annotate test-data/bgm-out1.json @ 6:b5d981229301 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f953137ef9ed4e9e1dcce3d93ee26fdc5d2bba53"

{
 "MLE":{
   "content":    [
[2, 3, 0.02851572177464722, 0.01992394838090668, 0.04843967015555389, 4, 3, 1],
    [2, 4, 0.2913031811286725, 0.1581095173619919, 0.4494126984906644, 4, 2, 2],
    [2, 5, 0.04313828130286183, 0.09337388689236253, 0.1365121681952244, 4, 3, 2],
    [2, 6, 0.05037434713194238, 0.07113225549859428, 0.1215066026305367, 4, 6, 3],
    [2, 7, 0.2804886800096655, 0.2001828066808252, 0.4806714866904907, 4, 4, 3],
    [2, 8, 0.07183821900324161, 0.1469389589305462, 0.2187771779337878, 4, 5, 3],
    [2, 9, 0.03082407077478325, 0.09900473652454521, 0.1298288072993285, 4, 3, 2],
    [2, 10, 0.02245776059232202, 0.02955557233236829, 0.05201333292469031, 4, 3, 1],
    [3, 4, 0.03717045364745913, 0.02520976460488304, 0.06238021825234218, 3, 2, 0],
    [3, 5, 0.02873335174526813, 0.03479214292405394, 0.06352549466932207, 3, 3, 1],
    [3, 6, 0.1236923855363388, 0.2512471049857198, 0.3749394905220587, 3, 6, 3],
    [3, 7, 0.01909635400892135, 0.02551889926711521, 0.04461525327603656, 3, 4, 1],
    [3, 8, 0.02488014112561441, 0.05406148356625361, 0.07894162469186802, 3, 5, 2],
    [3, 9, 0.08440837590482446, 0.2181470609147132, 0.3025554368195377, 3, 3, 2],
    [3, 10, 0.1267967238159999, 0.1611592144212058, 0.2879559382372058, 3, 3, 2],
    [4, 5, 0.03705892982325252, 0.07620033982326219, 0.1132592696465147, 2, 3, 1],
    [4, 6, 0.01210885428759886, 0.04049276326654051, 0.05260161755413936, 2, 6, 1],
    [4, 7, 0.03773982374178716, 0.04469577929352821, 0.08243560303531537, 2, 4, 1],
    [4, 8, 0.02406357502679824, 0.04542327412998536, 0.06948684915678359, 2, 5, 1],
    [4, 9, 0.04518375503528457, 0.08175199548949739, 0.126935750524782, 2, 3, 1],
    [4, 10, 0.05271458150974553, 0.07030981080391227, 0.1230243923136578, 2, 3, 1],
    [5, 6, 0.1359282078272841, 0.1540926795656895, 0.2900208873929736, 3, 6, 3],
    [5, 7, 0.09099743539437326, 0.04199316180345154, 0.1329905971978248, 3, 4, 2],
    [5, 8, 0.1895195673806065, 0.2930011407919719, 0.4825207081725784, 3, 5, 3],
    [5, 9, 0.1148199627842869, 0.1105571269028783, 0.2253770896871652, 3, 3, 2],
    [5, 10, 0.1270434887308012, 0.1100230063742557, 0.2370664951050569, 3, 3, 2],
    [6, 7, 0.09069770755435493, 0.0484084497358865, 0.1391061572902414, 6, 4, 3],
    [6, 8, 0.1325890592140632, 0.1385237411340729, 0.2711128003481361, 6, 5, 4],
    [6, 9, 0.1237432424538594, 0.1610336810828299, 0.2847769235366894, 6, 3, 3],
    [6, 10, 0.2074649804257667, 0.132053108013182, 0.3395180884389487, 6, 3, 3],
    [7, 8, 0.0894441901425615, 0.1431622704391284, 0.2326064605816899, 4, 5, 3],
    [7, 9, 0.06037024754303832, 0.114173814968622, 0.1745440625116604, 4, 3, 2],
    [7, 10, 0.02455907863678367, 0.02700169365828593, 0.0515607722950696, 4, 3, 1],
    [8, 9, 0.2356164682007381, 0.275411073609017, 0.5110275418097552, 5, 3, 3],
    [8, 10, 0.05927356969559661, 0.02598780235339034, 0.08526137204898694, 5, 3, 2],
    [9, 10, 0.1776480482199785, 0.09671451255218226, 0.2743625607721607, 3, 3, 2] 
    ],
   "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.codon.MG_REV.ModelDescription":0
      },
     "Cat":{
       "models.codon.MG_REV.ModelDescription":0.8288168941011919
      },
     "Chimp":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Cow":{
       "models.codon.MG_REV.ModelDescription":0.8164924147537205
      },
     "Horse":{
       "models.codon.MG_REV.ModelDescription":0.2841592907567805
      },
     "Human":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Mouse":{
       "models.codon.MG_REV.ModelDescription":0.1035113121392619
      },
     "Node1":{
       "models.codon.MG_REV.ModelDescription":0.5236339695213962
      },
     "Node12":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Node2":{
       "models.codon.MG_REV.ModelDescription":0.08766202644314423
      },
     "Node3":{
       "models.codon.MG_REV.ModelDescription":0.2629569437833751
      },
     "Node8":{
       "models.codon.MG_REV.ModelDescription":0.07018254851044582
      },
     "Node9":{
       "models.codon.MG_REV.ModelDescription":0.03334231749233734
      },
     "Pig":{
       "models.codon.MG_REV.ModelDescription":0
      },
     "Rat":{
       "models.codon.MG_REV.ModelDescription":0.1018034850081214
      },
     "RhMonkey":{
       "models.codon.MG_REV.ModelDescription":0
      }
    },
   "attributes":{
     "models.codon.MG_REV.ModelDescription":{
       "attribute type":"branch length",
       "display order":0
      }
    }
  },
 "data partitions":{
   "0":{
     "coverage":      [
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9] 
      ],
     "name":"bgm.filter.default"
    }
  },
 "fits":{
   "models.codon.MG_REV.ModelDescription":{
     "AIC-c":508.3788244913426,
     "Log Likelihood":-208.6011769515537,
     "Rate Distributions":null,
     "display order":0,
     "estimated parameters":31
    }
  },
 "input":{
   "datatype":"codon",
   "file name":"/tmp/tmp_Fhyr9/job_working_directory/000/3/working/./bgm_input.fa",
   "number of sequences":10,
   "number of sites":10,
   "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":"codon",
   "max-parents":1,
   "min-subs":1,
   "samples":100,
   "steps":100000,
   "threshold":0.5
  },
 "tested":0,
 "timers":{
   "Baseline fit":{
     "order":1,
     "timer":3
    },
   "Network inference":{
     "order":2,
     "timer":0
    },
   "Overall":{
     "order":0,
     "timer":3
    }
  }
}