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Several bugs dicoverd during the doc writing

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This commit is contained in:
Eric Coissac
2025-04-04 16:59:27 +02:00
parent 03b5ce9397
commit 7542e33010
6 changed files with 38 additions and 11 deletions
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26
cmd/obitools/obitaxonomy/main.go
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@ -4,9 +4,11 @@ import (
"os"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiitercsv"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicsv"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitaxonomy"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@ -37,13 +39,25 @@ func main() {
}
switch {
case obitaxonomy.CLIDownloadNCBI():
err := obitaxonomy.CLIDownloadNCBITaxdump()
if err != nil {
log.Errorf("Cannot download NCBI taxonomy: %s", err.Error())
os.Exit(1)
}
case obitaxonomy.CLIAskForRankList():
newIter := obiitercsv.NewICSVRecord()
newIter.Add(1)
newIter.AppendField("rank")
go func() {
ranks := obitax.DefaultTaxonomy().RankList()
data := make([]obiitercsv.CSVRecord, len(ranks))
for i, rank := range ranks {
record := make(obiitercsv.CSVRecord)
record["rank"] = rank
data[i] = record
}
newIter.Push(obiitercsv.MakeCSVRecordBatch(obitax.DefaultTaxonomy().Name(), 0, data))
newIter.Close()
newIter.Done()
}()
obicsv.CLICSVWriter(newIter, true)
obiutils.WaitForLastPipe()
os.Exit(0)
case obitaxonomy.CLIExtractTaxonomy():