millironx/SequenceVariation.jl
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SequenceVariation.jl/docs/src/compare.md

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CurrentModule = SequenceVariation

Comparing variations in sequences

Checking for variations in a known haplotype

Looking for a known Variation within a Haplotype is efficiently accomplished using the in operator.

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_haplotype = Haplotype(bos_ovis_alignment)
bos_human_haplotype = Haplotype(bos_human_alignment)

println("\tOvis aires\tHomo sapiens")
for v in vcat(variations(bos_ovis_haplotype), variations(bos_human_haplotype))
    is_sheep = v in bos_ovis_haplotype
    is_human = v in bos_human_haplotype
    println("$v\t$is_sheep\t\t$is_human")
end

Constructing new haplotypes based on other variations

New haplotypes can be constructed using variations. This might be useful to pool variations found on different reads or to filter variations from a haplotype that aren't validated by another haplotype.

sheeple = vcat(variations(bos_ovis_haplotype), variations(bos_human_haplotype));
Haplotype(bovine, sheeple)
reconstruct!(bovine, ans)