| Next changeset 1:57555f63bbd3 (2021-11-25) |
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Uploaded version 1.1 |
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._epibuilder-1.1.jar ._epibuilder-1.1.xml ._test-data epibuilder-1.1.jar epibuilder-1.1.xml test-data/._command-epifinder-epitope-detail.tsv test-data/._command-epifinder-epitopes-fasta.fasta test-data/._command-epifinder-parameters.txt test-data/._command-epifinder-protein-summary.tsv test-data/._command-epifinder-scores.tsv test-data/._command-epifinder-topology.tsv test-data/._command-epifinder.log test-data/._command-epifinder.txt test-data/._command-epifinder.xls test-data/._command-test_proteom.phr test-data/._command-test_proteom.pin test-data/._command-test_proteom.psq test-data/._command-test_proteom_blast.csv test-data/._input_bcell_command_line.txt test-data/._input_bepi_online.csv test-data/._online-epifinder-epitope-detail.tsv test-data/._online-epifinder-epitopes-fasta.fasta test-data/._online-epifinder-parameters.txt test-data/._online-epifinder-protein-summary.tsv test-data/._online-epifinder-scores.tsv test-data/._online-epifinder-topology.tsv test-data/._online-epifinder.log test-data/._online-epifinder.txt test-data/._online-epifinder.xls test-data/._online-test_proteom.phr test-data/._online-test_proteom.pin test-data/._online-test_proteom.psq test-data/._online-test_proteom_blast.csv test-data/._proteom.fasta test-data/command-epifinder-epitope-detail.tsv test-data/command-epifinder-epitopes-fasta.fasta test-data/command-epifinder-parameters.txt test-data/command-epifinder-protein-summary.tsv test-data/command-epifinder-scores.tsv test-data/command-epifinder-topology.tsv test-data/command-epifinder.log test-data/command-epifinder.txt test-data/command-epifinder.xls test-data/command-test_proteom.phr test-data/command-test_proteom.pin test-data/command-test_proteom.psq test-data/command-test_proteom_blast.csv test-data/input_bcell_command_line.txt test-data/input_bepi_online.csv test-data/online-epifinder-epitope-detail.tsv test-data/online-epifinder-epitopes-fasta.fasta test-data/online-epifinder-parameters.txt test-data/online-epifinder-protein-summary.tsv test-data/online-epifinder-scores.tsv test-data/online-epifinder-topology.tsv test-data/online-epifinder.log test-data/online-epifinder.txt test-data/online-epifinder.xls test-data/online-test_proteom.phr test-data/online-test_proteom.pin test-data/online-test_proteom.psq test-data/online-test_proteom_blast.csv test-data/proteom.fasta |
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| b'@@ -0,0 +1,586 @@\n+<tool id="epibuilder_1.1" name="EpiBuilder" version="1.1">\n+ <description>Predict B cell epitopes</description>\n+ <requirements>\n+\t\t<requirement type="package" version=">=1.8">Java</requirement>\n+\t\t<requirement type="package" version=">=2.11.0+">Blastp</requirement>\n+\t\t<requirement type="package" version=">=2.11.0+">Makeblastdb</requirement>\n+ </requirements>\n+\t<stdio>\n+\t\t<regex match="command not found"\n+ source="both"\n+ level="log"\n+ description="WARNING: some methods could not be applied -> check inputs and outputs files" />\n+\t\t<regex match="makeblastdb "\n+ source="both"\n+ level="log"\n+ description="makeblastdb and blastp must be in $PATH on your Galaxy server" /> \n+\t\t<regex match="blastp "\n+ source="both"\n+ level="log"\n+ description="makeblastdb and blastp must be in $PATH on your Galaxy server" /> \n+\t</stdio>\n+ <command><![CDATA[\n+\t#*<!-- \n+\t\tMethods used will be saved in $param with each threshold \n+\t\tThreshold is separated from method by ":"\n+\t\tEach method is separated by ";"\n+\t\texample: emini:0.8;parker:d;\n+\n+\t\t>> d means defalt threshold\n+\t-->*#\n+\n+\t#*<!-- Set variables that concatenate methods -->*#\n+\t#set param = \'\'\n+\t#set nomethod = \'\'\n+\t#set proteomes = \'\'\n+\n+\t#*<!-- Add Bepipred2.0 method -->*#\n+\t#if $bepi_type.bepipred_origin == \'y\':\n+\t\t#set bepipred_origin = \'-o\'\n+\t#*<!-- jobid -->*#\n+\t#elif $bepi_type.bepipred_origin == \'id\':\n+\t\t#set bepipred_origin = \'-jobid \' + str($bepi_type.job_id)\n+\t#else:\n+\t\t#set bepipred_origin = \'\'\n+\t#end if\n+\t\n+\t#*<!-- Add Emini method -->*#\n+\t#if $emini_method.emini_choice == \'eminiyes\':\n+\t\t#if $emini_method.emini_t.t_emini == \'t_emini_choice\'\n+\t\t\t#set param += \'emini:\' + str($emini_method.emini_t.thresh_em_value) + \';\'\n+\t\t#else:\n+\t\t\t#set param += \'emini:d;\'\t\t\n+\t\t#end if\n+\t#end if\n+\n+\t#*<!-- Add Parker method -->*#\n+\t#if $parker_method.parker_choice == \'parkeryes\':\n+\t\t#if $parker_method.parker_t.t_parker == \'t_parker_choice\'\n+\t\t\t#set param += \'parker:\' + str($parker_method.parker_t.thresh_park_value) + \';\'\n+\t\t#else:\n+\t\t\t#set param += \'parker:d;\'\t\t\n+\t\t#end if\n+ #end if\n+\n+\t#*<!-- Add Chou method -->*#\n+\t#if $chou_method.chou_choice == \'chouyes\':\n+\t\t#if $chou_method.chou_t.t_chou == \'t_chou_choice\'\n+\t\t\t#set param += \'chou_fosman:\' + str($chou_method.chou_t.thresh_chou_value) + \';\'\n+\t\t#else:\n+\t\t\t#set param += \'chou_fosman:d;\'\t\t\n+\t\t#end if\n+ #end if\n+\n+\t#*<!-- Add Karplus method -->*#\n+\t#if $karplus_method.karplus_choice == \'karplusyes\':\n+\t\t#if $karplus_method.karplus_t.t_karplus == \'t_karplus_choice\'\n+\t\t\t#set param += \'karplus_schulz:\' + str($karplus_method.karplus_t.thresh_karplus_value) + \';\'\n+\t\t#else:\n+\t\t\t#set param += \'karplus_schulz:d;\'\t\t\n+\t\t#end if\n+ #end if\n+\n+\t#*<!-- Add Kolaskar method -->*#\n+\t#if $kolaskar_method.kolaskar_choice == \'kolaskaryes\':\n+\t\t#if $kolaskar_method.kolaskar_t.t_kolaskar == \'t_kolaskar_choice\'\n+\t\t\t#set param += \'kolaskar:\' + str($kolaskar_method.kolaskar_t.thresh_kolaskar_value) + \';\'\n+\t\t#else:\n+\t\t\t#set param += \'kolaskar:d;\'\t\t\n+\t\t#end if\n+ #end if\n+\n+\n+\n+\t#*<!-- Clean $proteome if there\'s no protome -->*#\n+\t#if proteomes == \'-proteomes \':\n+\t\t#set proteomes = \'\'\t\n+\t#end if\n+\n+\n+\t#*<!-- Parse blast command -->*#\n+\t\n+\t#if $use_search.search_use_bool == "use":\n+\t\t#*<!-- Add proteomes, as many as given -->*#\n+\t\t#if $use_search.prot_input: \n+\t\t\t#for $file in $use_search.prot_input:\n+\t\t\t\t#set proteomes += str($file.prot_name) + \'=\' + str($file.prot_file) + \';\'\n+\t\t\t#end for\n+\t\t#end if\n+\t\t#if $use_search.prot_input:\n+\t\t\t#if $use_search.blast.blast_search == \'blastyes\':\n+\t\t\t\t#set blast_command = \'task=\' + str($use_search.blast.blast_task) \t\t\n+\t\t\t\t#set blast_command += \';identity=\' + str($use_search.blast.blast_id) + \';cover=\' + str($use_search.blast.blast_cover) + \';word-size=\' + str($use_search.blast.blast_wordsize)\n+\t\t\t\t#set blast_command += \';makeblastdb_path=makeblastdb;blastp_path=blastp\'\n+\t\t\t#end if\n+\t\t#end if\n+\t#end if\n+\n+\t#*<'..b'plus_choice"/>\n+\t\t\t\t\t<param name="thresh_karplus_value" value="0.8" />\n+\t\t\t\t</conditional>\n+\t\t\t</conditional>\n+\n+\n+\t\t\t<conditional name="kolaskar_method">\n+\t\t\t\t<param name="kolaskar_choice" value="kolaskaryes"/>\n+\t\t\t\t<conditional name="kolaskar_t">\n+\t\t\t\t\t<param name="t_kolaskar" value="t_kolaskar_choice"/>\n+\t\t\t\t\t<param name="thresh_kolaskar_value" value="0.8" />\n+\t\t\t\t</conditional>\n+\t\t\t</conditional>\n+\t\t\t<!