diff test-data/busted-out2-1.json @ 26:5f2ca10db92a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 18:07:06 +0000
parents
children 3f59ebfbfe3d
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/busted-out2-1.json	Tue Apr 27 18:07:06 2021 +0000
@@ -0,0 +1,338 @@
+{
+ "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. Version 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets\n",
+   "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
+   "version":"3.1"
+  },
+ "background":0,
+ "branch attributes":{
+   "0":{
+     "B_FR_83_HXB2":{
+       "MG94xREV with separate rates for branch sets":0.01243274064118979,
+       "Nucleotide GTR":0.01178680392701259,
+       "constrained":0.01256398347964253,
+       "original name":"B_FR_83_HXB2",
+       "unconstrained":0.01346367617740634
+      },
+     "B_US_83_RF":{
+       "MG94xREV with separate rates for branch sets":0.02861520854418918,
+       "Nucleotide GTR":0.02637179869727959,
+       "constrained":0.02907713203932123,
+       "original name":"B_US_83_RF",
+       "unconstrained":0.03296423032791345
+      },
+     "B_US_86_JRFL":{
+       "MG94xREV with separate rates for branch sets":0.01913497611653954,
+       "Nucleotide GTR":0.01766254318226218,
+       "constrained":0.01932498128977916,
+       "original name":"B_US_86_JRFL",
+       "unconstrained":0.02067264364489925
+      },
+     "B_US_90_WEAU160":{
+       "MG94xREV with separate rates for branch sets":0.02258152057123029,
+       "Nucleotide GTR":0.0208836028381146,
+       "constrained":0.02318748492797678,
+       "original name":"B_US_90_WEAU160",
+       "unconstrained":0.02519768979779986
+      },
+     "D_CD_83_ELI":{
+       "MG94xREV with separate rates for branch sets":0.02096470337130958,
+       "Nucleotide GTR":0.01905599613120992,
+       "constrained":0.02057807476219352,
+       "original name":"D_CD_83_ELI",
+       "unconstrained":0.02169258688744172
+      },
+     "D_CD_83_NDK":{
+       "MG94xREV with separate rates for branch sets":0.01034012674036274,
+       "Nucleotide GTR":0.009776698714183414,
+       "constrained":0.0105101167818647,
+       "original name":"D_CD_83_NDK",
+       "unconstrained":0.01040169158313715
+      },
+     "D_CD_84_84ZR085":{
+       "MG94xREV with separate rates for branch sets":0.03124894063248942,
+       "Nucleotide GTR":0.02822254903672137,
+       "constrained":0.03140845141419388,
+       "original name":"D_CD_84_84ZR085",
+       "unconstrained":0.03388014669054998
+      },
+     "D_UG_94_94UG114":{
+       "MG94xREV with separate rates for branch sets":0.0597102708893009,
+       "Nucleotide GTR":0.05323070232023583,
+       "constrained":0.06218362660429492,
+       "original name":"D_UG_94_94UG114",
+       "unconstrained":0.06804948826756697
+      },
+     "Node1":{
+       "MG94xREV with separate rates for branch sets":0.02639559777106507,
+       "Nucleotide GTR":0.02355240508560319,
+       "constrained":0.02779997592087442,
+       "unconstrained":0.02940126303315396
+      },
+     "Node10":{
+       "MG94xREV with separate rates for branch sets":0.00193736936681532,
+       "Nucleotide GTR":0.002230248981703367,
+       "constrained":0.001848018461605612,
+       "unconstrained":0.001859856019153286
+      },
+     "Node2":{
+       "MG94xREV with separate rates for branch sets":0.003944601108756816,
+       "Nucleotide GTR":0.003949360371801276,
+       "constrained":0.00346172246250584,
+       "unconstrained":0.002261770932022259
+      },
+     "Node3":{
+       "MG94xREV with separate rates for branch sets":0.01136485742287924,
+       "Nucleotide GTR":0.01048442975058683,
+       "constrained":0.01170820974676507,
+       "unconstrained":0.01401270546560647
+      },
+     "Node9":{
+       "MG94xREV with separate rates for branch sets":0.005522231785763113,
+       "Nucleotide GTR":0.004986123424162501,
+       "constrained":0.005522033787153708,
+       "unconstrained":0.005520113121560347
+      }
+    },
+   "attributes":{
+     "MG94xREV with separate rates for branch sets":{
+       "attribute type":"branch length",
+       "display order":1
+      },
+     "Nucleotide GTR":{
+       "attribute type":"branch length",
+       "display order":0
+      },
+     "constrained":{
+       "attribute type":"branch length",
+       "display order":1
+      },
+     "original name":{
+       "attribute type":"node label",
+       "display order":0
+      },
+     "unconstrained":{
+       "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, 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, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439] 
+      ],
+     "name":"busted.filter.default"
+    }
+  },
+ "fits":{
+   "Constrained model":{
+     "AIC-c":6398.612664722735,
+     "Log Likelihood":-3168.021928691643,
+     "Rate Distributions":{
+       "Test":{
+         "0":{
+           "omega":0,
+           "proportion":0.6914129319908371
+          },
+         "1":{
+           "omega":0,
+           "proportion":0.07568144722655729
