tests/testthat/_snaps/process_age.md

In poseidon-framework/poseidonR: Poseidon .janno file handling in R

processing age in a normal janno file works as expected

{
  "type": "list",
  "attributes": {
    "names": {
      "type": "character",
      "attributes": {},
      "value": ["source_file", "Poseidon_ID", "Genetic_Sex", "Group_Name", "Alternative_IDs", "Relation_To", "Relation_Degree", "Relation_Type", "Relation_Note", "Collection_ID", "Country", "Country_ISO", "Location", "Site", "Latitude", "Longitude", "Date_Type", "Date_C14_Labnr", "Date_C14_Uncal_BP", "Date_C14_Uncal_BP_Err", "Date_BC_AD_Start", "Date_BC_AD_Median", "Date_BC_AD_Stop", "Date_Note", "MT_Haplogroup", "Y_Haplogroup", "Source_Tissue", "Nr_Libraries", "Library_Names", "Capture_Type", "UDG", "Library_Built", "Genotype_Ploidy", "Data_Preparation_Pipeline_URL", "Endogenous", "Nr_SNPs", "Coverage_on_Target_SNPs", "Damage", "Contamination", "Contamination_Err", "Contamination_Meas", "Contamination_Note", "Genetic_Source_Accession_IDs", "Primary_Contact", "Publication", "Note", "Keywords", "AdditionalColumn1", "AdditionalColumn2", "Date_BC_AD_Prob", "Date_BC_AD_Start_Derived", "Date_BC_AD_Median_Derived", "Date_BC_AD_Stop_Derived", "Date_BC_AD_Sample"]
    },
    "row.names": {
      "type": "integer",
      "attributes": {},
      "value": [1, 2, 3]
    },
    "class": {
      "type": "character",
      "attributes": {},
      "value": ["janno", "tbl_df", "tbl", "data.frame"]
    }
  },
  "value": [
    {
      "type": "character",
      "attributes": {},
      "value": ["testJannoFiles/normal_full.janno", "testJannoFiles/normal_full.janno", "testJannoFiles/normal_full.janno"]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["XXX011", "XXX012", "XXX013"]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["M", "F", "M"]
    },
    {
      "type": "list",
      "attributes": {},
      "value": [
        {
          "type": "character",
          "attributes": {},
          "value": ["POP1", "POP3"]
        },
        {
          "type": "character",
          "attributes": {},
          "value": ["POP2"]
        },
        {
          "type": "character",
          "attributes": {},
          "value": ["POP1"]
        }
      ]
    },
    {
      "type": "list",
      "attributes": {},
      "value": [
        {
          "type": "character",
          "attributes": {},
          "value": ["Paul", "Peter"]
        },
        {
          "type": "NULL"
        },
        {
          "type": "character",
          "attributes": {},
          "value": ["Skeleton Joe"]
        }
      ]
    },
    {
      "type": "list",
      "attributes": {},
      "value": [
        {
          "type": "character",
          "attributes": {},
          "value": ["XXX012", "I1234"]
        },
        {
          "type": "character",
          "attributes": {},
          "value": ["XXX011"]
        },
        {
          "type": "character",
          "attributes": {},
          "value": ["XXX011"]
        }
      ]
    },
    {
      "type": "list",
      "attributes": {},
      "value": [
        {
          "type": "character",
          "attributes": {},
          "value": ["first", "second"]
        },
        {
          "type": "character",
          "attributes": {},
          "value": ["first"]
        },
        {
          "type": "character",
          "attributes": {},
          "value": ["sixthToTenth"]
        }
      ]
    },
    {
      "type": "list",
      "attributes": {},
      "value": [
        {
          "type": "character",
          "attributes": {},
          "value": ["father_of", "grandfather_of"]
        },
        {
          "type": "character",
          "attributes": {},
          "value": ["daughter_of"]
        },
        {
          "type": "NULL"
        }
      ]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["yyy", null, "xxx"]
    },
    {
      "type": "character",
      "attributes": {},
      "value": [null, null, null]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["xxx", "xxx", "xxx"]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["DE", "FR", "EG"]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["xxx", "xxx", "xxx"]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["xxx", "xxx", "xxx"]
    },
    {
      "type": "double",
      "attributes": {},
      "value": [0, -90, 90]
    },
    {
      "type": "double",
      "attributes": {},
      "value": [0, -180, 180]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["C14", "contextual", "modern"]
    },
    {
      "type": "list",
      "attributes": {},
      "value": [
        {
          "type": "character",
          "attributes": {},
          "value": ["A-1", "A-2", "A-3"]
        },
        {
          "type": "NULL"
        },
        {
          "type": "NULL"
        }
      ]
    },
    {
      "type": "list",
      "attributes": {},
      "value": [
        {
          "type": "integer",
          "attributes": {},
          "value": [3000, 3100, 2900]
        },
        {
          "type": "NULL"
        },
        {
          "type": "NULL"
        }
      ]
    },
    {
      "type": "list",
      "attributes": {},
      "value": [
        {
          "type": "integer",
          "attributes": {},
          "value": [30, 40, 20]
        },
        {
          "type": "NULL"
        },
        {
          "type": "NULL"
        }
