| Previous changeset 2:9a599f278852 (2018-07-26) Next changeset 4:3e510701a712 (2019-07-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b |
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modified:
pathwaymatcher.xml test-data/proteoforms_graphs/geneInternalEdges.tsv test-data/proteoforms_graphs/geneVertices.tsv test-data/proteoforms_graphs/proteinExternalEdges.tsv test-data/proteoforms_graphs/proteinInternalEdges.tsv test-data/proteoforms_graphs/proteinVertices.tsv test-data/proteoforms_graphs/proteoformExternalEdges.tsv test-data/proteoforms_graphs/proteoformInternalEdges.tsv test-data/proteoforms_graphs/proteoformVertices.tsv |
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removed:
test-data/proteoforms_graphs/geneExternalEdges.tsv |
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| diff -r 9a599f278852 -r 2cd67294abbd pathwaymatcher.xml --- a/pathwaymatcher.xml Thu Jul 26 17:00:38 2018 -0400 +++ b/pathwaymatcher.xml Wed May 08 13:41:47 2019 -0400 |
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| b'@@ -3,8 +3,8 @@\n PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome.\n </description>\n <macros>\n- <token name="@PATHWAYMATCHER_VERSION@">1.8.1</token>\n- <token name="@TOOL_SUBVERSION@">2</token>\n+ <token name="@PATHWAYMATCHER_VERSION@">1.9.1</token>\n+ <token name="@TOOL_SUBVERSION@">1</token>\n <xml name="input_fasta">\n <param format="fasta" name="input_database" type="data" label="Protein Database"\n help="Select FASTA database from history"/>\n@@ -33,73 +33,98 @@\n cwd=`pwd`;\n export HOME=\\$cwd;\n \n+ ## If we use peptideshaker files as inputs, firstly we need to uncompress their proteoforms files.\n+ #for $i, $s in enumerate($match_types)\n+ #if $s.match_type.match_type_selector == "peptideshakerzip_proteoforms"\n+ ##unzip -l $s.match_type.input_peptideshakerzip_proteoforms;\n+ unzip -j \'${$s.match_type.input_peptideshakerzip_proteoforms}\' \'output_reports/proteoforms.txt\' -d \'./\';\n+ mv proteoforms.txt ps_proteoforms_\'${$i}\'.txt;\n+ #end if\n+ #end for\n+\n #####################\n ## Pathway Matcher ##\n #####################\n- (pathwaymatcher src.main.java.no.uib.pap.pathwaymatcher.PathwayMatcher\n+ (pathwaymatcher\n+\n+ #for $i, $s in enumerate($match_types)\n+\n+\n+ ## PROTEOFORMS\n+\n+ #if $s.match_type.match_type_selector == "proteoforms"\n+ #if $s.match_type.proteoform_match_criteria:\n+ match-proteoforms -m \'${s.match_type.proteoform_match_criteria}\' -i \'${s.match_type.input_proteoforms}\' -r \'${s.match_type.proteoform_range}\'\n+ #else:\n+ match-proteoforms -i \'${s.match_type.input_proteoforms}\' -r \'${s.match_type.proteoform_range}\'\n+ #end if\n+ #end if\n+\n+ ## PROTEOFORMS FROM PEPTIDESHAKER FILE\n \n- #for $i, $s in enumerate($input_types)\n+ #if $s.match_type.match_type_selector == "peptideshakerzip_proteoforms"\n+ #if $s.match_type.proteoform_peptideshakerzip_match_criteria:\n+ match-proteoforms -m \'${s.match_type.proteoform_peptideshakerzip_match_criteria}\' -i ps_proteoforms_\'${$i}\'.txt -r \'${s.match_type.proteoform_peptideshakerzip_range}\'\n+ #else:\n+ match-proteoforms -i ps_proteoforms_\'${$i}\'.txt -r \'${s.match_type.proteoform_peptideshakerzip_range}\'\n+ #end if\n+ #end if\n+\n+\n+ ## GENES\n+\n+ #if $s.match_type.match_type_selector == "gene"\n+ match-genes -i \'${s.match_type.input_gene}\'\n+ #end if\n+\n+\n+ ## PROTEINS\n+\n+ #if $s.match_type.match_type_selector == "uniprot"\n+ match-uniprot -i \'${s.match_type.input_uniprot}\'\n+ #end if\n+\n+ #if $s.match_type.match_type_selector == "ensembl"\n+ match-ensembl -i \'${s.match_type.input_ensembl}\'\n+ #end if\n+\n \n ## GENETIC VARIANTS\n \n- #if $s.input_type.input_type_selector == "rsid"\n- -t rsid -i \'${s.input_type.input_rsid}\'\n- #end if\n-\n- #if $s.input_type.input_type_selector == "chrbp"\n- -t chrbp -i \'${s.input_type.input_chrbp}\'\n+ #if $s.match_type.match_type_selector == "vcf"\n+ match-vcf -i \'${s.match_type.input_vcf}\'\n #end if\n \n- #if $s.input_type.input_type_selector == "vcf"\n- -t vcf -i \'${s.input_type.input_vcf}\'\n+ #if $s.match_type.match_type_selector == "chrbp"\n+ match-chrbp -i \'${s.match_type.input_chrbp}\'\n #end if\n \n- ## GENES\n+ '..b' <option value="SUBSET">SUBSET</option>\n+ <option value="ONE_NO_TYPES">ONE_NO_TYPES</option>\n </param>\n+\n+ <param name="modifiedpeptide_ptm_range" type="integer" value="0" label="PTM position range" optional="true"\n+ help="Integer number margin error for sites of PTMs. Only for modified peptides."/>\n </when>\n \n+\n+\n </conditional>\n \n </repeat>\n \n <section name="output_options" expanded="true" title="Output options">\n \n- <param name="search_top_level_info" type="select" label="Add search top level info">\n+ <param name="search_top_level_info" type="select" label="Add Top Level Pathways in the search result.">\n <option value="0" selected="True">False</option>\n <option value="1">True</option>\n </param>\n@@ -269,9 +339,9 @@\n \n <!-- Test that genes search works -->\n <test>\n- <repeat name="input_types">\n- <conditional name="input_type">\n- <param name="input_type_selector" value="gene"/>\n+ <repeat name="match_types">\n+ <conditional name="match_type">\n+ <param name="match_type_selector" value="gene"/>\n <param name="input_gene" value="genes.txt" ftype="txt" />\n </conditional>\n </repeat>\n@@ -280,15 +350,16 @@\n \n <!-- Test graphs from proteoforms -->\n <test>\n- <repeat name="input_types">\n- <conditional name="input_type">\n- <param name="input_type_selector" value="proteoforms"/>\n+ <repeat name="match_types">\n+ <conditional name="match_type">\n+ <param name="match_type_selector" value="proteoforms"/>\n <param name="input_proteoforms" value="proteoforms.txt" ftype="txt" />\n+ <param name="proteoform_match_criteria" value="SUBSET"/>\n </conditional>\n </repeat>\n <param name="output_graphs" value="gg,gu,gp" />\n <output_collection name="graphs_files" type="list">\n- <element name="geneExternalEdges" ftype="tsv" file="proteoforms_graphs/geneExternalEdges.tsv" compare="sim_size" delta="1000" />\n+<!