #end if\n     ]]></command>\n@@ -178,57 +178,28 @@\n                     #end for\n                   #end if\n                   #if $pg.quant_method.iso_labels.labeling == \'tmt2plex\':\n-                    - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]\n-                    - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]\n+                    @TMT2PLEX@\n                   #end if\n                   #if $pg.quant_method.iso_labels.labeling == \'tmt6plex\':\n-                    - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True]\n-                    - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True]\n-                    - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True]\n-                    - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True]\n-                    - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True]\n-                    - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True]\n+                    @TMT6PLEX@\n                   #end if\n                   #if $pg.quant_method.iso_labels.labeling == \'tmt8plex\':\n-                    - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True]\n-                    - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True]\n-                    - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True]\n-                    - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True]\n-                    - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True]\n-                    - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True]\n-                    - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True]\n-                    - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True]\n+                    @TMT8PLEX@\n                   #end if\n                   #if $pg.quant_method.iso_labels.labeling == \'tmt10plex\':\n                     @TMT10PLEX@\n                   #end if\n                   #if $pg.quant_method.iso_labels.labeling == \'tmt11plex\':\n-                    @TMT10PLEX@\n-                    - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True]\n+                    @TMT11PLEX@\n                   #end if\n                   #if $pg.quant_method.iso_labels.labeling == \'itraq4plex\':\n-                    - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False]\n-                    - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False]\n-                    - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False]\n-                    - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False]\n+                    @ITRAQ4PLEX@\n                   #end if\n                   #if $pg.quant_method.iso_labels.labeling == \'itraq8plex\':\n-                    - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False]\n-                    - [iTRAQ4plex-Lys114,iTRAQ8plex-Nter114,0,0,0,0,False]\n-                    - [iTRAQ4plex-Lys115,iTRAQ8plex-Nter115,0,0,0,0,False]\n-                    - [iTRAQ4plex-Lys116,iTRAQ8plex-Nter116,0,0,0,0,False]\n-                    - [iTRAQ4plex-Lys117,iTRAQ8plex-Nter117,0,0,0,0,False]\n-                    - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False]\n-                    - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False]\n-                    - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False]\n+                    @ITRAQ8PLEX@\n                   #end if\n                   #if $pg.quant_method.iso_labels.labeling == \'iodotmt6plex\':\n-                    - [iodoTMT6plex-Cys126,\'\',0,0,0,0,True]\n-                    - [i'..b'                      <when value="tmt10plex"/>\n+                        <when value="tmt11plex"/>\n+                        <when value="itraq4plex"/>\n+                        <when value="itraq8plex"/>\n+                        <when value="iodotmt6plex"/>\n                         <when value="custom">\n                             <repeat name="iso_label" title="Isobaric Label" min="1" default="1">\n                                 <param name="internallabel" type="select" label="internal label" help="contains Lys">\n@@ -645,7 +585,7 @@\n                                    max="1"\n                                    help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>\n                         </when>\n-                        <when value="False"></when>\n+                        <when value="False"/>\n                     </conditional>\n                 </when>\n             </conditional>\n@@ -663,7 +603,7 @@\n                 <option value="mqpar">mqpar.xml</option>\n                 <option value="peptides">Peptides</option>\n                 <option value="evidence">Evidence</option>\n-                <option value="parameters">Tabular Paramters</option>\n+                <option value="parameters">Tabular Parameters</option>\n                 <option value="msms">MSMS</option>\n                 <option value="mzTab">mzTab</option>\n                 <option value="allPeptides">all peptides</option>\n@@ -780,7 +720,7 @@\n             </repeat>\n             <param name="dry_run" value="True" />\n             <param name="output" value="config,mqpar,mzTab" />\n-            <output name="config" file="02/config.yml" lines_diff="2" />\n+            <output name="config" file="02/config.yml" lines_diff="7" />\n             <!-- high difference due to unconsistant xml formatting in MQ -->\n             <output name="mqpar" file="02/mqpar.xml" lines_diff="24" />\n         </test>\n@@ -849,7 +789,7 @@\n             </repeat>\n             <param name="dry_run" value="True" />\n             <param name="output" value="config,mqpar,mzTab" />\n-            <output name="config" file="06/config.yml" lines_diff="2">\n+            <output name="config" file="06/config.yml" lines_diff="7">\n                 <assert_contents>\n                     <has_text_matching expression="lcmsRunType\\: \\\'Reporter ion MS3\\\'" />\n                 </assert_contents>\n@@ -936,6 +876,30 @@\n             <output name="config" file="04/config.yml" lines_diff="2" />\n             <output name="mqpar" file="04/mqpar.xml" lines_diff="12" />\n         </test>\n+        <!-- PTXQC Test -->\n+        <test expect_num_outputs="3">\n+            <param name="ftype" value=".mzxml" />\n+            <param name="fasta_files" value="ptxqc.fasta" />\n+            <param name="identifier_parse_rule" value="&gt;([^\\s]*)" />\n+            <param name="description_parse_rule" value="&gt;(.*)" />\n+            <repeat name="paramGroups">\n+                <param name="files" value="ptxqc.mzXML"/>\n+                <param name="variableModifications" value="Oxidation (M)" />\n+                <param name="fixedModifications" value="" />\n+                <conditional name="quant_method">\n+                    <param name="select_quant_method" value="reporter_ion_ms2" />\n+                    <conditional name="iso_labels">\n+                        <param name="labeling" value="tmt10plex" />\n+                    </conditional>\n+                </conditional>\n+            </repeat>\n+            <param name="do_it" value="True" />\n+            <param name="output" value="config,mqpar" />\n+            <output name="config" file="07/config.yml" lines_diff="2" />\n+            <!-- high difference due to unconsistant xml formatting in MQ -->\n+            <output name="mqpar" file="07/mqpar.xml" lines_diff="24" />\n+            <output name="ptxqc_report" file="07/combined/txt/report_v1.0.9_combined.pdf" compare="sim_size" />\n+        </test>\n     </tests>\n \n     <help><![CDATA[\n'