      ]
    },
    {
      "type": "integer",
      "attributes": {},
      "value": [-1200, -5500, 2000]
    },
    {
      "type": "integer",
      "attributes": {},
      "value": [-1000, -5000, 2000]
    },
    {
      "type": "integer",
      "attributes": {},
      "value": [-800, -4500, 2000]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["x x x", "yyy", null]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["A", "B", "C"]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["C", "B", "A"]
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    {
      "type": "list",
      "attributes": {},
      "value": [
        {
          "type": "character",
          "attributes": {},
          "value": ["xxx", "yyy"]
        },
        {
          "type": "character",
          "attributes": {},
          "value": ["xxx"]
        },
        {
          "type": "character",
          "attributes": {},
          "value": ["xxx"]
        }
      ]
    },
    {
      "type": "integer",
      "attributes": {},
      "value": [2, 0, 0]
    },
    {
      "type": "list",
      "attributes": {},
      "value": [
        {
          "type": "character",
          "attributes": {},
          "value": ["Lib1", "Lib2"]
        },
        {
          "type": "character",
          "attributes": {},
          "value": ["Lib3"]
        },
        {
          "type": "NULL"
        }
      ]
    },
    {
      "type": "list",
      "attributes": {},
      "value": [
        {
          "type": "character",
          "attributes": {},
          "value": ["Shotgun", "1240K"]
        },
        {
          "type": "character",
          "attributes": {},
          "value": ["1240K"]
        },
        {
          "type": "character",
          "attributes": {},
          "value": ["ReferenceGenome"]
        }
      ]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["minus", "half", "plus"]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["ds", "ss", "mixed"]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["diploid", "haploid", "diploid"]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["ftp://test.test", "https://www.google.de", "http://huhu.org/23&test"]
    },
    {
      "type": "double",
      "attributes": {},
      "value": [0, 0, 0]
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      "type": "integer",
      "attributes": {},
      "value": [0, 0, 0]
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      "type": "double",
      "attributes": {},
      "value": [0, 0, 0]
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      "type": "double",
      "attributes": {},
      "value": [0, 100, 50]
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      "type": "list",
      "attributes": {},
      "value": [
        {
          "type": "character",
          "attributes": {},
          "value": ["10"]
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        {
          "type": "character",
          "attributes": {},
          "value": ["20", "50", "70"]
        },
        {
          "type": "NULL"
        }
      ]
    },
    {
      "type": "list",
      "attributes": {},
      "value": [
        {
          "type": "character",
          "attributes": {},
          "value": ["1"]
        },
        {
          "type": "character",
          "attributes": {},
          "value": ["2", "5", "7.4"]
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          "type": "NULL"
        }
      ]
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      "type": "list",
      "attributes": {},
      "value": [
        {
          "type": "character",
          "attributes": {},
          "value": ["ANGSD v.123"]
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          "type": "character",
          "attributes": {},
          "value": ["Schmutzi v145", "Zwiebel", "other"]
        },
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      "type": "character",
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      "value": [null, "xxx", null]
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      "type": "list",
      "attributes": {},
      "value": [
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          "type": "character",
          "attributes": {},
          "value": ["Ich", "mag", "Kekse"]
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        {
          "type": "character",
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          "value": ["aus"]
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          "value": ["der Dose"]
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          "type": "character",
          "attributes": {},
          "value": ["unpublished"]
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          "type": "character",
          "attributes": {},
          "value": ["PaulNature2026"]
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          "type": "character",
          "attributes": {},
          "value": ["BovineCell1618"]
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      "type": "character",
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          "value": ["Hutschnur"]
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          "attributes": {
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}

poseidon-framework/poseidonR documentation built on March 15, 2024, 12:18 a.m.