-- This first part test all methods-->\n+\n+\t\t\t<conditional name="use_search">\n+\t\t\t\t<param name="search_use_bool" value="use"/>\n+\t\t\t\t\t<repeat name="prot_input">\n+\t\t\t\t\t\t<param name="prot_name" value="test_proteom" />\n+\t\t\t\t\t\t<param name="prot_file" value="proteom.fasta" />\n+\t\t\t\t\t</repeat>\n+\t\t\t\t\t<conditional name="check_use_hit" value="usehit"/>\n+\t\t\t\t\t<conditional name="blast">\n+\t\t\t\t\t\t<param name="blast_search" value="blastyes" />\n+\t\t\t\t\t\t<param name="blast_id" value="90" />\n+\t\t\t\t\t\t<param name="blast_cover" value="90"/>\n+\t\t\t\t\t\t<param name="blast_wordsize" value="4" />\n+\t\t\t\t\t\t<param name="blast_task" value="blastp-short" />\n+\t\t\t\t\t</conditional>\n+\t\t\t</conditional>\n+\t\n+\t\t\t<param name="basename" value="command" />\n+\n+\t\t\t<output name="epif_out" file="command-EpiBuilder.txt" />\n+\t\t\t<output name="ep_xls" file="command-EpiBuilder.xlsx" />\n+\t\t\t<output_collection name= "epif_collection">\n+\t\t\t\t<element name="ep_prot_sum" file="command-EpiBuilder-protein-summary.tsv" />\n+\t\t\t\t<element name="ep_top" file="command-EpiBuilder-topology.tsv" />\n+\t\t\t\t<element name="ep_score" file="command-EpiBuilder-socre.tsv" />\n+\t\t\t\t<element name="ep_detail" file="command-EpiBuilder-epitope-detail.tsv" />\n+\t\t\t\t<element name="ep_parameters" file="command-EpiBuilder-parameters.tsv" />\n+\t\t\t\t<element name="ep_fasta" file="command-EpiBuilder-fasta.fasta" />\n+\t\t\t</output_collection>\n+\t\t\t<output_collection name="blast_collection" >\n+\t\t\t\t<element name="test_proteom" file="command-test_proteom_blast.csv" ftype="csv" />\n+\t\t\t</output_collection >\n+\t\t</test>\n+\t</tests>\n+ <help>\n+**How to Run**\n+\n+First, you must have a file with epitopes predicted by Bepipred 2.0 or have one job submmited into bepipred\'s server.\n+\n+.. class:: warningmark \n+\n+Input this file (or jobID) and specify if Bepipred 2.0 was ran online or command-line based through bcell standalone suite.\n+\n+Select methods that you want to check your epitopes for validation.\n+\n+Give a threshold for each method (or use default threshold).\n+\n+Optionaly, you can search validated epitopes in proteomes datasets, as many as you wish.\n+\n+.. class:: warningmark \n+\n+If you want to search using Blastp, this software and Makeblastdb must be avaliable on your server\'s $PATH.\n+\n+-----\n+\n+**Outputs**\n+\n+\n+**Summary** : Prediction overview \n+\n+**Protein Summary** : Show proteins that have epitopes predicted\n+\n+**Fasta** : Epitopes\' sequences\n+\n+**Topology** : Show epitope match in each method, aminoacid per aminoacid\n+\n+**Score** : Detailed score for aminoacids\n+\n+**Epitope Detail** : Properties of each predicted epitope\n+\n+**Parameters** : Softwares, thresholds and parameters used for prediction\n+\n+**Xls Report** : Table with epitope detail, protein summary, topology and scores\n+\n+**Collection with blast files** : All blast results for each proteome \n+\n+\n+-----\n+\n+.. class:: infomark\n+\n+**For more information, checkout our GitHub page**: https://github.com/bioinfo-ufsc/EpiBuilder\n+\n+-----\n+\n+Please cite methods used in your analysis, available bellow\n+\n+| Bioinformatics Lab - UFSC - 2021\n+\n+</help>\n+<citations>\n+\t<citation type="doi">10.1093/nar/gkx346</citation>\n+\t<citation type="doi">10.1016/0014-5793(90)80535-q</citation>\n+\t<citation type="doi">10.1002/9780470122921.ch2</citation>\n+\t<citation type="doi">10.1021/bi00367a013</citation>\n+\t<citation type="doi">https://doi.org/10.1007/BF01195768</citation>\n+\t<citation type="doi">doi:10.1128/jvi.55.3.836-839.1985</citation>\n+\t<citation type="doi">10.1371/journal.pcbi.1006791</citation>\n+\t<citation type="doi">https://doi.org/10.1093/nar/gky379</citation>\n+</citations>\n+</tool>\n+\n' |
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| @@ -0,0 +1,4 @@ +N Id Epitope Start End N-Glyc N-Glyc-Count N-Glyc-Motifs Length MW(kDa) I.P Hydropathy All Matches Cover Avg Cover BepiPred2 Emini Parker Chou Fosman Karplus Schulz Kolaskar test_proteom_count test_proteom_acc test_proteom_count test_proteom_id +1 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation PETQSSHSAW 73 83 N 0 - 10 1.13 5.25 -1.40 0.90 0.98 0.65 2.57 4.19 1.13 1.04 0.99 1 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 1 4WFF_B(100.00,100.00) +2 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation AIFLKWHVPPELVR 149 163 N 0 - 14 1.71 8.80 0.42 0.07 0.60 0.64 0.82 -1.83 0.83 0.96 1.10 2 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation,4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 2 4WFF_B(100.00,100.00),4WFF_A(100.00,100.00) +3 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation LKWHVPPELVRVLSA 150 165 N 0 - 15 1.74 8.75 0.39 0.07 0.59 0.63 0.81 -1.70 0.84 0.96 1.11 2 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation,4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 2 4WFF_B(100.00,100.00),4WFF_A(100.00,100.00) |
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| @@ -0,0 +1,6 @@ +>1-PETQSSHSAW +PETQSSHSAW +>2-AIFLKWHVPPELVR +AIFLKWHVPPELVR +>3-LKWHVPPELVRVLSA +LKWHVPPELVRVLSA |
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| @@ -0,0 +1,28 @@ + +---- Running Parameters ---- +BepiPred-2.0 Threshold : 0.6 +Min epitope length : 10 +Max epitope length : 30 + +---- Softwares Threshold ---- +Emini : 0.8 +Parker : 0.8 +Chou Fosman : 0.8 +Karplus Schulz : 0.8 +Kolaskar : 0.8 + +---- Proteomes ---- +Alias File +test_proteom /usr/local/bioinfo/stingrayGalaxy/tools/stingray/epifinder/test-data/proteom.fasta + +---- Blast ---- +Identity : 90.0 +Cover : 90.0 +Word size : 4 +Task blastp-short: blastp-short + +---- Stats ---- +Processed proteins : 6 +NGlycosylated proteins : 0 +Identified epitopes : 3 +N-glycosylated epitopes: 0 |
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| @@ -0,0 +1,7 @@ +Id Epitopes N-Glyc +5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta 0 0 +4XAK_A Chain A of Crystal structure of potent neutralizing antibody m336 in complex with MERS Co-V RBD 0 0 +4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation 1 0 +4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 2 0 +5C0N_A Chain A of Development of a therapeutic monoclonal antibody that targets secreted fatty acid-binding protein aP2 to treat type 2 diabetes. 0 0 +4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2 0 0 |
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| diff -r 000000000000 -r ef26009cd70a test-data/command-epifinder-scores.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/command-epifinder-scores.tsv Thu Nov 25 01:26:36 2021 +0000 |
