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

Changeset 4:3e510701a712 (2019-07-14)
Previous changeset 3:2cd67294abbd (2019-05-08) Next changeset 5:a2ab72e994dc (2019-08-04)
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
modified:
pathwaymatcher.xml
removed:
test-data/genes_search.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
b
diff -r 2cd67294abbd -r 3e510701a712 pathwaymatcher.xml
--- a/pathwaymatcher.xml Wed May 08 13:41:47 2019 -0400
+++ b/pathwaymatcher.xml Sun Jul 14 05:09:33 2019 -0400
[
b'@@ -4,7 +4,7 @@\n     </description>\n     <macros>\n        <token name="@PATHWAYMATCHER_VERSION@">1.9.1</token>\n-       <token name="@TOOL_SUBVERSION@">1</token>\n+       <token name="@TOOL_SUBVERSION@">2</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@@ -18,6 +18,7 @@\n         <exit_code range="1:" level="fatal" description="Job Failed" />\n         <regex match="java.*Exception" level="fatal" description="Java Exception"/>\n         <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>\n+        <regex match="filename not matched:  reports/proteins_proteoforms.txt" level="fatal" description="PeptideShaker archive does not contain the proteoforms file. It may have been created by a 1.x PeptideShaker version."/>\n     </stdio>\n     <command>\n <![CDATA[\n@@ -33,12 +34,11 @@\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+        ## If we use peptideshaker 2.x 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 $s.match_type.input_peptideshakerzip_proteoforms;\n-                unzip -j \'${$s.match_type.input_peptideshakerzip_proteoforms}\' \'output_reports/proteoforms.txt\' -d \'./\';\n-                mv proteoforms.txt ps_proteoforms_\'${$i}\'.txt;\n+                unzip -j \'${$s.match_type.input_peptideshakerzip_proteoforms}\' \'reports/proteins_proteoforms.txt\' -d \'./\';\n+                mv proteins_proteoforms.txt ps_proteoforms_\'${$i}\'.txt;\n             #end if\n         #end for\n \n@@ -49,7 +49,6 @@\n \n             #for $i, $s in enumerate($match_types)\n \n-\n                 ## PROTEOFORMS\n \n                 #if $s.match_type.match_type_selector == "proteoforms"\n@@ -147,15 +146,12 @@\n         #if $output_options.output_graphs:\n             mkdir "graphs";\n         #end if\n-\n         #if \'gg\' in $output_graphs_list:\n             mv -t "graphs" "geneExternalEdges.tsv" "geneInternalEdges.tsv" "geneVertices.tsv" ;\n         #end if\n-\n         #if \'gu\' in $output_graphs_list:\n             mv -t "graphs" "proteinExternalEdges.tsv" "proteinInternalEdges.tsv" "proteinVertices.tsv";\n         #end if\n-\n         #if \'gp\' in $output_graphs_list:\n             mv -t "graphs" "proteoformExternalEdges.tsv" "proteoformInternalEdges.tsv" "proteoformVertices.tsv";\n         #end if\n@@ -172,7 +168,7 @@\n                   <param name="match_type_selector" type="select" label="Match type"\n                       help="">\n                       <option value="proteoforms">Proteoforms</option>\n-                      <option value="peptideshakerzip_proteoforms">Proteoforms from Peptideshaker Archive</option>\n+                      <option value="peptideshakerzip_proteoforms">Proteoforms from Peptideshaker 2.x Archive</option>\n                       <option value="gene">Genes</option>\n                       <option value="uniprot">Proteins - UniProt Accession list</option>\n                       <option value="ensembl">Proteins - Ensembl identifier list</option>\n@@ -181,7 +177,6 @@\n                       <option value="rsid">Genetic variants - SNP rsId list</option>\n                       <option value="peptide">Peptides - Simple list</option>\n                       <option value="modifiedpeptide">Peptides - Peptide List with PTM types and sites</option>\n-\n                   </param>\n \n \n@@ -202,6 +197,7 @@\n                           <option value="SUBSET_NO_TYPES">SUBSET NO TYPES</option>\n                           <option value="ONE">ONE</option>\n                           <option value="ONE_NO_TYPES">ONE_NO_TYPES</option>\n+                          <option value="ACCESSION">ACCESSION</option>\n      '..b'P27361;00047:202,00048:204\\tP28482;00047:185,00048:187\\tSet\\tR-HSA-450307\\tmember/candidate\\tmember/candidate"/>\n+                      <has_line_matching expression="P12931;00048:419\\tQ01196;\\tComplex\\tR-HSA-8937687\\tcomponent\\tcomponent"/>\n+                      <has_line_matching expression="P15509;\\tP42229;00048:694\\tSet\\tR-HSA-913465\\tmember/candidate\\tmember/candidate"/>\n+                      <has_n_columns n="6" />\n+                  </assert_contents>\n+              </element>\n+              <element name="proteoformInternalEdges" ftype="tsv">\n+                  <assert_contents>\n+                      <has_line_matching expression="P27361;00047:202,00048:204\\tQ15759;00047:180,00048:182\\tSet\\tR-HSA-450307\\tmember/candidate\\tmember/candidate"/>\n+                      <has_line_matching expression="P27361;00047:202,00048:204\\tQ15759;00047:180,00048:182\\tSet\\tR-HSA-450307\\tmember/candidate\\tmember/candidate"/>\n+                      <has_n_columns