| Next changeset 1:b5489f81c2fa (2023-10-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 |
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added:
macros.xml pepquery2.xml test-data/AgilentMassHunterTest.mzXML test-data/Uniprot.fasta test-data/iTRAQ_f4.mgf test-data/immunopeptidomics.mgf test-data/novel_peptides test-data/novel_proteins.fa test-data/pep.txt test-data/small-index-filter.mzML |
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| diff -r 000000000000 -r a07976bbc4d9 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Nov 06 16:25:25 2022 +0000 |
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| b'@@ -0,0 +1,1302 @@\n+ <macros>\n+ <token name="@TOOL_VERSION@">2.0.2</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1101/gr.235028.118</citation>\n+ <citation type="doi">10.1038/s41467-020-15456-w</citation>\n+ </citations>\n+ </xml>\n+ <token name="@PEPQUERY_DOCUMANTATION_URL@">http://pepquery.org/document.html</token>\n+\n+ <token name="@CMD_IMPORTS@">\n+#import re\n+#import os.path\n+#def identifier_or_name($input1)\n+ #if hasattr($input1, \'element_identifier\')\n+ #return $input1.element_identifier\n+ #else\n+ #return $input1.name\n+ #end if\n+#end def\n+#def clean($name1)\n+ #set $name_clean = $re.sub(\'[^\\w\\-_]\', \'_\', $re.sub(\'(?i)[.](fa|fas|fasta|imzml|mzml|mzxml|mgf|raw)$\',\'\', $re.sub(\'.*/\',\'\', $name1.rstrip(\'.gz\'))))\n+ #return $name_clean\n+#end def\n+#def ln_name($ds)\n+ #set $ext = \'\'\n+ #if $ds.is_of_type(\'mzml\') or $ds.is_of_type(\'imzml\')\n+ #set $ext = ".mzML"\n+ #else if $ds.is_of_type(\'mzxml\')\n+ #set $ext = ".mzXML"\n+ #else if $ds.is_of_type(\'mgf\')\n+ #set $ext = ".mgf"\n+ #else if $ds.is_of_type(\'thermo.raw\')\n+ #set $ext = ".raw"\n+ #else if $ds.is_of_type(\'fasta\')\n+ #set $ext = ".fasta"\n+ #end if\n+ #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)\n+ #return $name\n+#end def\n+ </token>\n+\n+ <token name="@INDEX_SPECTRUM_FILES@"><![CDATA[\n+#def index_spectrum_files($idx_dir,$spectrum_files)\n+#set global $input_dir = \'input_dir\'\n+#set global $index_dir = \'index_dir\'\n+mkdir -p $input_dir &&\n+#if $idx_dir\n+mkdir -p $idx_dir &&\n+ln -s $idx_dir $index_dir &&\n+#else\n+mkdir -p $index_dir &&\n+#end if\n+#if isinstance($spectrum_files, list)\n+ #set $sfiles = $spectrum_files\n+#else\n+ #set $sfiles = [$spectrum_files]\n+#end if\n+#for $sf in $sfiles\n+ #set $i_name = $ln_name($sf)\n+ #set $p_name = $os.path.join($input_dir, $i_name)\n+ ln -s \'$sf\' \'$p_name\' &&\n+#end for\n+pepquery index -i input_dir -o index_dir\n+#end def\n+ ]]></token>\n+\n+ <xml name="pepquerydb_options">\n+ <option value="all">all</option>\n+ <option value="w">w:global proteome</option>\n+ <option value="p">p:phosphorylation</option>\n+ <option value="a">a:acetylation</option>\n+ <option value="u">u:ubiquitination</option>\n+ <option value="g">g:glycosylation</option>\n+ <option value="Academia_Sinica_LUAD100_Phosphoproteome_PDC000220">Academia_Sinica_LUAD100_Phosphoproteome_PDC000220</option>\n+ <option value="Academia_Sinica_LUAD100_Proteome_PDC000219">Academia_Sinica_LUAD100_Proteome_PDC000219</option>\n+ <option value="CCLE_proteome_MSV000085836">CCLE_proteome_MSV000085836</option>\n+ <option value="CPTAC">CPTAC</option>\n+ <option value="CPTAC_CCRCC_Discovery_Study_Phosphoproteme_PDC000128">CPTAC_CCRCC_Discovery_Study_Phosphoproteme_PDC000128</option>\n+ <option value="CPTAC_CCRCC_Discovery_Study_Proteome_PDC000127">CPTAC_CCRCC_Discovery_Study_Proteome_PDC000127</option>\n+ <option value="CPTAC_GBM_Discovery_Study_Acetylome_PDC000245">CPTAC_GBM_Discovery_Study_Acetylome_PDC000245</option>\n+ <option value="CPTAC_GBM_Discovery_Study_Phosphoproteome_PDC000205">CPTAC_GBM_Discovery_Study_Phosphoproteome_PDC000205</option>\n+ <option