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

Patch a small bug on json write

Browse Source
This commit is contained in:
Eric Coissac
2024-12-20 19:42:03 +01:00
parent abfa8f357a
commit 5d0f996625
14 changed files with 458 additions and 79 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
pkg/obiseq/taxonomy_classifier.go
View File

@ -19,6 +19,8 @@ func TaxonomyClassifier(taxonomicRank string,
taxonomy *obitax.Taxonomy,
abortOnMissing bool) *BioSequenceClassifier {
taxonomy = taxonomy.OrDefault(true)
keys := make(map[*obitax.TaxNode]int)
codes := make([]*obitax.TaxNode, 1)
codes[0] = nil

15
pkg/obiseq/taxonomy_lca.go
View File

@ -12,6 +12,8 @@ func (sequence *BioSequence) TaxonomicDistribution(taxonomy *obitax.Taxonomy) ma
taxids := sequence.StatsOn(MakeStatsOnDescription("taxid"), "na")
taxons := make(map[*obitax.TaxNode]int, len(taxids))
taxonomy = taxonomy.OrDefault(true)
for taxid, v := range taxids {
t := taxonomy.Taxon(taxid)
if t == nil {
@ -27,6 +29,9 @@ func (sequence *BioSequence) TaxonomicDistribution(taxonomy *obitax.Taxonomy) ma
}
func (sequence *BioSequence) LCA(taxonomy *obitax.Taxonomy, threshold float64) (*obitax.Taxon, float64, int) {
taxonomy = taxonomy.OrDefault(true)
taxons := sequence.TaxonomicDistribution(taxonomy)
paths := make(map[*obitax.TaxNode]*obitax.TaxonSlice, len(taxons))
answer := (*obitax.TaxNode)(nil)
@ -34,11 +39,11 @@ func (sequence *BioSequence) LCA(taxonomy *obitax.Taxonomy, threshold float64) (
granTotal := 0
for t, w := range taxons {
p := (&obitax.Taxon{Taxonomy: taxonomy,
Node: t,
}).Path()
taxon := &obitax.Taxon{Taxonomy: taxonomy, Node: t}
p := taxon.Path()
if p == nil {
log.Panicf("Sequence %s: taxonomic path cannot be retreived from Taxid %d : %v", sequence.Id(), t.String(taxonomy.Code()))
log.Panicf("Sequence %s: taxonomic path cannot be retreived from Taxid : %s", sequence.Id(), taxon.String())
}
p.Reverse(true)
@ -103,6 +108,8 @@ func (sequence *BioSequence) LCA(taxonomy *obitax.Taxonomy, threshold float64) (
func AddLCAWorker(taxonomy *obitax.Taxonomy, slot_name string, threshold float64) SeqWorker {
taxonomy = taxonomy.OrDefault(true)
if !strings.HasSuffix(slot_name, "taxid") {
slot_name = slot_name + "_taxid"
}

32
pkg/obiseq/taxonomy_methods.go
View File

@ -9,6 +9,7 @@ import (
)
func (s *BioSequence) Taxon(taxonomy *obitax.Taxonomy) *obitax.Taxon {
taxid := s.Taxid()
if taxid == "NA" {
return nil
@ -21,16 +22,39 @@ func (s *BioSequence) Taxon(taxonomy *obitax.Taxonomy) *obitax.Taxon {
// Parameters:
//
// taxid - the taxid to set.
func (s *BioSequence) SetTaxid(taxid string) {
func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
if taxid == "" {
taxid = "NA"
} else {
taxonomy := obitax.DefaultTaxonomy()
taxon := (*obitax.Taxon)(nil)
if taxonomy != nil {
taxon = taxonomy.Taxon(taxid)
}
if taxon != nil {
taxid = taxon.String()
}
}
if len(rank) > 0 {
r := rank[0]
s.SetAttribute(r+"_taxid", taxid)
} else {
s.SetAttribute("taxid", taxid)
}
s.SetAttribute("taxid", taxid)
}
func (s *BioSequence) SetTaxon(taxon *obitax.Taxon) {
func (s *BioSequence) SetTaxon(taxon *obitax.Taxon, rank ...string) {
taxid := taxon.String()
s.SetTaxid(taxid)
if len(rank) > 0 {
r := rank[0]
s.SetAttribute(r+"_taxid", taxid)
} else {
s.SetAttribute("taxid", taxid)
}
}
// Taxid returns the taxonomic ID associated with the BioSequence.