diff --git a/cmd/obitools/obitaxonomy/main.go b/cmd/obitools/obitaxonomy/main.go index f1dcd4f..c067a47 100644 --- a/cmd/obitools/obitaxonomy/main.go +++ b/cmd/obitools/obitaxonomy/main.go @@ -20,6 +20,19 @@ func main() { var iterator *obitax.ITaxon + if obitaxonomy.CLIDownloadNCBI() { + err := obitaxonomy.CLIDownloadNCBITaxdump() + if err != nil { + log.Errorf("Cannot download NCBI taxonomy: %s", err.Error()) + os.Exit(1) + } + os.Exit(0) + } + + if !obidefault.HasSelectedTaxonomy() { + log.Fatal("you must indicate a taxonomy using the -t or --taxonomy option") + } + switch { case obitaxonomy.CLIDownloadNCBI(): err := obitaxonomy.CLIDownloadNCBITaxdump() diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go index f6fa64d..4846692 100644 --- a/pkg/obioptions/version.go +++ b/pkg/obioptions/version.go @@ -8,7 +8,7 @@ import ( // corresponds to the last commit, and not the one when the file will be // commited -var _Commit = "78df7db" +var _Commit = "b18c9b7" var _Version = "Release 4.4.0" // Version returns the version of the obitools package. diff --git a/pkg/obitools/obitaxonomy/obitaxonomy.go b/pkg/obitools/obitaxonomy/obitaxonomy.go index 1cdf668..da8dd1e 100644 --- a/pkg/obitools/obitaxonomy/obitaxonomy.go +++ b/pkg/obitools/obitaxonomy/obitaxonomy.go @@ -68,7 +68,7 @@ func CLICSVTaxaIterator(iterator *obitax.ITaxon) *obiitercsv.ICSVRecord { obitax.OptionsWithRank(CLIWithRank()), obitax.OptionsWithScientificName(CLIWithScientificName()), obitax.OptionsWithPath(CLIWithPath()), - obitax.OptionsRawTaxid(CLIRawTaxid()), + obitax.OptionsRawTaxid(obidefault.UseRawTaxids()), obitax.OptionsSource(obidefault.SelectedTaxonomy()), ) diff --git a/pkg/obitools/obitaxonomy/options.go b/pkg/obitools/obitaxonomy/options.go index 27bf15c..4a3079d 100644 --- a/pkg/obitools/obitaxonomy/options.go +++ b/pkg/obitools/obitaxonomy/options.go @@ -18,7 +18,6 @@ var __with_query__ = false var __without_rank__ = false var __without_parent__ = false var __without_scientific_name__ = false -var __raw_taxid__ = false var __taxid_path__ = "NA" var __taxid_sons__ = "NA" var __restrict_rank__ = "" @@ -67,8 +66,6 @@ func OptionSet(options *getoptions.GetOpt) { options.BoolVar(&__without_scientific_name__, "without-scientific-name", __without_scientific_name__, options.Alias("S"), options.Description("Supress the column containing the scientific name from the output.")) - options.BoolVar(&__raw_taxid__, "raw-taxid", false, - options.Description("Displays the raw taxid for each displayed taxon.")) options.StringVar(&__to_dump__, "dump", __to_dump__, options.Alias("D"), options.ArgName("TAXID"), @@ -132,10 +129,6 @@ func CLIWithScientificName() bool { return !__without_scientific_name__ } -func CLIRawTaxid() bool { - return __raw_taxid__ -} - func CLIRankRestriction() string { return __restrict_rank__ }