Mercurial > repos > rdvelazquez > hivclustering
diff test-data/hivclustering-out2.json @ 1:d975f8166fc8 draft
planemo upload for repository https://github.com/veg/hivclustering/ commit b'bf63b6fa0634630e46efafb2ba62a6554d7168a8\n'-dirty
author | rdvelazquez |
---|---|
date | Mon, 05 Mar 2018 10:57:10 -0500 |
parents | b2bdeb5c06ed |
children | 9dc36a1975e8 |
line wrap: on
line diff
--- a/test-data/hivclustering-out2.json Mon Mar 05 10:17:18 2018 -0500 +++ b/test-data/hivclustering-out2.json Mon Mar 05 10:57:10 2018 -0500 @@ -1,527 +1,527 @@ -{ - "Cluster sizes": [ - 8 - ], - "Degrees": { - "Distribution": [ - 0, - 0, - 0, - 0, - 0, - 0, - 8 - ], - "Model": "Negative Binomial", - "fitted": null, - "rho": 0.0, - "rho CI": [ - 0.0, - 0.0 - ] - }, - "Directed Edges": { - "Count": 0, - "Reasons for unresolved directions": { - "Missing dates": 28 - } - }, - "Edges": [ - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.045156, - "removed": false, - "sequences": [ - "B_FR_83_HXB2_ACC_K03455_5", - "B_US_83_RF_ACC_M17451" - ], - "source": 3, - "support": 0.0, - "target": 4 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0296218, - "removed": false, - "sequences": [ - "B_FR_83_HXB2_ACC_K03455_5", - "B_US_86_JRFL_ACC_U63632" - ], - "source": 3, - "support": 0.0, - "target": 0 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0327566, - "removed": false, - "sequences": [ - "B_FR_83_HXB2_ACC_K03455_5", - "B_US_90_WEAU160_ACC_U21135" - ], - "source": 3, - "support": 0.0, - "target": 1 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0669206, - "removed": false, - "sequences": [ - "B_FR_83_HXB2_ACC_K03455_5", - "D_CD_83_ELI_ACC_K03454_7" - ], - "source": 3, - "support": 0.0, - "target": 2 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0592586, - "removed": false, - "sequences": [ - "B_FR_83_HXB2_ACC_K03455_5", - "D_CD_83_NDK_ACC_M27323" - ], - "source": 3, - "support": 0.0, - "target": 5 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0663619, - "removed": false, - "sequences": [ - "B_FR_83_HXB2_ACC_K03455_5", - "D_CD_84_84ZR085_ACC_U88822" - ], - "source": 3, - "support": 0.0, - "target": 6 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0847988, - "removed": false, - "sequences": [ - "B_FR_83_HXB2_ACC_K03455_5", - "D_UG_94_94UG114_ACC_U88824" - ], - "source": 3, - "support": 0.0, - "target": 7 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.048328, - "removed": false, - "sequences": [ - "B_US_83_RF_ACC_M17451", - "B_US_86_JRFL_ACC_U63632" - ], - "source": 4, - "support": 0.0, - "target": 0 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0515908, - "removed": false, - "sequences": [ - "B_US_83_RF_ACC_M17451", - "B_US_90_WEAU160_ACC_U21135" - ], - "source": 4, - "support": 0.0, - "target": 1 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0810759, - "removed": false, - "sequences": [ - "B_US_83_RF_ACC_M17451", - "D_CD_83_ELI_ACC_K03454_7" - ], - "source": 4, - "support": 0.0, - "target": 2 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0661066, - "removed": false, - "sequences": [ - "B_US_83_RF_ACC_M17451", - "D_CD_83_NDK_ACC_M27323" - ], - "source": 4, - "support": 0.0, - "target": 5 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0769146, - "removed": false, - "sequences": [ - "B_US_83_RF_ACC_M17451", - "D_CD_84_84ZR085_ACC_U88822" - ], - "source": 4, - "support": 0.0, - "target": 6 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0955213, - "removed": false, - "sequences": [ - "B_US_83_RF_ACC_M17451", - "D_UG_94_94UG114_ACC_U88824" - ], - "source": 4, - "support": 0.0, - "target": 7 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0408994, - "removed": false, - "sequences": [ - "B_US_86_JRFL_ACC_U63632", - "B_US_90_WEAU160_ACC_U21135" - ], - "source": 0, - "support": 0.0, - "target": 1 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0771797, - "removed": false, - "sequences": [ - "B_US_86_JRFL_ACC_U63632", - "D_CD_83_ELI_ACC_K03454_7" - ], - "source": 0, - "support": 0.0, - "target": 2 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0609044, - "removed": false, - "sequences": [ - "B_US_86_JRFL_ACC_U63632", - "D_CD_83_NDK_ACC_M27323" - ], - "source": 0, - "support": 0.0, - "target": 5 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0705011, - "removed": false, - "sequences": [ - "B_US_86_JRFL_ACC_U63632", - "D_CD_84_84ZR085_ACC_U88822" - ], - "source": 0, - "support": 0.0, - "target": 6 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0882054, - "removed": false, - "sequences": [ - "B_US_86_JRFL_ACC_U63632", - "D_UG_94_94UG114_ACC_U88824" - ], - "source": 0, - "support": 0.0, - "target": 7 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0771856, - "removed": false, - "sequences": [ - "B_US_90_WEAU160_ACC_U21135", - "D_CD_83_ELI_ACC_K03454_7" - ], - "source": 1, - "support": 0.0, - "target": 2 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0609097, - "removed": false, - "sequences": [ - "B_US_90_WEAU160_ACC_U21135", - "D_CD_83_NDK_ACC_M27323" - ], - "source": 1, - "support": 0.0, - "target": 5 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0740203, - "removed": false, - "sequences": [ - "B_US_90_WEAU160_ACC_U21135", - "D_CD_84_84ZR085_ACC_U88822" - ], - "source": 1, - "support": 0.0, - "target": 6 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0890019, - "removed": false, - "sequences": [ - "B_US_90_WEAU160_ACC_U21135", - "D_UG_94_94UG114_ACC_U88824" - ], - "source": 1, - "support": 0.0, - "target": 7 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0287246, - "removed": false, - "sequences": [ - "D_CD_83_ELI_ACC_K03454_7", - "D_CD_83_NDK_ACC_M27323" - ], - "source": 2, - "support": 0.0, - "target": 5 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.055948, - "removed": false, - "sequences": [ - "D_CD_83_ELI_ACC_K03454_7", - "D_CD_84_84ZR085_ACC_U88822" - ], - "source": 2, - "support": 0.0, - "target": 6 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0742033, - "removed": false, - "sequences": [ - "D_CD_83_ELI_ACC_K03454_7", - "D_UG_94_94UG114_ACC_U88824" - ], - "source": 2, - "support": 0.0, - "target": 7 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0491974, - "removed": false, - "sequences": [ - "D_CD_83_NDK_ACC_M27323", - "D_CD_84_84ZR085_ACC_U88822" - ], - "source": 5, - "support": 0.0, - "target": 6 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0726626, - "removed": false, - "sequences": [ - "D_CD_83_NDK_ACC_M27323", - "D_UG_94_94UG114_ACC_U88824" - ], - "source": 5, - "support": 0.0, - "target": 7 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0805088, - "removed": false, - "sequences": [ - "D_CD_84_84ZR085_ACC_U88822", - "D_UG_94_94UG114_ACC_U88824" - ], - "source": 6, - "support": 0.0, - "target": 7 - } - ], - "HIV Stages": { - "Unknown": 8 - }, - "Multiple sequences": { - "Followup, days": null, - "Subjects with": 0 - }, - "Network Summary": { - "Clusters": 1, - "Edges": 28, - "Nodes": 8, - "Sequences used to make links": 8 - }, - "Nodes": [ - { - "attributes": [], - "baseline": null, - "cluster": 1, - "edi": null, - "id": "B_FR_83_HXB2_ACC_K03455_5" - }, - { - "attributes": [], - "baseline": null, - "cluster": 1, - "edi": null, - "id": "B_US_83_RF_ACC_M17451" - }, - { - "attributes": [], - "baseline": null, - "cluster": 1, - "edi": null, - "id": "B_US_86_JRFL_ACC_U63632" - }, - { - "attributes": [], - "baseline": null, - "cluster": 1, - "edi": null, - "id": "B_US_90_WEAU160_ACC_U21135" - }, - { - "attributes": [], - "baseline": null, - "cluster": 1, - "edi": null, - "id": "D_CD_83_ELI_ACC_K03454_7" - }, - { - "attributes": [], - "baseline": null, - "cluster": 1, - "edi": null, - "id": "D_CD_83_NDK_ACC_M27323" - }, - { - "attributes": [], - "baseline": null, - "cluster": 