n="6" />\n+                  </assert_contents>\n+              </element>\n+              <element name="proteoformVertices" ftype="tsv">\n+                  <assert_contents>\n+                      <has_line_matching expression="P16220;00046:133\\tCyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ]"/>\n+                      <has_line_matching expression="Q15759;00047:180,00048:182\\tMitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber"/>\n+                      <has_line_matching expression="P42229;00048:694\\tSignal transducer and activator of transcription 5A ]"/>\n+                      <has_n_columns n="2" />\n+                  </assert_contents>\n+              </element>\n+\n           </output_collection>\n       </test>\n \n@@ -418,13 +489,44 @@\n \n **Try it now**\n \n-You can easily test PathwayMatcher functionality using the example files we provide with proteoforms and proteins information of Cystic Fibrosis:\n+You can easily test PathwayMatcher functionality creating text files with the example data we provide with proteoforms and proteins information of Cystic Fibrosis:\n \n-https://media.githubusercontent.com/media/PathwayAnalysisPlatform/PathwayMatcher/master/src/test/resources/Proteoforms/Simple/CysticFibrosis.txt\n+**Proteoforms**:\n+\n+::\n \n-https://media.githubusercontent.com/media/PathwayAnalysisPlatform/PathwayMatcher/master/src/test/resources/Proteins/UniProt/CysticFibrosis.txt\n+ P01137;\n+ P10145;\n+ P12318;\n+ P12318;00048:288,00048:304\n+ P13569;\n+ P13569;01148:null\n+ P19438;\n+ P37088;\n+ P37088;01148:null\n+ P51168;\n+ P51170;\n+ P51170;01148:null\n+ Q14CN2;\n+ Q16623;\n+ Q9UJW0;\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+**Proteins**:\n+::\n+\n+  P13569\n+  P01137\n+  P12318\n+  Q9UJW0\n+  P51168\n+  P51170\n+  P37088\n+  P19438\n+  Q14CN2\n+  Q16623\n+  P10145\n+\n+After copying and pasting this data into new text files, you can upload them to Galaxy by directly using the Galaxy upload dialog (the button with the arrow pointing up in the top-left area, and then choosing *Choose local file*).\n \n Once they appear in green in your history, they have been uploaded and you can use them as inputs in PathwayMatcher.\n \n@@ -462,9 +564,9 @@\n http://www.nature.com/nbt/journal/v26/n8/full/nbt0808-864.html\n \n .. _dbSNP: https://www.ncbi.nlm.nih.gov/projects/SNP/\n-.. _PathwayMatcher: https://github.com/LuisFranciscoHS/PathwayMatcher\n-.. _Input: https://github.com/LuisFranciscoHS/PathwayMatcher/wiki/Input\n-.. _Output: https://github.com/LuisFranciscoHS/PathwayMatcher/wiki/Output\n+.. _PathwayMatcher: https://github.com/PathwayAnalysisPlatform/PathwayMatcher\n+.. _Input: https://github.com/PathwayAnalysisPlatform/PathwayMatcher/wiki/Input\n+.. _Output: https://github.com/PathwayAnalysisPlatform/PathwayMatcher/wiki/Output\n \n     </help>\n \n'
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diff -r 2cd67294abbd -r 3e510701a712 test-data/genes_search.tsv
--- a/test-data/genes_search.tsv Wed May 08 13:41:47 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,539 +0,0 @@\n-GENE\tUNIPROT\tREACTION_STID\tREACTION_DISPLAY_NAME\tPATHWAY_STID\tPATHWAY_DISPLAY_NAME\tTOP_LEVEL_PATHWAY_STID\tTOP_LEVEL_PATHWAY_DISPLAY_NAME\n-CFTR\tP13569\tR-HSA-1454916\tThe ABCC family mediates organic anion transport\tR-HSA-382556\tABC-family proteins mediated transport\tR-HSA-382551\tTransport of small molecules\n-CFTR\tP13569\tR-HSA-1454916\tThe ABCC family mediates organic anion transport\tR-HSA-382551\tTransport of small molecules\tR-HSA-382551\tTransport of small molecules\n-CFTR\tP13569\tR-HSA-383190\tHCO3- transport through ion channel\tR-HSA-382556\tABC-family proteins mediated transport\tR-HSA-382551\tTransport of small molecules\n-CFTR\tP13569\tR-HSA-383190\tHCO3- transport through ion channel\tR-HSA-382551\tTransport of small molecules\tR-HSA-382551\tTransport of small molecules\n-CFTR\tP13569\tR-HSA-5678863\tCFTR transports Cl- from cytosol to extracellular region\tR-HSA-382556\tABC-family proteins mediated transport\tR-HSA-382551\tTransport of small molecules\n-CFTR\tP13569\tR-HSA-5678863\tCFTR transports Cl- from cytosol to extracellular region\tR-HSA-382551\tTransport of small molecules\tR-HSA-382551\tTransport of small molecules\n-CFTR\tP13569\tR-HSA-5627071\tRHOQ positively regulates trafficking of GOPC:CFTR to the plasma membrane\tR-HSA-162582\tSignal Transduction\tR-HSA-162582\tSignal Transduction\n-CFTR\tP13569\tR-HSA-5627071\tRHOQ positively regulates trafficking of GOPC:CFTR to the plasma membrane\tR-HSA-194315\tSignaling by Rho GTPases\tR-HSA-162582\tSignal Transduction\n-CFTR\tP13569\tR-HSA-5627071\tRHOQ positively regulates trafficking of GOPC:CFTR to the plasma membrane\tR-HSA-195258\tRHO GTPase Effectors\tR-HSA-162582\tSignal Transduction\n-CFTR\tP13569\tR-HSA-5627071\tRHOQ positively regulates trafficking of GOPC:CFTR to the plasma membrane\tR-HSA-5627083\tRHO GTPases regulate CFTR trafficking\tR-HSA-162582\tSignal Transduction\n-CFTR\tP13569\tR-HSA-8866542\tVCP-catalyzed ATP hydrolysis promotes the translocation of misfolded CFTR into the cytosol\tR-HSA-382556\tABC-family proteins mediated