b
diff -r f522c08e900c -r d72c96ad9a16 test-data/07/combined/txt/report_v1.0.9_combined.pdf
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Binary file test-data/07/combined/txt/report_v1.0.9_combined.pdf has changed
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diff -r f522c08e900c -r d72c96ad9a16 test-data/07/config.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/07/config.yml Tue Jun 15 07:55:59 2021 +0000
[
@@ -0,0 +1,52 @@
+
+            fastaFiles: [/tmp/tmpaa0pqa83/files/b/b/8/dataset_bb8c7384-70b6-410c-8efd-e0cfdf7cb971.dat]
+            parseRules:
+              identifierParseRule: '>([^\s]*)'
+              descriptionParseRule: '>(.*)'
+            minUniquePeptides: 0
+            minPepLen: 7
+            maxPeptideMass: 4600
+            calcPeakProperties: False
+            writeMzTab: False
+            separateLfq: False
+            lfqStabilizeLargeRatios: True
+            lfqRequireMsms: True
+            advancedSiteIntensities: True
+            matchBetweenRuns: False
+            includeContaminants: True
+            minPeptideLengthForUnspecificSearch: 8
+            maxPeptideLengthForUnspecificSearch: 25
+            decoyMode: revert
+            peptideFdr: 0.01
+            proteinFdr: 0.01
+            quantMode: 1
+            restrictProteinQuantification: True
+            restrictMods: [Oxidation (M),Acetyl (Protein N-term)]
+            useCounterparts: True
+            paramGroups:
+              - files: ['ptxqc.mzXML']
+                maxMissedCleavages: 2
+                fixedModifications: []
+                variableModifications: [Oxidation (M)]
+                enzymes: [Trypsin/P]
+                enzymeMode: 0
+                lcmsRunType: 'Reporter ion MS2'
+                reporterMassTolerance: 0.003
+                reporterPif: 0
+                reporterFraction: 0
+                reporterBasePeakRatio: 0
+                filterPif: False
+                isobaricLabels:
+                    
+                    - [TMT10plex-Lys126C,TMT10plex-Nter126C,0,0,0,0,True]
+                    - [TMT10plex-Lys127N,TMT10plex-Nter127N,0,0,0,0,True]
+                    - [TMT10plex-Lys127C,TMT10plex-Nter127C,0,0,0,0,True]
+                    - [TMT10plex-Lys128N,TMT10plex-Nter128N,0,0,0,0,True]
+                    - [TMT10plex-Lys128C,TMT10plex-Nter128C,0,0,0,0,True]
+                    - [TMT10plex-Lys129N,TMT10plex-Nter129N,0,0,0,0,True]
+                    - [TMT10plex-Lys129C,TMT10plex-Nter129C,0,0,0,0,True]
+                    - [TMT10plex-Lys130N,TMT10plex-Nter130N,0,0,0,0,True]
+                    - [TMT10plex-Lys130C,TMT10plex-Nter130C,0,0,0,0,True]
+                    - [TMT10plex-Lys131N,TMT10plex-Nter131N,0,0,0,0,True]
+    
+        
\ No newline at end of file
b
diff -r f522c08e900c -r d72c96ad9a16 test-data/07/mqpar.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/07/mqpar.xml Tue Jun 15 07:55:59 2021 +0000
[
b'@@ -0,0 +1,539 @@\n+<?xml version="1.0" ?>\n+<MaxQuantParams>\n+\t<fastaFiles>\n+\t\t<FastaFileInfo>\n+\t\t\t<fastaFilePath>/tmp/tmpfqvn4g0u/files/5/b/8/dataset_5b803772-27b2-44fa-a4cf-8da6ee3cdfb8.dat</fastaFilePath>\n+\t\t\t<identifierParseRule>&gt;([^\\s]*)</identifierParseRule>\n+\t\t\t<descriptionParseRule>&gt;(.