ioUtils.jl

PopGenCore.jl/src/Utils/ioUtils.jl

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

📦 isbinary

isbinary(filepath::String)

Returns true if the filepath is a binary file.

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🟪 findploidy

findploidy(genotypes::T) where T<:AbstractVector

Used internally in the genepop and delimited file parsers to scan the genotypes of a sample and return the ploidy of the first non-missing locus.

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🟪 phase

phase(loc::T, type::DataType, digit::Int) where T<:AbstractString
phase(loc::Missing, type::DataType, digit::Int) = missing
phase(loc::T, type::DataType, digits::T) where T<:Integer

Takes a String of numbers or Integers and returns a typed locus appropriate for PopGen.jl as used in the genepop and csv file parsers. Use type to specify output type (Int8 or Int16), and digit to specify the number of digits/characters used per allele in a locus.

Examples

ph_locus = phase("128114", Int16, 3)
map(i -> phase(i, Int16, 3), ["112131", "211112", "001003", "516500"])
# or #
[phase(i, Int8, 2) for i in ["0101", "0103", "0202", "0103"]]

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🟪 unphase

unphase(geno::T; digits::Int = 3, ploidy::Int = 2, miss::Int = 0) where T <: Genotype
unphase(geno::Missing; digits::Int = 3, ploidy::Int, miss::Int = 0)

Takes a Genotype (e.g. (131, 94)) and returns a string of concatenated alleles padded with n number of zeroes, where n is given by digits = . missing values are returned as either a string of 'digits × ploidy' zeroes (miss = 0) or "-9" (miss = -9). The ploidy flag is only relevant for unphasing missing genotypes and not used otherwise.

Example

unphase((1,2,3,4), digits = 3)
"001002003004"
unphase(missing, digits = 2, ploidy = 2, miss = -9)
"-9"
unphase(missing, digits = 2, ploidy = 2, miss = 0)
"0000"