value="CPTAC_GBM_Discovery_Study_Proteome_PDC000204">CPTAC_GBM_Discovery_Study_Proteome_PDC000204</option>\n+ <option value="CPTAC_HNSCC_Discovery_Study_Phosphoproteome_PDC000222">CPTAC_HNSCC_Discovery_Study_Phosphoproteome_PDC000222</option>\n+ <option value="CPTAC_HNSCC_Discovery_Study_Proteome_PDC000221">CPTAC_HNSCC_Discovery_Study_Proteome_PDC000221</optio'..b'735]</option>\n+ <option value="1122">1122: Trimethyl of K [42.04695]</option>\n+ <option value="1123">1123: Trimethyl of protein A [42.04695]</option>\n+ <option value="1124">1124: Trimethyl of R [42.04695]</option>\n+ <option value="1125">1125: Trimethyl:13C(3)2H(9) of K [54.113505]</option>\n+ <option value="1126">1126: Trimethyl:13C(3)2H(9) of R [54.113505]</option>\n+ <option value="1127">1127: Trimethyl:2H(9) of K [51.103441]</option>\n+ <option value="1128">1128: Trimethyl:2H(9) of R [51.103441]</option>\n+ <option value="1129">1129: Trioxidation of W [47.984744]</option>\n+ <option value="1130">1130: Trioxidation of Y [47.984744]</option>\n+ <option value="1131">1131: Tris of N [104.071154]</option>\n+ <option value="1132">1132: Triton of C-term [188.156501]</option>\n+ <option value="1133">1133: Triton of N-term [188.156501]</option>\n+ <option value="1134">1134: Trp->Hydroxykynurenin of W [19.989829]</option>\n+ <option value="1135">1135: Trp->Kynurenin of W [3.994915]</option>\n+ <option value="1136">1136: Trp->Oxolactone of W [13.979265]</option>\n+ <option value="1137">1137: Tween20 of N-term [165.164326]</option>\n+ <option value="1138">1138: Tyr->Dha of Y [-94.041865]</option>\n+ <option value="1139">1139: Ub-amide of C [196.108602]</option>\n+ <option value="1140">1140: Ub-Br2 of C [100.063663]</option>\n+ <option value="1141">1141: Ub-VME of C [173.092617]</option>\n+ <option value="1142">1142: UgiJoullieProGly of D [154.074228]</option>\n+ <option value="1143">1143: UgiJoullieProGly of E [154.074228]</option>\n+ <option value="1144">1144: Xlink:BMOE of C [220.048407]</option>\n+ <option value="1145">1145: Xlink:DFDNB of K [203.998263]</option>\n+ <option value="1146">1146: Xlink:DFDNB of N [203.998263]</option>\n+ <option value="1147">1147: Xlink:DFDNB of Q [203.998263]</option>\n+ <option value="1148">1148: Xlink:DFDNB of R [203.998263]</option>\n+ <option value="1149">1149: Xlink:DMP of K [122.084398]</option>\n+ <option value="1150">1150: Xlink:DMP of protein N-term [122.084398]</option>\n+ <option value="1151">1151: Xlink:DMP-de of K [140.094963]</option>\n+ <option value="1152">1152: Xlink:DMP-de of protein N-term [140.094963]</option>\n+ <option value="1153">1153: Xlink:DMP-s of K [154.110613]</option>\n+ <option value="1154">1154: Xlink:DMP-s of protein N-term [154.110613]</option>\n+ <option value="1155">1155: Xlink:DSS of K [156.078644]</option>\n+ <option value="1156">1156: Xlink:DSS of protein N-term [156.078644]</option>\n+ <option value="1157">1157: Xlink:DSS-NH2 of K [155.094629]</option>\n+ <option value="1158">1158: Xlink:DSS-NH2 of protein N-term [155.094629]</option>\n+ <option value="1159">1159: Xlink:DST of K [132.005873]</option>\n+ <option value="1160">1160: Xlink:DST of protein N-term [132.005873]</option>\n+ <option value="1161">1161: Xlink:DTBPc of K [87.01427]</option>\n+ <option value="1162">1162: Xlink:DTBPc of N [87.01427]</option>\n+ <option value="1163">1163: Xlink:DTBPc of protein N-term [87.01427]</option>\n+ <option value="1164">1164: Xlink:DTBPc of Q [87.01427]</option>\n+ <option value="1165">1165: Xlink:DTBPc of R [87.01427]</option>\n+ <option value="1166">1166: Xlink:DTSSP of K [191.991486]</option>\n+ <option value="1167">1167: Xlink:DTSSP of protein N-term [191.991486]</option>\n+ <option value="1168">1168: Xlink:EGS115 of K [115.026943]</option>\n+ <option value="1169">1169: Xlink:EGS115 of protein N-term [115.026943]</option>\n+ <option value="1170">1170: Xlink:EGS244 of K [244.058303]</option>\n+ <option value="1171">1171: Xlink:EGS244 of protein N-term [244.058303]</option>\n+ <option value="1172">1172: Xlink:SMCC of C [237.100108]</option>\n+ </xml>\n+</macros>\n' |