*)</descriptionParseRule>\n+\t\t\t<taxonomyParseRule/>\n+\t\t\t<variationParseRule/>\n+\t\t\t<modificationParseRule/>\n+\t\t\t<taxonomyId/>\n+\t\t</FastaFileInfo>\n+\t</fastaFiles>\n+\t<fastaFilesProteogenomics>\n+   </fastaFilesProteogenomics>\n+\t<fastaFilesFirstSearch>\n+   </fastaFilesFirstSearch>\n+\t<fixedSearchFolder/>\n+\t<andromedaCacheSize>350000</andromedaCacheSize>\n+\t<advancedRatios>True</advancedRatios>\n+\t<pvalThres>0.005</pvalThres>\n+\t<neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>\n+\t<neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>\n+\t<rtShift>False</rtShift>\n+\t<separateLfq>False</separateLfq>\n+\t<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>\n+\t<lfqRequireMsms>True</lfqRequireMsms>\n+\t<decoyMode>revert</decoyMode>\n+\t<boxCarMode>all</boxCarMode>\n+\t<includeContaminants>True</includeContaminants>\n+\t<maxPeptideMass>4600</maxPeptideMass>\n+\t<epsilonMutationScore>True</epsilonMutationScore>\n+\t<mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>\n+\t<proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>\n+\t<minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>\n+\t<minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>\n+\t<minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>\n+\t<minScoreModifiedPeptides>40</minScoreModifiedPeptides>\n+\t<secondPeptide>True</secondPeptide>\n+\t<matchBetweenRuns>False</matchBetweenRuns>\n+\t<matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>\n+\t<matchBetweenRunsFdr>False</matchBetweenRunsFdr>\n+\t<dependentPeptides>False</dependentPeptides>\n+\t<dependentPeptideFdr>0</dependentPeptideFdr>\n+\t<dependentPeptideMassBin>0</dependentPeptideMassBin>\n+\t<dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>\n+\t<dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>\n+\t<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>\n+\t<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>\n+\t<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>\n+\t<msmsConnection>False</msmsConnection>\n+\t<ibaq>False</ibaq>\n+\t<top3>False</top3>\n+\t<independentEnzymes>False</independentEnzymes>\n+\t<useDeltaScore>False</useDeltaScore>\n+\t<splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>\n+\t<taxonomyLevel>Species</taxonomyLevel>\n+\t<avalon>False</avalon>\n+\t<nModColumns>3</nModColumns>\n+\t<ibaqLogFit>False</ibaqLogFit>\n+\t<razorProteinFdr>True</razorProteinFdr>\n+\t<deNovoSequencing>False</deNovoSequencing>\n+\t<deNovoVarMods>True</deNovoVarMods>\n+\t<massDifferenceSearch>False</massDifferenceSearch>\n+\t<isotopeCalc>False</isotopeCalc>\n+\t<writePeptidesForSpectrumFile/>\n+\t<intensityPredictionsFile>\n+   </intensityPredictionsFile>\n+\t<minPepLen>7</minPepLen>\n+\t<psmFdrCrosslink>0.01</psmFdrCrosslink>\n+\t<peptideFdr>0.01</peptideFdr>\n+\t<proteinFdr>0.01</proteinFdr>\n+\t<siteFdr>0.01</siteFdr>\n+\t<minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>\n+\t<maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>\n+\t<useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>\n+\t<minPeptides>1</minPeptides>\n+\t<minRazorPeptides>1</minRazorPeptides>\n+\t<minUniquePeptides>0</minUniquePeptides>\n+\t<useCounterparts>True</useCounterparts>\n+\t<advancedSiteIntensities>True</advancedSiteIntensities>\n+\t<customProteinQuantification>False</customProteinQuantification>\n+\t<customProteinQuantificationFile/>\n+\t<minRatioCount>2</minRatioCount>\n+\t<restrictProteinQuantification>True</restrictProteinQuantification>\n+\t<restrictMods>\n+\t\t<string>Oxidation (M)</string>\n+\t\t<string>Acetyl (Protein