Add some basic tests, define more methods

src/Common.jl

@@ -0,0 +1,36 @@
+function length(x::T) where {T <: GeneticSeq}
+  return size(x.data, 2)
+end
+
+
+function show(io::IO, x::T) where {T <: GeneticSeq}
+  len = length(x)
+  println(io, "$(len)nt DNA sequence")
+  if len <= 26
+    print(io, prod([onehot(T, x.data[:, i]) for i=1:len]))
+  else
+    print(io, prod([onehot(T, x.data[:, i]) for i=1:13]) *
+              "..." *
+              prod([onehot(T, x.data[:, i]) for i=len-13:len]))
+  end
+end
+
+
+function getindex(x::T, i::Int64) where {T <: GeneticSeq}
+  return T(x.data[:, i])
+end
+
+
+function setindex(x::T, a::BitArray{1}, i) where {T <: GeneticSeq}
+  return x.data[:, i] = a
+end
+
+
+function setindex(x::T, a::Char, i) where {T <: GeneticSeq}
+  return x.data[:, i] = onehot(T, a)
+end
+
+
+function ==(x::T, y::T) where {T <: GeneticSeq}
+  return x.data == y.data
+end

src/DNA.jl

@@ -1,21 +1,22 @@
-function onehotDNA(x::Char)
-  return ['A', 'C', 'G', 'T'] .== Ref(x)
+struct DNASeq <: GeneticSeq
+  data::BitArray{2}
 end
 
 
-function onehotDNA(x::BitArray{1})
-  return ['A', 'C', 'G', 'T'][x][1]
+function onehot(::Type{DNASeq}, x::Char)
+  return ['A', 'C', 'G', 'T'] .== Ref(x)
 end
 
-struct DNASeq
-  data::BitArray{2}
+
+function onehot(::Type{DNASeq}, x::BitArray{1})
+  return ['A', 'C', 'G', 'T'][x][1]
 end
 
 
 function DNASeq(seq::Vector{Char})
   x = BitArray(undef, (4, length(seq)))
   for i in 1:length(seq)
-    x[:, i] = onehotDNA(seq[i])
+    x[:, i] = onehot(DNASeq, seq[i])
   end
   return DNASeq(x)
 end
@@ -26,19 +27,6 @@ function DNASeq(x::String)
 end
 
 
-function length(x::DNASeq)
-  return size(x.data, 2)
-end
-
-
-function show(io::IO, x::DNASeq)
-  len = length(x)
-  println(io, "$(len)nt DNA sequence")
-  if len <= 26
-    print(io, prod([onehotDNA(x.data[:, i]) for i=1:len]))
-  else
-    print(io, prod([onehotDNA(x.data[:, i]) for i=1:13]) *
-              "..." *
-              prod([onehotDNA(x.data[:, i]) for i=len-13:len]))
-  end
+function DNASeq(x::BitArray{1})
+  return DNASeq(reshape(x, (4, 1)))
 end

src/GeneticBitArrays.jl

@@ -1,10 +1,16 @@
 module GeneticBitArrays
 
 import Base.show,
-       Base.length
+       Base.length,
+       Base.getindex,
+       Base.setindex,
+       Base.==
+
+abstract type GeneticSeq end
 
 include("DNA.jl")
 include("RNA.jl")
+include("Common.jl")
 
 export DNASeq, RNASeq
 

src/RNA.jl

@@ -1,21 +1,22 @@
-function onehotRNA(x::Char)
-  return ['A', 'C', 'G', 'U'] .== Ref(x)
+struct RNASeq <: GeneticSeq
+  data::BitArray{2}
 end
 
 
-function onehotRNA(x::BitArray{1})
-  return ['A', 'C', 'G', 'U'][x][1]
+function onehot(::Type{RNASeq}, x::Char)
+  return ['A', 'C', 'G', 'U'] .== Ref(x)
 end
 
-struct RNASeq
-  data::BitArray{2}
+
+function onehot(::Type{RNASeq}, x::BitArray{1})
+  return ['A', 'C', 'G', 'U'][x][1]
 end
 
 
 function RNASeq(seq::Vector{Char})
   x = BitArray(undef, (4, length(seq)))
   for i in 1:length(seq)
-    x[:, i] = onehotRNA(seq[i])
+    x[:, i] = onehot(RNASeq, seq[i])
   end
   return RNASeq(x)
 end
@@ -26,19 +27,6 @@ function RNASeq(x::String)
 end
 
 
-function length(x::RNASeq)
-  return size(x.data, 2)
-end
-
-
-function show(io::IO, x::RNASeq)
-  len = length(x)
-  println(io, "$(len)nt RNA sequence")
-  if len <= 26
-    print(io, prod([onehotRNA(x.data[:, i]) for i=1:len]))
-  else
-    print(io, prod([onehotRNA(x.data[:, i]) for i=1:13]) *
-              "..." *
-              prod([onehotRNA(x.data[:, i]) for i=len-13:len]))
-  end
+function RNASeq(x::BitArray{1})
+  return RNASeq(reshape(x, (4, 1)))
 end

test/runtests.jl

@@ -0,0 +1,12 @@
+using Test,
+      GeneticBitArrays
+
+@testset "GeneticBitArrays" begin
+  @test sum(DNASeq("AAAA").data, dims=2)[:] == [4;0;0;0]
+  @test sum(DNASeq("CCCC").data, dims=2)[:] == [0;4;0;0]
+  @test sum(DNASeq("GGGG").data, dims=2)[:] == [0;0;4;0]
+  @test sum(DNASeq("TTTT").data, dims=2)[:] == [0;0;0;4]
+  @test DNASeq("TTTT").data == RNASeq("UUUU").data
+  @test length(DNASeq("ACGT")[2]) == length(DNASeq("C"))
+  @test DNASeq("ACGT")[2] == DNASeq("C")
+end