1, - "edi": null, - "id": "D_CD_84_84ZR085_ACC_U88822" - }, - { - "attributes": [], - "baseline": null, - "cluster": 1, - "edi": null, - "id": "D_UG_94_94UG114_ACC_U88824" - } - ], - "Settings": { - "contaminants": null, - "edge-filtering": null, - "threshold": 0.8 - } -} +{ + "Cluster sizes": [ + 8 + ], + "Degrees": { + "Distribution": [ + 0, + 0, + 0, + 0, + 0, + 0, + 8 + ], + "Model": "Negative Binomial", + "fitted": null, + "rho": 0.0, + "rho CI": [ + 0.0, + 0.0 + ] + }, + "Directed Edges": { + "Count": 0, + "Reasons for unresolved directions": { + "Missing dates": 28 + } + }, + "Edges": [ + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.045156, + "removed": false, + "sequences": [ + "B_FR_83_HXB2_ACC_K03455_5", + "B_US_83_RF_ACC_M17451" + ], + "source": 3, + "support": 0.0, + "target": 4 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0296218, + "removed": false, + "sequences": [ + "B_FR_83_HXB2_ACC_K03455_5", + "B_US_86_JRFL_ACC_U63632" + ], + "source": 3, + "support": 0.0, + "target": 0 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0327566, + "removed": false, + "sequences": [ + "B_FR_83_HXB2_ACC_K03455_5", + "B_US_90_WEAU160_ACC_U21135" + ], + "source": 3, + "support": 0.0, + "target": 1 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0669206, + "removed": false, + "sequences": [ + "B_FR_83_HXB2_ACC_K03455_5", + "D_CD_83_ELI_ACC_K03454_7" + ], + "source": 3, + "support": 0.0, + "target": 2 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0592586, + "removed": false, + "sequences": [ + "B_FR_83_HXB2_ACC_K03455_5", + "D_CD_83_NDK_ACC_M27323" + ], + "source": 3, + "support": 0.0, + "target": 5 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0663619, + "removed": false, + "sequences": [ + "B_FR_83_HXB2_ACC_K03455_5", + "D_CD_84_84ZR085_ACC_U88822" + ], + "source": 3, + "support": 0.0, + "target": 6 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0847988, + "removed": false, + "sequences": [ + "B_FR_83_HXB2_ACC_K03455_5", + "D_UG_94_94UG114_ACC_U88824" + ], + "source": 3, + "support": 0.0, + "target": 7 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.048328, + "removed": false, + "sequences": [ + "B_US_83_RF_ACC_M17451", + "B_US_86_JRFL_ACC_U63632" + ], + "source": 4, + "support": 0.0, + "target": 0 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0515908, + "removed": false, + "sequences": [ + "B_US_83_RF_ACC_M17451", + "B_US_90_WEAU160_ACC_U21135" + ], + "source": 4, + "support": 0.0, + "target": 1 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0810759, + "removed": false, + "sequences": [ + "B_US_83_RF_ACC_M17451", + "D_CD_83_ELI_ACC_K03454_7" + ], + "source": 4, + "support": 0.0, + "target": 2 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0661066, + "removed": false, + "sequences": [ + "B_US_83_RF_ACC_M17451", + "D_CD_83_NDK_ACC_M27323" + ], + "source": 4, + "support": 0.0, + "target": 5 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0769146, + "removed": false, + "sequences": [ + "B_US_83_RF_ACC_M17451", + "D_CD_84_84ZR085_ACC_U88822" + ], + "source": 4, + "support": 0.0, + "target": 6 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0955213, + "removed": false, + "sequences": [ + "B_US_83_RF_ACC_M17451", + "D_UG_94_94UG114_ACC_U88824" + ], + "source": 4, + "support": 0.0, + "target": 7 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0408994, + "removed": false, + "sequences": [ + "B_US_86_JRFL_ACC_U63632", + "B_US_90_WEAU160_ACC_U21135" + ], + "source": 0, + "support": 0.0, + "target": 1 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0771797, + "removed": false, + "sequences": [ + "B_US_86_JRFL_ACC_U63632", + "D_CD_83_ELI_ACC_K03454_7" + ], + "source": 0, + "support": 0.0, + "target": 2 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0609044, + "removed": false, + "sequences": [ + "B_US_86_JRFL_ACC_U63632", + "D_CD_83_NDK_ACC_M27323" + ], + "source": 