N-term)</string>\n+\t</restrictMods>\n+\t<matchingTimeWindow>0</matchingTimeWindow>'..b'<IncludeWater>True</IncludeWater>\n+\t\t\t<IncludeAmmonia>True</IncludeAmmonia>\n+\t\t\t<DependentLosses>True</DependentLosses>\n+\t\t\t<Recalibration>False</Recalibration>\n+\t\t</msmsParams>\n+\t\t<msmsParams>\n+\t\t\t<Name>Unknown</Name>\n+\t\t\t<MatchTolerance>20</MatchTolerance>\n+\t\t\t<MatchToleranceInPpm>True</MatchToleranceInPpm>\n+\t\t\t<DeisotopeTolerance>7</DeisotopeTolerance>\n+\t\t\t<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>\n+\t\t\t<DeNovoTolerance>10</DeNovoTolerance>\n+\t\t\t<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>\n+\t\t\t<Deisotope>True</Deisotope>\n+\t\t\t<Topx>12</Topx>\n+\t\t\t<TopxInterval>100</TopxInterval>\n+\t\t\t<HigherCharges>True</HigherCharges>\n+\t\t\t<IncludeWater>True</IncludeWater>\n+\t\t\t<IncludeAmmonia>True</IncludeAmmonia>\n+\t\t\t<DependentLosses>True</DependentLosses>\n+\t\t\t<Recalibration>False</Recalibration>\n+\t\t</msmsParams>\n+\t</msmsParamsArray>\n+\t<fragmentationParamsArray>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>CID</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>HCD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>PQD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETHCD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>ETCID</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>UVPD</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t\t<fragmentationParams>\n+\t\t\t<Name>Unknown</Name>\n+\t\t\t<Connected>False</Connected>\n+\t\t\t<ConnectedScore0>1</ConnectedScore0>\n+\t\t\t<ConnectedScore1>1</ConnectedScore1>\n+\t\t\t<ConnectedScore2>1</ConnectedScore2>\n+\t\t\t<InternalFragments>False</InternalFragments>\n+\t\t\t<InternalFragmentWeight>1</InternalFragmentWeight>\n+\t\t\t<InternalFragmentAas>KRH</InternalFragmentAas>\n+\t\t</fragmentationParams>\n+\t</fragmentationParamsArray>\n+</MaxQuantParams>\n+\n'
b
diff -r f522c08e900c -r d72c96ad9a16 test-data/ptxqc.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ptxqc.fasta Tue Jun 15 07:55:59 2021 +0000
b
b'@@ -0,0 +1,998 @@\n+>sp|P16402|H13_HUMAN Histone H1.3 OS=Homo sapiens OX=9606 GN=H1-3 PE=1 SV=2\n+MSETAPLAPTIPAPAEKTPVKKKAKKAGATAGKRKASGPPVSELITKAVAASKERSGVSL\n+AALKKALAAAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEGKPK\n+AKKAGAAKPRKPAGAAKKPKKVAGAATPKKSIKKTPKKVKKPATAAGTKKVAKSAKKVKT\n+PQPKKAAKSPAKAKAPKPKAAKPKSGKPKVTKAKKAAPKKK\n+>sp|P49736|MCM2_HUMAN DNA replication licensing factor MCM2 OS=Homo sapiens OX=9606 GN=MCM2 PE=1 SV=4\n+MAESSESFTMASSPAQRRRGNDPLTSSPGRSSRRTDALTSSPGRDLPPFEDESEGLLGTE\n+GPLEEEEDGEELIGDGMERDYRAIPELDAYEAEGLALDDEDVEELTASQREAAERAMRQR\n+DREAGRGLGRMRRGLLYDSDEEDEERPARKRRQVERATEDGEEDEEMIESIENLEDLKGH\n+SVREWVSMAGPRLEIHHRFKNFLRTHVDSHGHNVFKERISDMCKENRESLVVNYEDLAAR\n+EHVLAYFLPEAPAELLQIFDEAALEVVLAMYPKYDRITNHIHVRISHLPLVEELRSLRQL\n+HLNQLIRTSGVVTSCTGVLPQLSMVKYNCNKCNFVLGPFCQSQNQEVKPGSCPECQSAGP\n+FEVNMEETIYQNYQRIRIQESPGKVAAGRLPRSKDAILLADLVDSCKPGDEIELTGIYHN\n+NYDGSLNTANGFPVFATVILANHVAKKDNKVAVGELTDEDVKMITSLSKDQQIGEKIFAS\n+IAPSIYGHEDIKRGLALALFGGEPKNPGGKHKVRGDINVLLCGDPGTAKSQFLKYIEKVS\n+SRAIFTTGQGASAVGLTAYVQRHPVSREWTLEAGALVLADRGVCLIDEFDKMNDQDRTSI\n+HEAMEQQSISISKAGIVTSLQARCTVIAAANPIGGRYDPSLTFSENVDLTEPIISRFDIL\n+CVVRDTVDPVQDEMLARFVVGSHVRHHPSNKEEEGLANGSAAEPAMPNTYGVEPLPQEVL\n+KKYIIYAKERVHPKLNQMDQDKVAKMYSDLRKESMATGSIPITVRHIESMIRMAEAHARI\n+HLRDYVIEDDVNMAIRVMLESFIDTQKFSVMRSMRKTFARYLSFRRDNNELLLFILKQLV\n+AEQVTYQRNRFGAQQDTIEVPEKDLVDKARQINIHNLSAFYDSELFRMNKFSHDLKRKMI\n+LQQF\n+>sp|P78414|IRX1_HUMAN Iroquois-class homeodomain protein IRX-1 OS=Homo sapiens OX=9606 GN=IRX1 PE=2 SV=3\n+MSFPQLGYPQYLSAAGPGAYGGERPGVLAAAAAAAAAASSGRPGAAELGGGAGAAAVTSV\n+LGMYAAAGPYAGAPNYSAFLPYAADLSLFSQMGSQYELKDNPGVHPATFAAHTAPAYYPY\n+GQFQYGDPGRPKNATRESTSTLKAWLNEHRKNPYPTKGEKIMLAIITKMTLTQVSTWFAN\n+ARRRLKKENKVTWGARSKDQEDGALFGSDTEGDPEKAEDDEEIDLESIDIDKIDEHDGDQ\n+SNEDDEDKAEAPHAPAAPSALARDQGSPLAAADVLKPQDSPLGLAKEAPEPGSTRLLSPG\n+AAAGGLQGAPHGKPKIWSLAETATSPDGAPKASPPPPAGHPGAHGPSAGAPLQHPAFLPS\n+HGLYTCHIGKFSNWTNSAFLAQGSLLNMRSFLGVGAPHAAPHGPHLPAPPPPQPPVAIAP\n+GALNGDKASVRSSPTLPERDLVPRPDSPAQQLKSPFQPVRDNSLAPQEGTPRILAALPSA\n+>sp|Q8N163|CCAR2_HUMAN Cell cycle and