| Previous changeset 0:f66af2b04a98 (2018-06-20) Next changeset 2:9a599f278852 (2018-07-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 7e04827e48352f6b28cf2e2c93a89a270e5bf026 |
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modified:
README.rst pathwaymatcher.xml test-data/proteoforms_graphs/geneExternalEdges.tsv test-data/proteoforms_graphs/proteinExternalEdges.tsv test-data/proteoforms_graphs/proteoformExternalEdges.tsv test-data/proteoforms_graphs/proteoformInternalEdges.tsv test-data/proteoforms_graphs/proteoformVertices.tsv |
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| diff -r f66af2b04a98 -r 5d0c44bc354d README.rst --- a/README.rst Wed Jun 20 14:21:10 2018 -0400 +++ b/README.rst Wed Jul 04 04:28:07 2018 -0400 |
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| @@ -15,14 +15,10 @@ General Requirements -------------------- -This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell: +This tool requires a Java runtime 1.8 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell: export _JAVA_OPTIONS='-Xmx1500M' -On some systems you may also need to adjust the amount of memory available for class definitions in addition to the maximum heapspace. For example: - - export _JAVA_OPTIONS='-Xmx1500M -XX:MaxPermSize=256M' - It is also possible to set this on a per tool basis using advanced features of the galaxy job config system. |
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| diff -r f66af2b04a98 -r 5d0c44bc354d pathwaymatcher.xml --- a/pathwaymatcher.xml Wed Jun 20 14:21:10 2018 -0400 +++ b/pathwaymatcher.xml Wed Jul 04 04:28:07 2018 -0400 |
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| @@ -3,7 +3,7 @@ PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome. </description> <macros> - <token name="@PATHWAYMATCHER_VERSION@">1.8</token> + <token name="@PATHWAYMATCHER_VERSION@">1.8.1</token> <token name="@TOOL_SUBVERSION@">0</token> <xml name="input_fasta"> <param format="fasta" name="input_database" type="data" label="Protein Database" @@ -87,13 +87,11 @@ ## PROTEOFORMS #if $s.input_type.input_type_selector == "proteoforms" - #if $s.input_type.proteoform_match_criteria: -t proteoform -m '${s.input_type.proteoform_match_criteria}' -i '${s.input_type.input_proteoforms}' #else: -t proteoform -i '${s.input_type.input_proteoforms}' #end if - #end if #end for |
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| diff -r f66af2b04a98 -r 5d0c44bc354d test-data/proteoforms_graphs/geneExternalEdges.tsv --- a/test-data/proteoforms_graphs/geneExternalEdges.tsv Wed Jun 20 14:21:10 2018 -0400 +++ b/test-data/proteoforms_graphs/geneExternalEdges.tsv Wed Jul 04 04:28:07 2018 -0400 |
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| b'@@ -1,1 +1,18387 @@\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\tReactio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| diff -r f66af2b04a98 -r 5d0c44bc354d test-data/proteoforms_graphs/proteinExternalEdges.tsv --- a/test-data/proteoforms_graphs/proteinExternalEdges.tsv Wed Jun 20 14:21:10 2018 -0400 +++ b/test-data/proteoforms_graphs/proteinExternalEdges.tsv Wed Jul 04 04:28:07 2018 -0400 |
