millironx/SequenceVariation.jl
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Update documentation wording to reflect new type names

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Thomas A. Christensen II 2023-01-04 13:05:56 -06:00
parent 46c84b06bb
commit 1384783fcc
4 changed files with 26 additions and 25 deletions
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22
docs/src/compare.md
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@ -4,7 +4,7 @@ CurrentModule = SequenceVariation
# Comparing variations in sequences # Comparing variations in sequences
## Checking for variations in a known variant ## Checking for variations in a known haplotype
Looking for a known [`Variation`](@ref) within a [`Haplotype`](@ref) is Looking for a known [`Variation`](@ref) within a [`Haplotype`](@ref) is
efficiently accomplished using the `in` operator. efficiently accomplished using the `in` operator.
@ -21,27 +21,27 @@ bos_ovis_alignment =
bos_human_alignment = bos_human_alignment =
PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine); PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);
bos_ovis_variant = Haplotype(bos_ovis_alignment) bos_ovis_haplotype = Haplotype(bos_ovis_alignment)
bos_human_variant = Haplotype(bos_human_alignment) bos_human_haplotype = Haplotype(bos_human_alignment)
``` ```
```@example call_variants ```@example call_variants
println("\tOvis aires\tHomo sapiens") println("\tOvis aires\tHomo sapiens")
for v in vcat(variations(bos_ovis_variant), variations(bos_human_variant)) for v in vcat(variations(bos_ovis_haplotype), variations(bos_human_haplotype))
is_sheep = v in bos_ovis_variant is_sheep = v in bos_ovis_haplotype
is_human = v in bos_human_variant is_human = v in bos_human_haplotype
println("$v\t$is_sheep\t\t$is_human") println("$v\t$is_sheep\t\t$is_human")
end end
``` ```
## Constructing new variants based on other variations ## Constructing new haplotypes based on other variations
New variants can be constructed using variations. This might be useful to pool New haplotypes can be constructed using variations. This might be useful to pool
variations found on different reads or to filter variations from a variant variations found on different reads or to filter variations from a haplotype
that aren't validated by another variant. that aren't validated by another haplotype.
```@repl call_variants ```@repl call_variants
sheeple = vcat(variations(bos_ovis_variant), variations(bos_human_variant)); sheeple = vcat(variations(bos_ovis_haplotype), variations(bos_human_haplotype));
Haplotype(bovine, sheeple) Haplotype(bovine, sheeple)
reconstruct!(bovine, ans) reconstruct!(bovine, ans)
``` ```

15
docs/src/haplotypes.md
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@ -2,13 +2,14 @@
CurrentModule = SequenceVariation CurrentModule = SequenceVariation
``` ```
# Working with variants # Working with haplotypes
## Calling variants ## Calling variants
The first step in working with sequence variation is to identify (call) The first step in working with sequence variation is to identify (call)
variations. SequenceVariation can directly call variants using the variations between two sequences. SequenceVariation can directly call variants
`Haplotype(::PairwiseAlignment)` constructor of the [`Haplotype`](@ref) type. using the `Haplotype(::PairwiseAlignment)` constructor of the
[`Haplotype`](@ref) type.
```@repl call_variants ```@repl call_variants
using SequenceVariation, BioAlignments, BioSequences using SequenceVariation, BioAlignments, BioSequences
@ -22,19 +23,19 @@ bos_ovis_alignment =
bos_human_alignment = bos_human_alignment =
PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine); PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);
bos_ovis_variant = Haplotype(bos_ovis_alignment) bos_ovis_haplotype = Haplotype(bos_ovis_alignment)
bos_human_variant = Haplotype(bos_human_alignment) bos_human_haplotype = Haplotype(bos_human_alignment)
``` ```
## Sequence reconstruction ## Sequence reconstruction
If the alternate sequence of a variant is no longer available (as is often the If the alternate sequence of a haplotype is no longer available (as is often the
case when calling variants from alignment files), then the sequence can be case when calling variants from alignment files), then the sequence can be
retrieved using the [`reconstruct!`](@ref) function. retrieved using the [`reconstruct!`](@ref) function.
```@repl call_variants ```@repl call_variants
human2 = copy(bovine); human2 = copy(bovine);
reconstruct!(human2, bos_human_variant) reconstruct!(human2, bos_human_haplotype)
human2 == bovine human2 == bovine
human2 == human human2 == human
``` ```

12
docs/src/variations.md
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@ -42,13 +42,13 @@ bos_ovis_alignment =
bos_human_alignment = bos_human_alignment =
PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine); PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);
bos_ovis_variant = Haplotype(bos_ovis_alignment) bos_ovis_haplotype = Haplotype(bos_ovis_alignment)
bos_human_variant = Haplotype(bos_human_alignment) bos_human_haplotype = Haplotype(bos_human_alignment)
``` ```
```@repl call_variants ```@repl call_variants
variations(bos_ovis_variant) variations(bos_ovis_haplotype)
variations(bos_human_variant) variations(bos_human_haplotype)
``` ```
## Reference switching ## Reference switching
@ -59,8 +59,8 @@ alignment between the new and old references using the [`translate`](@ref).
```@repl call_variants ```@repl call_variants
ovis_human_alignment = ovis_human_alignment =
PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), ovine) PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), ovine)
human_variation = first(variations(bos_ovis_variant)) human_variation = first(variations(bos_ovis_haplotype))
reference(ans) == bovine reference(ans) == bovine
SequenceVariation.translate(human_variation, ovis_human_alignment) SequenceVariation.translate(human_variation, ovis_human_haplotype)
reference(ans) == bovine reference(ans) == bovine
``` ```

2
src/Haplotype.jl
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@ -2,7 +2,7 @@
Haplotype{S<:BioSequence,T<:BioSymbol} Haplotype{S<:BioSequence,T<:BioSymbol}
A set of variations within a given sequence that are all found together. Depending on the A set of variations within a given sequence that are all found together. Depending on the
field, it might also be referred to as a "genotype," "haplotype," or "strain." field, it might also be referred to as a "genotype" or "strain."
# Constructors # Constructors