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Patch a bug in obitag on the identification of the best match

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Former-commit-id: e551b3b83e79a517dd5409ea8112fb005c39c2ee
This commit is contained in:
Eric Coissac
2024-04-03 12:30:40 +02:00
parent e25c3b7365
commit bf41d16e67
3 changed files with 15 additions and 12 deletions
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2
Release-notes.md
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@ -33,6 +33,8 @@
### Bug fixes ### Bug fixes
- Fix a bug in the parsing of the JSON header of FASTA and FASTQ files occurring when a string includes a curly - Fix a bug in the parsing of the JSON header of FASTA and FASTQ files occurring when a string includes a curly
brace. brace.
- Fix a bug in the function looking for the closest match in `obitag`. This error led to some wrong taxonomic
assignment.
## February 16th, 2024. Release 4.1.2 ## February 16th, 2024. Release 4.1.2

23
pkg/obitools/obitag/obitag.go
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@ -101,10 +101,6 @@ func FindClosests(sequence *obiseq.BioSequence,
ref := references[order] ref := references[order]
score := int(1e9) score := int(1e9)
if maxe != -1 {
wordmin = obiutils.MaxInt(sequence.Len(), ref.Len()) - 3 - 4*maxe
}
if cw[order] < wordmin { if cw[order] < wordmin {
break break
} }
@ -124,12 +120,17 @@ func FindClosests(sequence *obiseq.BioSequence,
} }
} }
//
// We have found a better candidate than never
//
if maxe == -1 || score < maxe { if maxe == -1 || score < maxe {
bests = bests[:0] bests = bests[:0] // Empty the best lists
bestidxs = bestidxs[:0] bestidxs = bestidxs[:0] //
maxe = score
maxe = score // Memorize the best scores
wordmin = max(0, max(sequence.Len(), ref.Len())-3-4*maxe)
bestId = float64(lcs) / float64(alilength) bestId = float64(lcs) / float64(alilength)
// log.Println(ref.Id(), maxe, bestId,bestidxs) // log.Warnln(sequence.Id(), ref.Id(), cw[order], maxe, bestId, wordmin)
} }
if score == maxe { if score == maxe {
@ -279,7 +280,7 @@ func CLIAssignTaxonomy(iterator obiiter.IBioSequence,
buffer := make([]byte, 0, 1000) buffer := make([]byte, 0, 1000)
var err error var err error
j:= 0 j := 0
for _, seq := range references { for _, seq := range references {
references[j] = seq references[j] = seq
refcounts[j] = obikmer.Count4Mer(seq, &buffer, nil) refcounts[j] = obikmer.Count4Mer(seq, &buffer, nil)
@ -287,12 +288,12 @@ func CLIAssignTaxonomy(iterator obiiter.IBioSequence,
if err == nil { if err == nil {
j++ j++
} else { } else {
log.Warnf("Taxid %d is not described in the taxonomy. Sequence %s is discared from the reference database",seq.Taxid(),seq.Id()) log.Warnf("Taxid %d is not described in the taxonomy. Sequence %s is discared from the reference database", seq.Taxid(), seq.Id())
} }
} }
references = references[:j] references = references[:j]
refcounts = refcounts[:j] refcounts = refcounts[:j]
worker := IdentifySeqWorker(references, refcounts, taxa, taxo, CLIRunExact()) worker := IdentifySeqWorker(references, refcounts, taxa, taxo, CLIRunExact())

2
pkg/obitools/obitag/options.go
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@ -34,7 +34,7 @@ func TagOptionSet(options *getoptions.GetOpt) {
// options.BoolVar(&_RunExact, "exact", _RunExact, // options.BoolVar(&_RunExact, "exact", _RunExact,
// options.Alias("E"), // options.Alias("E"),
// options.Description("Unactivate the heuristic limatitating the sequence comparisons")) // options.Description("Desactivate the heuristic limitating the sequence comparisons"))
} }