diff test-data/busted-out1.json @ 2:6943fbec145c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
author iuc
date Thu, 13 Feb 2020 15:01:46 -0500
parents fe399429a5d2
children cd41e7a4d35f
line wrap: on
line diff
--- a/test-data/busted-out1.json	Wed Aug 21 12:24:34 2019 -0400
+++ b/test-data/busted-out1.json	Thu Feb 13 15:01:46 2020 -0500
@@ -1,361 +1,394 @@
 {
- "analysis":{
-   "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted jointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. Assuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio style analysis to explore which individual sites may have been subject to selection.",
-   "version":"1.2",
-   "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
-   "authors":"Sergei L Kosakovsky Pond",
-   "contact":"spond@temple.edu",
-   "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})"
+ "Evidence Ratios":{
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+  ],
+ "analysis":{
+   "authors":"Sergei L Kosakovsky Pond",
+   "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
+   "contact":"spond@temple.edu",
+   "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted \njointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1),  BUSTED will also perform a quick evidence-ratio \nstyle analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. Version 3.0 implements the option\nfor branch-site variation in synonymous substitution rates\n",
+   "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
+   "version":"3.0"
   },
  "background":0,
- "fits":{
-   "Nucleotide GTR":{
-     "Log Likelihood":-3531.963798530155,
-     "estimated parameters":24,
-     "AIC-c":7112.142458295762,
-     "Equilibrium frequencies":[
-      [0.3563279857397504],
-      [0.1837789661319073],
-      [0.2402852049910873],
-      [0.2196078431372549]
-      ],
-     "Rate Distributions":{
-       "Substitution rate from nucleotide A to nucleotide C":0.5474490057204714,
-       "Substitution rate from nucleotide A to nucleotide G":1,
-       "Substitution rate from nucleotide A to nucleotide T":0.2645352969683238,
-       "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331,
-       "Substitution rate from nucleotide C to nucleotide T":1.018028772244997,
-       "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378
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-     "display order":0
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-   "MG94xREV with separate rates for branch sets":{
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-      [0.01634417558076203],
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-      [0.02055210293142003],
-      [0.009176034326710849],
-      [0.007500393094996483],
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-      [0.01154535713247913],
-      [0.01429258425298098],
-      [0.01201267864744234]
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-   "Constrained model":{
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- "Evidence Ratios":{
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- "tested":{
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-     "Cow":"test",
-     "Node3":"test",
-     "Horse":"test",
-     "Cat":"test",
-     "Node2":"test",
-     "RhMonkey":"test",
-     "Baboon":"test",
-     "Node9":"test",
-     "Human":"test",
-     "Chimp":"test",
-     "Node12":"test",
-     "Node8":"test",
-     "Node1":"test",
-     "Rat":"test",
-     "Mouse":"test"
-    }
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- "data partitions":{
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-     "name":"busted.filter.default",
-     "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, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186]
-      ]
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  "branch attributes":{
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-       "constrained":0.001827227299324197
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      "Baboon":{
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-       "MG94xREV with separate rates for branch sets":0.2111575880588217,
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-       "constrained":0.218486450878766
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      "Cat":{
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-       "constrained":0.28483085314287
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+     "Human":{
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+       "constrained":0,
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      "Mouse":{
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+       "constrained":0.04601717170435755,
        "original name":"Mouse",
-       "Nucleotide GTR":0.1181831744338598,
-       "MG94xREV with separate rates for branch sets":0.1201847378516324,
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-       "constrained":0.1233480139851019
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-     "Rat":{
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-       "MG94xREV with separate rates for branch sets":0.0670850471739789,
