annotate test-data/bgm-out1.json @ 1:5c87e4907e08 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"

{
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    [26, 30, 0.008888531742284057, 0.0220072024775357, 0.03089573421981976, 1, 2, 0],
    [28, 29, 0.3253931306175987, 0.3786081317863912, 0.70400126240399, 2, 2, 2],
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    [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":"[e-mail]",
   "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
    }
  }
}