annotate test-data/PRIME/gene2.json @ 0:dd2d60b55e0d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drhip commit 15c654c3d27df68a47483031961ace7f5b8d998d

{
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      [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [5.24043352637176, 0.0004338156767874127, 5.20859751191156, 0.0004338156767874127, 0.1357666032748778, 0, 1, -5.894933720870095, -5.895005662002102, 0.9999999999867918, 1, 0.886606480448811, 1, -5.894957967156203, 6.632621509002536, 1, -5.894956725977382, 14.18143511951259, 1, -5.894958091629903, 14.18143511951259, 1, -5.894956502696569, 14.18143511951259, 1, -5.894957058566754],
      [7.737689682919324, 0.0002059368534316897, 7.796546118142354, 0.0002059368534316897, 0.200464301315868, 0, 1, -5.185312974623315, -5.185375021116818, 0.9999999999908757, 1, 1.697672244826404, 1, -5.185319913350097, 0.639872503016355, 1, -5.185320726580621, 14.42273103529203, 1, -5.185322382170208, 14.42273103529203, 1, -5.185318999805737, 14.67233899949953, 1, -5.185320891586968],
      [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
      [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0]
      ]
    },
   "headers":    [
["α", "Synonymous substitution rate at a site"],
    ["β", "Property independent non-synonymous rate a site"],
    ["FEL α", "Synonymous substitution rate at a site (FEL model)"],
    ["FEL 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"],
    ["# subs", "The number of amino-acid substitutions that occurred at this site"],
    ["# aa", "The number of unique amino-acids occurring at that site"],
    ["PRIME LogL", "Site Log-likelihood under the PRIME model"],
    ["FEL LogL", "Site Log-likelihood under the FEL model"],
    ["p-value", "Omnibus q-value (any property is important)"],
    ["q-value", "Importance for Factor I bipolar"],
    ["λ1", "p-value for non-zero effect of Factor I bipolar"],
    ["p1", "Log likelihood when there is no effect of Factor I bipolar"],
    ["LogL1", "Importance for Factor II secondary structure"],
    ["λ2", "p-value for non-zero effect of Factor II secondary structure"],
    ["p2", "Log likelihood when there is no effect of Factor II secondary structure"],
    ["LogL2", "Importance for Factor III volume"],
    ["λ3", "p-value for non-zero effect of Factor III volume"],
    ["p3", "Log likelihood when there is no effect of Factor III volume"],
    ["LogL3", "Importance for Factor IV composition"],
    ["λ4", "p-value for non-zero effect of Factor IV composition"],
    ["p4", "Log likelihood when there is no effect of Factor IV composition"],
    ["LogL4", "Importance for Factor V charge"],
    ["λ5", "p-value for non-zero effect of Factor V charge"],
    ["p5", "Log likelihood when there is no effect of Factor V charge"],
    ["LogL5", "0"]
    ],
   "substitutions":{
     "0":{
       "0":null,
       "1":null,
       "10":null,
       "11":null,
       "12":null,
       "13":null,
       "14":null,
       "15":null,
       "16":null,
       "17":null,
       "18":null,
       "19":null,
       "2":null,
       "20":null,
       "21":null,
       "22":null,
       "23":null,
       "24":null,
       "25":{
         "PP564823_1_2023_10_06":"GGT",
         "root":"GTT"
        },
       "26":{
         "Node2":"TCA",
         "Node3":"CCA",
         "PP564823_1_2023_10_06":"TCA",
         "root":"CCA"
        },
       "27":null,
       "28":null,
       "29":null,
       "3":null,
       "30":null,
