obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

Add a --valid-taxid option to obigrep

Browse Source
This commit is contained in:
Eric Coissac
2025-02-27 18:12:55 +01:00
parent 573acafafc
commit 75dd535201
1 changed files with 27 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files

28
pkg/obitools/obigrep/options.go
View File

@ -6,6 +6,7 @@ import (
log "github.com/sirupsen/logrus" log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
@ -16,6 +17,7 @@ import (
var _BelongTaxa = make([]string, 0) var _BelongTaxa = make([]string, 0)
var _NotBelongTaxa = make([]string, 0) var _NotBelongTaxa = make([]string, 0)
var _RequiredRanks = make([]string, 0) var _RequiredRanks = make([]string, 0)
var _ValidateTaxonomy = false
var _MinimumLength = 1 var _MinimumLength = 1
var _MaximumLength = int(2e9) var _MaximumLength = int(2e9)
@ -62,6 +64,9 @@ func TaxonomySelectionOptionSet(options *getoptions.GetOpt) {
options.ArgName("RANK_NAME"), options.ArgName("RANK_NAME"),
options.Description("Select sequences belonging a taxon with a rank <RANK_NAME>")) options.Description("Select sequences belonging a taxon with a rank <RANK_NAME>"))
options.BoolVar(&_ValidateTaxonomy, "valid-taxid", _ValidateTaxonomy,
options.Description("Validate the taxonomic classification of the sequences."))
} }
func SequenceSelectionOptionSet(options *getoptions.GetOpt) { func SequenceSelectionOptionSet(options *getoptions.GetOpt) {
@ -271,6 +276,27 @@ func CLIRestrictTaxonomyPredicate() obiseq.SequencePredicate {
return nil return nil
} }
func CLIIsValidTaxonomyPredicate() obiseq.SequencePredicate {
if _ValidateTaxonomy {
if !obidefault.HasSelectedTaxonomy() {
log.Fatal("Taxonomy not found")
}
taxonomy := obitax.DefaultTaxonomy()
if taxonomy == nil {
log.Fatal("Taxonomy not found")
}
predicat := func(sequences *obiseq.BioSequence) bool {
taxon := sequences.Taxon(taxonomy)
return taxon != nil
}
return predicat
}
return nil
}
func CLIAvoidTaxonomyPredicate() obiseq.SequencePredicate { func CLIAvoidTaxonomyPredicate() obiseq.SequencePredicate {
var p obiseq.SequencePredicate var p obiseq.SequencePredicate
var p2 obiseq.SequencePredicate var p2 obiseq.SequencePredicate
@ -319,7 +345,7 @@ func CLIHasRankDefinedPredicate() obiseq.SequencePredicate {
} }
func CLITaxonomyFilterPredicate() obiseq.SequencePredicate { func CLITaxonomyFilterPredicate() obiseq.SequencePredicate {
return CLIHasRankDefinedPredicate().And(CLIRestrictTaxonomyPredicate()).And(CLIAvoidTaxonomyPredicate()) return CLIIsValidTaxonomyPredicate().And(CLIAvoidTaxonomyPredicate()).And(CLIHasRankDefinedPredicate()).And(CLIRestrictTaxonomyPredicate())
} }
func CLIPredicatesPredicate() obiseq.SequencePredicate { func CLIPredicatesPredicate() obiseq.SequencePredicate {