-- <element name="geneExternalEdges" ftype="tsv" file="proteoforms_graphs/geneExternalEdges.tsv" compare="sim_size" delta="1000" /> -->\n <element name="geneInternalEdges" ftype="tsv" file="proteoforms_graphs/geneInternalEdges.tsv" compare="sim_size" delta="1000"/>\n <element name="geneVertices" ftype="tsv" file="proteoforms_graphs/geneVertices.tsv" compare="sim_size" delta="1000"/>\n <element name="proteinExternalEdges" ftype="tsv" file="proteoforms_graphs/proteinExternalEdges.tsv" compare="sim_size" delta="10000"/>\n@@ -349,9 +420,9 @@\n \n You can easily test PathwayMatcher functionality using the example files we provide with proteoforms and proteins information of Cystic Fibrosis:\n \n-https://raw.githubusercontent.com/PathwayAnalysisPlatform/PathwayMatcher/master/resources/input/Proteoforms/Simple/CysticFibrosis.txt\n+https://media.githubusercontent.com/media/PathwayAnalysisPlatform/PathwayMatcher/master/src/test/resources/Proteoforms/Simple/CysticFibrosis.txt\n \n-https://raw.githubusercontent.com/PathwayAnalysisPlatform/PathwayMatcher/master/resources/input/Proteins/UniProt/CysticFibrosis.txt\n+https://media.githubusercontent.com/media/PathwayAnalysisPlatform/PathwayMatcher/master/src/test/resources/Proteins/UniProt/CysticFibrosis.txt\n \n You can upload them to Galaxy by directly copying and pasting their URL into the Galaxy upload dialog (the button with the arrow pointing up in the top-left area, and then choosing *Pasta/Fetch data*).\n \n@@ -397,4 +468,8 @@\n \n </help>\n \n+ <citations>\n+ <citation type="doi">doi:10.1101/375097</citation>\n+ </citations>\n+\n </tool>\n' |
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| diff -r 9a599f278852 -r 2cd67294abbd test-data/proteoforms_graphs/geneExternalEdges.tsv --- a/test-data/proteoforms_graphs/geneExternalEdges.tsv Thu Jul 26 17:00:38 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,18387 +0,0 @@\n-id1\tid2\ttype\tcontainer_id\trole1\trole2\n-AKT3\tPDK1\tReaction\tR-HSA-198270\tinput\tinput\n-AKT3\tPDPK1\tReaction\tR-HSA-198270\tinput\tinput\n-PKBG\tPDK1\tReaction\tR-HSA-198270\tinput\tinput\n-PKBG\tPDPK1\tReaction\tR-HSA-198270\tinput\tinput\n-AKT3\tAKT1\tReaction\tR-HSA-198270\tinput\tinput\n-AKT3\tPKB\tReaction\tR-HSA-198270\tinput\tinput\n-AKT3\tRAC\tReaction\tR-HSA-198270\tinput\tinput\n-PKBG\tAKT1\tReaction\tR-HSA-198270\tinput\tinput\n-PKBG\tPKB\tReaction\tR-HSA-198270\tinput\tinput\n-PKBG\tRAC\tReaction\tR-HSA-198270\tinput\tinput\n-PDK1\tAKT3\tReaction\tR-HSA-198270\tinput\tinput\n-PDK1\tPKBG\tReaction\tR-HSA-198270\tinput\tinput\n-PDPK1\tAKT3\tReaction\tR-HSA-198270\tinput\tinput\n-PDPK1\tPKBG\tReaction\tR-HSA-198270\tinput\tinput\n-PDK1\tAKT2\tReaction\tR-HSA-198270\tinput\tinput\n-PDPK1\tAKT2\tReaction\tR-HSA-198270\tinput\tinput\n-AKT1\tAKT3\tReaction\tR-HSA-198270\tinput\tinput\n-AKT1\tPKBG\tReaction\tR-HSA-198270\tinput\tinput\n-PKB\tAKT3\tReaction\tR-HSA-198270\tinput\tinput\n-PKB\tPKBG\tReaction\tR-HSA-198270\tinput\tinput\n-RAC\tAKT3\tReaction\tR-HSA-198270\tinput\tinput\n-RAC\tPKBG\tReaction\tR-HSA-198270\tinput\tinput\n-AKT1\tAKT2\tReaction\tR-HSA-198270\tinput\tinput\n-PKB\tAKT2\tReaction\tR-HSA-198270\tinput\tinput\n-RAC\tAKT2\tReaction\tR-HSA-198270\tinput\tinput\n-AKT2\tPDK1\tReaction\tR-HSA-198270\tinput\tinput\n-AKT2\tPDPK1\tReaction\tR-HSA-198270\tinput\tinput\n-AKT2\tAKT1\tReaction\tR-HSA-198270\tinput\tinput\n-AKT2\tPKB\tReaction\tR-HSA-198270\tinput\tinput\n-AKT2\tRAC\tReaction\tR-HSA-198270\tinput\tinput\n-PAK1\tPDK1\tReaction\tR-HSA-5623667\tinput\tinput\n-PAK1\tPDPK1\tReaction\tR-HSA-5623667\tinput\tinput\n-PKN\tPDK1\tReaction\tR-HSA-5623667\tinput\tinput\n-PKN\tPDPK1\tReaction\tR-HSA-5623667\tinput\tinput\n-PKN1\tPDK1\tReaction\tR-HSA-5623667\tinput\tinput\n-PKN1\tPDPK1\tReaction\tR-HSA-5623667\tinput\tinput\n-PRK1\tPDK1\tReaction\tR-HSA-5623667\tinput\tinput\n-PRK1\tPDPK1\tReaction\tR-HSA-5623667\tinput\tinput\n-PRKCL1\tPDK1\tReaction\tR-HSA-5623667\tinput\tinput\n-PRKCL1\tPDPK1\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tPAK1\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tPKN\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tPKN1\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tPRK1\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tPRKCL1\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tPAK1\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tPKN\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tPKN1\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tPRK1\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tPRKCL1\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tPKN2\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tPRK2\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tPRKCL2\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tPKN2\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tPRK2\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tPRKCL2\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tPKN3\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tPKNBETA\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tPKN3\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tPKNBETA\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tMIG5\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tRAC1\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tTC25\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tMIG5\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tRAC1\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tTC25\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tARH9\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tARHC\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tRHOC\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tARH9\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tARHC\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tRHOC\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tARH6\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tARHB\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tRHOB\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tARH6\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tARHB\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tRHOB\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tARH12\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tARHA\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tRHO12\tReaction\tR-HSA-5623667\tinput\tinput\n-PDK1\tRHOA\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tARH12\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tARHA\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tRHO12\tReaction\tR-HSA-5623667\tinput\tinput\n-PDPK1\tRHOA\tReaction\t'..b'tion\tR-HSA-8855508\tinput\tinput\n-RET51\tGAB2\tReaction\tR-HSA-8855508\tinput\tinput\n-RET51\tKIAA0571\tReaction\tR-HSA-8855508\tinput\tinput\n-GDNFRB\tGAB2\tReaction\tR-HSA-8855508\tinput\tinput\n-GDNFRB\tKIAA0571\tReaction\tR-HSA-8855508\tinput\tinput\n-GFRA2\tGAB2\tReaction\tR-HSA-8855508\tinput\tinput\n-GFRA2\tKIAA0571\tReaction\tR-HSA-8855508\tinput\tinput\n-RETL2\tGAB2\tReaction\tR-HSA-8855508\tinput\tinput\n-RETL2\tKIAA0571\tReaction\tR-HSA-8855508\tinput\tinput\n-TRNR2\tGAB2\tRe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| diff -r 9a599f278852 -r 2cd67294abbd test-data/proteoforms_graphs/geneInternalEdges.tsv --- a/test-data/proteoforms_graphs/geneInternalEdges.tsv Thu Jul 26 17:00:38 2018 -0400 +++ b/test-data/proteoforms_graphs/geneInternalEdges.tsv Wed May 08 13:41:47 2019 -0400 |
