From d1dd370e05a97f5f84e2ae7fb6541a4a17c6d1d1 Mon Sep 17 00:00:00 2001
From: Justin Angevaare <jangevaa@uoguelph.ca>
Date: Tue, 10 Sep 2019 19:52:31 -0400
Subject: [PATCH] DNA RNA

update README

update README

let's keep the type names short

new

new

>1.0
---
 Project.toml            |  2 +-
 README.md               | 34 ++++++++++++++++++++++++-
 src/DNA.jl              | 44 +++++++++++++++++++++++++++++++++
 src/GeneticBitArrays.jl | 55 +++--------------------------------------
 src/RNA.jl              | 44 +++++++++++++++++++++++++++++++++
 5 files changed, 126 insertions(+), 53 deletions(-)
 create mode 100644 src/DNA.jl
 create mode 100644 src/RNA.jl

diff --git a/Project.toml b/Project.toml
index a490246..8854dfe 100644
--- a/Project.toml
+++ b/Project.toml
@@ -4,7 +4,7 @@ authors = ["Justin Angevaare <justinangevaare@gmail.com>"]
 version = "0.1.0"
 
 [compat]
-julia = "≥ 0.7.0"
+julia = "≥ 1.0.0"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
diff --git a/README.md b/README.md
index 03bb901..a786c82 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,34 @@
 # GeneticBitArrays.jl
-BitArray representations of Genetic sequences
+Minimal representations of genetic sequences.
+
+## Use
+Input using `String`, `Vector{Char}`, or use an appropriate `BitArray`.
+
+*e.g.*
+```
+julia> DNASeq("AAAAGCCT")
+
+8 nt DNA sequence
+AAAAGCCT
+```
+
+## Representation
+A 4 x n `BitArray` is used to represent sequences internally, where n is sequence length.
+
+
+```
+julia> x = DNASeq("AAAAGCCT")
+
+julia> x.data
+
+4×8 BitArray{2}:
+ 1  1  1  1  0  0  0  0
+ 0  0  0  0  0  1  1  0
+ 0  0  0  0  1  0  0  0
+ 0  0  0  0  0  0  0  1
+```
+
+## Notes
+* Ambiguities are not currently supported.
+* No error checking for I/O is provided.
+* For a full featured package for genetic sequences see [BioSequences.jl](https://github.com/BioJulia/BioSequences.jl).
diff --git a/src/DNA.jl b/src/DNA.jl
new file mode 100644
index 0000000..48e11a1
--- /dev/null
+++ b/src/DNA.jl
@@ -0,0 +1,44 @@
+function onehotDNA(x::Char)
+  return ['A', 'C', 'G', 'T'] .== Ref(x)
+end
+
+
+function onehotDNA(x::BitArray{1})
+  return ['A', 'C', 'G', 'T'][x][1]
+end
+
+struct DNASeq
+  data::BitArray{2}
+end
+
+
+function DNASeq(seq::Vector{Char})
+  x = BitArray(undef, (4, length(seq)))
+  for i in 1:length(seq)
+    x[:, i] = onehotDNA(seq[i])
+  end
+  return DNASeq(x)
+end
+
+
+function DNASeq(x::String)
+  return DNASeq(Vector{Char}(x))
+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
+end
diff --git a/src/GeneticBitArrays.jl b/src/GeneticBitArrays.jl
index 79748aa..7cc72b9 100644
--- a/src/GeneticBitArrays.jl
+++ b/src/GeneticBitArrays.jl
@@ -1,58 +1,11 @@
 module GeneticBitArrays
 
-import Base.getindex,
-       Base.setindex,
-       Base.show,
+import Base.show,
        Base.length
 
-function onehotDNA(x::Char)
-  return ['A', 'C', 'G', 'T'] .== Ref(x)
-end
+include("DNA.jl")
+include("RNA.jl")
 
-
-function onehotDNA(x::BitArray{1})
-  return ['A', 'C', 'G', 'T'][x]
-end
-
-
-struct DNABitArray
-  data::BitArray{2}
-
-  function DNABitArray(seq::Vector{Char})
-     x = BitArray(undef, (4, length(seq)))
-    for i in 1:length(seq)
-      x[onehotDNA(i), i] += 1
-    end
-    return new(x)
-  end
-end
-
-
-function DNABitArray(x::String)
-  return DNABitArray(Vector{Char}(x))
-end
-
-
-function length(x::DNABitArray)
-  return size(x.data, 1)
-end
-
-
-function getindex(x::DNABitArray, i)
-  return DNABitArray(x.data[i, :])
-end
-
-
-function show(io::IO, x::DNABitArray)
-  if length(x) <= 26
-    print(io, prod([onehotDNA(x[i]) for i=1:length(object)]))
-  else
-    print(io, prod([onehotDNA(x[i]) for i=1:13]) *
-              "..." *
-              prod([onehotDNA(x[i]) for i=length(x)-13:length(x)]))
-  end
-end
-
-export DNABitArray
+export DNASeq, RNASeq
 
 end # module
diff --git a/src/RNA.jl b/src/RNA.jl
new file mode 100644
index 0000000..4981cab
--- /dev/null
+++ b/src/RNA.jl
@@ -0,0 +1,44 @@
+function onehotRNA(x::Char)
+  return ['A', 'C', 'G', 'U'] .== Ref(x)
+end
+
+
+function onehotRNA(x::BitArray{1})
+  return ['A', 'C', 'G', 'U'][x][1]
+end
+
+struct RNASeq
+  data::BitArray{2}
+end
+
+
+function RNASeq(seq::Vector{Char})
+  x = BitArray(undef, (4, length(seq)))
+  for i in 1:length(seq)
+    x[:, i] = onehotRNA(seq[i])
+  end
+  return RNASeq(x)
+end
+
+
+function RNASeq(x::String)
+  return RNASeq(Vector{Char}(x))
+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
+end