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https://github.com/MillironX/SequenceVariation.jl.git
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Rename Variant type to Haplotype
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8 changed files with 62 additions and 60 deletions
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@ -18,8 +18,8 @@ Insertion
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## Variants
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```@docs
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Variant
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reference(::Variant)
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Haplotype
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reference(::Haplotype)
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variations
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reconstruct!
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```
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@ -49,7 +49,7 @@ _lendiff
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```@docs
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_edits
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_is_valid(::Variant)
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_is_valid(::Haplotype)
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```
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### Variations
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@ -6,7 +6,7 @@ CurrentModule = SequenceVariation
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## Checking for variations in a known variant
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Looking for a known [`Variation`](@ref) within a [`Variant`](@ref) is
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Looking for a known [`Variation`](@ref) within a [`Haplotype`](@ref) is
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efficiently accomplished using the `in` operator.
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```@setup call_variants
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@ -21,8 +21,8 @@ bos_ovis_alignment =
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bos_human_alignment =
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PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);
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bos_ovis_variant = Variant(bos_ovis_alignment)
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bos_human_variant = Variant(bos_human_alignment)
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bos_ovis_variant = Haplotype(bos_ovis_alignment)
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bos_human_variant = Haplotype(bos_human_alignment)
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```
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```@example call_variants
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@ -42,6 +42,6 @@ that aren't validated by another variant.
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```@repl call_variants
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sheeple = vcat(variations(bos_ovis_variant), variations(bos_human_variant));
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Variant(bovine, sheeple)
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Haplotype(bovine, sheeple)
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reconstruct!(bovine, ans)
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```
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@ -8,7 +8,7 @@ CurrentModule = SequenceVariation
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The first step in working with sequence variation is to identify (call)
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variations. SequenceVariation can directly call variants using the
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`Variant(::PairwiseAlignment)` constructor of the [`Variant`](@ref) type.
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`Haplotype(::PairwiseAlignment)` constructor of the [`Haplotype`](@ref) type.
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```@repl call_variants
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using SequenceVariation, BioAlignments, BioSequences
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@ -22,8 +22,8 @@ bos_ovis_alignment =
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bos_human_alignment =
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PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);
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bos_ovis_variant = Variant(bos_ovis_alignment)
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bos_human_variant = Variant(bos_human_alignment)
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bos_ovis_variant = Haplotype(bos_ovis_alignment)
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bos_human_variant = Haplotype(bos_human_alignment)
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```
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## Sequence reconstruction
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@ -27,7 +27,7 @@ mutation(Variation(bovine_ins, "25ACA"))
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## Extraction
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Sequence variations may also be extracted wholesale from a [`Variant`](@ref)
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Sequence variations may also be extracted wholesale from a [`Haplotype`](@ref)
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using the [`variations`](@ref) function.
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```@setup call_variants
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@ -42,8 +42,8 @@ bos_ovis_alignment =
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bos_human_alignment =
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PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);
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bos_ovis_variant = Variant(bos_ovis_alignment)
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bos_human_variant = Variant(bos_human_alignment)
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bos_ovis_variant = Haplotype(bos_ovis_alignment)
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bos_human_variant = Haplotype(bos_human_alignment)
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```
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```@repl call_variants
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@ -1,41 +1,43 @@
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"""
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Variant{S<:BioSequence,T<:BioSymbol}
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Haplotype{S<:BioSequence,T<:BioSymbol}
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A set of variations within a given sequence that are all found together. Depending on the
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field, it might also be referred to as a "genotype," "haplotype," or "strain."
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# Constructors
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Variant(ref::S, edits::Vector{Edit{S,T}}) where {S<:BioSequence,T<:BioSymbol}
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Variant(ref::S, vars::Vector{Variation{S,T}}) where {S<:BioSequence,T<:BioSymbol}
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Variant(
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Haplotype(ref::S, edits::Vector{Edit{S,T}}) where {S<:BioSequence,T<:BioSymbol}
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Haplotype(ref::S, vars::Vector{Variation{S,T}}) where {S<:BioSequence,T<:BioSymbol}
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Haplotype(
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aln::PairwiseAlignment{T,T}
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) where {T<:LongSequence{<:Union{BS.AminoAcidAlphabet,BS.NucleicAcidAlphabet}}}
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When constructing a `Variant` from a vector of [`Edit`](@ref)s or [`Variation`](@ref)s, the
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edits are applied sequentially from first to last position, therefore the vector must always
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be sorted by position. These edits are sorted automatically if constructing from an
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When constructing a `Haplotype` from a vector of [`Edit`](@ref)s or [`Variation`](@ref)s,
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the edits are applied sequentially from first to last position, therefore the vector must
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always be sorted by position. These edits are sorted automatically if constructing from an
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alignment.