       "31":null,
       "32":null,
       "33":null,
       "34":{
         "PP563831_1_2023_08_29":"GAA",
         "root":"AAA"
        },
       "35":null,
       "36":null,
       "37":{
         "Node8":"CTT",
         "root":"CTC"
        },
       "38":null,
       "39":null,
       "4":{
         "Node2":"CGG",
         "PP564823_1_2023_10_06":"CGG",
         "root":"CGA"
        },
       "40":{
         "Node2":"CAG",
         "root":"CAA"
        },
       "41":null,
       "42":null,
       "43":null,
       "44":null,
       "45":{
         "PP564823_1_2023_10_06":"ATG",
         "root":"CTG"
        },
       "46":null,
       "47":null,
       "48":null,
       "49":{
         "Node3":"TTT",
         "root":"TTC"
        },
       "5":{
         "PP564823_1_2023_10_06":"AAG",
         "root":"AAA"
        },
       "50":null,
       "51":null,
       "52":null,
       "53":null,
       "54":null,
       "55":{
         "Node2":"TTC",
         "root":"TTT"
        },
       "56":null,
       "57":null,
       "58":null,
       "59":{
         "Node3":"CCT",
         "root":"CCC"
        },
       "6":null,
       "60":null,
       "61":null,
       "62":null,
       "63":{
         "Node2":"GGG",
         "root":"GGA"
        },
       "64":null,
       "65":null,
       "66":null,
       "67":null,
       "68":null,
       "69":{
         "Node2":"GGT",
         "PP564823_1_2023_10_06":"AGC",
         "root":"GGC"
        },
       "7":null,
       "70":null,
       "71":null,
       "72":null,
       "73":null,
       "74":null,
       "75":null,
       "76":null,
       "77":null,
       "78":null,
       "79":null,
       "8":{
         "PP564823_1_2023_10_06":"GGT",
         "root":"GCT"
        },
       "80":{
         "PP563838_1_2023_09_30":"CTG",
         "PP564823_1_2023_10_06":"TTA",
         "root":"CTA"
        },
       "81":null,
       "82":null,
       "83":{
         "PP563832_1_2023_08_28":"TTT",
         "root":"TTC"
        },
       "84":{
         "PP564823_1_2023_10_06":"AAA",
         "root":"AAG"
        },
       "85":null,
       "86":{
         "PP564823_1_2023_10_06":"GAG",
         "root":"GAA"
        },
       "87":null,
       "88":null,
       "89":null,
       "9":null,
       "90":null,
       "91":{
         "Node2":"CTG",
         "PP564823_1_2023_10_06":"CTG",
         "root":"TTG"
        },
       "92":{
         "PP564823_1_2023_10_06":"AAC",
         "root":"AAT"
        },
       "93":null,
       "94":null,
       "95":{
         "PP564823_1_2023_10_06":"AAC",
         "root":"AAT"
        },
       "96":{
         "PP564823_1_2023_10_06":"AGG",
         "root":"AGA"
        },
       "97":null,
       "98":null,
       "99":null
      }
    }
  },
 "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",
   "residue_properties":null,
   "version":"0.2.0"
  },
 "branch attributes":{
   "0":{
     "Node2":{
       "Global MG94xREV":0.0155536653271895,
       "Nucleotide GTR":0.01391650578382423
      },
     "Node3":{
       "Global MG94xREV":0.007028463160179066,
       "Nucleotide GTR":0.007313844682570613
      },
     "Node8":{
       "Global MG94xREV":0.006625904948639312,
       "Nucleotide GTR":0.006196659368038242
      },
     "PP563830_1_2023_09_02":{
       "Global MG94xREV":0,
       "Nucleotide GTR":1e-06,
       "original name":"PP563830_1_2023_09_02"
      },
     "PP563831_1_2023_08_29":{
       "Global MG94xREV":0.003308074904952416,
       "Nucleotide GTR":0.003339882520232537,
