ReadWrite.jl

PopGenCore.jl/src/io/ReadWrite.jl

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

📦 read

PopGen.read(infile::String; kwargs...)

Wraps the individual file importers to read a file in as a PopData object. File type is inferred from the file extension (case insensitive):

File Format	Extensions	Docstring
delimited	.csv, .txt, .tsv	?delimited
genepop	.gen, .genepop	?genepop
structure	.str, .structure	?structure
plink	.bed, .ped	?plink
variant call format (vcf)	.vcf, .vcf.gz	?vcf
variant call format (bcf)	.bcf, .bcf.gz	?bcf

This function uses the same keyword arguments (and defaults) as the file importing functions it wraps; please see their respective docstrings in the Julia help console. for specific usage details (e.g. ?genepop).

Examples

PopGen.read("cavernous_assfish.gen", digits = 3)
PopGen.read("juglans_nigra.vcf")

---

📦 write

PopGen.write(data::PopData, filename::String, kwargs...)
PopGen.write(data::PopData; filename::String, kwargs...)

Writes PopData to a specified file type inferred from the extension of filename = (case insensitive). Additional keyword arguments kwargs... are specific to the intended file type, and are listed in the docstrings of the specific file writer with the format ?filetype. For example, to find the appropriate keywords for a conversion to Genepop format, call up the ?genepop docstring.

File Format	Extensions	Docstring
genepop	.gen, .genepop	?genepop
delimited	.csv, .txt, .tsv	?delimited
structure	.str, .structure	?structure

Example

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