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BioSequences v3 and BioSymbols v5 #72

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merged 5 commits into from
Jun 8, 2022
+16 −15
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BioSequences v3 and BioSymbols v5 #72

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ff57108
Increment compatibilities for BioSequences v3
CiaranOMara Mar 22, 2022
9a61761
Adjust test matrix for minimum compatibility
CiaranOMara Jun 8, 2022
6e1a548
Remove doctest version adjustments
CiaranOMara Jun 7, 2022
7e6d24b
Doctest corrections
CiaranOMara Jun 8, 2022
8125f96
CHANGELOG entries
CiaranOMara Jun 8, 2022
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1 change: 0 additions & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -13,7 +13,6 @@ jobs:
fail-fast: false
matrix:
version:
- '1.0'
- '1.6'
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Oh man, this is long overdue...

- '1'
- 'nightly'
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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -20,11 +20,16 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- *master* set as the main development branch (#49, #50)
- Updated chat links (#ebea200c)
- Expanded test matrix, adding julia v1.6 (#77)
- Incremented BioSequences compatibility to v3 (#72)
- Incremented BioSymbols compatibility to v5 (#72)
- Adjusted test matrix for minimum compatibility (#72)
- Updated doctests (#72)

### Removed
- :exclamation: Reverted the use of *BioJulia* registry,
the package switched to [General Julia Registry](https://github.com/JuliaRegistries/General) (#48)
- :exclamation: Removed Gitter chat links (#ebea200c)
- :exclamation: Dropped support for julia less than v1.6 (#72)

### Fixed
- Doctests (#78)
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4 changes: 2 additions & 2 deletions Project.toml
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Expand Up @@ -12,8 +12,8 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"

[compat]
BioGenerics = "0.1"
BioSequences = "2"
BioSymbols = "4"
BioSequences = "3"
BioSymbols = "5"
IntervalTrees = "1"
julia = "1"

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8 changes: 4 additions & 4 deletions docs/src/pairalign.md
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Expand Up @@ -74,7 +74,7 @@ julia> s2 = dna"ACCTGGTATGATAGCG";
julia> scoremodel = AffineGapScoreModel(EDNAFULL, gap_open=-5, gap_extend=-1);

julia> res = pairalign(GlobalAlignment(), s1, s2, scoremodel) # run pairwise alignment
PairwiseAlignmentResult{Int64, BioSequences.LongDNASeq, BioSequences.LongDNASeq}:
PairwiseAlignmentResult{Int64, BioSequences.LongSequence{BioSequences.DNAAlphabet{4}}, BioSequences.LongSequence{BioSequences.DNAAlphabet{4}}}:
score: 13
seq: 0 -CCTAGG------AGGG 10
||| || || |
Expand All @@ -85,7 +85,7 @@ julia> score(res) # get the achieved score of this alignment
13

julia> aln = alignment(res)
PairwiseAlignment{BioSequences.LongDNASeq, BioSequences.LongDNASeq}:
PairwiseAlignment{BioSequences.LongSequence{BioSequences.DNAAlphabet{4}}, BioSequences.LongSequence{BioSequences.DNAAlphabet{4}}}:
seq: 0 -CCTAGG------AGGG 10
||| || || |
ref: 1 ACCT-GGTATGATAGCG 16
Expand Down Expand Up @@ -126,11 +126,11 @@ julia> collect(aln) # pairwise alignment is iterable
(DNA_G, DNA_C)
(DNA_G, DNA_G)

julia> LongDNASeq([x for (x, _) in aln]) # create aligned `s1` with gaps
julia> LongDNA{4}([x for (x, _) in aln]) # create aligned `s1` with gaps
17nt DNA Sequence:
-CCTAGG------AGGG

julia> LongDNASeq([y for (_, y) in aln]) # create aligned `s2` with gaps
julia> LongDNA{4}([y for (_, y) in aln]) # create aligned `s2` with gaps
17nt DNA Sequence:
ACCT-GGTATGATAGCG

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4 changes: 2 additions & 2 deletions src/submat.jl
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Expand Up @@ -137,12 +137,12 @@ end

# Return the row/column index of `nt`.
function index(nt::BioSymbols.NucleicAcid)
return convert(Int, nt)
return reinterpret(Int8, nt)
end

# Return the row/column index of `aa`.
function index(aa::BioSymbols.AminoAcid)
return convert(Int, aa) + 1
return reinterpret(Int8, aa) + 1
end


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9 changes: 3 additions & 6 deletions test/runtests.jl
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Expand Up @@ -1012,15 +1012,12 @@ end
seq2 = aa"EPSHPKAVSPTETKRCPTEKVQHLPVSAPPKITQFLKAEASKEIAKLTCVVESSVLRA"
model = AffineGapScoreModel(BLOSUM62, gap_open=-10, gap_extend=-1)
aln = alignment(pairalign(GlobalAlignment(), seq1, seq2, model))
# julia 1.6+ uses shorter type aliases when printing types
seqtype = VERSION >= v"1.6" ?
"BioSequences.LongAminoAcidSeq" :
"BioSequences.LongSequence{BioSequences.AminoAcidAlphabet}"
seqtype = "BioSequences.LongAA"
buf = IOBuffer()
show(buf, MIME"text/plain"(), aln)
@test String(take!(buf)) ==
"""
PairwiseAlignment{$(seqtype),$(VERSION >= v"1.6" ? " " : "")$(seqtype)}:
PairwiseAlignment{$seqtype, $seqtype}:
seq: 1 EPVTSHPKAVSPTETK--PTEKGQHLPVSAPPKITQSLKAEASKDIAKLTCAVESSALCA 58
|| |||||||||||| |||| ||||||||||||| ||||||| |||||| |||| | |
ref: 1 EP--SHPKAVSPTETKRCPTEKVQHLPVSAPPKITQFLKAEASKEIAKLTCVVESSVLRA 58
Expand All @@ -1046,7 +1043,7 @@ end
buf = IOBuffer()
print(buf, (aln,))
@test String(take!(buf)) == (
"""(PairwiseAlignment{$seqtype,$(VERSION >= v"1.6" ? " " : "")$(seqtype)}""" *
"""(PairwiseAlignment{$seqtype, $seqtype}""" *
"""(lengths=(58, 58)/60),)"""
)
# Result from EMBOSS Needle:
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