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Patch a small bug on json write

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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
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10
pkg/obitools/obiannotate/obiannotate.go
View File

@@ -273,31 +273,31 @@ func CLIAnnotationWorker() obiseq.SeqWorker {
}
if CLIHasTaxonAtRank() {
taxo := obigrep.CLILoadSelectedTaxonomy()
taxo := obitax.DefaultTaxonomy()
w := AddTaxonAtRankWorker(taxo, CLITaxonAtRank()...)
annotator = annotator.ChainWorkers(w)
}
if CLISetTaxonomicPath() {
taxo := obigrep.CLILoadSelectedTaxonomy()
taxo := obitax.DefaultTaxonomy()
w := obiseq.MakeSetPathWorker(taxo)
annotator = annotator.ChainWorkers(w)
}
if CLISetTaxonomicRank() {
taxo := obigrep.CLILoadSelectedTaxonomy()
taxo := obitax.DefaultTaxonomy()
w := AddTaxonRankWorker(taxo)
annotator = annotator.ChainWorkers(w)
}
if CLISetScientificName() {
taxo := obigrep.CLILoadSelectedTaxonomy()
taxo := obitax.DefaultTaxonomy()
w := AddScientificNameWorker(taxo)
annotator = annotator.ChainWorkers(w)
}
if CLIHasAddLCA() {
taxo := obigrep.CLILoadSelectedTaxonomy()
taxo := obitax.DefaultTaxonomy()
w := obiseq.AddLCAWorker(taxo, CLILCASlotName(), CLILCAThreshold())
annotator = annotator.ChainWorkers(w)
}

3
pkg/obitools/obicleandb/obicleandb.go
View File

@@ -11,6 +11,7 @@ import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obistats"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obigrep"
)
@@ -245,7 +246,7 @@ func ICleanDB(itertator obiiter.IBioSequence) obiiter.IBioSequence {
log.Fatal(err)
}
taxonomy := obigrep.CLILoadSelectedTaxonomy()
taxonomy := obitax.DefaultTaxonomy()
if len(obigrep.CLIRequiredRanks()) > 0 {
rankPredicate = obigrep.CLIHasRankDefinedPredicate()

2
pkg/obitools/obiconvert/options.go
View File

@@ -3,6 +3,7 @@ package obiconvert
import (
"os"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
log "github.com/sirupsen/logrus"
"github.com/DavidGamba/go-getoptions"
@@ -115,6 +116,7 @@ func PairedFilesOptionSet(options *getoptions.GetOpt) {
}
func OptionSet(options *getoptions.GetOpt) {
obioptions.LoadTaxonomyOptionSet(options, false, false)
InputOptionSet(options)
OutputOptionSet(options)
PairedFilesOptionSet(options)

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:] {

6
pkg/obitools/obirefidx/geomindexing.go
View File

@@ -70,11 +70,7 @@ func GeomIndexSesquence(seqidx int,
new_lca, _ := lca.LCA(taxa.Taxon(o))
if new_lca.SameAs(lca) {
lca = new_lca
index[int(seq_dist[o])] = fmt.Sprintf(
"%s@%s",
lca.String(),
lca.Rank(),
)
index[int(seq_dist[o])] = lca.String()
if lca.IsRoot() {
break

14
pkg/obitools/obirefidx/obirefidx.go
View File

@@ -1,7 +1,6 @@
package obirefidx
import (
"fmt"
"os"
log "github.com/sirupsen/logrus"
@@ -172,11 +171,7 @@ func IndexSequence(seqidx int,
for i, d := range closest {
if i < (len(closest)-1) && d < closest[i+1] {
current_taxon := pseq.Taxon(i)
obitag_index[d] = fmt.Sprintf(
"%s@%s",
current_taxon.String(),
current_taxon.Rank(),
)
obitag_index[d] = current_taxon.String()
}
}
@@ -197,9 +192,10 @@ func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
source, references := iterator.Load()
log.Infof("Done. Database contains %d sequences", len(references))
taxo, error := obioptions.CLILoadSelectedTaxonomy()
if error != nil {
log.Panicln(error)
taxo := obitax.DefaultTaxonomy()
if taxo == nil {
log.Fatal("No taxonomy loaded.")
}
log.Infoln("Indexing sequence taxids...")