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| b'@@ -0,0 +1,1141 @@\n+Id\tPosition\tResidue\tBepipred2\tEmini\tParker\tChou Fosman\tKarplus Schulz\tKolaskar\tMW\tIP\tHydropathy\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t1\tV\t0.23\t0.00\t0.00\t0.00\t0.00\t0.00\t117.15\t5.49\t4.20\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t2\tR\t0.27\t0.00\t0.00\t0.00\t0.00\t0.00\t174.20\t9.75\t-4.50\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t3\tS\t0.31\t0.23\t0.00\t0.00\t0.00\t0.00\t105.09\t5.24\t-0.80\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t4\tL\t0.33\t0.45\t1.63\t1.03\t0.98\t1.09\t131.17\t5.52\t3.80\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t5\tN\t0.39\t0.19\t0.84\t1.04\t0.97\t1.07\t132.12\t5.52\t-3.50\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t6\tC\t0.40\t0.28\t0.84\t1.04\t0.96\t1.07\t121.15\t5.52\t2.50\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t7\tT\t0.41\t0.56\t1.34\t1.04\t0.96\t1.05\t119.12\t5.19\t-0.70\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t8\tL\t0.42\t0.47\t3.59\t1.16\t0.99\t1.01\t131.17\t5.52\t3.80\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t9\tR\t0.44\t1.50\t3.44\t1.08\t1.03\t1.05\t174.20\t9.75\t-4.50\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t10\tD\t0.45\t1.80\t4.10\t1.05\t1.07\t0.99\t133.10\t3.80\t-3.50\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t11\tS\t0.46\t4.37\t4.17\t1.06\t1.11\t0.99\t105.09\t5.24\t-0.80\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t12\tQ\t0.45\t2.99\t6.41\t1.18\t1.12\t0.96\t146.15\t5.52\t-3.50\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t13\tQ\t0.45\t1.48\t4.50\t1.13\t1.12\t1.01\t146.15\t5.52\t-3.50\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t14\tK\t0.43\t0.82\t2.54\t0.99\t1.08\t1.09\t146.19\t8.75\t-3.90\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t15\tS\t0.43\t0.47\t1.01\t0.87\t1.03\t1.06\t105.09\t5.24\t-0.80\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t16\tL\t0.43\t0.36\t1.09\t0.93\t0.99\t1.06\t131.17\t5.52\t3.80\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t17\tV\t0.42\t0.18\t1.04\t1.02\t0.97\t1.04\t117.15\t5.49\t4.20\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t18\tM\t0.42\t0.21\t0.53\t1.09\t0.98\t1.06\t149.21\t5.28\t1.90\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t19\tS\t0.41\t0.39\t-0.67\t1.05\t1.01\t1.08\t105.09\t5.24\t-0.80\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta\t20\tG\t0.39\t0.92\t1.76\t1.07\t1.03\t1.02\t75.07\t5.52\t-0.40\n+5BVP_A Chain A of The molecular mode of action and species specificity of cana'..b'\t0.44\t0.94\t-1.84\t0.81\t0.98\t1.06\t131.17\t5.52\t4.50\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t111\tT\t0.44\t0.45\t-1.84\t0.81\t0.96\t1.09\t119.12\t5.19\t-0.70\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t112\tL\t0.47\t0.46\t-1.89\t0.82\t0.95\t1.08\t131.17\t5.52\t3.80\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t113\tY\t0.48\t1.13\t-1.37\t0.79\t0.95\t1.07\t181.19\t5.52\t-1.30\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t114\tL\t0.47\t1.56\t0.59\t0.86\t0.98\t1.04\t131.17\t5.52\t3.80\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t115\tK\t0.50\t3.79\t0.66\t0.87\t1.02\t1.04\t146.19\t8.75\t-3.90\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t116\tE\t0.49\t3.79\t1.70\t0.95\t1.05\t1.03\t147.13\t4.00\t-3.50\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t117\tK\t0.48\t6.16\t2.90\t0.99\t1.06\t1.01\t146.19\t8.75\t-3.90\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t118\tK\t0.48\t4.76\t4.51\t1.12\t1.06\t0.98\t146.19\t8.75\t-3.90\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t119\tY\t0.49\t1.47\t3.90\t1.15\t1.04\t1.05\t181.19\t5.52\t-1.30\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t120\tS\t0.48\t0.74\t3.09\t1.14\t1.01\t1.08\t105.09\t5.24\t-0.80\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t121\tP\t0.46\t0.39\t0.84\t1.13\t0.99\t1.08\t115.13\t5.96\t-1.60\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t122\tC\t0.45\t0.43\t1.14\t1.09\t0.95\t1.07\t121.15\t5.52\t2.50\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t123\tA\t0.41\t0.24\t0.89\t1.00\t0.94\t1.10\t89.09\t5.57\t1.80\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t124\tW\t0.40\t0.11\t-0.57\t0.87\t0.92\t1.15\t204.23\t5.52\t-0.90\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t125\tE\t0.39\t0.42\t-0.27\t0.79\t0.92\t1.12\t147.13\t4.00\t-3.50\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t126\tV\t0.38\t0.42\t-0.17\t0.71\t0.93\t1.07\t117.15\t5.49\t4.20\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t127\tV\t0.36\t0.69\t0.64\t0.72\t0.94\t1.04\t117.15\t5.49\t4.20\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t128\tR\t0.39\t0.28\t0.93\t0.65\t0.94\t1.08\t174.20\t9.75\t-4.50\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t129\tA\t0.40\t0.37\t-0.79\t0.63\t0.94\t1.08\t89.09\t5.57\t1.80\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t130\tE\t0.39\t0.99\t0.34\t0.70\t0.94\t1.00\t147.13\t4.00\t-3.50\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t131\tI\t0.37\t0.67\t1.80\t0.83\t0.94\t0.95\t131.17\t5.52\t4.50\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t132\tM\t0.40\t0.58\t-0.11\t0.78\t0.95\t0.98\t149.21\t5.28\t1.90\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t133\tR\t0.41\t0.45\t0.51\t0.89\t0.96\t0.97\t174.20\t9.75\t-4.50\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t134\tS\t0.41\t0.53\t-1.91\t0.87\t0.97\t1.03\t105.09\t5.24\t-0.80\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t135\tF\t0.42\t0.71\t0.16\t1.00\t0.97\t1.01\t165.19\t5.52\t2.80\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t136\tS\t0.45\t0.52\t1.50\t1.06\t0.98\t1.02\t105.09\t5.24\t-0.80\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t137\tL\t0.43\t0.63\t1.90\t1.14\t0.99\t1.01\t131.17\t5.52\t3.80\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t138\tS\t0.43\t0.60\t-0.34\t1.02\t1.00\t1.04\t105.09\t5.24\t-0.80\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t139\tT\t0.45\t0.78\t1.83\t1.08\t1.02\t1.03\t119.12\t5.19\t-0.70\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t140\tN\t0.47\t1.63\t2.01\t0.98\t1.02\t1.01\t132.12\t5.52\t-3.50\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t141\tL\t0.45\t1.63\t4.26\t1.10\t1.02\t0.97\t131.17\t5.52\t3.80\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t142\tQ\t0.39\t0.93\t2.01\t0.98\t0.00\t1.01\t146.15\t5.52\t-3.50\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t143\tE\t0.36\t0.00\t0.00\t0.00\t0.00\t0.00\t147.13\t4.00\t-3.50\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t144\tS\t0.29\t0.00\t0.00\t0.00\t0.00\t0.00\t105.09\t5.24\t-0.80\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\t145\tL\t0.24\t0.00\t0.00\t0.00\t0.00\t0.00\t131.17\t5.52\t3.80\n' |
| b |
| diff -r 000000000000 -r ef26009cd70a test-data/command-epifinder-topology.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/command-epifinder-topology.tsv Thu Nov 25 01:26:36 2021 +0000 |
| b |