apoptosis regulator protein 2 OS=Homo sapiens OX=9606 GN=CCAR2 PE=1 SV=2\n+MSQFKRQRINPLPGGRNFSGTASTSLLGPPPGLLTPPVATELSQNARHLQGGEKQRVFTG\n+IVTSLHDYFGVVDEEVFFQLSVVKGRLPQLGEKVLVKAAYNPGQAVPWNAVKVQTLSNQP\n+LLKSPAPPLLHVAALGQKQGILGAQPQLIFQPHRIPPLFPQKPLSLFQTSHTLHLSHLNR\n+FPARGPHGRLDQGRSDDYDSKKRKQRAGGEPWGAKKPRHDLPPYRVHLTPYTVDSPICDF\n+LELQRRYRSLLVPSDFLSVHLSWLSAFPLSQPFSLHHPSRIQVSSEKEAAPDAGAEPITA\n+DSDPAYSSKVLLLSSPGLEELYRCCMLFVDDMAEPRETPEHPLKQIKFLLGRKEEEAVLV\n+GGEWSPSLDGLDPQADPQVLVRTAIRCAQAQTGIDLSGCTKWWRFAEFQYLQPGPPRRLQ\n+TVVVYLPDVWTIMPTLEEWEALCQQKAAEAAPPTQEAQGETEPTEQAPDALEQAADTSRR\n+NAETPEATTQQETDTDLPEAPPPPLEPAVIARPGCVNLSLHGIVEDRRPKERISFEVMVL\n+AELFLEMLQRDFGYRVYKMLLSLPEKVVSPPEPEKEEAAKEEATKEEEAIKEEVVKEPKD\n+EAQNEGPATESEAPLKEDGLLPKPLSSGGEEEEKPRGEASEDLCEMALDPELLLLRDDGE\n+EEFAGAKLEDSEVRSVASNQSEMEFSSLQDMPKELDPSAVLPLDCLLAFVFFDANWCGYL\n+HRRDLERILLTLGIRLSAEQAKQLVSRVVTQNICQYRSLQYSRQEGLDGGLPEEVLFGNL\n+DLLPPPGKSTKPGAAPTEHKALVSHNGSLINVGSLLQRAEQQDSGRLYLENKIHTLELKL\n+EESHNRFSATEVTNKTLAAEMQELRVRLAEAEETARTAERQKSQLQRLLQELRRRLTPLQ\n+LEIQRVVEKADSWVEKEEPAPSN\n+>sp|Q9UKA8|RCAN3_HUMAN Calcipressin-3 OS=Homo sapiens OX=9606 GN=RCAN3 PE=1 SV=1\n+MLRDTMKSWNDSQSDLCSTDQEEEEEMIFGENEDDLDEMMDLSDLPTSLFACSVHEAVFE\n+AREQKERFEALFTIYDDQVTFQLFKSFRRVRINFSKPEAAARARIELHETDFNGQKLKLY\n+FAQVQMSGEVRDKSYLLPPQPVKQFLISPPASPPVGWKQSEDAMPVINYDLLCAVSKLGP\n+GEKYELHAGTESTPSVVVHVCESETEEEEETKNPKQKIAQTRRPDPPTAALNEPQTFDCA\n+L\n+>sp|Q6ZU80|CE128_HUMAN Centrosomal protein of 128 kDa OS=Homo sapiens OX=9606 GN=CEP128 PE=1 SV=2\n+MAESSSESDHFRCRDRLSPWAARSTHRGTRSLPTVEVTEKVNTITSTLQDTSRNLRQVDQ\n+MLGRYREYSNGQAGAIEHLKESLEQSIDQLRSQRLLRNSGGRSISVTSLSASDLDGGTGS\n+ELHHFPPTSPLKDYGDPQGIKRMRSRTGVRFVQETDDMTQLHGFHQSLRDLSSEQIRLGD\n+DFNRELSRRSRSDAETKRALEELTEKLNEAQKQEVVSDRVERRLQELEREMRTERELVER\n+RQDQLGLMSLQLQEALKKQEAKADEHEGAIKNKLRQTETEKNQLEQELELSRRLLNQSEG\n+SRETLLHQVEELRTQLTKAEGDRKGLQHQVSQISKQQSNYQDEQGEDWRFRRGVEREKQD\n+LEKQMSDLRVQLNFSAMASELEEVKRCMERKDKEKAHLASQVENLTRELENGEKQQLQML\n+DRLKEIQNHFDTCEAERKHADLQISELTRHAEDATKQAERYLSELQQSEALKEEAEKRRE\n+DLKLKAQESIRQWKLKHKKLERALEKQSETVDELTGKN'..b'KEPPWCDGSYCYECTARFGVTTRKHHCRHCGRLLCHKCSTK\n+EIPIIKFDLNKPVRVCNICFDVLTLGGVS\n+>sp|Q9H4A4|AMPB_HUMAN Aminopeptidase B OS=Homo sapiens OX=9606 GN=RNPEP PE=1 SV=2\n+MASGEHSPGSGAARRPLHSAQAVDVASASNFRAFELLHLHLDLRAEFGPPGPGAGSRGLS\n+GTAVLDLRCLEPEGAAELRLDSHPCLEVTAAALRRERPGSEEPPAEPVSFYTQPFSHYGQ\n+ALCVSFPQPCRAAERLQVLLTYRVGEGPGVCWLAPEQTAGKKKPFVYTQGQAVLNRAFFP\n+CFDTPAVKYKYSALIEVPDGFTAVMSASTWEKRGPNKFFFQMCQPIPSYLIALAIGDLVS\n+AEVGPRSRVWAEPCLIDAAKEEYNGVIEEFLATGEKLFGPYVWGRYDLLFMPPSFPFGGM\n+ENPCLTFVTPCLLAGDRSLADVIIHEISHSWFGNLVTNANWGEFWLNEGFTMYAQRRIST\n+ILFGAAYTCLEAATGRALLRQHMDITGEENPLNKLRVKIEPGVDPDDTYNETPYEKGFCF\n+VSYLAHLVGDQDQFDSFLKAYVHEFKFRSILADDFLDFYLEYFPELKKKRVDIIPGFEFD\n+RWLNTPGWPPYLPDLSPGDSLMKPAEELAQLWAAEELDMKAIEAVAISPWKTYQLVYFLD\n+KILQKSPLPPGNVKKLGDTYPSISNARNAELRLRWGQIVLKNDHQEDFWKVKEFLHNQGK\n+QKYTLPLYHAMMGGSEVAQTLAKETFASTASQLHSNVVNYVQQIVAPKGS\n+>sp|Q8TBH0|ARRD2_HUMAN Arrestin domain-containing protein 2 OS=Homo sapiens OX=9606 GN=ARRDC2 PE=1 SV=2\n+MLFDKVKAFSVQLDGATAGVEPVFSGGQAVAGRVLLELSSAARVGALRLRARGRAHVHWT\n+ESRSAGSSTAYTQSYSERVEVVSHRATLLAPDTGETTTLPPGRHEFLFSFQLPPTLVTSF\n+EGKHGSVRYCIKATLHRPWVPARRARKVFTVIEPVDINTPALLAPQAGAREKVARSWYCN\n+RGLVSLSAKIDRKGYTPGEVIPVFAEIDNGSTRPVLPRAAVVQTQTFMARGARKQKRAVV\n+ASLAGEPVGPGQRALWQGRALRIPPVGPSILHCRVLHVDYALKVCVDIPGTSKLLLELPL\n+VIGTIPLHPFGSRSSSVGSHASFLLDWRLGALPERPEAPPEYSEVVADTEEAALGQSPFP\n+LPQDPDMSLEGPFFAYIQEFRYRPPPLYSEEDPNPLLGDMRPRCMTC\n+>sp|P00966|ASSY_HUMAN Argininosuccinate synthase OS=Homo sapiens OX=9606 GN=ASS1 PE=1 SV=2\n+MSSKGSVVLAYSGGLDTSCILVWLKEQGYDVIAYLANIGQKEDFEEARKKALKLGAKKVF\n+IEDVSREFVEEFIWPAIQSSALYEDRYLLGTSLARPCIARKQVEIAQREGAKYVSHGATG\n+KGNDQVRFELSCYSLAPQIKVIAPWRMPEFYNRFKGRNDLMEYAKQHGIPIPVTPKNPWS\n+MDENLMHISYEAGILENPKNQAPPGLYTKTQDPAKAPNTPDILEIEFKKGVPVKVTNVKD\n+GTTHQTSLELFMYLNEVAGKHGVGRIDIVENRFIGMKSRGIYETPAGTILYHAHLDIEAF\n+TMDREVRKIKQGLGLKFAELVYTGFWHSPECEFVRHCIAKSQERVEGKVQVSVLKGQVYI\n+LGRESPLSLYNEELVSMNVQGDYEPTDATGFININSLRLKEYHRLQSKVTAK\n+>sp|Q7L266|ASGL1_HUMAN