       "original name":"PP563831_1_2023_08_29"
      },
     "PP563832_1_2023_08_28":{
       "Global MG94xREV":0.003305744077013286,
       "Nucleotide GTR":0.003342518270787742,
       "original name":"PP563832_1_2023_08_28"
      },
     "PP563838_1_2023_09_30":{
       "Global MG94xREV":0.003316134050292535,
       "Nucleotide GTR":0.003339882520180704,
       "original name":"PP563838_1_2023_09_30"
      },
     "PP563839_1_2023_09_29":{
       "Global MG94xREV":0,
       "Nucleotide GTR":1e-06,
       "original name":"PP563839_1_2023_09_29"
      },
     "PP563845_1_2023_10_22":{
       "Global MG94xREV":0.005917829644775162,
       "Nucleotide GTR":0.007157676157708746,
       "original name":"PP563845_1_2023_10_22"
      },
     "PP564823_1_2023_10_06":{
       "Global MG94xREV":0.04452770118405119,
       "Nucleotide GTR":0.04195089101557686,
       "original name":"PP564823_1_2023_10_06"
      }
    },
   "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, 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]
      ],
     "name":"prime.filter.default"
    }
  },
 "fits":{
   "Global MG94xREV":{
     "AIC-c":1098.164186625619,
     "Equilibrium frequencies":      [
[0.04022787530103862],
      [0.01934493712337751],
      [0.03425741450905353],
      [0.01425856648080257],
      [0.03379960463533115],
      [0.01625368532572285],
      [0.0287832021345848],
      [0.01198009852897374],
      [0.03434841386947805],
      [0.01651759884459136],
      [0.02925055929127961],
      [0.01217462118004102],
      [0.04856425764989153],
      [0.02335376908798366],
      [0.04135654424169535],
      [0.01721335494628832],
      [0.01826098626758108],
      [0.008781414094422619],
      [0.01555076352482647],
      [0.006472514015538997],
      [0.01534294594175388],
      [0.007378175514105413],
      [0.01306580710473399],
      [0.005438229413926055],
      [0.01559207164907205],
      [0.007497976053105356],
      [0.01327795856827995],
      [0.005526530758038588],
      [0.02204519218088164],
      [0.01060117775101382],
      [0.01877333269084459],
      [0.00781380661894053],
      [0.02001283201397348],
      [0.009623848489980729],
      [0.0170426073132688],
      [0.007093446860043523],
      [0.01681485300040535],
      [0.008085991904804354],
      [0.0143192595888557],
      [0.005959939409601683],
      [0.01708787828271292],
      [0.008217285364372072],
      [0.0145517635478013],
      [0.006056711836919557],
      [0.02416007116849923],
      [0.01161818898347029],
      [0.02057432977490965],
      [0.008563414755540757],
      [0.01095174735555056],
      [0.008072200842739543],
      [0.01913496685581441],
      [0.009201697278655068],
      [0.01629503140027161],
      [0.006782292004731834],
      [0.009351106613197152],
      [0.01655961626153459],
      [0.006892417094094173],
      [0.02749367841825353],
      [0.0132212670023302],
      [0.02341317633368553],
      [0.009744994946783913]
      ],
     "Log Likelihood":-522.0390026738794,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *background*":        [
[0.2130897909742414, 1]
        ],
       "non-synonymous/synonymous rate ratio for *test*":        [
[0.05367176447095212, 1]
        ]
      },
     "display order":1,
     "estimated parameters":26
    },
   "Nucleotide GTR":{
     "AIC-c":1130.795872905925,
     "Equilibrium frequencies":      [
[0.3347619047619048],
      [0.2033333333333333],