| @@ -0,0 +1,28 @@ +N Id Method Threshold Avg Score Cover Epitope Start End N-Glyc N-Glyc-Count N-Glyc-Motifs Length kDa I.P Avg Hydropathy Avg Cover +1 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation BepiPred-2.0 0.60 0.65 - PETQSSHSAW 73 83 N 0 - 10 1.13 5.25 -1.40 0.98 + Emini 0.80 2.57 0.90 EEEEEEEEE. + Parker 0.80 4.19 1.00 EEEEEEEEEE + Chou Fosman 0.80 1.13 1.00 EEEEEEEEEE + Karplus Schulz 0.80 1.04 1.00 EEEEEEEEEE + Kolaskar 0.80 0.99 1.00 EEEEEEEEEE + All matches - - 0.90 EEEEEEEEE. + N-Glyc - - - .......... + Hydropathy - -1.40 - --------+- +2 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation BepiPred-2.0 0.60 0.64 - AIFLKWHVPPELVR 149 163 N 0 - 14 1.71 8.80 0.42 0.60 + Emini 0.80 0.82 0.43 .....EEEE.EE.. + Parker 0.80 -1.83 0.07 .......E...... + Chou Fosman 0.80 0.83 0.50 .....EEEEEEE.. + Karplus Schulz 0.80 0.96 1.00 EEEEEEEEEEEEEE + Kolaskar 0.80 1.10 1.00 EEEEEEEEEEEEEE + All matches - - 0.07 .......E...... + N-Glyc - - - .............. + Hydropathy - 0.42 - ++++---+---++- +3 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation BepiPred-2.0 0.60 0.63 - LKWHVPPELVRVLSA 150 165 N 0 - 15 1.74 8.75 0.39 0.59 + Emini 0.80 0.81 0.40 ..EEEE.EE...... + Parker 0.80 -1.70 0.07 ....E.......... + Chou Fosman 0.80 0.84 0.47 ..EEEEEEE...... + Karplus Schulz 0.80 0.96 1.00 EEEEEEEEEEEEEEE + Kolaskar 0.80 1.11 1.00 EEEEEEEEEEEEEEE + All matches - - 0.07 ....E.......... + N-Glyc - - - ............... + Hydropathy - 0.39 - +---+---++-++-+ |
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| diff -r 000000000000 -r ef26009cd70a test-data/command-epifinder.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/command-epifinder.log Thu Nov 25 01:26:36 2021 +0000 |
| b |
| @@ -0,0 +1,14 @@ +makeblastdb -dbtype prot -in /usr/local/bioinfo/stingrayGalaxy/tools/stingray/epifinder/test-data/proteom.fasta -out ./command-test_proteom Success: + + +Building a new DB, current time: 03/20/2021 00:04:04 +New DB name: /usr/local/bioinfo/stingrayGalaxy/tools/stingray/epifinder/command-test_proteom +New DB title: /usr/local/bioinfo/stingrayGalaxy/tools/stingray/epifinder/test-data/proteom.fasta +Sequence type: Protein +Keep Linkouts: T +Keep MBits: T +Maximum file size: 1000000000B +Adding sequences from FASTA; added 6 sequences in 0.00420094 seconds. +Error: +blastp -query ./command-epifinder-epitopes-fasta.fasta -db ./command-test_proteom -outfmt 6 qacc sacc pident qcovs qseq sseq qacc -task blastp-short -word_size 4 -out ./command-test_proteom_blast.csv Success: +Error: |
| b |
| diff -r 000000000000 -r ef26009cd70a test-data/command-epifinder.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/command-epifinder.txt Thu Nov 25 01:26:36 2021 +0000 |
| b |
| b'@@ -0,0 +1,80 @@\n+\n+---- Running Parameters ----\n+BepiPred-2.0 Threshold : 0.6\n+Min epitope length : 10\n+Max epitope length : 30\n+\n+---- Softwares Threshold ----\n+Emini : 0.8\n+Parker : 0.8\n+Chou Fosman : 0.8\n+Karplus Schulz : 0.8\n+Kolaskar : 0.8\n+\n+---- Proteomes ----\n+Alias \tFile\n+test_proteom \t/usr/local/bioinfo/stingrayGalaxy/tools/stingray/epifinder/test-data/proteom.fasta\n+\n+---- Blast ----\n+Identity : 90.0\n+Cover : 90.0\n+Word size : 4\n+Task blastp-short: blastp-short\n+\n+---- Stats ----\n+Processed proteins : 6\n+NGlycosylated proteins : 0\n+Identified epitopes : 3\n+N-glycosylated epitopes: 0\n+\n+---- Protein Summary ----\n+Id \tEpitopes\tN-Glyc\t\n+5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta \t0 \t0 \t\n+4XAK_A Chain A of Crystal structure of potent neutralizing antibody m336 in complex with MERS Co-V RBD \t0 \t0 \t\n+4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation \t1 \t0 \t\n+4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation \t2 \t0 \t\n+5C0N_A Chain A of Development of a therapeutic monoclonal antibody that targets secreted fatty acid-binding protein aP2 to treat type 2 diabetes.\t0 \t0 \t\n+4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2 \t0 \t0 \t\n+\n+---- Epitopes list ----\n+N\tId \tEpitope \tStart\tEnd\tN-Glyc\tN-Glyc-Count\tN-Glyc-Motifs\tLength\tMW(kDa)\tI.P \tHydropathy\tAll Matches Cover\tAvg Cover\tBepiPred2\tEmini\tParker\tChou Fosman\tKarplus Schulz\tKolaskar\ttest_proteom_count\ttest_proteom_acc \ttest_proteom_count\ttest_proteom_id \t\n+1\t4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation\tPETQSSHSAW \t73 \t83 \tN \t0 \t- \t10 \t1.13 \t5.25\t-1.40 \t0.90 \t0.98 \t0.65 \t2.57 \t4.19 \t1.13 \t1.04 \t0.99 \t1 \t4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation \t1 \t4WFF_B(100.00,100.00) \t\n+2\t4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation\tAIFLKWHVPPELVR \t149 \t163\tN \t0 \t- \t14 \t1.71 \t8.80\t0.42 \t0.07 \t0.60 \t0.64 \t0.82 \t-1.83 \t0.83 \t0.96 \t1.10 \t2 \t4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation,4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation\t2 \t4WFF_B(100.00,100.00),4WFF_A(100.00,100.00)\t\n+3\t4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation\tLKWHVPPELVRVLSA\t150 \t165\tN \t0 \t- \t15 \t1.74 \t8.75\t0.39 \t0.07 \t0.59 \t0.63 \t0.81 \t-1.70 \t0.84 \t0.96 \t1.11 \t2 \t4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation,4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation\t2 \t4WFF_B(100.00,100.00),4WFF_A(100.00,100.00)\t\n+\n+---- Epitopes topology ----\n+N'..b'.00 \tEEEEEEEEEE \t\n+ \t \t Karplus Schulz\t0.80 \t1.04 \t1.00 \tEEEEEEEEEE \t\n+ \t \t Kolaskar\t0.80 \t0.99 \t1.00 \tEEEEEEEEEE \t\n+ \t \t All matches\t- \t- \t0.90 \tEEEEEEEEE. \t\n+ \t \t N-Glyc\t- \t- \t- \t.......... \t\n+ \t \t Hydropathy\t- \t-1.40 \t- \t--------+- \t\n+2\t4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation\t BepiPred-2.0\t0.60 \t0.64 \t- \tAIFLKWHVPPELVR \t149 \t163\tN \t0 \t- \t14 \t1.71\t8.80\t0.42 \t0.60 \t\n+ \t \t Emini\t0.80 \t0.82 \t0.43 \t.....EEEE.EE.. \t\n+ \t \t Parker\t0.80 \t-1.83 \t0.07 \t.......E...... \t\n+ \t \t Chou Fosman\t0.80 \t0.83 \t0.50 \t.....EEEEEEE.. \t\n+ \t \t Karplus Schulz\t0.80 \t0.96 \t1.00 \tEEEEEEEEEEEEEE \t\n+ \t \t Kolaskar\t0.80 \t1.10 \t1.00 \tEEEEEEEEEEEEEE \t\n+ \t \t All matches\t- \t- \t0.07 \t.......E...... \t\n+ \t \t N-Glyc\t- \t- \t- \t.............. \t\n+ \t \t Hydropathy\t- \t0.42 \t- \t++++---+---++- \t\n+3\t4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation\t BepiPred-2.0\t0.60 \t0.63 \t- \tLKWHVPPELVRVLSA \t150 \t165\tN \t0 \t- \t15 \t1.74\t8.75\t0.39 \t0.59 \t\n+ \t \t Emini\t0.80 \t0.81 \t0.40 \t..EEEE.EE...... \t\n+ \t \t Parker\t0.80 \t-1.70 \t0.07 \t....E.......... \t\n+ \t \t Chou Fosman\t0.80 \t0.84 \t0.47 \t..EEEEEEE...... \t\n+ \t \t Karplus Schulz\t0.80 \t0.96 \t1.00 \tEEEEEEEEEEEEEEE \t\n+ \t \t Kolaskar\t0.80 \t1.11 \t1.00 \tEEEEEEEEEEEEEEE \t\n+ \t \t All matches\t- \t- \t0.07 \t....E.......... \t\n+ \t \t N-Glyc\t- \t- \t- \t............... \t\n+ \t \t Hydropathy\t- \t0.39 \t- \t+---+---++-++-+ \t\n+Generated files:\n+\t./command-epifinder-parameters.txt\n+\t./command-epifinder-protein-summary.tsv\n+\t./command-epifinder-topology.tsv\n+\t./command-epifinder-epitope-detail.tsv\n+\t./command-epifinder-scores.tsv\n+\t./command-epifinder-epitopes-fasta.fasta\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r ef26009cd70a test-data/command-epifinder.xls |
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| diff -r 000000000000 -r ef26009cd70a test-data/command-test_proteom.phr |