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| diff -r 000000000000 -r a07976bbc4d9 pepquery2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pepquery2.xml Sun Nov 06 16:25:25 2022 +0000 |
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| b'@@ -0,0 +1,790 @@\n+<tool id="pepquery2" name="PepQuery2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n+ <description>Peptide-centric search engine for novel peptide identification and validation.</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <requirements> \n+ <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="Failed" />\n+ <regex match="Exception"\n+ source="stderr"\n+ level="fatal"\n+ description="java Exception" />\n+ </stdio>\n+ <command><![CDATA[\n+@CMD_IMPORTS@\n+#if $req_inputs.db_type.db_type_selector == \'history\'\n+ #set $db_file = $re.sub(\'\\s\',\'_\',$re.sub(\'[.][^.]*$\',\'\',$req_inputs.db_type.db_file.display_name.split(\'/\')[-1])) + ".fa"\n+ ln -s \'$req_inputs.db_type.db_file\' \'$db_file\' &&\n+#end if\n+#if $req_inputs.ms_dataset.ms_dataset_type == \'history\'\n+ @INDEX_SPECTRUM_FILES@\n+ $index_spectrum_files($ms_index.files_path, $req_inputs.ms_dataset.spectrum_files) &&\n+#elif $req_inputs.ms_dataset.ms_dataset_type == \'indexed\'\n+ #if $os.path.exists($os.path.join($req_inputs.ms_dataset.index.extra_files_path, \'summary.txt\'))\n+ #set $index_dir = \'index_dir\'\n+ ln -s \'$req_inputs.ms_dataset.index.extra_files_path\' index_dir &&\n+ #else\n+ #raise ValueError\n+ #end if\n+#end if\n+## PepQuery command\n+pepquery \n+ -Xmx\\$[ \\${GALAXY_MEMORY_MB:-8192} / 1024 ]g\n+#if $validation.task_type == "known"\n+ -s 2 $validation.decoy\n+#else\n+ -s 1\n+#end if\n+#if $req_inputs.ms_dataset.ms_dataset_type in [\'history\', \'indexed\']\n+ -ms \'$index_dir\'\n+#elif $req_inputs.ms_dataset.ms_dataset_type in [\'PepQueryDB\', \'public\']\n+ -b \'$req_inputs.ms_dataset.dataset\' \n+#end if\n+\n+#if $req_inputs.db_type.db_type_selector == \'history\'\n+ -db \'$db_file\'\n+#else\n+ -db \'$req_inputs.db_type.db_id\' \n+#end if\n+#if $req_inputs.input_type.input_type_selector == \'peptide\'\n+ -t $req_inputs.input_type.input_type_selector\n+ -i \'$req_inputs.input_type.multiple.input\'\n+#else\n+ -t $req_inputs.input_type.input_type_selector\n+ #if $req_inputs.input_type.input_type_selector == \'protein\'\n+ #if $req_inputs.input_type.multiple.protein_input_selector == \'identifier\'\n+ #set $prot_id = str($req_inputs.input_type.multiple.input).replace(\'|\',\'\\|\')\n+ -i \'"$prot_id"\'\n+ #else\n+ -i \'$req_inputs.input_type.multiple.input\'\n+ #end if\n+ #else\n+ -i \'$req_inputs.input_type.input\'\n+ #if $req_inputs.input_type.input_type_selector == \'DNA\'\n+ #if $req_inputs.input_type.frame == \'None\'\n+ -frame \'0\'\n+ #else\n+ -frame \'$req_inputs.input_type.frame\'\n+ #end if\n+ #else\n+ -anno \'$req_inputs.input_type.anno\'\n+ #end if\n+ #end if\n+#end if\n+#if $req_inputs.indexType\n+ -indexType $req_inputs.indexType\n+#end if\n+\n+#if $modifications.fixed_mod\n+ -fixMod \'$modifications.fixed_mod\'\n+#end if\n+#if $modifications.var_mod\n+ -varMod \'$modifications.var_mod\'\n+#end if\n+#if $digestion.enzyme\n+ -e \'$digestion.enzyme\'\n+#end if\n+#if $digestion.max_missed_cleavages\n+ -c \'$digestion.max_missed_cleavages\'\n+#end if\n+\n+#if $modifications.max_mods\n+ -maxVar \'$modifications.max_mods\'\n+#end if\n+ $modifications.unmodified\n+ $modifications.aa\n+#if $ms_params.tolerance_params.precursor_tolerance\n+ -tol \'$ms_params.tolerance_params.precursor_tolerance\'\n+#end if\n+\n+#if $ms_params.tolerance_params.precursor_unit\n+ -tolu \'$ms_params.tolerance_params.precursor_unit\'\n+#end if\n+#if $ms_params.tolerance_params.tolerance\n+ -itol \'$ms_params.tolerance_params.tolerance\'\n+#end if\n+#if $ms_params.search.frag_method\n+ -fragmentMethod \'$ms_params.search.frag_method\'\n+#end if\n+#if $ms_params.search.scoring_method\n+ -m \'$ms_params.search.scoring_method\'\n+#end if\n+ $ms_params.search.extra_score_validation\n+#if $ms_params.search.max_charge\n+ -maxCharge \'$ms_params.search.max_charge\'\n+#end if\n+#if $ms_params.search.min_char'..b' identification, one of the following:\n+\n+ - Mass Spectrometry history datasets in MGF, mzML, or mzXML format \n+ - An Indexed MS/MS dataset (from previous PepQuery2 run or from **PepQuery2 index** tool.)\n+ - PepQueryDB dataset IDs \n+ \n+ .. \n+\n+ Multiple datasets from PepQueryDB must be separated by comma. A pattern to match datasets in PepQueryDB is also supported, for example, use \'CPTAC\' to search all datasets contain \'CPTAC\'. In addition, dataset selection from PepQueryDB based on data type (w:global proteome, p:phosphorylation, a:acetylation, u:ubiquitination, g:glycosylation) is also supported. For example, use \'p\' to search all phosphoproteomics datasets in PepQueryDB. The **PepQuery2 Show Sets** tool will list available PepQueryDB datasets.\n+\n+\n+ - Dataset IDs from public proteomics data repositories: PRIDE, MassIVE, jPOSTrepo and iProX\n+\n+ ..\n+\n+ Dataset ID from public proteomics data repositories, one dataset is supported for each analysis. For example, use \'PXD000529\' to use all MS/MS data from dataset PXD000529 or use \'PXD000529:LM3\' to use data files containing LM3 from dataset PXD000529\n+\n+ - A reference protein fasta database, novel peptides matching a reference sequence will be excluded. \n+\n+ - A protein fasta file\n+ - The ID for a public reference protein database from RefSeq, GENCODE, Ensembl or UniProt.\n+\n+\n+**Options**\n+\n+ - MS/MS searching parameter set name \n+\n+ .. \n+\n+ Setting a *parameter set name* will change defaults for various options, These may be overridden by manually setting the option.\n+ The **PepQuery2 Show Sets** tool *PepQuery Predefined Parameter Sets* will list those available along with the option values that will be set.\n+ The **PepQuery2 Show Sets** tool *PepQuery Datasets* column *parameter_set* column for each PepQueryDB dataset.\n+\n+\n+ - Override default options\n+\n+ .. \n+\n+ Values for modifications are provided in a select list. \n+ The **PepQuery2 Show Sets** tool *PepQuery Modifications* lists all available modifications.\n+\n+**Outputs**\n+ - Log.txt: \n+\n+ - Logging output from PepQuery2\n+ - When searching for *novel* peptides ignored peptide have a log message similar to: \n+\n+ - Ignore peptide (reason: exist in reference database): *PEPTIDE*\n+\n+ - When searching for *known* proteins, ignored protein have a log message similar to:\n+\n+ - Target protein is not present in database *DATABASE_NAME*: *PROTEIN_NAME*, ignored!\n+\n+ - Parameters: \n+ \n+ - parameters used in the search\n+\n+ - PSM - tabular with columns: \n+ \n+ - peptide modification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue\n+\n+ - PSM Rank - tabular with columns: \n+ \n+ - peptide mo/dification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank n_ptm\n+\n+ - An MGF with the best matching spectrums\n+\n+ - Detail - tabular with columns: \n+ \n+ - spectrum_title peptide modification pep_mass score\n+\n+ - PSM annotation - tabular with columns: \n+ \n+ - peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity\n+\n+ - PTM - tabular with columns: \n+ \n+ - spectrum_title peptide charge exp_mass pep_mass tol_ppm tol_da isotope_error