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https://github.com/MillironX/SequenceVariation.jl.git
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Move Variation-related code to Variation.jl
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commit
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2 changed files with 135 additions and 133 deletions
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@ -33,139 +33,7 @@ struct Inapplicable end
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include("Edit.jl")
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include("Edit.jl")
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include("Variant.jl")
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include("Variant.jl")
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include("Variation.jl")
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struct Variation{S <: BioSequence, T <: BioSymbol}
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ref::S
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edit::Edit{S, T}
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function Variation{S, T}(ref::S, e::Edit{S, T}, ::Unsafe) where {S <: BioSequence, T <: BioSymbol}
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new(ref, e)
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end
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end
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function Variation{S, T}(ref::S, e::Edit{S, T}) where {S <: BioSequence, T <: BioSymbol}
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v = Variation{S, T}(ref, e, Unsafe())
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is_valid(v) ? v : throw(ArgumentError("Invalid variant"))
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end
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Variation(ref::S, edit::Edit{S, T}) where {S, T} = Variation{S, T}(ref, edit)
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function Variation(ref::S, edit::AbstractString) where {S<:BioSequence}
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T = eltype(ref)
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e = parse(Edit{S,T}, edit)
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return Variation{S,T}(ref, e)
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end
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function Variant(ref::S, vars::Vector{Variation{S,T}}) where {S<:BioSequence, T<:BioSymbol}
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edits = edit.(vars)
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return Variant{S, T}(ref, edits)
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end
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reference(v::Variation) = v.ref
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edit(v::Variation) = v.edit
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mutation(v::Variation) = mutation(edit(v))
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BioGenerics.leftposition(v::Variation) = leftposition(edit(v))
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BioGenerics.rightposition(v::Variation) = rightposition(edit(v))
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Base.:(==)(x::Variation, y::Variation) = x.ref == y.ref && x.edit == y.edit
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Base.hash(x::Variation, h::UInt) = hash(Variation, hash((x.ref, x.edit), h))
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function is_valid(v::Variation)
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isempty(v.ref) && return false
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op = v.edit.x
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pos = v.edit.pos
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if op isa Substitution
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return pos in eachindex(v.ref)
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elseif op isa Insertion
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return pos in 0:lastindex(v.ref)+1
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elseif op isa Deletion
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return pos in 1:(lastindex(v.ref)-length(op) + 1)
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end
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end
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function Base.show(io::IO, x::Variation)
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content = x.edit.x
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pos = x.edit.pos
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if content isa Substitution
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print(io, x.ref[pos], pos, content.x)
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elseif content isa Deletion
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print(io, 'Δ', pos, '-', pos + content.len - 1)
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elseif content isa Insertion
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print(io, pos, content.seq)
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else
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print(io, pos, content.x)
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end
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end
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function Base.in(v::Variation, var::Variant)
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if v.ref != var.ref
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error("References must be equal")
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end
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any(v.edit == edit for edit in var.edits)
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end
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function translate(var::Variation{S, T}, aln::PairwiseAlignment{S, S}) where {S, T}
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kind = var.edit.x
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pos = var.edit.pos
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seq, ref = aln.seq, aln.b
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# Special case: Insertions may have a pos of 0, which cannot be mapped to
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# the seq using ref2seq
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if iszero(pos)
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(s, r), _ = iterate(aln)
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(isgap(s) | isgap(r)) && return Inapplicable()
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return Variation{S, T}(seq, Edit{S, T}(Insertion(var.edit.x), 0))
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end
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(seqpos, op) = BA.ref2seq(aln, pos)
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if kind isa Substitution
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# If it's a substitution, return nothing if it maps to a deleted
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# position, or substitutes to same base.
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op in (BA.OP_MATCH, BA.OP_SEQ_MATCH, BA.OP_SEQ_MISMATCH) || return nothing
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seq[seqpos] == kind.x && return nothing
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edit = Edit{S, T}(kind, seqpos)
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return Variation{S, T}(seq, edit, Unsafe())
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elseif kind isa Deletion
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# If it's a deletion, return nothing if the deleted part is already missing
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# from the new reference.
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(stop, op2) = BA.ref2seq(aln, pos + length(kind) - 1)
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start = seqpos + op == BA.OP_DELETE
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start < stop && return nothing
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edit = Edit{S, T}(Deletion(stop - start + 1), start)
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return Variation{S, T}(seq, edit, Unsafe())
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else
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# If it maps directly to a symbol, just insert
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if op in (BA.OP_MATCH, BA.OP_SEQ_MATCH, BA.OP_SEQ_MISMATCH)
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# This happens if there is already an insertion at the position
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if pos != lastindex(ref) && first(ref2seq(aln, pos+1)) != seqpos + 1
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return Inapplicable()
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else
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edit = Edit{S, T}(Insertion(var.edit.x), seqpos)
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return Variation{S, T}(seq, edit, Unsafe())
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end
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# Alternatively, it can map to a deletion. In that case, it become really
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# tricky to talk about the "same" insertion.