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| diff -r 000000000000 -r ef26009cd70a test-data/command-test_proteom.pin |
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| Binary file test-data/command-test_proteom.pin has changed |
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| diff -r 000000000000 -r ef26009cd70a test-data/command-test_proteom.psq |
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| Binary file test-data/command-test_proteom.psq has changed |
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| diff -r 000000000000 -r ef26009cd70a test-data/command-test_proteom_blast.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/command-test_proteom_blast.csv Thu Nov 25 01:26:36 2021 +0000 |
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| @@ -0,0 +1,6 @@ +qacc sacc pident qcovs qseq sseq qacc +1-PETQSSHSAW 4WFF_B 100.00 100 PETQSSHSAW PETQSSHSAW +2-AIFLKWHVPPELVR 4WFF_B 100.00 100 AIFLKWHVPPELVR AIFLKWHVPPELVR +2-AIFLKWHVPPELVR 4WFF_A 100.00 100 AIFLKWHVPPELVR AIFLKWHVPPELVR +3-LKWHVPPELVRVLSA 4WFF_B 100.00 100 LKWHVPPELVRVLSA LKWHVPPELVRVLSA +3-LKWHVPPELVRVLSA 4WFF_A 100.00 100 LKWHVPPELVRVLSA LKWHVPPELVRVLSA |
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| diff -r 000000000000 -r ef26009cd70a test-data/input_bcell_command_line.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_bcell_command_line.txt Thu Nov 25 01:26:36 2021 +0000 |
| b |
| b'@@ -0,0 +1,1153 @@\n+input: 5C0N_A Chain A of Development of a therapeutic monoclonal antibody that targets secreted fatty acid-binding protein aP2 to treat type 2 diabetes.\n+Position\tResidue\tScore\tAssignment\n+0\tC\t0.243\tE\n+1\tD\t0.294\tE\n+2\tA\t0.340\tE\n+3\tF\t0.402\tE\n+4\tV\t0.452\tE\n+5\tG\t0.469\tE\n+6\tT\t0.488\tE\n+7\tW\t0.502\tE\n+8\tK\t0.522\tE\n+9\tL\t0.533\tE\n+10\tV\t0.554\tE\n+11\tS\t0.562\tE\n+12\tS\t0.573\tE\n+13\tE\t0.582\tE\n+14\tN\t0.576\tE\n+15\tF\t0.554\tE\n+16\tD\t0.546\tE\n+17\tD\t0.545\tE\n+18\tY\t0.535\tE\n+19\tM\t0.529\tE\n+20\tK\t0.527\tE\n+21\tE\t0.520\tE\n+22\tV\t0.526\tE\n+23\tG\t0.536\tE\n+24\tV\t0.547\tE\n+25\tG\t0.548\tE\n+26\tF\t0.544\tE\n+27\tA\t0.542\tE\n+28\tT\t0.517\tE\n+29\tR\t0.525\tE\n+30\tK\t0.521\tE\n+31\tV\t0.512\tE\n+32\tA\t0.510\tE\n+33\tG\t0.508\tE\n+34\tM\t0.497\tE\n+35\tA\t0.479\tE\n+36\tK\t0.472\tE\n+37\tP\t0.463\tE\n+38\tN\t0.452\tE\n+39\tM\t0.450\tE\n+40\tI\t0.453\tE\n+41\tI\t0.448\tE\n+42\tS\t0.458\tE\n+43\tV\t0.468\tE\n+44\tN\t0.468\tE\n+45\tG\t0.466\tE\n+46\tD\t0.467\tE\n+47\tL\t0.467\tE\n+48\tV\t0.460\tE\n+49\tT\t0.457\tE\n+50\tI\t0.454\tE\n+51\tR\t0.447\tE\n+52\tS\t0.448\tE\n+53\tE\t0.469\tE\n+54\tS\t0.486\tE\n+55\tT\t0.502\tE\n+56\tF\t0.508\tE\n+57\tK\t0.509\tE\n+58\tN\t0.501\tE\n+59\tT\t0.486\tE\n+60\tE\t0.477\tE\n+61\tI\t0.473\tE\n+62\tS\t0.458\tE\n+63\tF\t0.454\tE\n+64\tK\t0.464\tE\n+65\tL\t0.462\tE\n+66\tG\t0.468\tE\n+67\tV\t0.489\tE\n+68\tE\t0.519\tE\n+69\tF\t0.531\tE\n+70\tD\t0.538\tE\n+71\tE\t0.556\tE\n+72\tI\t0.569\tE\n+73\tT\t0.582\tE\n+74\tA\t0.589\tE\n+75\tD\t0.577\tE\n+76\tD\t0.557\tE\n+77\tR\t0.543\tE\n+78\tK\t0.523\tE\n+79\tV\t0.494\tE\n+80\tK\t0.475\tE\n+81\tS\t0.455\tE\n+82\tI\t0.432\tE\n+83\tI\t0.421\tE\n+84\tT\t0.427\tE\n+85\tL\t0.427\tE\n+86\tD\t0.426\tE\n+87\tG\t0.437\tE\n+88\tG\t0.461\tE\n+89\tA\t0.458\tE\n+90\tL\t0.473\tE\n+91\tV\t0.486\tE\n+92\tQ\t0.502\tE\n+93\tV\t0.515\tE\n+94\tQ\t0.529\tE\n+95\tK\t0.540\tE\n+96\tW\t0.547\tE\n+97\tD\t0.551\tE\n+98\tG\t0.560\tE\n+99\tK\t0.551\tE\n+100\tS\t0.547\tE\n+101\tT\t0.543\tE\n+102\tT\t0.530\tE\n+103\tI\t0.520\tE\n+104\tK\t0.515\tE\n+105\tR\t0.505\tE\n+106\tK\t0.505\tE\n+107\tR\t0.507\tE\n+108\tD\t0.499\tE\n+109\tG\t0.490\tE\n+110\tD\t0.468\tE\n+111\tK\t0.458\tE\n+112\tL\t0.438\tE\n+113\tV\t0.433\tE\n+114\tV\t0.433\tE\n+115\tE\t0.426\tE\n+116\tC\t0.415\tE\n+117\tV\t0.413\tE\n+118\tM\t0.415\tE\n+119\tK\t0.424\tE\n+120\tG\t0.426\tE\n+121\tV\t0.448\tE\n+122\tT\t0.442\tE\n+123\tS\t0.436\tE\n+124\tT\t0.439\tE\n+125\tR\t0.447\tE\n+126\tV\t0.453\tE\n+127\tY\t0.401\tE\n+128\tE\t0.353\tE\n+129\tR\t0.308\tE\n+130\tA\t0.251\tE\n+input: 5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing 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4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2\n+Position\tResidue\tScore\tAssignment\n+0\tL\t0.257\tE\n+1\tG\t0.312\tE\n+2\tS\t0.367\tE\n+3\tR\t0.427\tE\n+4\tR\t0.476\tE\n+5\tT\t0.462\tE\n+6\tL\t0.471\tE\n+7\tM\t0.472\tE\n+8\tL\t0.444\tE\n+9\tL\t0.458\tE\n+10\tA\t0.472\tE\n+11\tQ\t0.484\tE\n+12\tM\t0.492\tE\n+13\tR\t0.505\tE\n+14\tK\t0.544\tE\n+15\tI\t0.553\tE\n+16\tS\t0.552\tE\n+17\tL\t0.588\tE\n+18\tF\t0.578\tE\n+19\tS\t0.571\tE\n+20\tC\t0.572\tE\n+21\tL\t0.575\tE\n+22\tK\t0.579\tE\n+23\tD\t0.564\tE\n+24\tR\t0.569\tE\n+25\tH\t0.568\tE\n+26\tD\t0.555\tE\n+27\tF\t0.552\tE\n+28\tG\t0.550\tE\n+29\tF\t0.542\tE\n+30\tP\t0.533\tE\n+31\tQ\t0.542\tE\n+32\tE\t0.554\tE\n+33\tE\t0.562\tE\n+34\tF\t0.583\tE\n+35\tG\t0.602\tE\n+36\tN\t0.603\tE\n+37\tQ\t0.605\tE\n+38\tF\t0.608\tE\n+39\tQ\t0.600\tE\n+40\tK\t0.568\tE\n+41\tA\t0.552\tE\n+42\tE\t0.509\tE\n+43\tT\t0.464\tE\n+44\tI\t0.439\tE\n+45\tP\t0.414\tE\n+46\tV\t0.378\tE\n+47\tL\t0.349\tE\n+48\tH\t0.343\tE\n+49\tE\t0.352\tE\n+50\tM\t0.338\tE\n+51\tI\t0.355\tE\n+52\tQ\t0.391\tE\n+53\tQ\t0.377\tE\n+54\tI\t0.377\tE\n+55\tF\t0.409\tE\n+56\tN\t0.438\tE\n+57\tL\t0.461\tE\n+58\tF\t0.491\tE\n+59\tS\t0.535\tE\n+60\tT\t0.563\tE\n+61\tK\t0.575\tE\n+62\tD\t0.604\tE\n+63\tS\t0.621\tE\n+64\tS\t0.624\tE\n+65\tA\t0.626\tE\n+66\tA\t0.617\tE\n+67\tW\t0.593\tE\n+68\tD\t0.556\tE\n+69\tE\t0.530\tE\n+70\tT\t0.517\tE\n+71\tL\t0.479\tE\n+72\tL\t0.478\tE\n+73\tD\t0.467\tE\n+74\tK\t0.449\tE\n+75\tF\t0.417\tE\n+76\tY\t0.426\tE\n+77\tT\t0.442\tE\n+78\tE\t0.443\tE\n+79\tL\t0.434\tE\n+80\tY\t0.463\tE\n+81\tQ\t0.468\tE\n+82\tQ\t0.458\tE\n+83\tL\t0.484\tE\n+84\tN\t0.508\tE\n+85\tD\t0.476\tE\n+86\tL\t0.476\tE\n+87\tE\t0.482\tE\n+88\tA\t0.497\tE\n+89\tC\t0.502\tE\n+90\tV\t0.512\tE\n+91\tI\t0.535\tE\n+92\tQ\t0.528\tE\n+93\tG\t0.538\tE\n+94\tM\t0.560\tE\n+95\tK\t0.568\tE\n+96\tE\t0.570\tE\n+97\tD\t0.560\tE\n+98\tS\t0.531\tE\n+99\tI\t0.524\tE\n+100\tL\t0.525\tE\n+101\tA\t0.513\tE\n+102\tV\t0.486\tE\n+103\tR\t0.482\tE\n+104\tK\t0.480\tE\n+105\tY\t0.455\tE\n+106\tF\t0.456\tE\n+107\tQ\t0.486\tE\n+108\tR\t0.476\tE\n+109\tI\t0.444\tE\n+110\tT\t0.444\tE\n+111\tL\t0.468\tE\n+112\tY\t0.480\tE\n+113\tL\t0.472\tE\n+114\tK\t0.495\tE\n+115\tE\t0.491\tE\n+116\tK\t0.480\tE\n+117\tK\t0.481\tE\n+118\tY\t0.485\tE\n+119\tS\t0.475\tE\n+120\tP\t0.463\tE\n+121\tC\t0.445\tE\n+122\tA\t0.414\tE\n+123\tW\t0.402\tE\n+124\tE\t0.394\tE\n+125\tV\t0.384\tE\n+126\tV\t0.362\tE\n+127\tR\t0.389\tE\n+128\tA\t0.398\tE\n+129\tE\t0.387\tE\n+130\tI\t0.370\tE\n+131\tM\t0.400\tE\n+132\tR\t0.411\tE\n+133\tS\t0.405\tE\n+134\tF\t0.423\tE\n+135\tS\t0.446\tE\n+136\tL\t0.429\tE\n+137\tS\t0.432\tE\n+138\tT\t0.446\tE\n+139\tN\t0.468\tE\n+140\tL\t0.447\tE\n+141\tQ\t0.392\tE\n+142\tE\t0.355\tE\n+143\tS\t0.294\tE\n+144\tL\t0.242\tE\n+\n' |
| b |
| diff -r 000000000000 -r ef26009cd70a test-data/input_bepi_online.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_bepi_online.csv Thu Nov 25 01:26:36 2021 +0000 |
| b |
