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Error when translating gaps #278

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merged 1 commit into from
Jun 22, 2023
Merged

Error when translating gaps #278

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2 changes: 1 addition & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "BioSequences"
uuid = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
authors = ["Sabrina Jaye Ward <[email protected]>", "Jakob Nissen <[email protected]>"]
version = "3.1.4"
version = "3.1.5"

[deps]
BioSymbols = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
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10 changes: 6 additions & 4 deletions src/geneticcode.jl
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Expand Up @@ -372,7 +372,11 @@ function translate!(aaseq::LongAA,
a = reinterpret(RNA, ntseq[3i-2])
b = reinterpret(RNA, ntseq[3i-1])
c = reinterpret(RNA, ntseq[3i])
if isambiguous(a) | isambiguous(b) | isambiguous(c)
if isgap(a) | isgap(b) | isgap(c)
error("Cannot translate nucleotide sequences with gaps.")
elseif iscertain(a) & iscertain(b) & iscertain(c)
aaseq[i] = code[unambiguous_codon(a, b, c)]
else
aa = try_translate_ambiguous_codon(code, a, b, c)
if aa === nothing
if allow_ambiguous_codons
Expand All @@ -382,8 +386,6 @@ function translate!(aaseq::LongAA,
end
end
aaseq[i] = aa
else
aaseq[i] = code[unambiguous_codon(a, b, c)]
end
end
alternative_start && !isempty(aaseq) && (@inbounds aaseq[1] = AA_M)
Expand Down Expand Up @@ -421,4 +423,4 @@ function try_translate_ambiguous_codon(code::GeneticCode,
end
end
return found
end
end
7 changes: 6 additions & 1 deletion test/translation.jl
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Expand Up @@ -75,6 +75,11 @@
# can't translate N
@test_throws Exception translate(rna"ACGUACGNU", allow_ambiguous_codons=false)

# Can't translate gaps
@test_throws Exception translate(dna"A-G")
@test_throws Exception translate(dna"---")
@test_throws Exception translate(dna"AACGAT-A-")

# issue #133
@test translate(rna"GAN") == aa"X"
end
end