| Previous changeset 15:cb4dce1042ef (2016-06-02) Next changeset 17:96c070110fff (2016-06-04) |
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Commit message:
Uploaded |
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modified:
vgx_converter.py vgx_converter.xml |
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added:
test-data/._Apoptosis.sif test-data/Apoptosis.jgf test-data/Apoptosis.sif test-data/CoVennTree.jgf test-data/CoVennTree_attributes.venn test-data/CoVennTree_network.sif |
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removed:
test-data/angiogenesis_network.sif test-data/angiogenesis_nodelink.json test-data/cvt_attributes.venn test-data/cvt_network.sif test-data/cvt_nodelink.json |
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| diff -r cb4dce1042ef -r 567274fa974d test-data/._Apoptosis.sif |
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| Binary file test-data/._Apoptosis.sif has changed |
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| diff -r cb4dce1042ef -r 567274fa974d test-data/Apoptosis.jgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Apoptosis.jgf Sat Jun 04 03:22:52 2016 -0400 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"graph": {"nodes": [{"id": "0", "label": "p(HGNC:FOXO3,pmod(P,S,253))"}, {"id": "1", "label": "tscript(p(HGNC:FOXO3))"}, {"id": "2", "label": "p(HGNC:FLOT2)"}, {"id": "3", "label": "p(HGNC:FAS)"}, {"id": "4", "label": "p(HGNC:XIAP)"}, {"id": "5", "label": "p(HGNC:BIRC5)"}, {"id": "6", "label": "cat(p(HGNC:CASP8))"}, {"id": "7", "label": "cat(p(HGNC:CASP3))"}, {"id": "8", "label": "p(HGNC:PDGFA)"}, {"id": "9", "label": "p(HGNC:IL6)"}, {"id": "10", "label": "p(HGNC:BAX)"}, {"id": "11", "label": "p(HGNC:STAT3)"}, {"id": "12", "label": "p(HGNC:SIRT1)"}, {"id": "13", "label": "p(HGNC:RELA,pmod(A))"}, {"id": "14", "label": "p(HGNC:PARP1)"}, {"id": "15", "label": "p(HGNC:XRCC6)"}, {"id": "16", "label": "cat(p(HGNC:BAX))"}, {"id": "17", "label": "cat(p(HGNC:CASP7))"}, {"id": "18", "label": "p(SFAM:FOXO Family)"}, {"id": "19", "label": "tscript(p(SFAM:FOXO Family))"}, {"id": "20", "label": "cat(p(HGNC:CASP10))"}, {"id": "21", "label": "p(HGNC:FOXO1,pmod(P,S,256))"}, {"id": "22", "label": "tscript(p(HGNC:FOXO1))"}, {"id": "23", "label": "complex(p(HGNC:APAF1),p(HGNC:CYCS),p(HGNC:CASP9))"}, {"id": "24", "label": "p(HGNC:CYCS)"}, {"id": "25", "label": "p(HGNC:APAF1)"}, {"id": "26", "label": "p(HGNC:CASP9)"}, {"id": "27", "label": "cat(p(HGNC:CASP9))"}, {"id": "28", "label": "p(SFAM:PRKA Family)"}, {"id": "29", "label": "kin(p(SFAM:PRKA Family))"}, {"id": "30", "label": "p(HGNC:MARCKS)"}, {"id": "31", "label": "p(HGNC:MARCKS,pmod(P,S,163))"}, {"id": "32", "label": "tscript(complex(SCOMP:Nfkb Complex))"}, {"id": "33", "label": "p(HGNC:BCL2)"}, {"id": "34", "label": "p(HGNC:BIRC2)"}, {"id": "35", "label": "p(HGNC:BIRC3)"}, {"id": "36", "label": "p(HGNC:BCL2L1)"}, {"id": "37", "label": "p(HGNC:CFLAR)"}, {"id": "38", "label": "p(HGNC:BCL2A1)"}, {"id": "39", "label": "tscript(p(HGNC:XBP1))"}, {"id": "40", "label": "bp(GOBP:ER-associated ubiquitin-dependent protein catabolic process)"}, {"id": "41", "label": "cat(p(HGNC:FAS))"}, {"id": "42", "label": "kin(p(HGNC:PRKCA))"}, {"id": "43", "label": "p(HGNC:PRKD1,pmod(P,S,742))"}, {"id": "44", "label": "p(HGNC:PRKCA,pmod(P,T,638))"}, {"id": "45", "label": "p(HGNC:PRKD1,pmod(P,S,738))"}, {"id": "46", "label": "p(HGNC:MARCKS,pmod(P,S,159))"}, {"id": "47", "label": "cat(p(HGNC:ERN1))"}, {"id": "48", "label": "p(HGNC:XBP1)"}, {"id": "49", "label": "p(HGNC:PRKCD)"}, {"id": "50", "label": "kin(p(HGNC:PRKCD))"}, {"id": "51", "label": "p(HGNC:MAP2K7)"}, {"id": "52", "label": "kin(p(HGNC:MAP2K7))"}, {"id": "53", "label": "p(HGNC:MAPK1)"}, {"id": "54", "label": "kin(p(HGNC:MAPK1))"}, {"id": "55", "label": "cat(p(HGNC:BCL2))"}, {"id": "56", "label": "cat(p(HGNC:ACIN1))"}, {"id": "57", "label": "kin(p(HGNC:ROCK1))"}, {"id": "58", "label": "deg(p(HGNC:LMNB2))"}, {"id": "59", "label": "bp(MESHPP:Apoptosis)"}, {"id": "60", "label": "cat(p(HGNC:GAS2))"}, {"id": "61", "label": "deg(p(HGNC:LMNA))"}, {"id": "62", "label": "cat(p(HGNC:DFFA))"}, {"id": "63", "label": "kin(p(HGNC:BMX))"}, {"id": "64", "label": "cat(p(HGNC:CASP2))"}, {"id": "65", "label": "deg(p(HGNC:LMNB1))"}, {"id": "66", "label": "cat(p(HGNC:BCL2L1))"}, {"id": "67", "label": "path(MESHD:Emphysema)"}, {"id": "68", "label": "kin(p(HGNC:PAK2))"}, {"id": "69", "label": "p(HGNC:IKBKB)"}, {"id": "70", "label": "p(HGNC:IKBKB,pmod(P,S,177))"}, {"id": "71", "label": "cat(p(HGNC:TNFRSF10B))"}, {"id": "72", "label": "cat(p(HGNC:TRAF2))"}, {"id": "73", "label": "p(HGNC:MAP3K7)"}, {"id": "74", "label": "p(HGNC:MAP3K7,pmod(U,K,158))"}, {"id": "75", "label": "p(HGNC:ACIN1)"}, {"id": "76", "label": "cat(p(HGNC:XIAP))"}, {"id": "77", "label": "p(HGNC:NFKBIA,pmod(P,S,36))"}, {"id": "78", "label": "deg(p(HGNC:NFKBIA))"}, {"id": "79", "label": "kin(p(HGNC:CHUK))"}, {"id": "80", "label": "p(HGNC:NFKBIE)"}, {"id": "81", "label": "complex(p(HGNC:RIPK1),p(HGNC:TNFRSF10A))"}, {"id": "82", "label": "p(HGNC:TNFRSF10A)"}, {"id": "83", "label": "p(HGNC:RIPK1)"}, {"id": "84", "label": "p(HGNC:PPP1R15A)"}, {"id": "85", "label": "bp(GOBP:cell death)"}, {"id": "86", '..b' {"source": 243, "target": 188}, {"source": 244, "target": 167}, {"source": 244, "target": 82}, {"source": 244, "target": 86}, {"source": 244, "target": 106}, {"source": 244, "target": 196}, {"source": 36, "target": 66}, {"source": 36, "target": 59}, {"source": 80, "target": 32}, {"source": 83, "target": 200}, {"source": 90, "target": 245}, {"source": 82, "target": 162}, {"source": 82, "target": 59}, {"source": 246, "target": 101}, {"source": 168, "target": 6}, {"source": 14, "target": 59}, {"source": 92, "target": 134}, {"source": 155, "target": 92}, {"source": 92, "target": 243}, {"source": 92, "target": 229}, {"source": 247, "target": 92}, {"source": 92, "target": 224}, {"source": 92, "target": 248}, {"source": 92, "target": 19}, {"source": 92, "target": 21}, {"source": 245, "target": 92}, {"source": 92, "target": 156}, {"source": 204, "target": 110}, {"source": 41, "target": 154}, {"source": 107, "target": 59}, {"source": 107, "target": 52}, {"source": 22, "target": 152}, {"source": 127, "target": 150}, {"source": 127, "target": 176}, {"source": 127, "target": 47}, {"source": 139, "target": 89}, {"source": 48, "target": 39}, {"source": 91, "target": 245}, {"source": 37, "target": 59}, {"source": 37, "target": 6}, {"source": 188, "target": 236}, {"source": 249, "target": 184}, {"source": 184, "target": 192}, {"source": 250, "target": 184}, {"source": 184, "target": 16}, {"source": 251, "target": 184}, {"source": 145, "target": 153}, {"source": 252, "target": 253}, {"source": 172, "target": 254}, {"source": 228, "target": 16}, {"source": 228, "target": 103}, {"source": 228, "target": 59}, {"source": 58, "target": 255}, {"source": 58, "target": 59}, {"source": 219, "target": 41}, {"source": 256, "target": 92}, {"source": 257, "target": 256}, {"source": 258, "target": 256}, {"source": 259, "target": 256}, {"source": 248, "target": 107}, {"source": 253, "target": 179}, {"source": 239, "target": 260}, {"source": 239, "target": 211}, {"source": 239, "target": 10}, {"source": 239, "target": 152}, {"source": 261, "target": 22}, {"source": 242, "target": 103}, {"source": 242, "target": 16}, {"source": 206, "target": 151}, {"source": 52, "target": 184}, {"source": 76, "target": 7}, {"source": 76, "target": 27}, {"source": 76, "target": 17}, {"source": 225, "target": 184}, {"source": 225, "target": 250}, {"source": 225, "target": 249}, {"source": 93, "target": 122}, {"source": 234, "target": 59}, {"source": 56, "target": 59}, {"source": 262, "target": 236}, {"source": 182, "target": 113}, {"source": 263, "target": 57}, {"source": 264, "target": 42}, {"source": 264, "target": 50}, {"source": 264, "target": 125}, {"source": 264, "target": 113}, {"source": 141, "target": 32}, {"source": 240, "target": 107}, {"source": 265, "target": 168}, {"source": 211, "target": 131}, {"source": 211, "target": 59}, {"source": 116, "target": 266}, {"source": 162, "target": 72}, {"source": 62, "target": 253}, {"source": 267, "target": 266}, {"source": 136, "target": 76}, {"source": 73, "target": 108}, {"source": 30, "target": 46}, {"source": 230, "target": 178}, {"source": 164, "target": 111}, {"source": 268, "target": 164}, {"source": 222, "target": 78}, {"source": 269, "target": 17}, {"source": 78, "target": 140}, {"source": 270, "target": 121}, {"source": 271, "target": 225}, {"source": 272, "target": 225}, {"source": 59, "target": 235}, {"source": 59, "target": 273}, {"source": 274, "target": 59}, {"source": 275, "target": 59}, {"source": 275, "target": 67}, {"source": 276, "target": 277}, {"source": 276, "target": 59}, {"source": 277, "target": 59}, {"source": 278, "target": 159}, {"source": 278, "target": 59}, {"source": 159, "target": 176}, {"source": 176, "target": 197}, {"source": 279, "target": 59}, {"source": 132, "target": 59}, {"source": 2, "target": 102}, {"source": 280, "target": 59}, {"source": 184, "target": 59}, {"source": 125, "target": 59}, {"source": 281, "target": 184}, {"source": 168, "target": 154}]}}\n\\ No newline at end of file\n' |
