Encoding biological sequences into Voss representation

BioVossEncoder

A Julia package for encoding biological sequences into Voss representations

Installation

BioVossEncoder is a   Julia Language   package. To install BioVossEncoder, please open Julia's interactive session (known as REPL) and press ] key in the REPL to use the package mode, then type the following command

pkg> add BioVossEncoder

Encoding BioSequences

This package provides a simple and fast way to encode biological sequences into Voss representations. The main struct provided by this package is VossEncoder which is a wrapper of BitMatrix that encodes a biological sequence into a bit matrix and its corresponding alphabet. The following example shows how to encode a DNA sequence into a Voss matrix.

julia> using BioSequences, BioVossEncoder

julia> seq = dna"ACGT"

julia> VossEncoder(seq)

4×4 Voss Matrix of DNAAlphabet{4}():
 1  0  0  0
 0  1  0  0
 0  0  1  0
 0  0  0  1

For simplicity the VossEncoder struct provides a property bitmatrix that returns the BitMatrix representation of the sequence.

julia> VossEncoder(seq).bitmatrix

4×4 BitMatrix:
 1  0  0  0
 0  1  0  0
 0  0  1  0
 0  0  0  1

Similarly another function that makes use of the VossEncoder structure is vossmatrix which returns the BitMatrix representation of a sequence directly.

julia> vossmatrix(seq)

4×4 BitMatrix:
 1  0  0  0
 0  1  0  0
 0  0  1  0
 0  0  0  1

Creating a Voss vector of a sequence

Sometimes it proves to be useful to encode a sequence into a Voss vector representation (i.e a bit vector of the sequence from the corresponding molecule alphabet).

This package provides a function vossvector that returns a Voss vector of a sequence given a BioSequence and the specific molecule (BioSymbol) that could be DNA or AA.

julia> vossvector(seq, DNA_A)

4-element view(::BitMatrix, 1, :) with eltype Bool:
 1
 0
 0
 0

Note that the output is actually using behind the scenes a view of the BitMatrix representation of the sequence. This is done for performance reasons.