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Merge pull request #58 from pdimens/dev
pull 0.4.5 into release
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,10 @@ | ||
| using .GZip | ||
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| # if GZip is loaded in, overwrite openvcf to this method | ||
| function openvcf(infile::String) | ||
| if endswith(infile, ".gz") | ||
| return GZip.open(infile, "r") | ||
| else | ||
| return open(infile, "r") | ||
| end | ||
| end |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,140 @@ | ||
| using .GeneticVariation | ||
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| export bcf, vcf | ||
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| """ | ||
| openvcf(::String) | ||
| Open VCF file (`.vcf(.gz)`, or `.bcf(.gz)`) and return an `IO` stream in reading mode `"r"`. | ||
| """ | ||
| function openvcf(infile::String) | ||
| if endswith(infile, ".gz") | ||
| throw(ArgumentError("Please load in GZip.jl with \`using GZip\`")) | ||
| else | ||
| return open(infile, "r") | ||
| end | ||
| end | ||
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| function bcf(infile::String; rename_loci::Bool = false, silent::Bool = false, allow_monomorphic::Bool = false) | ||
| bases = (A = Int8(1), T = Int8(2), C = Int8(3), G = Int8(4), miss = Int8(0)) | ||
| stream = BCF.Reader(openvcf(infile)) | ||
| nmarkers = countlines(openvcf(infile)) - length(BCF.header(stream)) - 1 | ||
| sample_ID = header(stream).sampleID | ||
| nsamples = length(sample_ID) | ||
| loci_names = fill("marker", nmarkers) | ||
| geno_df = DataFrame(:name => sample_ID, :population => "missing") | ||
| if silent == false | ||
| @info "\n$(abspath(infile))\n$nsamples samples detected\n$nmarkers markers detected\npopulation info must be added <---" | ||
| end | ||
| for record in stream | ||
| ref_alt = Dict(-1 => "miss", 0 => BCF.ref(record), [i => j for (i,j) in enumerate(BCF.alt(record))]...) | ||
| raw_geno = BCF.genotype(record, 1:nsamples, "GT") | ||
| conv_geno = map(raw_geno) do rg | ||
| tmp = replace.(rg, "." => "-1") | ||
| ig = collect(parse.(Int8, split(tmp, r"\/|\|"))) | ||
| [bases[Symbol(ref_alt[i])] for i in ig] |> sort |> Tuple | ||
| end | ||
| insertcols!(geno_df, Symbol(BCF.chrom(record) * "_" * string(BCF.pos(record))) => conv_geno) | ||
| end | ||
| close(stream) | ||
| if rename_snp | ||
| rnm = append!([:name, :population], [Symbol.("snp_" * i) for i in string.(1:nmarkers)]) | ||
| rename!(geno_df, rnm) | ||
| end | ||
| stacked_geno_df = DataFrames.stack(geno_df, DataFrames.Not(1:2)) | ||
| rename!(stacked_geno_df, [:name, :population, :locus, :genotype]) | ||
| # set columns as PooledArrays | ||
| select!( | ||
| stacked_geno_df, | ||
| :name => PooledArray => :name, | ||
| :population => PooledArray => :population, | ||
| :locus => (i -> PooledArray(i |> Vector{String})) => :locus, | ||
| :genotype | ||
| ) | ||
| # replace missing genotypes as missing | ||
| stacked_geno_df.genotype = map(stacked_geno_df.genotype) do geno | ||
| if all(0 .== geno) | ||
| return missing | ||
| else | ||
| return geno | ||
| end | ||
| end | ||
| sort!(stacked_geno_df, [:name, :locus]) | ||
| #meta_df = generate_meta(stacked_geno_df) | ||
| # ploidy finding | ||
| meta_df = DataFrames.combine(DataFrames.groupby(stacked_geno_df, :name), | ||
| :genotype => (i -> Int8(length(first(skipmissing(i))))) => :ploidy | ||