| b |
| b'@@ -1,411 +1,1 @@\n id1\tid2\ttype\tcontainer_id\trole1\trole2\n-PDK1\tPDPK1\tReaction\tR-HSA-198270\tinput\tinput\n-PDPK1\tPDK1\tReaction\tR-HSA-198270\tinput\tinput\n-PDK1\tAKT1\tReaction\tR-HSA-198270\tinput\tinput\n-PDK1\tPKB\tReaction\tR-HSA-198270\tinput\tinput\n-PDK1\tRAC\tReaction\tR-HSA-198270\tinput\tinput\n-PDPK1\tAKT1\tReaction\tR-HSA-198270\tinput\tinput\n-PDPK1\tPKB\tReaction\tR-HSA-198270\tinput\tinput\n-PDPK1\tRAC\tReaction\tR-HSA-198270\tinput\tinput\n-AKT1\tPDK1\tReaction\tR-HSA-198270\tinput\tinput\n-AKT1\tPDPK1\tReaction\tR-HSA-198270\tinput\tinput\n-PKB\tPDK1\tReaction\tR-HSA-198270\tinput\tinput\n-PKB\tPDPK1\tReaction\tR-HSA-198270\tinput\tinput\n-RAC\tPDK1\tReaction\tR-HSA-198270\tinput\tinput\n-RAC\tPDPK1\tReaction\tR-HSA-198270\tinput\tinput\n-AKT1\tPKB\tReaction\tR-HSA-198270\tinput\tinput\n-AKT1\tRAC\tReaction\tR-HSA-198270\tinput\tinput\n-PKB\tAKT1\tReaction\tR-HSA-198270\tinput\tinput\n-PKB\tRAC\tReaction\tR-HSA-198270\tinput\tinput\n-RAC\tAKT1\tReaction\tR-HSA-198270\tinput\tinput\n-RAC\tPKB\tReaction\tR-HSA-198270\tinput\tinput\n-PDK1\tGAB2\tReaction\tR-HSA-198284\tinput\tregulator\n-PDK1\tKIAA0571\tReaction\tR-HSA-198284\tinput\tregulator\n-PDPK1\tGAB2\tReaction\tR-HSA-198284\tinput\tregulator\n-PDPK1\tKIAA0571\tReaction\tR-HSA-198284\tinput\tregulator\n-AKT1\tGAB2\tReaction\tR-HSA-198284\tinput\tregulator\n-AKT1\tKIAA0571\tReaction\tR-HSA-198284\tinput\tregulator\n-PKB\tGAB2\tReaction\tR-HSA-198284\tinput\tregulator\n-PKB\tKIAA0571\tReaction\tR-HSA-198284\tinput\tregulator\n-RAC\tGAB2\tReaction\tR-HSA-198284\tinput\tregulator\n-RAC\tKIAA0571\tReaction\tR-HSA-198284\tinput\tregulator\n-GAB2\tPDK1\tReaction\tR-HSA-198284\tregulator\tinput\n-GAB2\tPDPK1\tReaction\tR-HSA-198284\tregulator\tinput\n-KIAA0571\tPDK1\tReaction\tR-HSA-198284\tregulator\tinput\n-KIAA0571\tPDPK1\tReaction\tR-HSA-198284\tregulator\tinput\n-GAB2\tAKT1\tReaction\tR-HSA-198284\tregulator\tinput\n-GAB2\tPKB\tReaction\tR-HSA-198284\tregulator\tinput\n-GAB2\tRAC\tReaction\tR-HSA-198284\tregulator\tinput\n-KIAA0571\tAKT1\tReaction\tR-HSA-198284\tregulator\tinput\n-KIAA0571\tPKB\tReaction\tR-HSA-198284\tregulator\tinput\n-KIAA0571\tRAC\tReaction\tR-HSA-198284\tregulator\tinput\n-GAB2\tKIAA0571\tReaction\tR-HSA-198284\tregulator\tregulator\n-KIAA0571\tGAB2\tReaction\tR-HSA-198284\tregulator\tregulator\n-AKT1\tAKT1\tComplex\tR-HSA-2317313\tcomponent\tcomponent\n-PKB\tPKB\tComplex\tR-HSA-2317313\tcomponent\tcomponent\n-RAC\tRAC\tComplex\tR-HSA-2317313\tcomponent\tcomponent\n-PDK1\tPDK1\tComplex\tR-HSA-2317313\tcomponent\tcomponent\n-PDPK1\tPDPK1\tComplex\tR-HSA-2317313\tcomponent\tcomponent\n-PDK1\tPDK1\tSet\tR-HSA-432180\tmember/candidate\tmember/candidate\n-PDPK1\tPDPK1\tSet\tR-HSA-432180\tmember/candidate\tmember/candidate\n-AKT1\tAKT1\tSet\tR-HSA-432180\tmember/candidate\tmember/candidate\n-PKB\tPKB\tSet\tR-HSA-432180\tmember/candidate\tmember/candidate\n-RAC\tRAC\tSet\tR-HSA-432180\tmember/candidate\tmember/candidate\n-ABL\tABL1\tReaction\tR-HSA-8985227\tregulator\tregulator\n-ABL\tJTK7\tReaction\tR-HSA-8985227\tregulator\tregulator\n-ABL1\tABL\tReaction\tR-HSA-8985227\tregulator\tregulator\n-ABL1\tJTK7\tReaction\tR-HSA-8985227\tregulator\tregulator\n-JTK7\tABL\tReaction\tR-HSA-8985227\tregulator\tregulator\n-JTK7\tABL1\tReaction\tR-HSA-8985227\tregulator\tregulator\n-SRC\tSRC1\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-SRC1\tSRC\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-SRC\tABL\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-SRC\tABL1\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-SRC\tJTK7\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-SRC1\tABL\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-SRC1\tABL1\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-SRC1\tJTK7\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-ABL\tSRC\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-ABL\tSRC1\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-ABL1\tSRC\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-ABL1\tSRC1\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-JTK7\tSRC\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-JTK7\tSRC1\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-MAPK11\tPRKM11\tReaction\tR-HSA-448957\tinput\tinput\n-MAPK11\tSAPK2\tReaction\tR-HSA-448957\tinput\tinput\n-MAPK11\tSAPK2B\tReaction\tR-HSA-448957\tinput\tinput\n-PRKM11\tMAPK11\tReaction\tR-HSA-448957\tinput\tinput\n-PRKM11\tSAPK2\tReaction\tR-HSA-448957\tinput\tinput\n-PRKM11\tSAPK2B\tReaction\tR-HSA-448957\tinput\tinput\n-SAPK2\tMAPK11\tReactio'..b'r/candidate\tmember/candidate\n-PRKM11\tPRKM11\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate\n-SAPK2\tSAPK2\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate\n-SAPK2B\tSAPK2B\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate\n-AKT1\tPKB\tReaction\tR-HSA-198599\tcatalyst\tcatalyst\n-AKT1\tRAC\tReaction\tR-HSA-198599\tcatalyst\tcatalyst\n-PKB\tAKT1\tReaction\tR-HSA-198599\tcatalyst\tcatalyst\n-PKB\tRAC\tReaction\tR-HSA-198599\tcatalyst\tcatalyst\n-RAC\tAKT1\tReaction\tR-HSA-198599\tcatalyst\tcatalyst\n-RAC\tPKB\tReaction\tR-HSA-198599\tcatalyst\tcatalyst\n-AKT1\tAKT1\tComplex\tR-HSA-2317310\tcomponent\tcomponent\n-PKB\tPKB\tComplex\tR-HSA-2317310\tcomponent\tcomponent\n-RAC\tRAC\tComplex\tR-HSA-2317310\tcomponent\tcomponent\n-AKT1\tAKT1\tSet\tR-HSA-202074\tmember/candidate\tmember/candidate\n-PKB\tPKB\tSet\tR-HSA-202074\tmember/candidate\tmember/candidate\n-RAC\tRAC\tSet\tR-HSA-202074\tmember/candidate\tmember/candidate\n-APRF\tSTAT3\tReaction\tR-HSA-8875816\tinput\tinput\n-STAT3\tAPRF\tReaction\tR-HSA-8875816\tinput\tinput\n-STAT5\tSTAT5A\tReaction\tR-HSA-380782\tinput\tinput\n-STAT5A\tSTAT5\tReaction\tR-HSA-380782\tinput\tinput\n-STAT5\tAPRF\tReaction\tR-HSA-380782\tinput\tinput\n-STAT5\tSTAT3\tReaction\tR-HSA-380782\tinput\tinput\n-STAT5A\tAPRF\tReaction\tR-HSA-380782\tinput\tinput\n-STAT5A\tSTAT3\tReaction\tR-HSA-380782\tinput\tinput\n-APRF\tSTAT5\tReaction\tR-HSA-380782\tinput\tinput\n-APRF\tSTAT5A\tReaction\tR-HSA-380782\tinput\tinput\n-STAT3\tSTAT5\tReaction\tR-HSA-380782\tinput\tinput\n-STAT3\tSTAT5A\tReaction\tR-HSA-380782\tinput\tinput\n-APRF\tAPRF\tComplex\tR-HSA-1112576\tcomponent\tcomponent\n-STAT3\tSTAT3\tComplex\tR-HSA-1112576\tcomponent\tcomponent\n-STAT5\tSTAT5\tComplex\tR-HSA-1469975\tcomponent\tcomponent\n-STAT5A\tSTAT5A\tComplex\tR-HSA-1469975\tcomponent\tcomponent\n-APRF\tAPRF\tSet\tR-HSA-1112559\tmember/candidate\tmember/candidate\n-STAT3\tSTAT3\tSet\tR-HSA-1112559\tmember/candidate\tmember/candidate\n-STAT5\tSTAT5\tSet\tR-HSA-1433551\tmember/candidate\tmember/candidate\n-STAT5A\tSTAT5A\tSet\tR-HSA-1433551\tmember/candidate\tmember/candidate\n-STAT5\tSTAT5A\tReaction\tR-HSA-1671691\tinput\tinput\n-STAT5A\tSTAT5\tReaction\tR-HSA-1671691\tinput\tinput\n-STAT5\tSTAT5\tComplex\tR-HSA-507927\tcomponent\tcomponent\n-STAT5A\tSTAT5A\tComplex\tR-HSA-507927\tcomponent\tcomponent\n-STAT5\tSTAT5\tSet\tR-HSA-452094\tmember/candidate\tmember/candidate\n-STAT5A\tSTAT5A\tSet\tR-HSA-452094\tmember/candidate\tmember/candidate\n-CRKL\tCRKL\tComplex\tR-HSA-8875574\tcomponent\tcomponent\n-CRKL\tCRKL\tSet\tR-HSA-381945\tmember/candidate\tmember/candidate\n-OK/SW-cl.2\tRPS6\tReaction\tR-HSA-165726\tinput\tinput\n-RPS6\tOK/SW-cl.2\tReaction\tR-HSA-165726\tinput\tinput\n-OK/SW-cl.2\tOK/SW-cl.2\tComplex\tR-HSA-72505\tcomponent\tcomponent\n-RPS6\tRPS6\tComplex\tR-HSA-72505\tcomponent\tcomponent\n-MAPK11\tPRKM11\tReaction\tR-HSA-450257\tinput\tinput\n-MAPK11\tSAPK2\tReaction\tR-HSA-450257\tinput\tinput\n-MAPK11\tSAPK2B\tReaction\tR-HSA-450257\tinput\tinput\n-PRKM11\tMAPK11\tReaction\tR-HSA-450257\tinput\tinput\n-PRKM11\tSAPK2\tReaction\tR-HSA-450257\tinput\tinput\n-PRKM11\tSAPK2B\tReaction\tR-HSA-450257\tinput\tinput\n-SAPK2\tMAPK11\tReaction\tR-HSA-450257\tinput\tinput\n-SAPK2\tPRKM11\tReaction\tR-HSA-450257\tinput\tinput\n-SAPK2\tSAPK2B\tReaction\tR-HSA-450257\tinput\tinput\n-SAPK2B\tMAPK11\tReaction\tR-HSA-450257\tinput\tinput\n-SAPK2B\tPRKM11\tReaction\tR-HSA-450257\tinput\tinput\n-SAPK2B\tSAPK2\tReaction\tR-HSA-450257\tinput\tinput\n-MAPK11\tMAPK11\tComplex\tR-HSA-450254\tcomponent\tcomponent\n-PRKM11\tPRKM11\tComplex\tR-HSA-450254\tcomponent\tcomponent\n-SAPK2\tSAPK2\tComplex\tR-HSA-450254\tcomponent\tcomponent\n-SAPK2B\tSAPK2B\tComplex\tR-HSA-450254\tcomponent\tcomponent\n-MAPK11\tMAPK11\tSet\tR-HSA-198703\tmember/candidate\tmember/candidate\n-PRKM11\tPRKM11\tSet\tR-HSA-198703\tmember/candidate\tmember/candidate\n-SAPK2\tSAPK2\tSet\tR-HSA-198703\tmember/candidate\tmember/candidate\n-SAPK2B\tSAPK2B\tSet\tR-HSA-198703\tmember/candidate\tmember/candidate\n-GAB2\tKIAA0571\tReaction\tR-HSA-2730870\tcatalyst\tcatalyst\n-KIAA0571\tGAB2\tReaction\tR-HSA-2730870\tcatalyst\tcatalyst\n-GAB2\tGAB2\tComplex\tR-HSA-2685700\tcomponent\tcomponent\n-KIAA0571\tKIAA0571\tComplex\tR-HSA-2685700\tcomponent\tcomponent\n-GAB2\tGAB2\tSet\tR-HSA-912533\tmember/candidate\tmember/candidate\n-KIAA0571\tKIAA0571\tSet\tR-HSA-912533\tmember/candidate\tmember/candidate\n' |
| b |
| diff -r 9a599f278852 -r 2cd67294abbd test-data/proteoforms_graphs/geneVertices.tsv --- a/test-data/proteoforms_graphs/geneVertices.tsv Thu Jul 26 17:00:38 2018 -0400 +++ b/test-data/proteoforms_graphs/geneVertices.tsv Wed May 08 13:41:47 2019 -0400 |
| [ |
| @@ -1,36 +1,17 @@ id name -ABL Tyrosine-protein kinase ABL1 ecNumber evidence="65 70"2.7.10.2/ecNumber -ABL1 Tyrosine-protein kinase ABL1 ecNumber evidence="65 70"2.7.10.2/ecNumber -AKT1 RAC-alpha serine/threonine-protein kinase ecNumber2.7.11.1/ecNumber -APRF fullName evidence="52"Signal transducer and activator of transcription 3 -BCR Breakpoint cluster region protein ecNumber2.7.11.1/ecNumber -BCR1 Breakpoint cluster region protein ecNumber2.7.11.1/ecNumber CBL E3 ubiquitin-protein ligase CBL ecNumber evidence="23 33 39"2.3.2.27/ecNumber CBL2 E3 ubiquitin-protein ligase CBL ecNumber evidence="23 33 39"2.3.2.27/ecNumber CREB1 Cyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ] -CRKL Crk-like protein ] -D22S11 Breakpoint cluster region protein ecNumber2.7.11.1/ecNumber ERK1 Mitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber -GAB2 GRB2-associated-binding protein 2 -JTK7 Tyrosine-protein kinase ABL1 ecNumber evidence="65 70"2.7.10.2/ecNumber -KIAA0571 GRB2-associated-binding protein 2 MAPK11 Mitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber MAPK3 Mitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber -OK/SW-cl.2 40S ribosomal protein S6 -PDK1 3-phosphoinositide-dependent protein kinase 1 shortName:hPDK1 ecNumber2.7.11.1/ecNumber ] -PDK1 [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial ecNumber2.7.11.2/ecNumber -PDPK1 3-phosphoinositide-dependent protein kinase 1 shortName:hPDK1 ecNumber2.7.11.1/ecNumber ] -PKB RAC-alpha serine/threonine-protein kinase ecNumber2.7.11.1/ecNumber PRKM11 Mitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber PRKM3 Mitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber -RAC RAC-alpha serine/threonine-protein kinase ecNumber2.7.11.1/ecNumber RNF55 E3 ubiquitin-protein ligase CBL ecNumber evidence="23 33 39"2.3.2.27/ecNumber -RPS6 40S ribosomal protein S6 SAPK2 Mitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber SAPK2B Mitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber SRC Proto-oncogene tyrosine-protein kinase Src ecNumber evidence="28 42 49 63 65 66"2.7.10.2/ecNumber SRC1 Proto-oncogene tyrosine-protein kinase Src ecNumber evidence="28 42 49 63 65 66"2.7.10.2/ecNumber SRC1 Nuclear receptor coactivator 1 shortName:NCoA-1 ecNumber2.3.1.48/ecNumber -STAT3 fullName evidence="52"Signal transducer and activator of transcription 3 STAT5 Signal transducer and activator of transcription 5A ] STAT5A Signal transducer and activator of transcription 5A ] |
| b |
| diff -r 9a599f278852 -r 2cd67294abbd test-data/proteoforms_graphs/proteinExternalEdges.tsv --- a/test-data/proteoforms_graphs/proteinExternalEdges.tsv Thu Jul 26 17:00:38 2018 -0400 +++ b/test-data/proteoforms_graphs/proteinExternalEdges.tsv Wed May 08 13:41:47 2019 -0400 |
| b |
| b'@@ -1,2164 +1,110 @@\n 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|
| b |
| diff -r 9a599f278852 -r 2cd67294abbd test-data/proteoforms_graphs/proteinInternalEdges.tsv --- a/test-data/proteoforms_graphs/proteinInternalEdges.tsv Thu Jul 26 17:00:38 2018 -0400 +++ b/test-data/proteoforms_graphs/proteinInternalEdges.tsv Wed May 08 13:41:47 2019 -0400 |
| b |
