obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

Changes to be committed:

Browse Source 
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
Download Patch File Download Diff File Expand all files Collapse all files

36
pkg/obiseq/taxonomy_methods.go
View File

@ -1,6 +1,10 @@
package obiseq
import (
"fmt"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
)
@ -12,6 +16,23 @@ func (s *BioSequence) Taxon(taxonomy *obitax.Taxonomy) *obitax.Taxon {
return taxonomy.Taxon(taxid)
}
// SetTaxid sets the taxid for the BioSequence.
//
// Parameters:
//
// taxid - the taxid to set.
func (s *BioSequence) SetTaxid(taxid string) {
if taxid == "" {
taxid = "NA"
}
s.SetAttribute("taxid", taxid)
}
func (s *BioSequence) SetTaxon(taxon *obitax.Taxon) {
taxid := taxon.String()
s.SetTaxid(taxid)
}
// Taxid returns the taxonomic ID associated with the BioSequence.
//
// It retrieves the "taxid" attribute from the BioSequence's attributes map.
@ -25,7 +46,20 @@ func (s *BioSequence) Taxid() (taxid string) {
taxid = s.taxon.String()
ok = true
} else {
taxid, ok = s.GetStringAttribute("taxid")
var ta interface{}
ta, ok = s.GetAttribute("taxid")
if ok {
switch tv := ta.(type) {
case string:
taxid = tv
case int:
taxid = fmt.Sprintf("%d", tv)
case float64:
taxid = fmt.Sprintf("%d", int(tv))
default:
log.Fatalf("Taxid: %v is not a string or an integer (%T)", ta, ta)
}
}
}
if !ok {