millironx/SequenceVariation.jl
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Apply Blue style to tests file

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This commit is contained in:
Thomas A. Christensen II 2023-01-03 21:59:42 -06:00
parent fb9ab68cca
commit d29764d2bc
1 changed files with 17 additions and 7 deletions
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24
test/runtests.jl
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@ -29,7 +29,7 @@ using BioSequences
using SequenceVariation
using Test
const DNA_MODEL = BioAlignments.AffineGapScoreModel(EDNAFULL, gap_open=-25, gap_extend=-2)
const DNA_MODEL = BioAlignments.AffineGapScoreModel(EDNAFULL; gap_open=-25, gap_extend=-2)
align(a::BioSequence, b::BioSequence) = pairalign(GlobalAlignment(), a, b, DNA_MODEL).aln
seq1 = ungap!(dna"--ATGCGTGTTAGCAAC--TTATCGCG")
@ -112,23 +112,33 @@ end
refseq = dna"GATTACA"
mutseq = dna"GATTACAAAA"
refvar = Variant(refseq, SequenceVariation.Edit{typeof(refseq), eltype(refseq)}[])
refvar = Variant(refseq, SequenceVariation.Edit{typeof(refseq),eltype(refseq)}[])
# Test for ending soft clip
@test Variant(PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3S", 1, 1)), refseq)) == refvar
@test Variant(
PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3S", 1, 1)), refseq)
) == refvar
# Test for ending soft+hard clip
@test Variant(PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3S2H", 1, 1)), refseq)) == refvar
@test Variant(
PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3S2H", 1, 1)), refseq)
) == refvar
# Test that ending insertions are still valid
@test length(Variant(PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3I", 1, 1)), refseq)).edits) == 1
@test length(
Variant(
PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3I", 1, 1)), refseq)
).edits,
) == 1
# Test that out-of-bounds bases are still caught
@test_throws BoundsError Variant(PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3X", 1, 1)), refseq))
@test_throws BoundsError Variant(
PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3X", 1, 1)), refseq)
)
end
@testset "Aqua" begin
Aqua.test_ambiguities(SequenceVariation;recursive=false)
Aqua.test_ambiguities(SequenceVariation; recursive=false)
# TODO: Refactor `Edit` so that this test doesn't fail
# TODO: This test _should_ be set to @test_fails, but Aqua's syntax doesn't allow that
# Aqua.test_unbound_args(SequenceVariation)