0, + "support": 0.0, + "target": 5 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0705011, + "removed": false, + "sequences": [ + "B_US_86_JRFL_ACC_U63632", + "D_CD_84_84ZR085_ACC_U88822" + ], + "source": 0, + "support": 0.0, + "target": 6 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0882054, + "removed": false, + "sequences": [ + "B_US_86_JRFL_ACC_U63632", + "D_UG_94_94UG114_ACC_U88824" + ], + "source": 0, + "support": 0.0, + "target": 7 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0771856, + "removed": false, + "sequences": [ + "B_US_90_WEAU160_ACC_U21135", + "D_CD_83_ELI_ACC_K03454_7" + ], + "source": 1, + "support": 0.0, + "target": 2 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0609097, + "removed": false, + "sequences": [ + "B_US_90_WEAU160_ACC_U21135", + "D_CD_83_NDK_ACC_M27323" + ], + "source": 1, + "support": 0.0, + "target": 5 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0740203, + "removed": false, + "sequences": [ + "B_US_90_WEAU160_ACC_U21135", + "D_CD_84_84ZR085_ACC_U88822" + ], + "source": 1, + "support": 0.0, + "target": 6 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0890019, + "removed": false, + "sequences": [ + "B_US_90_WEAU160_ACC_U21135", + "D_UG_94_94UG114_ACC_U88824" + ], + "source": 1, + "support": 0.0, + "target": 7 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0287246, + "removed": false, + "sequences": [ + "D_CD_83_ELI_ACC_K03454_7", + "D_CD_83_NDK_ACC_M27323" + ], + "source": 2, + "support": 0.0, + "target": 5 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.055948, + "removed": false, + "sequences": [ + "D_CD_83_ELI_ACC_K03454_7", + "D_CD_84_84ZR085_ACC_U88822" + ], + "source": 2, + "support": 0.0, + "target": 6 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0742033, + "removed": false, + "sequences": [ + "D_CD_83_ELI_ACC_K03454_7", + "D_UG_94_94UG114_ACC_U88824" + ], + "source": 2, + "support": 0.0, + "target": 7 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0491974, + "removed": false, + "sequences": [ + "D_CD_83_NDK_ACC_M27323", + "D_CD_84_84ZR085_ACC_U88822" + ], + "source": 5, + "support": 0.0, + "target": 6 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0726626, + "removed": false, + "sequences": [ + "D_CD_83_NDK_ACC_M27323", + "D_UG_94_94UG114_ACC_U88824" + ], + "source": 5, + "support": 0.0, + "target": 7 + }, + { + "attributes": [ + "BULK" + ], + "directed": false, + "length": 0.0805088, + "removed": false, + "sequences": [ + "D_CD_84_84ZR085_ACC_U88822", + "D_UG_94_94UG114_ACC_U88824" + ], + "source": 6, + "support": 0.0, + "target": 7 + } + ], + "HIV Stages": { + "Unknown": 8 + }, + "Multiple sequences": { + "Followup, days": null, + "Subjects with": 0 + }, + "Network Summary": { + "Clusters": 1, + "Edges": 28, + "Nodes": 8, + "Sequences used to make links": 8 + }, + "Nodes": [ + { + "attributes": [], + "baseline": null, + "cluster": 1, + "edi": null, + "id": "B_FR_83_HXB2_ACC_K03455_5" + }, + { + "attributes": [], + "baseline": null, + "cluster": 1, + "edi": null, + "id": "B_US_83_RF_ACC_M17451" + }, + { + "attributes": [], + "baseline": null, + "cluster": 1, + "edi": null, + "id": "B_US_86_JRFL_ACC_U63632" + }, + { + "attributes": [], + "baseline": null, + "cluster": 1, + "edi": null, + "id": "B_US_90_WEAU160_ACC_U21135" + }, + { + "attributes": [], + "baseline": null, + "cluster": 1, + "edi": null, + "id": "D_CD_83_ELI_ACC_K03454_7" + }, + { + "attributes": [], + "baseline": null, + "cluster": 1, + "edi": null, + "id": "D_CD_83_NDK_ACC_M27323" + }, + { + "attributes": [], + "baseline": null, + "cluster": 1, + "edi": null, + "id": "D_CD_84_84ZR085_ACC_U88822" + }, + { + "attributes": [], + "baseline": null, + "cluster": 1, + "edi": null, + "id": "D_UG_94_94UG114_ACC_U88824" + } + ], + "Settings": { + "contaminants": null, + "edge-filtering": null, + "threshold": 0.8 + } +}