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Xprize update

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Former-commit-id: d38919a897961e4d40da3b844057c3fb94fdb6d7
This commit is contained in:
Eric Coissac
2024-07-25 18:09:03 -04:00
parent 4e4fac491f
commit 67665a6b40
18 changed files with 895 additions and 29 deletions
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25
pkg/obitools/obigrep/options.go
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@@ -1,6 +1,7 @@
package obigrep
import (
"strconv"
"strings"
log "github.com/sirupsen/logrus"
@@ -13,7 +14,7 @@ import (
"github.com/DavidGamba/go-getoptions"
)
var _BelongTaxa = make([]int, 0)
var _BelongTaxa = make([]string, 0)
var _NotBelongTaxa = make([]int, 0)
var _RequiredRanks = make([]string, 0)
@@ -48,7 +49,7 @@ func TaxonomySelectionOptionSet(options *getoptions.GetOpt) {
options.Alias("t"),
options.Description("Points to the directory containing the NCBI Taxonomy database dump."))
options.IntSliceVar(&_BelongTaxa, "restrict-to-taxon", 1, 1,
options.StringSliceVar(&_BelongTaxa, "restrict-to-taxon", 1, 1,
options.Alias("r"),
options.ArgName("TAXID"),
options.Description("Require that the actual taxon of the sequence belongs the provided taxid."))
@@ -231,13 +232,27 @@ func CLILoadSelectedTaxonomy() *obitax.Taxonomy {
}
func CLIRestrictTaxonomyPredicate() obiseq.SequencePredicate {
var p obiseq.SequencePredicate
var p2 obiseq.SequencePredicate
if len(_BelongTaxa) > 0 {
taxonomy := CLILoadSelectedTaxonomy()
p := taxonomy.IsSubCladeOf(_BelongTaxa[0])
for _, taxid := range _BelongTaxa[1:] {
p = p.Or(taxonomy.IsSubCladeOf(taxid))
taxid, err := strconv.Atoi(_BelongTaxa[0])
if err != nil {
p = taxonomy.IsSubCladeOfSlot(_BelongTaxa[0])
} else {
p = taxonomy.IsSubCladeOf(taxid)
}
for _, staxid := range _BelongTaxa[1:] {
taxid, err := strconv.Atoi(staxid)
if err != nil {
p2 = taxonomy.IsSubCladeOfSlot(staxid)
} else {
p2 = taxonomy.IsSubCladeOf(taxid)
}
p = p.Or(p2)
}
return p