GeneticBitArrays.jl

BitArray representation of genetic sequences in Julia
Author jangevaare
Popularity
4 Stars
Updated Last
3 Years Ago
Started In
September 2019

GeneticBitArrays.jl

DOI Latest Release License

test-lts test-stable test-nightly codecov.io

Description

Minimal representations of DNA and RNA genetic sequences using BitArrays in Julia.

Installation

The current release can be installed from the Julia REPL with:

pkg> add GeneticBitArrays

The development version (master branch) can be installed with:

pkg> add GeneticBitArrays#master

Use

Input using String, Vector{Char} with nucleotides indicated by their IUPAC code. You may also construct a sequence with a 4 x n BitArray - the same way sequences are represented internally with this package.

Example

julia> x = DNASeq("NVHMDRWABSYCKGT-")

16nt DNA sequence
NVHMDRWABSYCKGT-

julia> x.data

4×16 BitArray{2}:
 1  1  1  1  1  1  1  1  0  0  0  0  0  0  0  0
 1  1  1  1  0  0  0  0  1  1  1  1  0  0  0  0
 1  1  0  0  1  1  0  0  1  1  0  0  1  1  0  0
 1  0  1  0  1  0  1  0  1  0  1  0  1  0  1  0

Notes

  • For a full featured package for biological sequences see BioSequences.jl.

Used By Packages