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Genepop.jl

PopGenCore.jl/src/io/Genepop.jl​

📦 not exported🟪 exported by PopGenCore.jl🔵 exported by PopGen.jl

🟪 genepop​

genepop(infile::String; kwargs...)

Load a Genepop format file into memory as a PopData object.

  • infile::String : path to Genepop file

Keyword Arguments

  • digits::Integer: number of digits denoting each allele (default: 3)
  • popsep::String : word that separates populations in infile (default: "POP")
  • diploid::Bool : whether samples are diploid for parsing optimizations (default: true)
  • silent::Bool : whether to print file information during import (default: true)
  • allow_monomorphic : whether to keep monomorphic loci in the dataset (default: false)

File must follow standard Genepop formatting

  • First line is a comment (and skipped)
  • Loci are listed after first line as one-per-line without commas or in single comma-separated row
  • A line with a particular keyword (default POP) must delimit populations
  • Sample name is immediately followed by a comma
  • File is tab or space delimted (but not both!)

Genepop file example:

wasp_hive.gen: Wasp populations in New York \n
Locus1
Locus2
Locus3
pop
Oneida_01,  250230  564568  110100
Oneida_02,  252238  568558  100120
Oneida_03,  254230  564558  090100
pop
Newcomb_01, 254230  564558  080100
Newcomb_02, 000230  564558  090080
Newcomb_03, 254230  000000  090100
Newcomb_04, 254230  564000  090120

Example

waspsNY = genepop("wasp_hive.gen", digits = 3, popsep = "pop")
genepop(data::PopData; filename::String = "output.gen", digits::Int = 3, format::String = "vertical")

Writes a PopData object to a Genepop-formatted file

  • data: the PopData object you wish to convert to a Genepop file

Keyword arguments

  • filename: a String of the output filename
  • digits : an Integer indicating how many digits to format each allele as (e.g. (1, 2) => 001002 for digits = 3)
  • format : a String indicating whether loci should be formatted
    • vertically ("v" or "vertical")
    • hortizontally ("h", or "horizontal")
    • Genepop Isolation-By-Distance ("ibd") where each sample is a population with long/lat data prepended

Example

cats = @nancycats;
fewer_cats = omit_samplenames(cats, samplenames(cats)[1:10]);
julia> genepop(fewer_cats, filename = "filtered_nancycats.gen", digits = 3, format = "h")