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| b'@@ -8394,8 +8394,8 @@\n P12931\tP32121\tReaction\tR-HSA-6802942\tinput\toutput\n P12931\tP30086\tReaction\tR-HSA-6802942\tinput\tregulator\n P12931\tP15056\tReaction\tR-HSA-6802942\tinput\tinput\n+P12931\tP15056\tReaction\tR-HSA-6802942\tinput\toutput\n P12931\tP15056\tReaction\tR-HSA-6802942\tinput\tregulator\n-P12931\tP15056\tReaction\tR-HSA-6802942\tinput\toutput\n P12931\tP62834\tReaction\tR-HSA-6802942\tinput\tinput\n P12931\tP62834\tReaction\tR-HSA-6802942\tinput\toutput\n P12931\tP46940\tReaction\tR-HSA-6802942\tinput\tinput\n@@ -8407,11 +8407,11 @@\n P12931\tQ9Y490\tReaction\tR-HSA-6802942\tinput\tinput\n P12931\tQ9Y490\tReaction\tR-HSA-6802942\tinput\toutput\n P12931\tP31946\tReaction\tR-HSA-6802942\tinput\tinput\n+P12931\tP31946\tReaction\tR-HSA-6802942\tinput\toutput\n P12931\tP31946\tReaction\tR-HSA-6802942\tinput\tregulator\n-P12931\tP31946\tReaction\tR-HSA-6802942\tinput\toutput\n P12931\tQ8IVT5\tReaction\tR-HSA-6802942\tinput\tinput\n+P12931\tQ8IVT5\tReaction\tR-HSA-6802942\tinput\toutput\n P12931\tQ8IVT5\tReaction\tR-HSA-6802942\tinput\tregulator\n-P12931\tQ8IVT5\tReaction\tR-HSA-6802942\tinput\toutput\n P12931\tQ02750\tReaction\tR-HSA-6802942\tinput\tinput\n P12931\tQ02750\tReaction\tR-HSA-6802942\tinput\toutput\n P12931\tQ7Z5R6\tReaction\tR-HSA-6802942\tinput\tinput\n@@ -8436,8 +8436,8 @@\n P12931\tP32121\tReaction\tR-HSA-6802942\toutput\toutput\n P12931\tP30086\tReaction\tR-HSA-6802942\toutput\tregulator\n P12931\tP15056\tReaction\tR-HSA-6802942\toutput\tinput\n+P12931\tP15056\tReaction\tR-HSA-6802942\toutput\toutput\n P12931\tP15056\tReaction\tR-HSA-6802942\toutput\tregulator\n-P12931\tP15056\tReaction\tR-HSA-6802942\toutput\toutput\n P12931\tP62834\tReaction\tR-HSA-6802942\toutput\tinput\n P12931\tP62834\tReaction\tR-HSA-6802942\toutput\toutput\n P12931\tP46940\tReaction\tR-HSA-6802942\toutput\tinput\n@@ -8449,11 +8449,11 @@\n P12931\tQ9Y490\tReaction\tR-HSA-6802942\toutput\tinput\n P12931\tQ9Y490\tReaction\tR-HSA-6802942\toutput\toutput\n P12931\tP31946\tReaction\tR-HSA-6802942\toutput\tinput\n+P12931\tP31946\tReaction\tR-HSA-6802942\toutput\toutput\n P12931\tP31946\tReaction\tR-HSA-6802942\toutput\tregulator\n-P12931\tP31946\tReaction\tR-HSA-6802942\toutput\toutput\n P12931\tQ8IVT5\tReaction\tR-HSA-6802942\toutput\tinput\n+P12931\tQ8IVT5\tReaction\tR-HSA-6802942\toutput\toutput\n P12931\tQ8IVT5\tReaction\tR-HSA-6802942\toutput\tregulator\n-P12931\tQ8IVT5\tReaction\tR-HSA-6802942\toutput\toutput\n P12931\tQ02750\tReaction\tR-HSA-6802942\toutput\tinput\n P12931\tQ02750\tReaction\tR-HSA-6802942\toutput\toutput\n P12931\tQ7Z5R6\tReaction\tR-HSA-6802942\toutput\tinput\n@@ -8472,58 +8472,58 @@\n P10398\tP27361\tReaction\tR-HSA-6802942\tregulator\toutput\n P15056\tP27361\tReaction\tR-HSA-6802942\tinput\tinput\n P15056\tP27361\tReaction\tR-HSA-6802942\tinput\toutput\n+P15056\tP27361\tReaction\tR-HSA-6802942\toutput\tinput\n+P15056\tP27361\tReaction\tR-HSA-6802942\toutput\toutput\n P15056\tP27361\tReaction\tR-HSA-6802942\tregulator\tinput\n P15056\tP27361\tReaction\tR-HSA-6802942\tregulator\toutput\n-P15056\tP27361\tReaction\tR-HSA-6802942\toutput\tinput\n-P15056\tP27361\tReaction\tR-HSA-6802942\toutput\toutput\n P01116\tP12931\tReaction\tR-HSA-6802942\tinput\tinput\n P01116\tP12931\tReaction\tR-HSA-6802942\tinput\toutput\n P01116\tP27361\tReaction\tR-HSA-6802942\tinput\tinput\n