transport\tR-HSA-382551\tTransport of small molecules\n-CFTR\tP13569\tR-HSA-8866542\tVCP-catalyzed ATP hydrolysis promotes the translocation of misfolded CFTR into the cytosol\tR-HSA-382551\tTransport of small molecules\tR-HSA-382551\tTransport of small molecules\n-CFTR\tP13569\tR-HSA-8866546\tRNF5 and RNF185 ubiquitinate misfolded CFTR\tR-HSA-382556\tABC-family proteins mediated transport\tR-HSA-382551\tTransport of small molecules\n-CFTR\tP13569\tR-HSA-8866546\tRNF5 and RNF185 ubiquitinate misfolded CFTR\tR-HSA-382551\tTransport of small molecules\tR-HSA-382551\tTransport of small molecules\n-CFTR\tP13569\tR-HSA-8866551\tCFTR binds components of the ERAD machinery for ubiquitination and degradation\tR-HSA-382556\tABC-family proteins mediated transport\tR-HSA-382551\tTransport of small molecules\n-CFTR\tP13569\tR-HSA-8866551\tCFTR binds components of the ERAD machinery for ubiquitination and degradation\tR-HSA-382551\tTransport of small molecules\tR-HSA-382551\tTransport of small molecules\n-CFTR\tP13569\tR-HSA-5678992\tIvacaftor:CFTR G551D transports Cl- from cytosol to extracellular region\tR-HSA-1643685\tDisease\tR-HSA-1643685\tDisease\n-CFTR\tP13569\tR-HSA-5678992\tIvacaftor:CFTR G551D transports Cl- from cytosol to extracellular region\tR-HSA-5619115\tDisorders of transmembrane transporters\tR-HSA-1643685\tDisease\n-CFTR\tP13569\tR-HSA-5678992\tIvacaftor:CFTR G551D transports Cl- from cytosol to extracellular region\tR-HSA-5619084\tABC transporter disorders\tR-HSA-1643685\tDisease\n-CFTR\tP13569\tR-HSA-5678992\tIvacaftor:CFTR G551D transports Cl- from cytosol to extracellular region\tR-HSA-5678895\tDefective CFTR causes cystic fibrosis\tR-HSA-1643685\tDisease\n-CFTR\tP13569\tR-HSA-5679000\tIvacaftor binds CFTR G551D\tR-HSA-1643685\tDisease\tR-HSA-1643685\tDisease\n-CFTR\tP13569\tR-HSA-5679000\tIvacaftor binds CFTR G551D\tR-HSA-5619115\tDisorders of transmembrane transporters\tR-HSA-1643685\tDisease\n-CFTR\tP13569\tR-HSA-5679000\tIvacaftor binds CFTR G551D\tR-HSA-5619084\tABC transporter disorders\tR-HSA-1643685\tDisease\n-CFTR\tP13569\tR-HSA-5679000\tIvacaftor binds CFTR '..b'582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-380073\tLiganded Gi-activating GPCR acts as a GEF for Gi\tR-HSA-372790\tSignaling by GPCR\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-380073\tLiganded Gi-activating GPCR acts as a GEF for Gi\tR-HSA-388396\tGPCR downstream signalling\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-749456\tLiganded Gi-activating GPCRs bind inactive heterotrimeric G-protein Gi\tR-HSA-418594\tG alpha (i) signalling events\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-749456\tLiganded Gi-activating GPCRs bind inactive heterotrimeric G-protein Gi\tR-HSA-162582\tSignal Transduction\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-749456\tLiganded Gi-activating GPCRs bind inactive heterotrimeric G-protein Gi\tR-HSA-372790\tSignaling by GPCR\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-749456\tLiganded Gi-activating GPCRs bind inactive heterotrimeric G-protein Gi\tR-HSA-388396\tGPCR downstream signalling\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-749454\tThe Ligand:GPCR:Gi complex dissociates\tR-HSA-418594\tG alpha (i) signalling events\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-749454\tThe Ligand:GPCR:Gi complex dissociates\tR-HSA-162582\tSignal Transduction\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-749454\tThe Ligand:GPCR:Gi complex dissociates\tR-HSA-372790\tSignaling by GPCR\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-749454\tThe Ligand:GPCR:Gi complex dissociates\tR-HSA-388396\tGPCR downstream signalling\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-373813\tReceptor CXCR2 binds ligands CXCL1 to 7\tR-HSA-373076\tClass A/1 (Rhodopsin-like receptors)\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-373813\tReceptor CXCR2 binds ligands CXCL1 to 7\tR-HSA-375276\tPeptide ligand-binding receptors\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-373813\tReceptor CXCR2 binds ligands CXCL1 to 7\tR-HSA-380108\tChemokine receptors bind chemokines\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-373813\tReceptor CXCR2 binds ligands CXCL1 to 7\tR-HSA-162582\tSignal Transduction\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-373813\tReceptor CXCR2 binds ligands CXCL1 to 7\tR-HSA-372790\tSignaling by GPCR\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-373813\tReceptor CXCR2 binds ligands CXCL1 to 7\tR-HSA-500792\tGPCR ligand binding\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-373791\tReceptor CXCR1 binds CXCL6 and CXCL8 ligands\tR-HSA-373076\tClass A/1 (Rhodopsin-like receptors)\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-373791\tReceptor CXCR1 binds CXCL6 and CXCL8 ligands\tR-HSA-375276\tPeptide ligand-binding receptors\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-373791\tReceptor CXCR1 binds CXCL6 and CXCL8 ligands\tR-HSA-380108\tChemokine receptors bind chemokines\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-373791\tReceptor CXCR1 binds CXCL6 and CXCL8 ligands\tR-HSA-162582\tSignal