obitools/obitools4
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Rename obifind obitaxonomy and introduce the new CSV format for taxonomy.

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This commit is contained in:
Eric Coissac
2025-01-29 10:45:26 +01:00
parent c50a0f409d
commit 00f2dc2697
11 changed files with 4571 additions and 55 deletions
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24
cmd/obitools/obifind/main.go → cmd/obitools/obitaxonomy/main.go
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@ -6,25 +6,29 @@ import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obifind"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitaxonomy"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
func main() {
optionParser := obioptions.GenerateOptionParser(obifind.OptionSet)
optionParser := obioptions.GenerateOptionParser(obitaxonomy.OptionSet)
_, args := optionParser(os.Args)
var iterator *obitax.ITaxon
switch {
case obifind.CLIRequestsPathForTaxid() != "NA":
taxon := obitax.DefaultTaxonomy().Taxon(obifind.CLIRequestsPathForTaxid())
case obitaxonomy.CLIDumpSubtaxonomy():
iterator = obitaxonomy.CLISubTaxonomyIterator()
case obitaxonomy.CLIRequestsPathForTaxid() != "NA":
taxon := obitax.DefaultTaxonomy().Taxon(obitaxonomy.CLIRequestsPathForTaxid())
if taxon == nil {
log.Fatalf("Cannot identify the requested taxon: %s",
obifind.CLIRequestsPathForTaxid())
obitaxonomy.CLIRequestsPathForTaxid())
}
s := taxon.Path()
@ -35,7 +39,7 @@ func main() {
iterator = s.Iterator()
if obifind.CLIWithQuery() {
if obitaxonomy.CLIWithQuery() {
iterator = iterator.AddMetadata("query", taxon.String())
}
@ -45,8 +49,8 @@ func main() {
iters := make([]*obitax.ITaxon, len(args))
for i, pat := range args {
ii := obitax.DefaultTaxonomy().IFilterOnName(pat, obifind.CLIFixedPattern(), true)
if obifind.CLIWithQuery() {
ii := obitax.DefaultTaxonomy().IFilterOnName(pat, obitaxonomy.CLIFixedPattern(), true)
if obitaxonomy.CLIWithQuery() {
ii = ii.AddMetadata("query", pat)
}
iters[i] = ii
@ -59,8 +63,8 @@ func main() {
}
}
iterator = obifind.CLITaxonRestrictions(iterator)
obifind.CLICSVTaxaWriter(iterator, true)
iterator = obitaxonomy.CLITaxonRestrictions(iterator)
obitaxonomy.CLICSVTaxaWriter(iterator, true)
obiutils.WaitForLastPipe()