| b'@@ -1,79 +1,4 @@\n id1\tid2\ttype\tcontainer_id\trole1\trole2\n-O15530\tP31749\tReaction\tR-HSA-198270\tinput\tinput\n-O15530\tP31749\tReaction\tR-HSA-198270\tinput\toutput\n-O15530\tP31749\tReaction\tR-HSA-198270\tinput\tcatalyst\n-O15530\tP31749\tReaction\tR-HSA-198270\toutput\tinput\n-O15530\tP31749\tReaction\tR-HSA-198270\toutput\toutput\n-O15530\tP31749\tReaction\tR-HSA-198270\toutput\tcatalyst\n-O15530\tP31749\tReaction\tR-HSA-198270\tcatalyst\tinput\n-O15530\tP31749\tReaction\tR-HSA-198270\tcatalyst\toutput\n-O15530\tP31749\tReaction\tR-HSA-198270\tcatalyst\tcatalyst\n-O15530\tP31749\tReaction\tR-HSA-2317314\tinput\tinput\n-O15530\tP31749\tReaction\tR-HSA-2317314\tinput\toutput\n-O15530\tP31749\tReaction\tR-HSA-2317314\toutput\tinput\n-O15530\tP31749\tReaction\tR-HSA-2317314\toutput\toutput\n-O15530\tP31749\tReaction\tR-HSA-2243942\tinput\tinput\n-O15530\tP31749\tReaction\tR-HSA-2243942\tinput\toutput\n-O15530\tP31749\tReaction\tR-HSA-2243942\tinput\tcatalyst\n-O15530\tP31749\tReaction\tR-HSA-2243942\toutput\tinput\n-O15530\tP31749\tReaction\tR-HSA-2243942\toutput\toutput\n-O15530\tP31749\tReaction\tR-HSA-2243942\toutput\tcatalyst\n-O15530\tP31749\tReaction\tR-HSA-2243942\tcatalyst\tinput\n-O15530\tP31749\tReaction\tR-HSA-2243942\tcatalyst\toutput\n-O15530\tP31749\tReaction\tR-HSA-2243942\tcatalyst\tcatalyst\n-O15530\tP31749\tReaction\tR-HSA-2243937\tinput\tinput\n-O15530\tP31749\tReaction\tR-HSA-2243937\tinput\toutput\n-O15530\tP31749\tReaction\tR-HSA-2243937\toutput\tinput\n-O15530\tP31749\tReaction\tR-HSA-2243937\toutput\toutput\n-O15530\tP31749\tReaction\tR-HSA-198284\tinput\tinput\n-O15530\tP31749\tReaction\tR-HSA-198284\tinput\toutput\n-O15530\tQ9UQC2\tReaction\tR-HSA-198284\tinput\tregulator\n-O15530\tP31749\tReaction\tR-HSA-198284\toutput\tinput\n-O15530\tP31749\tReaction\tR-HSA-198284\toutput\toutput\n-O15530\tQ9UQC2\tReaction\tR-HSA-198284\toutput\tregulator\n-P31749\tQ9UQC2\tReaction\tR-HSA-198284\tinput\tregulator\n-P31749\tQ9UQC2\tReaction\tR-HSA-198284\toutput\tregulator\n-O15530\tP31749\tReaction\tR-HSA-432110\tcatalyst\tcatalyst\n-O15530\tP31749\tComplex\tR-HSA-2317313\tcomponent\tcomponent\n-O15530\tP31749\tComplex\tR-HSA-2243941\tcomponent\tcomponent\n-O15530\tP31749\tComplex\tR-HSA-198360\tcomponent\tcomponent\n-O15530\tP31749\tSet\tR-HSA-432180\tmember/candidate\tmember/candidate\n-P00519\tP12931\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-P00519\tQ15759\tReaction\tR-HSA-448957\tinput\tinput\n-P00519\tQ15759\tReaction\tR-HSA-448957\tinput\toutput\n-P00519\tQ15759\tReaction\tR-HSA-448957\toutput\tinput\n-P00519\tQ15759\tReaction\tR-HSA-448957\toutput\toutput\n-P00519\tQ15759\tComplex\tR-HSA-448881\tcomponent\tcomponent\n-P00519\tQ15759\tComplex\tR-HSA-448887\tcomponent\tcomponent\n-P00519\tP12931\tSet\tR-HSA-8942611\tmember/candidate\tmember/candidate\n-P11274\tP42229\tReaction\tR-HSA-1839112\tcatalyst\tinput\n-P11274\tP42229\tReaction\tR-HSA-1839112\tcatalyst\toutput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839102\tinput\tinput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839102\tinput\toutput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839102\toutput\tinput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839102\toutput\toutput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839107\tcatalyst\tcatalyst\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839114\tinput\tinput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839114\tinput\toutput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839114\toutput\tinput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839114\toutput\toutput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839110\tinput\tinput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839110\tinput\toutput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839110\tinput\tcatalyst\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839110\toutput\tinput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839110\toutput\toutput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839110\toutput\tcatalyst\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839110\tcatalyst\tinput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839110\tcatalyst\toutput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839110\tcatalyst\tcatalyst\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839095\tinput\tinput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839095\tinput\toutput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839095\toutput\tinput\n-P11274\tQ9UQC2\tReaction\tR-HSA-1839095\toutput\toutput\n-P11274\tQ9UQC2\tComplex\tR-HSA-1839048\tcomponent\tcomponent\n-P11274\tQ9UQC2\tComplex\tR-HSA-1839047\tcomponent\tcomponent\n-P11274\tQ9UQC2\tComplex\tR-HSA-1839051\tcomponent\tcomponent\n-P11274\tQ9UQC2\tComplex\tR-HSA-1839045'..b'9112\toutput\toutput\n P40763\tP42229\tReaction\tR-HSA-380782\tinput\tinput\n P40763\tP42229\tReaction\tR-HSA-380782\tinput\toutput\n P40763\tP42229\tReaction\tR-HSA-380782\toutput\tinput\n P40763\tP42229\tReaction\tR-HSA-380782\toutput\toutput\n+P40763\tP42229\tReaction\tR-HSA-8985988\tinput\tinput\n+P40763\tP42229\tReaction\tR-HSA-8985988\tinput\toutput\n+P40763\tP42229\tReaction\tR-HSA-8985988\toutput\tinput\n+P40763\tP42229\tReaction\tR-HSA-8985988\toutput\toutput\n+P40763\tP42229\tReaction\tR-HSA-8985929\tinput\tinput\n+P40763\tP42229\tReaction\tR-HSA-8985929\tinput\toutput\n+P40763\tP42229\tReaction\tR-HSA-8985929\toutput\tinput\n+P40763\tP42229\tReaction\tR-HSA-8985929\toutput\toutput\n+P12931\tP42229\tReaction\tR-HSA-1470012\tinput\tinput\n+P12931\tP42229\tReaction\tR-HSA-1470012\tinput\toutput\n+P12931\tP42229\tReaction\tR-HSA-1470012\toutput\tinput\n+P12931\tP42229\tReaction\tR-HSA-1470012\toutput\toutput\n+P40763\tP42229\tReaction\tR-HSA-1470012\tinput\tinput\n+P40763\tP42229\tReaction\tR-HSA-1470012\tinput\toutput\n+P40763\tP42229\tReaction\tR-HSA-1470012\toutput\tinput\n+P40763\tP42229\tReaction\tR-HSA-1470012\toutput\toutput\n+P12931\tP42229\tReaction\tR-HSA-1470010\tinput\tinput\n+P12931\tP42229\tReaction\tR-HSA-1470010\tinput\toutput\n+P12931\tP42229\tReaction\tR-HSA-1470010\toutput\tinput\n+P12931\tP42229\tReaction\tR-HSA-1470010\toutput\toutput\n+P40763\tP42229\tReaction\tR-HSA-1470010\tinput\tinput\n+P40763\tP42229\tReaction\tR-HSA-1470010\tinput\toutput\n+P40763\tP42229\tReaction\tR-HSA-1470010\toutput\tinput\n+P40763\tP42229\tReaction\tR-HSA-1470010\toutput\toutput\n+P12931\tP42229\tComplex\tR-HSA-1433527\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-1433527\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-1469999\tcomponent\tcomponent\n+P12931\tP42229\tComplex\tR-HSA-1469999\tcomponent\tcomponent\n P40763\tP42229\tComplex\tR-HSA-1469975\tcomponent\tcomponent\n P40763\tP42229\tComplex\tR-HSA-1566924\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-1470000\tcomponent\tcomponent\n+P12931\tP42229\tComplex\tR-HSA-1470000\tcomponent\tcomponent\n