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a functional new version of obifind

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This commit is contained in:
Eric Coissac
2024-11-24 19:33:24 +01:00
parent 36327c79c8
commit 3d06978808
21 changed files with 1805 additions and 343 deletions
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10
pkg/obitools/obiannotate/obiannotate.go
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@@ -207,7 +207,7 @@ func EvalAttributeWorker(expression map[string]string) obiseq.SeqWorker {
func AddTaxonAtRankWorker(taxonomy *obitax.Taxonomy, ranks ...string) obiseq.SeqWorker {
f := func(s *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
for _, r := range ranks {
taxonomy.SetTaxonAtRank(s, r)
s.SetTaxonAtRank(taxonomy, r)
}
return obiseq.BioSequenceSlice{s}, nil
}
@@ -217,7 +217,7 @@ func AddTaxonAtRankWorker(taxonomy *obitax.Taxonomy, ranks ...string) obiseq.Seq
func AddTaxonRankWorker(taxonomy *obitax.Taxonomy) obiseq.SeqWorker {
f := func(s *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
taxonomy.SetTaxonomicRank(s)
s.SetTaxonomicRank(taxonomy)
return obiseq.BioSequenceSlice{s}, nil
}
@@ -226,7 +226,7 @@ func AddTaxonRankWorker(taxonomy *obitax.Taxonomy) obiseq.SeqWorker {
func AddScientificNameWorker(taxonomy *obitax.Taxonomy) obiseq.SeqWorker {
f := func(s *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
taxonomy.SetScientificName(s)
s.SetScientificName(taxonomy)
return obiseq.BioSequenceSlice{s}, nil
}
@@ -280,7 +280,7 @@ func CLIAnnotationWorker() obiseq.SeqWorker {
if CLISetTaxonomicPath() {
taxo := obigrep.CLILoadSelectedTaxonomy()
w := taxo.MakeSetPathWorker()
w := obiseq.MakeSetPathWorker(taxo)
annotator = annotator.ChainWorkers(w)
}
@@ -298,7 +298,7 @@ func CLIAnnotationWorker() obiseq.SeqWorker {
if CLIHasAddLCA() {
taxo := obigrep.CLILoadSelectedTaxonomy()
w := obitax.AddLCAWorker(taxo, CLILCASlotName(), CLILCAThreshold())
w := obiseq.AddLCAWorker(taxo, CLILCASlotName(), CLILCAThreshold())
annotator = annotator.ChainWorkers(w)
}