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Add the --taxonomic-path option to obiannotate

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Former-commit-id: 385309a1c4bc5ed33aeaafc63eedb9fc552f78a6
This commit is contained in:
Eric Coissac
2024-02-27 20:10:26 +01:00
parent 4127ddb26f
commit 4a0b20484f
5 changed files with 72 additions and 0 deletions
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6
pkg/obitools/obiannotate/obiannotate.go
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@@ -256,6 +256,12 @@ func CLIAnnotationWorker() obiseq.SeqWorker {
annotator = annotator.ChainWorkers(w)
}
if CLISetTaxonomicPath() {
taxo := obigrep.CLILoadSelectedTaxonomy()
w := taxo.MakeSetPathWorker()
annotator = annotator.ChainWorkers(w)
}
if CLIHasAddLCA() {
taxo := obigrep.CLILoadSelectedTaxonomy()
w := obitax.AddLCAWorker(taxo, CLILCASlotName(), CLILCAThreshold())

8
pkg/obitools/obiannotate/options.go
View File

@@ -31,6 +31,7 @@ var _lcaSlot = ""
var _lcaError = 0.0
var _setId = ""
var _cut = ""
var _taxonomicPath = false
func SequenceAnnotationOptionSet(options *getoptions.GetOpt) {
// options.BoolVar(&_addRank, "seq-rank", _addRank,
@@ -113,6 +114,9 @@ func SequenceAnnotationOptionSet(options *getoptions.GetOpt) {
options.ArgName("RANK_NAME"),
options.Description("Adds taxonomic annotation at taxonomic rank <RANK_NAME>."))
options.BoolVar(&_taxonomicPath, "taxonomic-path", _taxonomicPath,
options.Description("Annotate the sequence with its taxonomic path"))
// options.StringVar(&_tagList, "tag-list", _tagList,
// options.ArgName("FILENAME"),
// options.Description("<FILENAME> points to a file containing attribute names"+
@@ -299,3 +303,7 @@ func CLIPatternError() int {
func CLIPatternInDels() bool {
return _pattern_indel
}
func CLISetTaxonomicPath() bool {
return _taxonomicPath
}