P40763\tP42229\tComplex\tR-HSA-380766\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-8983180\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-8983137\tcomponent\tcomponent\n P40763\tP42229\tComplex\tR-HSA-8983118\tcomponent\tcomponent\n P40763\tP42229\tComplex\tR-HSA-9007112\tcomponent\tcomponent\n-P40763\tP42229\tComplex\tR-HSA-8983137\tcomponent\tcomponent\n-P40763\tP42229\tComplex\tR-HSA-8983180\tcomponent\tcomponent\n P40763\tP42229\tComplex\tR-HSA-8983197\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-8985982\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-8985893\tcomponent\tcomponent\n P40763\tP42229\tComplex\tR-HSA-9006875\tcomponent\tcomponent\n P40763\tP42229\tComplex\tR-HSA-9006869\tcomponent\tcomponent\n P40763\tP42229\tComplex\tR-HSA-8987135\tcomponent\tcomponent\n+P40763\tP42229\tComplex\tR-HSA-8987029\tcomponent\tcomponent\n P40763\tP42229\tSet\tR-HSA-1433551\tmember/candidate\tmember/candidate\n P40763\tP42229\tSet\tR-HSA-1433413\tmember/candidate\tmember/candidate\n P40763\tP42229\tSet\tR-HSA-1469979\tmember/candidate\tmember/candidate\n P40763\tP42229\tSet\tR-HSA-380756\tmember/candidate\tmember/candidate\n+P40763\tP42229\tSet\tR-HSA-9007110\tmember/candidate\tmember/candidate\n P40763\tP42229\tSet\tR-HSA-9007142\tmember/candidate\tmember/candidate\n-P40763\tP42229\tSet\tR-HSA-9007110\tmember/candidate\tmember/candidate\n+P40763\tP42229\tSet\tR-HSA-9010175\tmember/candidate\tmember/candidate\n+P40763\tP42229\tSet\tR-HSA-9005640\tmember/candidate\tmember/candidate\n P40763\tP42229\tSet\tR-HSA-9006868\tmember/candidate\tmember/candidate\n P40763\tP42229\tSet\tR-HSA-9006876\tmember/candidate\tmember/candidate\n P40763\tP42229\tSet\tR-HSA-9009216\tmember/candidate\tmember/candidate\n+P40763\tP42229\tSet\tR-HSA-9009214\tmember/candidate\tmember/candidate\n+P27361\tQ15759\tReaction\tR-HSA-168053\tcatalyst\tcatalyst\n+P00519\tQ15759\tReaction\tR-HSA-448957\tinput\tinput\n+P00519\tQ15759\tReaction\tR-HSA-448957\tinput\toutput\n+P00519\tQ15759\tReaction\tR-HSA-448957\toutput\tinput\n+P00519\tQ15759\tReaction\tR-HSA-448957\toutput\toutput\n+P00519\tQ15759\tComplex\tR-HSA-448881\tcomponent\tcomponent\n+P00519\tQ15759\tComplex\tR-HSA-448887\tcomponent\tcomponent\n+P27361\tQ15759\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate\n' |
| b |
| diff -r 9a599f278852 -r 2cd67294abbd test-data/proteoforms_graphs/proteinVertices.tsv --- a/test-data/proteoforms_graphs/proteinVertices.tsv Thu Jul 26 17:00:38 2018 -0400 +++ b/test-data/proteoforms_graphs/proteinVertices.tsv Wed May 08 13:41:47 2019 -0400 |
| b |
| @@ -1,15 +1,7 @@ id name -O15530 3-phosphoinositide-dependent protein kinase 1 shortName:hPDK1 ecNumber2.7.11.1/ecNumber ] -P00519 Tyrosine-protein kinase ABL1 ecNumber evidence="65 70"2.7.10.2/ecNumber -P11274 Breakpoint cluster region protein ecNumber2.7.11.1/ecNumber P12931 Proto-oncogene tyrosine-protein kinase Src ecNumber evidence="28 42 49 63 65 66"2.7.10.2/ecNumber P16220 Cyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ] P22681 E3 ubiquitin-protein ligase CBL ecNumber evidence="23 33 39"2.3.2.27/ecNumber P27361 Mitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber -P31749 RAC-alpha serine/threonine-protein kinase ecNumber2.7.11.1/ecNumber -P40763 fullName evidence="52"Signal transducer and activator of transcription 3 P42229 Signal transducer and activator of transcription 5A ] -P46109 Crk-like protein ] -P62753 40S ribosomal protein S6 Q15759 Mitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber -Q9UQC2 GRB2-associated-binding protein 2 |
| b |
| diff -r 9a599f278852 -r 2cd67294abbd test-data/proteoforms_graphs/proteoformExternalEdges.tsv --- a/test-data/proteoforms_graphs/proteoformExternalEdges.tsv Thu Jul 26 17:00:38 2018 -0400 +++ b/test-data/proteoforms_graphs/proteoformExternalEdges.tsv Wed May 08 13:41:47 2019 -0400 |
| b |
| b'@@ -1,1316 +1,4 @@\n id1\tid2\ttype\tcontainer_id\trole1\trole2\n-P01880;\tP22681;\tReaction\tR-HSA-983703\tinput\tinput\n-P01880;\tP22681;\tReaction\tR-HSA-983703\tinput\toutput\n-P01880;\tP22681;\tReaction\tR-HSA-983703\toutput\tinput\n-P01880;\tP22681;\tReaction\tR-HSA-983703\toutput\toutput\n-P01880;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\tinput\n-P01880;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\toutput\n-P04433;\tP22681;\tReaction\tR-HSA-983703\tinput\tinput\n-P04433;\tP22681;\tReaction\tR-HSA-983703\tinput\toutput\n-P04433;\tP22681;\tReaction\tR-HSA-983703\toutput\tinput\n-P04433;\tP22681;\tReaction\tR-HSA-983703\toutput\toutput\n-P04433;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\tinput\n-P04433;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\toutput\n-A0A075B6S6;\tP22681;\tReaction\tR-HSA-983703\tinput\tinput\n-A0A075B6S6;\tP22681;\tReaction\tR-HSA-983703\tinput\toutput\n-A0A075B6S6;\tP22681;\tReaction\tR-HSA-983703\toutput\tinput\n-A0A075B6S6;\tP22681;\tReaction\tR-HSA-983703\toutput\toutput\n-A0A075B6S6;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\tinput\n-A0A075B6S6;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\toutput\n-A2KUC3;\tP22681;\tReaction\tR-HSA-983703\tinput\tinput\n-A2KUC3;\tP22681;\tReaction\tR-HSA-983703\tinput\toutput\n-A2KUC3;\tP22681;\tReaction\tR-HSA-983703\toutput\tinput\n-A2KUC3;\tP22681;\tReaction\tR-HSA-983703\toutput\toutput\n-A2KUC3;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\tinput\n-A2KUC3;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\toutput\n-P0CG06;\tP22681;\tReaction\tR-HSA-983703\tinput\tinput\n-P0CG06;\tP22681;\tReaction\tR-HSA-983703\tinput\toutput\n-P0CG06;\tP22681;\tReaction\tR-HSA-983703\toutput\tinput\n-P0CG06;\tP22681;\tReaction\tR-HSA-983703\toutput\toutput\n-P0CG06;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\tinput\n-P0CG06;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\toutput\n-P0CG05;\tP22681;\tReaction\tR-HSA-983703\tinput\tinput\n-P0CG05;\tP22681;\tReaction\tR-HSA-983703\tinput\toutput\n-P0CG05;\tP22681;\tReaction\tR-HSA-983703\toutput\tinput\n-P0CG05;\tP22681;\tReaction\tR-HSA-983703\toutput\toutput\n-P0CG05;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\tinput\n-P0CG05;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\toutput\n-P0CG04;\tP22681;\tReaction\tR-HSA-983703\tinput\tinput\n-P0CG04;\tP22681;\tReaction\tR-HSA-983703\tinput\toutput\n-P0CG04;\tP22681;\tReaction\tR-HSA-983703\toutput\tinput\n-P0CG04;\tP22681;\tReaction\tR-HSA-983703\toutput\toutput\n-P0CG04;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\tinput\n-P0CG04;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\toutput\n-P01718;\tP22681;\tReaction\tR-HSA-983703\tinput\tinput\n-P01718;\tP22681;\tReaction\tR-HSA-983703\tinput\