SequenceVariation.jl/docs/src/variations.md

CurrentModule = SequenceVariation

Working with individual variations

Construction

Individual Variations can be made using a reference sequence and string syntax

Variation type	Syntax	Interpretation	Example
Substitutions	<REF><POS><ALT>	<ALT> is substituted for <REF> in position <POS>	"G16C"
Deletions	Δ<START>-<END>	All bases (inclusive) between <START> and <END> are deleted. It is valid to have <START> equal <END>: that is a deletion of one base.	"Δ1-2"
Insertions	<POS><ALT>	<ALT> is inserted between positions <POS> and <POS>+1	"11T"

using BioSequences: @dna_str
using SequenceVariation
bovine_ins = dna"GACCGGCTGCATTCGAGGCTGCCAGCAAGCAG"
Variation(bovine_ins, "C4A")
mutation(ans)
typeof(mutation(Variation(bovine_ins, "Δ13-14")))
mutation(Variation(bovine_ins, "25ACA"))

Extraction

Sequence variations may also be extracted wholesale from a Haplotype using the variations function.

using SequenceVariation, BioAlignments, BioSequences

bovine = dna"GACCGGCTGCATTCGAGGCTGCCAGCAAGCAG";
ovine  = dna"GACCGGCTGCATTCGAGGCTGTCAGCAAACAG";
human  = dna"GACAGGCTGCATCAGAAGAGGCCATCAAGCAG";

bos_ovis_alignment =
    PairwiseAlignment(AlignedSequence(ovine, Alignment("32M", 1, 1)), bovine);
bos_human_alignment =
    PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);

bos_ovis_haplotype = Haplotype(bos_ovis_alignment)
bos_human_haplotype = Haplotype(bos_human_alignment)

variations(bos_ovis_haplotype)
variations(bos_human_haplotype)

Reference switching

An individual variation can be mapped to a new reference sequence given an alignment between the new and old references using the [translate](@ref translate(::Variation{S,T}, ::PairwiseAlignment{S,S}) where {S,T}) function.

ovis_human_alignment =
    PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), ovine)
human_variation = first(variations(bos_ovis_haplotype))
reference(ans) == bovine
SequenceVariation.translate(human_variation, ovis_human_alignment)
reference(ans) == bovine