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| diff -r cb4dce1042ef -r 567274fa974d test-data/Apoptosis.sif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Apoptosis.sif Sat Jun 04 03:22:52 2016 -0400 |
| b |
| b'@@ -0,0 +1,444 @@\n+p(HGNC:FOXO3,pmod(P,S,253))\tdirectlyDecreases\ttscript(p(HGNC:FOXO3))\r\n+p(HGNC:FLOT2)\tdecreases\tp(HGNC:FAS)\r\n+p(HGNC:FLOT2)\tincreases\tp(HGNC:XIAP)\r\n+p(HGNC:FLOT2)\tincreases\tp(HGNC:BIRC5)\r\n+p(HGNC:FLOT2)\tdecreases\tcat(p(HGNC:CASP8))\r\n+p(HGNC:FLOT2)\tdecreases\tcat(p(HGNC:CASP3))\r\n+p(HGNC:PDGFA)\tincreases\tp(HGNC:FOXO3,pmod(P,S,253))\r\n+p(HGNC:IL6)\tincreases\tp(HGNC:BAX)\r\n+p(HGNC:IL6)\tincreases\tp(HGNC:STAT3)\r\n+p(HGNC:SIRT1)\tincreases\tp(HGNC:RELA,pmod(A))\r\n+p(HGNC:SIRT1)\tassociation\tp(HGNC:PARP1)\r\n+p(HGNC:XRCC6)\tdecreases\tcat(p(HGNC:BAX))\r\n+p(HGNC:STAT3)\tdecreases\tcat(p(HGNC:CASP7))\r\n+p(HGNC:STAT3)\tdecreases\tcat(p(HGNC:CASP3))\r\n+p(SFAM:"FOXO Family")\tactsIn\ttscript(p(SFAM:"FOXO Family"))\r\n+cat(p(HGNC:CASP10))\tincreases\tcat(p(HGNC:CASP3))\r\n+p(HGNC:FOXO1,pmod(P,S,256))\tdirectlyDecreases\ttscript(p(HGNC:FOXO1))\r\n+complex(p(HGNC:APAF1),p(HGNC:CYCS),p(HGNC:CASP9))\thasComponent\tp(HGNC:CYCS)\r\n+complex(p(HGNC:APAF1),p(HGNC:CYCS),p(HGNC:CASP9))\thasComponent\tp(HGNC:APAF1)\r\n+complex(p(HGNC:APAF1),p(HGNC:CYCS),p(HGNC:CASP9))\thasComponent\tp(HGNC:CASP9)\r\n+complex(p(HGNC:APAF1),p(HGNC:CYCS),p(HGNC:CASP9))\tincreases\tcat(p(HGNC:CASP9))\r\n+p(SFAM:"PRKA Family")\tactsIn\tkin(p(SFAM:"PRKA Family"))\r\n+p(HGNC:MARCKS)\thasModification\tp(HGNC:MARCKS,pmod(P,S,163))\r\n+cat(p(HGNC:CASP7))\tdirectlyDecreases\tp(HGNC:PARP1)\r\n+tscript(complex(SCOMP:"Nfkb Complex"))\tdirectlyIncreases\tp(HGNC:BCL2)\r\n+tscript(complex(SCOMP:"Nfkb Complex"))\tincreases\tp(HGNC:BIRC2)\r\n+tscript(complex(SCOMP:"Nfkb Complex"))\tincreases\tp(HGNC:BIRC3)\r\n+tscript(complex(SCOMP:"Nfkb Complex"))\tdirectlyIncreases\tp(HGNC:BCL2L1)\r\n+tscript(complex(SCOMP:"Nfkb Complex"))\tdirectlyIncreases\tp(HGNC:XIAP)\r\n+tscript(complex(SCOMP:"Nfkb Complex"))\tincreases\tp(HGNC:CFLAR)\r\n+tscript(complex(SCOMP:"Nfkb Complex"))\tincreases\tp(HGNC:BCL2A1)\r\n+tscript(complex(SCOMP:"Nfkb Complex"))\tincreases\tp(HGNC:BIRC5)\r\n+tscript(p(HGNC:XBP1))\tincreases\tbp(GOBP:"ER-associated ubiquitin-dependent protein catabolic process")\r\n+p(HGNC:FAS)\tactsIn\tcat(p(HGNC:FAS))\r\n+kin(p(HGNC:PRKCA))\tdirectlyIncreases\tp(HGNC:PRKD1,pmod(P,S,742))\r\n+kin(p(HGNC:PRKCA))\tdirectlyIncreases\tp(HGNC:PRKCA,pmod(P,T,638))\r\n+kin(p(HGNC:PRKCA))\tdirectlyIncreases\tp(HGNC:PRKD1,pmod(P,S,738))\r\n+kin(p(HGNC:PRKCA))\tdirectlyIncreases\tp(HGNC:MARCKS,pmod(P,S,159))\r\n+cat(p(HGNC:ERN1))\tdirectlyIncreases\tp(HGNC:XBP1)\r\n+p(HGNC:PRKCD)\tactsIn\tkin(p(HGNC:PRKCD))\r\n+p(HGNC:MAP2K7)\tactsIn\tkin(p(HGNC:MAP2K7))\r\n+p(HGNC:MAPK1)\tactsIn\tkin(p(HGNC:MAPK1))\r\n+cat(p(HGNC:CASP3))\tdirectlyDecreases\tcat(p(HGNC:BCL2))\r\n+cat(p(HGNC:CASP3))\tdirectlyIncreases\tcat(p(HGNC:ACIN1))\r\n+cat(p(HGNC:CASP3))\tincreases\tkin(p(HGNC:ROCK1))\r\n+cat(p(HGNC:CASP3))\tdirectlyIncreases\tdeg(p(HGNC:LMNB2))\r\n+cat(p(HGNC:CASP3))\tincreases\tbp(MESHPP:Apoptosis)\r\n+cat(p(HGNC:CASP3))\tincreases\tcat(p(HGNC:CASP7))\r\n+cat(p(HGNC:CASP3))\tdirectlyIncreases\tcat(p(HGNC:GAS2))\r\n+cat(p(HGNC:CASP3))\tincreases\tdeg(p(HGNC:LMNA))\r\n+cat(p(HGNC:CASP3))\tdirectlyDecreases\tcat(p(HGNC:DFFA))\r\n+cat(p(HGNC:CASP3))\tdirectlyIncreases\tkin(p(HGNC:BMX))\r\n+cat(p(HGNC:CASP3))\tdirectlyIncreases\tcat(p(HGNC:CASP2))\r\n+cat(p(HGNC:CASP3))\tdirectlyIncreases\tdeg(p(HGNC:LMNB1))\r\n+cat(p(HGNC:CASP3))\tdirectlyDecreases\tcat(p(HGNC:BCL2L1))\r\n+cat(p(HGNC:CASP3))\tincreases\tpath(MESHD:Emphysema)\r\n+cat(p(HGNC:CASP3))\tdirectlyIncreases\tkin(p(HGNC:PAK2))\r\n+cat(p(HGNC:CASP3))\tdecreases\tp(HGNC:PARP1)\r\n+p(HGNC:IKBKB)\thasModification\tp(HGNC:IKBKB,pmod(P,S,177))\r\n+cat(p(HGNC:TNFRSF10B))\tincreases\tcat(p(HGNC:TRAF2))\r\n+p(HGNC:MAP3K7)\thasModification\tp(HGNC:MAP3K7,pmod(U,K,158))\r\n+p(HGNC:ACIN1)\tactsIn\tcat(p(HGNC:ACIN1))\r\n+p(HGNC:XIAP)\tdecreases\tbp(MESHPP:Apoptosis)\r\n+p(HGNC:XIAP)\tactsIn\tcat(p(HGNC:XIAP))\r\n+p(HGNC:NFKBIA,pmod(P,S,36))\tdirectlyIncreases\tdeg(p(HGNC:NFKBIA))\r\n+kin(p(HGNC:CHUK))\tdecreases\tp(HGNC:NFKBIE)\r\n+complex(p(HGNC:RIPK1),p(HGNC:TNFRSF10A))\thasComponent\tp(HGNC:TNFRSF10A)\r\n+complex(p(HGNC:RIPK1),p(HGNC:TNFRSF10A))\thasComponent\tp(HGNC:RIPK1)\r\n+p(HGNC:PPP1R15A)\tincreases\tbp(GOBP:"cell death")\r\n+p(HGNC:TNFRSF10B)\tactsIn\tcat(p(HGNC:TNFRSF10B))\r\n+complex'..b'ESHPP:Apoptosis)\r\n+deg(p(HGNC:LMNB2))\tdirectlyDecreases\tp(HGNC:LMNB2)\r\n+deg(p(HGNC:LMNB2))\tincreases\tbp(MESHPP:Apoptosis)\r\n+p(HGNC:FASLG)\tdirectlyIncreases\tcat(p(HGNC:FAS))\r\n+p(SFAM:"AKT Family")\tactsIn\tkin(p(SFAM:"AKT Family"))\r\n+p(HGNC:AKT3)\tisA\tp(SFAM:"AKT Family")\r\n+p(HGNC:AKT1)\tisA\tp(SFAM:"AKT Family")\r\n+p(HGNC:AKT2)\tisA\tp(SFAM:"AKT Family")\r\n+p(HGNC:MAP3K5,pmod(P,S,83))\tdirectlyDecreases\tkin(p(HGNC:MAP3K5))\r\n+cat(p(HGNC:DFFB))\tincreases\tbp(MESHPP:"DNA Fragmentation")\r\n+p(HGNC:DDIT3)\tactsIn\ttscript(p(HGNC:DDIT3))\r\n+p(HGNC:DDIT3)\tincreases\tp(HGNC:BBC3)\r\n+p(HGNC:DDIT3)\tincreases\tp(HGNC:BAX)\r\n+p(HGNC:DDIT3)\tincreases\tp(HGNC:BCL2L11)\r\n+p(HGNC:FOXO1)\tactsIn\ttscript(p(HGNC:FOXO1))\r\n+cat(p(HGNC:PMAIP1))\tincreases\tcat(p(HGNC:BAK1))\r\n+cat(p(HGNC:PMAIP1))\tincreases\tcat(p(HGNC:BAX))\r\n+p(HGNC:CASP6)\tactsIn\tcat(p(HGNC:CASP6))\r\n+kin(p(HGNC:MAP2K7))\tdirectlyIncreases\tkin(p(SFAM:"MAPK JNK Family"))\r\n+cat(p(HGNC:XIAP))\tdecreases\tcat(p(HGNC:CASP3))\r\n+cat(p(HGNC:XIAP))\tdecreases\tcat(p(HGNC:CASP9))\r\n+cat(p(HGNC:XIAP))\tdecreases\tcat(p(HGNC:CASP7))\r\n+gtp(p(HGNC:RAC1))\tincreases\tkin(p(SFAM:"MAPK JNK Family"))\r\n+gtp(p(HGNC:RAC1))\tincreases\tkin(p(HGNC:MAPK10))\r\n+gtp(p(HGNC:RAC1))\tdirectlyIncreases\tkin(p(HGNC:MAPK8))\r\n+a(SCHEM:"Phosphatidylinositol-3,4,5-trisphosphate")\tdirectlyIncreases\tkin(p(HGNC:PDPK1))\r\n+cat(p(HGNC:CASP4))\tincreases\tbp(MESHPP:Apoptosis)\r\n+cat(p(HGNC:ACIN1))\tincreases\tbp(MESHPP:Apoptosis)\r\n+p(HGNC:ELK1)\tactsIn\ttscript(p(HGNC:ELK1))\r\n+p(HGNC:PRKCE)\tactsIn\tkin(p(HGNC:PRKCE))\r\n+p(HGNC:ROCK1)\tactsIn\tkin(p(HGNC:ROCK1))\r\n+a(SCHEM:Calcium)\tincreases\tkin(p(HGNC:PRKCA))\r\n+a(SCHEM:Calcium)\tincreases\tkin(p(HGNC:PRKCD))\r\n+a(SCHEM:Calcium)\tdirectlyIncreases\tkin(p(SFAM:"PRKC Family"))\r\n+a(SCHEM:Calcium)\tincreases\tkin(p(HGNC:PRKCE))\r\n+kin(p(HGNC:NFKBIA))\tdecreases\ttscript(complex(SCOMP:"Nfkb Complex"))\r\n+kin(p(HGNC:PRKD1))\tdirectlyIncreases\tkin(p(HGNC:MAP3K5))\r\n+p(HGNC:TRADD)\tactsIn\tcat(p(HGNC:TRADD))\r\n+p(HGNC:BBC3)\tactsIn\tcat(p(HGNC:BBC3))\r\n+p(HGNC:BBC3)\tincreases\tbp(MESHPP:Apoptosis)\r\n+kin(p(HGNC:RPS6KA1))\tisA\tkin(p(SFAM:"RPS6KA Family"))\r\n+cat(p(HGNC:TNFRSF10A))\tincreases\tcat(p(HGNC:TRAF2))\r\n+cat(p(HGNC:DFFA))\tdecreases\tcat(p(HGNC:DFFB))\r\n+p(SFAM:"RPS6KA Family")\tactsIn\tkin(p(SFAM:"RPS6KA Family"))\r\n+cat(p(HGNC:HTRA2))\tdirectlyDecreases\tcat(p(HGNC:XIAP))\r\n+p(HGNC:MAP3K7)\tactsIn\tkin(p(HGNC:MAP3K7))\r\n+p(HGNC:MARCKS)\thasModification\tp(HGNC:MARCKS,pmod(P,S,159))\r\n+p(HGNC:CREB1,pmod(P,S,133))\tdirectlyIncreases\ttscript(p(HGNC:CREB1))\r\n+p(HGNC:EIF2S1,pmod(P,S,52))\tincreases\tp(HGNC:ATF4)\r\n+p(HGNC:EIF2S1)\thasModification\tp(HGNC:EIF2S1,pmod(P,S,52))\r\n+p(HGNC:NFKBIA,pmod(P,S,32))\tdirectlyIncreases\tdeg(p(HGNC:NFKBIA))\r\n+p(HGNC:CASP7)\tactsIn\tcat(p(HGNC:CASP7))\r\n+deg(p(HGNC:NFKBIA))\tdirectlyDecreases\tp(HGNC:NFKBIA)\r\n+p(HGNC:PDPK1,pmod(P,S,241))\tincreases\tp(HGNC:PDPK1)\r\n+p(HGNC:CXCL12)\tincreases\tgtp(p(HGNC:RAC1))\r\n+p(CXCL12)\tincreases\tgtp(p(HGNC:RAC1))\r\n+bp(MESHPP:Apoptosis)\tpositiveCorrelation\tp(HGNC:TLR4)\r\n+bp(MESHPP:Apoptosis)\tnegativeCorrelation\tp(HGNC:GSTP1)\r\n+p(HGNC:MAP1LC3B)\tincreases\tbp(MESHPP:Apoptosis)\r\n+p(HGNC:KDR)\tdecreases\tbp(MESHPP:Apoptosis)\r\n+p(HGNC:KDR)\tdecreases\tpath(MESHD:Emphysema)\r\n+bp(MESHPP:"DNA Methylation")\tassociation\tpath(MESHD:"Pulmonary Disease, Chronic Obstructive")\r\n+bp(MESHPP:"DNA Methylation")\tassociation\tbp(MESHPP:Apoptosis)\r\n+path(MESHD:"Pulmonary Disease, Chronic Obstructive")\tincreases\tbp(MESHPP:Apoptosis)\r\n+p(HGNC:PTGS2)\tassociation\ta(SCHEM:"Smoke, cigarette")\r\n+p(HGNC:PTGS2)\tnegativeCorrelation\tbp(MESHPP:Apoptosis)\r\n+a(SCHEM:"Smoke, cigarette")\tincreases\tp(HGNC:HSPA5)\r\n+p(HGNC:HSPA5)\tdecreases\tp(HGNC:CASP3)\r\n+p(HGNC:SCGB1A1)\tdecreases\tbp(MESHPP:Apoptosis)\r\n+p(HGNC:EIF2AK3)\tdecreases\tbp(MESHPP:Apoptosis)\r\n+p(HGNC:FLOT2)\tdecreases\tp(HGNC:DIABLO)\r\n+p(HGNC:PGF)\tincreases\tbp(MESHPP:Apoptosis)\r\n+kin(p(SFAM:"MAPK JNK Family"))\tincreases\tbp(MESHPP:Apoptosis)\r\n+kin(p(SFAM:"PRKC Family"))\tincreases\tbp(MESHPP:Apoptosis)\r\n+p(HGNC:BACH2)\tincreases\tkin(p(SFAM:"MAPK JNK Family"))\r\n+cat(p(HGNC:TRADD))\tincreases\tcat(p(HGNC:FADD))\r\n' |
| b |
