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This commit is contained in:
Eric Coissac
2023-02-02 23:11:08 +01:00
parent 2002299b7f
commit 7756aebab1
4 changed files with 181 additions and 114 deletions
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35
pkg/obitools/obiannotate/options.go
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@@ -17,9 +17,9 @@ var _setSeqLength = false
var _uniqueID = false
func SequenceAnnotationOptionSet(options *getoptions.GetOpt) {
options.BoolVar(&_addRank, "seq-rank", _addRank,
options.Description("Adds a new attribute named seq_rank to the sequence record indicating its entry number in the sequence file."),
)
// options.BoolVar(&_addRank, "seq-rank", _addRank,
// options.Description("Adds a new attribute named seq_rank to the sequence record indicating its entry number in the sequence file."),
// )
options.BoolVar(&_clearAll, "clear", _clearAll,
options.Description("Clears all attributes associated to the sequence records."),
@@ -29,9 +29,10 @@ func SequenceAnnotationOptionSet(options *getoptions.GetOpt) {
options.Description("Adds attribute with seq_length as a key and sequence length as a value."),
)
options.BoolVar(&_uniqueID, "uniq-id", _uniqueID,
options.Description("Forces sequence record ids to be unique."),
)
// options.BoolVar(&_uniqueID, "uniq-id", _uniqueID,
// options.Description("Forces sequence record ids to be unique."),
// )
options.StringMapVar(&_toBeRenamed, "rename-tag", 1, 1,
options.Alias("R"),
options.ArgName("NEW_NAME=OLD_NAME"),
@@ -47,10 +48,10 @@ func SequenceAnnotationOptionSet(options *getoptions.GetOpt) {
options.ArgName("RANK_NAME"),
options.Description("Adds taxonomic annotation at taxonomic rank <RANK_NAME>."))
options.StringVar(&_tagList, "tag-list", _tagList,
options.ArgName("FILENAME"),
options.Description("<FILENAME> points to a file containing attribute names"+
" and values to modify for specified sequence records."))
// options.StringVar(&_tagList, "tag-list", _tagList,
// options.ArgName("FILENAME"),
// options.Description("<FILENAME> points to a file containing attribute names"+
// " and values to modify for specified sequence records."))
options.StringSliceVar(&_keepOnly, "keep", 1, 1,
options.Alias("k"),
@@ -111,14 +112,8 @@ func CLIHasToBeKeptAttributes() bool {
return len(_keepOnly) > 0
}
func CLIToBeKeptAttributes() map[string]bool {
d := make(map[string]bool, len(_keepOnly))
for _, v := range _keepOnly {
d[v] = true
}
return d
func CLIToBeKeptAttributes() []string {
return _keepOnly
}
func CLIHasTaxonAtRank() bool {
@@ -131,4 +126,8 @@ func CLITaxonAtRank() []string {
func CLIHasSetLengthFlag() bool {
return _setSeqLength
}
func CLIHasClearAllFlag() bool {
return _clearAll
}