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Delimited.jl

PopGenCore.jl/src/io/Delimited.jl​

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

🟪 delimited​

delimited(infile::String; delim::Union{Char,String,Regex} = "auto", digits::Int64 = 3, silent::Bool = false)

Load a delimited-type file into memory as a PopData object. There should be no empty cells in your file

Arguments​

  • infile : path to file

Keyword Arguments​

  • delim : delimiter characters. By default uses auto-parsing of CSV.File
  • digits : number of digits denoting each allele (default: 3)
  • diploid : whether samples are diploid for parsing optimizations (default: true)
  • silent : whether to print file information during import (default: true)
  • allow_monomorphic : whether to keep monomorphic loci in the dataset (default: false)

File formatting:​

  • The first row is column names (names don't matter)
  • The columns must be in this order:
    1. sample name
    2. population name
    3. longitude
    4. latitude
    5. locus_1 genotypes
    6. locus_2 genotypes
    7. etc...

Missing data​

Genotypes​

Missing genotypes can be formatted as all-zeros 000000, left empty, or negative-nine -9

Location data​

If location data is missing for a sample (which is ok!), make sure the value is blank, otherwise there will be transcription errors! (look at line 3 in the example below)

Example

lizardsCA = delimited("CA_lizards.csv", digits = 3);

Formatting example​

name,population,long,lat,Locus1,Locus2,Locus3
sierra_01,mountain,11.11,-22.22,001001,-9,001001
sierra_02,mountain,11.12,-22.21,001001,001001,001002
snbarb_01,coast,,,001001,001001,001002
snbarb_02,coast,11.14,-22.24,001001,001001,001001
snbarb_03,coast,11.15,,001002,001001,001001

Example

lizardsCA = delimited("CA_lizards.csv", digits = 3);
delimited(data::PopData; filename::String, delim::String = ",", digits::Integer = 3, format::String = "wide")

Write PopData to a text-delimited 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 to output in"wide" or "long" (aka "tidy") format
  • delim : the String delimiter to use for writing the file.

Example

cats = @nancycats;
fewer_cats = omit_samplenames(cats, samplenames(cats)[1:10]);
delimited(fewer_cats, filename = "filtered_nancycats.csv", digits = 3, format = "wide", delim = " ")