annotate test-data/prime-out1.json @ 8:c257fa0a98a7 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"

{
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    },
   "headers":    [
["alpha;", "Synonymous substitution rate at a site"],
    ["β", "Log of property independent non-synonymous rate a site"],
    ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
    ["PRIME LogL", "Site Log-likelihood under the PRIME model"],
    ["FEL LogL", "Site Log-likelihood under the FEL model"],
    ["p-value", "Omnibus p-value (any property is important)"],
    ["λ1", "Importance for Factor I bipolar"],
    ["p1", "p-value for non-zero effect of Factor I bipolar"],
    ["LogL1", "Log likelihood when there is no effect of Factor I bipolar"],
    ["λ2", "Importance for Factor II secondary structure"],
    ["p2", "p-value for non-zero effect of Factor II secondary structure"],
    ["LogL2", "Log likelihood when there is no effect of Factor II secondary structure"],
    ["λ3", "Importance for Factor III volume"],
    ["p3", "p-value for non-zero effect of Factor III volume"],
    ["LogL3", "Log likelihood when there is no effect of Factor III volume"],
    ["λ4", "Importance for Factor IV composition"],
    ["p4", "p-value for non-zero effect of Factor IV composition"],
    ["LogL4", "Log likelihood when there is no effect of Factor IV composition"],
    ["λ5", "Importance for Factor V charge"],
    ["p5", "p-value for non-zero effect of Factor V charge"],
    ["LogL5", "Log likelihood when there is no effect of Factor V charge"] 
    ]
  },
 "analysis":{
   "authors":"Sergei L. Kosakovsky Pond",
   "citation":"TBD",
   "contact":"[e-mail]",
   "info":"PRIME (PRoperty Informed Model of Evolution). Given a set of N amino-acid properties,\n    fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the \n    properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...).\n    When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted.\n    At each site, N tests are performed\n    A subset of branches can be selected\n    for testing as well, in which case an additional (nuisance) parameter will be\n    inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n    for recombination - aware analysis.\n    ",
   "requirements":"in-frame codon alignment and a phylogenetic tree",
   "version":"0.0.1"
  },
 "branch attributes":{
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       "Nucleotide GTR":0.006740765844759078,
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       "Nucleotide GTR":0.02817726192677478,
       "original name":"CHICKEN_HEBEI_326_2005"
      },
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       "original name":"CHICKEN_HONGKONG_915_97"
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      },
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       "original name":"HONGKONG_1_97_98"
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       "original name":"HUMAN_VIETNAM_3062_2004"
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       "Nucleotide GTR":0
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       "Nucleotide GTR":0.005534464552270369
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       "Nucleotide GTR":0.004793454999477672
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   "attributes":{
     "Global MG94xREV":{
       "attribute type":"branch length",
       "display order":1
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     "Nucleotide GTR":{
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       "display order":0
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     "original name":{
       "attribute type":"node label",
       "display order":-1
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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] 
      ],
     "name":"prime.filter.default"
    }
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 "fits":{
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     "Log Likelihood":-277.7176481414617,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *test*":        [
[0.4074296362572946, 1] 
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     "display order":1,
     "estimated parameters":43
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   "Nucleotide GTR":{
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     "Equilibrium frequencies":      [
[0.3543689320388349],
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     "Log Likelihood":-292.5311130078037,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0,
       "Substitution rate from nucleotide C to nucleotide G":0,
       "Substitution rate from nucleotide C to nucleotide T":1.816257034982832,
       "Substitution rate from nucleotide G to nucleotide T":0
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     "display order":0,
     "estimated parameters":36
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 "input":{
   "file name":"/Users/sergei/Development/tools-iuc/tools/hyphy/test-data/prime-in1.fa",
   "number of sequences":13,
   "number of sites":50,
   "partition count":1,
   "trees":{
     "0":"(((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516)Node7:0.002095219592954275)Node5:0.003887237703073042)Node4:0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-1,(GOOSE_HONGKONG_W355_97:-1)Node13:0.002899766890966483)Node11:0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716)Node10:0.000182535836694054,HONGKONG_1_538_97:-1)Node9:0.02096173714686362)Node3:0.003130608143291779,(((GOOSE_SHANTOU_2216_2005:0.006207842095177651)Node19:0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232)Node18:0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774)Node17:0.004655295319725731)Node2:0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001)Node25:0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184)Node24:0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072)Node23:0.0004125980823087554,CHICKEN_CK_160_2005:0.006168335080088849)"
    }
  },
 "tested":{
   "0":{
     "CHICKEN_CK_160_2005":"test",
     "CHICKEN_HEBEI_326_2005":"test",
     "CHICKEN_HONGKONG_915_97":"test",
     "CK_HK_WF157_2003":"test",
     "GOOSE_HONGKONG_W355_97":"test",
     "GOOSE_SHANTOU_2216_2005":"test",
     "HONGKONG_1_538_97":"test",
     "HONGKONG_1_97_98":"test",
     "HUMAN_VIETNAM_3062_2004":"test",
     "HUMAN_VIETNAM_CL105_2005":"test",
     "MALLARD_VIETNAM_16_2003":"test",
     "Node10":"test",
     "Node11":"test",
     "Node13":"test",
     "Node17":"test",
     "Node18":"test",
     "Node19":"test",
     "Node2":"test",
     "Node23":"test",
     "Node24":"test",
     "Node25":"test",
     "Node3":"test",
     "Node4":"test",
     "Node5":"test",
     "Node7":"test",
     "Node9":"test",
     "PEREGRINEFALCON_HK_D0028_2004":"test",
     "SWINE_ANHUI_1_2004":"test"
    }
  },
 "timers":{
   "Model fitting":{
     "order":1,
     "timer":3
    },
   "PRIME analysis":{
     "order":2,
     "timer":86
    },
   "Total time":{
     "order":0,
     "timer":89
    }
  }
}