Transduction\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-373791\tReceptor CXCR1 binds CXCL6 and CXCL8 ligands\tR-HSA-372790\tSignaling by GPCR\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-373791\tReceptor CXCR1 binds CXCL6 and CXCL8 ligands\tR-HSA-500792\tGPCR ligand binding\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-374251\tDARC  is a non-specific receptor for many chemokines\tR-HSA-373076\tClass A/1 (Rhodopsin-like receptors)\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-374251\tDARC  is a non-specific receptor for many chemokines\tR-HSA-375276\tPeptide ligand-binding receptors\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-374251\tDARC  is a non-specific receptor for many chemokines\tR-HSA-162582\tSignal Transduction\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-374251\tDARC  is a non-specific receptor for many chemokines\tR-HSA-372790\tSignaling by GPCR\tR-HSA-162582\tSignal Transduction\n-CXCL8\tP10145\tR-HSA-374251\tDARC  is a non-specific receptor for many chemokines\tR-HSA-500792\tGPCR ligand binding\tR-HSA-162582\tSignal Transduction\n'
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diff -r 2cd67294abbd -r 3e510701a712 test-data/proteoforms_graphs/geneVertices.tsv
--- a/test-data/proteoforms_graphs/geneVertices.tsv Wed May 08 13:41:47 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,17 +0,0 @@
-id  name
-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 ]
-ERK1 Mitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber
-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
-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
-RNF55 E3 ubiquitin-protein ligase CBL ecNumber evidence="23 33 39"2.3.2.27/ecNumber
-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
-STAT5 Signal transducer and activator of transcription 5A ]
-STAT5A Signal transducer and activator of transcription 5A ]
b
diff -r 2cd67294abbd -r 3e510701a712 test-data/proteoforms_graphs/proteinExternalEdges.tsv
--- a/test-data/proteoforms_graphs/proteinExternalEdges.tsv Wed May 08 13:41:47 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,31020 +0,0 @@\n-id1\tid2\ttype\tcontainer_id\trole1\trole2\n-P12931\tP56975\tReaction\tR-HSA-1963586\tcatalyst\tinput\n-P12931\tP56975\tReaction\tR-HSA-1963586\tcatalyst\toutput\n-P12931\tQ15303\tReaction\tR-HSA-1963586\tcatalyst\tinput\n-P12931\tQ15303\tReaction\tR-HSA-1963586\tcatalyst\toutput\n-P07947\tP12931\tReaction\tR-HSA-1963586\tcatalyst\tcatalyst\n-P04626\tP12931\tReaction\tR-HSA-1963586\tcatalyst\tcatalyst\n-P12931\tQ8WWG1\tReaction\tR-HSA-1963586\tcatalyst\tinput\n-P12931\tQ8WWG1\tReaction\tR-HSA-1963586\tcatalyst\toutput\n-P12931\tQ02297\tReaction\tR-HSA-1963586\tcatalyst\tinput\n-P12931\tQ02297\tReaction\tR-HSA-1963586\tcatalyst\toutput\n-P12931\tQ99075\tReaction\tR-HSA-1963586\tcatalyst\tinput\n-P12931\tQ99075\tReaction\tR-HSA-1963586\tcatalyst\toutput\n-P06241\tP12931\tReaction\tR-HSA-1963586\tcatalyst\tcatalyst\n-P12931\tP21860\tReaction\tR-HSA-1963586\tcatalyst\tinput\n-P12931\tP21860\tReaction\tR-HSA-1963586\tcatalyst\toutput\n-O14511\tP12931\tReaction\tR-HSA-1963586\tcatalyst\tcatalyst\n-P00533\tP12931\tReaction\tR-HSA-1963586\tcatalyst\tcatalyst\n-P12931\tP35070\tReaction\tR-HSA-1963586\tcatalyst\tinput\n-P12931\tP35070\tReaction\tR-HSA-1963586\tcatalyst\toutput\n-O14944\tP12931\tReaction\tR-HSA-1963586\tcatalyst\tcatalyst\n-P01133\tP12931\tReaction\tR-HSA-1963586\tcatalyst\tcatalyst\n-P12931\tQ9Y6W8\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ6PIZ9\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-O95750\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P11487\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ9Y4K3\tReaction\tR-HSA-2316434\tcatalyst\tregulator\n-P12931\tP15498\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tP21802\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tP62993\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tP33681\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tP63000\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ92731\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P04085\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tP55075\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ13480\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tP27986\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-O14944\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tP22455\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-O43320\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ15303\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ9GZV9\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P10767\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P09619\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ9Y4H2\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ02297\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ9NWZ3\tReaction\tR-HSA-2316434\tcatalyst\tregulator\n-P10721\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-O95760\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tP35568\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tP14210\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tP16