integrate plink

BioJulia · Jul 25, 2022 · 98f6d8b · 98f6d8b · pdimens · Jul 25, 2022
1 parent 033ba7f
commit 98f6d8b
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Showing 3 changed files with 12 additions and 3 deletions.
diff --git a/src/PopGenCore.jl b/src/PopGenCore.jl
@@ -73,6 +73,9 @@ export bcf, vcf
 include("io/Baypass.jl")
 export baypass
 
+include("io/Plink.jl")
+export plink
+
 include("io/ReadWrite.jl")
 ##
 include("Datasets.jl")

diff --git a/src/io/Plink.jl b/src/io/Plink.jl
@@ -217,7 +217,7 @@ plink(sharks, filename = "biallelic_sharks.ped")
 ```
 """
 function plink(data::PopData; filename::String)
-    data.metadata.biallelic != true && throw(ArgumentError("To write to PLINK format, data must be biallelic.\nThis can be done with dropmultiallelic(::PopData)\n"))
+    data.metadata.biallelic != true && throw(ArgumentError("To write to PLINK format, data must be biallelic.\nThis can be done with dropmultiallelic())\n"))
     basename = endswith(filename, r".bed|.ped") ? splitext(filename)[1] : filename
     # the .fam file
     tmp = data.metadata[:, r"population|name|sire|dam|sex|phenotype"]

diff --git a/src/io/ReadWrite.jl b/src/io/ReadWrite.jl
@@ -64,6 +64,8 @@ to Genepop format, call up the `?genepop` docstring.
 | genepop     | `.gen`, `.genepop`     | ?genepop   |
 | delimited   | `.csv`, `.txt`, `.tsv` | ?delimited |
 | structure   | `.str`, `.structure`   | ?structure |
+| plink       | `.ped`                 | ?plink     |
+| baypass     | `.baypass`             | ?baypass   |
 
 ### Example
 ```
@@ -80,8 +82,10 @@ function Base.write(data::PopData; filename::String, kwargs...)
         structure(data, filename = filename; kwargs...)
     elseif ext in ["csv", "txt", "tsv"]
         delimited(data, filename = filename; kwargs...)
+    elseif ext == "baypass"
+        baypass(data, filename = filename)
     else
-        @error "File type not recognized by filename extension. Please see the docstring"
+        throw(ArgumentError("File type not recognized by filename extension. Please see the docstring"))
     end
 end
 
@@ -93,7 +97,9 @@ function Base.write(data::PopData, filename::String, kwargs...)
         structure(data, filename = filename; kwargs...)
     elseif ext in ["csv", "txt", "tsv"]
         delimited(data, filename = filename; kwargs...)
+    elseif ext == "baypass"
+        baypass(data, filename = filename)
     else
-        @error "File type not recognized by filename extension. Please see the docstring"
+        throw(ArgumentError("File type not recognized by filename extension. Please see the docstring"))
     end
 end