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Adds the ability to read gzip-tar file for the taxonomy dump

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This commit is contained in:
Eric Coissac
2025-01-24 11:47:59 +01:00
parent ffd67252c3
commit 3137c1f841
17 changed files with 305 additions and 64 deletions
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28
pkg/obioptions/options.go
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@ -6,8 +6,8 @@ import (
"os"
"runtime"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats/ncbitaxdump"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitaxformat"
log "github.com/sirupsen/logrus"
"github.com/DavidGamba/go-getoptions"
@ -32,7 +32,7 @@ var _Quality_Shift_Input = byte(33)
var _Quality_Shift_Output = byte(33)
var _Read_Qualities = true
var __taxdump__ = ""
var __taxonomy__ = ""
var __alternative_name__ = false
type ArgumentParser func([]string) (*getoptions.GetOpt, []string)
@ -131,8 +131,8 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
log.Info(" go tool pprof -http=127.0.0.1:8080 'http://localhost:6060/debug/pprof/block'")
}
if options.Called("taxdump") {
taxonomy, err := ncbitaxdump.LoadNCBITaxDump(CLISelectedNCBITaxDump(),
if options.Called("taxonomy") {
taxonomy, err := obitaxformat.LoadTaxonomy(CLISelectedTaxonomy(),
!CLIAreAlternativeNamesSelected())
if err != nil {
log.Fatalf("Loading taxonomy error: %v", err)
@ -186,14 +186,14 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
func LoadTaxonomyOptionSet(options *getoptions.GetOpt, required, alternatiive bool) {
if required {
options.StringVar(&__taxdump__, "taxdump", "",
options.StringVar(&__taxonomy__, "taxonomy", "",
options.Alias("t"),
options.Required(),
options.Description("Points to the directory containing the NCBI Taxonomy database dump."))
options.Description("Path to the taxonomy database."))
} else {
options.StringVar(&__taxdump__, "taxdump", "",
options.StringVar(&__taxonomy__, "taxonomy", "",
options.Alias("t"),
options.Description("Points to the directory containing the NCBI Taxonomy database dump."))
options.Description("Path to the taxonomy database."))
}
if alternatiive {
options.BoolVar(&__alternative_name__, "alternative-names", false,
@ -462,12 +462,12 @@ func SetParallelFilesRead(n int) {
_ParallelFilesRead = n
}
func CLISelectedNCBITaxDump() string {
return __taxdump__
func CLISelectedTaxonomy() string {
return __taxonomy__
}
func CLIHasSelectedTaxonomy() bool {
return __taxdump__ != ""
return __taxonomy__ != ""
}
func CLIAreAlternativeNamesSelected() bool {
@ -479,8 +479,8 @@ func CLILoadSelectedTaxonomy() (*obitax.Taxonomy, error) {
return obitax.DefaultTaxonomy(), nil
}
if CLISelectedNCBITaxDump() != "" {
taxonomy, err := ncbitaxdump.LoadNCBITaxDump(CLISelectedNCBITaxDump(),
if CLISelectedTaxonomy() != "" {
taxonomy, err := obitaxformat.LoadTaxonomy(CLISelectedTaxonomy(),
!CLIAreAlternativeNamesSelected())
if err != nil {
return nil, err
@ -489,5 +489,5 @@ func CLILoadSelectedTaxonomy() (*obitax.Taxonomy, error) {
return taxonomy, nil
}
return nil, errors.New("no NCBI taxdump selected using option -t|--taxdump")
return nil, errors.New("no taxonomy selected using option -t|--taxonomy")
}