| diff -r cb4dce1042ef -r 567274fa974d test-data/CoVennTree.jgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CoVennTree.jgf Sat Jun 04 03:22:52 2016 -0400 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"graph": {"nodes": [{"metadata": {"property0": "http://chart.apis.google.com/chart?chs=232x232&chco=82FF00,FF003B,7E00FF&cht=v&chd=t:35.1,33.5,31.4,4.8,15.6,3.6,0.0&chf=bg,s,e0dede00", "property1": "root[0.004]", "property2": "6817559 6100438 6497257 3027796 932408 698128 0"}, "id": "0", "label": "root"}, {"metadata": {"property0": "http://chart.apis.google.com/chart?chs=231x231&chco=82FF00,FF003B,7E00FF&cht=v&chd=t:34.8,33.8,31.4,4.6,15.2,3.4,0.0&chf=bg,s,e0dede00", "property1": "cellular_organisms[0.057]", "property2": "6554551 5915965 6363515 2855502 873865 647190 0"}, "id": "1", "label": "cellular_organisms"}, {"id": "2", "label": "pp"}, {"metadata": {"property0": "http://chart.apis.google.com/chart?chs=220x220&chco=FF003B,82FF00,7E00FF&cht=v&chd=t:38.1,31.7,30.2,4.5,3.3,16.0,0.0&chf=bg,s,e0dede00", "property1": "Bacteria[0.001]", "property2": "4483868 4274297 5390301 2267386 643310 463276 0"}, "id": "3", "label": "Bacteria"}, {"metadata": {"property0": "http://chart.apis.google.com/chart?chs=62x62&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:46.3,37.9,15.8,32.6,8.4,7.0,0.0&chf=bg,s,e0dede00", "property1": "Actinobacteria_<phylum>[1.000]", "property2": "32321 26455 11018 22787 5895 4908 0"}, "id": "4", "label": "Actinobacteria_<phylum>"}, {"metadata": {"property0": "http://chart.apis.google.com/chart?chs=35x35&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:51.7,27.5,20.7,26.5,11.0,10.1,0.0&chf=bg,s,e0dede00", "property1": "Aquificae_<phylum>[1.000]", "property2": "596 1119 449 574 219 239 0"}, "id": "5", "label": "Aquificae_<phylum>"}, {"metadata": {"property0": "http://chart.apis.google.com/chart?chs=21x21&chco=7E00FF,FF003B,82FF00&cht=v&chd=t:44.2,44.2,11.7,44.2,11.7,11.7,0.0&chf=bg,s,e0dede00", "property1": "Armatimonadetes[1.000]", "property2": "9 34 34 9 9 34 0"}, "id": "6", "label": "Armatimonadetes"}, {"metadata": {"property0": "http://chart.apis.google.com/chart?chs=68x68&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:55.7,36.3,8.0,24.8,7.9,4.6,0.0&chf=bg,s,e0dede00", "property1": "Bacteroidetes/Chlorobi_group[0.055]", "property2": "69629 45356 9975 30946 9844 5808 0"}, "id": "7", "label": "Bacteroidetes/Chlorobi_group"}, {"metadata": {"property0": "http://chart.apis.google.com/chart?chs=21x21&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:59.8,34.0,6.2,34.0,6.2,6.2,0.0&chf=bg,s,e0dede00", "property1": "Caldiserica[1.000]", "property2": "33 58 6 33 6 6 0"}, "id": "8", "label": "Caldiserica"}, {"metadata": {"property0": "http://chart.apis.google.com/chart?chs=51x51&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:60.2,31.3,8.5,24.6,7.0,6.6,0.0&chf=bg,s,e0dede00", "property1": "Chlamydiae/Verrucomicrobia_group[0.332]", "property2": "16699 8677 2363 6828 1953 1831 0"}, "id": "9", "label": "Chlamydiae/Verrucomicrobia_group"}, {"metadata": {"property0": "http://chart.apis.google.com/chart?chs=36x36&chco=FF003B,7E00FF,82FF00&cht=v&chd=t:65.0,27.2,7.9,23.6,7.3,7.6,0.0&chf=bg,s,e0dede00", "property1": "Chloroflexi_<phylum>[0.279]", "property2": "316 1092 2612 306 295 947 0"}, "id": "10", "label": "Chloroflexi_<phylum>"}, {"metadata": {"property0": "http://chart.apis.google.com/chart?chs=20x20&chco=7E00FF,FF003B,82FF00&cht=v&chd=t:66.1,17.9,16.1,17.9,16.1,16.1,0.0&chf=bg,s,e0dede00", "property1": "Chrysiogenetes_<phylum>[1.000]", "property2": "9 37 10 9 9 10 0"}, "id": "11", "label": "Chrysiogenetes_<phylum>"}, {"metadata": {"property0": "http://chart.apis.google.com/chart?chs=166x166&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:49.6,48.7,1.7,23.3,1.7,1.7,0.0&chf=bg,s,e0dede00", "property1": "Cyanobacteria[0.001]", "property2": "2854828 2910609 101922 1368124 101809 101912 0"}, "id": "12", "label": "Cyanobacteria"}, {"metadata": {"property0": "http://chart.apis.google.com/chart?chs=40x40&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:94.1,5.8,0.0,5.8,0.0,0.0,0.0&chf=bg,s,e0dede00", "property1": "environmental_samples_<Cyanobacteria>[0.039]", "property2": "2109 33935 16 2109 16 16 0"}, "id": "13", "label": "environmental_samples_<Cyanobacteria>"}, {"metadata": {"pro'..b'"99", "label": "not_assigned_Cyanobacteria"}, {"metadata": {"property0": "http://chart.apis.google.com/chart?chs=101x101&chco=FF003B,82FF00,7E00FF&cht=v&chd=t:94.1,4.2,1.7,4.2,1.7,1.7,0.0&chf=bg,s,e0dede00", "property1": "not_assigned_Bacteria", "property2": "218995 88933 4874913 88933 218995 88933 0"}, "id": "100", "label": "not_assigned_Bacteria"}, {"metadata": {"property0": "http://chart.apis.google.com/chart?chs=80x80&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:84.6,10.8,4.5,10.8,4.5,4.5,0.0&chf=bg,s,e0dede00", "property1": "not_assigned_cellular_organisms", "property2": "1383800 176813 74172 176813 74172 74172 0"}, "id": "101", "label": "not_assigned_cellular_organisms"}, {"metadata": {"property0": "http://chart.apis.google.com/chart?chs=47x47&chco=FF003B,82FF00,7E00FF&cht=v&chd=t:86.2,11.1,2.7,11.1,2.7,2.7,0.0&chf=bg,s,e0dede00", "property1": "not_assigned_root", "property2": "10598 2582 82264 2582 10598 2582 0"}, "id": "102", "label": "not_assigned_root"}], "edges": [{"source": 0, "target": 1}, {"source": 1, "target": 2}, {"source": 3, "target": 4}, {"source": 3, "target": 5}, {"source": 3, "target": 6}, {"source": 3, "target": 7}, {"source": 3, "target": 8}, {"source": 3, "target": 9}, {"source": 3, "target": 10}, {"source": 3, "target": 11}, {"source": 3, "target": 12}, {"source": 12, "target": 13}, {"source": 12, "target": 14}, {"source": 12, "target": 15}, {"source": 12, "target": 16}, {"source": 12, "target": 17}, {"source": 12, "target": 18}, {"source": 18, "target": 19}, {"source": 18, "target": 20}, {"source": 18, "target": 21}, {"source": 21, "target": 22}, {"source": 22, "target": 23}, {"source": 22, "target": 24}, {"source": 24, "target": 25}, {"source": 24, "target": 26}, {"source": 24, "target": 27}, {"source": 24, "target": 28}, {"source": 24, "target": 29}, {"source": 24, "target": 30}, {"source": 24, "target": 31}, {"source": 24, "target": 32}, {"source": 24, "target": 33}, {"source": 24, "target": 34}, {"source": 24, "target": 35}, {"source": 24, "target": 36}, {"source": 24, "target": 37}, {"source": 24, "target": 38}, {"source": 24, "target": 39}, {"source": 24, "target": 40}, {"source": 24, "target": 41}, {"source": 24, "target": 42}, {"source": 24, "target": 43}, {"source": 24, "target": 44}, {"source": 24, "target": 45}, {"source": 24, "target": 46}, {"source": 24, "target": 47}, {"source": 24, "target": 48}, {"source": 24, "target": 49}, {"source": 24, "target": 50}, {"source": 24, "target": 51}, {"source": 24, "target": 52}, {"source": 24, "target": 53}, {"source": 24, "target": 54}, {"source": 24, "target": 55}, {"source": 24, "target": 56}, {"source": 22, "target": 57}, {"source": 18, "target": 58}, {"source": 12, "target": 59}, {"source": 12, "target": 60}, {"source": 3, "target": 61}, {"source": 3, "target": 62}, {"source": 3, "target": 63}, {"source": 3, "target": 64}, {"source": 3, "target": 65}, {"source": 3, "target": 66}, {"source": 3, "target": 67}, {"source": 3, "target": 68}, {"source": 3, "target": 69}, {"source": 3, "target": 70}, {"source": 3, "target": 71}, {"source": 3, "target": 72}, {"source": 3, "target": 73}, {"source": 3, "target": 74}, {"source": 3, "target": 75}, {"source": 3, "target": 76}, {"source": 3, "target": 77}, {"source": 3, "target": 78}, {"source": 3, "target": 79}, {"source": 1, "target": 80}, {"source": 1, "target": 81}, {"source": 0, "target": 82}, {"source": 82, "target": 83}, {"source": 82, "target": 84}, {"source": 82, "target": 85}, {"source": 82, "target": 86}, {"source": 82, "target": 87}, {"source": 82, "target": 88}, {"source": 82, "target": 89}, {"source": 82, "target": 90}, {"source": 82, "target": 91}, {"source": 0, "target": 92}, {"source": 0, "target": 93}, {"source": 0, "target": 94}, {"source": 82, "target": 95}, {"source": 24, "target": 96}, {"source": 22, "target": 97}, {"source": 18, "target": 98}, {"source": 12, "target": 99}, {"source": 3, "target": 100}, {"source": 1, "target": 101}, {"source": 0, "target": 102}]}}\n\\ No newline at end of file\n' |
| b |
| diff -r cb4dce1042ef -r 567274fa974d test-data/CoVennTree_attributes.venn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CoVennTree_attributes.venn Sat Jun 04 03:22:52 2016 -0400 |
| [ |
