obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2026-03-26 14:00:51 +00:00
Code Issues Packages Projects Releases Wiki Activity

Patch a small bug on json write

Browse Source
This commit is contained in:
Eric Coissac
2024-12-20 19:42:03 +01:00
parent abfa8f357a
commit 5d0f996625
14 changed files with 458 additions and 79 deletions
Download Patch File Download Diff File Expand all files Collapse all files

33
pkg/obitools/obigrep/options.go
View File

@@ -6,7 +6,7 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats/ncbitaxdump"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
@@ -33,7 +33,6 @@ var _Predicats = make([]string, 0)
var _IdList = ""
var _Taxdump = ""
var _Taxonomy = (*obitax.Taxonomy)(nil)
var _RequiredAttributes = make([]string, 0)
var _AttributePatterns = make(map[string]string, 0)
@@ -49,10 +48,7 @@ var _pattern_indel = false
var _pattern_only_forward = false
func TaxonomySelectionOptionSet(options *getoptions.GetOpt) {
options.StringVar(&_Taxdump, "taxdump", _Taxdump,
options.Alias("t"),
options.Description("Points to the directory containing the NCBI Taxonomy database dump."))
obioptions.LoadTaxonomyOptionSet(options, false, false)
options.StringSliceVar(&_BelongTaxa, "restrict-to-taxon", 1, 1,
options.Alias("r"),
@@ -246,31 +242,12 @@ func CLIPatternBothStrand() bool {
return !_pattern_only_forward
}
func CLILoadSelectedTaxonomy() *obitax.Taxonomy {
if CLISelectedNCBITaxDump() != "" {
if _Taxonomy == nil {
var err error
_Taxonomy, err = ncbitaxdump.LoadNCBITaxDump(CLISelectedNCBITaxDump(), true)
if err != nil {
log.Fatalf("cannot load taxonomy %s : %v",
CLISelectedNCBITaxDump(), err)
return nil
}
}
return _Taxonomy
}
log.Fatalln("no NCBI taxdump selected using option -t|--taxdump")
return nil
}
func CLIRestrictTaxonomyPredicate() obiseq.SequencePredicate {
var p obiseq.SequencePredicate
var p2 obiseq.SequencePredicate
if len(_BelongTaxa) > 0 {
taxonomy := CLILoadSelectedTaxonomy()
taxonomy := obitax.DefaultTaxonomy()
taxon := taxonomy.Taxon(_BelongTaxa[0])
if taxon == nil {
@@ -300,7 +277,7 @@ func CLIAvoidTaxonomyPredicate() obiseq.SequencePredicate {
var p2 obiseq.SequencePredicate
if len(_NotBelongTaxa) > 0 {
taxonomy := CLILoadSelectedTaxonomy()
taxonomy := obitax.DefaultTaxonomy()
taxon := taxonomy.Taxon(_NotBelongTaxa[0])
if taxon == nil {
@@ -329,7 +306,7 @@ func CLIAvoidTaxonomyPredicate() obiseq.SequencePredicate {
func CLIHasRankDefinedPredicate() obiseq.SequencePredicate {
if len(_RequiredRanks) > 0 {
taxonomy := CLILoadSelectedTaxonomy()
taxonomy := obitax.DefaultTaxonomy()
p := obiseq.HasRequiredRank(taxonomy, _RequiredRanks[0])
for _, rank := range _RequiredRanks[1:] {