annotate test-data/prime-out1.json @ 10:188452adcaa0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e86817831c8ab0d0f8f86e32c25027cc370947c5"

{
 "MLE":{
   "content":{
     "0":      [
[0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 4.123712641737602, 511.6499971244988, -5.608842688620929, -7.031699805798055, 1, 3.180962375542725, 1, -5.599238755695894, 0.7828049218517579, 1, -5.608352884924835, -2.115291881920681, 1, -5.604784076919627, -5.404956845857691, 1, -5.615111503355894, 2.462902938936584, 1, -5.607953657572869],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 4.849174446703908, 0.2440623951294166, -7.530855366772653, -8.547881040478554, 1, 8.833984038052169, 1, -7.53445935473729, 1.725573110573239, 1, -7.53079217870133, -0.2671292981572289, 1, -7.530980113687253, -0.4804669617756561, 1, -7.530833122267245, -0.1532486612226931, 1, -7.530868793694735],
      [10.63135649145974, 0, 0.7502380884715356, -7.750335490678291, -7.750335610925491, 1, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839],
      [0, 2.202981274414969, 0.397462976308795, -6.144243972107117, -7.361850215781605, 1, -2.763157788623757, 1, -6.146863972828472, -0.02286865932396898, 1, -6.141696705195292, 2.56489740323532, 1, -6.144140070703968, 3.673465169891661, 1, -6.162164086824393, -0.3782299185469108, 1, -6.140399389962398],
      [0, 6.509531966707992, 0.7279903564537584, -7.452295439546786, -8.507460649598423, 1, 6.763405786911178, 1, -7.454926555248795, 0.6678772051425989, 1, -7.451746683657063, -0.5798067642619018, 1, -7.452771449125621, -0.2211171350169704, 1, -7.452165845137638, 0.1663073214171773, 1, -7.450195387750036],
      [8.776439958358919, 2.284512411822656, 1.336576511778388, -9.655786100846457, -10.49206003395885, 1, 5.383393783342485, 1, -9.664210115841298, -3.158949692311737, 1, -9.655544560079083, -0.3018714845472609, 1, -9.655318226877892, 3.597509240461804, 1, -9.653746338822806, -0.0948988112495659, 1, -9.655669896512631],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 2.425089497235808, 0.5977083182449383, -7.256204136892792, -8.1869045859499, 1, 5.146566146987978, 1, -7.264970053927162, -2.513623140671756, 1, -7.255847818578761, -0.3554384584781068, 1, -7.256424962957591, 4.119925682148564, 1, -7.254165622670933, -0.1223190226259517, 1, -7.255886801654065],
      [6.419869332267623, 0, 0.4530400706576413, -5.863592599386944, -5.863592751403759, 1, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 2.699658477079707, 0.4801615193392039, -5.903524182207455, -6.898872136243598, 1, -0.8716130556024849, 1, -5.903538930457988, -0.4627800379305517, 1, -5.903694932983693, 3.044105631862708, 1, -5.908943461477226, -0.07628230444039112, 1, -5.903502621374115, 0.3057953308962, 1, -5.903488680659473],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [5.437286509277304, 0, 0.3837007479214133, -9.641801767536267, -9.641801993340092, 1, -0.06122935182163709, 1, -9.641801767535474, -0.06122935182163709, 1, -9.641801767535474, -0.06122935182163709, 1, -9.641801767535474, -0.06122935182163709, 1, -9.641801767535474, -0.06122935182163709, 1, -9.641801767535474],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [2.976165780520339, 0, 0.2100233331415074, -6.510110085668789, -6.510110085669312, 1, -0.06122935182163709, 1, -6.510110085668789, -0.06122935182163709, 1, -6.510110085668789, -0.06122935182163709, 1, -6.510110085668789, -0.06122935182163709, 1, -6.510110085668789, -0.06122935182163709, 1, -6.510110085668789],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [7.811867907041998, 0, 0.5512712183698597, -8.853002619643194, -8.85300270595488, 1, -0.06122935182163709, 1, -8.853002619609974, -0.06122935182163709, 1, -8.853002619609974, -0.06122935182163709, 1, -8.853002619609974, -0.06122935182163709, 1, -8.853002619609974, -0.06122935182163709, 1, -8.853002619609974],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [5.250193239862218, 0, 0.370497870478199, -7.813932328397811, -7.813933401024069, 1, -0.06122935182163709, 1, -7.81393232835335, -0.06122935182163709, 1, -7.81393232835335, -0.06122935182163709, 1, -7.81393232835335, -0.06122935182163709, 1, -7.81393232835335, -0.06122935182163709, 1, -7.81393232835335],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [7.592268336906083, 0, 0.5357744224661302, -5.63867473098278, -5.638674842181149, 1, -0.06122935182163709, 1, -5.638674730981298, -0.06122935182163709, 1, -5.638674730981298, -0.06122935182163709, 1, -5.638674730981298, -0.06122935182163709, 1, -5.638674730981298, -0.06122935182163709, 1, -5.638674730981298] 
      ]
    },
   "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":{
   "0":{
     "CHICKEN_CK_160_2005":{
       "Global MG94xREV":0.006875905528136641,
       "Nucleotide GTR":0.006740765844759078,
       "original name":"CHICKEN_CK_160_2005"
      },
     "CHICKEN_HEBEI_326_2005":{
       "Global MG94xREV":0.03000509055831138,
       "Nucleotide GTR":0.02817726192677478,
       "original name":"CHICKEN_HEBEI_326_2005"
      },
     "CHICKEN_HONGKONG_915_97":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"CHICKEN_HONGKONG_915_97"
      },
     "CK_HK_WF157_2003":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"CK_HK_WF157_2003"
      },
     "GOOSE_HONGKONG_W355_97":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"GOOSE_HONGKONG_W355_97"
      },
     "GOOSE_SHANTOU_2216_2005":{
       "Global MG94xREV":0.008912012248907763,
       "Nucleotide GTR":0.007985902570718373,