| ) | ||
| insertcols!(meta_df, 2, :population => "missing") | ||
| insertcols!(meta_df, 4, :longitude => Vector{Union{Missing, Float32}}(undef, nsamples), :latitude => Vector{Union{Missing, Float32}}(undef, nsamples)) | ||
|
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| if allow_monomorphic | ||
| pd_out = PopData(meta_df, stacked_geno_df) | ||
| else | ||
| pd_out = drop_monomorphic!(PopData(meta_df, stacked_geno_df)) | ||
| end | ||
| return pd_out | ||
| end | ||
|
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| ### VCF parsing ### | ||
|
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| function vcf(infile::String; rename_snp::Bool = false, silent::Bool = false, allow_monomorphic::Bool = false) | ||
| bases = (A = Int8(1), T = Int8(2), C = Int8(3), G = Int8(4), miss = Int8(0)) | ||
| stream = VCF.Reader(openvcf(infile)) | ||
| nmarkers = countlines(openvcf(infile)) - length(VCF.header(stream)) - 1 | ||
| sample_ID = header(stream).sampleID | ||
| nsamples = length(sample_ID) | ||
| loci_names = fill("marker", nmarkers) | ||
| geno_df = DataFrame(:name => sample_ID, :population => "missing") | ||
| if silent == false | ||
| @info "\n$(abspath(infile))\n$nsamples samples detected\n$nmarkers markers detected\npopulation info must be added <---" | ||
| end | ||
| for record in stream | ||
| ref_alt = Dict(-1 => "miss", 0 => VCF.ref(record), [i => j for (i,j) in enumerate(VCF.alt(record))]...) | ||
| raw_geno = VCF.genotype(record, 1:nsamples, "GT") | ||
| conv_geno = map(raw_geno) do rg | ||
| tmp = replace.(rg, "." => "-1") | ||
| ig = collect(parse.(Int8, split(tmp, r"\/|\|"))) | ||
| [bases[Symbol(ref_alt[i])] for i in ig] |> sort |> Tuple | ||
| end | ||
| insertcols!(geno_df, Symbol(VCF.chrom(record) * "_" * string(VCF.pos(record))) => conv_geno) | ||
| end | ||
| close(stream) | ||
| if rename_snp | ||
| rnm = append!([:name, :population], [Symbol.("snp_" * i) for i in string.(1:nmarkers)]) | ||
| rename!(geno_df, rnm) | ||
| end | ||
| stacked_geno_df = DataFrames.stack(geno_df, DataFrames.Not(1:2)) | ||
| rename!(stacked_geno_df, [:name, :population, :locus, :genotype]) | ||
| # set columns as PooledArrays | ||
| select!( | ||
| stacked_geno_df, | ||
| :name => PooledArray => :name, | ||
| :population => PooledArray => :population, | ||
| :locus => (i -> PooledArray(i |> Vector{String})) => :locus, | ||
| :genotype | ||
| ) | ||
| # replace missing genotypes as missing | ||
| stacked_geno_df.genotype = map(stacked_geno_df.genotype) do geno | ||
| if all(0 .== geno) | ||
| return missing | ||
| else | ||
| return geno | ||
| end | ||
| end | ||
| sort!(stacked_geno_df, [:name, :locus]) | ||
| # ploidy finding | ||
| #meta_df = generate_meta(stacked_geno_df) | ||
| meta_df = DataFrames.combine(DataFrames.groupby(stacked_geno_df, :name), | ||
| :genotype => (i -> Int8(length(first(skipmissing(i))))) => :ploidy | ||
| ) | ||
| insertcols!(meta_df, 2, :population => "missing") | ||
| insertcols!(meta_df, 4, :longitude => Vector{Union{Missing, Float32}}(undef, nsamples), :latitude => Vector{Union{Missing, Float32}}(undef, nsamples)) | ||
|
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| if allow_monomorphic | ||
| pd_out = PopData(meta_df, stacked_geno_df) | ||
| else | ||
| pd_out = drop_monomorphic!(PopData(meta_df, stacked_geno_df)) | ||
| end | ||
| return pd_out | ||
| end |