234\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tP84095\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-O60258\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ9NPH3\tReaction\tR-HSA-2316434\tcatalyst\tregulator\n-P12931\tP31371\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-O14511\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-O15520\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P00533\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ99836\tReaction\tR-HSA-2316434\tcatalyst\tregulator\n-P12931\tP42338\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ01638\tReaction\tR-HSA-2316434\tcatalyst\tregulator\n-P12931\tQ92569\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tP42336\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tP56975\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-O00329\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P06239\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ8WWG1\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ06124\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ9UEF7\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12931\tQ99075\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst\n-P12034\tP12931\tReaction\tR-HSA-2316434\tcatalyst\tcat'..b'onent\n-Q15759\tQ16539\tComplex\tR-HSA-3239017\tcomponent\tcomponent\n-Q15759\tQ8IW41\tComplex\tR-HSA-3239009\tcomponent\tcomponent\n-Q15759\tQ16539\tComplex\tR-HSA-3239009\tcomponent\tcomponent\n-Q15759\tQ16539\tComplex\tR-HSA-3239002\tcomponent\tcomponent\n-Q15759\tQ8IW41\tComplex\tR-HSA-3239002\tcomponent\tcomponent\n-Q15759\tQ16539\tComplex\tR-HSA-450241\tcomponent\tcomponent\n-P49137\tQ15759\tComplex\tR-HSA-450241\tcomponent\tcomponent\n-Q15759\tQ16644\tComplex\tR-HSA-450241\tcomponent\tcomponent\n-Q15759\tQ16539\tComplex\tR-HSA-170993\tcomponent\tcomponent\n-Q15759\tQ16539\tComplex\tR-HSA-189828\tcomponent\tcomponent\n-P53778\tQ15759\tComplex\tR-HSA-189828\tcomponent\tcomponent\n-O15264\tQ15759\tComplex\tR-HSA-189828\tcomponent\tcomponent\n-O60271\tQ15759\tComplex\tR-HSA-448881\tcomponent\tcomponent\n-P60953\tQ15759\tComplex\tR-HSA-448881\tcomponent\tcomponent\n-Q15759\tQ4KMG0\tComplex\tR-HSA-448881\tcomponent\tcomponent\n-Q15759\tQ9BWV1\tComplex\tR-HSA-448881\tcomponent\tcomponent\n-P55283\tQ15759\tComplex\tR-HSA-448881\tcomponent\tcomponent\n-P19022\tQ15759\tComplex\tR-HSA-448881\tcomponent\tcomponent\n-P55291\tQ15759\tComplex\tR-HSA-448881\tcomponent\tcomponent\n-P35222\tQ15759\tComplex\tR-HSA-448881\tcomponent\tcomponent\n-P35221\tQ15759\tComplex\tR-HSA-448881\tcomponent\tcomponent\n-P26232\tQ15759\tComplex\tR-HSA-448881\tcomponent\tcomponent\n-Q12982\tQ15759\tComplex\tR-HSA-448881\tcomponent\tcomponent\n-Q15759\tQ16539\tComplex\tR-HSA-448881\tcomponent\tcomponent\n-P53778\tQ15759\tComplex\tR-HSA-448881\tcomponent\tcomponent\n-Q15759\tQ16539\tComplex\tR-HSA-448887\tcomponent\tcomponent\n-P53778\tQ15759\tComplex\tR-HSA-448887\tcomponent\tcomponent\n-O60271\tQ15759\tComplex\tR-HSA-448887\tcomponent\tcomponent\n-P60953\tQ15759\tComplex\tR-HSA-448887\tcomponent\tcomponent\n-Q15759\tQ4KMG0\tComplex\tR-HSA-448887\tcomponent\tcomponent\n-Q15759\tQ9BWV1\tComplex\tR-HSA-448887\tcomponent\tcomponent\n-P55283\tQ15759\tComplex\tR-HSA-448887\tcomponent\tcomponent\n-P19022\tQ15759\tComplex\tR-HSA-448887\tcomponent\tcomponent\n-P55291\tQ15759\tComplex\tR-HSA-448887\tcomponent\tcomponent\n-P35222\tQ15759\tComplex\tR-HSA-448887\tcomponent\tcomponent\n-P35221\tQ15759\tComplex\tR-HSA-448887\tcomponent\tcomponent\n-P26232\tQ15759\tComplex\tR-HSA-448887\tcomponent\tcomponent\n-Q12982\tQ15759\tComplex\tR-HSA-448887\tcomponent\tcomponent\n-Q14814\tQ15759\tComplex\tR-HSA-448874\tcomponent\tcomponent\n-Q02080\tQ15759\tComplex\tR-HSA-448874\tcomponent\tcomponent\n-Q06413\tQ15759\tComplex\tR-HSA-448874\tcomponent\tcomponent\n-Q02078\tQ15759\tComplex\tR-HSA-448874\tcomponent\tcomponent\n-Q15759\tQ16539\tComplex\tR-HSA-448874\tcomponent\tcomponent\n-P53778\tQ15759\tComplex\tR-HSA-448874\tcomponent\tcomponent\n-Q15759\tQ16539\tSet\tR-HSA-198703\tmember/candidate\tmember/candidate\n-P28482\tQ15759\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate\n-P53779\tQ15759\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate\n-P45984\tQ15759\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate\n-P45983\tQ15759\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate\n-Q15759\tQ16539\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate\n-Q15759\tQ16539\tSet\tR-HSA-203795\tmember/candidate\tmember/candidate\n-Q15759\tQ16539\tSet\tR-HSA-170997\tmember/candidate\tmember/candidate\n-Q15759\tQ16539\tSet\tR-HSA-171016\tmember/candidate\tmember/candidate\n-P53778\tQ15759\tSet\tR-HSA-171016\tmember/candidate\tmember/candidate\n-O15264\tQ15759\tSet\tR-HSA-171016\tmember/candidate\tmember/candidate\n-Q15759\tQ16539\tSet\tR-HSA-1250102\tmember/candidate\tmember/candidate\n-P53778\tQ15759\tSet\tR-HSA-1250102\tmember/candidate\tmember/candidate\n-O15264\tQ15759\tSet\tR-HSA-1250102\tmember/candidate\tmember/candidate\n-Q15759\tQ16539\tSet\tR-HSA-1250100\tmember/candidate\tmember/candidate\n-O15264\tQ15759\tSet\tR-HSA-1250100\tmember/candidate\tmember/candidate\n-P53778\tQ15759\tSet\tR-HSA-1250100\tmember/candidate\tmember/candidate\n-Q15759\tQ16539\tSet\tR-HSA-448858\tmember/candidate\tmember/candidate\n-P53778\tQ15759\tSet\tR-HSA-448858\tmember/candidate\tmember/candidate\n-Q15759\tQ16539\tSet\tR-HSA-448861\tmember/candidate\tmember/candidate\n-P53778\tQ15759\tSet\tR-HSA-448861\tmember/candidate\tmember/candidate\n-Q15759\tQ16539\tSet\tR-HSA-448855\tmember/candidate\tmember/candidate\n-P53778\tQ15759\tSet\tR-HSA-448855\tmember/candidate\tmember/candidate\n'
