| Previous changeset 1:f009d54be92b (2016-02-23) Next changeset 3:acb0ce730695 (2016-02-23) |
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Commit message:
Uploaded |
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added:
._vgx_converter.py.bz2 test-data/.DS_Store test-data/._.DS_Store test-data/._angiogenesis_network.sif test-data/._cvt_attributes.venn test-data/._cvt_network.sif 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 vgx_converter.py.bz2 vgx_converter.xml.bz2 |
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removed:
vgx_converter.py vgx_converter.xml |
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| diff -r f009d54be92b -r f5e05d6382c8 test-data/._cvt_attributes.venn |
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| diff -r f009d54be92b -r f5e05d6382c8 test-data/angiogenesis_network.sif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/angiogenesis_network.sif Tue Feb 23 09:17:36 2016 -0500 |
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| b'@@ -0,0 +1,322 @@\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 f009d54be92b -r f5e05d6382c8 test-data/angiogenesis_nodelink.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/angiogenesis_nodelink.json Tue Feb 23 09:17:36 2016 -0500 |
| [ |
| b'@@ -0,0 +1,1 @@\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 f009d54be92b -r f5e05d6382c8 test-data/cvt_attributes.venn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cvt_attributes.venn Tue Feb 23 09:17:36 2016 -0500 |
| [ |
| 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 f009d54be92b -r f5e05d6382c8 test-data/cvt_network.sif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cvt_network.sif Tue Feb 23 09:17:36 2016 -0500 |
| 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 f009d54be92b -r f5e05d6382c8 test-data/cvt_nodelink.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cvt_nodelink.json Tue Feb 23 09:17:36 2016 -0500 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"nodes": [{"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, "name": "root"}, {"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, "name": "cellular_organisms"}, {"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": 2, "name": "Bacteria"}, {"property0": 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11, "target": 58}, {"source": 11, "target": 59}, {"source": 2, "target": 60}, {"source": 2, "target": 61}, {"source": 2, "target": 62}, {"source": 2, "target": 63}, {"source": 2, "target": 64}, {"source": 2, "target": 65}, {"source": 2, "target": 66}, {"source": 2, "target": 67}, {"source": 2, "target": 68}, {"source": 2, "target": 69}, {"source": 2, "target": 70}, {"source": 2, "target": 71}, {"source": 2, "target": 72}, {"source": 2, "target": 73}, {"source": 2, "target": 74}, {"source": 2, "target": 75}, {"source": 2, "target": 76}, {"source": 2, "target": 77}, {"source": 2, "target": 78}, {"source": 1, "target": 79}, {"source": 1, "target": 80}, {"source": 0, "target": 81}, {"source": 81, "target": 82}, {"source": 81, "target": 83}, {"source": 81, "target": 84}, {"source": 81, "target": 85}, {"source": 81, "target": 86}, {"source": 81, "target": 87}, {"source": 81, "target": 88}, {"source": 81, "target": 89}, {"source": 81, "target": 90}, {"source": 0, "target": 91}, {"source": 0, "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' |
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| diff -r f009d54be92b -r f5e05d6382c8 vgx_converter.py --- a/vgx_converter.py Tue Feb 23 09:03:17 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,71 +0,0 @@ -#!/usr/bin/python - -import sys # -import csv -import json -import shlex - - -def __main__(): - - arg_names = ['command', "network", "delimiter", "attributes", "output"] - args = dict(zip(arg_names, sys.argv)) - print args - - idc = 0 # counter for the ids - ids = {} # dictionary with id and name correlation - keys = [] - - nodes = [] - links = [] - - delim = {} - delim['tab'] = '\t' - delim['space'] = ' ' - - - ################################################# - data = {} - with open(sys.argv[1], 'r') as f: - reader = csv.reader(f, delimiter=delim[sys.argv[2]]) - for row in reader: # iterate through each line - p1 = shlex.split(row[0])[0] - p2 = shlex.split(row[2])[0] - - if p1 not in ids: - ids[p1] = idc - idc = idc + 1 - nodes.append({'id': ids[p1], 'name': p1 }) - if p2 not in ids: - ids[p2] = idc - idc = idc + 1 - nodes.append({'id': ids[p2], 'name': p2 }) - - links.append({'source': ids[p1], 'target': ids[p2]}) - f.close() - - data = {'nodes': nodes, 'links': links} - - if args['attributes'] != 'None': # None for Galaxy - data['some'] = 'not in here' - - # process attributes list - with open(sys.argv[3]) as f: - reader = csv.reader(f, delimiter='\t') - ids_keys = ids.keys() - for row in reader: - propscnt = 0 - if row[0] in ids_keys: - pos = ids[row[0]] - for props in range(len(row)-1): - nodes[pos]['property'+str(propscnt)] = row[props+1] - propscnt = propscnt +1 - f.close() - - # write json data back to spec ified output file - with open(sys.argv[4], 'w') as out: - json.dump(data, out) - out.close() - -if __name__ == "__main__": - __main__() \ No newline at end of file |
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| diff -r f009d54be92b -r f5e05d6382c8 vgx_converter.xml --- a/vgx_converter.xml Tue Feb 23 09:03:17 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,37 +0,0 @@ -<tool id="vgx_converter" name="SIF-to-VGX" version="0.0.1"> - <description>Converts a SIF file to a JSON file in node-link format for visualization in VisualGraphX</description> - <command interpreter="python">vgx_converter.py $input1 $delimiter $input2 $output</command> - <inputs> - <param format="txt" name="input1" type="data" label="Network"/> - <param format="tabular" name="input2" type="data" optional="true" label="Attributes"/> - <param name="delimiter" type="select" label="Delimiter"> - <option value="tab" selected="true">tab-delimited</option> - <option value="space">space-delimited</option> - </param> - </inputs> - <outputs> - <data format="json" name="output"/> - </outputs> - - <help> - This tool converts the simple interaction format (.sif) to the JavaScript Object Notation (.json) - that can be visualized using VisualGraphX. Furthermore, a attributes list can be provided to enhance - the information of the nodes in the graph. - </help> - - <tests> - <test> - <param name="input1" value="cvt_network.sif"/> - <param name="delimiter" value="space"/> - <param name="input2" value="cvt_attributes.venn"/> - <param name="output" value="cvt_nodelink.json"/> - </test> - <test> - <param name="input1" value="angiogenesis_network.sif"/> - <param name="delimiter" value="tab"/> - <param name="output" value="angiogenesis_nodelink.json"/> - </test> - </tests> - -</tool> - |
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