annotate test-data/absrel-out2.json @ 7:f3e408cc2546 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d

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 "analysis":{
   "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
   "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. v2.2 adds support for multiple-hit models. v2.3 adds support for SRV",
   "contact":"[e-mail]",
   "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.",
   "requirements":"in-frame codon alignment and a phylogenetic tree",
   "version":"2.3"
  },
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       "Nucleotide GTR":0,
       "Rate Distributions":        [
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       "Rate classes":1,
       "Uncorrected P-value":1,
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       "Full adaptive model (non-synonymous subs/site)":0.01619043357790366,
       "Full adaptive model (synonymous subs/site)":0.01400929685896962,
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       "rate at which 2 nucleotides are changed instantly within a single codon":0
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       "Baseline MG94xREV omega ratio":1.283370430439691,
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       "Full adaptive model":0.2181331361104026,
       "Full adaptive model (non-synonymous subs/site)":0.1712686263446052,
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       "Rate Distributions":        [
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       "original name":"Pig",
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       "Baseline MG94xREV omega ratio":0.9234518387715737,
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       "Full adaptive model":0.06783877994658692,
       "Full adaptive model (non-synonymous subs/site)":0.04934287026354431,
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       "Rate Distributions":        [
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       "Uncorrected P-value":1,
       "original name":"Rat",
       "rate at which 2 nucleotides are changed instantly within a single codon":0.02234985038534893
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     "RhMonkey":{
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       "Baseline MG94xREV omega ratio":10000000000,
       "Corrected P-value":1,
       "Full adaptive model":0.003691831254195047,
       "Full adaptive model (non-synonymous subs/site)":0.003691831254195047,
       "Full adaptive model (synonymous subs/site)":1e-10,
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       "Nucleotide GTR":0.003778804730491441,
       "Rate Distributions":        [
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       "Rate classes":1,
       "Uncorrected P-value":0.2385766813428075,
       "original name":"RhMonkey",
       "rate at which 2 nucleotides are changed instantly within a single codon":0
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    },
   "attributes":{
     "Baseline MG94xREV":{
       "attribute type":"branch length",
       "display order":1
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     "Baseline MG94xREV omega ratio":{
       "attribute type":"branch label",
       "display order":1
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     "Corrected P-value":{
       "attribute type":"branch label",
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     "Full adaptive model":{
       "attribute type":"branch length",
       "display order":2
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     "Full adaptive model (non-synonymous subs/site)":{
       "attribute type":"branch label",
       "display order":10
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     "Full adaptive model (synonymous subs/site)":{
       "attribute type":"branch label",
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     "LRT":{
       "attribute type":"branch label",
       "display order":4
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     "Nucleotide GTR":{
       "attribute type":"branch length",
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     "Rate Distributions":{
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       "display order":3
      },
     "Rate classes":{
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     "Uncorrected P-value":{
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     "original name":{
       "attribute type":"node label",
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      },
     "rate at which 2 nucleotides are changed instantly within a single codon":{
       "attribute type":"branch label",
       "display order":7
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    }
  },
 "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] 
      ],
     "name":"absrel.filter.default"
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 "fits":{
   "Baseline MG94xREV":{
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     "Equilibrium frequencies":      [
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      [0.005274916061901906],
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     "Log Likelihood":-3399.656647852504,
     "Rate Distributions":{
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         "Mean":666666667.5178814,
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       "Synonymous site-to-site rates":{
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     "estimated parameters":67
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   "Full adaptive model":{
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     "Log Likelihood":-3399.405413285916,
     "Rate Distributions":{
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     "display order":2,
     "estimated parameters":67
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   "Nucleotide GTR":{
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     "Equilibrium frequencies":      [
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     "Log Likelihood":-3532.321213744258,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,
       "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,
       "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
       "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
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     "display order":0,
     "estimated parameters":24
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 "input":{
   "file name":"/tmp/tmpasswxnks/job_working_directory/000/9/working/./input.fasta",
   "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)"
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 "runtime":"2.5.36",
 "test results":{
   "P-value threshold":0.05,
   "positive test results":0,
   "tested":16
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 "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":{
   "Baseline model fitting":{
     "order":2,
     "timer":129
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   "Complexity analysis":{
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     "timer":406
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   "Full adaptive model fitting":{
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     "timer":46
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   "Overall":{
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     "timer":1006
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   "Preliminary model fitting":{
     "order":1,
     "timer":0
    },
   "Testing for selection":{
     "order":5,
     "timer":424
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  }
}