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

Chang log package

Browse Source
This commit is contained in:
Eric Coissac
2022-08-23 11:10:04 +02:00
parent abaede48b5
commit 4df99cec5b
2 changed files with 14 additions and 8 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3
pkg/obitools/obiclean/graph.go
View File

@ -3,7 +3,6 @@ package obiclean
import ( import (
"bytes" "bytes"
"fmt" "fmt"
"log"
"math" "math"
"os" "os"
"path" "path"
@ -11,6 +10,8 @@ import (
"sync" "sync"
"text/template" "text/template"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign" "git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"github.com/schollz/progressbar/v3" "github.com/schollz/progressbar/v3"
) )

19
pkg/obitools/obigrep/options.go
View File

@ -1,9 +1,10 @@
package obigrep package obigrep
import ( import (
"log"
"strings" "strings"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils" "git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats/ncbitaxdump" "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats/ncbitaxdump"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq" "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
@ -177,6 +178,10 @@ func CLIMaxSequenceCount() int {
return _MaximumCount return _MaximumCount
} }
func CLIRequiredRanks() []string {
return _RequiredRanks
}
func CLISequenceCountPredicate() obiseq.SequencePredicate { func CLISequenceCountPredicate() obiseq.SequencePredicate {
if _MinimumCount > 1 { if _MinimumCount > 1 {
p := obiseq.IsMoreAbundantOrEqualTo(_MinimumCount) p := obiseq.IsMoreAbundantOrEqualTo(_MinimumCount)
@ -222,10 +227,10 @@ func CLIRestrictTaxonomyPredicate() obiseq.SequencePredicate {
if len(_BelongTaxa) > 0 { if len(_BelongTaxa) > 0 {
taxonomy := CLILoadSelectedTaxonomy() taxonomy := CLILoadSelectedTaxonomy()
p := obitax.IsSubCladeOf(*taxonomy, _BelongTaxa[0]) p := taxonomy.IsSubCladeOf(_BelongTaxa[0])
for _, taxid := range _BelongTaxa[1:] { for _, taxid := range _BelongTaxa[1:] {
p = p.Or(obitax.IsSubCladeOf(*taxonomy, taxid)) p = p.Or(taxonomy.IsSubCladeOf(taxid))
} }
return p return p
@ -238,10 +243,10 @@ func CLIAvoidTaxonomyPredicate() obiseq.SequencePredicate {
if len(_NotBelongTaxa) > 0 { if len(_NotBelongTaxa) > 0 {
taxonomy := CLILoadSelectedTaxonomy() taxonomy := CLILoadSelectedTaxonomy()
p := obitax.IsSubCladeOf(*taxonomy, _NotBelongTaxa[0]) p := taxonomy.IsSubCladeOf(_NotBelongTaxa[0])
for _, taxid := range _NotBelongTaxa[1:] { for _, taxid := range _NotBelongTaxa[1:] {
p = p.Or(obitax.IsSubCladeOf(*taxonomy, taxid)) p = p.Or(taxonomy.IsSubCladeOf(taxid))
} }
return p.Not() return p.Not()
@ -254,10 +259,10 @@ func CLIHasRankDefinedPredicate() obiseq.SequencePredicate {
if len(_RequiredRanks) > 0 { if len(_RequiredRanks) > 0 {
taxonomy := CLILoadSelectedTaxonomy() taxonomy := CLILoadSelectedTaxonomy()
p := obitax.HasRankDefined(*taxonomy, _RequiredRanks[0]) p := taxonomy.HasRequiredRank(_RequiredRanks[0])
for _, rank := range _RequiredRanks[1:] { for _, rank := range _RequiredRanks[1:] {
p = p.And(obitax.HasRankDefined(*taxonomy, rank)) p = p.And(taxonomy.HasRequiredRank(rank))
} }
return p return p