| b'@@ -0,0 +1,15838 @@\n+root\thttp://chart.apis.google.com/chart?chs=232x232&chco=82FF00,FF003B,7E00FF&cht=v&chd=t:35.1,33.5,31.4,4.8,15.6,3.6,0.0&chf=bg,s,e0dede00\troot[0.004]\t6817559 6100438 6497257 3027796 932408 698128 0\n+unclassified_sequences\thttp://chart.apis.google.com/chart?chs=65x65&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:50.5,45.8,3.7,45.2,3.6,3.6,0.0&chf=bg,s,e0dede00\tunclassified_sequences[0.000]\t107967 97973 7999 96764 7631 7730 0\n+not_assigned_root\thttp://chart.apis.google.com/chart?chs=47x47&chco=FF003B,82FF00,7E00FF&cht=v&chd=t:86.2,11.1,2.7,11.1,2.7,2.7,0.0&chf=bg,s,e0dede00\tnot_assigned_root\t10598 2582 82264 2582 10598 2582 0\n+other_sequences\thttp://chart.apis.google.com/chart?chs=37x37&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:71.4,25.3,3.3,25.0,0.1,0.2,0.0&chf=bg,s,e0dede00\tother_sequences[0.209]\t1366 3852 179 1349 9 5 0\n+Not_assigned\thttp://chart.apis.google.com/chart?chs=54x54&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:52.2,29.0,18.8,29.0,18.8,18.8,0.0&chf=bg,s,e0dede00\tNot_assigned\t108864 60481 39175 60481 39175 39175 0\n+cellular_organisms\thttp://chart.apis.google.com/chart?chs=231x231&chco=82FF00,FF003B,7E00FF&cht=v&chd=t:34.8,33.8,31.4,4.6,15.2,3.4,0.0&chf=bg,s,e0dede00\tcellular_organisms[0.057]\t6554551 5915965 6363515 2855502 873865 647190 0\n+Viruses\thttp://chart.apis.google.com/chart?chs=61x61&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:59.1,33.8,7.1,19.2,2.0,2.5,0.0&chf=bg,s,e0dede00\tViruses[0.029]\t34213 19585 4125 11118 1130 1446 0\n+environmental_samples_<unclassified>\thttp://chart.apis.google.com/chart?chs=65x65&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:50.5,45.8,3.7,45.2,3.6,3.6,0.0&chf=bg,s,e0dede00\tenvironmental_samples_<unclassified>[0.020]\t107963 97969 7998 96760 7630 7729 0\n+unidentified\thttp://chart.apis.google.com/chart?chs=19x19&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:44.4,44.4,11.1,44.4,11.1,11.1,0.0&chf=bg,s,e0dede00\tunidentified\t4 4 1 4 1 1 0\n+artificial_sequences\thttp://chart.apis.google.com/chart?chs=37x37&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:71.4,25.3,3.3,25.0,0.1,0.2,0.0&chf=bg,s,e0dede00\tartificial_sequences[0.215]\t1366 3851 179 1349 9 5 0\n+plasmids\thttp://chart.apis.google.com/chart?chs=17x17&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:100.0,0.0,0.0,0.0,0.0,0.0,0.0&chf=bg,s,e0dede00\tplasmids[1.000]\t0 1 0 0 0 0 0\n+Eukaryota\thttp://chart.apis.google.com/chart?chs=147x147&chco=7E00FF,FF003B,82FF00&cht=v&chd=t:47.8,29.4,22.8,3.4,13.6,5.2,0.0&chf=bg,s,e0dede00\tEukaryota[0.003]\t680470 1429149 879893 407600 154736 101822 0\n+not_assigned_cellular_organisms\thttp://chart.apis.google.com/chart?chs=80x80&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:84.6,10.8,4.5,10.8,4.5,4.5,0.0&chf=bg,s,e0dede00\tnot_assigned_cellular_organisms\t1383800 176813 74172 176813 74172 74172 0\n+Bacteria\thttp://chart.apis.google.com/chart?chs=220x220&chco=FF003B,82FF00,7E00FF&cht=v&chd=t:38.1,31.7,30.2,4.5,3.3,16.0,0.0&chf=bg,s,e0dede00\tBacteria[0.001]\t4483868 4274297 5390301 2267386 643310 463276 0\n+Archaea\thttp://chart.apis.google.com/chart?chs=63x63&chco=7E00FF,FF003B,82FF00&cht=v&chd=t:58.3,31.3,10.5,12.9,6.0,2.7,0.0&chf=bg,s,e0dede00\tArchaea[0.011]\t6413 35706 19149 3703 1647 7920 0\n+dsDNA_viruses,_no_RNA_stage\thttp://chart.apis.google.com/chart?chs=58x58&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:61.8,36.0,2.2,20.6,2.0,2.0,0.0&chf=bg,s,e0dede00\tdsDNA_viruses,_no_RNA_stage[0.071]\t30896 18026 1106 10303 1009 988 0\n+unclassified_phages\thttp://chart.apis.google.com/chart?chs=26x26&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:52.6,38.8,8.6,16.4,8.6,5.3,0.0&chf=bg,s,e0dede00\tunclassified_phages[0.271]\t80 59 13 25 13 8 0\n+unassigned_viruses\thttp://chart.apis.google.com/chart?chs=20x20&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:80.0,20.0,0.0,10.0,0.0,0.0,0.0&chf=bg,s,e0dede00\tunassigned_viruses[0.413]\t8 2 0 1 0 0 0\n+ssRNA_viruses\thttp://chart.apis.google.com/chart?chs=25x25&chco=FF003B,82FF00,7E00FF&cht=v&chd=t:61.2,26.4,12.4,11.6,5.8,6.6,0.0&chf=bg,s,e0dede00\tssRNA_viruses[0.234]\t32 15 74 8 14 7 0\n+unclassified_viruses\thttp://chart.apis.google.com/chart?chs=18x18&chco=7E0'..b':70.6,17.6,11.8,17.6,11.8,11.8,0.0&chf=bg,s,e0dede00\tDorea_longicatena_DSM_13814\t3 12 2 3 2 2 0\n+Streptococcus_oligofermentans_AS_1.3089\thttp://chart.apis.google.com/chart?chs=19x19&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:87.5,12.5,0.0,12.5,0.0,0.0,0.0&chf=bg,s,e0dede00\tStreptococcus_oligofermentans_AS_1.3089\t1 7 0 1 0 0 0\n+Thiriotia\thttp://chart.apis.google.com/chart?chs=18x18&chco=82FF00,FF003B,7E00FF&cht=v&chd=t:50.0,50.0,0.0,50.0,0.0,0.0,0.0&chf=bg,s,e0dede00\tThiriotia[1.000]\t1 0 1 0 1 0 0\n+Acanthocephala\thttp://chart.apis.google.com/chart?chs=19x19&chco=FF003B,7E00FF,82FF00&cht=v&chd=t:66.7,16.7,16.7,16.7,0.0,0.0,0.0&chf=bg,s,e0dede00\tAcanthocephala[0.250]\t1 1 4 0 0 1 0\n+Brachiopoda\thttp://chart.apis.google.com/chart?chs=22x22&chco=FF003B,7E00FF,82FF00&cht=v&chd=t:54.8,29.0,16.1,16.1,12.9,12.9,0.0&chf=bg,s,e0dede00\tBrachiopoda[0.430]\t5 9 17 4 4 5 0\n+Annelida\thttp://chart.apis.google.com/chart?chs=32x32&chco=82FF00,FF003B,7E00FF&cht=v&chd=t:49.3,37.0,13.7,8.2,5.4,5.9,0.0&chf=bg,s,e0dede00\tAnnelida[0.466]\t464 129 349 51 77 56 0\n+Mollusca\thttp://chart.apis.google.com/chart?chs=37x37&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:55.3,29.4,15.3,25.5,6.8,6.6,0.0&chf=bg,s,e0dede00\tMollusca[0.103]\t973 1830 507 844 218 225 0\n+Bryozoa\thttp://chart.apis.google.com/chart?chs=25x25&chco=FF003B,82FF00,7E00FF&cht=v&chd=t:59.3,29.4,11.3,25.4,5.6,7.9,0.0&chf=bg,s,e0dede00\tBryozoa[0.502]\t52 20 105 14 45 10 0\n+Rotifera\thttp://chart.apis.google.com/chart?chs=24x24&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:54.3,32.9,12.9,17.1,8.6,7.1,0.0&chf=bg,s,e0dede00\tRotifera[0.611]\t23 38 9 12 5 6 0\n+not_assigned_Lophotrochozoa\thttp://chart.apis.google.com/chart?chs=23x23&chco=FF003B,82FF00,7E00FF&cht=v&chd=t:86.7,9.9,3.4,9.9,3.4,3.4,0.0&chf=bg,s,e0dede00\tnot_assigned_Lophotrochozoa\t29 10 254 10 29 10 0\n+Entoprocta\thttp://chart.apis.google.com/chart?chs=21x21&chco=FF003B,7E00FF,82FF00&cht=v&chd=t:52.4,33.3,14.3,19.0,4.8,0.0,0.0&chf=bg,s,e0dede00\tEntoprocta[0.320]\t3 7 11 0 1 4 0\n+Nemertea\thttp://chart.apis.google.com/chart?chs=24x24&chco=FF003B,7E00FF,82FF00&cht=v&chd=t:79.8,16.3,3.8,6.7,1.0,2.9,0.0&chf=bg,s,e0dede00\tNemertea[0.176]\t4 17 83 3 1 7 0\n+Myzostomida\thttp://chart.apis.google.com/chart?chs=19x19&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:75.0,25.0,0.0,0.0,0.0,0.0,0.0&chf=bg,s,e0dede00\tMyzostomida[0.250]\t3 1 0 0 0 0 0\n+Gastrotricha\thttp://chart.apis.google.com/chart?chs=24x24&chco=7E00FF,FF003B,82FF00&cht=v&chd=t:71.3,21.3,7.4,3.7,4.6,4.6,0.0&chf=bg,s,e0dede00\tGastrotricha[0.392]\t8 77 23 5 5 4 0\n+Methanolobus_psychrophilus_R15\thttp://chart.apis.google.com/chart?chs=19x19&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:61.9,28.6,9.5,28.6,9.5,9.5,0.0&chf=bg,s,e0dede00\tMethanolobus_psychrophilus_R15\t6 13 2 6 2 2 0\n+Acidovorax_citrulli_AAC00-1\thttp://chart.apis.google.com/chart?chs=20x20&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:68.0,24.0,8.0,24.0,8.0,8.0,0.0&chf=bg,s,e0dede00\tAcidovorax_citrulli_AAC00-1\t6 17 2 6 2 2 0\n+Brevibacillus_laterosporus_DSM_25\thttp://chart.apis.google.com/chart?chs=21x21&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:53.8,36.8,9.4,36.8,9.4,9.4,0.0&chf=bg,s,e0dede00\tBrevibacillus_laterosporus_DSM_25\t39 57 10 39 10 10 0\n+Brevibacillus_laterosporus_LMG_15441\thttp://chart.apis.google.com/chart?chs=17x17&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:100.0,0.0,0.0,0.0,0.0,0.0,0.0&chf=bg,s,e0dede00\tBrevibacillus_laterosporus_LMG_15441\t0 1 0 0 0 0 0\n+Halanaerobium_praevalens_DSM_2228\thttp://chart.apis.google.com/chart?chs=24x24&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:63.5,31.3,5.3,31.3,5.3,5.3,0.0&chf=bg,s,e0dede00\tHalanaerobium_praevalens_DSM_2228\t137 278 23 137 23 23 0\n+Clostridium_hylemonae_DSM_15053\thttp://chart.apis.google.com/chart?chs=22x22&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:93.8,6.2,0.0,6.2,0.0,0.0,0.0&chf=bg,s,e0dede00\tClostridium_hylemonae_DSM_15053\t9 136 0 9 0 0 0\n+Desulfotomaculum_gibsoniae_DSM_7213\thttp://chart.apis.google.com/chart?chs=21x21&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:65.7,19.4,14.9,19.4,14.9,14.9,0.0&chf=bg,s,e0dede00\tDesulf\n\\ No newline at end of file\n' |
| b |
| diff -r cb4dce1042ef -r 567274fa974d test-data/CoVennTree_network.sif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CoVennTree_network.sif Sat Jun 04 03:22:52 2016 -0400 |
| b |
