mirror of
https://github.com/MillironX/SequenceVariation.jl.git
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48 lines
1.4 KiB
Markdown
48 lines
1.4 KiB
Markdown
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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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