-       "unconstrained":0.07366345007817726,
-       "constrained":0.06713082546371778
+       "unconstrained":0.04942545223877414
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      "Node1":{
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-       "MG94xREV with separate rates for branch sets":0.2843521449765504,
-       "unconstrained":0.459085769955035,
-       "constrained":0.3115534692518958
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      "Node12":{
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-       "MG94xREV with separate rates for branch sets":0.01788794906051452,
-       "unconstrained":0.01828498503175797,
-       "constrained":0.01770410398930177
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+       "unconstrained":0.00572208893382143
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      "Node2":{
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-       "MG94xREV with separate rates for branch sets":0.06447679597474805,
-       "unconstrained":0.0623969317369398,
-       "constrained":0.06097949807503514
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+       "constrained":0.02253286838656328,
+       "unconstrained":0.02248978054488407
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      "Node3":{
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-       "MG94xREV with separate rates for branch sets":0.1017497956116402,
-       "unconstrained":0.1285021744856729,
-       "constrained":0.1065011238088613
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      "Node8":{
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-       "MG94xREV with separate rates for branch sets":0.1093806684969149,
-       "unconstrained":0.1348034716617685,
-       "constrained":0.1118205234697939
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+       "constrained":0.04415239867414091,
+       "unconstrained":0.04768889036449767
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      "Node9":{
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-       "MG94xREV with separate rates for branch sets":0.02593963430985144,
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-       "constrained":0.02639493109700932
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+       "constrained":0.00997308939110993,
+       "unconstrained":0.009841415288506062
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+     "Pig":{
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+       "constrained":0.07816490289585476,
+       "original name":"Pig",
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+     "Rat":{
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+       "constrained":0.02277034233250765,
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+     "RhMonkey":{
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+       "constrained":0.001359450941376631,
+       "original name":"RhMonkey",
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    "attributes":{
-     "original name":{
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-     "Nucleotide GTR":{
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-       "display order":0
-      },
      "MG94xREV with separate rates for branch sets":{
        "attribute type":"branch length",
        "display order":1
       },
-     "unconstrained":{
+     "Nucleotide GTR":{
        "attribute type":"branch length",
        "display order":0
       },
      "constrained":{
        "attribute type":"branch length",
        "display order":1
+      },
+     "original name":{
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+     "unconstrained":{
+       "attribute type":"branch length",
+       "display order":0
       }
     }
   },
+ "data partitions":{
+   "0":{
+     "coverage":      [
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+      ],
+     "name":"busted.filter.default"
+    }
+  },
+ "fits":{
+   "Constrained model":{
+     "AIC-c":6918.851822592964,
+     "Log Likelihood":-3419.573452280089,
+     "Rate Distributions":{
+       "Synonymous site-to-site rates":{
+         "0":{
+           "proportion":0.3289898788632067,
+           "rate":0.3124849036133048
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+         "1":{
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+           "rate":1.039520868895482
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+         "2":{
+           "proportion":0.09619034764544485,
+           "rate":3.115265578623139
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+       "Test":{
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+           "proportion":0.02093092071081848
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+         "1":{
+           "omega":0,
+           "proportion":0.1387433808480476
+          },
+         "2":{
+           "omega":1,
+           "proportion":0.8403256984411339
+          }
+        }
+      },
+     "display order":3,
+     "estimated parameters":39
+    },
+   "MG94xREV with separate rates for branch sets":{
