mirror of
https://github.com/MillironX/SequenceVariation.jl.git
synced 2024-11-21 21:16:05 +00:00
Add tutorial-type documentation
This commit is contained in:
parent
134ee771b9
commit
6510ee3fc0
5 changed files with 170 additions and 0 deletions
|
|
@ -1,6 +1,16 @@
|
|||
[deps]
|
||||
BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
|
||||
BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
|
||||
BioSymbols = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
|
||||
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
|
||||
Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
|
||||
Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
|
||||
SequenceVariation = "eef6e190-9969-4f06-a38f-35a110a8fdc8"
|
||||
|
||||
[compat]
|
||||
BioAlignments = "3"
|
||||
BioSequences = "3"
|
||||
BioSymbols = "5"
|
||||
Documenter = "0.27"
|
||||
Revise = "3.4"
|
||||
julia = "1.6"
|
||||
|
|
|
|||
|
|
@ -1,6 +1,10 @@
|
|||
using Pkg
|
||||
using Documenter
|
||||
using SequenceVariation
|
||||
using Revise
|
||||
|
||||
# see https://github.com/tlienart/LiveServer.jl/issues/140#issuecomment-1271591251
|
||||
Revise.revise()
|
||||
|
||||
makedocs(;
|
||||
checkdocs = :exports,
|
||||
|
|
@ -10,6 +14,9 @@ makedocs(;
|
|||
modules = [SequenceVariation],
|
||||
pages = [
|
||||
"Home" => "index.md",
|
||||
"Working with variants" => "variants.md",
|
||||
"Working with variations" => "variations.md",
|
||||
"Comparing variations" => "compare.md",
|
||||
"API Reference" => "api.md",
|
||||
],
|
||||
authors = replace(join(Pkg.TOML.parsefile("Project.toml")["authors"], ", "), r" <.*?>" => "" ) * ", The BioJulia Organisation, and other contributors."
|
||||
|
|
|
|||
47
docs/src/compare.md
Normal file
47
docs/src/compare.md
Normal file
|
|
@ -0,0 +1,47 @@
|
|||
```@meta
|
||||
CurrentModule = SequenceVariation
|
||||
```
|
||||
|
||||
# Comparing variations in sequences
|
||||
|
||||
## Checking for variations in a known variant
|
||||
|
||||
Looking for a known [`Variation`](@ref) within a [`Variant`](@ref) is
|
||||
efficiently accomplished using the `in` operator.
|
||||
|
||||
```@setup call_variants
|
||||
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_variant = Variant(bos_ovis_alignment)
|
||||
bos_human_variant = Variant(bos_human_alignment)
|
||||
```
|
||||
|
||||
```@example call_variants
|
||||
println("\tOvis aires\tHomo sapiens")
|
||||
for v in vcat(variations(bos_ovis_variant), variations(bos_human_variant))
|
||||
is_sheep = v in bos_ovis_variant
|
||||
is_human = v in bos_human_variant
|
||||
println("$v\t$is_sheep\t\t$is_human")
|
||||
end
|
||||
```
|
||||
|
||||
## Constructing new variants based on other variations
|
||||
|
||||
New variants can be constructed using variations. This might be useful to pool
|
||||
variations found on different reads or to filter variations from a variant
|
||||
that aren't validated by another variant.
|
||||
|
||||
```@repl call_variants
|
||||
sheeple = vcat(variations(bos_ovis_variant), variations(bos_human_variant));
|
||||
Variant(bovine, sheeple)
|
||||
reconstruct!(bovine, ans)
|
||||
```
|
||||
40
docs/src/variants.md
Normal file
40
docs/src/variants.md
Normal file
|
|
@ -0,0 +1,40 @@
|
|||
```@meta
|
||||
CurrentModule = SequenceVariation
|
||||
```
|
||||
|
||||
# Working with variants
|
||||
|
||||
## Calling variants
|
||||
|
||||
The first step in working with sequence variation is to identify (call)
|
||||
variations. SequenceVariation can directly call variants using the
|
||||
`Variant(::PairwiseAlignment)` constructor of the [`Variant`](@ref) type.
|
||||
|
||||
```@repl call_variants
|
||||
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_variant = Variant(bos_ovis_alignment)
|
||||
bos_human_variant = Variant(bos_human_alignment)
|
||||
```
|
||||
|
||||
## Sequence reconstruction
|
||||
|
||||
If the alternate sequence of a variant is no longer available (as is often the
|
||||
case when calling variants from alignment files), then the sequence can be
|
||||
retrieved using the [`reconstruct!`](@ref) function.
|
||||
|
||||
```@repl call_variants
|
||||
human2 = copy(bovine);
|
||||
reconstruct!(human2, bos_human_variant)
|
||||
human2 == bovine
|
||||
human2 == human
|
||||
```
|
||||
66
docs/src/variations.md
Normal file
66
docs/src/variations.md
Normal file
|
|
@ -0,0 +1,66 @@
|
|||
```@meta
|
||||
CurrentModule = SequenceVariation
|
||||
```
|
||||
|
||||
# Working with individual variations
|
||||
|
||||
## Construction
|
||||
|
||||
Individual [`Variation`](@ref)s 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"` |
|
||||
|
||||
```@repl
|
||||
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 [`Variant`](@ref)
|
||||
using the [`variations`](@ref) function.
|
||||
|
||||
```@setup call_variants
|
||||
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_variant = Variant(bos_ovis_alignment)
|
||||
bos_human_variant = Variant(bos_human_alignment)
|
||||
```
|
||||
|
||||
```@repl call_variants
|
||||
variations(bos_ovis_variant)
|
||||
variations(bos_human_variant)
|
||||
```
|
||||
|
||||
## 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).
|
||||
|
||||
```@repl call_variants
|
||||
ovis_human_alignment =
|
||||
PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), ovine)
|
||||
human_variation = first(variations(bos_ovis_variant))
|
||||
reference(ans) == bovine
|
||||
SequenceVariation.translate(human_variation, ovis_human_alignment)
|
||||
reference(ans) == bovine
|
||||
```
|
||||
Loading…
Reference in a new issue