      [0.2466666666666667],
      [0.2152380952380952]
      ],
     "Log Likelihood":-546.2152441452704,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.1157280802219541,
       "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":0.1604122535118794,
       "Substitution rate from nucleotide C to nucleotide T":2.313607104947681,
       "Substitution rate from nucleotide G to nucleotide T":0.1528462357734212
      },
     "display order":0,
     "estimated parameters":19
    }
  },
 "input":{
   "file name":"/home/dcallan-adm/Documents/veg/CAPHEINE/work/6a/8adfdc16ef877c493cc257d23c98ea/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1-nodups.fasta",
   "number of sequences":7,
   "number of sites":100,
   "partition count":1,
   "trees":{
     "0":"(PP564823_1_2023_10_06,((PP563832_1_2023_08_28,PP563830_1_2023_09_02,PP563831_1_2023_08_29)Node3,(PP563839_1_2023_09_29,PP563838_1_2023_09_30)Node8)Node2,PP563845_1_2023_10_22)"
    }
  },
 "model":{
   "Q":    [
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    ],
   "alphabet":    [
["AAA", "AAC", "AAG", "AAT", "ACA", "ACC", "ACG", "ACT", "AGA", "AGC", "AGG", "AGT", "ATA", "ATC", "ATG", "ATT", "CAA", "CAC", "CAG", "CAT", "CCA", "CCC", "CCG", "CCT", "CGA", "CGC", "CGG", "CGT", "CTA", "CTC", "CTG", "CTT", "GAA", "GAC", "GAG", "GAT", "GCA", "GCC", "GCG", "GCT", "GGA", "GGC", "GGG", "GGT", "GTA", "GTC", "GTG", "GTT", "TAC", "TAT", "TCA", "TCC", "TCG", "TCT", "TGC", "TGG", "TGT", "TTA", "TTC", "TTG", "TTT"]
    ],
   "ordering":{
     "Factor I bipolar":0,
     "Factor II secondary structure":1,
     "Factor III volume":2,
     "Factor IV composition":3,
     "Factor V charge":4
    },
   "parameters":{
     "lambda_Factor_III_volume":"Factor III volume",
     "lambda_Factor_II_secondary_structure":"Factor II secondary structure",
     "lambda_Factor_IV_composition":"Factor IV composition",
     "lambda_Factor_I_bipolar":"Factor I bipolar",
     "lambda_Factor_V_charge":"Factor V charge"
    },
   "residue_properties":{
     "Factor I bipolar":{
       "A":-0.6038471648233061,
       "C":-1.372194149505415,
       "D":1.072824912122625,
       "E":1.38649848166705,
       "F":-1.027868439614629,
       "G":-0.3923473964334172,
       "H":0.3433039718792401,
       "I":-1.265933396304698,
       "K":1.870802299139549,
       "L":-1.041151033764719,
       "M":-0.6774123016545719,
       "N":0.9655424209103626,
       "P":0.1931084841820725,
       "Q":0.9512380887487276,
       "R":1.571433061756759,
       "S":-0.2329562666323415,
       "T":-0.03269561636945143,
       "V":-1.366063721436143,
       "W":-0.6079341168694875,
       "Y":0.2656518830017929
      },
     "Factor II secondary structure":{
       "A":-1.330232386778897,
       "C":0.475221663023938,
       "D":0.3086744020630652,
       "E":-1.48451849969357,
       "F":-0.6027376027044098,
       "G":1.688053557260477,
       "H":-0.4259727183717044,
       "I":-0.5588018222055293,
       "K":-0.5731064949260951,
       "L":-1.008377250566167,
       "M":-1.557063625633582,
       "N":0.8461213914214641,
       "P":2.126389599912099,
       "Q":-0.1827932821220867,
       "R":-0.05609475231136144,
       "S":1.42954768595311,
       "T":0.3331966981554637,
       "V":-0.2849695158404135,
       "W":0.009298037268367709,
       "Y":0.8481649160958307
      },
     "Factor III volume":{
       "A":-0.3445293132340136,
       "C":-0.4051709852318138,
       "D":-1.718603788036881,
       "E":0.6943706488988424,
