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Changes to be committed:

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modified:   cmd/obitools/obitag/main.go
	modified:   cmd/obitools/obitag2/main.go
	modified:   go.mod
	modified:   go.sum
	modified:   pkg/obiformats/ncbitaxdump/read.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/attributes.go
	modified:   pkg/obiseq/taxonomy_lca.go
	modified:   pkg/obiseq/taxonomy_methods.go
	modified:   pkg/obiseq/taxonomy_predicate.go
	modified:   pkg/obitax/inner.go
	modified:   pkg/obitax/lca.go
	new file:   pkg/obitax/taxid.go
	modified:   pkg/obitax/taxon.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonslice.go
	modified:   pkg/obitools/obicleandb/obicleandb.go
	modified:   pkg/obitools/obigrep/options.go
	modified:   pkg/obitools/obilandmark/obilandmark.go
	modified:   pkg/obitools/obilandmark/options.go
	modified:   pkg/obitools/obirefidx/famlilyindexing.go
	modified:   pkg/obitools/obirefidx/geomindexing.go
	modified:   pkg/obitools/obirefidx/obirefidx.go
	modified:   pkg/obitools/obirefidx/options.go
	modified:   pkg/obitools/obitag/obigeomtag.go
	modified:   pkg/obitools/obitag/obitag.go
	modified:   pkg/obitools/obitag/options.go
	modified:   pkg/obiutils/strings.go
This commit is contained in:
Eric Coissac
2024-12-19 13:36:59 +01:00
parent f41a6fbb60
commit 795df34d1a
28 changed files with 590 additions and 280 deletions
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44
pkg/obitools/obigrep/options.go
View File

@@ -1,7 +1,6 @@
package obigrep
import (
"strconv"
"strings"
log "github.com/sirupsen/logrus"
@@ -16,7 +15,7 @@ import (
)
var _BelongTaxa = make([]string, 0)
var _NotBelongTaxa = make([]int, 0)
var _NotBelongTaxa = make([]string, 0)
var _RequiredRanks = make([]string, 0)
var _MinimumLength = 1
@@ -60,7 +59,7 @@ func TaxonomySelectionOptionSet(options *getoptions.GetOpt) {
options.ArgName("TAXID"),
options.Description("Require that the actual taxon of the sequence belongs the provided taxid."))
options.IntSliceVar(&_NotBelongTaxa, "ignore-taxon", 1, 1,
options.StringSliceVar(&_NotBelongTaxa, "ignore-taxon", 1, 1,
options.Alias("i"),
options.ArgName("TAXID"),
options.Description("Require that the actual taxon of the sequence doesn't belong the provided taxid."))
@@ -273,18 +272,18 @@ func CLIRestrictTaxonomyPredicate() obiseq.SequencePredicate {
if len(_BelongTaxa) > 0 {
taxonomy := CLILoadSelectedTaxonomy()
taxid, err := strconv.Atoi(_BelongTaxa[0])
if err != nil {
p = taxonomy.IsSubCladeOfSlot(_BelongTaxa[0])
taxon := taxonomy.Taxon(_BelongTaxa[0])
if taxon == nil {
p = obiseq.IsSubCladeOfSlot(taxonomy, _BelongTaxa[0])
} else {
p = taxonomy.IsSubCladeOf(taxid)
p = obiseq.IsSubCladeOf(taxonomy, taxon)
}
for _, staxid := range _BelongTaxa[1:] {
taxid, err := strconv.Atoi(staxid)
if err != nil {
p2 = taxonomy.IsSubCladeOfSlot(staxid)
taxon := taxonomy.Taxon(staxid)
if taxon == nil {
p2 = obiseq.IsSubCladeOfSlot(taxonomy, staxid)
} else {
p2 = taxonomy.IsSubCladeOf(taxid)
p2 = obiseq.IsSubCladeOf(taxonomy, taxon)
}
p = p.Or(p2)
@@ -297,13 +296,28 @@ func CLIRestrictTaxonomyPredicate() obiseq.SequencePredicate {
}
func CLIAvoidTaxonomyPredicate() obiseq.SequencePredicate {
var p obiseq.SequencePredicate
var p2 obiseq.SequencePredicate
if len(_NotBelongTaxa) > 0 {
taxonomy := CLILoadSelectedTaxonomy()
p := taxonomy.IsSubCladeOf(_NotBelongTaxa[0])
taxon := taxonomy.Taxon(_NotBelongTaxa[0])
if taxon == nil {
p = obiseq.IsSubCladeOfSlot(taxonomy, _NotBelongTaxa[0])
} else {
p = obiseq.IsSubCladeOf(taxonomy, taxon)
}
for _, taxid := range _NotBelongTaxa[1:] {
p = p.Or(taxonomy.IsSubCladeOf(taxid))
taxon := taxonomy.Taxon(taxid)
if taxon == nil {
p2 = obiseq.IsSubCladeOfSlot(taxonomy, taxid)
} else {
p2 = obiseq.IsSubCladeOf(taxonomy, taxon)
}
p = p.Or(p2)
}
return p.Not()
@@ -316,10 +330,10 @@ func CLIHasRankDefinedPredicate() obiseq.SequencePredicate {
if len(_RequiredRanks) > 0 {
taxonomy := CLILoadSelectedTaxonomy()
p := taxonomy.HasRequiredRank(_RequiredRanks[0])
p := obiseq.HasRequiredRank(taxonomy, _RequiredRanks[0])
for _, rank := range _RequiredRanks[1:] {
p = p.And(taxonomy.HasRequiredRank(rank))
p = p.And(obiseq.HasRequiredRank(taxonomy, rank))
}
return p