| b'@@ -0,0 +1,1142 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|
| b |
| diff -r 000000000000 -r ef26009cd70a test-data/online-epifinder-epitope-detail.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/online-epifinder-epitope-detail.tsv Thu Nov 25 01:26:36 2021 +0000 |
| b |
| @@ -0,0 +1,3 @@ +N Id Epitope Start End N-Glyc N-Glyc-Count N-Glyc-Motifs Length MW(kDa) I.P Hydropathy All Matches Cover Avg Cover BepiPred2 Emini Parker Chou Fosman Karplus Schulz Kolaskar test_proteom_count test_proteom_acc test_proteom_count test_proteom_id +1 4WFF_A FLKWHVPPELVRVLSA 149 165 N 0 - 16 1.89 8.75 0.54 0.06 0.58 0.64 0.78 -1.78 0.83 0.96 1.11 2 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation,4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 2 4WFF_B(100.00,100.00),4WFF_A(100.00,100.00) +2 4WFF_B AIFLKWHVPPELVRVLSAML 149 169 N 0 - 20 2.32 8.80 1.03 0.05 0.54 0.64 0.67 -2.18 0.80 0.95 1.11 2 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation,4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 2 4WFF_B(100.00,100.00),4WFF_A(100.00,100.00) |
| b |
| diff -r 000000000000 -r ef26009cd70a test-data/online-epifinder-epitopes-fasta.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/online-epifinder-epitopes-fasta.fasta Thu Nov 25 01:26:36 2021 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>1-FLKWHVPPELVRVLSA +FLKWHVPPELVRVLSA +>2-AIFLKWHVPPELVRVLSAML +AIFLKWHVPPELVRVLSAML |
| b |
| diff -r 000000000000 -r ef26009cd70a test-data/online-epifinder-parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/online-epifinder-parameters.txt Thu Nov 25 01:26:36 2021 +0000 |
| b |
| @@ -0,0 +1,28 @@ + +---- Running Parameters ---- +BepiPred-2.0 Threshold : 0.6 +Min epitope length : 10 +Max epitope length : 30 + +---- Softwares Threshold ---- +Emini : 0.8 +Parker : 0.8 +Chou Fosman : 0.8 +Karplus Schulz : 0.8 +Kolaskar : 0.8 + +---- Proteomes ---- +Alias File +test_proteom /usr/local/bioinfo/stingrayGalaxy/tools/stingray/epifinder/test-data/proteom.fasta + +---- Blast ---- +Identity : 90.0 +Cover : 90.0 +Word size : 4 +Task blastp-short: blastp-short + +---- Stats ---- +Processed proteins : 6 +NGlycosylated proteins : 0 +Identified epitopes : 2 +N-glycosylated epitopes: 0 |
| b |
| diff -r 000000000000 -r ef26009cd70a test-data/online-epifinder-protein-summary.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/online-epifinder-protein-summary.tsv Thu Nov 25 01:26:36 2021 +0000 |
| b |
| @@ -0,0 +1,7 @@ +Id Epitopes N-Glyc +4WFF_B 1 0 +5BVP_A 0 0 +4XAK_A 0 0 +4WFF_A 1 0 +5C0N_A 0 0 +4Z5R_A 0 0 |
| b |
| diff -r 000000000000 -r ef26009cd70a test-data/online-epifinder-scores.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/online-epifinder-scores.tsv Thu Nov 25 01:26:36 2021 +0000 |
| b |
| b'@@ -0,0 +1,1141 @@\n+Id\tPosition\tResidue\tBepipred2\tEmini\tParker\tChou Fosman\tKarplus Schulz\tKolaskar\tMW\tIP\tHydropathy\n+4WFF_B\t1\tR\t0.18\t0.00\t0.00\t0.00\t0.00\t0.00\t174.20\t9.75\t-4.50\n+4WFF_B\t2\tS\t0.22\t0.00\t0.00\t0.00\t0.00\t0.00\t105.09\t5.24\t-0.80\n+4WFF_B\t3\tT\t0.26\t1.27\t0.00\t0.00\t0.00\t0.00\t119.12\t5.19\t-0.70\n+4WFF_B\t4\tT\t0.28\t0.66\t0.69\t0.88\t1.03\t1.04\t119.12\t5.19\t-0.70\n+4WFF_B\t5\tL\t0.31\t0.40\t-1.23\t0.83\t0.99\t1.09\t131.17\t5.52\t3.80\n+4WFF_B\t6\tL\t0.31\t0.23\t-3.47\t0.71\t0.95\t1.13\t131.17\t5.52\t3.80\n+4WFF_B\t7\tA\t0.31\t0.16\t-3.91\t0.66\t0.93\t1.15\t89.09\t5.57\t1.80\n+4WFF_B\t8\tL\t0.29\t0.16\t-5.97\t0.61\t0.91\t1.20\t131.17\t5.52\t3.80\n+4WFF_B\t9\tL\t0.28\t0.15\t-5.19\t0.60\t0.91\t1.22\t131.17\t5.52\t3.80\n+4WFF_B\t10\tA\t0.27\t0.12\t-5.19\t0.60\t0.91\t1.22\t89.09\t5.57\t1.80\n+4WFF_B\t11\tL\t0.26\t0.12\t-6.80\t0.59\t0.91\t1.24\t131.17\t5.52\t3.80\n+4WFF_B\t12\tV\t0.24\t0.23\t-5.76\t0.67\t0.91\t1.23\t117.15\t5.49\t4.20\n+4WFF_B\t13\tL\t0.24\t0.18\t-5.76\t0.67\t0.91\t1.23\t131.17\t5.52\t3.80\n+4WFF_B\t14\tL\t0.26\t0.17\t-6.59\t0.64\t0.90\t1.28\t131.17\t5.52\t3.80\n+4WFF_B\t15\tY\t0.26\t0.30\t-4.34\t0.76\t0.91\t1.24\t181.19\t5.52\t-1.30\n+4WFF_B\t16\tL\t0.28\t0.36\t-3.00\t0.91\t0.93\t1.17\t131.17\t5.52\t3.80\n+4WFF_B\t17\tV\t0.30\t0.44\t-1.39\t0.92\t0.95\t1.14\t117.15\t5.49\t4.20\n+4WFF_B\t18\tS\t0.31\t0.23\t-1.39\t0.92\t0.97\t1.14\t105.09\t5.24\t-0.80\n+4WFF_B\t19\tG\t0.30\t0.21\t-1.64\t0.83\t0.98\t1.17\t75.07\t5.52\t-0.40\n+4WFF_B\t20\tA\t0.32\t0.24\t-1.64\t0.83\t0.96\t1.15\t89.09\t5.57\t1.80\n+4WFF_B\t21\tL\t0.34\t0.36\t-0.51\t0.90\t0.94\t1.08\t131.17\t5.52\t3.80\n+4WFF_B\t22\tV\t0.36\t0.36\t-1.14\t0.79\t0.93\t1.09\t117.15\t5.49\t4.20\n+4WFF_B\t23\tF\t0.38\t0.30\t-3.27\t0.65\t0.92\t1.14\t165.19\t5.52\t2.80\n+4WFF_B\t24\tR\t0.42\t0.62\t-2.46\t0.66\t0.93\t1.11\t174.20\t9.75\t-4.50\n+4WFF_B\t25\tA\t0.45\t1.45\t-0.29\t0.72\t0.96\t1.08\t89.09\t5.57\t1.80\n+4WFF_B\t26\tL\t0.47\t2.59\t0.54\t0.86\t0.99\t1.03\t131.17\t5.52\t3.80\n+4WFF_B\t27\tE\t0.50\t1.80\t2.16\t0.91\t1.03\t1.03\t147.13\t4.00\t-3.50\n+4WFF_B\t28\tQ\t0.54\t3.09\t2.67\t0.88\t1.06\t1.03\t146.15\t5.52\t-3.50\n+4WFF_B\t29\tP\t0.55\t6.48\t3.23\t0.93\t1.07\t1.02\t115.13\t5.96\t-1.60\n+4WFF_B\t30\tH\t0.57\t6.48\t5.40\t0.98\t1.06\t0.99\t155.16\t6.74\t-3.20\n+4WFF_B\t31\tE\t0.61\t3.78\t4.59\t0.97\t1.06\t1.02\t147.13\t4.00\t-3.50\n+4WFF_B\t32\tQ\t0.61\t4.23\t4.59\t0.97\t1.06\t1.02\t146.15\t5.52\t-3.50\n+4WFF_B\t33\tQ\t0.61\t6.09\t4.89\t0.89\t1.05\t0.99\t146.15\t5.52\t-3.50\n+4WFF_B\t34\tA\t0.58\t6.09\t5.70\t0.86\t1.05\t0.95\t89.09\t5.57\t1.80\n+4WFF_B\t35\tQ\t0.58\t2.90\t3.27\t0.84\t1.04\t1.01\t146.15\t5.52\t-3.50\n+4WFF_B\t36\tR\t0.57\t1.66\t3.23\t0.92\t1.03\t0.99\t174.20\t9.75\t-4.50\n+4WFF_B\t37\tE\t0.57\t2.84\t3.49\t0.89\t1.02\t0.97\t147.13\t4.00\t-3.50\n+4WFF_B\t38\tL\t0.57\t1.22\t2.66\t0.87\t1.02\t1.01\t131.17\t5.52\t3.80\n+4WFF_B\t39\tG\t0.58\t1.22\t2.40\t0.86\t1.02\t0.99\t75.07\t5.52\t-0.40\n+4WFF_B\t40\tE\t0.57\t1.22\t2.91\t0.83\t1.02\t0.99\t147.13\t4.00\t-3.50\n+4WFF_B\t41\tV\t0.54\t2.95\t2.61\t0.87\t1.03\t1.00\t117.15\t5.49\t4.20\n+4WFF_B\t42\tR\t0.51\t2.58\t2.61\t0.87\t1.03\t0.98\t174.20\t9.75\t-4.50\n+4WFF_B\t43\tE\t0.54\t1.23\t0.49\t0.73\t1.03\t1.03\t147.13\t4.00\t-3.50\n+4WFF_B\t44\tK\t0.54\t3.25\t-0.03\t0.76\t1.01\t1.04\t146.19\t8.75\t-3.90\n+4WFF_B\t45\tF\t0.53\t1.68\t0.80\t0.79\t0.98\t0.99\t165.19\t5.52\t2.80\n+4WFF_B\t46\tL\t0.52\t1.32\t0.50\t0.79\t0.96\t1.02\t131.17\t5.52\t3.80\n+4WFF_B\t47\tR\t0.52\t1.02\t-0.31\t0.90\t0.94\t1.05\t174.20\t9.75\t-4.50\n+4WFF_B\t48\tA\t0.51\t0.63\t-0.93\t0.92\t0.93\t1.12\t89.09\t5.57\t1.80\n+4WFF_B\t49\tH\t0.51\t0.57\t-0.14\t0.91\t0.93\t1.16\t155.16\t6.74\t-3.20\n+4WFF_B\t50\tP\t0.54\t0.39\t2.10\t1.03\t0.93\t1.13\t115.13\t5.96\t-1.60\n+4WFF_B\t51\tC\t0.56\t0.64\t2.93\t1.10\t0.94\t1.13\t121.15\t5.52\t2.50\n+4WFF_B\t52\tV\t0.57\t0.82\t3.49\t1.15\t0.97\t1.12\t117.15\t5.49\t4.20\n+4WFF_B\t53\tS\t0.57\t0.91\t4.30\t1.12\t1.01\t1.09\t105.09\t5.24\t-0.80\n+4WFF_B\t54\tD\t0.58\t1.41\t2.69\t0.98\t1.03\t1.11\t133.10\t3.80\t-3.50\n+4WFF_B\t55\tQ\t0.58\t1.88\t3.30\t1.04\t1.05\t1.04\t146.15\t5.52\t-3.50\n+4WFF_B\t56\tE\t0.55\t1.15\t2.51\t1.05\t1.03\t1.02\t147.13\t4.00\t-3.50\n+4WFF_B\t57\tL\t0.53\t0.57\t0.27\t0.93\t1.00\t1.05\t131.17\t5.52\t3.80\n+4WFF_B\t58\tG\t0.52\t0.23\t-2.30\t0.79\t0.97\t1.