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Obitag, allow for reference sequences with bad taxid, which are discarded with the emission of a warning

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Former-commit-id: a8781da1afa86de9c34b008959f0705ae69fc64f
This commit is contained in:
Eric Coissac
2024-03-18 19:11:41 +01:00
parent aa07ef2127
commit b428c48353
2 changed files with 16 additions and 5 deletions
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4
pkg/obitax/lca.go
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@ -12,11 +12,11 @@ import (
func (t1 *TaxNode) LCA(t2 *TaxNode) (*TaxNode, error) { func (t1 *TaxNode) LCA(t2 *TaxNode) (*TaxNode, error) {
if t1 == nil { if t1 == nil {
log.Fatalf("Try to get LCA of nil taxon") log.Panicf("Try to get LCA of nil taxon")
} }
if t2 == nil { if t2 == nil {
log.Fatalf("Try to get LCA of nil taxon") log.Panicf("Try to get LCA of nil taxon")
} }
p1, err1 := t1.Path() p1, err1 := t1.Path()

17
pkg/obitools/obitag/obitag.go
View File

@ -278,11 +278,22 @@ func CLIAssignTaxonomy(iterator obiiter.IBioSequence,
buffer := make([]byte, 0, 1000) buffer := make([]byte, 0, 1000)
for i, seq := range references { var err error
refcounts[i] = obikmer.Count4Mer(seq, &buffer, nil) j:= 0
taxa[i], _ = taxo.Taxon(seq.Taxid()) for _, seq := range references {
references[j] = seq
refcounts[j] = obikmer.Count4Mer(seq, &buffer, nil)
taxa[j], err = taxo.Taxon(seq.Taxid())
if err == nil {
j++
} else {
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]
refcounts = refcounts[:j]
worker := IdentifySeqWorker(references, refcounts, taxa, taxo, CLIRunExact()) worker := IdentifySeqWorker(references, refcounts, taxa, taxo, CLIRunExact())
return iterator.MakeIWorker(worker, false, obioptions.CLIParallelWorkers(), 0) return iterator.MakeIWorker(worker, false, obioptions.CLIParallelWorkers(), 0)