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"`

julia> using BioSequences: @dna_str
julia> using SequenceVariation
julia> bovine_ins = dna"GACCGGCTGCATTCGAGGCTGCCAGCAAGCAG"32nt DNA Sequence:
GACCGGCTGCATTCGAGGCTGCCAGCAAGCAG
julia> Variation(bovine_ins, "C4A")C4A
julia> mutation(ans)Substitution{BioSymbols.DNA}(DNA_A)
julia> typeof(mutation(Variation(bovine_ins, "Δ13-14")))Deletion
julia> mutation(Variation(bovine_ins, "25ACA"))Insertion{BioSequences.LongSequence{BioSequences.DNAAlphabet{4}}}(ACA)

Extraction

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

julia> variations(bos_ovis_haplotype)2-element Vector{Variation{BioSequences.LongSequence{BioSequences.DNAAlphabet{4}}, BioSymbols.DNA}}:
 C22T
 G29A
julia> variations(bos_human_haplotype)7-element Vector{Variation{BioSequences.LongSequence{BioSequences.DNAAlphabet{4}}, BioSymbols.DNA}}:
 C4A
 T13C
 C14A
 G17A
 C19A
 T20G
 G25T

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 function.

julia> ovis_human_alignment =
           PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), ovine)BioAlignments.PairwiseAlignment{BioSequences.LongSequence{BioSequences.DNAAlphabet{4}}, BioSequences.LongSequence{BioSequences.DNAAlphabet{4}}}:
  seq:  1 GACAGGCTGCATCAGAAGAGGCCATCAAGCAG 32
          ||| ||||||||  || |  | || ||| |||
  ref:  1 GACCGGCTGCATTCGAGGCTGTCAGCAAACAG 32
julia> human_variation = first(variations(bos_ovis_haplotype))C22T
julia> reference(ans) == bovinetrue
julia> SequenceVariation.translate(human_variation, ovis_human_alignment)C22T
julia> reference(ans) == bovinefalse