GeneticBitArrays.jl

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

GeneticBitArrays.jl

DOI Latest Release License Build Status 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