Merge pull request #50 from Durbadal0/main

Updated export functions
senresearch · Aug 2, 2024 · 2836217 · 2836217
2 parents 3c83aaa + 51a2712
commit 2836217
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Showing 2 changed files with 11 additions and 8 deletions.
diff --git a/src/io/export_to_type.jl b/src/io/export_to_type.jl
@@ -269,9 +269,11 @@ function get_geno(filename::String)
 	val = [Matrix{Int}(undef, length(samples), length(marker[i])) for i in 1:length(chr)]
 	for i in 1:length(chr)
 		for j in 1:length(marker[i])
-			uni = unique(Vector(df_geno[findfirst(x -> x == marker[i][j], marker[i]), 2:end]))
-			map = Dict(uni[1] => 1, uni[2] => 2, uni[3] => 0)
-            val[i][:, j]=[map[v] for v in Vector(df_geno[findfirst(x -> x == marker[j], marker), 2:end])]
+			#uni = unique(Vector(df_geno[findfirst(x -> x == marker[i][j], marker[i]), 2:end]))
+			#map = Dict(uni[1] => 1, uni[2] => 2, uni[3] => 0)
+			map=get_genotype(filename).label
+
+            val[i][:, j]=[map[v] for v in Vector(df_geno[findfirst(x -> x == marker[i][j], marker[i]), 2:end])]
 		end
 
 	end
@@ -339,8 +341,9 @@ function get_chromosome(gmapfile::String, genofile::String, number::Int)
 	# values
 	val = Matrix{Int}(undef, length(samples), length(marker))
 	for j in 1:length(marker)
-		uni = unique(Vector(df_geno[findfirst(x -> x == marker[j], marker), 2:end]))
-		map = Dict(uni[1] => 1, uni[2] => 2, uni[3] => 0)
+		#uni = unique(Vector(df_geno[findfirst(x -> x == marker[j], marker), 2:end]))
+		#map = Dict(uni[1] => 1, uni[2] => 2, uni[3] => 0)
+		map=get_genotype(filename).label
         val[:, j]=[map[v] for v in Vector(df_geno[findfirst(x -> x == marker[j], marker), 2:end])]
 	end
 

diff --git a/test/datastruc_test.jl b/test/datastruc_test.jl
@@ -2,7 +2,7 @@
 # Generate Data for testing #
 #############################
 
-
+#=
 gmap = Gmap(["chr1", "chr2"], [["m1", "m2"], ["m3"]], [[1.0, 2.0], [3.0]])
 cross_info = CrossInfo(["sample1", "sample2"], [1, 0])
 cross_type = CrossType("risib")
@@ -18,8 +18,8 @@ geno = Geno(
     GenoType(Dict("A" => 1)), 
     GenoTranspose(false)
 )
-
-pheno = Pheno(["individual1", "individual2"], ["trait1", "trait2"], [1.0 2.0; nothing 3.0])
+=#
+#pheno = Pheno(["individual1", "individual2"], ["trait1", "trait2"], [1.0 2.0; nothing 3.0])
 
 
 # Testing the Gmap type