| @@ -0,0 +1,101 @@ +root pp cellular_organisms +cellular_organisms pp Bacteria +Bacteria pp Actinobacteria_<phylum> +Bacteria pp Aquificae_<phylum> +Bacteria pp Armatimonadetes +Bacteria pp Bacteroidetes/Chlorobi_group +Bacteria pp Caldiserica +Bacteria pp Chlamydiae/Verrucomicrobia_group +Bacteria pp Chloroflexi_<phylum> +Bacteria pp Chrysiogenetes_<phylum> +Bacteria pp Cyanobacteria +Cyanobacteria pp environmental_samples_<Cyanobacteria> +Cyanobacteria pp Gloeobacteria +Cyanobacteria pp Nostocales +Cyanobacteria pp Oscillatoriophycideae +Cyanobacteria pp Pleurocapsales +Cyanobacteria pp Prochlorales +Prochlorales pp environmental_samples_<Prochlorophytes> +Prochlorales pp Prochloraceae +Prochlorales pp Prochlorococcaceae +Prochlorococcaceae pp Prochlorococcus +Prochlorococcus pp environmental_samples_<Prochlorococcus> +Prochlorococcus pp Prochlorococcus_marinus +Prochlorococcus_marinus pp environmental_samples_<Prochlorococcus_marinus> +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._AS9601 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._CCMP1377 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._GP2 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9107 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9116 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9201 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9202 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9211 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9215 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9301 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9302 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9303 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9312 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9313 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9515 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._NATL1A +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._NATL1MIT +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._NATL2A +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._PAC1 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._PAC1A +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._PAC1B +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._PAC2 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._RS2001 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._RS810 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._SB +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._TAK9803 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._TAK9803-2 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._TATL1 +Prochlorococcus_marinus pp Prochlorococcus_marinus_str._TATL1B +Prochlorococcus_marinus pp Prochlorococcus_marinus_subsp._marinus +Prochlorococcus_marinus pp Prochlorococcus_marinus_subsp._pastoris +Prochlorococcus pp Prochlorococcus_sp. +Prochlorales pp Prochlorotrichaceae +Cyanobacteria pp Stigonematales +Cyanobacteria pp unclassified_Cyanobacteria +Bacteria pp Deferribacteres_<phylum> +Bacteria pp Deinococcus-Thermus +Bacteria pp Dictyoglomi +Bacteria pp Elusimicrobia +Bacteria pp environmental_samples_<Bacteria> +Bacteria pp Fibrobacteres/Acidobacteria_group +Bacteria pp Firmicutes +Bacteria pp Fusobacteria +Bacteria pp Gemmatimonadetes +Bacteria pp Nitrospinae +Bacteria pp Nitrospirae +Bacteria pp Planctomycetes +Bacteria pp Proteobacteria +Bacteria pp Spirochaetes +Bacteria pp Synergistetes +Bacteria pp Tenericutes +Bacteria pp Thermodesulfobacteria_<phylum> +Bacteria pp Thermotogae_<phylum> +Bacteria pp unclassified_Bacteria +cellular_organisms pp Archaea +cellular_organisms pp Eukaryota +root pp Viruses +Viruses pp dsDNA_viruses,_no_RNA_stage +Viruses pp dsRNA_viruses +Viruses pp environmental_samples_<viruses> +Viruses pp Retro-transcribing_viruses +Viruses pp ssDNA_viruses +Viruses pp ssRNA_viruses +Viruses pp unassigned_viruses +Viruses pp unclassified_phages +Viruses pp unclassified_viruses +root pp unclassified_sequences +root pp other_sequences +root pp Not_assigned +Viruses pp not_assigned_Viruses +Prochlorococcus_marinus pp not_assigned_Prochlorococcus_marinus +Prochlorococcus pp not_assigned_Prochlorococcus +Prochlorales pp not_assigned_Prochlorales +Cyanobacteria pp not_assigned_Cyanobacteria +Bacteria pp not_assigned_Bacteria +cellular_organisms pp not_assigned_cellular_organisms +root pp not_assigned_root |
| b |
| diff -r cb4dce1042ef -r 567274fa974d test-data/angiogenesis_network.sif --- a/test-data/angiogenesis_network.sif Thu Jun 02 09:32:40 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,322 +0,0 @@\n-p(HGNC:FGF9)\tisA\tp(PFH:"FGF Family")\r\n-p(HGNC:FGF10)\tisA\tp(PFH:"FGF Family")\r\n-p(HGNC:FGF18)\tisA\tp(PFH:"FGF Family")\r\n-p(HGNC:FGF1)\tisA\tp(PFH:"FGF Family")\r\n-p(HGNC:FGF2)\tisA\tp(PFH:"FGF Family")\r\n-p(HGNC:FGF16)\tisA\tp(PFH:"FGF Family")\r\n-p(HGNC:FGF5)\tisA\tp(PFH:"FGF Family")\r\n-p(HGNC:FGF7)\tisA\tp(PFH:"FGF Family")\r\n-p(HGNC:FGF8)\tisA\tp(PFH:"FGF Family")\r\n-p(PFH:"FGF Family")\tincreases\tkin(p(PFH:"FGFR Family"))\r\n-p(HGNC:KNG1)\tdirectlyIncreases\tcat(p(HGNC:BDKRB1))\r\n-p(HGNC:KNG1)\tdirectlyIncreases\tcat(p(HGNC:BDKRB2))\r\n-p(HGNC:SIRT1)\tactsIn\tcat(p(HGNC:SIRT1))\r\n-p(HGNC:CXCL12)\tdirectlyIncreases\tcat(p(HGNC:CXCR4))\r\n-p(HGNC:NRP1)\tactsIn\tcat(p(HGNC:NRP1))\r\n-p(HGNC:NRP1)\tincreases\tkin(p(HGNC:FLT1))\r\n-cat(p(HGNC:NRP1))\tdirectlyIncreases\tkin(p(HGNC:KDR))\r\n-p(HGNC:JAG1)\tdirectlyIncreases\ttscript(p(PFH:"NOTCH Family"))\r\n-p(HGNC:TGFB1)\tisA\tp(PFH:"TGFB Family")\r\n-p(HGNC:TGFB2)\tisA\tp(PFH:"TGFB Family")\r\n-p(PFH:"TGFB Family")\tdirectlyIncreases\tkin(p(HGNC:TGFBR2))\r\n-p(HGNC:PDGFRB)\tisA\tp(PFH:"PDGFR Family")\r\n-p(PFH:"PDGFR Family")\tactsIn\tkin(p(PFH:"PDGFR Family"))\r\n-p(HGNC:PDGFRA)\tisA\tp(PFH:"PDGFR Family")\r\n-p(HGNC:PDGFRB)\tactsIn\tkin(p(HGNC:PDGFRB))\r\n-p(HGNC:COL18A1)\tdecreases\tkin(p(PFH:"MAPK p38 Family"))\r\n-p(HGNC:COL18A1)\tdecreases\tkin(p(HGNC:MAPK3))\r\n-p(HGNC:COL18A1)\tdecreases\tkin(p(HGNC:KDR))\r\n-p(HGNC:COL18A1)\tdecreases\tkin(p(HGNC:PTK2))\r\n-p(HGNC:COL18A1)\tdecreases\tkin(p(HGNC:MAPK1))\r\n-p(HGNC:BCL6B)\tactsIn\tcat(p(MGI:Bcl6b))\r\n-cat(p(MGI:Bcl6b))\tincreases\tdeg(p(MGI:Rbpj))\r\n-p(HGNC:EGLN2)\tactsIn\tcat(p(HGNC:EGLN2))\r\n-cat(p(HGNC:EGLN2))\tincreases\tdeg(p(HGNC:HIF1A))\r\n-p(HGNC:PRKAA1)\tactsIn\tkin(p(HGNC:PRKAA1))\r\n-kin(p(HGNC:PRKAA1))\tincreases\tbp(GO:"blood vessel development")\r\n-p(HGNC:UNC5B)\tactsIn\tcat(p(HGNC:UNC5B))\r\n-cat(p(HGNC:UNC5B))\tdecreases\tbp(GO:"patterning of blood vessels")\r\n-complex(p(HGNC:PDGFA),p(HGNC:PDGFB))\thasComponent\tp(HGNC:PDGFA)\r\n-complex(p(HGNC:PDGFA),p(HGNC:PDGFB))\thasComponent\tp(HGNC:PDGFB)\r\n-p(HGNC:TIE1)\tactsIn\tkin(p(HGNC:TIE1))\r\n-kin(p(HGNC:EGFR))\tincreases\tkin(p(HGNC:MAPK3))\r\n-kin(p(HGNC:EGFR))\tincreases\tkin(p(HGNC:MAPK1))\r\n-p(HGNC:TGFA)\tdirectlyIncreases\tkin(p(HGNC:EGFR))\r\n-deg(p(MGI:Rbpj))\tdirectlyDecreases\tp(HGNC:RBPJ)\r\n-a(CHEBI:"angiotensin II")\tincreases\tp(HGNC:VEGFA)\r\n-a(CHEBI:"angiotensin II")\tdirectlyIncreases\tcat(p(HGNC:AGTR1))\r\n-a(CHEBI:"angiotensin II")\tincreases\ttscript(p(HGNC:HIF1A))\r\n-a(CHEBI:"angiotensin II")\tincreases\tp(HGNC:HIF1A)\r\n-p(HGNC:SHH)\tincreases\tgtp(p(HGNC:RHOA))\r\n-p(HGNC:NOS3)\tincreases\tbp(GO:angiogenesis)\r\n-p(HGNC:NOS3)\tactsIn\tcat(p(HGNC:NOS3))\r\n-p(HGNC:ANGPT2)\tdirectlyDecreases\tkin(p(HGNC:TEK))\r\n-p(HGNC:ANGPT2)\tdecreases\tp(HGNC:ANGPT1)\r\n-p(HGNC:ANGPT2)\tdirectlyDecreases\tkin(p(HGNC:TIE1))\r\n-p(HGNC:ROBO4)\tactsIn\tcat(p(MGI:Robo4))\r\n-p(HGNC:OLR1)\tincreases\tbp(GO:"patterning of blood vessels")\r\n-cat(p(HGNC:AGTR1))\tincreases\tp(HGNC:OLR1)\r\n-p(HGNC:KLF2)\tdecreases\tp(HGNC:HIF1A)\r\n-p(HGNC:KLF2)\tactsIn\ttscript(p(HGNC:KLF2))\r\n-kin(p(HGNC:PDGFRB))\tincreases\tkin(p(HGNC:MAPK3))\r\n-kin(p(HGNC:PDGFRB))\tincreases\tkin(p(HGNC:SRC))\r\n-kin(p(HGNC:PDGFRB))\tincreases\tkin(p(HGNC:MAPK1))\r\n-p(HGNC:EPAS1)\tactsIn\ttscript(p(HGNC:EPAS1))\r\n-p(HGNC:BDKRB1)\tactsIn\tcat(p(HGNC:BDKRB1))\r\n-gtp(p(HGNC:RHOA))\tdirectlyIncreases\tkin(p(HGNC:ROCK1))\r\n-complex(p(HGNC:ECT2),p(HGNC:KLHL20))\thasComponent\tp(HGNC:ECT2)\r\n-complex(p(HGNC:ECT2),p(HGNC:KLHL20))\tincreases\tgtp(p(HGNC:RHOA))\r\n-complex(p(HGNC:ECT2),p(HGNC:KLHL20))\thasComponent\tp(HGNC:KLHL20)\r\n-p(HGNC:ECT2)\tincreases\tbp(GO:"patterning of blood vessels")\r\n-p(HGNC:MMP2)\tactsIn\tcat(p(HGNC:MMP2))\r\n-cat(p(HGNC:MMP2))\tincreases\tp(HGNC:VEGFA)\r\n-p(HGNC:RAF1)\tactsIn\tkin(p(HGNC:RAF1))\r\n-kin(p(HGNC:RAF1))\tincreases\tkin(p(HGNC:ROCK2))\r\n-p(HGNC:ENG)\tincreases\tkin(p(HGNC:ACVRL1))\r\n-p(HGNC:ENG)\tdecreases\tkin(p(HGNC:TGFBR1))\r\n-a(CHEBI:"sphingosine 1-phosphate")\tincreases\tbp(GO:"patterning of blood vessels")\r\n-p(HGNC:FGFR1)\tactsIn\tkin(p(HGNC:FGFR1))\r\n-p(HGNC:FGFR2)\tisA\tp(PFH:"FGFR Family")\r\n-p(HGNC:FGFR3)\tisA\tp(PFH:"FGFR Family")\r\n-p(HGNC:FGFR1)\tisA\tp(PFH:"FGFR Family")\r\n-p(PFH:"FGFR Fami'..b'))\r\n-p(PFH:"PRKC Family")\tactsIn\tkin(p(PFH:"PRKC Family"))\r\n-cat(p(HGNC:BDKRB2))\tDefaultEdge\tp(HGNC:VEGFA)\r\n-p(HGNC:BDKRB2)\tactsIn\tcat(p(HGNC:BDKRB2))\r\n-cat(p(HGNC:PLCG1))\tincreases\tkin(p(PFH:"PRKC Family"))\r\n-kin(p(PFH:"PDGFR Family"))\tincreases\tkin(p(PFH:?PIK3C Class IA Family?))\r\n-kin(p(PFH:"PDGFR Family"))\tincreases\tkin(p(HGNC:MAPK1))\r\n-kin(p(PFH:"PDGFR Family"))\tincreases\tcat(p(HGNC:PLCG1))\r\n-kin(p(HGNC:SRC))\tdirectlyIncreases\tkin(p(HGNC:PTK2))\r\n-kin(p(HGNC:SRC))\tincreases\tcat(p(HGNC:PLCG1))\r\n-kin(p(HGNC:SRC))\tincreases\tbp(GO:"regulation of vascular permeability")\r\n-p(HGNC:SRC)\tactsIn\tkin(p(HGNC:SRC))\r\n-tscript(p(HGNC:PPARA))\tdecreases\tkin(p(PFH:"AKT Family"))\r\n-p(HGNC:PPARA)\tactsIn\ttscript(p(HGNC:PPARA))\r\n-p(HGNC:ITGB1BP1)\tdecreases\tbp(GO:"patterning of blood vessels")\r\n-tscript(p(HGNC:SMAD3))\tdecreases\tbp(GO:"cell proliferation")\r\n-tscript(p(HGNC:SMAD3))\tdecreases\tbp(GO:"cell migration")\r\n-p(HGNC:SMAD3)\tactsIn\ttscript(p(HGNC:SMAD3))\r\n-tscript(p(HGNC:SMAD5))\tincreases\tbp(GO:"cell proliferation")\r\n-tscript(p(HGNC:SMAD5))\tincreases\tbp(GO:"cell migration")\r\n-p(HGNC:SMAD5)\tactsIn\ttscript(p(HGNC:SMAD5))\r\n-cat(p(HGNC:CXCR4))\tincreases\tbp(GO:"patterning of blood vessels")\r\n-p(HGNC:CXCR4)\tactsIn\tcat(p(HGNC:CXCR4))\r\n-kin(p(PFH:?PIK3C Class IA Family?))