Isoaspartyl peptidase/L-asparaginase OS=Homo sapiens OX=9606 GN=ASRGL1 PE=1 SV=2\n+MNPIVVVHGGGAGPISKDRKERVHQGMVRAATVGYGILREGGSAVDAVEGAVVALEDDPE\n+FNAGCGSVLNTNGEVEMDASIMDGKDLSAGAVSAVQCIANPIKLARLVMEKTPHCFLTDQ\n+GAAQFAAAMGVPEIPGEKLVTERNKKRLEKEKHEKGAQKTDCQKNLGTVGAVALDCKGNV\n+AYATSTGGIVNKMVGRVGDSPCLGAGGYADNDIGAVSTTGHGESILKVNLARLTLFHIEQ\n+GKTVEEAADLSLGYMKSRVKGLGGLIVVSKTGDWVAKWTSTSMPWAAAKDGKLHFGIDPD\n+DTTITDLP\n+>sp|P46597|ASMT_HUMAN Acetylserotonin O-methyltransferase OS=Homo sapiens OX=9606 GN=ASMT PE=1 SV=1\n+MGSSEDQAYRLLNDYANGFMVSQVLFAACELGVFDLLAEAPGPLDVAAVAAGVRASAHGT\n+ELLLDICVSLKLLKVETRGGKAFYRNTELSSDYLTTVSPTSQCSMLKYMGRTSYRCWGHL\n+ADAVREGRNQYLETFGVPAEELFTAIYRSEGERLQFMQALQEVWSVNGRSVLTAFDLSVF\n+PLMCDLGGGAGALAKECMSLYPGCKITVFDIPEVVWTAKQHFSFQEEEQIDFQEGDFFKD\n+PLPEADLYILARVLHDWADGKCSHLLERIYHTCKPGGGILVIESLLDEDRRGPLLTQLYS\n+LNMLVQTEGQERTPTHYHMLLSSAGFRDFQFKKTGAIYDAILARK\n+>sp|O43683|BUB1_HUMAN Mitotic checkpoint serine/threonine-protein kinase BUB1 OS=Homo sapiens OX=9606 GN=BUB1 PE=1 SV=1\n+MDTPENVLQMLEAHMQSYKGNDPLGEWERYIQWVEENFPENKEYLITLLEHLMKEFLDKK\n+KYHNDPRFISYCLKFAEYNSDLHQFFEFLYNHGIGTLSSPLYIAWAGHLEAQGELQHASA\n+VLQRGIQNQAEPREFLQQQYRLFQTRLTETHLPAQARTSEPLHNVQVLNQMITSKSNPGN\n+NMACISKNQGSELSGVISSACDKESNMERRVITISKSEYSVHSSLASKVDVEQVVMYCKE\n+KLIRGESEFSFEELRAQKYNQRRKHEQWVNEDRHYMKRKEANAFEEQLLKQKMDELHKKL\n+HQVVETSHEDLPASQERSEVNPARMGPSVGSQQELRAPCLPVTYQQTPVNMEKNPREAPP\n+VVPPLANAISAALVSPATSQSIAPPVPLKAQTVTDSMFAVASKDAGCVNKSTHEFKPQSG\n+AEIKEGCETHKVANTSSFHTTPNTSLGMVQATPSKVQPSPTVHTKEALGFIMNMFQAPTL\n+PDISDDKDEWQSLDQNEDAFEAQFQKNVRSSGAWGVNKIISSLSSAFHVFEDGNKENYGL\n+PQPKNKPTGARTFGERSVSRLPSKPKEEVPHAEEFLDDSTVWGIRCNKTLAPSPKSPGDF\n+TSAAQLASTPFHKLPVESVHILEDKENVVAKQCTQATLDSCEENMVVPSRDGKFSPIQEK\n+SPKQALSSHMYSASLLRLSQPAAGGVLTCEAELGVEACRLTDTDAAIAEDPPDAIAGLQA\n+EWMQMSSLGTVDAPNFIVGNPWDDKLIFKLLSGLSKPVSSYPNTFEWQCKLPAIKPKTEF\n+QLGSKLVYVHHLLGEGAFAQVYEATQGDLNDAKNKQKFVLKVQKPANPWEFYIGTQLMER\n+LKPSMQHMFMKFYSAHLFQNGSVLVGELYSYGTLLNAINLYKNTPEKVMPQGLVISFAMR\n+MLYMIEQVHDCEIIHGDIKPDNFILGNGFLEQDDEDDLSAGLALIDLGQSIDMKLFPKGT\n+IFTAKCETSGFQCVEMLSNKPWNYQIDYFGVAATVYCMLFGTYMKVKNEGGECKPEGLFR\n+RLPHLDMWNEFFHVMLNIPDCHHLPSLDLLRQKLKKVFQQHYTNKIRALRNRLIVLLLEC\n+KRSRK\n'
b
diff -r f522c08e900c -r d72c96ad9a16 test-data/ptxqc.mzXML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ptxqc.mzXML Tue Jun 15 07:55:59 2021 +0000
[
b'@@ -0,0 +1,1697 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.1" \n+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" \n+ xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.1 http://sashimi.sourceforge.net/schema_revision/mzXML_3.1/mzXML_idx_3.1.xsd">\n+\t<msRun scanCount="100" startTime="PT1000.14828S" endTime="PT1019.82204S" >\n+\t\t<parentFile fileName="FileFilter_on_data_13__out.mzML" fileType="processedData" fileSha1="70ccfd499ae5f6dcf702437f45812d8a5a1582c5"/>\n+\t\t<msInstrument>\n+\t\t\t<msManufacturer category="msManufacturer" value="Thermo Scientific"/>\n+\t\t\t<msModel category="msModel" value=""/>\n+\t\t\t<msIonisation category="msIonisation" value="NSI"/>\n+\t\t\t<msMassAnalyzer category="msMassAnalyzer" value="Quadrupole"/>\n+\t\t\t<msDetector category="msDetector" value=""/>\n+\t\t\t<software type="acquisition" name="Xcalibur" version="2.8-280502/2.8.1.2806"/>\n+\t\t\t<nameValue name="instrument serial number" value="Exactive Series slot #0012"/>\n+\t\t</msInstrument>\n+\t\t<dataProcessing deisotoped="0" chargeDeconvoluted="0" centroided="0">\n+\t\t\t<software type="processing" name="ProteoWizard software" version="3.0.20287"/>\n+\t\t</dataProcessing>\n+\t\t<dataProcessing