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https://github.com/MillironX/SequenceVariation.jl.git
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Add tutorial-type documentation
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[deps]
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BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
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BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
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BioSymbols = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
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Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
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Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
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Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
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SequenceVariation = "eef6e190-9969-4f06-a38f-35a110a8fdc8"
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[compat]
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BioAlignments = "3"
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BioSequences = "3"
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BioSymbols = "5"
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Documenter = "0.27"
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Revise = "3.4"
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julia = "1.6"
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using Pkg
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using Documenter
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using SequenceVariation
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using Revise
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# see https://github.com/tlienart/LiveServer.jl/issues/140#issuecomment-1271591251
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Revise.revise()
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makedocs(;
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checkdocs = :exports,
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@ -10,6 +14,9 @@ makedocs(;
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modules = [SequenceVariation],
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pages = [
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"Home" => "index.md",
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"Working with variants" => "variants.md",
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"Working with variations" => "variations.md",
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"Comparing variations" => "compare.md",
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"API Reference" => "api.md",
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],
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authors = replace(join(Pkg.TOML.parsefile("Project.toml")["authors"], ", "), r" <.*?>" => "" ) * ", The BioJulia Organisation, and other contributors."
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47
docs/src/compare.md
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47
docs/src/compare.md
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```@meta
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CurrentModule = SequenceVariation
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```
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# Comparing variations in sequences
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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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efficiently accomplished using the `in` operator.
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```@setup call_variants
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using SequenceVariation, BioAlignments, BioSequences
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bovine = dna"GACCGGCTGCATTCGAGGCTGCCAGCAAGCAG";
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ovine = dna"GACCGGCTGCATTCGAGGCTGTCAGCAAACAG";
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human = dna"GACAGGCTGCATCAGAAGAGGCCATCAAGCAG";
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bos_ovis_alignment =
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PairwiseAlignment(AlignedSequence(ovine, Alignment("32M", 1, 1)), bovine);
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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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```
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```@example call_variants
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println("\tOvis aires\tHomo sapiens")
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for v in vcat(variations(bos_ovis_variant), variations(bos_human_variant))
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is_sheep = v in bos_ovis_variant
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is_human = v in bos_human_variant
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println("$v\t$is_sheep\t\t$is_human")
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end
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```
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## Constructing new variants based on other variations
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New variants can be constructed using variations. This might be useful to pool
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variations found on different reads or to filter variations from a variant
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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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reconstruct!(bovine, ans)
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```
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40
docs/src/variants.md
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40
docs/src/variants.md
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```@meta
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CurrentModule = SequenceVariation
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```
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# Working with variants
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## Calling variants
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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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```@repl call_variants
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using SequenceVariation, BioAlignments, BioSequences
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bovine = dna"GACCGGCTGCATTCGAGGCTGCCAGCAAGCAG";
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ovine = dna"GACCGGCTGCATTCGAGGCTGTCAGCAAACAG";
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human = dna"GACAGGCTGCATCAGAAGAGGCCATCAAGCAG";
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bos_ovis_alignment =
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PairwiseAlignment(AlignedSequence(ovine, Alignment("32M", 1, 1)), bovine);
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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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```
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## Sequence reconstruction
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If the alternate sequence of a variant is no longer available (as is often the
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case when calling variants from alignment files), then the sequence can be
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retrieved using the [`reconstruct!`](@ref) function.
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```@repl call_variants
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human2 = copy(bovine);
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reconstruct!(human2, bos_human_variant)
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human2 == bovine
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human2 == human
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```
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66
docs/src/variations.md
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66
docs/src/variations.md
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```@meta
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CurrentModule = SequenceVariation
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```
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# Working with individual variations
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## Construction
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Individual [`Variation`](@ref)s can be made using a reference sequence and
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string syntax
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| Variation type | Syntax | Interpretation | Example |
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|:--- |:--- |:--- |:--- |
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| Substitutions | `<REF><POS><ALT>` | `<ALT>` is substituted for `<REF>` in position `<POS>` | `"G16C"` |
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| 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"` |
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| Insertions | `<POS><ALT>` | `<ALT>` is inserted between positions `<POS>` and `<POS>+1` | `"11T"` |
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```@repl
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using BioSequences: @dna_str
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using SequenceVariation
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bovine_ins = dna"GACCGGCTGCATTCGAGGCTGCCAGCAAGCAG"
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Variation(bovine_ins, "C4A")
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mutation(ans)
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typeof(mutation(Variation(bovine_ins, "Δ13-14")))
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mutation(Variation(bovine_ins, "25ACA"))
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```
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## Extraction
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Sequence variations may also be extracted wholesale from a [`Variant`](@ref)
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using the [`variations`](@ref) function.
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```@setup call_variants
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using SequenceVariation, BioAlignments, BioSequences
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bovine = dna"GACCGGCTGCATTCGAGGCTGCCAGCAAGCAG";
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ovine = dna"GACCGGCTGCATTCGAGGCTGTCAGCAAACAG";
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human = dna"GACAGGCTGCATCAGAAGAGGCCATCAAGCAG";
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bos_ovis_alignment =
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PairwiseAlignment(AlignedSequence(ovine, Alignment("32M", 1, 1)), bovine);
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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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```
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```@repl call_variants
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variations(bos_ovis_variant)
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variations(bos_human_variant)
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```
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## Reference switching
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An individual variation can be mapped to a new reference sequence given an
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alignment between the new and old references using the [`translate`](@ref).
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```@repl call_variants
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ovis_human_alignment =
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PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), ovine)
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human_variation = first(variations(bos_ovis_variant))
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reference(ans) == bovine
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SequenceVariation.translate(human_variation, ovis_human_alignment)
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reference(ans) == bovine
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```
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