toutput\n-P01718;\tP22681;\tReaction\tR-HSA-983703\toutput\tinput\n-P01718;\tP22681;\tReaction\tR-HSA-983703\toutput\toutput\n-P01718;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\tinput\n-P01718;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\toutput\n-P01717;\tP22681;\tReaction\tR-HSA-983703\tinput\tinput\n-P01717;\tP22681;\tReaction\tR-HSA-983703\tinput\toutput\n-P01717;\tP22681;\tReaction\tR-HSA-983703\toutput\tinput\n-P01717;\tP22681;\tReaction\tR-HSA-983703\toutput\toutput\n-P01717;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\tinput\n-P01717;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\toutput\n-P01715;\tP22681;\tReaction\tR-HSA-983703\tinput\tinput\n-P01715;\tP22681;\tReaction\tR-HSA-983703\tinput\toutput\n-P01715;\tP22681;\tReaction\tR-HSA-983703\toutput\tinput\n-P01715;\tP22681;\tReaction\tR-HSA-983703\toutput\toutput\n-P01715;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\tinput\n-P01715;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\toutput\n-P01714;\tP22681;\tReaction\tR-HSA-983703\tinput\tinput\n-P01714;\tP22681;\tReaction\tR-HSA-983703\tinput\toutput\n-P01714;\tP22681;\tReaction\tR-HSA-983703\toutput\tinput\n-P01714;\tP22681;\tReaction\tR-HSA-983703\toutput\toutput\n-P01714;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\tinput\n-P01714;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\toutput\n-P01834;\tP22681;\tReaction\tR-HSA-983703\tinput\tinput\n-P01834;\tP22681;\tReaction\tR-HSA-983703\tinput\toutput\n-P01834;\tP22681;\tReaction\tR-HSA-983703\toutput\tinput\n-P01834;\tP22681;\tReaction\tR-HSA-983703\toutput\toutput\n-P01834;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\tinput\n-P01834;\tP22681;\tReaction\tR-HSA-983703\tcatalyst\toutput\n-A2NXD2;\tP22681;\tReaction\tR-HSA-983703\tinput\tinput\n-A2NXD2;\tP22681;\tReaction\tR-HSA-983703\tinput\toutput\n-A2NXD2;\tP'..b'onent\n-P40763;\tP50991;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ92526;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tP49368;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tP48643;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ99832;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tP78371;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tP50990;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ9Y6D5;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ9UKT8;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tP51784;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ9H0D6;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ9NRD1;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ9UKT5;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ9BVG8-2;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tP57775;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ969H0;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ5XX13;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ969U6;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ9H1H9;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ9UKA1;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ15477;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ9UKT7;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ9Y2T2;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ86WA8;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ5XUX1;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tQ9BUR4;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tP61962;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-O15379;\tP40763;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-O96020;\tP40763;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P24864;\tP40763;\tComplex\tR-HSA-390481\tcomponent\tcomponent\n-P40763;\tP42224;\tSet\tR-HSA-1112559\tmember/candidate\tmember/candidate\n-P40763;\tP42226;\tSet\tR-HSA-6786055\tmember/candidate\tmember/candidate\n-P40763;\tP42226;\tSet\tR-HSA-6788573\tmember/candidate\tmember/candidate\n-P40763;\tP42224;\tSet\tR-HSA-6788573\tmember/candidate\tmember/candidate\n-P40763;\tP42224;\tSet\tR-HSA-1888196\tmember/candidate\tmember/candidate\n-O14556;\tP40763;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-O95302;\tP40763;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-O00567;\tP40763;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P04062;\tP40763;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P04637;\tP40763;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ9Y6D5;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ9UKT8;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tP51784;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ9H0D6;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ9NRD1;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ9UKT5;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ9BVG8-2;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tP57775;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ969H0;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ5XX13;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ969U6;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ9H1H9;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ9UKA1;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ15477;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ9UKT7;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ9Y2T2;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ86WA8;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ5XUX1;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tQ9BUR4;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P40763;\tP61962;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-O15379;\tP40763;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-O96020;\tP40763;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n-P24864;\tP40763;\tSet\tR-HSA-391287\tmember/candidate\tmember/candidate\n' |
| b |
| diff -r 9a599f278852 -r 2cd67294abbd test-data/proteoforms_graphs/proteoformInternalEdges.tsv --- a/test-data/proteoforms_graphs/proteoformInternalEdges.tsv Thu Jul 26 17:00:38 2018 -0400 +++ b/test-data/proteoforms_graphs/proteoformInternalEdges.tsv Wed May 08 13:41:47 2019 -0400 |
| b |