b
diff -r 2cd67294abbd -r 3e510701a712 test-data/proteoforms_graphs/proteinInternalEdges.tsv
--- a/test-data/proteoforms_graphs/proteinInternalEdges.tsv Wed May 08 13:41:47 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,524 +0,0 @@\n-id1\tid2\ttype\tcontainer_id\trole1\trole2\n-P12931\tQ9UQC2\tReaction\tR-HSA-1562641\tinput\tinput\n-P12931\tQ9UQC2\tReaction\tR-HSA-1562641\tinput\toutput\n-P12931\tQ9UQC2\tReaction\tR-HSA-1562641\toutput\tinput\n-P12931\tQ9UQC2\tReaction\tR-HSA-1562641\toutput\toutput\n-P12931\tQ9UQC2\tReaction\tR-HSA-1433514\tcatalyst\tcatalyst\n-P12931\tQ9UQC2\tReaction\tR-HSA-205234\tinput\tinput\n-P12931\tQ9UQC2\tReaction\tR-HSA-205234\tinput\toutput\n-P12931\tQ9UQC2\tReaction\tR-HSA-205234\toutput\tinput\n-P12931\tQ9UQC2\tReaction\tR-HSA-205234\toutput\toutput\n-P12931\tP22681\tReaction\tR-HSA-205244\tinput\tinput\n-P12931\tP22681\tReaction\tR-HSA-205244\tinput\toutput\n-P12931\tP22681\tReaction\tR-HSA-205244\toutput\tinput\n-P12931\tP22681\tReaction\tR-HSA-205244\toutput\toutput\n-P12931\tP42229\tReaction\tR-HSA-1433456\tinput\tinput\n-P12931\tP42229\tReaction\tR-HSA-1433456\tinput\toutput\n-P12931\tP42229\tReaction\tR-HSA-1433456\toutput\tinput\n-P12931\tP42229\tReaction\tR-HSA-1433456\toutput\toutput\n-P12931\tP40763\tReaction\tR-HSA-1433456\tinput\tinput\n-P12931\tP40763\tReaction\tR-HSA-1433456\tinput\toutput\n-P12931\tP40763\tReaction\tR-HSA-1433456\toutput\tinput\n-P12931\tP40763\tReaction\tR-HSA-1433456\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-P12931\tP40763\tReaction\tR-HSA-1470012\tinput\tinput\n-P12931\tP40763\tReaction\tR-HSA-1470012\tinput\toutput\n-P12931\tP40763\tReaction\tR-HSA-1470012\toutput\tinput\n-P12931\tP40763\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-P12931\tP40763\tReaction\tR-HSA-1470010\tinput\tinput\n-P12931\tP40763\tReaction\tR-HSA-1470010\tinput\toutput\n-P12931\tP40763\tReaction\tR-HSA-1470010\toutput\tinput\n-P12931\tP40763\tReaction\tR-HSA-1470010\toutput\toutput\n-P12931\tP27361\tReaction\tR-HSA-418176\tinput\tinput\n-P12931\tP27361\tReaction\tR-HSA-418176\tinput\toutput\n-P12931\tP27361\tReaction\tR-HSA-418176\toutput\tinput\n-P12931\tP27361\tReaction\tR-HSA-418176\toutput\toutput\n-P12931\tP27361\tReaction\tR-HSA-418170\tinput\tinput\n-P12931\tP27361\tReaction\tR-HSA-418170\tinput\toutput\n-P12931\tP27361\tReaction\tR-HSA-418170\toutput\tinput\n-P12931\tP27361\tReaction\tR-HSA-418170\toutput\toutput\n-P00519\tP12931\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst\n-P12931\tP27361\tReaction\tR-HSA-6803234\tinput\tinput\n-P12931\tP27361\tReaction\tR-HSA-6803234\tinput\toutput\n-P12931\tP27361\tReaction\tR-HSA-6803234\toutput\tinput\n-P12931\tP27361\tReaction\tR-HSA-6803234\toutput\toutput\n-P12931\tP27361\tReaction\tR-HSA-6803230\tinput\tinput\n-P12931\tP27361\tReaction\tR-HSA-6803230\tinput\toutput\n-P12931\tP27361\tReaction\tR-HSA-6803230\toutput\tinput\n-P12931\tP27361\tReaction\tR-HSA-6803230\toutput\toutput\n-P12931\tP27361\tReaction\tR-HSA-6803227\tinput\tinput\n-P12931\tP27361\tReaction\tR-HSA-6803227\tinput\toutput\n-P12931\tP27361\tReaction\tR-HSA-6803227\toutput\tinput\n-P12931\tP27361\tReaction\tR-HSA-6803227\toutput\toutput\n-P12931\tP27361\tReaction\tR-HSA-6803233\tinput\tinput\n-P12931\tP27361\tReaction\tR-HSA-6803233\tinput\toutput\n-P12931\tP27361\tReaction\tR-HSA-6803233\toutput\tinput\n-P12931\tP27361\tReaction\tR-HSA-6803233\toutput\toutput\n-P12931\tP27361\tReaction\tR-HSA-5672980\tinput\tinput\n-P12931\tP27361\tReaction\tR-HSA-5672980\tinput\toutput\n-P12931\tP27361\tReaction\tR-HSA-5672980\toutput\tinput\n-P12931\tP27361\tReaction\tR-HSA-5672980\toutput\toutput\n-P12931\tP27361\tReaction\tR-HSA-6802932\tinput\tinput\n-P12931\tP27361\tReaction\tR-HSA-6802932\tinput\toutput\n-P12931\tP27361\tReaction\tR-HSA-6802932\toutput\tinput\n-P12931\tP27361\tReaction\tR-HSA-6802932\toutput\toutput\n-P12931\tP27361\tReaction\tR-HSA-6802943\tinput\tinput\n-P12931\tP27361\tReaction\tR-HSA-6802943\tinput\toutput\n-P12931\tP27361\tReaction\tR-HSA-6802943\tinput\tcatalyst\n-P12931\tP27361\tReaction\tR-HSA-6802943\toutput\tinput\n-P12931\tP27361\tReaction\tR-HSA-6802943\toutput\toutput\n-P12931\tP27361\tReaction\tR-HSA-6802943\toutput\tcatalyst\n-P12931\tP27361\tReaction\tR-HSA-6802943\tcatalyst\tinput\n-P12931\tP27361'..b'274\tP42229\tReaction\tR-HSA-1839112\tinput\tinput\n-P11274\tP42229\tReaction\tR-HSA-1839112\tinput\toutput\n-P11274\tP42229\tReaction\tR-HSA-1839112\toutput\tinput\n-P11274\tP42229\tReaction\tR-HSA-1839112\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-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-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 2cd67294abbd -r 3e510701a712 test-data/proteoforms_graphs/proteinVertices.tsv
