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Changes to be committed:

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modified:   cmd/obitools/obitag/main.go
	modified:   cmd/obitools/obitag2/main.go
	modified:   go.mod
	modified:   go.sum
	modified:   pkg/obiformats/ncbitaxdump/read.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/attributes.go
	modified:   pkg/obiseq/taxonomy_lca.go
	modified:   pkg/obiseq/taxonomy_methods.go
	modified:   pkg/obiseq/taxonomy_predicate.go
	modified:   pkg/obitax/inner.go
	modified:   pkg/obitax/lca.go
	new file:   pkg/obitax/taxid.go
	modified:   pkg/obitax/taxon.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonslice.go
	modified:   pkg/obitools/obicleandb/obicleandb.go
	modified:   pkg/obitools/obigrep/options.go
	modified:   pkg/obitools/obilandmark/obilandmark.go
	modified:   pkg/obitools/obilandmark/options.go
	modified:   pkg/obitools/obirefidx/famlilyindexing.go
	modified:   pkg/obitools/obirefidx/geomindexing.go
	modified:   pkg/obitools/obirefidx/obirefidx.go
	modified:   pkg/obitools/obirefidx/options.go
	modified:   pkg/obitools/obitag/obigeomtag.go
	modified:   pkg/obitools/obitag/obitag.go
	modified:   pkg/obitools/obitag/options.go
	modified:   pkg/obiutils/strings.go
This commit is contained in:
Eric Coissac
2024-12-19 13:36:59 +01:00
parent f41a6fbb60
commit 795df34d1a
28 changed files with 590 additions and 280 deletions
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9
pkg/obiseq/taxonomy_predicate.go
View File

@@ -47,14 +47,7 @@ func IsAValidTaxon(taxonomy *obitax.Taxonomy, withAutoCorrection ...bool) Sequen
// A function that takes a taxonomy and a taxid as arguments and returns a function that takes a
// pointer to a BioSequence as an argument and returns a boolean.
func IsSubCladeOf(taxonomy *obitax.Taxonomy, taxid string) SequencePredicate {
parent := taxonomy.Taxon(taxid)
if parent == nil {
log.Fatalf("Cannot find taxon : %s in taxonomy %s",
taxid,
taxonomy.Name())
}
func IsSubCladeOf(taxonomy *obitax.Taxonomy, parent *obitax.Taxon) SequencePredicate {
f := func(sequence *BioSequence) bool {
taxon := sequence.Taxon(taxonomy)