       "original name":"GOOSE_SHANTOU_2216_2005"
      },
     "HONGKONG_1_538_97":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"HONGKONG_1_538_97"
      },
     "HONGKONG_1_97_98":{
       "Global MG94xREV":0.02020234274992877,
       "Nucleotide GTR":0.02001220163799822,
       "original name":"HONGKONG_1_97_98"
      },
     "HUMAN_VIETNAM_3062_2004":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"HUMAN_VIETNAM_3062_2004"
      },
     "HUMAN_VIETNAM_CL105_2005":{
       "Global MG94xREV":0.006025788919462983,
       "Nucleotide GTR":0.005802088014335368,
       "original name":"HUMAN_VIETNAM_CL105_2005"
      },
     "MALLARD_VIETNAM_16_2003":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0,
       "original name":"MALLARD_VIETNAM_16_2003"
      },
     "Node10":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0
      },
     "Node11":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0
      },
     "Node13":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0
      },
     "Node17":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0
      },
     "Node18":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0
      },
     "Node19":{
       "Global MG94xREV":0.004922199772633382,
       "Nucleotide GTR":0.005534464552270369
      },
     "Node2":{
       "Global MG94xREV":0.006872306486383904,
       "Nucleotide GTR":0.006718147482064949
      },
     "Node23":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0
      },
     "Node24":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0
      },
     "Node25":{
       "Global MG94xREV":0.0008268367968756879,
       "Nucleotide GTR":0.0009189593587976459
      },
     "Node3":{
       "Global MG94xREV":0,
       "Nucleotide GTR":0
      },
     "Node4":{
       "Global MG94xREV":0.002648185777377607,
       "Nucleotide GTR":0.00251461257430795
      },
     "Node5":{
       "Global MG94xREV":0.003268514528883674,
       "Nucleotide GTR":0.003965274251091903
      },
     "Node7":{
       "Global MG94xREV":0.005023432525711092,
       "Nucleotide GTR":0.004793454999477672
      },
     "Node9":{
       "Global MG94xREV":0.01391813691986412,
       "Nucleotide GTR":0.01351408611669037
      },
     "PEREGRINEFALCON_HK_D0028_2004":{
       "Global MG94xREV":0.006920710269269024,
       "Nucleotide GTR":0.006722811033712868,
       "original name":"PEREGRINEFALCON_HK_D0028_2004"
      },
     "SWINE_ANHUI_1_2004":{
       "Global MG94xREV":0.01018798286684916,
       "Nucleotide GTR":0.009150633137551082,
       "original name":"SWINE_ANHUI_1_2004"
      }
    },
   "attributes":{
     "Global MG94xREV":{
       "attribute type":"branch length",
       "display order":1
      },
     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
      },
     "original name":{
       "attribute type":"node label",
       "display order":-1
      }
    }
  },
 "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"
    }
  },
 "fits":{
   "Global MG94xREV":{
     "AIC-c":647.6795207053656,
     "Equilibrium frequencies":      [
[0.04488063522282697],
      [0.02743154763030629],
      [0.03260676907658289],
      [0.05361444334761576],
      [0.01878621141548667],
      [0.0114823431236735],
      [0.01364859597925394],
      [0.02244202343953587],
      [0.00898846188937465],
      [0.005493848721556544],
      [0.006530315351495689],
      [0.01073762388516669],
      [0.04007728102844568],
      [0.02449568367218243],
      [0.02911702655775225],
      [0.04787635251947601],
      [0.02154103095825152],
      [0.01316611972632322],
      [0.01565003299619046],
      [0.02573293310637029],
      [0.009016680795182521],
      [0.005511096433290134],
      [0.006550817007515099],
      [0.01077133421300087],
      [0.004314126457096238],
      [0.002636842477907016],
      [0.003134307802358531],
      [0.005153658975191914],
      [0.01923560009946569],
      [0.01175701452767408],
      [0.01397508674685076],
      [0.02297886352699522],
      [0.03843194498464033],
      [0.02349003582808618],
      [0.02792165371671785],
      [0.04591083274306419],
      [0.01608690786137961],
      [0.00983249851595989],
      [0.0116874925496928],
      [0.01921743321791434],
      [0.00769695150511784],
      [0.004704463089092132],
      [0.005592004637968804],
      [0.00919478452948895],
      [0.03431876246786721],
      [0.02097601254029597],
      [0.02493333610872543],
      [0.04099722156245031],
      [0.006131000492593795],
      [0.01198292502502543],
      [0.004198752217504174],
      [0.002566324448628536],
      [0.003050485878513492],
      [0.005015832814718212],
      [0.001227885122343091],
      [0.001459537288103269],
      [0.002399878352343215],
      [0.008957344771016727],
      [0.00547482958980595],
      [0.006507708080284218],
      [0.01070045135026252] 
      ],
     "Log Likelihood":-277.7176481414617,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *test*":        [
[0.4074296362572946, 1] 
        ]
      },
     "display order":1,
     "estimated parameters":43
    },
   "Nucleotide GTR":{
     "AIC-c":658.4548031196325,
     "Equilibrium frequencies":      [
[0.3543689320388349],
      [0.1790722761596548],
      [0.2076591154261057],
      [0.2588996763754045] 
      ],
     "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
      },
     "display order":0,
     "estimated parameters":36
    }
  },
 "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
    }
  }
}