+          },
+         "2":{
+           "omega":1,
+           "proportion":0.2329056207826056
+          }
+        }
+      },
+     "display order":3,
+     "estimated parameters":31
+    },
+   "MG94xREV with separate rates for branch sets":{
+     "AIC-c":6408.899382280021,
+     "Equilibrium frequencies":      [
+[0.07535940345366139],
+      [0.01443006409728228],
+      [0.02915821068672351],
+      [0.02954870567752823],
+      [0.03219408024958758],
+      [0.006164627375802654],
+      [0.01245659774045292],
+      [0.01262342001471309],
+      [0.0276793164843978],
+      [0.005300125700761717],
+      [0.01070973633984303],
+      [0.01085316415297191],
+      [0.0418125103783387],
+      [0.008006395714089126],
+      [0.01617817990958604],
+      [0.0163948426631036],
+      [0.0409913146415633],
+      [0.007849150478922548],
+      [0.01586044121725868],
+      [0.01607284872448998],
+      [0.01751178502783737],
+      [0.003353213651232053],
+      [0.006775694789785172],
+      [0.006866436807635995],
+      [0.01505600521072376],
+      [0.002882972930821469],
+      [0.005825499564956559],
+      [0.005903516300053625],
+      [0.02274367484777162],
+      [0.004355032959661065],
+      [0.008800028033786655],
+      [0.008917880494044083],
+      [0.06143704799998004],
+      [0.01176416611541591],
+      [0.0237713451467977],
+      [0.0240896977132239],
+      [0.0262463496652457],
+      [0.005025736545566795],
+      [0.01015528996016046],
+      [0.01029129247081581],
+      [0.02256567087217255],
+      [0.004320948178469224],
+      [0.008731154380523415],
+      [0.00884808446536876],
+      [0.034087812394816],
+      [0.006527245376826684],
+      [0.01318932435908579],
+      [0.01336595951511979],
+      [0.01178447449308153],
+      [0.02413128354890585],
+      [0.0262916585104385],
+      [0.005034412430862358],
+      [0.01017282094890981],
+      [0.01030905823951665],
+      [0.004328407393735399],
+      [0.008746226896405704],
+      [0.008863358836639712],
+      [0.03414665788893068],
+      [0.006538513303760755],
+      [0.0132120929750345],
+      [0.01338903305480236] 
+      ],
+     "Log Likelihood":-3176.217093030587,
+     "Rate Distributions":{
+       "non-synonymous/synonymous rate ratio for *test*":        [
+[0.231720664913378, 1] 
+        ]
+      },
+     "display order":1,
+     "estimated parameters":28
+    },
+   "Nucleotide GTR":{
+     "AIC-c":6683.094244259512,
+     "Equilibrium frequencies":      [
+[0.4044507575757576],
+      [0.1662878787878788],
+      [0.2095643939393939],
+      [0.2196969696969697] 
+      ],
+     "Log Likelihood":-3320.503280793639,
+     "Rate Distributions":{
+       "Substitution rate from nucleotide A to nucleotide C":0.1815218119292989,
+       "Substitution rate from nucleotide A to nucleotide G":1,
+       "Substitution rate from nucleotide A to nucleotide T":0.08433479296165451,
+       "Substitution rate from nucleotide C to nucleotide G":0.1775869374255926,
+       "Substitution rate from nucleotide C to nucleotide T":1.184827038118431,
+       "Substitution rate from nucleotide G to nucleotide T":0.04288318031815568
+      },
+     "display order":0,
+     "estimated parameters":21
+    },
+   "Unconstrained model":{
+     "AIC-c":6391.938375474656,
+     "Log Likelihood":-3163.666348620609,
+     "Rate Distributions":{
+       "Test":{
+         "0":{
+           "omega":0.1490485393860332,
+           "proportion":0.02658974082564446
+          },
+         "1":{
+           "omega":0.169565784922581,
+           "proportion":0.9641001770967245
+          },
+         "2":{
+           "omega":15.09387961636913,
+           "proportion":0.009310082077631076
+          }
+        }
+      },
+     "display order":2,
+     "estimated parameters":32
+    }
+  },
+ "input":{
+   "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/5/working/./input.nex",
+   "number of sequences":8,
+   "number of sites":440,
+   "partition count":1,
+   "trees":{
+     "0":"((((D_CD_83_ELI,D_CD_83_NDK)Node3,D_UG_94_94UG114)Node2,D_CD_84_84ZR085)Node1,B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL)Node10,B_US_90_WEAU160)Node9)"
+    }
+  },
+ "test results":{
+   "LRT":8.711160142067456,
+   "p-value":0.006417496108925114
+  },
+ "tested":{
+   "0":{
+     "B_FR_83_HXB2":"test",
+     "B_US_83_RF":"test",
+     "B_US_86_JRFL":"test",
+     "B_US_90_WEAU160":"test",
+     "D_CD_83_ELI":"test",
+     "D_CD_83_NDK":"test",
+     "D_CD_84_84ZR085":"test",
+     "D_UG_94_94UG114":"test",
+     "Node1":"test",
+     "Node10":"test",
+     "Node2":"test",
+     "Node3":"test",
+     "Node9":"test"
+    }
+  },
+ "timers":{
+   "Constrained BUSTED model fitting":{
+     "order":3,
+     "timer":23
+    },
+   "Overall":{
+     "order":0,
+     "timer":133
+    },
+   "Preliminary model fitting":{
+     "order":1,
+     "timer":4
+    },
+   "Unconstrained BUSTED model fitting":{
+     "order":2,
+     "timer":105
+    }
+  }
+}
\ No newline at end of file