+     "AIC-c":6997.089050462658,
+     "Equilibrium frequencies":      [
+[0.04875339327772683],
+      [0.03982858547830345],
+      [0.04946803524790992],
+      [0.04152216138298744],
+      [0.01811683453600613],
+      [0.01480036248560469],
+      [0.0183823965708893],
+      [0.01542969784826435],
+      [0.01894694796506697],
+      [0.01547851515238824],
+      [0.01922467805342367],
+      [0.01613668666381816],
+      [0.02832099415740372],
+      [0.02313654621336914],
+      [0.02873613184734657],
+      [0.02412034959764736],
+      [0.01662182431200483],
+      [0.01357902918971745],
+      [0.01686547203528639],
+      [0.01415643148428886],
+      [0.006176695005242439],
+      [0.005045987744654046],
+      [0.006267234867003878],
+      [0.005260551308914496],
+      [0.006459711194459957],
+      [0.005277194922783805],
+      [0.006554399593040238],
+      [0.005501589790395056],
+      [0.009655668202293983],
+      [0.007888099278638223],
+      [0.009797203904398108],
+      [0.008223514024394991],
+      [0.03326722643528176],
+      [0.02717732003095303],
+      [0.03375486749252685],
+      [0.02833294365668738],
+      [0.01236215156074466],
+      [0.01009913314808799],
+      [0.01254335971371867],
+      [0.01052856463184265],
+      [0.01292858539344675],
+      [0.0105618754683007],
+      [0.0131180965046964],
+      [0.01101098350431497],
+      [0.0193250328267319],
+      [0.01578738770911659],
+      [0.0196083049972345],
+      [0.01645869298147252],
+      [0.01962343746171723],
+      [0.02045785777700414],
+      [0.008926115885166477],
+      [0.007292098982657142],
+      [0.009056957588961733],
+      [0.007602170831388156],
+      [0.007626222986467745],
+      [0.009471947420992787],
+      [0.007950502328516303],
+      [0.01395367801862353],
+      [0.01139931439306339],
+      [0.01415821524731906],
+      [0.01188403168729233] 
+      ],
+     "Log Likelihood":-3467.004808147542,
+     "Rate Distributions":{
+       "non-synonymous/synonymous rate ratio for *test*":        [
+[0.9950576192409499, 1] 
+        ]
+      },
+     "display order":1,
+     "estimated parameters":31
+    },
+   "Nucleotide GTR":{
+     "AIC-c":7112.85745601076,
+     "Equilibrium frequencies":      [
+[0.3592490842490842],
+      [0.181959706959707],
+      [0.240018315018315],
+      [0.2187728937728937] 
+      ],
+     "Log Likelihood":-3532.321297387654,
+     "Rate Distributions":{
+       "Substitution rate from nucleotide A to nucleotide C":0.5497129763145497,
+       "Substitution rate from nucleotide A to nucleotide G":1,
+       "Substitution rate from nucleotide A to nucleotide T":0.264666902964203,
+       "Substitution rate from nucleotide C to nucleotide G":0.4916303643305098,
+       "Substitution rate from nucleotide C to nucleotide T":1.027924764411573,
+       "Substitution rate from nucleotide G to nucleotide T":0.304615404570875
+      },
+     "display order":0,
+     "estimated parameters":24
+    },
+   "Unconstrained model":{
+     "AIC-c":6910.766610587704,
+     "Log Likelihood":-3414.486640449675,
+     "Rate Distributions":{
+       "Synonymous site-to-site rates":{
+         "0":{
+           "proportion":0.2645541257391169,
+           "rate":0.2747941124675511
+          },
+         "1":{
+           "proportion":0.6325830460054784,
+           "rate":0.9734675888351726
+          },
+         "2":{
+           "proportion":0.1028628282554047,
+           "rate":3.028333913894314
+          }
+        },
+       "Test":{
+         "0":{
+           "omega":0,
+           "proportion":0.04809457608200497
+          },
+         "1":{
+           "omega":0,
+           "proportion":0.3410012743721951
+          },
+         "2":{
+           "omega":1.89363684081788,
+           "proportion":0.6109041495458
+          }
+        }
+      },
+     "display order":2,
+     "estimated parameters":40
+    }
+  },
+ "input":{
+   "file name":"/tmp/tmp7qHfo2/job_working_directory/000/3/working/./busted_input.fa",
+   "number of sequences":10,
+   "number of sites":187,
+   "partition count":1,
+   "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)"
+    }
+  },
  "test results":{
-   "LRT":44.77492170961614,
-   "p-value":1.893429857346973e-10
+   "LRT":10.17362366082671,
+   "p-value":0.003088842014430382
+  },
+ "tested":{
+   "0":{
+     "Baboon":"test",
+     "Cat":"test",
+     "Chimp":"test",
+     "Cow":"test",
+     "Horse":"test",
+     "Human":"test",
+     "Mouse":"test",
+     "Node1":"test",
+     "Node12":"test",
+     "Node2":"test",
+     "Node3":"test",
+     "Node8":"test",
+     "Node9":"test",
+     "Pig":"test",
+     "Rat":"test",
+     "RhMonkey":"test"
+    }
+  },
+ "timers":{
+   "Constrained BUSTED model fitting":{
+     "order":3,
+     "timer":62
+    },
+   "Overall":{
+     "order":0,
+     "timer":228
+    },
+   "Preliminary model fitting":{
+     "order":1,
+     "timer":3
+    },
+   "Unconstrained BUSTED model fitting":{
+     "order":2,
+     "timer":161
+    }
   }
 }
\ No newline at end of file