diff test-data/hivclustering-out2.json @ 0:ef842bb94d1f draft default tip

planemo upload for repository https://github.com/veg/hivclustering/ commit 7d666f963da2c5e3b17c313526cc6169f3242c3c
author iuc
date Thu, 14 Jun 2018 07:04:38 -0400
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hivclustering-out2.json	Thu Jun 14 07:04:38 2018 -0400
@@ -0,0 +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
+    }
+}