--- a/test-data/proteoforms_graphs/proteinVertices.tsv Wed May 08 13:41:47 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,7 +0,0 @@
-id  name
-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
-P42229 Signal transducer and activator of transcription 5A ]
-Q15759 Mitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber
b
diff -r 2cd67294abbd -r 3e510701a712 test-data/proteoforms_graphs/proteoformExternalEdges.tsv
--- a/test-data/proteoforms_graphs/proteoformExternalEdges.tsv Wed May 08 13:41:47 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,512 +0,0 @@\n-id1\tid2\ttype\tcontainer_id\trole1\trole2\n-P22681;\tQ07889;\tComplex\tR-HSA-205200\tcomponent\tcomponent\n-P22681;\tP62993-1;\tComplex\tR-HSA-205200\tcomponent\tcomponent\n-P10721;00048:568,00048:570,00048:703,00048:721,00048:730,00048:823,00048:936\tP22681;\tComplex\tR-HSA-205200\tcomponent\tcomponent\n-P21583-1;\tP22681;\tComplex\tR-HSA-205200\tcomponent\tcomponent\n-P06241;\tP22681;\tComplex\tR-HSA-205200\tcomponent\tcomponent\n-P06239;\tP22681;\tComplex\tR-HSA-205200\tcomponent\tcomponent\n-P12931-1;\tP22681;\tComplex\tR-HSA-205200\tcomponent\tcomponent\n-P07947;\tP22681;\tComplex\tR-HSA-205200\tcomponent\tcomponent\n-P07948;\tP22681;\tComplex\tR-HSA-205200\tcomponent\tcomponent\n-O14492;00048:629\tP22681;\tComplex\tR-HSA-205200\tcomponent\tcomponent\n-O43597;00048:55\tP22681;\tComplex\tR-HSA-182935\tcomponent\tcomponent\n-O43609;00048:53\tP22681;\tComplex\tR-HSA-182935\tcomponent\tcomponent\n-P01133;\tP22681;\tComplex\tR-HSA-182935\tcomponent\tcomponent\n-P00533;00048:992,00048:1045,00048:1068,00048:1086,00048:1148,00048:1173\tP22681;\tComplex\tR-HSA-182935\tcomponent\tcomponent\n-P01133;\tP22681;\tComplex\tR-HSA-182960\tcomponent\tcomponent\n-P00533;00048:992,00048:1045,00048:1068,00048:1086,00048:1148,00048:1173\tP22681;\tComplex\tR-HSA-182960\tcomponent\tcomponent\n-P01133;\tP22681;\tComplex\tR-HSA-182939\tcomponent\tcomponent\n-P00533;00048:992,00048:1045,00048:1068,00048:1086,00048:1148,00048:1173\tP22681;\tComplex\tR-HSA-182939\tcomponent\tcomponent\n-O43597;00048:55\tP22681;\tComplex\tR-HSA-182939\tcomponent\tcomponent\n-O43609;00048:53\tP22681;\tComplex\tR-HSA-182939\tcomponent\tcomponent\n-P0CG48;\tP22681;\tComplex\tR-HSA-182939\tcomponent\tcomponent\n-P0CG47;\tP22681;\tComplex\tR-HSA-182939\tcomponent\tcomponent\n-P22681;\tP62987;\tComplex\tR-HSA-182939\tcomponent\tcomponent\n-P22681;\tP62979;\tComplex\tR-HSA-182939\tcomponent\tcomponent\n-P22681;\tP62993-1;\tComplex\tR-HSA-182910\tcomponent\tcomponent\n-O43597;\tP22681;\tComplex\tR-HSA-182914\tcomponent\tcomponent\n-O43609;\tP22681;\tComplex\tR-HSA-182914\tcomponent\tcomponent\n-P01133;\tP22681;\tComplex\tR-HSA-182928\tcomponent\tcomponent\n-P00533;00048:992,00048:1045,00048:1068,00048:1086,00048:1148,00048:1173\tP22681;\tComplex\tR-HSA-182928\tcomponent\tcomponent\n-P22681;\tP62993-1;\tComplex\tR-HSA-182928\tcomponent\tcomponent\n-P22681;\tP60953;\tComplex\tR-HSA-182956\tcomponent\tcomponent\n-P22681;\tQ14155;\tComplex\tR-HSA-182956\tcomponent\tcomponent\n-O43597;00048:55,00048:227\tP22681;\tComplex\tR-HSA-934576\tcomponent\tcomponent\n-O43597;00048:55,00048:227\tP22681;\tComplex\tR-HSA-934572\tcomponent\tcomponent\n-P0CG48;\tP22681;\tComplex\tR-HSA-934572\tcomponent\tcomponent\n-P0CG47;\tP22681;\tComplex\tR-HSA-934572\tcomponent\tcomponent\n-P22681;\tP62987;\tComplex\tR-HSA-934572\tcomponent\tcomponent\n-P22681;\tP62979;\tComplex\tR-HSA-934572\tcomponent\tcomponent\n-P22681;\tP43405;\tComplex\tR-HSA-912623\tcomponent\tcomponent\n-P07947;\tP22681;\tComplex\tR-HSA-912623\tcomponent\tcomponent\n-P08631;\tP22681;\tComplex\tR-HSA-912623\tcomponent\tcomponent\n-P07948;\tP22681;\tComplex\tR-HSA-912623\tcomponent\tcomponent\n-P06241;\tP22681;\tComplex\tR-HSA-912623\tcomponent\tcomponent\n-P22681;\tP62993-1;\tComplex\tR-HSA-912623\tcomponent\tcomponent\n-P22681;\tP42338;\tComplex\tR-HSA-912623\tcomponent\tcomponent\n-P22681;\tQ92569;\tComplex\tR-HSA-912623\tcomponent\tcomponent\n-O00459;\tP22681;\tComplex\tR-HSA-912623\tcomponent\tcomponent\n-P22681;\tP27986;\tComplex\tR-HSA-912623\tcomponent\tcomponent\n-O00329;\tP22681;\tComplex\tR-HSA-912623\tcomponent\tcomponent\n-P22681;\tP42336;\tComplex\tR-HSA-912623\tcomponent\tcomponent\n-P22681;\tP37173;\tComplex\tR-HSA-4332229\tcomponent\tcomponent\n-P22681;\tQ06124;\tComplex\tR-HSA-1112744\tcomponent\tcomponent\n-P22681;\tP40189-1;00048:759,00048:767,00048:814,00048:905,00048:915\tComplex\tR-HSA-1112744\tcomponent\tcomponent\n-P22681;\tP29597;00048:1054\tComplex\tR-HSA-1112744\tcomponent\tcomponent\n-O60674;00048:1007\tP22681;\tComplex\tR-HSA-1112744\tcomponent\tcomponent\n-P22681;\tP23458;00048:1034\tComplex\tR-HSA-1112744\tcomponent\tcomponent\n-P08887;\tP22681;\tComplex\tR-HSA-1112744\tcomponent\tcomponent\n-P05231;\tP22681;\tComplex\tR-HSA-1112744\tcomponent\tcomponent\n-P08887-2;\tP22681;\tComplex\tR-HSA-1112744\tcomponent\tcomponent\n-P14210;\tP2268'..b'1696\tcomponent\tcomponent\n-P42229;00048:694\tP51692;00048:699\tComplex\tR-HSA-1671696\tcomponent\tcomponent\n-P42229;00