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add the --download-ncbi option to obitaxonomy

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This commit is contained in:
Eric Coissac
2025-01-29 12:38:39 +01:00
parent b6b18c0fa1
commit 8a28c9ae7c
5 changed files with 87 additions and 3 deletions
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20
pkg/obitools/obitaxonomy/obifind.go → pkg/obitools/obitaxonomy/obitaxonomy.go
View File

@@ -1,10 +1,15 @@
package obitaxonomy
import (
"fmt"
"time"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiitercsv"
"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/obiutils"
log "github.com/sirupsen/logrus"
)
@@ -73,3 +78,18 @@ func CLICSVTaxaIterator(iterator *obitax.ITaxon) *obiitercsv.ICSVRecord {
func CLICSVTaxaWriter(iterator *obitax.ITaxon, terminalAction bool) *obiitercsv.ICSVRecord {
return obicsv.CLICSVWriter(CLICSVTaxaIterator(iterator), terminalAction)
}
func CLIDownloadNCBITaxdump() error {
now := time.Now()
dateStr := now.Format("20060102") // In Go, this specific date is used as reference for formatting
filename := fmt.Sprintf("ncbitaxo_%s.tgz", dateStr)
if obiconvert.CLIOutPutFileName() != "-" {
filename = obiconvert.CLIOutPutFileName()
}
log.Infof("Downloading NCBI Taxdump to %s", filename)
return obiutils.DownloadFile("https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz", filename)
}

11
pkg/obitools/obitaxonomy/options.go
View File

@@ -22,6 +22,7 @@ var __taxid_path__ = "NA"
var __taxid_sons__ = "NA"
var __restrict_rank__ = ""
var __to_dump__ = ""
var __download_ncbi__ = false
func FilterTaxonomyOptionSet(options *getoptions.GetOpt) {
options.BoolVar(&__rank_list__, "rank-list", false,
@@ -34,7 +35,7 @@ func FilterTaxonomyOptionSet(options *getoptions.GetOpt) {
}
func OptionSet(options *getoptions.GetOpt) {
obioptions.LoadTaxonomyOptionSet(options, true, true)
obioptions.LoadTaxonomyOptionSet(options, false, true)
FilterTaxonomyOptionSet(options)
options.BoolVar(&__fixed_pattern__, "fixed", false,
options.Alias("F"),
@@ -70,6 +71,10 @@ func OptionSet(options *getoptions.GetOpt) {
options.ArgName("TAXID"),
options.Description("Dump a sub-taxonomy corresponding to the precised clade"),
)
options.BoolVar(&__download_ncbi__, "download-ncbi", __download_ncbi__,
options.Description("Download the current NCBI taxonomy taxdump"),
)
}
func CLITaxonomicalRestrictions() (*obitax.TaxonSet, error) {
@@ -144,3 +149,7 @@ func CLIDumpSubtaxonomy() bool {
func CLISubTaxonomyNode() string {
return __to_dump__
}
func CLIDownloadNCBI() bool {
return __download_ncbi__
}