ReferenceSequences.jl provides a data structure for reference sequences. It is
common that a reference sequence contains only five kinds of nucleotides
("ACGTN") and the occurrence of 'N' is sparse and clustered. In such a case,
ReferenceSequence can compress positions of 'N' and aggressively save memory
space.
julia> using Bio.Seq
julia> using ReferenceSequences
# create ReferenceSequence from DNASequence of Bio.Seq
julia> seq = ReferenceSequence(dna"ACGT"^5 * dna"N"^10)
30nt Reference Sequence:
ACGTACGTACGTACGTACGTNNNNNNNNNN
julia> DNASequence(seq) # round trip
30nt DNA Sequence:
ACGTACGTACGTACGTACGTNNNNNNNNNN
julia> seq[4] # access an element
T
julia> seq[15:25] # make a subsequence (copy-free)
11nt Reference Sequence:
GTACGTNNNNN
julia> seq[1:4] == dna"ACGT" # comparison
true
- FASTA parser