048:694\tQ15303-1;00048:1056,00048:1188,00048:1242\tComplex\tR-HSA-1254288\tcomponent\tcomponent\n-P42229;00048:694\tQ15303-3;00048:1172,00048:1226\tComplex\tR-HSA-1254288\tcomponent\tcomponent\n-P42229;00048:694\tQ15303-1;00048:1056,00048:1188,00048:1242\tComplex\tR-HSA-8954223\tcomponent\tcomponent\n-P42229;00048:694\tQ15303-3;00048:1172,00048:1226\tComplex\tR-HSA-8954223\tcomponent\tcomponent\n-P31785;\tP42229;00048:694\tComplex\tR-HSA-9006869\tcomponent\tcomponent\n-P42229;00048:694\tP52333;00048:null\tComplex\tR-HSA-9006869\tcomponent\tcomponent\n-P23458;00048:null\tP42229;00048:694\tComplex\tR-HSA-9006869\tcomponent\tcomponent\n-P42229;00048:694\tQ9HBE5;\tComplex\tR-HSA-9006869\tcomponent\tcomponent\n-P42229;00048:694\tQ9HBE4;\tComplex\tR-HSA-9006869\tcomponent\tcomponent\n-P42224;00048:701\tP42229;00048:694\tComplex\tR-HSA-9006869\tcomponent\tcomponent\n-P42229;00048:694\tP51692;00048:699\tComplex\tR-HSA-9006869\tcomponent\tcomponent\n-P40763;00048:705\tP42229;00048:694\tComplex\tR-HSA-9006869\tcomponent\tcomponent\n-P42229;00048:694\tQ14765;00048:693\tComplex\tR-HSA-9006869\tcomponent\tcomponent\n-P42229;00048:694\tP51692;00048:699\tComplex\tR-HSA-8865622\tcomponent\tcomponent\n-P01241;\tP42229;00048:694\tComplex\tR-HSA-1168901\tcomponent\tcomponent\n-P01242;\tP42229;00048:694\tComplex\tR-HSA-1168901\tcomponent\tcomponent\n-P10912;00048:332,00048:487,00048:534,00048:566,00048:627\tP42229;00048:694\tComplex\tR-HSA-1168901\tcomponent\tcomponent\n-O60674;00048:1007\tP42229;00048:694\tComplex\tR-HSA-1168901\tcomponent\tcomponent\n-P42229;00048:694\tP51692;00048:699\tComplex\tR-HSA-1168901\tcomponent\tcomponent\n-P42229;00048:694\tP51692;00048:699\tComplex\tR-HSA-9012668\tcomponent\tcomponent\n-O60674;00048:119,00048:221,00048:372,00048:373,00048:570,00048:637,00048:813,00048:868,00048:966,00048:972,00048:1007,00048:1008\tP42229;00048:694\tComplex\tR-HSA-2671835\tcomponent\tcomponent\n-P42229;00048:694\tP48357-1;00048:986,00048:1079,00048:1141\tComplex\tR-HSA-2671835\tcomponent\tcomponent\n-P41159;\tP42229;00048:694\tComplex\tR-HSA-2671835\tcomponent\tcomponent\n-P42229;00048:694\tP51692;00048:699\tComplex\tR-HSA-2671835\tcomponent\tcomponent\n-P42224-1;00048:701\tP42229;00048:694\tSet\tR-HSA-1433413\tmember/candidate\tmember/candidate\n-P42229;00048:694\tP51692;00048:699\tSet\tR-HSA-1433413\tmember/candidate\tmember/candidate\n-P40763;00048:705\tP42229;00048:694\tSet\tR-HSA-1433413\tmember/candidate\tmember/candidate\n-P42229;00048:694\tP51692;00048:699\tSet\tR-HSA-1469979\tmember/candidate\tmember/candidate\n-P42224-1;00048:701\tP42229;00048:694\tSet\tR-HSA-1469979\tmember/candidate\tmember/candidate\n-P40763;00048:705\tP42229;00048:694\tSet\tR-HSA-1469979\tmember/candidate\tmember/candidate\n-P15509;\tP42229;00048:694\tSet\tR-HSA-913465\tmember/candidate\tmember/candidate\n-P04141;\tP42229;00048:694\tSet\tR-HSA-913465\tmember/candidate\tmember/candidate\n-P32927;\tP42229;00048:694\tSet\tR-HSA-913465\tmember/candidate\tmember/candidate\n-O60674;00048:1007\tP42229;00048:694\tSet\tR-HSA-913465\tmember/candidate\tmember/candidate\n-P42229;00048:694\tP51692;00048:699\tSet\tR-HSA-913465\tmember/candidate\tmember/candidate\n-P08700;\tP42229;00048:694\tSet\tR-HSA-913465\tmember/candidate\tmember/candidate\n-P26951;\tP42229;00048:694\tSet\tR-HSA-913465\tmember/candidate\tmember/candidate\n-P05113;\tP42229;00048:694\tSet\tR-HSA-913465\tmember/candidate\tmember/candidate\n-P42229;00048:694\tQ01344;\tSet\tR-HSA-913465\tmember/candidate\tmember/candidate\n-P42229;00048:694\tP51692;00048:699\tSet\tR-HSA-507929\tmember/candidate\tmember/candidate\n-P42229;00048:694\tP51692;00048:699\tSet\tR-HSA-1469978\tmember/candidate\tmember/candidate\n-P42224;00048:701\tP42229;00048:694\tSet\tR-HSA-9006876\tmember/candidate\tmember/candidate\n-P42229;00048:694\tP51692;00048:699\tSet\tR-HSA-9006876\tmember/candidate\tmember/candidate\n-P40763;00048:705\tP42229;00048:694\tSet\tR-HSA-9006876\tmember/candidate\tmember/candidate\n-P42229;00048:694\tQ14765;00048:693\tSet\tR-HSA-9006876\tmember/candidate\tmember/candidate\n-P42229;00048:694\tP51692;00048:699\tSet\tR-HSA-1295524\tmember/candidate\tmember/candidate\n'
b
diff -r 2cd67294abbd -r 3e510701a712 test-data/proteoforms_graphs/proteoformInternalEdges.tsv
--- a/test-data/proteoforms_graphs/proteoformInternalEdges.tsv Wed May 08 13:41:47 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,3 +0,0 @@
-id1 id2 type container_id role1 role2
-P27361;00047:202,00048:204 Q15759;00047:180,00048:182 Set R-HSA-450307 member/candidate member/candidate
-P27361;00047:202,00048:204 Q15759;00047:180,00048:182 Set R-HSA-450307 member/candidate member/candidate
b
diff -r 2cd67294abbd -r 3e510701a712 test-data/proteoforms_graphs/proteoformVertices.tsv
--- a/test-data/proteoforms_graphs/proteoformVertices.tsv Wed May 08 13:41:47 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,7 +0,0 @@
-id  name
-P22681; E3 ubiquitin-protein ligase CBL ecNumber evidence="23 33 39"2.3.2.27/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
-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
-P42229;00048:694 Signal transducer and activator of transcription 5A ]