modification score\n+\n+ - PTM Detail - tabular with columns: \n+ \n+ - peptide modification n spectrum_title charge exp_mass tol_ppm tol_da isotope_error pep_mass mz score n_db total_db n_random total_random pvalue rank ptm_spectrum_title ptm_peptide ptm_charge ptm_exp_mass ptm_pep_mass ptm_tol_ppm ptm_tol_da ptm_isotope_error ptm_modification ptm_score\n+\n+ - An Indexed MS/MS dataset *when MS/MS data is MGF, mzML, or mzXML history datasets*\n+\n+\n+.. _PepQuery: http://pepquery.org/document.html\n+\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r a07976bbc4d9 test-data/AgilentMassHunterTest.mzXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AgilentMassHunterTest.mzXML Sun Nov 06 16:25:25 2022 +0000 |
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| b'@@ -0,0 +1,4263 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2"\n+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\n+ xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_idx_3.2.xsd">\n+ <msRun scanCount="212" startTime="PT0.668S" endTime="PT209.708S">\n+ <msInstrument msInstrumentID="1">\n+ <msManufacturer category="msManufacturer" value="instrument model"/>\n+ <msModel category="msModel" value="Agilent instrument model"/>\n+ <msIonisation category="msIonisation" value="microelectrospray"/>\n+ <msMassAnalyzer category="msMassAnalyzer" value="time-of-flight"/>\n+ <msDetector category="msDetector" value="microchannel plate detector"/>\n+ <software type="acquisition" name="MassHunter Data Acquisition" version="8.0"/>\n+ </msInstrument>\n+ <dataProcessing>\n+ <software type="conversion" name="ProteoWizard software" version="3.0.20287"/>\n+ <processingOperation name="Conversion to mzML"/>\n+ </dataProcessing>\n+ <scan num="676"\n+ scanType="Full"\n+ centroided="1"\n+ msLevel="1"\n+ peaksCount="164"\n+ polarity="+"\n+ retentionTime="PT0.668S"\n+ lowMz="101.059547842973"\n+ highMz="961.958412367698"\n+ basePeakMz="622.030137146612"\n+ basePeakIntensity="69123.5234"\n+ totIonCurrent="248205.188"\n+ msInstrumentID="1">\n+ <peaks compressionType="zlib"\n+ compressedLen="2042"\n+ precision="64"\n+ byteOrder="network"\n+ 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| b |
| diff -r 000000000000 -r a07976bbc4d9 test-data/Uniprot.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Uniprot.fasta Sun Nov 06 16:25:25 2022 +0000 |
| b |
| b'@@ -0,0 +1,20 @@\n+>sp|Q8C4J7|TBL3_MOUSE Transducin beta-like protein 3 OS=Mus musculus GN=Tbl3 PE=2 SV=1\n+MAETAAGLCRFKANYAVERKIEPFYKGGKAQLDQTGHYLFCVCGTKVNILDVASGALLRSLEQEDQEDITSFDLSPDDEVLVTASRALLLAQWAWREGTVTRLWKAIHTAPVASMAFDATSTLLATGGCDGAVRVWDIVQHYGTHHFRGSPGVVHLVAFHPDPTRLLLFSSAVDTSIRVWSLQDRSCLAVLTAHYSAVTSLSFSEGGHTMLSSGRDKICIVWDLQSYQTTRTVPVFESVEASVLLPEQPAPALGVKSSGLHFLTAGDQGILRVWEAASGQCVYTQPQMPGLRQELTHCTLARAADLLLTVTADHNLLLYEAHSLQLQKQFAGYSEEVLDVRFLGPSDSHIVVASNSPCLKVFELQTLACQILHGHTDIVLALDVFRKGWLFASCAKDQSIRIWKMNKAGQVACVAQGSGHTHSVGTICCSRLKESFLVTGSQDCTVKLWPLPEALLAKSTAADSGPVLLQAQTTRRCHDKDINSLAVSPNDKLLATGSQDRTAKLWALPQCQLLGVFTGHRRGLWNVQFSPTDQVLATASADGTIKLWALQDFSCLKTFEGHDASVLKVAFVSRGSQLLSSGSDGLLKLWTIKSNECVRTLDAHEDKVWGLHCSQLDDHAITGGSDSRIILWKDVTEAEQAEEQAKREEQVIKQQELDNLLHEKRYLRALGLAISLDRPHTVLTVIQAIRRDPEACEKLEATVLRLRRDQKEALLRFCVTWNTNSRHCHEAQAVLGVLLRHEAPEELLAYDGVRGSLEALLPYTERHFQRLSRTLQAATFLDFLWHNMKLSPCPAAAPPAL\n+>tr|Q80ZP8|Q80ZP8_MOUSE Armet protein OS=Mus musculus GN=Manf PE=1 SV=1\n+METNNYLPSPPSFPVCISYLGRFYQDLKDRDVTFSPATIEEELIKFCREARGKENRLCYYIGATDDAATKIINEVSKPLAHHIPVEKICEKLKKKDSQICELKYDKQIDLSTVDLKKLRVKELKKILDDWGEMCKGCAEKSDYIRKINELMPKYAPKAASARTDL\n+>sp|Q60847|COCA1_MOUSE Collagen alpha-1(XII) chain OS=Mus musculus GN=Col12a1 PE=2 