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Patch a small bug on json write

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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
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15
pkg/obiseq/taxonomy_lca.go
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@@ -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"
}