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Adds possibility to extract a taxonomy from taxonomic path included in sequence files

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This commit is contained in:
Eric Coissac
2025-01-30 11:18:21 +01:00
parent 2452aef7a9
commit 0df082da06
20 changed files with 460 additions and 173 deletions
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8
pkg/obiformats/fastseq_json_header.go
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@ -292,8 +292,8 @@ func _parse_json_header_(header string, sequence *obiseq.BioSequence) string {
case skey == "taxid":
if dataType == jsonparser.Number || dataType == jsonparser.String {
taxid := obiutils.UnsafeString(value)
taxon := taxonomy.Taxon(taxid)
if taxon != nil {
taxon, err := taxonomy.Taxon(taxid)
if err == nil {
sequence.SetTaxon(taxon)
} else {
sequence.SetTaxid(string(value))
@ -307,9 +307,9 @@ func _parse_json_header_(header string, sequence *obiseq.BioSequence) string {
rank, _ := obiutils.SplitInTwo(skey, '_')
taxid := obiutils.UnsafeString(value)
taxon := taxonomy.Taxon(taxid)
taxon, err := taxonomy.Taxon(taxid)
if taxon != nil {
if err == nil {
taxid = taxon.String()
} else {
taxid = string(value)