SV=3\n+MQTRLPRALAALGVALLLSSIEAEVDPPSDLNFKIIDENTVHMSWERPVDPIVGYRITVDPTTDGPTKEFTLAASTTETLLSDLIPETQYVVTITSYNEVEESVPVIGQLTIQTGGPTKPGEKKPGKTEIQKCSVSAWTDLVFLVDGSWSVGRNNFKYILDFIVALVSAFDIGEEKTRVGVVQYSSDTRTEFNLNQYYRREDLLAAVKKIPYKGGNTMTGDAIDYLVKNTFTESAGSRAGFPKVAIIITDGKSQDEVEIPARELRNIGVEVFSLGIKAADAKELKQIASTPSLNHVFNVANFDAIVDIQNEIISQVCSGVDEQLGELVSGEEVIEPPSNLVVTELSSKYIRLSWDPSPSAVTGYKILLTPMAAGSRHHALSVGPQTTTLNVRDLTADTEYQISVFAMKGLTSSEPTSVMEKTQPMKVQVECSRGVDIKADIVFLVDGSYSIGIANFVKVRAFLEVLAKSFEISPNRVQISLVQYSRDPHTEFTLKEFNRVEDIIKAINTFPYRGGSTNTGKAMTYVREKIFVPNKGSRSNVPKVMILITDGKSSDAFRDPAIKLRNSDVEIFAVGVKDAVRSELEAIASPPAETHVFTVEDFDAFQRISFELTQSICLRIEQELAAIKKKAYVPPKDLRFTQVTANSFKAEWSPPGDNVFSYHVTYKDANGDDEVTVVEPASSTSVVLNNLRPETLYLVNVTAEYEDGFSVPITGEETTAEVKGVPRNLKVTDETTDSFKLTWSQAPGRVLRYRIRYRPVSGGESKEVSTPANQRRKTLENLTPDTKYEISVIAEYSSGPGSPLTGNAATEEVRGNPRDLRVSDATTSTLKLSWSRAPGKVKQYLVTYTPAAGGETQEVTVRGDTTTTMLRKLKEGTQYDLSVTALYASGAGEALSGKGSTLEERGSPQNLVTKDITDTSIGAYWTSAPGMVRGYRVSWKSLYDDIEAGETTLPGDAIHTMIENLQPETKYKISVFATYSSGEGEPVTGDATTELSQDSKILRVDEETEHTMRVTWKAAPGKVVNYRVVYRPQGGGRQMVAKVPPTVTSTVLKRLQPQTTYDITVLPMYKTGEGKLRQGSGTTASRFKSPRNLKTSDPTMSSFRVTWEPAPGEVKGYKVTFHPTGDDRRLGELVLGPYDNTVVLEELRAGTTYRVNVFGMFDGGESLPLVGQEMTTLSDTTVTPFLSSGMDCLTRAEADIVLLVDGSWSIGRANFRTVRSFISRIVEVFEIGPKRVQIALAQYSGDPRTEWQLNAHRDKKSLLQAVANLPYKGGNTLTGMALNFIRQQSFKTQAGMRPRARKIGVLITDGKSQDDVEAPSKKLKDEGVELFAIGIKNADEVELKMIATDPDDTHAYNVADFESLSKIVDDLTINLCNSVKGPGDLEAPTNLVISERTHRSFRVSWTPPSDSVDRYKVEYYPVSGGKRQEFYVSRLDTSTVLKDLKPETDYVVNVYSVVEDEYSEPLKGTEKTLPVPVVSLNIYDVGPTTMHVQWQPVGGATGYTVSYQPTRSPEGTKPKEMRVGPTVNDVQLTGLLPNTEYEVTVQAVLYDLTSEPAKAREVTLPLPRPQDVKLRDVTHSTMNVVWEPVLGKVRKYIVRYKTPDEEFKEVEVDRSRASTILKDLSSQTQYTVSVSAVYDEGTSPPATAYDTTRRVPAPTNLQFTEVTPESFRGTWDHGASDVSLYRITWAPVGNPDKMETILNGDENTLVFENLNPNTPYEVSITAIYPDESESEDLSGTERTLRLIPLTTQAPKSGPRNLQVYNATSNSLTVKWDPASGRVQKYRITYQPSTGEGNEQTITVGGRQNSVLLQKLKPDTPYTITVYSQYPDGEGGRMTGRGKTKPLNTVRNLRVYDPSTSSLSVRWDHAEGNPRQYKLFYAPTSGGPEELVPIPGNTNYAILRNLQPDTPYTITVVPVYTEGDGGRTSDTGRTLVRGLARNIQVYNPTPNSLDVRWDPAPGPVQQYRIVYSPVAGTRPSESIVVPGNTRTVHLERLIPDTPYSVNIVALYSDGEGNPSPSQGRTLPRSGPRNIRVFGETTNSLSVAWDHADGPVQQYRIIYSPTVGDPIDEYTTVPGRRNNVILQPLQPDTPYKITVIAIYEDGDGGHLTGNGRTVGLLPPQNIHIFDEWYTRFRVSWDPSPSPVLGYKIVYKPVGSNEPMEAFVGEVTSYTLHNLNPSTTYDVSVYAQYDSGLSVPLTDQGTTLYLNVTDLKTYQVGWDTFCVKWSPHRAATSYRLKLSPADGTRGQEITVRGSETSHCFTGLSPEAEYGVTVFVQTPNLEGPGVPIKEQTTVKPTEAPTEPPTPSPPPTIPPARDVCKGAKADIVFLTDASWSIGDDNFNKVVKFIFNTVGAFDEVNPAGIQVSFVQYSDEVKSEFKLNTYNDKALALGALQNIRYRGGNTRTGKALTFIKEKVLTWESGMRKNVPKVLVVVTDGRSQDEVKKAAFVIQQSGFSVFVVGVADVDYNELANIASKPSERHVFIVDDFESFEKIEDNLITFVCETATSSCPLIYLDGYTSPGFKMLEAYNLTEKNFASVQGVSLESGSFPSYSAYRLQKNAFINQPTAELHPNGLPPSYTIILLFRLLPETPSDPFAIWQITDRDYRPQVGVIADPSSKTLSFFNKDTRGEVQTVTFDTDEVKTLFYGSFHKVHIVVTSKSVKIYIDCYEIIEKDIKEAGNITTDGYEILGKLLKGERKSATFQIQSFDIVCSPVWTSRDRCCDIPSRRDEAKCPALPNACTCTQDSVGPPGPPGPAGGPG'..b'GPPGPRGDTGPPGPQGPPGPQGPNGLSIPGEQGRQGMKGDAGEPGLPGRTGTPGLPGPPGPMGPPGDRGFTGKDGAMGPRGPPGPPGSPGSPGVTGPSGKPGKPGDHGRPGQSGLKGEKGDRGDIASQNMMRAVARQVCEQLISGQMSRFNQMLNQIPNDYHSSRNQPGPPGPPGPPGSAGARGEPGPGGRPGFPGTPGMQGPPGERGLPGEKGERGTGSQGPRGPPGPPGPQGESRTGPPGSTGSRGPPGPPGRPGNSGIRGPPGPPGYCDSSQCASIPYNGQGYPEPYVPEGGAYLPEREPFIVPVEPERTAEYEDDYGADEPDQQHPDHMRWRRALRPGPAE\n+>tr|D6RFR8|D6RFR8_MOUSE Choline/ethanolaminephosphotransferase 1 OS=Mus musculus GN=Cept1 PE=4 SV=1\n+MSGHRSTRKRCGDSHPESPVGFGHMSTTGHLCGLILPVLVAFSFTSLWMP\n+>tr|Q91VK2|Q91VK2_MOUSE Eef1d protein OS=Mus musculus GN=Eef1d PE=1 SV=1\n+MATNFLAHEKIWFDKFKYDDAERRFYEQMNGPVTSGSRQLKVMLPNSPEALGQATPGTSSGPGASSGPGGDHSELIVRITSLEVENQNLRGVVQDLQQAISKLEARLSSLEKSSPTPRATAPQTQHVSPMRQVEPPTKKGATPAEDDEDKDIDLFGSDEEEEDKEAARLREERLRQYAEKKAKKPTLVAKSSILLDVKPWDDETDMAQLETCVRSIQLDGLVWGASKLVPVGYGIRKLQIQCVVEDDKVGTDLLEEEITKFEEHVQSVDIAAFNKI\n+>tr|F6WN43|F6WN43_MOUSE Iron-sulfur cluster co-chaperone protein HscB, mitochondrial (Fragment) OS=Mus musculus GN=Hscb PE=1 SV=1\n+XQKSQTEKHFSDKHSTLVNDAYKTLQAPLTRGLYLVS\n+>sp|Q6NXK2|ZN532_MOUSE Zinc finger protein 532 OS=Mus musculus GN=Znf532 PE=1 