09\t75.07\t5.52\t-0.40\n+4WFF_B\t59\tL\t0.50\t0.27\t-2.34\t0.79\t0.95\t1.08\t131.17\t5.52\t3.80\n+4WFF_B\t60\tL\t0.47\t0.56\t-2.34\t0.79\t0.95\t1.08\t131.17\t5.52\t3.80\n+4WFF_B\t61\tI\t0.44\t0.42\t-1.56\t0.78\t0.96\t1.10\t131.17\t5.52\t4.50\n+4WFF_B\t62\tK\t0.44\t0.51\t-2.07\t0.65\t0.98\t1.13\t146.19\t8.75\t-3.90\n+4WFF_B\t63\tE\t0.44\t1.04\t0.67\t0.78\t0.98\t1.07\t147.13\t4.00\t-3.50\n+4WFF_B\t64\tV\t0.42\t1.50\t2.29\t0.79\t0.97\t1.04\t117.15\t5.49\t4.2'..b'0\n+4Z5R_A\t81\tY\t0.46\t1.17\t0.67\t0.85\t0.99\t1.06\t181.19\t5.52\t-1.30\n+4Z5R_A\t82\tQ\t0.46\t1.09\t0.93\t0.94\t0.99\t1.05\t146.15\t5.52\t-3.50\n+4Z5R_A\t83\tQ\t0.45\t2.20\t1.24\t1.04\t1.00\t1.05\t146.15\t5.52\t-3.50\n+4Z5R_A\t84\tL\t0.48\t1.16\t1.24\t1.04\t1.01\t1.05\t131.17\t5.52\t3.80\n+4Z5R_A\t85\tN\t0.50\t1.16\t2.63\t0.99\t1.01\t1.00\t132.12\t5.52\t-3.50\n+4Z5R_A\t86\tD\t0.47\t0.68\t2.07\t0.94\t1.00\t1.01\t133.10\t3.80\t-3.50\n+4Z5R_A\t87\tL\t0.47\t0.44\t1.41\t0.97\t0.98\t1.07\t131.17\t5.52\t3.80\n+4Z5R_A\t88\tE\t0.47\t0.20\t2.20\t0.96\t0.96\t1.09\t147.13\t4.00\t-3.50\n+4Z5R_A\t89\tA\t0.49\t0.09\t0.06\t0.80\t0.94\t1.14\t89.09\t5.57\t1.80\n+4Z5R_A\t90\tC\t0.48\t0.18\t-0.51\t0.73\t0.93\t1.16\t121.15\t5.52\t2.50\n+4Z5R_A\t91\tV\t0.50\t0.10\t1.61\t0.87\t0.94\t1.11\t117.15\t5.49\t4.20\n+4Z5R_A\t92\tI\t0.52\t0.10\t-0.10\t0.85\t0.95\t1.10\t131.17\t5.52\t4.50\n+4Z5R_A\t93\tQ\t0.51\t0.37\t0.41\t0.90\t0.98\t1.08\t146.15\t5.52\t-3.50\n+4Z5R_A\t94\tG\t0.52\t0.87\t1.33\t0.84\t1.00\t1.00\t75.07\t5.52\t-0.40\n+4Z5R_A\t95\tM\t0.54\t2.08\t3.29\t0.97\t1.02\t0.93\t149.21\t5.28\t1.90\n+4Z5R_A\t96\tK\t0.55\t1.61\t5.36\t1.11\t1.04\t0.91\t146.19\t8.75\t-3.90\n+4Z5R_A\t97\tE\t0.56\t1.14\t3.36\t1.04\t1.04\t0.93\t147.13\t4.00\t-3.50\n+4Z5R_A\t98\tD\t0.55\t0.95\t1.23\t0.90\t1.02\t0.98\t133.10\t3.80\t-3.50\n+4Z5R_A\t99\tS\t0.53\t0.48\t2.13\t0.91\t1.00\t1.02\t105.09\t5.24\t-0.80\n+4Z5R_A\t100\tI\t0.52\t0.21\t0.79\t0.84\t0.96\t1.08\t131.17\t5.52\t4.50\n+4Z5R_A\t101\tL\t0.52\t0.24\t0.27\t0.87\t0.94\t1.09\t131.17\t5.52\t3.80\n+4Z5R_A\t102\tA\t0.52\t0.36\t-0.34\t0.80\t0.94\t1.09\t89.09\t5.57\t1.80\n+4Z5R_A\t103\tV\t0.50\t0.80\t-1.54\t0.76\t0.96\t1.12\t117.15\t5.49\t4.20\n+4Z5R_A\t104\tR\t0.50\t0.84\t-1.71\t0.78\t0.98\t1.11\t174.20\t9.75\t-4.50\n+4Z5R_A\t105\tK\t0.51\t1.45\t0.46\t0.83\t0.99\t1.07\t146.19\t8.75\t-3.90\n+4Z5R_A\t106\tY\t0.48\t3.82\t0.76\t0.88\t0.99\t1.05\t181.19\t5.52\t-1.30\n+4Z5R_A\t107\tF\t0.48\t1.37\t0.14\t0.87\t0.99\t1.01\t165.19\t5.52\t2.80\n+4Z5R_A\t108\tQ\t0.51\t0.99\t0.29\t0.87\t0.99\t1.02\t146.15\t5.52\t-3.50\n+4Z5R_A\t109\tR\t0.50\t0.52\t-1.84\t0.81\t0.99\t1.06\t174.20\t9.75\t-4.50\n+4Z5R_A\t110\tI\t0.47\t0.94\t-1.84\t0.81\t0.98\t1.06\t131.17\t5.52\t4.50\n+4Z5R_A\t111\tT\t0.46\t0.45\t-1.84\t0.81\t0.96\t1.09\t119.12\t5.19\t-0.70\n+4Z5R_A\t112\tL\t0.48\t0.46\t-1.89\t0.82\t0.95\t1.08\t131.17\t5.52\t3.80\n+4Z5R_A\t113\tY\t0.49\t1.13\t-1.37\t0.79\t0.95\t1.07\t181.19\t5.52\t-1.30\n+4Z5R_A\t114\tL\t0.48\t1.56\t0.59\t0.86\t0.98\t1.04\t131.17\t5.52\t3.80\n+4Z5R_A\t115\tK\t0.50\t3.79\t0.66\t0.87\t1.02\t1.04\t146.19\t8.75\t-3.90\n+4Z5R_A\t116\tE\t0.49\t3.79\t1.70\t0.95\t1.05\t1.03\t147.13\t4.00\t-3.50\n+4Z5R_A\t117\tK\t0.48\t6.16\t2.90\t0.99\t1.06\t1.01\t146.19\t8.75\t-3.90\n+4Z5R_A\t118\tK\t0.48\t4.76\t4.51\t1.12\t1.06\t0.98\t146.19\t8.75\t-3.90\n+4Z5R_A\t119\tY\t0.48\t1.47\t3.90\t1.15\t1.04\t1.05\t181.19\t5.52\t-1.30\n+4Z5R_A\t120\tS\t0.48\t0.74\t3.09\t1.14\t1.01\t1.08\t105.09\t5.24\t-0.80\n+4Z5R_A\t121\tP\t0.46\t0.39\t0.84\t1.13\t0.99\t1.08\t115.13\t5.96\t-1.60\n+4Z5R_A\t122\tC\t0.44\t0.43\t1.14\t1.09\t0.95\t1.07\t121.15\t5.52\t2.50\n+4Z5R_A\t123\tA\t0.41\t0.24\t0.89\t1.00\t0.94\t1.10\t89.09\t5.57\t1.80\n+4Z5R_A\t124\tW\t0.40\t0.11\t-0.57\t0.87\t0.92\t1.15\t204.23\t5.52\t-0.90\n+4Z5R_A\t125\tE\t0.39\t0.42\t-0.27\t0.79\t0.92\t1.12\t147.13\t4.00\t-3.50\n+4Z5R_A\t126\tV\t0.38\t0.42\t-0.17\t0.71\t0.93\t1.07\t117.15\t5.49\t4.20\n+4Z5R_A\t127\tV\t0.36\t0.69\t0.64\t0.72\t0.94\t1.04\t117.15\t5.49\t4.20\n+4Z5R_A\t128\tR\t0.38\t0.28\t0.93\t0.65\t0.94\t1.08\t174.20\t9.75\t-4.50\n+4Z5R_A\t129\tA\t0.39\t0.37\t-0.79\t0.63\t0.94\t1.08\t89.09\t5.57\t1.80\n+4Z5R_A\t130\tE\t0.38\t0.99\t0.34\t0.70\t0.94\t1.00\t147.13\t4.00\t-3.50\n+4Z5R_A\t131\tI\t0.36\t0.67\t1.80\t0.83\t0.94\t0.95\t131.17\t5.52\t4.50\n+4Z5R_A\t132\tM\t0.39\t0.58\t-0.11\t0.78\t0.95\t0.98\t149.21\t5.28\t1.90\n+4Z5R_A\t133\tR\t0.40\t0.45\t0.51\t0.89\t0.96\t0.97\t174.20\t9.75\t-4.50\n+4Z5R_A\t134\tS\t0.39\t0.53\t-1.91\t0.87\t0.97\t1.03\t105.09\t5.24\t-0.80\n+4Z5R_A\t135\tF\t0.41\t0.71\t0.16\t1.00\t0.97\t1.01\t165.19\t5.52\t2.80\n+4Z5R_A\t136\tS\t0.44\t0.52\t1.50\t1.06\t0.98\t1.02\t105.09\t5.24\t-0.80\n+4Z5R_A\t137\tL\t0.42\t0.63\t1.90\t1.14\t0.99\t1.01\t131.17\t5.52\t3.80\n+4Z5R_A\t138\tS\t0.42\t0.60\t-0.34\t1.02\t1.00\t1.04\t105.09\t5.24\t-0.80\n+4Z5R_A\t139\tT\t0.44\t0.78\t1.83\t1.08\t1.02\t1.03\t119.12\t5.19\t-0.70\n+4Z5R_A\t140\tN\t0.46\t1.63\t2.01\t0.98\t1.02\t1.01\t132.12\t5.52\t-3.50\n+4Z5R_A\t141\tL\t0.44\t1.63\t4.26\t1.10\t1.02\t0.97\t131.17\t5.52\t3.80\n+4Z5R_A\t142\tQ\t0.39\t0.93\t2.01\t0.98\t0.00\t1.01\t146.15\t5.52\t-3.50\n+4Z5R_A\t143\tE\t0.36\t0.00\t0.00\t0.00\t0.00\t0.00\t147.13\t4.00\t-3.50\n+4Z5R_A\t144\tS\t0.30\t0.00\t0.00\t0.00\t0.00\t0.00\t105.09\t5.24\t-0.80\n+4Z5R_A\t145\tL\t0.24\t0.00\t0.00\t0.00\t0.00\t0.00\t131.17\t5.52\t3.80\n' |
| b |
| diff -r 000000000000 -r ef26009cd70a test-data/online-epifinder-topology.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/online-epifinder-topology.tsv Thu Nov 25 01:26:36 2021 +0000 |
| b |
| @@ -0,0 +1,19 @@ +N Id Method Threshold Avg Score Cover Epitope Start End N-Glyc N-Glyc-Count N-Glyc-Motifs Length kDa I.P Avg Hydropathy Avg Cover +1 4WFF_A BepiPred-2.0 0.60 0.64 - FLKWHVPPELVRVLSA 149 165 N 0 - 16 1.89 8.75 0.54 0.58 + Emini 0.80 0.78 0.38 ...EEEE.EE...... + Parker 0.80 -1.78 0.06 .....E.......... + Chou Fosman 0.80 0.83 0.44 ...EEEEEEE...... + Karplus Schulz 0.80 0.96 1.00 EEEEEEEEEEEEEEEE + Kolaskar 0.80 1.11 1.00 EEEEEEEEEEEEEEEE + All matches - - 0.06 .....E.......... + N-Glyc - - - ................ + Hydropathy - 0.54 - ++---+---++-++-+ +2 4WFF_B BepiPred-2.0 0.60 0.64 - AIFLKWHVPPELVRVLSAML 149 169 N 0 - 20 2.32 8.80 1.03 0.54 + Emini 0.80 0.67 0.30 .....EEEE.EE........ + Parker 0.80 -2.18 0.05 .......E............ + Chou Fosman 0.80 0.80 0.35 .....EEEEEEE........ + Karplus Schulz 0.80 0.95 1.00 EEEEEEEEEEEEEEEEEEEE + Kolaskar 0.80 1.11 1.00 EEEEEEEEEEEEEEEEEEEE + All matches - - 0.05 .......E............ + N-Glyc - - - .................... + Hydropathy - 1.03 - ++++---+---++-++-+++ |
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| diff -r 000000000000 -r ef26009cd70a test-data/online-epifinder.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/online-epifinder.log Thu Nov 25 01:26:36 2021 +0000 |