| @@ -1,79 +1,3 @@ id1 id2 type container_id role1 role2 -Q15759; Q15759;00047:180,00048:182 Reaction R-HSA-1247960 input output -P00519; Q15759; Reaction R-HSA-448957 input input -P00519; Q15759; Reaction R-HSA-448957 input output -P00519; Q15759; Reaction R-HSA-448957 output input -P00519; Q15759; Reaction R-HSA-448957 output output -Q15759; Q15759;00047:180,00048:182 Reaction R-HSA-450333 input output -Q15759; Q15759;00047:180,00048:182 Reaction R-HSA-3238999 input output -P00519; Q15759; Complex R-HSA-448887 component component -P27361;00047:202,00048:204 Q15759;00047:180,00048:182 Reaction R-HSA-168053 catalyst catalyst -P00519; Q15759;00047:180,00048:182 Complex R-HSA-448881 component component P27361;00047:202,00048:204 Q15759;00047:180,00048:182 Set R-HSA-450307 member/candidate member/candidate -O15530; P31749; Reaction R-HSA-198284 input input -O15530; P31749; Reaction R-HSA-198284 input output -O15530; P31749; Reaction R-HSA-198284 output input -O15530; P31749; Reaction R-HSA-198284 output output -O15530; P31749; Complex R-HSA-198360 component component -P27361; P27361;00047:202,00048:204 Reaction R-HSA-199959 output input -P27361; P27361;00047:202,00048:204 Reaction R-HSA-5675373 output input -P27361; P27361;00047:202,00048:204 Reaction R-HSA-203797 output input -P27361; P27361;00047:202,00048:204 Reaction R-HSA-109860 input output -P27361; P27361;00047:202,00048:204 Reaction R-HSA-109860 catalyst output -P27361; P27361;00047:202,00048:204 Reaction R-HSA-5672973 input output -P27361; P27361;00047:202,00048:204 Reaction R-HSA-5672973 catalyst output -P27361; P27361;00047:202,00048:204 Reaction R-HSA-5675376 output input -P27361; P27361;00047:202,00048:204 Reaction R-HSA-5674373 input output -P27361; P27361;00047:202,00048:204 Reaction R-HSA-5674373 catalyst output -P27361; P27361;00047:202,00048:204 Reaction R-HSA-6802922 input output -P27361; P27361;00047:202,00048:204 Reaction R-HSA-6802922 catalyst output -P27361; P27361;00047:202,00048:204 Reaction R-HSA-6802910 input output -P27361; P27361;00047:202,00048:204 Reaction R-HSA-6802910 catalyst output -P27361; P27361;00047:202,00048:204 Reaction R-HSA-6802921 input output -P27361; P27361;00047:202,00048:204 Reaction R-HSA-6802921 catalyst output -P27361; P27361;00047:202,00048:204 Reaction R-HSA-6802918 input output -P27361; P27361;00047:202,00048:204 Reaction R-HSA-6802918 catalyst output -P27361; P27361;00047:202,00048:204 Reaction R-HSA-6802935 input output -P27361; P27361;00047:202,00048:204 Reaction R-HSA-6802935 catalyst output -P16220; P16220;00046:133 Reaction R-HSA-199298 input output -P16220; P16220;00046:133 Reaction R-HSA-199935 input output -P16220; P16220;00046:133 Reaction R-HSA-199917 input output -P16220; P16220;00046:133 Reaction R-HSA-199895 input output -P16220; P16220;00046:133 Reaction R-HSA-111912 input output -P16220; P16220;00046:133 Reaction R-HSA-111919 input output -P16220; P16220;00046:133 Reaction R-HSA-443474 input output -P16220; P16220;00046:133 Reaction R-HSA-442724 input output -P16220; P16220;00046:133 Reaction R-HSA-443475 input output -P16220; P16220;00046:133 Reaction R-HSA-443480 input output -P16220; P16220;00046:133 Reaction R-HSA-2399996 input output -P40763; P42229; Reaction R-HSA-1433456 input input -P40763; P42229; Reaction R-HSA-1433456 input output -P40763; P42229; Reaction R-HSA-1433456 output input -P40763; P42229; Reaction R-HSA-1433456 output output -P40763; P42229; Reaction R-HSA-380782 input input -P40763; P42229; Reaction R-HSA-380782 input output -P40763; P42229; Reaction R-HSA-380782 output input -P40763; P42229; Reaction R-HSA-380782 output output -P42229; P42229;00048:694 Reaction R-HSA-1671691 input output -P42229; P42229;00048:694 Reaction R-HSA-1671691 catalyst output -P42229; P42229;00048:694 Reaction R-HSA-452097 input output -P42229; P42229;00048:694 Reaction R-HSA-452097 catalyst output -P42229; P42229;00048:694 Reaction R-HSA-879909 input output -P42229; P42229;00048:694 Reaction R-HSA-879909 catalyst output -P42229; P42229;00048:694 Reaction R-HSA-1839112 input output -P42229; P42229;00048:694 Reaction R-HSA-1168394 input output -P42229; P42229;00048:694 Reaction R-HSA-1168394 catalyst output -P42229; P42229;00048:694 Reaction R-HSA-2671829 input output -P42229; P42229;00048:694 Reaction R-HSA-2671829 catalyst output -P40763; P42229; Complex R-HSA-1433527 component component -P40763; P42229; Complex R-HSA-380766 component component -P40763; P42229; Complex R-HSA-8983118 component component -P40763; P42229; Complex R-HSA-9007112 component component -P40763; P42229; Complex R-HSA-9006875 component component -P40763; P42229; Complex R-HSA-8987135 component component -P40763; P42229; Set R-HSA-1433551 member/candidate member/candidate -P40763; P42229; Set R-HSA-380756 member/candidate member/candidate -P40763; P42229; Set R-HSA-9007142 member/candidate member/candidate -P40763; P42229; Set R-HSA-9006868 member/candidate member/candidate -P40763; P42229; Set R-HSA-9009216 member/candidate member/candidate -P40763; P40763;00046:727 Reaction R-HSA-198732 input output +P27361;00047:202,00048:204 Q15759;00047:180,00048:182 Set R-HSA-450307 member/candidate member/candidate |
| b |
| diff -r 9a599f278852 -r 2cd67294abbd test-data/proteoforms_graphs/proteoformVertices.tsv --- a/test-data/proteoforms_graphs/proteoformVertices.tsv Thu Jul 26 17:00:38 2018 -0400 +++ b/test-data/proteoforms_graphs/proteoformVertices.tsv Wed May 08 13:41:47 2019 -0400 |
| b |
| @@ -1,21 +1,7 @@ id name P22681; E3 ubiquitin-protein ligase CBL ecNumber evidence="23 33 39"2.3.2.27/ecNumber -Q15759; Mitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber +P16220;00046:133 Cyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ] Q15759;00047:180,00048:182 Mitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber -O15530; 3-phosphoinositide-dependent protein kinase 1 shortName:hPDK1 ecNumber2.7.11.1/ecNumber ] -P31749; RAC-alpha serine/threonine-protein kinase ecNumber2.7.11.1/ecNumber -P31749;00047:308 RAC-alpha serine/threonine-protein kinase ecNumber2.7.11.1/ecNumber -P27361; Mitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber P27361;00047:202,00048:204 Mitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber P12931;00048:419 Proto-oncogene tyrosine-protein kinase Src ecNumber evidence="28 42 49 63 65 66"2.7.10.2/ecNumber -Q9UQC2; GRB2-associated-binding protein 2 -P46109; Crk-like protein ] -P11274; Breakpoint cluster region protein ecNumber2.7.11.1/ecNumber -P00519; Tyrosine-protein kinase ABL1 ecNumber evidence="65 70"2.7.10.2/ecNumber -P16220; Cyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ] -P16220;00046:133 Cyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ] -P42229; Signal transducer and activator of transcription 5A ] P42229;00048:694 Signal transducer and activator of transcription 5A ] -P62753; 40S ribosomal protein S6 -P40763; fullName evidence="52"Signal transducer and activator of transcription 3 -P40763;00046:727 fullName evidence="52"Signal transducer and activator of transcription 3 |