diff test-data/absrel-out1.json @ 0:6164d9298db9 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/absrel-out1.json	Wed Aug 21 12:25:26 2019 -0400
@@ -0,0 +1,456 @@
+{
+ "analysis":{
+   "info":"aBSREL (Adaptive branch-site random effects likelihood)\n                            uses an adaptive random effects branch-site model framework\n                            to test whether each branch has evolved under positive selection,\n                            using a procedure which infers an optimal number of rate categories per branch.",
+   "version":"2.0",
+   "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353",
+   "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
+   "contact":"[e-mail]",
+   "requirements":"in-frame codon alignment and a phylogenetic tree"
+  },
+ "input":{
+   "file name":"/tmp/tmpCAMqUO/job_working_directory/002/2602/working/absrel_input.fa",
+   "number of sequences":10,
+   "number of sites":187,
+   "partition count":1,
+   "trees":{
+     "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,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)"
+    }
+  },
+ "fits":{
+   "Nucleotide GTR":{
+     "Log Likelihood":-3531.96369518556,
+     "estimated parameters":24,
+     "AIC-c":7112.577796875186,
+     "Equilibrium frequencies":[
+      [0.3563279857397504],
+      [0.1837789661319073],
+      [0.2402852049910873],
+      [0.2196078431372549]
+      ],
+     "Rate Distributions":{
+       "Substitution rate from nucleotide A to nucleotide C":0.5474707834424497,
+       "Substitution rate from nucleotide A to nucleotide G":1,
+       "Substitution rate from nucleotide A to nucleotide T":0.2645731370379643,
+       "Substitution rate from nucleotide C to nucleotide G":0.4867482826410435,
+       "Substitution rate from nucleotide C to nucleotide T":1.018295973581558,
+       "Substitution rate from nucleotide G to nucleotide T":0.3026112531229544
+      },
+     "display order":0
+    },
+   "Baseline MG94xREV":{
+     "Log Likelihood":-3450.669934819203,
+     "estimated parameters":46,
+     "AIC-c":6995.711784065174,
+     "Equilibrium frequencies":[
+      [0.04787662253946073],
+      [0.03913388100305117],
+      [0.04844580322128512],
+      [0.0407178971288476],
+      [0.01817959331488358],
+      [0.01485982100934833],
+      [0.01839572120297191],
+      [0.01546129971531724],
+      [0.0190238172858878],
+      [0.01554988139098808],
+      [0.01924998172104109],
+      [0.01617929156565557],
+      [0.02798385246472159],
+      [0.02287372613761008],
+      [0.02831653817605838],
+      [0.02379958245776909],
+      [0.01680670574479072],
+      [0.01373763619452979],
+      [0.01700651207463693],
+      [0.01429369239710176],
+      [0.006381800954137531],
+      [0.005216421415661322],
+      [0.006457670922102578],
+      [0.00542756570877943],
+      [0.006678159032689796],
+      [0.005458661598138652],
+      [0.00675755225029668],
+      [0.00567961101013393],
+      [0.009823507779659469],
+      [0.008029638769211124],
+      [0.009940294440024354],
+      [0.008354653231583485],
+      [0.0329096029621651],
+      [0.02689998621179963],
+      [0.03330084840219455],
+      [0.02798881284619018],
+      [0.01249635346589736],
+      [0.01021439657952951],
+      [0.01264491622176376],
+      [0.01062784315018763],
+      [0.01307665913959002],
+      [0.01068873273724336],
+      [0.0132321208528494],
+      [0.01112137894012831],
+      [0.01923563996618058],
+      [0.01572302316926395],
+      [0.01946432265285621],
+      [0.01635944157725275],
+      [0.01977100255021048],
+      [0.02057127040149398],
+      [0.009184593415672956],
+      [0.007507396443725858],
+      [0.009293784349897772],
+      [0.007811272183233558],
+      [0.007856024926654371],
+      [0.009725369116048951],
+      [0.008174012048031599],
+      [0.01413784690564137],
+      [0.01155613719386138],
+      [0.01430592453757226],
+      [0.01202389319448819]
+      ],
+     "Rate Distributions":{
+       "Per-branch omega":{
+         "Mean":666666667.6064719,
+         "Median":1.103169534345197,
+         "2.5%":0,
+         "97.5%":10000000000
+        }
+      },
+     "display order":1
+    },
+   "Full adaptive model":{
+     "Log Likelihood":-3414.992415597899,
+     "estimated parameters":60,
+     "AIC-c":6954.031265689993,
+     "Rate Distributions":{
+      },
+     "display order":2
+    }
+  },
+ "timers":{
+   "Overall":{
+     "timer":98,
+     "order":0
+    },
+   "Preliminary model fitting":{
+     "timer":0,
+     "order":1
+    },
+   "Baseline model fitting":{
+     "timer":1,
+     "order":2
+    },
+   "Complexity analysis":{