P01116\tP27361\tReaction\tR-HSA-6802942\tinput\toutput\n+P01116\tP12931\tReaction\tR-HSA-6802942\toutput\tinput\n+P01116\tP12931\tReaction\tR-HSA-6802942\toutput\toutput\n+P01116\tP27361\tReaction\tR-HSA-6802942\toutput\tinput\n+P01116\tP27361\tReaction\tR-HSA-6802942\toutput\toutput\n P01116\tP12931\tReaction\tR-HSA-6802942\tregulator\tinput\n P01116\tP12931\tReaction\tR-HSA-6802942\tregulator\toutput\n P01116\tP27361\tReaction\tR-HSA-6802942\tregulator\tinput\n P01116\tP27361\tReaction\tR-HSA-6802942\tregulator\toutput\n-P01116\tP12931\tReaction\tR-HSA-6802942\toutput\tinput\n-P01116\tP12931\tReaction\tR-HSA-6802942\toutput\toutput\n-P01116\tP27361\tReaction\tR-HSA-6802942\toutput\tinput\n-P01116\tP27361\tReaction\tR-HSA-6802942\toutput\toutput\n P01112\tP12931\tReaction\tR-HSA-6802942\tinput\tinput\n P01112\tP12931\tReaction\tR-HSA-6802942\tinput\toutput\n P01112\tP27361\tReaction\tR-HSA-6802942\tinput\tinput\n P01112\tP27361\tReaction\tR-HSA-6802942\tinput\toutput\n+P01112\tP12931\tReaction\tR-HSA-6802942\toutput\tinput\n+P01112\tP12931\tReaction\tR-HSA-6802942\toutput\toutput\n+'..b'3\tReaction\tR-HSA-1112602\tinput\toutput\n P40189\tP40763\tReaction\tR-HSA-1112602\tinput\tcatalyst\n@@ -33424,9 +33421,9 @@\n P40189\tP40763\tReaction\tR-HSA-1112602\tcatalyst\tinput\n P40189\tP40763\tReaction\tR-HSA-1112602\tcatalyst\toutput\n P40189\tP40763\tReaction\tR-HSA-1112602\tcatalyst\tcatalyst\n-O60674\tP40763\tReaction\tR-HSA-1112602\toutput\tinput\n-O60674\tP40763\tReaction\tR-HSA-1112602\toutput\toutput\n-O60674\tP40763\tReaction\tR-HSA-1112602\toutput\tcatalyst\n+P40189\tP40763\tReaction\tR-HSA-1112602\toutput\tinput\n+P40189\tP40763\tReaction\tR-HSA-1112602\toutput\toutput\n+P40189\tP40763\tReaction\tR-HSA-1112602\toutput\tcatalyst\n O60674\tP40763\tReaction\tR-HSA-1112602\tinput\tinput\n O60674\tP40763\tReaction\tR-HSA-1112602\tinput\toutput\n O60674\tP40763\tReaction\tR-HSA-1112602\tinput\tcatalyst\n@@ -33436,9 +33433,9 @@\n O60674\tP40763\tReaction\tR-HSA-1112602\tcatalyst\tinput\n O60674\tP40763\tReaction\tR-HSA-1112602\tcatalyst\toutput\n O60674\tP40763\tReaction\tR-HSA-1112602\tcatalyst\tcatalyst\n-P23458\tP40763\tReaction\tR-HSA-1112602\toutput\tinput\n-P23458\tP40763\tReaction\tR-HSA-1112602\toutput\toutput\n-P23458\tP40763\tReaction\tR-HSA-1112602\toutput\tcatalyst\n+O60674\tP40763\tReaction\tR-HSA-1112602\toutput\tinput\n+O60674\tP40763\tReaction\tR-HSA-1112602\toutput\toutput\n+O60674\tP40763\tReaction\tR-HSA-1112602\toutput\tcatalyst\n P23458\tP40763\tReaction\tR-HSA-1112602\tinput\tinput\n P23458\tP40763\tReaction\tR-HSA-1112602\tinput\toutput\n P23458\tP40763\tReaction\tR-HSA-1112602\tinput\tcatalyst\n@@ -33448,12 +33445,12 @@\n P23458\tP40763\tReaction\tR-HSA-1112602\tcatalyst\tinput\n P23458\tP40763\tReaction\tR-HSA-1112602\tcatalyst\toutput\n P23458\tP40763\tReaction\tR-HSA-1112602\tcatalyst\tcatalyst\n+P23458\tP40763\tReaction\tR-HSA-1112602\toutput\tinput\n+P23458\tP40763\tReaction\tR-HSA-1112602\toutput\toutput\n+P23458\tP40763\tReaction\tR-HSA-1112602\toutput\tcatalyst\n O14543\tP40763\tReaction\tR-HSA-1112602\tregulator\tinput\n O14543\tP40763\tReaction\tR-HSA-1112602\tregulator\toutput\n O14543\tP40763\tReaction\tR-HSA-1112602\tregulator\tcatalyst\n-P05231\tP40763\tReaction\tR-HSA-1112602\toutput\tinput\n-P05231\tP40763\tReaction\tR-HSA-1112602\toutput\toutput\n-P05231\tP40763\tReaction\tR-HSA-1112602\toutput\tcatalyst\n P05231\tP40763\tReaction\tR-HSA-1112602\tinput\tinput\n