diff test-data/bgm-out1.json @ 1:c2bed8cc8fc1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:27:21 -0400
parents
children a603e2f909e5
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bgm-out1.json	Wed Aug 21 12:27:21 2019 -0400
@@ -0,0 +1,408 @@
+{
+ "MLE":{
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+    [25, 30, 0.1123773177282409, 0.107330048901509, 0.2197073666297499, 3, 2, 2],
+    [26, 28, 0.01202310187965289, 0.0100752849569055, 0.0220983868365584, 1, 2, 0],
+    [26, 29, 0.01098659894875614, 0.0106778458846393, 0.02166444483339544, 1, 2, 0],
+    [26, 30, 0.008888531742284057, 0.0220072024775357, 0.03089573421981976, 1, 2, 0],
+    [28, 29, 0.3253931306175987, 0.3786081317863912, 0.70400126240399, 2, 2, 2],
+    [28, 30, 0.007946759742122602, 0.03360599467213372, 0.04155275441425633, 2, 2, 1],
+    [29, 30, 0.01669873349292508, 0.03504162520377113, 0.05174035869669621, 2, 2, 1] 
+    ],
+   "headers":    [
+["Site 1", "Index of site 1"],
+    ["Site 2", "Index of site 2"],
+    ["P [Site 1 –> Site 2]", "Probability that site 2 is conditionally dependent on site 1"],
+    ["P [Site 2 –> Site 1]", "Probability that site 1 is conditionally dependent on site 2"],
+    ["P [Site 1 <–> Site 2]", "Probability that sites 1 and 2 are not conditionally independent"],
+    ["Site 1 subs", "Substitution counts inferred for Site 1"],
+    ["Site 2 subs", "Substitution counts inferred for Site 2"],
+    ["Shared subs", "Substitutions shared by both sites"] 
+    ]
+  },
+ "analysis":{
+   "authors":"Art FY Poon, Fraser I Lewis, Simon DW Frost and Sergei L Kosakovsky Pond",
+   "citation":"Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models (2008). _Bioinformatics_ 24(17): 1949-1950",
+   "contact":"apoon42@uwo.ca",
+   "info":"BGM (Bayesian Graphical Model) uses a maximum likelihood ancestral state reconstruction to\nmap substitution (non-synonymous only for coding data) events to branches in the\nphylogeny and then analyzes the joint distribution of the\nsubstitution map using a Bayesian graphical model (network).\nNext, a Markov chain Monte Carlo analysis is used to generate\na random sample of network structures from the posterior\ndistribution given the data.  Each node in the network\nrepresents a codon site in the alignment, and links (edges)\nbetween nodes indicate high posterior support for correlated\nsubstitutions at the two sites over time, which implies coevolution.",
+   "requirements":"in-frame codon alignment and a phylogenetic tree",
+   "version":"1.1"
+  },
+ "branch attributes":{
+   "0":{
+     "Baboon":{
+       "models.DNA.GTR.ModelDescription":0
+      },
+     "Cat":{
+       "models.DNA.GTR.ModelDescription":0.7933191636859576
+      },
+     "Chimp":{
+       "models.DNA.GTR.ModelDescription":0
+      },
+     "Cow":{
+       "models.DNA.GTR.ModelDescription":0.8094119333244753
+      },
+     "Horse":{
+       "models.DNA.GTR.ModelDescription":0.2769077630163064
+      },
+     "Human":{
+       "models.DNA.GTR.ModelDescription":0
+      },
+     "Mouse":{
+       "models.DNA.GTR.ModelDescription":0.1094921058577506
+      },
+     "Node1":{
+       "models.DNA.GTR.ModelDescription":0.4820782253393885
+      },
+     "Node12":{
+       "models.DNA.GTR.ModelDescription":0
+      },
+     "Node2":{
+       "models.DNA.GTR.ModelDescription":0.08259105925424247
+      },
+     "Node3":{
+       "models.DNA.GTR.ModelDescription":0.2526911684326281
+      },
+     "Node8":{
+       "models.DNA.GTR.ModelDescription":0.06531857233184223
+      },
+     "Node9":{
+       "models.DNA.GTR.ModelDescription":0.03361817454867485
+      },
+     "Pig":{
+       "models.DNA.GTR.ModelDescription":0
+      },
+     "Rat":{
+       "models.DNA.GTR.ModelDescription":0.0888784436278628
+      },
+     "RhMonkey":{
+       "models.DNA.GTR.ModelDescription":0
+      }
+    },
+   "attributes":{
+     "models.DNA.GTR.ModelDescription":{
+       "attribute type":"branch length",
+       "display order":0
+      }
+    }
+  },
+ "data partitions":{
+   "0":{
+     "coverage":      [
+[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29] 
+      ],
+     "name":"bgm.filter.default"
+    }
+  },
+ "fits":{
+   "models.DNA.GTR.ModelDescription":{
+     "AIC-c":472.7691802214979,
+     "Log Likelihood":-210.2027719289308,
+     "Rate Distributions":null,
+     "display order":0,
+     "estimated parameters":24
+    }
+  },
+ "input":{
+   "datatype":"nucleotide",
+   "file name":"/tmp/tmpSz4m4X/job_working_directory/000/3/working/bgm_input.fa",
+   "number of sequences":10,
+   "number of sites":30,
+   "trees":{
+     "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"
+    }
+  },
+ "settings":{
+   "burn-in":10000,
+   "data-type":"nucleotide",
+   "max-parents":1,
+   "min-subs":1,
+   "samples":100,
+   "steps":100000,
+   "threshold":0.5
+  },
+ "tested":0,
+ "timers":{
+   "Baseline fit":{
+     "order":1,
+     "timer":0
+    },
+   "Network inference":{
+     "order":2,
+     "timer":1
+    },
+   "Overall":{
+     "order":0,
+     "timer":1
+    }
+  }
+}
\ No newline at end of file