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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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14
pkg/obitax/ncbitaxdump_read.go
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@ -91,7 +91,13 @@ func loadNameTable(reader io.Reader, taxonomy *Taxonomy, onlysn bool) int {
if !onlysn || classname == "scientific name" {
n++
taxonomy.Taxon(taxid).SetName(name, classname)
taxon, err := taxonomy.Taxon(taxid)
if err != nil {
log.Fatalf("%s: is unknown from the taxonomy", taxid)
}
taxon.SetName(name, classname)
}
}
@ -196,7 +202,11 @@ func LoadNCBITaxDump(directory string, onlysn bool) (*Taxonomy, error) {
n = loadMergedTable(buffered, taxonomy)
log.Printf("%d merged taxa read\n", n)
root := taxonomy.Taxon("1")
root, err := taxonomy.Taxon("1")
if err != nil {
log.Fatal("cannot find the root taxon (1) in the NCBI tax dump")
}
taxonomy.SetRoot(root)
return taxonomy, nil