SV=1\n+MTMGDMKTPDFDDLLAAFDIPDMVDPKAAIESGHDDHESHIKQNAHVDDDSHTPSSSDVGVSVIVKNVRNIDSSEGVEKDGHNPTGNGLHNGFLTASSLDSYGKDGAKSLKGDTPASEVTLKDPAFSQFSPISSAEEFEDDEKIEVDDPPDKEEARAGFRSNVLTGSAPQQDFDKLKALGGENSSKTGVSTSGHTDKNKVKREAESNSITLSVYEPFKVRKAEDKLKENSEKMLESRVLDGKPSSEKSDSGIAAAASSKTKPSSKLSSCIAAIAALSAKKAASDSCKEPVANSREASPLPKEVNDSPKAADKSPESQNLIDGTKKASLKPSDSPRSVSSENSSKGSPSSPVGSTPAIPKVRIKTIKTSSGEIKRTVTRVLPEVDLDSGKKPSEQAASVMASVTSLLSSSASATVLSSPPRAPLQTAMVTSAVSSAELTPKQVTIKPVATAFLPVSAVKTAGSQVINLKLANNTTVKATVISAASVQSASSAIIKAANAIQQQTVVVPASSLANAKLVPKTVHLANLNLLPQGAQATSELRQVLTKPQQQIKQAIINAAASQPPKKVSRVQVVSSLQSSVVEAFNKVLSSVNPVPVYTPNLSPPANAGITLPMRGYKCLECGDAFALEKSLSQHYDRRSVRIEVTCNHCTKNLVFYNKCSLLSHARGHKEKGVVMQCSHLILKPVPADQMIVPPSSNTAASTLQSSVGAATHTVPKVQPGIAGAVISAPASTPMSPAMPLDEDPSKLCRHSLKCLECNEVFQDEPSLATHFQHAADTSGQQMKKHPCRQCDKSFSSSHSLCRHNRIKHKGIRKVYACSHCPDSRRTFTKRLMLERHIQLMHGIKDPDVKELSDDAGDVTNDEEEEAEIKEDAKVPSPKRKLEEPVLEFRPPRGAITQPLKKLKINVFKVHKCAVCGFTTENLLQFHEHIPQHRSDGSSHQCRECGLCYTSHGSLARHLFIVHKLKEPQPVSKQNGAGEDSQQENKPSPEDEAAEGAASDRKCKVCAKTFETEAALNTHMRTHGMAFIKSKRMSSAEK\n+>sp|P58006|SESN1_MOUSE Sestrin-1 OS=Mus musculus GN=Sesn1 PE=1 SV=3\n+MRLAAASNEAYAASLAVSELLSCHQCGGDRGQDEELGIRIPRPLGHGPSRFIPEKEMLQVGSEDAQMHALFADSFAALGRLDNITLVMVFHPQYLESFLKTQHYLLQMDGPLPLHYRHYIGIMAAARHQCSYLVNLHVSDFLHVGGDPKWLNGLENAPQKLQNLGELNKVLAHRPWLITKEHIEGLLKAEEHSWSLAELVHAVVLLTHYHSLASFTFGCGISPEIHCDGGHTFRPPSVSNYCICDITNGNHSVDEMQVNSAGNASVSDSFFEVEALMEKMRQLQECREEEEASQEEMASRFEMEKRESMFVFSSDDDEVTPARDVSRHFEDTSYGYKDFSRHGMHVPTFRVQDYCWEDHGYSLVNRLYPDVGQLIDEKFHIAYNLTYNTMAMHKDVDTSMLRRAIWNYIHCMFGIRYDDYDYGEINQLLDRSFKVYIKTVVCTPEKVTKRMYDSFWRQFKHSEKVHVNLLLIEARMQAELLYALRAITRYMT\n+>tr|A0A1B0GSE5|A0A1B0GSE5_MOUSE Ubiquitin carboxyl-terminal hydrolase CYLD OS=Mus musculus GN=Cyld PE=1 SV=1\n+MSSGLWSQEKVTSPYWEERIFYLLLQECSVTDKQTQKLLKVPKGSIGQYIQDRSVGHSRVPSTKGKKNQIGLKILEQPHAVLFVDEKDVVEINEKFTELLLAITNCEERLSLFRNRLRLSKGLQVDVGSPVKVQLRSGEEKFPGVVRFRGPLLAERTVSGIFFGVELLEEGRGQGFTDGVYQGKQLFQCDEDCGVFVALDKLELIEDDDNGLESDFAGPGDTMQVEPPPLEINSRVSLKVGESTESGTVIFCDVLPGKESLGYFVGVDMDNPIGNWDGRFDGVQLCSFASVESTILLHINDIIPDSVTQERRPPKLAFMSRGVGDKGSSSHNKPKVTGSTSDPGSRNRSELFYTLNGSSVDSQQSKSKNPWYIDEAFGGYLSEVVEENTPPKMEKEGLEIMIGKKKGIQGHYNSCYLDSTLFCLFAFSSALDTVLLRPKEKNDIEYYSETQELLRTEIVNPLRIYGYVCATKIMKLRKILEKVEAASGFTSEEKDPEEFLNILFHDILRVEPLLKIRSAGQKVQDCNFYQIFMEKNEKVGVPTIQQLLEWSFINSNLKFAEAPSCLIIQMPRFGKDFKLFKKIFPSLELNITDLLEDTPRQCRICGGLAMYECRECYDDPDISAGKIKQFCKTCSTQVHLHPRRLNHSYHPVSLPKDLPDWDWRHGCIPCQKMELFAVLCIETSHYVAFVKYGKDDSAWLFFDSMADRDGGQNGFNIPQVTPCPEVGEYLKMSLEDLHSLDSRRIQGCARRLLCDAYMCMYQSPTMSLYK\n+>sp|Q60880|OL141_MOUSE Olfactory receptor 141 OS=Mus musculus GN=Olfr141 PE=3 SV=2\n+MRNITEATFFVLKGLTDNNELQIILFLLFLAIYIFTLIGNVGLIILVVGDSQLHNPMYCFLSVLSSVDACYSTDITPNMLVGFMSKSKIISFYGCATQMFLAVTFGTTECFLLAAMAYDRYVAIHDPLLYAVSMSPRVYIPLIIASYAGGIVHAIIHTVATFSLSFCRSNEVKHIFCDIPPLLAISCSETYVNELLLFFFVSFIELVTILIVLVSYAFILLSILKMNSSEGRRKVFSTCGAHLTAVSIYYGTILFMYVRPSSNYSLEHDMIVSTFYTIGIPMLNPIIYSLRNKDVKEAMKRVLRKKINIKHRIKKLNDFSVFLMP\n' |
| b |
| diff -r 000000000000 -r a07976bbc4d9 test-data/iTRAQ_f4.mgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/iTRAQ_f4.mgf Sun Nov 06 16:25:25 2022 +0000 |
| b |
| b'@@ -0,0 +1,753 @@\n+COM=Conversion to mascot generic\n+CHARGE=2+ and 3+\n+BEGIN IONS\n+PEPMASS=740.462952\n+CHARGE=3+\n+SCANS=277\n+TITLE=Mo_Tai_iTRAQ_f4.00277.00277.3\n+111.017494 85.198502\n+112.240982 97.204994\n+114.110542 168.274780\n+115.107582 369.265503\n+115.650398 84.005325\n+117.296082 86.641182\n+117.595589 82.974037\n+120.657990 81.247025\n+123.208023 88.939392\n+126.714996 76.470490\n+126.995316 81.651260\n+129.369080 82.580246\n+129.410400 90.817963\n+132.734039 124.614685\n+143.307465 87.847046\n+178.966888 94.961578\n+179.972855 89.878273\n+183.256714 104.533241\n+188.080093 123.015953\n+212.102753 442.314178\n+213.104324 84.621696\n+233.001801 107.842552\n+244.242355 102.163200\n+281.079132 97.696259\n+291.216034 243.588058\n+309.183807 104.681831\n+325.188324 