P05231\tP40763\tReaction\tR-HSA-1112602\tinput\toutput\n P05231\tP40763\tReaction\tR-HSA-1112602\tinput\tcatalyst\n@@ -33463,9 +33460,9 @@\n P05231\tP40763\tReaction\tR-HSA-1112602\tcatalyst\tinput\n P05231\tP40763\tReaction\tR-HSA-1112602\tcatalyst\toutput\n P05231\tP40763\tReaction\tR-HSA-1112602\tcatalyst\tcatalyst\n-P08887\tP40763\tReaction\tR-HSA-1112602\toutput\tinput\n-P08887\tP40763\tReaction\tR-HSA-1112602\toutput\toutput\n-P08887\tP40763\tReaction\tR-HSA-1112602\toutput\tcatalyst\n+P05231\tP40763\tReaction\tR-HSA-1112602\toutput\tinput\n+P05231\tP40763\tReaction\tR-HSA-1112602\toutput\toutput\n+P05231\tP40763\tReaction\tR-HSA-1112602\toutput\tcatalyst\n P08887\tP40763\tReaction\tR-HSA-1112602\tinput\tinput\n P08887\tP40763\tReaction\tR-HSA-1112602\tinput\toutput\n P08887\tP40763\tReaction\tR-HSA-1112602\tinput\tcatalyst\n@@ -33475,6 +33472,9 @@\n P08887\tP40763\tReaction\tR-HSA-1112602\tcatalyst\tinput\n P08887\tP40763\tReaction\tR-HSA-1112602\tcatalyst\toutput\n P08887\tP40763\tReaction\tR-HSA-1112602\tcatalyst\tcatalyst\n+P08887\tP40763\tReaction\tR-HSA-1112602\toutput\tinput\n+P08887\tP40763\tReaction\tR-HSA-1112602\toutput\toutput\n+P08887\tP40763\tReaction\tR-HSA-1112602\toutput\tcatalyst\n P40763\tP42224\tReaction\tR-HSA-1112602\tinput\tinput\n P40763\tP42224\tReaction\tR-HSA-1112602\tinput\toutput\n P40763\tP42224\tReaction\tR-HSA-1112602\tinput\tcatalyst\n@@ -44583,10 +44583,10 @@\n P55884\tP62753\tReaction\tR-HSA-72619\toutput\toutput\n P55010\tP62753\tReaction\tR-HSA-72619\tinput\tinput\n P55010\tP62753\tReaction\tR-HSA-72619\tinput\toutput\n+P55010\tP62753\tReaction\tR-HSA-72619\toutput\tinput\n+P55010\tP62753\tReaction\tR-HSA-72619\toutput\toutput\n P55010\tP62753\tReaction\tR-HSA-72619\tregulator\tinput\n P55010\tP62753\tReaction\tR-HSA-72619\tregulator\toutput\n-P55010\tP62753\tReaction\tR-HSA-72619\toutput\tinput\n-P55010\tP62753\tReaction\tR-HSA-72619\toutput\toutput\n P61247\tP62753\tReaction\tR-HSA-72619\tinput\tinput\n P61247\tP62753\tReaction\tR-HSA-72619\tinput\toutput\n P61247\tP62753\tReaction\tR-HSA-72619\toutput\tinput\n' |
| b |
| diff -r f66af2b04a98 -r 5d0c44bc354d test-data/proteoforms_graphs/proteoformExternalEdges.tsv --- a/test-data/proteoforms_graphs/proteoformExternalEdges.tsv Wed Jun 20 14:21:10 2018 -0400 +++ b/test-data/proteoforms_graphs/proteoformExternalEdges.tsv Wed Jul 04 04:28:07 2018 -0400 |
| b |
| b'@@ -1,1 +1,26209 @@\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;\t'..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 f66af2b04a98 -r 5d0c44bc354d test-data/proteoforms_graphs/proteoformInternalEdges.tsv --- a/test-data/proteoforms_graphs/proteoformInternalEdges.tsv Wed Jun 20 14:21:10 2018 -0400 +++ b/test-data/proteoforms_graphs/proteoformInternalEdges.tsv Wed Jul 04 04:28:07 2018 -0400 |
| b |
| @@ -1,1 +1,79 @@ 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 |
| b |
| diff -r f66af2b04a98 -r 5d0c44bc354d test-data/proteoforms_graphs/proteoformVertices.tsv --- a/test-data/proteoforms_graphs/proteoformVertices.tsv Wed Jun 20 14:21:10 2018 -0400 +++ b/test-data/proteoforms_graphs/proteoformVertices.tsv Wed Jul 04 04:28:07 2018 -0400 |
| b |
| @@ -1,1 +1,21 @@ 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 +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 |