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"""
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struct Variant{S<:BioSequence,T<:BioSymbol}
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struct Haplotype{S<:BioSequence,T<:BioSymbol}
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ref::S
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edits::Vector{Edit{S,T}}
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Variant{S,T}(ref::S, edits::Vector{Edit{S,T}}, ::Unsafe) where {S,T} = new(ref, edits)
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Haplotype{S,T}(ref::S, edits::Vector{Edit{S,T}}, ::Unsafe) where {S,T} = new(ref, edits)
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end
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function Variant{S,T}(ref::S, edits::Vector{Edit{S,T}}) where {S<:BioSequence,T<:BioSymbol}
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function Haplotype{S,T}(
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ref::S, edits::Vector{Edit{S,T}}
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) where {S<:BioSequence,T<:BioSymbol}
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sort!(edits; by=x -> x.pos)
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result = Variant{S,T}(ref, edits, Unsafe())
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result = Haplotype{S,T}(ref, edits, Unsafe())
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_is_valid(result) || error("TODO") # report what kind of error message?
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return result
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end
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function Variant(ref::S, edits::Vector{Edit{S,T}}) where {S<:BioSequence,T<:BioSymbol}
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return Variant{S,T}(ref, edits)
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function Haplotype(ref::S, edits::Vector{Edit{S,T}}) where {S<:BioSequence,T<:BioSymbol}
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return Haplotype{S,T}(ref, edits)
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end
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function Base.show(io::IO, x::Variant)
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function Base.show(io::IO, x::Haplotype)
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n = length(x.edits)
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print(io, summary(x), " with $n edit$(n > 1 ? "s" : ""):")
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for i in x.edits
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@ -46,12 +48,12 @@ function Base.show(io::IO, x::Variant)
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end
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"""
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is_valid(v::Variant)
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is_valid(v::Haplotype)
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Validate `v`. `v` is invalid if any of its operations are out of bounds, or the same
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position is affected by multiple edits.
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"""
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function _is_valid(v::Variant)
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function _is_valid(v::Haplotype)
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isempty(v.ref) && return false
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valid_positions = 1:length(v.ref)
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last_was_insert = false
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@ -87,7 +89,7 @@ function _is_valid(v::Variant)
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return true
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end
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function Variant(
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function Haplotype(
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aln::PairwiseAlignment{T,T}
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) where {T<:LongSequence{<:Union{BS.AminoAcidAlphabet,BS.NucleicAcidAlphabet}}}
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ref = aln.b
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@ -141,30 +143,30 @@ function Variant(
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end
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end
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return Variant(ref, edits)
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return Haplotype(ref, edits)
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end
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"""
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_edits(v::Variant)
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_edits(v::Haplotype)
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Gets the [`Edit`](@ref)s that comprise `v`
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"""
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_edits(v::Variant) = v.edits
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_edits(v::Haplotype) = v.edits
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"""
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reference(v::Variant)
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reference(v::Haplotype)
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Gets the reference sequence of `v`.
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"""
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reference(v::Variant) = v.ref
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Base.:(==)(x::Variant, y::Variant) = x.ref == y.ref && x.edits == y.edits
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reference(v::Haplotype) = v.ref
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Base.:(==)(x::Haplotype, y::Haplotype) = x.ref == y.ref && x.edits == y.edits
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"""
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reconstruct!(seq::S, x::Variant{S}) where {S}
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reconstruct!(seq::S, x::Haplotype{S}) where {S}
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Apply the edits in `x` to `seq` and return the mutated sequence
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"""
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function reconstruct!(seq::S, x::Variant{S}) where {S}
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function reconstruct!(seq::S, x::Haplotype{S}) where {S}
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len = length(x.ref) + sum(edit -> _lendiff(edit), _edits(x))
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resize!(seq, len % UInt)
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refpos = seqpos = 1
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@ -2,10 +2,10 @@ module SequenceVariation
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"""
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Needs to be able to:
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* Given a sequence and a reference, create a `Variant` that unambiguously represents
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* Given a sequence and a reference, create a `Haplotype` that unambiguously represents
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the sequence
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* Given a `Variant` and a new reference, translate the variant to the new reference.
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* Given a `Haplotype` and a new reference, translate the variant to the new reference.
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* Given a mutation and a reference and a sequence, determine if the sequence has that
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mutation
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@ -26,9 +26,9 @@ using BioSequences: BioSequences, BioSequence, NucleotideSeq, LongSequence, isga
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using BioSymbols: BioSymbol
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export Deletion
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export Haplotype
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export Insertion
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export Substitution
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export Variant
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export Variation
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export altbases
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export mutation
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@ -12,7 +12,7 @@ and built-in validation.