+     "timer":36,
+     "order":3
+    },
+   "Full adaptive model fitting":{
+     "timer":8,
+     "order":4
+    },
+   "Testing for selection":{
+     "timer":53,
+     "order":5
+    }
+  },
+ "test results":{
+   "P-value threshold":0.05,
+   "tested":16,
+   "positive test results":3
+  },
+ "tested":{
+   "0":{
+     "Pig":"test",
+     "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"
+    }
+  },
+ "data partitions":{
+   "0":{
+     "name":"absrel.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]
+      ]
+    }
+  },
+ "branch attributes":{
+   "0":{
+     "Human":{
+       "original name":"Human",
+       "Nucleotide GTR":0,
+       "Baseline MG94xREV":0,
+       "Baseline MG94xREV omega ratio":1,
+       "Rate classes":1,
+       "Full adaptive model":0,
+       "Rate Distributions":[
+        [1, 1]
+        ],
+       "LRT":0,
+       "Uncorrected P-value":1,
+       "Corrected P-value":1
+      },
+     "Chimp":{
+       "original name":"Chimp",
+       "Nucleotide GTR":0.001818174796225333,
+       "Baseline MG94xREV":0.001839770270131542,
+       "Baseline MG94xREV omega ratio":10000000000,
+       "Rate classes":1,
+       "Full adaptive model":0.001845806111200226,
+       "Rate Distributions":[
+        [10000000000, 1]
+        ],
+       "LRT":0.6362875427803374,
+       "Uncorrected P-value":0.303261123771571,
+       "Corrected P-value":1
+      },
+     "Baboon":{
+       "original name":"Baboon",
+       "Nucleotide GTR":0.001682034724848474,
+       "Baseline MG94xREV":0.001821072110941238,
+       "Baseline MG94xREV omega ratio":0,
+       "Rate classes":1,
+       "Full adaptive model":0.001808294153407354,
+       "Rate Distributions":[
+        [0, 1]
+        ],
+       "LRT":0,
+       "Uncorrected P-value":1,
+       "Corrected P-value":1
+      },
+     "RhMonkey":{
+       "original name":"RhMonkey",
+       "Nucleotide GTR":0.003775509884015639,
+       "Baseline MG94xREV":0.003671340584166445,
+       "Baseline MG94xREV omega ratio":10000000000,
+       "Rate classes":1,
+       "Full adaptive model":0.003682180830540259,
+       "Rate Distributions":[
+        [10000000000, 1]
+        ],
+       "LRT":1.200615147074132,
+       "Uncorrected P-value":0.2192326116145807,
+       "Corrected P-value":1
+      },
+     "Cow":{
+       "original name":"Cow",
+       "Nucleotide GTR":0.248257545271419,
+       "Baseline MG94xREV":0.2535517510207829,
+       "Baseline MG94xREV omega ratio":1.957039676836281,
+       "Rate classes":2,
+       "Full adaptive model":0.3959632497370367,
+       "Rate Distributions":[
+        [0, 0.5384412409742189],
+        [10.58123012791267, 0.4615587590257811]
+        ],
+       "LRT":24.50128746473001,
+       "Uncorrected P-value":1.583131814197891e-06,
+       "Corrected P-value":2.533010902716626e-05
+      },
+     "Pig":{
+       "original name":"Pig",
+       "Nucleotide GTR":0.1872143003439852,
+       "Baseline MG94xREV":0.1913752025483544,
+       "Baseline MG94xREV omega ratio":1.354835319497051,
+       "Rate classes":1,
+       "Full adaptive model":0.1823079562415392,
+       "Rate Distributions":[
+        [1.270031670375847, 1]
+        ],
+       "LRT":0.5083013304356427,
+       "Uncorrected P-value":0.3278475069550038,
+       "Corrected P-value":1
+      },
+     "Horse":{
+       "original name":"Horse",
+       "Nucleotide GTR":0.2092211101976542,
+       "Baseline MG94xREV":0.2093433205074538,
+       "Baseline MG94xREV omega ratio":1.262933703792719,
+       "Rate classes":2,
+       "Full adaptive model":0.2696870893488891,
+       "Rate Distributions":[
+        [0, 0.5494326491453121],
+        [4.447670371762946, 0.4505673508546879]
+        ],
+       "LRT":9.839972152766677,
+       "Uncorrected P-value":0.002531289908698275,
+       "Corrected P-value":0.03543805872177586
+      },
+     "Cat":{
+       "original name":"Cat",
+       "Nucleotide GTR":0.2662269345134692,
+       "Baseline MG94xREV":0.2773733494290757,
+       "Baseline MG94xREV omega ratio":1.619113019542315,
+       "Rate classes":2,
+       "Full adaptive model":0.3637840333790108,
+       "Rate Distributions":[
+        [0.3427137549260186, 0.5775012741005606],
+        [6.025097508634321, 0.4224987258994394]
+        ],
+       "LRT":13.05292728184577,
+       "Uncorrected P-value":0.000499814517576469,
+       "Corrected P-value":0.007497217763647035
+      },
+     "Mouse":{
+       "original name":"Mouse",
+       "Nucleotide GTR":0.1181551390736968,
+       "Baseline MG94xREV":0.1220127721537473,
+       "Baseline MG94xREV omega ratio":0.5307054960008202,
+       "Rate classes":1,