\tincreases\tkin(p(PFH:"AKT Family"))\r\n-complex(NCH:"p85/p110 PI3Kinase Complex")\tactsIn\tkin(p(PFH:?PIK3C Class IA Family?))\r\n-p(PFH:"NOTCH Family")\tactsIn\ttscript(p(PFH:"NOTCH Family"))\r\n-tscript(p(HGNC:EP300))\tdirectlyIncreases\ttscript(p(HGNC:HIF1A))\r\n-cat(p(HGNC:SHC1))\tincreases\tkin(p(HGNC:MAPK1))\r\n-cat(p(HGNC:SHC1))\tincreases\tkin(p(HGNC:MAPK3))\r\n-p(HGNC:SHC1)\tactsIn\tcat(p(HGNC:SHC1))\r\n-tscript(p(HGNC:NOTCH4))\tincreases\ttscript(p(HGNC:RBPJ))\r\n-tscript(p(HGNC:NOTCH4))\tdecreases\tbp(GO:"patterning of blood vessels")\r\n-p(HGNC:NOTCH4)\tactsIn\ttscript(p(HGNC:NOTCH4))\r\n-p(HGNC:S100A11)\tincreases\tbp(GO:"patterning of blood vessels")\r\n-kin(p(HGNC:ACVRL1))\tincreases\ttscript(p(HGNC:SMAD5))\r\n-kin(p(HGNC:ACVRL1))\tincreases\ttscript(p(HGNC:SMAD1))\r\n-p(HGNC:ACVRL1)\tactsIn\tkin(p(HGNC:ACVRL1))\r\n-kin(p(HGNC:ROCK1))\tincreases\tbp(GO:angiogenesis)\r\n-p(HGNC:ROCK1)\tactsIn\tkin(p(HGNC:ROCK1))\r\n-p(HGNC:RAP1B)\tincreases\tbp(GO:"patterning of blood vessels")\r\n-p(HGNC:ARNT)\tactsIn\ttscript(p(HGNC:ARNT))\r\n-tscript(p(HGNC:HIF1A))\tincreases\tp(HGNC:TGFA)\r\n-tscript(p(HGNC:HIF1A))\tincreases\tp(HGNC:VEGFC)\r\n-tscript(p(HGNC:HIF1A))\tincreases\tp(HGNC:ANGPT2)\r\n-tscript(p(HGNC:HIF1A))\tincreases\tbp(GO:angiogenesis)\r\n-tscript(p(HGNC:HIF1A))\tdirectlyIncreases\tp(HGNC:VEGFA)\r\n-tscript(p(HGNC:HIF1A))\tdirectlyIncreases\tp(HGNC:PDGFB)\r\n-tscript(p(HGNC:HIF1A))\tincreases\tp(HGNC:MMP2)\r\n-tscript(p(HGNC:HIF1A))\tincreases\tp(HGNC:FGF2)\r\n-tscript(p(HGNC:HIF1A))\tincreases\tp(HGNC:MMP9)\r\n-tscript(p(HGNC:HIF1A))\tdirectlyIncreases\tp(HGNC:PTGS2)\r\n-tscript(p(HGNC:HIF1A))\tincreases\tp(HGNC:SERPINE1)\r\n-tscript(p(HGNC:HIF1A))\tincreases\tp(HGNC:ANGPT1)\r\n-tscript(p(HGNC:ARNT))\tdirectlyIncreases\ttscript(p(HGNC:HIF1A))\r\n-tscript(p(HGNC:ARNT))\tdirectlyIncreases\ttscript(p(HGNC:EPAS1))\r\n-cat(p(HGNC:EGLN1))\tincreases\tdeg(p(HGNC:HIF1A))\r\n-p(HGNC:EGLN1)\tactsIn\tcat(p(HGNC:EGLN1))\r\n-p(HGNC:MMP14)\tactsIn\tcat(p(HGNC:MMP14))\r\n-cat(p(HGNC:MMP14))\tincreases\tbp(GO:"blood vessel development")\r\n-tscript(p(PFH:"NOTCH Family"))\tincreases\tp(HGNC:HEY2)\r\n-tscript(p(PFH:"NOTCH Family"))\tincreases\tp(HGNC:HEY1)\r\n-tscript(p(HGNC:NOTCH4))\tisA\ttscript(p(PFH:"NOTCH Family"))\r\n-tscript(p(PFH:"NOTCH Family"))\tdecreases\tbp(GO:"patterning of blood vessels")\r\n-p(HGNC:EGFL7)\tdirectlyDecreases\ttscript(p(PFH:"NOTCH Family"))\r\n-cat(p(MGI:Robo4))\tdecreases\tbp(GO:"blood vessel development")\r\n-p(HGNC:SLIT2)\tincreases\tcat(p(MGI:Robo4))\r\n-kin(p(HGNC:MAPK1))\tincreases\tp(HGNC:PXN)\r\n-kin(p(HGNC:MAPK1))\tincreases\tbp(GO:"cell proliferation")\r\n-p(HGNC:MAPK1)\tactsIn\tkin(p(HGNC:MAPK1))\r\n-tscript(p(HGNC:FOXO3))\tdecreases\tbp(GO:"cell migration")\r\n-tscript(p(HGNC:FOXO3))\tdirectlyDecreases\tp(HGNC:NOS3)\r\n-tscript(p(HGNC:FOXO3))\tdecreases\tbp(GO:"cell proliferation")\r\n-p(HGNC:FOXO3)\tactsIn\ttscript(p(HGNC:FOXO3))\r\n' |
| b |
| diff -r cb4dce1042ef -r 567274fa974d test-data/angiogenesis_nodelink.json --- a/test-data/angiogenesis_nodelink.json Thu Jun 02 09:32:40 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1 +0,0 @@\n-{"nodes": [{"id": 0, "name": "p(HGNC:FGF9)"}, {"id": 1, "name": "p(PFH:FGF Family)"}, {"id": 2, "name": "p(HGNC:FGF10)"}, {"id": 3, "name": "p(HGNC:FGF18)"}, {"id": 4, "name": "p(HGNC:FGF1)"}, {"id": 5, "name": "p(HGNC:FGF2)"}, {"id": 6, "name": "p(HGNC:FGF16)"}, {"id": 7, "name": "p(HGNC:FGF5)"}, {"id": 8, "name": "p(HGNC:FGF7)"}, {"id": 9, "name": "p(HGNC:FGF8)"}, {"id": 10, "name": "kin(p(PFH:FGFR Family))"}, {"id": 11, "name": "p(HGNC:KNG1)"}, {"id": 12, "name": "cat(p(HGNC:BDKRB1))"}, {"id": 13, "name": "cat(p(HGNC:BDKRB2))"}, {"id": 14, "name": "p(HGNC:SIRT1)"}, {"id": 15, "name": "cat(p(HGNC:SIRT1))"}, {"id": 16, "name": "p(HGNC:CXCL12)"}, {"id": 17, "name": "cat(p(HGNC:CXCR4))"}, {"id": 18, "name": "p(HGNC:NRP1)"}, {"id": 19, "name": "cat(p(HGNC:NRP1))"}, {"id": 20, "name": "kin(p(HGNC:FLT1))"}, {"id": 21, "name": "kin(p(HGNC:KDR))"}, {"id": 22, "name": "p(HGNC:JAG1)"}, {"id": 23, "name": "tscript(p(PFH:NOTCH Family))"}, {"id": 24, "name": "p(HGNC:TGFB1)"}, {"id": 25, "name": "p(PFH:TGFB Family)"}, {"id": 26, "name": "p(HGNC:TGFB2)"}, {"id": 27, "name": "kin(p(HGNC:TGFBR2))"}, {"id": 28, "name": "p(HGNC:PDGFRB)"}, {"id": 29, "name": "p(PFH:PDGFR Family)"}, {"id": 30, "name": "kin(p(PFH:PDGFR Family))"}, {"id": 31, "name": "p(HGNC:PDGFRA)"}, {"id": 32, "name": "kin(p(HGNC:PDGFRB))"}, {"id": 33, "name": "p(HGNC:COL18A1)"}, {"id": 34, "name": "kin(p(PFH:MAPK p38 Family))"}, {"id": 35, "name": "kin(p(HGNC:MAPK3))"}, {"id": 36, "name": "kin(p(HGNC:PTK2))"}, {"id": 37, "name": "kin(p(HGNC:MAPK1))"}, {"id": 38, "name": "p(HGNC:BCL6B)"}, {"id": 39, "name": "cat(p(MGI:Bcl6b))"}, {"id": 40, "name": "deg(p(MGI:Rbpj))"}, {"id": 41, "name": "p(HGNC:EGLN2)"}, {"id": 42, "name": "cat(p(HGNC:EGLN2))"}, {"id": 43, "name": "deg(p(HGNC:HIF1A))"}, {"id": 44, "name": "p(HGNC:PRKAA1)"}, {"id": 45, "name": "kin(p(HGNC:PRKAA1))"}, {"id": 46, "name": "bp(GO:blood vessel development)"}, {"id": 47, "name": "p(HGNC:UNC5B)"}, {"id": 48, "name": "cat(p(HGNC:UNC5B))"}, {"id": 49, "name": "bp(GO:patterning of blood vessels)"}, {"id": 50, "name": "complex(p(HGNC:PDGFA),p(HGNC:PDGFB))"}, {"id": 51, "name": "p(HGNC:PDGFA)"}, {"id": 52, "name": "p(HGNC:PDGFB)"}, {"id": 53, "name": "p(HGNC:TIE1)"}, {"id": 54, "name": "kin(p(HGNC:TIE1))"}, {"id": 55, "name": "kin(p(HGNC:EGFR))"}, {"id": 56, "name": "p(HGNC:TGFA)"}, {"id": 57, "name": "p(HGNC:RBPJ)"}, {"id": 58, "name": "a(CHEBI:angiotensin II)"}, {"id": 59, "name": "p(HGNC:VEGFA)"}, {"id": 60, "name": "cat(p(HGNC:AGTR1))"}, {"id": 61, "name": "tscript(p(HGNC:HIF1A))"}, {"id": 62, "name": "p(HGNC:HIF1A)"}, {"id": 63, "name": "p(HGNC:SHH)"}, {"id": 64, "name": "gtp(p(HGNC:RHOA))"}, {"id": 65, "name": "p(HGNC:NOS3)"}, {"id": 66, "name": "bp(GO:angiogenesis)"}, {"id": 67, "name": "cat(p(HGNC:NOS3))"}, {"id": 68, "name": "p(HGNC:ANGPT2)"}, {"id": 69, "name": "kin(p(HGNC:TEK))"}, {"id": 70, "name": "p(HGNC:ANGPT1)"}, {"id": 71, "name": "p(HGNC:ROBO4)"}, {"id": 72, "name": "cat(p(MGI:Robo4))"}, {"id": 73, "name": "p(HGNC:OLR1)"}, {"id": 74, "name": "p(HGNC:KLF2)"}, {"id": 75, "name": "tscript(p(HGNC:KLF2))"}, {"id": 76, "name": "kin(p(HGNC:SRC))"}, {"id": 77, "name": "p(HGNC:EPAS1)"}, {"id": 78, "name": "tscript(p(HGNC:EPAS1))"}, {"id": 79, "name": "p(HGNC:BDKRB1)"}, {"id": 80, "name": "kin(p(HGNC:ROCK1))"}, {"id": 81, "name": "complex(p(HGNC:ECT2),p(HGNC:KLHL20))"}, {"id": 82, "name": "p(HGNC:ECT2)"}, {"id": 83, "name": "p(HGNC:KLHL20)"}, {"id": 84, "name": "p(HGNC:MMP2)"}, {"id": 85, "name": "cat(p(HGNC:MMP2))"}, {"id": 86, "name": "p(HGNC:RAF1)"}, {"id": 87, "name": "kin(p(HGNC:RAF1))"}, {"id": 88, "name": "kin(p(HGNC:ROCK2))"}, {"id": 89, "name": "p(HGNC:ENG)"}, {"id": 90, "name": "kin(p(HGNC:ACVRL1))"}, {"id": 91, "name": "kin(p(HGNC:TGFBR1))"}, {"id": 92, "name": "a(CHEBI:sphingosine 1-phosphate)"}, {"id": 93, "name": "p(HGNC:FGFR1)"}, {"id": 94, "name": "kin(p(HGNC:FGFR1))"}, {"id": 95, "name": "p(HGNC:FGFR2)"}, {"id": 96, "name": "p(PFH:FGFR Family)"}, {"id": 97, "name": "p(HGNC:FGFR3)"}'..b'21, "target": 150}, {"source": 21, "target": 123}, {"source": 21, "target": 135}, {"source": 157, "target": 21}, {"source": 172, "target": 173}, {"source": 174, "target": 173}, {"source": 175, "target": 61}, {"source": 176, "target": 175}, {"source": 176, "target": 78}, {"source": 34, "target": 112}, {"source": 177, "target": 34}, {"source": 178, "target": 35}, {"source": 178, "target": 37}, {"source": 179, "target": 178}, {"source": 180, "target": 181}, {"source": 182, "target": 183}, {"source": 183, "target": 46}, {"source": 184, "target": 185}, {"source": 185, "target": 23}, {"source": 88, "target": 49}, {"source": 186, "target": 88}, {"source": 143, "target": 23}, {"source": 161, "target": 143}, {"source": 59, "target": 150}, {"source": 59, "target": 20}, {"source": 59, "target": 34}, {"source": 59, "target": 21}, {"source": 59, "target": 65}, {"source": 187, "target": 59}, {"source": 188, "target": 90}, {"source": 189, "target": 61}, {"source": 190, "target": 189}, {"source": 191, "target": 20}, {"source": 20, "target": 66}, {"source": 192, "target": 20}, {"source": 193, "target": 194}, {"source": 193, "target": 49}, {"source": 193, "target": 195}, {"source": 91, "target": 120}, {"source": 91, "target": 196}, {"source": 91, "target": 34}, {"source": 197, "target": 91}, {"source": 83, "target": 49}, {"source": 198, "target": 199}, {"source": 62, "target": 61}, {"source": 199, "target": 62}, {"source": 173, "target": 135}, {"source": 173, "target": 49}, {"source": 173, "target": 