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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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20
pkg/obitools/obilandmark/obilandmark.go
View File

@@ -11,7 +11,6 @@ import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obistats"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obifind"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obirefidx"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"github.com/schollz/progressbar/v3"
@@ -155,19 +154,20 @@ func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSeque
}
}
if obifind.CLIHasSelectedTaxonomy() {
taxo, err := obifind.CLILoadSelectedTaxonomy()
if err != nil {
log.Fatal(err)
if obioptions.CLIHasSelectedTaxonomy() {
taxo := obitax.DefaultTaxonomy()
if taxo == nil {
log.Fatal("No taxonomy available")
}
taxa := make(obitax.TaxonSet, len(library))
taxa := obitax.DefaultTaxonomy().NewTaxonSlice(len(library), len(library))
for i, seq := range library {
taxa[i], err = taxo.Taxon(seq.Taxid())
if err != nil {
log.Fatal(err)
taxon := seq.Taxon(taxo)
if taxon == nil {
log.Fatal("%s: Cannot identify taxid %s in %s", seq.Id(), seq.Taxid(), taxo.Name())
}
taxa.Set(i, taxon)
}
pbopt := make([]progressbar.Option, 0, 5)
@@ -182,7 +182,7 @@ func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSeque
bar := progressbar.NewOptions(len(library), pbopt...)
for i, seq := range library {
idx := obirefidx.GeomIndexSesquence(i, library, &taxa, taxo)
idx := obirefidx.GeomIndexSesquence(i, library, taxa, taxo)
seq.SetOBITagGeomRefIndex(idx)
if i%10 == 0 {

4
pkg/obitools/obilandmark/options.go
View File

@@ -1,8 +1,8 @@
package obilandmark
import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obifind"
"github.com/DavidGamba/go-getoptions"
)
@@ -25,7 +25,7 @@ func LandmarkOptionSet(options *getoptions.GetOpt) {
func OptionSet(options *getoptions.GetOpt) {
obiconvert.InputOptionSet(options)
obiconvert.OutputOptionSet(options)
obifind.LoadTaxonomyOptionSet(options, false, false)
obioptions.LoadTaxonomyOptionSet(options, false, false)
LandmarkOptionSet(options)
}