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| @@ -0,0 +1,14 @@ +makeblastdb -dbtype prot -in /usr/local/bioinfo/stingrayGalaxy/tools/stingray/epifinder/test-data/proteom.fasta -out ./online-test_proteom Success: + + +Building a new DB, current time: 03/20/2021 00:12:41 +New DB name: /usr/local/bioinfo/stingrayGalaxy/tools/stingray/epifinder/online-test_proteom +New DB title: /usr/local/bioinfo/stingrayGalaxy/tools/stingray/epifinder/test-data/proteom.fasta +Sequence type: Protein +Keep Linkouts: T +Keep MBits: T +Maximum file size: 1000000000B +Adding sequences from FASTA; added 6 sequences in 0.00433183 seconds. +Error: +blastp -query ./online-epifinder-epitopes-fasta.fasta -db ./online-test_proteom -outfmt 6 qacc sacc pident qcovs qseq sseq qacc -task blastp-short -word_size 4 -out ./online-test_proteom_blast.csv Success: +Error: |
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| diff -r 000000000000 -r ef26009cd70a test-data/online-epifinder.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/online-epifinder.txt Thu Nov 25 01:26:36 2021 +0000 |
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| @@ -0,0 +1,70 @@ + +---- Running Parameters ---- +BepiPred-2.0 Threshold : 0.6 +Min epitope length : 10 +Max epitope length : 30 + +---- Softwares Threshold ---- +Emini : 0.8 +Parker : 0.8 +Chou Fosman : 0.8 +Karplus Schulz : 0.8 +Kolaskar : 0.8 + +---- Proteomes ---- +Alias File +test_proteom /usr/local/bioinfo/stingrayGalaxy/tools/stingray/epifinder/test-data/proteom.fasta + +---- Blast ---- +Identity : 90.0 +Cover : 90.0 +Word size : 4 +Task blastp-short: blastp-short + +---- Stats ---- +Processed proteins : 6 +NGlycosylated proteins : 0 +Identified epitopes : 2 +N-glycosylated epitopes: 0 + +---- Protein Summary ---- +Id Epitopes N-Glyc +4WFF_B 1 0 +5BVP_A 0 0 +4XAK_A 0 0 +4WFF_A 1 0 +5C0N_A 0 0 +4Z5R_A 0 0 + +---- Epitopes list ---- +N Id Epitope Start End N-Glyc N-Glyc-Count N-Glyc-Motifs Length MW(kDa) I.P Hydropathy All Matches Cover Avg Cover BepiPred2 Emini Parker Chou Fosman Karplus Schulz Kolaskar test_proteom_count test_proteom_acc test_proteom_count test_proteom_id +1 4WFF_A FLKWHVPPELVRVLSA 149 165 N 0 - 16 1.89 8.75 0.54 0.06 0.58 0.64 0.78 -1.78 0.83 0.96 1.11 2 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation,4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 2 4WFF_B(100.00,100.00),4WFF_A(100.00,100.00) +2 4WFF_B AIFLKWHVPPELVRVLSAML 149 169 N 0 - 20 2.32 8.80 1.03 0.05 0.54 0.64 0.67 -2.18 0.80 0.95 1.11 2 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation,4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 2 4WFF_B(100.00,100.00),4WFF_A(100.00,100.00) + +---- Epitopes topology ---- +N Id Method Threshold Avg Score Cover Epitope Start End N-Glyc N-Glyc-Count N-Glyc-Motifs Length kDa I.P Avg Hydropathy Avg Cover +1 4WFF_A BepiPred-2.0 0.60 0.64 - FLKWHVPPELVRVLSA 149 165 N 0 - 16 1.89 8.75 0.54 0.58 + Emini 0.80 0.78 0.38 ...EEEE.EE...... + Parker 0.80 -1.78 0.06 .....E.......... + Chou Fosman 0.80 0.83 0.44 ...EEEEEEE...... + Karplus Schulz 0.80 0.96 1.00 EEEEEEEEEEEEEEEE + Kolaskar 0.80 1.11 1.00 EEEEEEEEEEEEEEEE + All matches - - 0.06 .....E.......... + N-Glyc - - - ................ + Hydropathy - 0.54 - ++---+---++-++-+ +2 4WFF_B BepiPred-2.0 0.60 0.64 - AIFLKWHVPPELVRVLSAML 149 169 N 0 - 20 2.32 8.80 1.03 0.54 + Emini 0.80 0.67 0.30 .....EEEE.EE........ + Parker 0.80 -2.18 0.05 .......E............ + Chou Fosman 0.80 0.80 0.35 .....EEEEEEE........ + Karplus Schulz 0.80 0.95 1.00 EEEEEEEEEEEEEEEEEEEE + Kolaskar 0.80 1.11 1.00 EEEEEEEEEEEEEEEEEEEE + All matches - - 0.05 .......E............ + N-Glyc - - - .................... + Hydropathy - 1.03 - ++++---+---++-++-+++ +Generated files: + ./online-epifinder-parameters.txt + ./online-epifinder-protein-summary.tsv + ./online-epifinder-topology.tsv + ./online-epifinder-epitope-detail.tsv + ./online-epifinder-scores.tsv + ./online-epifinder-epitopes-fasta.fasta \ No newline at end of file |
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| diff -r 000000000000 -r ef26009cd70a test-data/online-epifinder.xls |
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| Binary file test-data/online-epifinder.xls has changed |
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| diff -r 000000000000 -r ef26009cd70a test-data/online-test_proteom.phr |
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| Binary file test-data/online-test_proteom.phr has changed |
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| diff -r 000000000000 -r ef26009cd70a test-data/online-test_proteom.pin |
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| Binary file test-data/online-test_proteom.pin has changed |
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| diff -r 000000000000 -r ef26009cd70a test-data/online-test_proteom.psq |
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| Binary file test-data/online-test_proteom.psq has changed |
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| diff -r 000000000000 -r ef26009cd70a test-data/online-test_proteom_blast.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/online-test_proteom_blast.csv Thu Nov 25 01:26:36 2021 +0000 |
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| @@ -0,0 +1,5 @@ +qacc sacc pident qcovs qseq sseq qacc +1-FLKWHVPPELVRVLSA 4WFF_B 100.00 100 FLKWHVPPELVRVLSA FLKWHVPPELVRVLSA +1-FLKWHVPPELVRVLSA 4WFF_A 100.00 100 FLKWHVPPELVRVLSA FLKWHVPPELVRVLSA +2-AIFLKWHVPPELVRVLSAML 4WFF_B 100.00 100 AIFLKWHVPPELVRVLSAML AIFLKWHVPPELVRVLSAML +2-AIFLKWHVPPELVRVLSAML 4WFF_A 100.00 100 AIFLKWHVPPELVRVLSAML AIFLKWHVPPELVRVLSAML |
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| diff -r 000000000000 -r ef26009cd70a test-data/proteom.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteom.fasta Thu Nov 25 01:26:36 2021 +0000 |
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| @@ -0,0 +1,12 @@ +>5C0N_A Chain A of Development of a therapeutic monoclonal antibody that targets secreted fatty acid-binding protein aP2 to treat type 2 diabetes. +CDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDLVTIRSESTFKNTEISFKLGVEFDEITADDRKVKSIITLDGGALVQVQKWDGKSTTIKRKRDGDKLVVECVMKGVTSTRVYERA +>5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta +VRSLNCTLRDSQQKSLVMSGPYELKALHLQGQDMEQQVVFSMSFVQGEESNDKIPVALGLKEKNLYLSCVLKDDKPTLQLESVDPKNYPKKKMEKRFVFNKIEINNKLEFESAQFPNWYISTSQAENMPVFLGGGGQDITDFTMQFVSS +>4XAK_A Chain A of Crystal structure of potent neutralizing antibody m336 in complex with MERS Co-V RBD +VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRFLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTTNSVCPKLEFA +>4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation +RSTTLLALLALVLLYLVSGALVFRALEQPHEQQAQRELGEVREKFLRAHPCVSDQELGLLIKEVADALGGGADPETSHSAWDLGSAFFFSGTIITTIGYGNVALRTDAGRLFCIFYALVGIPLFGILLAGVGDRLGSSLRHGIGHIEAIFLKWHVPPELVRVLSAMLFLLIGCLLFVLTPTFVFCYMEDWSKLEAIYFVVTLTTVGFGDYVAGADPRQDSPAYQPLVWFWILLGLAYFASVLTTIGNWLRVV +>4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation +RSTTLLALLALVLLYLVSGALVFRALEQPHEQQAQRELGEVREKFLRAHPCVSDQELGLLIKEVADALGGGADPETQSSHSAWDLGSAFFFSGTIITTIGYGNVALRTDAGRLFCIFYALVGIPLFGILLAGVGDRLGSSLRHGIGHIEAIFLKWHVPPELVRVLSAMLFLLIGCLLFVLTPTFVFCYMEDWSKLEAIYFVIVTLTTVGFGDYVAGADPRQDSPAYQPLVWFWILLGLAYFASVLTTIGNWLR +>4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2 +LGSRRTLMLLAQMRKISLFSCLKDRHDFGFPQEEFGNQFQKAETIPVLHEMIQQIFNLFSTKDSSAAWDETLLDKFYTELYQQLNDLEACVIQGMKEDSILAVRKYFQRITLYLKEKKYSPCAWEVVRAEIMRSFSLSTNLQESL |