obitools/obitools4
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Changes to be committed:

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modified:   cmd/obitools/obitag/main.go
	modified:   cmd/obitools/obitaxonomy/main.go
	modified:   pkg/obiformats/csvtaxdump_read.go
	modified:   pkg/obiformats/ecopcr_read.go
	modified:   pkg/obiformats/ncbitaxdump_read.go
	modified:   pkg/obiformats/ncbitaxdump_readtar.go
	modified:   pkg/obiformats/newick_write.go
	modified:   pkg/obiformats/options.go
	modified:   pkg/obiformats/taxonomy_read.go
	modified:   pkg/obiformats/universal_read.go
	modified:   pkg/obiiter/extract_taxonomy.go
	modified:   pkg/obioptions/options.go
	modified:   pkg/obioptions/version.go
	new file:   pkg/obiphylo/tree.go
	modified:   pkg/obiseq/biosequenceslice.go
	modified:   pkg/obiseq/taxonomy_methods.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonset.go
	modified:   pkg/obitools/obiconvert/sequence_reader.go
	modified:   pkg/obitools/obitag/obitag.go
	modified:   pkg/obitools/obitaxonomy/obitaxonomy.go
	modified:   pkg/obitools/obitaxonomy/options.go
	deleted:    sample/.DS_Store
This commit is contained in:
Eric Coissac
2025-06-04 09:48:10 +02:00
parent 3424d3057f
commit 6cb7a5a352
23 changed files with 230 additions and 56 deletions
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10
pkg/obioptions/options.go
View File

@ -17,10 +17,10 @@ import (
)
var _Debug = false
var _BatchSize = 2000
var _Pprof = false
var _PprofMudex = 10
var _PprofGoroutine = 6060
var __seq_as_taxa__ = false
var __defaut_taxonomy_mutex__ sync.Mutex
@ -102,6 +102,7 @@ func GenerateOptionParser(program string,
taxonomy, err := obiformats.LoadTaxonomy(
obidefault.SelectedTaxonomy(),
!obidefault.AreAlternativeNamesSelected(),
SeqAsTaxa(),
)
if err != nil {
@ -218,6 +219,9 @@ func LoadTaxonomyOptionSet(options *getoptions.GetOpt, required, alternatiive bo
options.BoolVar(obidefault.UseRawTaxidsPtr(), "raw-taxid", obidefault.UseRawTaxids(),
options.Description("When set, taxids are printed in files with any supplementary information (taxon name and rank)"),
)
options.BoolVar(&__seq_as_taxa__, "with-leaves", __seq_as_taxa__,
options.Description("If taxonomy is extracted from a sequence file, sequences are added as leave of their taxid annotation"),
)
}
// CLIIsDebugMode returns whether the CLI is in debug mode.
@ -232,6 +236,10 @@ func CLIIsDebugMode() bool {
return _Debug
}
func SeqAsTaxa() bool {
return __seq_as_taxa__
}
// SetDebugOn sets the debug mode on.
func SetDebugOn() {
_Debug = true

2
pkg/obioptions/version.go
View File

@ -8,7 +8,7 @@ import (
// corresponds to the last commit, and not the one when the file will be
// commited
var _Commit = "f9324dd"
var _Commit = "3424d30"
var _Version = "Release 4.4.0"
// Version returns the version of the obitools package.