deisotoped="0" chargeDeconvoluted="0" centroided="0">\n+\t\t\t<software type="processing" name="FileFilter" version="2.6.0-pre-exported-20201001" completionTime="2021-04-09T08:45:00"/>\n+\t\t\t<processingOperation name="parameter: in" value="in/http___ftp_pride_ebi_ac_uk_pride_data_archive_2020_05_PXD014145_MFA390_mzML.mzML"/>\n+\t\t\t<processingOperation name="parameter: in_type" value=""/>\n+\t\t\t<processingOperation name="parameter: out" value="out/output.mzML"/>\n+\t\t\t<processingOperation name="parameter: out_type" value="mzML"/>\n+\t\t\t<processingOperation name="parameter: rt" value="1000:1200"/>\n+\t\t\t<processingOperation name="parameter: mz" value=":"/>\n+\t\t\t<processingOperation name="parameter: int" value=":"/>\n+\t\t\t<processingOperation name="parameter: sort" value="false"/>\n+\t\t\t<processingOperation name="parameter: log" value="log.txt"/>\n+\t\t\t<processingOperation name="parameter: debug" value="0"/>\n+\t\t\t<processingOperation name="parameter: threads" value="1"/>\n+\t\t\t<processingOperation name="parameter: no_progress" value="true"/>\n+\t\t\t<processingOperation name="parameter: force" value="false"/>\n+\t\t\t<processingOperation name="parameter: test" value="false"/>\n+\t\t\t<processingOperation name="parameter: peak_options:sn" value="0.0"/>\n+\t\t\t<processingOperation name="parameter: peak_options:rm_pc_charge" value="[]"/>\n+\t\t\t<processingOperation name="parameter: peak_options:pc_mz_range" value=":"/>\n+\t\t\t<processingOperation name="parameter: peak_options:pc_mz_list" value="[]"/>\n+\t\t\t<processingOperation name="parameter: peak_options:level" value="[1, 2, 3]"/>\n+\t\t\t<processingOperation name="parameter: peak_options:sort_peaks" value="false"/>\n+\t\t\t<processingOperation name="parameter: peak_options:no_chromatograms" value="false"/>\n+\t\t\t<processingOperation name="parameter: peak_options:remove_chromatograms" value="false"/>\n+\t\t\t<processingOperation name="parameter: peak_options:remove_empty" value="false"/>\n+\t\t\t<processingOperation name="parameter: peak_options:mz_precision" value="64"/>\n+\t\t\t<processingOperation name="parameter: peak_options:int_precision" value="32"/>\n+\t\t\t<processingOperation name="parameter: peak_options:indexed_file" value="true"/>\n+\t\t\t<processingOperation name="parameter: peak_options:zlib_compression" value="false"/>\n+\t\t\t<processingOperation name="parameter: peak_options:numpress:masstime" value="none"/>\n+\t\t\t<processingOperation name="parameter: peak_options:numpress:lossy_mass_accuracy" value="-1.0"/>\n+\t\t\t<processingOperation name="parameter: peak_options:numpress:intensity" value="none"/>\n+\t\t\t<processingOperation name="parameter: peak_options:numpress:float_da" value="none"/>\n+\t\t\t<processingOperation name="parameter: spectra:remove_zoom" value="false"/>\n+\t\t\t<processingOperation name="parameter: spectra:remov'..b'15618668535978"/>\n+\t\t\t<nameValue name="highest observed m/z" value="2020.220186465410961"/>\n+\t\t\t<nameValue name="filter string" value="FTMS + p NSI Full ms [300.0000-2000.0000]"/>\n+\t\t\t<nameValue name="preset scan configuration" value="1"/>\n+\t\t</scan>\n+\t</msRun>\n+<index name = "scan" >\n+<offset id = "1" >10006</offset>\n+<offset id = "2" >88366</offset>\n+<offset id = "3" >166720</offset>\n+<offset id = "4" >241577</offset>\n+<offset id = "5" >245018</offset>\n+<offset id = "6" >247738</offset>\n+<offset id = "7" >325024</offset>\n+<offset id = "8" >410926</offset>\n+<offset id = "9" >488873</offset>\n+<offset id = "10" >491619</offset>\n+<offset id = "11" >494878</offset>\n+<offset id = "12" >499192</offset>\n+<offset id = "13" >502797</offset>\n+<offset id = "14" >505189<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