+       "Full adaptive model":0.1200052061883895,
+       "Rate Distributions":[
+        [0.5418818043457002, 1]
+        ],
+       "LRT":0,
+       "Uncorrected P-value":1,
+       "Corrected P-value":1
+      },
+     "Rat":{
+       "original name":"Rat",
+       "Nucleotide GTR":0.06673994656462794,
+       "Baseline MG94xREV":0.06546903135094065,
+       "Baseline MG94xREV omega ratio":1.103169534345197,
+       "Rate classes":1,
+       "Full adaptive model":0.06894368446818594,
+       "Rate Distributions":[
+        [1.162844601638596, 1]
+        ],
+       "LRT":0.04180897168953379,
+       "Uncorrected P-value":0.4613906175252571,
+       "Corrected P-value":1
+      },
+     "Node1":{
+       "Nucleotide GTR":0.2772613398768408,
+       "Baseline MG94xREV":0.2903229694372956,
+       "Baseline MG94xREV omega ratio":0.4389914526526448,
+       "Rate classes":2,
+       "Full adaptive model":0.3664538683295676,
+       "Rate Distributions":[
+        [0.1934444279004118, 0.7920338324503209],
+        [2.595458156723663, 0.2079661675496791]
+        ],
+       "LRT":1.095302853601424,
+       "Uncorrected P-value":0.232551772988317,
+       "Corrected P-value":1
+      },
+     "Node12":{
+       "Nucleotide GTR":0.01783922546179193,
+       "Baseline MG94xREV":0.01797212760838867,
+       "Baseline MG94xREV omega ratio":0.3712490894908597,
+       "Rate classes":1,
+       "Full adaptive model":0.01648897148329989,
+       "Rate Distributions":[
+        [0.3341484726344874, 1]
+        ],
+       "LRT":0,
+       "Uncorrected P-value":1,
+       "Corrected P-value":1
+      },
+     "Node2":{
+       "Nucleotide GTR":0.06619058539001231,
+       "Baseline MG94xREV":0.06580724801157116,
+       "Baseline MG94xREV omega ratio":0.6811307469311604,
+       "Rate classes":2,
+       "Full adaptive model":0.1259563484776556,
+       "Rate Distributions":[
+        [0, 0.902872882268449],
+        [33.80023214939837, 0.09712711773155103]
+        ],
+       "LRT":7.670975764417562,
+       "Uncorrected P-value":0.007599562698001494,
+       "Corrected P-value":0.09119475237601793
+      },
+     "Node3":{
+       "Nucleotide GTR":0.09883236156840018,
+       "Baseline MG94xREV":0.102749851157051,
+       "Baseline MG94xREV omega ratio":1.47449378631578,
+       "Rate classes":2,
+       "Full adaptive model":0.1389308407753113,
+       "Rate Distributions":[
+        [0, 0.7024206790833775],
+        [8.065310624699681, 0.2975793209166225]
+        ],
+       "LRT":6.598417720076213,
+       "Uncorrected P-value":0.0131150962965953,
+       "Corrected P-value":0.1442660592625483
+      },
+     "Node8":{
+       "Nucleotide GTR":0.1061134663636472,
+       "Baseline MG94xREV":0.110140333084973,
+       "Baseline MG94xREV omega ratio":1.896243438714738,
+       "Rate classes":2,
+       "Full adaptive model":0.2165540926910564,
+       "Rate Distributions":[
+        [1, 0.9077840705139004],
+        [33.32075865076668, 0.09221592948609958]
+        ],
+       "LRT":7.97288393366216,
+       "Uncorrected P-value":0.006519360772582139,
+       "Corrected P-value":0.08475169004356781
+      },
+     "Node9":{
+       "Nucleotide GTR":0.02566719422260768,
+       "Baseline MG94xREV":0.02590165433349057,
+       "Baseline MG94xREV omega ratio":0.4071738826525522,
+       "Rate classes":1,
+       "Full adaptive model":0.02766629863085238,
+       "Rate Distributions":[
+        [0.4488424899910019, 1]
+        ],
+       "LRT":0,
+       "Uncorrected P-value":1,
+       "Corrected P-value":1
+      }
+    },
+   "attributes":{
+     "original name":{
+       "attribute type":"node label",
+       "display order":-1
+      },
+     "Nucleotide GTR":{
+       "attribute type":"branch length",
+       "display order":0
+      },
+     "Baseline MG94xREV":{
+       "attribute type":"branch length",
+       "display order":1
+      },
+     "Baseline MG94xREV omega ratio":{
+       "attribute type":"branch label",
+       "display order":1
+      },
+     "Rate classes":{
+       "attribute type":"branch label",
+       "display order":2
+      },
+     "Full adaptive model":{
+       "attribute type":"branch length",
+       "display order":2
+      },
+     "Rate Distributions":{
+       "attribute type":"branch label",
+       "display order":3
+      },
+     "LRT":{
+       "attribute type":"branch label",
+       "display order":4
+      },
+     "Uncorrected P-value":{
+       "attribute type":"branch label",
+       "display order":5
+      },
+     "Corrected P-value":{
+       "attribute type":"branch label",
+       "display order":6
+      }
+    }
+  }
+}
\ No newline at end of file