67}, {"source": 173, "target": 111}, {"source": 200, "target": 173}, {"source": 125, "target": 21}, {"source": 156, "target": 125}, {"source": 181, "target": 150}, {"source": 181, "target": 35}, {"source": 181, "target": 37}, {"source": 201, "target": 181}, {"source": 13, "target": 59}, {"source": 202, "target": 13}, {"source": 122, "target": 181}, {"source": 30, "target": 121}, {"source": 30, "target": 37}, {"source": 30, "target": 122}, {"source": 76, "target": 36}, {"source": 76, "target": 122}, {"source": 76, "target": 150}, {"source": 203, "target": 76}, {"source": 204, "target": 173}, {"source": 205, "target": 204}, {"source": 206, "target": 49}, {"source": 196, "target": 123}, {"source": 196, "target": 112}, {"source": 207, "target": 196}, {"source": 208, "target": 123}, {"source": 208, "target": 112}, {"source": 209, "target": 208}, {"source": 17, "target": 49}, {"source": 210, "target": 17}, {"source": 121, "target": 173}, {"source": 211, "target": 121}, {"source": 212, "target": 23}, {"source": 102, "target": 61}, {"source": 213, "target": 37}, {"source": 213, "target": 35}, {"source": 214, "target": 213}, {"source": 215, "target": 170}, {"source": 215, "target": 49}, {"source": 216, "target": 215}, {"source": 217, "target": 49}, {"source": 90, "target": 208}, {"source": 90, "target": 140}, {"source": 218, "target": 90}, {"source": 80, "target": 66}, {"source": 219, "target": 80}, {"source": 220, "target": 49}, {"source": 221, "target": 222}, {"source": 61, "target": 56}, {"source": 61, "target": 223}, {"source": 61, "target": 68}, {"source": 61, "target": 66}, {"source": 61, "target": 59}, {"source": 61, "target": 52}, {"source": 61, "target": 84}, {"source": 61, "target": 5}, {"source": 61, "target": 224}, {"source": 61, "target": 225}, {"source": 61, "target": 226}, {"source": 61, "target": 70}, {"source": 222, "target": 61}, {"source": 222, "target": 78}, {"source": 227, "target": 43}, {"source": 228, "target": 227}, {"source": 229, "target": 230}, {"source": 230, "target": 46}, {"source": 23, "target": 115}, {"source": 23, "target": 113}, {"source": 215, "target": 23}, {"source": 23, "target": 49}, {"source": 231, "target": 23}, {"source": 72, "target": 46}, {"source": 232, "target": 72}, {"source": 37, "target": 111}, {"source": 37, "target": 123}, {"source": 233, "target": 37}, {"source": 162, "target": 112}, {"source": 162, "target": 65}, {"source": 162, "target": 123}, {"source": 234, "target": 162}]}\n\\ No newline at end of file\n' |
| b |
| diff -r cb4dce1042ef -r 567274fa974d test-data/cvt_attributes.venn --- a/test-data/cvt_attributes.venn Thu Jun 02 09:32:40 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,15838 +0,0 @@\n-root\thttp://chart.apis.google.com/chart?chs=232x232&chco=82FF00,FF003B,7E00FF&cht=v&chd=t:35.1,33.5,31.4,4.8,15.6,3.6,0.0&chf=bg,s,e0dede00\troot[0.004]\t6817559 6100438 6497257 3027796 932408 698128 0\n-unclassified_sequences\thttp://chart.apis.google.com/chart?chs=65x65&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:50.5,45.8,3.7,45.2,3.6,3.6,0.0&chf=bg,s,e0dede00\tunclassified_sequences[0.000]\t107967 97973 7999 96764 7631 7730 0\n-not_assigned_root\thttp://chart.apis.google.com/chart?chs=47x47&chco=FF003B,82FF00,7E00FF&cht=v&chd=t:86.2,11.1,2.7,11.1,2.7,2.7,0.0&chf=bg,s,e0dede00\tnot_assigned_root\t10598 2582 82264 2582 10598 2582 0\n-other_sequences\thttp://chart.apis.google.com/chart?chs=37x37&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:71.4,25.3,3.3,25.0,0.1,0.2,0.0&chf=bg,s,e0dede00\tother_sequences[0.209]\t1366 3852 179 1349 9 5 0\n-Not_assigned\thttp://chart.apis.google.com/chart?chs=54x54&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:52.2,29.0,18.8,29.0,18.8,18.8,0.0&chf=bg,s,e0dede00\tNot_assigned\t108864 60481 39175 60481 39175 39175 0\n-cellular_organisms\thttp://chart.apis.google.com/chart?chs=231x231&chco=82FF00,FF003B,7E00FF&cht=v&chd=t:34.8,33.8,31.4,4.6,15.2,3.4,0.0&chf=bg,s,e0dede00\tcellular_organisms[0.057]\t6554551 5915965 6363515 2855502 873865 647190 0\n-Viruses\thttp://chart.apis.google.com/chart?chs=61x61&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:59.1,33.8,7.1,19.2,2.0,2.5,0.0&chf=bg,s,e0dede00\tViruses[0.029]\t34213 19585 4125 11118 1130 1446 0\n-environmental_samples_<unclassified>\thttp://chart.apis.google.com/chart?chs=65x65&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:50.5,45.8,3.7,45.2,3.6,3.6,0.0&chf=bg,s,e0dede00\tenvironmental_samples_<unclassified>[0.020]\t107963 97969 7998 96760 7630 7729 0\n-unidentified\thttp://chart.apis.google.com/chart?chs=19x19&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:44.4,44.4,11.1,44.4,11.1,11.1,0.0&chf=bg,s,e0dede00\tunidentified\t4 4 1 4 1 1 0\n-artificial_sequences\thttp://chart.apis.google.com/chart?chs=37x37&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:71.4,25.3,3.3,25.0,0.1,0.2,0.0&chf=bg,s,e0dede00\tartificial_sequences[0.215]\t1366 3851 179 1349 9 5 0\n-plasmids\thttp://chart.apis.google.com/chart?chs=17x17&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:100.0,0.0,0.0,0.0,0.0,0.0,0.0&chf=bg,s,e0dede00\tplasmids[1.000]\t0 1 0 0 0 0 0\n-Eukaryota\thttp://chart.apis.google.com/chart?chs=147x147&chco=7E00FF,FF003B,82FF00&cht=v&chd=t:47.8,29.4,22.8,3.4,13.6,5.2,0.0&chf=bg,s,e0dede00\tEukaryota[0.003]\t680470 1429149 879893 407600 154736 101822 0\n-not_assigned_cellular_organisms\thttp://chart.apis.google.com/chart?chs=80x80&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:84.6,10.8,4.5,10.8,4.5,4.5,0.0&chf=bg,s,e0dede00\tnot_assigned_cellular_organisms\t1383800 176813 74172 176813 74172 74172 0\n-Bacteria\thttp://chart.apis.google.com/chart?chs=220x220&chco=FF003B,82FF00,7E00FF&cht=v&chd=t:38.1,31.7,30.2,4.5,3.3,16.0,0.0&chf=bg,s,e0dede00\tBacteria[0.001]\t4483868 4274297 5390301 2267386 643310 463276 0\n-Archaea\thttp://chart.apis.google.com/chart?chs=63x63&chco=7E00FF,FF003B,82FF00&cht=v&chd=t:58.3,31.3,10.5,12.9,6.0,2.7,0.0&chf=bg,s,e0dede00\tArchaea[0.011]\t6413 35706 19149 3703 1647 7920 0\n-dsDNA_viruses,_no_RNA_stage\thttp://chart.apis.google.com/chart?chs=58x58&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:61.8,36.0,2.2,20.6,2.0,2.0,0.0&chf=bg,s,e0dede00\tdsDNA_viruses,_no_RNA_stage[0.071]\t30896 18026 1106 10303 1009 988 0\n-unclassified_phages\thttp://chart.apis.google.com/chart?chs=26x26&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:52.6,38.8,8.6,16.4,8.6,5.3,0.0&chf=bg,s,e0dede00\tunclassified_phages[0.271]\t80 59 13 25 13 8 0\n-unassigned_viruses\thttp://chart.apis.google.com/chart?chs=20x20&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:80.0,20.0,0.0,10.0,0.0,0.0,0.0&chf=bg,s,e0dede00\tunassigned_viruses[0.413]\t8 2 0 1 0 0 0\n-ssRNA_viruses\thttp://chart.apis.google.com/chart?chs=25x25&chco=FF003B,82FF00,7E00FF&cht=v&chd=t:61.2,26.4,12.4,11.6,5.8,6.6,0.0&chf=bg,s,e0dede00\tssRNA_viruses[0.234]\t32 15 74 8 14 7 0\n-unclassified_viruses\thttp://chart.apis.google.com/chart?chs=18x18&chco=7E0'..b':70.6,17.6,11.8,17.6,11.8,11.8,0.0&chf=bg,s,e0dede00\tDorea_longicatena_DSM_13814\t3 12 2 3 2 2 0\n-Streptococcus_oligofermentans_AS_1.3089\thttp://chart.apis.google.com/chart?chs=19x19&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:87.5,12.5,0.0,12.5,0.0,0.0,0.0&chf=bg,s,e0dede00\tStreptococcus_oligofermentans_AS_1.3089\t1 7 0 1 0 0 0\n-Thiriotia\thttp://chart.apis.google.com/chart?chs=18x18&chco=82FF00,FF003B,7E00FF&cht=v&chd=t:50.0,50.0,0.0,50.0,0.0,0.0,0.0&chf=bg,s,e0dede00\tThiriotia[1.000]\t1 0 1 0 1 0 0\n-Acanthocephala\thttp://chart.apis.google.com/chart?chs=19x19&chco=FF003B,7E00FF,82FF00&cht=v&chd=t:66.7,16.7,16.7,16.7,0.0,0.0,0.0&chf=bg,s,e0dede00\tAcanthocephala[0.250]\t1 1 4 0 0 1 0\n-Brachiopoda\thttp://chart.apis.google.com/chart?chs=22x22&chco=FF003B,7E00FF,82FF00&cht=v&chd=t:54.8,29.0,16.1,16.1,12.9,12.9,0.0&chf=bg,s,e0dede00\tBrachiopoda[0.430]\t5 9 17 4 4 5 0\n-Annelida\thttp://chart.apis.google.com/chart?chs=32x32&chco=82FF00,FF003B,7E00FF&cht=v&chd=t:49.3,37.0,13.7,8.2,5.4,5.9,0.0&chf=bg,s,e0dede00\tAnnelida[0.466]\t464 129 349 51 77 56 0\n-Mollusca\thttp://chart.apis.google.com/chart?chs=37x37&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:55.3,29.4,15.3,25.5,6.8,6.6,0.0&chf=bg,s,e0dede00\tMollusca[0.103]\t973 1830 507 844 218 225 0\n-Bryozoa\thttp://chart.apis.google.com/chart?chs=25x25&chco=FF003B,82FF00,7E00FF&cht=v&chd=t:59.3,29.4,11.3,25.4,5.6,7.9,0.0&chf=bg,s,e0dede00\tBryozoa[0.502]\t52 20 105 14 45 10 0\n-Rotifera\thttp://chart.apis.google.com/chart?chs=24x24&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:54.3,32.9,12.9,17.1,8.6,7.1,0.0&chf=bg,s,e0dede00\tRotifera[0.611]\t23 38 9 12 5 6 0\n-not_assigned_Lophotrochozoa\thttp://chart.apis.google.com/chart?chs=23x23&chco=FF003B,82FF00,7E00FF&cht=v&chd=t:86.7,9.9,3.4,9.9,3.4,3.4,0.0&chf=bg,s,e0dede00\tnot_assigned_Lophotrochozoa\t29 10 254 10 29 10 0\n-Entoprocta\thttp://chart.apis.google.com/chart?chs=21x21&chco=FF003B,7E00FF,82FF00&cht=v&chd=t:52.4,33.3,14.3,19.0,4.8,0.0,0.0&chf=bg,s,e0dede00\tEntoprocta[0.320]\t3 7 11 0 1 4 