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else
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return Inapplicable()
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end
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end
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end
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function variations(v::Variant{S,T}) where {S,T}
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vs = Vector{Variation{S,T}}(undef, length(edits(v)))
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for (i, e) in enumerate(edits(v))
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vs[i] = Variation{S,T}(reference(v), e)
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end
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return vs
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end
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function refbases(v::Variation)
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return _refbases(mutation(v), reference(v), leftposition(v))
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end
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function altbases(v::Variation)
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return _altbases(mutation(v), reference(v), leftposition(v))
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end
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export Insertion,
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export Insertion,
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Deletion,
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Deletion,
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134
src/Variation.jl
Normal file
134
src/Variation.jl
Normal file
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@ -0,0 +1,134 @@
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struct Variation{S<:BioSequence,T<:BioSymbol}
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ref::S
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edit::Edit{S,T}
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function Variation{S,T}(
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ref::S, e::Edit{S,T}, ::Unsafe
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) where {S<:BioSequence,T<:BioSymbol}
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return new(ref, e)
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end
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end
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function Variation{S,T}(ref::S, e::Edit{S,T}) where {S<:BioSequence,T<:BioSymbol}
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v = Variation{S,T}(ref, e, Unsafe())
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return is_valid(v) ? v : throw(ArgumentError("Invalid variant"))
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end
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Variation(ref::S, edit::Edit{S,T}) where {S,T} = Variation{S,T}(ref, edit)
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function Variation(ref::S, edit::AbstractString) where {S<:BioSequence}
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T = eltype(ref)
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e = parse(Edit{S,T}, edit)
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return Variation{S,T}(ref, e)
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end
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function Variant(ref::S, vars::Vector{Variation{S,T}}) where {S<:BioSequence,T<:BioSymbol}
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edits = edit.(vars)
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return Variant{S,T}(ref, edits)
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end
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reference(v::Variation) = v.ref
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edit(v::Variation) = v.edit
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mutation(v::Variation) = mutation(edit(v))
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BioGenerics.leftposition(v::Variation) = leftposition(edit(v))
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BioGenerics.rightposition(v::Variation) = rightposition(edit(v))
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Base.:(==)(x::Variation, y::Variation) = x.ref == y.ref && x.edit == y.edit
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Base.hash(x::Variation, h::UInt) = hash(Variation, hash((x.ref, x.edit), h))
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function is_valid(v::Variation)
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isempty(v.ref) && return false
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op = v.edit.x
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pos = v.edit.pos
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if op isa Substitution
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return pos in eachindex(v.ref)
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elseif op isa Insertion
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return pos in 0:(lastindex(v.ref) + 1)
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elseif op isa Deletion
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return pos in 1:(lastindex(v.ref) - length(op) + 1)
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end
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end
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function Base.show(io::IO, x::Variation)
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content = x.edit.x
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pos = x.edit.pos
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if content isa Substitution
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print(io, x.ref[pos], pos, content.x)
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elseif content isa Deletion
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print(io, 'Δ', pos, '-', pos + content.len - 1)
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elseif content isa Insertion
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print(io, pos, content.seq)
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else
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print(io, pos, content.x)
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end
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end
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function Base.in(v::Variation, var::Variant)
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if v.ref != var.ref
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error("References must be equal")
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end
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return any(v.edit == edit for edit in var.edits)
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end
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function translate(var::Variation{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}
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kind = var.edit.x
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pos = var.edit.pos
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seq, ref = aln.seq, aln.b
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# Special case: Insertions may have a pos of 0, which cannot be mapped to
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# the seq using ref2seq
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if iszero(pos)
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(s, r), _ = iterate(aln)
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(isgap(s) | isgap(r)) && return Inapplicable()
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return Variation{S,T}(seq, Edit{S,T}(Insertion(var.edit.x), 0))
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end
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(seqpos, op) = BA.ref2seq(aln, pos)
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if kind isa Substitution
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# If it's a substitution, return nothing if it maps to a deleted
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# position, or substitutes to same base.
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op in (BA.OP_MATCH, BA.OP_SEQ_MATCH, BA.OP_SEQ_MISMATCH) || return nothing
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seq[seqpos] == kind.x && return nothing
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edit = Edit{S,T}(kind, seqpos)
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return Variation{S,T}(seq, edit, Unsafe())
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elseif kind isa Deletion
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# If it's a deletion, return nothing if the deleted part is already missing
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# from the new reference.
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(stop, op2) = BA.ref2seq(aln, pos + length(kind) - 1)
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start = seqpos + op == BA.OP_DELETE
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start < stop && return nothing
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edit = Edit{S,T}(Deletion(stop - start + 1), start)
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return Variation{S,T}(seq, edit, Unsafe())
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else
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# If it maps directly to a symbol, just insert
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if op in (BA.OP_MATCH, BA.OP_SEQ_MATCH, BA.OP_SEQ_MISMATCH)
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# This happens if there is already an insertion at the position
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if pos != lastindex(ref) && first(ref2seq(aln, pos + 1)) != seqpos + 1
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return Inapplicable()
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else
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edit = Edit{S,T}(Insertion(var.edit.x), seqpos)
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return Variation{S,T}(seq, edit, Unsafe())
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end
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# Alternatively, it can map to a deletion. In that case, it become really
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# tricky to talk about the "same" insertion.
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else
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return Inapplicable()
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end
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end
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end
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function variations(v::Variant{S,T}) where {S,T}
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vs = Vector{Variation{S,T}}(undef, length(edits(v)))
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for (i, e) in enumerate(edits(v))
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vs[i] = Variation{S,T}(reference(v), e)
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end
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return vs
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end
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function refbases(v::Variation)
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return _refbases(mutation(v), reference(v), leftposition(v))
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end
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function altbases(v::Variation)
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return _altbases(mutation(v), reference(v), leftposition(v))
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end
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