282.187622\n+345.226288 167.099777\n+347.629883 88.744476\n+357.377533 105.747673\n+388.266266 1321.324341\n+430.317047 94.113419\n+458.310547 310.033203\n+489.807434 100.114334\n+490.700165 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597.036011\n+572.329102 704.391174\n+575.329651 597.594116\n+578.266602 569.538757\n+584.834595 1397.603638\n+585.341125 596.237427\n+585.828064 634.964417\n+592.849548 948.947998\n+593.338867 8331.064453\n+593.809753 1243.525757\n+593.850098 3570.665283\n+594.347534 5469.266113\n+601.328064 1251.846069\n+612.421753 868.523682\n+615.363525 1159.816772\n+635.785217 692.349304\n+645.406799 926.912354\n+647.354187 1344.844971\n+660.368103 1515.965698\n+667.035950 629.281006\n+678.553528 864.705811\n+686.401672 1415.408081\n+687.406799 956.555176\n+701.317932 638.253906\n+713.436462 577.175781\n+714.438171 979.025330\n+721.332031 1133.021240\n+734.864807 659.578308\n+758.495483 1101.013306\n+759.436768 1680.954834\n+814.488220 766.761841\n+825.458008 2101.567139\n+873.476807 3603.638672\n+876.500122 1146.794800\n+877.493591 2904.569092\n+878.501526 2154.676025\n+879.500305 1179.630981\n+896.207703 648.875244\n+914.434082 1090.736938\n+914.517822 1977.191284\n+928.515015 1886.298706\n+930.495483 1311.800903\n+952.429504 625.323181\n+965.766296 606.633911\n+972.546692 2437.769531\n+999.546753 632.162537\n+1026.609131 980.280151\n+1040.573853 1742.042114\n+1041.564087 3165.200439\n+1042.581787 3063.955566\n+1043.577515 6683.765625\n+1045.518311 945.700500\n+1147.621704 832.881104\n+1148.635742 1159.247681\n+1467.104980 653.335815\n+1533.474243 661.718018\n+1620.307251 616.238525\n+1664.717529 648.275024\n+END IONS\n' |
| b |
| diff -r 000000000000 -r a07976bbc4d9 test-data/immunopeptidomics.mgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/immunopeptidomics.mgf Sun Nov 06 16:25:25 2022 +0000 |
| b |
| b'@@ -0,0 +1,464 @@\n+BEGIN IONS\n+TITLE=controllerType=0 controllerNumber=1 scan=19846\n+RTINSECONDS=2320.06458\n+PEPMASS=383.529876708984\n+CHARGE=3+\n+84.0449677 46347.0703125\n+84.0813446 85493.9453125\n+86.0719299 7175.7060546875\n+86.0969772 135316.21875\n+87.0795746 57686.53515625\n+89.5852509 6013.955078125\n+91.0547638 26870.0390625\n+100.0871506 10508.3408203125\n+101.0712357 8028.2236328125\n+102.0548477 7109.3364257813\n+110.071434 72448.5390625\n+112.0872192 68537.90625\n+116.0708847 66026.75\n+116.6829987 7043.2426757813\n+119.0492325 28436.21484375\n+120.0808487 28182.986328125\n+123.0442657 6282.2768554688\n+127.0979004 32528.88671875\n+129.1026154 74929.3046875\n+129.1124268 15517.341796875\n+132.1023407 7616.8291015625\n+136.075592 267654.46875\n+137.0793915 44604.71484375\n+140.0816498 8406.1591796875\n+145.4732819 7887.0209960938\n+147.0440521 10594.44921875\n+147.1123962 10032.357421875\n+155.0816803 6984.1274414063\n+157.1085968 34948.90234375\n+165.0540466 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| diff -r 000000000000 -r a07976bbc4d9 test-data/novel_peptides --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/novel_peptides Sun Nov 06 16:25:25 2022 +0000 |
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| b |
| diff -r 000000000000 -r a07976bbc4d9 test-data/novel_proteins.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/novel_proteins.fa Sun Nov 06 16:25:25 2022 +0000 |
| b |
| @@ -0,0 +1,6 @@ +>DSGASGSILEASAAR +DSGASGSILEASAAR +>ELGSSDLTAR +ELGSSDLTAR +>SPYREFTDHLVK +SPYREFTDHLVK |
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| diff -r 000000000000 -r a07976bbc4d9 test-data/pep.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pep.txt Sun Nov 06 16:25:25 2022 +0000 |
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| @@ -0,0 +1,2 @@ +LVVVGADGVGK +AHSSMVGVNLPQK |
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