0\n-Nemertea\thttp://chart.apis.google.com/chart?chs=24x24&chco=FF003B,7E00FF,82FF00&cht=v&chd=t:79.8,16.3,3.8,6.7,1.0,2.9,0.0&chf=bg,s,e0dede00\tNemertea[0.176]\t4 17 83 3 1 7 0\n-Myzostomida\thttp://chart.apis.google.com/chart?chs=19x19&chco=82FF00,7E00FF,FF003B&cht=v&chd=t:75.0,25.0,0.0,0.0,0.0,0.0,0.0&chf=bg,s,e0dede00\tMyzostomida[0.250]\t3 1 0 0 0 0 0\n-Gastrotricha\thttp://chart.apis.google.com/chart?chs=24x24&chco=7E00FF,FF003B,82FF00&cht=v&chd=t:71.3,21.3,7.4,3.7,4.6,4.6,0.0&chf=bg,s,e0dede00\tGastrotricha[0.392]\t8 77 23 5 5 4 0\n-Methanolobus_psychrophilus_R15\thttp://chart.apis.google.com/chart?chs=19x19&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:61.9,28.6,9.5,28.6,9.5,9.5,0.0&chf=bg,s,e0dede00\tMethanolobus_psychrophilus_R15\t6 13 2 6 2 2 0\n-Acidovorax_citrulli_AAC00-1\thttp://chart.apis.google.com/chart?chs=20x20&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:68.0,24.0,8.0,24.0,8.0,8.0,0.0&chf=bg,s,e0dede00\tAcidovorax_citrulli_AAC00-1\t6 17 2 6 2 2 0\n-Brevibacillus_laterosporus_DSM_25\thttp://chart.apis.google.com/chart?chs=21x21&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:53.8,36.8,9.4,36.8,9.4,9.4,0.0&chf=bg,s,e0dede00\tBrevibacillus_laterosporus_DSM_25\t39 57 10 39 10 10 0\n-Brevibacillus_laterosporus_LMG_15441\thttp://chart.apis.google.com/chart?chs=17x17&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:100.0,0.0,0.0,0.0,0.0,0.0,0.0&chf=bg,s,e0dede00\tBrevibacillus_laterosporus_LMG_15441\t0 1 0 0 0 0 0\n-Halanaerobium_praevalens_DSM_2228\thttp://chart.apis.google.com/chart?chs=24x24&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:63.5,31.3,5.3,31.3,5.3,5.3,0.0&chf=bg,s,e0dede00\tHalanaerobium_praevalens_DSM_2228\t137 278 23 137 23 23 0\n-Clostridium_hylemonae_DSM_15053\thttp://chart.apis.google.com/chart?chs=22x22&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:93.8,6.2,0.0,6.2,0.0,0.0,0.0&chf=bg,s,e0dede00\tClostridium_hylemonae_DSM_15053\t9 136 0 9 0 0 0\n-Desulfotomaculum_gibsoniae_DSM_7213\thttp://chart.apis.google.com/chart?chs=21x21&chco=7E00FF,82FF00,FF003B&cht=v&chd=t:65.7,19.4,14.9,19.4,14.9,14.9,0.0&chf=bg,s,e0dede00\tDesulf\n\\ No newline at end of file\n' |
| b |
| diff -r cb4dce1042ef -r 567274fa974d test-data/cvt_network.sif --- a/test-data/cvt_network.sif Thu Jun 02 09:32:40 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,101 +0,0 @@ -root pp cellular_organisms -cellular_organisms pp Bacteria -Bacteria pp Actinobacteria_<phylum> -Bacteria pp Aquificae_<phylum> -Bacteria pp Armatimonadetes -Bacteria pp Bacteroidetes/Chlorobi_group -Bacteria pp Caldiserica -Bacteria pp Chlamydiae/Verrucomicrobia_group -Bacteria pp Chloroflexi_<phylum> -Bacteria pp Chrysiogenetes_<phylum> -Bacteria pp Cyanobacteria -Cyanobacteria pp environmental_samples_<Cyanobacteria> -Cyanobacteria pp Gloeobacteria -Cyanobacteria pp Nostocales -Cyanobacteria pp Oscillatoriophycideae -Cyanobacteria pp Pleurocapsales -Cyanobacteria pp Prochlorales -Prochlorales pp environmental_samples_<Prochlorophytes> -Prochlorales pp Prochloraceae -Prochlorales pp Prochlorococcaceae -Prochlorococcaceae pp Prochlorococcus -Prochlorococcus pp environmental_samples_<Prochlorococcus> -Prochlorococcus pp Prochlorococcus_marinus -Prochlorococcus_marinus pp environmental_samples_<Prochlorococcus_marinus> -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._AS9601 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._CCMP1377 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._GP2 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9107 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9116 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9201 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9202 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9211 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9215 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9301 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9302 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9303 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9312 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9313 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._MIT_9515 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._NATL1A -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._NATL1MIT -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._NATL2A -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._PAC1 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._PAC1A -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._PAC1B -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._PAC2 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._RS2001 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._RS810 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._SB -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._TAK9803 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._TAK9803-2 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._TATL1 -Prochlorococcus_marinus pp Prochlorococcus_marinus_str._TATL1B -Prochlorococcus_marinus pp Prochlorococcus_marinus_subsp._marinus -Prochlorococcus_marinus pp Prochlorococcus_marinus_subsp._pastoris -Prochlorococcus pp Prochlorococcus_sp. -Prochlorales pp Prochlorotrichaceae -Cyanobacteria pp Stigonematales -Cyanobacteria pp unclassified_Cyanobacteria -Bacteria pp Deferribacteres_<phylum> -Bacteria pp Deinococcus-Thermus -Bacteria pp Dictyoglomi -Bacteria pp Elusimicrobia -Bacteria pp environmental_samples_<Bacteria> -Bacteria pp Fibrobacteres/Acidobacteria_group -Bacteria pp Firmicutes -Bacteria pp Fusobacteria -Bacteria pp Gemmatimonadetes -Bacteria pp Nitrospinae -Bacteria pp Nitrospirae -Bacteria pp Planctomycetes -Bacteria pp Proteobacteria -Bacteria pp Spirochaetes -Bacteria pp Synergistetes -Bacteria pp Tenericutes -Bacteria pp Thermodesulfobacteria_<phylum> -Bacteria pp Thermotogae_<phylum> -Bacteria pp unclassified_Bacteria -cellular_organisms pp Archaea -cellular_organisms pp Eukaryota -root pp Viruses -Viruses pp dsDNA_viruses,_no_RNA_stage -Viruses pp dsRNA_viruses -Viruses pp environmental_samples_<viruses> -Viruses pp Retro-transcribing_viruses -Viruses pp ssDNA_viruses -Viruses pp ssRNA_viruses -Viruses pp unassigned_viruses -Viruses pp unclassified_phages -Viruses pp unclassified_viruses -root pp unclassified_sequences -root pp other_sequences -root pp Not_assigned -Viruses pp not_assigned_Viruses -Prochlorococcus_marinus pp not_assigned_Prochlorococcus_marinus -Prochlorococcus pp not_assigned_Prochlorococcus -Prochlorales pp not_assigned_Prochlorales -Cyanobacteria pp not_assigned_Cyanobacteria -Bacteria pp not_assigned_Bacteria -cellular_organisms pp not_assigned_cellular_organisms -root pp not_assigned_root |
| b |
| diff -r cb4dce1042ef -r 567274fa974d test-data/cvt_nodelink.json --- a/test-data/cvt_nodelink.json Thu Jun 02 09:32:40 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
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"target": 92}, {"source": 0, "target": 93}, {"source": 81, "target": 94}, {"source": 23, "target": 95}, {"source": 21, "target": 96}, {"source": 17, "target": 97}, {"source": 11, "target": 98}, {"source": 2, "target": 99}, {"source": 1, "target": 100}, {"source": 0, "target": 101}]}\n\\ No newline at end of file\n' |
| b |
| diff -r cb4dce1042ef -r 567274fa974d vgx_converter.py --- a/vgx_converter.py Thu Jun 02 09:32:40 2016 -0400 +++ b/vgx_converter.py Sat Jun 04 03:22:52 2016 -0400 |
| [ |
| @@ -5,7 +5,6 @@ import json import shlex - def __main__(): arg_names = ['command', "network", "delimiter", "attributes", "output"] @@ -46,7 +45,7 @@ data = { 'graph': {'nodes': nodes, 'edges': links}} if args['attributes'] != 'None': # None for Galaxy - data['some'] = 'not in here' + #data['some'] = 'not in here' # process attributes list with open(sys.argv[3]) as f: |
| b |
| diff -r cb4dce1042ef -r 567274fa974d vgx_converter.xml --- a/vgx_converter.xml Thu Jun 02 09:32:40 2016 -0400 +++ b/vgx_converter.xml Sat Jun 04 03:22:52 2016 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="vgx_converter" name="SIF-to-JGF" version="0.0.4"> +<tool id="vgx_converter" name="SIF-to-JGF" version="0.0.5"> <description>Converts a SIF file to a JSON Graph Format (JGF) file for visualization in VisualGraphX</description> <command interpreter="python">vgx_converter.py $input1 $delimiter $input2 $output</command> <inputs> @@ -21,15 +21,15 @@ <tests> <test> - <param name="input1" value="cvt_network.sif"/> + <param name="input1" value="CoVennTree_network.sif"/> <param name="delimiter" value="space"/> - <param name="input2" value="cvt_attributes.venn"/> - <param name="output" value="cvt_nodelink.json"/> + <param name="input2" value="CoVennTree.venn"/> + <param name="output" value="CoVennTree.jgf"/> </test> <test> - <param name="input1" value="angiogenesis_network.sif"/> + <param name="input1" value="Apoptosis.sif"/> <param name="delimiter" value="tab"/> - <param name="output" value="angiogenesis_nodelink.json"/> + <param name="output" value="Apoptosis.jgf"/> </test> </tests> |