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Variation(ref::S, edit::AbstractString) where {S<:BioSequence}
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Generally speaking, the `Edit` constructor should be avoided to ensure corectness: use of
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[`variations(::Variant)`](@ref) is encouraged, instead.
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[`variations(::Haplotype)`](@ref) is encouraged, instead.
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Constructing a `Variation` from an `AbstractString` will parse the from `edit` using the
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following syntax:
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@ -45,9 +45,9 @@ function Variation(ref::S, edit::AbstractString) where {S<:BioSequence}
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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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function Haplotype(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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return Haplotype{S,T}(ref, edits)
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end
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"""
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@ -108,7 +108,7 @@ function Base.show(io::IO, x::Variation)
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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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function Base.in(v::Variation, var::Haplotype)
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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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@ -171,11 +171,11 @@ function translate(var::Variation{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}
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end
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"""
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variations(v::Variant{S,T}) where {S,T}
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variations(v::Haplotype{S,T}) where {S,T}
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Converts the [`Edit`](@ref)s of `v` into a vector of [`Variation`](@ref)s.
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"""
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function variations(v::Variant{S,T}) where {S,T}
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function variations(v::Haplotype{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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@ -1,9 +1,9 @@
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"""
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Needs to be able to:
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* Given a sequence and a reference, create a `Variant` that unambiguously represents
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* Given a sequence and a reference, create a `Haplotype` that unambiguously represents
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the sequence
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* Given a `Variant` and a new reference, translate the variant to the new reference.
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* Given a `Haplotype` and a new reference, translate the variant to the new reference.
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* Given a mutation and a reference and a sequence, determine if the sequence has that
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mutation
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@ -34,12 +34,12 @@ const DNA_MODEL = BioAlignments.AffineGapScoreModel(EDNAFULL; gap_open=-25, gap_
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align(a::BioSequence, b::BioSequence) = pairalign(GlobalAlignment(), a, b, DNA_MODEL).aln
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seq1 = ungap!(dna"--ATGCGTGTTAGCAAC--TTATCGCG")
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seq2 = ungap!(dna"TGATGCGTGT-AGCAACACTTATAGCG")
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var = Variant(align(seq1, seq2))
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var = Haplotype(align(seq1, seq2))
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@testset "VariantRoundtrip" begin
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@testset "HaplotypeRoundtrip" begin
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for v in variations(var)
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@test v in var
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@test v in Variant(seq2, [v])
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@test v in Haplotype(seq2, [v])
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end
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end
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@ -51,7 +51,7 @@ end
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read02 = AlignedSequence(mutseq[3:12], Alignment("10M", 1, 3))
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aln01 = PairwiseAlignment(read01, refseq)
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aln02 = PairwiseAlignment(read02, refseq)
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@test Variant(aln01).edits == Variant(aln02).edits
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@test Haplotype(aln01).edits == Haplotype(aln02).edits
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end
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@testset "VariationParsing" begin
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@ -72,7 +72,7 @@ end
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read = AlignedSequence(mutseq[1:10], Alignment("10M", 1, 1))
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aln = PairwiseAlignment(read, refseq)
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var = Variant(aln)
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var = Haplotype(aln)
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sub = Variation(refseq, "A4T")
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@test first(variations(var)) == sub
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@ -108,31 +108,31 @@ end
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@test altbases(Variation(dna"ATCGA", "1C")) == dna"CA"
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end
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@testset "SoftclipVariant" begin
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@testset "SoftclipHaplotype" begin
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refseq = dna"GATTACA"
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mutseq = dna"GATTACAAAA"
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refvar = Variant(refseq, SequenceVariation.Edit{typeof(refseq),eltype(refseq)}[])
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refvar = Haplotype(refseq, SequenceVariation.Edit{typeof(refseq),eltype(refseq)}[])
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# Test for ending soft clip
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@test Variant(
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@test Haplotype(
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PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3S", 1, 1)), refseq)
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) == refvar
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# Test for ending soft+hard clip
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@test Variant(
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@test Haplotype(
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PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3S2H", 1, 1)), refseq)
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) == refvar
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# Test that ending insertions are still valid
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@test length(
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Variant(
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Haplotype(
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PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3I", 1, 1)), refseq)
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).edits,
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) == 1
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# Test that out-of-bounds bases are still caught
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@test_throws BoundsError Variant(
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@test_throws BoundsError Haplotype(
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PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3X", 1, 1)), refseq)
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)
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end
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