Skip to main content

Delimited

Import a delimited file as PopData​

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

Arguments​

  • infile::String : path to the input file, in quotes

Keyword Arguments​

  • delim::String : delimiter characters. The default ("auto") uses auto-parsing of CSV.File

  • digits::Integer : the number of digits used to denote an allele (default: 3)

  • diploid::Bool : whether samples are diploid for parsing optimizations (default: true)

  • silent::Bool : whether to print file information during import (default: false)

Example​

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

Format​

First row is column names, and they occur in this order:

  1. name
  2. population
  3. longitude
  4. latitude
  5. locus_1_name
  6. locus_2_name
  7. etc...

Formatting example:

name,population,longitude,latitude,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

Missing data​

Genotypes​

Missing genotypes can be formatted as all-zeros (ex.000000) 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! (example at line 3 in the example above)

alias

You can also use the command csv() synonymously with delimited().

Writing to a delimited file​

All file writing options can be performed using PopGen.write(), which calls delimited when writing to a delimited file.

delimited(data::PopData; filename::String, delim::String = ",", digits::Integer = 3, format::String = "wide", miss::Int = 0)

Write PopData to a text-delimited file.

Keyword Arguments​

  • filename::String: the output filename
  • digits::Integer : how many digits to format each allele (default: 3)
    • e.g. digits = 3 will turn (1, 2) into 001002
  • format::String: whether to output in"wide" or "long" (aka "tidy") format
    • wide : the standard-format CSV for importing into PopGen.jl (default)
    • long : the loci table with longitude and latitude columns added
  • delim::String: delimiter to use for writing the file (default: ",")
  • miss::Integer: how you would like missing values written
    • 0 : As a genotype represented as a number of zeroes equal to digits × ploidy like 000000 (default)
    • -9 : As a single value -9

Example​

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

Acknowledgements​

Thanks to the efforts of the CSV.jl team, we are able leverage that package to do much of the heavy lifting within this parser.