       "F":0.8889881078685267,
       "G":0.6252673482501864,
       "H":-0.7864143650009298,
       "I":1.001809823213271,
       "K":0.2506052352095138,
       "L":-0.7074391642596085,
       "M":1.043177785506344,
       "N":0.6106945433514901,
       "P":-0.7652602933737901,
       "Q":-1.412574885164262,
       "R":0.7061229109139199,
       "S":-2.237583678622706,
       "T":1.040357242622726,
       "V":-0.2556822124000274,
       "W":0.315947812013345,
       "Y":1.455917227475868
      },
     "Factor IV composition":{
       "A":1.630293655002852,
       "C":-1.059000381337118,
       "D":-0.2688255698874202,
       "E":0.1174359673783979,
       "F":-0.4121161401634496,
       "G":1.08516648547448,
       "H":-1.530405590795939,
       "I":0.4081704577935299,
       "K":-0.2875156442712501,
       "L":1.314639065409281,
       "M":-1.043425319350593,
       "N":-0.1753751979682707,
       "P":0.4372439068350431,
       "Q":-0.5221799115348923,
       "R":0.4569723186846413,
       "S":0.6957899358113568,
       "T":0.942914252664219,
       "V":1.289718966230841,
       "W":-2.209478293408426,
       "Y":-0.8700229625672823
      },
     "Factor V charge":{
       "A":-0.09353709405505788,
       "C":-0.1633935055110449,
       "D":-2.077715533208598,
       "E":-0.5363882896154895,
       "F":0.2640764618388941,
       "G":1.322817670327799,
       "H":-0.0499569474586623,
       "I":0.5229938033821855,
       "K":1.056209714679261,
       "L":-0.5844546277732787,
       "M":0.7767840688553127,
       "N":0.5979772909083368,
       "P":-0.8920791919831299,
       "Q":-1.187526950526341,
       "R":1.856674466133644,
       "S":-1.696389250490137,
       "T":0.8415134042411355,
       "V":-0.8087642058429619,
       "W":-0.1178907053883378,
       "Y":0.9690494214864698
      }
    },
   "translation-table":{
     "AAA":"K",
     "AAC":"N",
     "AAG":"K",
     "AAT":"N",
     "ACA":"T",
     "ACC":"T",
     "ACG":"T",
     "ACT":"T",
     "AGA":"R",
     "AGC":"S",
     "AGG":"R",
     "AGT":"S",
     "ATA":"I",
     "ATC":"I",
     "ATG":"M",
     "ATT":"I",
     "CAA":"Q",
     "CAC":"H",
     "CAG":"Q",
     "CAT":"H",
     "CCA":"P",
     "CCC":"P",
     "CCG":"P",
     "CCT":"P",
     "CGA":"R",
     "CGC":"R",
     "CGG":"R",
     "CGT":"R",
     "CTA":"L",
     "CTC":"L",
     "CTG":"L",
     "CTT":"L",
     "GAA":"E",
     "GAC":"D",
     "GAG":"E",
     "GAT":"D",
     "GCA":"A",
     "GCC":"A",
     "GCG":"A",
     "GCT":"A",
     "GGA":"G",
     "GGC":"G",
     "GGG":"G",
     "GGT":"G",
     "GTA":"V",
     "GTC":"V",
     "GTG":"V",
     "GTT":"V",
     "TAA":"X",
     "TAC":"Y",
     "TAG":"X",
     "TAT":"Y",
     "TCA":"S",
     "TCC":"S",
     "TCG":"S",
     "TCT":"S",
     "TGA":"X",
     "TGC":"C",
     "TGG":"W",
     "TGT":"C",
     "TTA":"L",
     "TTC":"F",
     "TTG":"L",
     "TTT":"F"
    }
  },
 "runtime":"2.5.73",
 "tested":{
   "0":{
     "Node2":"test",
     "Node3":"test",
     "Node8":"test",
     "PP563830_1_2023_09_02":"background",
     "PP563831_1_2023_08_29":"background",
     "PP563832_1_2023_08_28":"background",
     "PP563838_1_2023_09_30":"background",
     "PP563839_1_2023_09_29":"background",
     "PP563845_1_2023_10_22":"background",
     "PP564823_1_2023_10_06":"background"
    }
  },
 "timers":{
   "Model fitting":{
     "order":1,
     "timer":0
    },
   "PRIME analysis":{
     "order":2,
     "timer":41
    },
   "Total time":{
     "order":0,
     "timer":43
    }
  }
}