obitools/obitools4
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a functional new version of obifind

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This commit is contained in:
Eric Coissac
2024-11-24 19:33:24 +01:00
parent 36327c79c8
commit 3d06978808
21 changed files with 1805 additions and 343 deletions
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2
cmd/obitools/obicsv/main.go
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@ -17,7 +17,7 @@ func main() {
fs, err := obiconvert.CLIReadBioSequences(args...)
obiconvert.OpenSequenceDataErrorMessage(args, err)
obicsv.CLIWriteCSV(fs, true)
obicsv.CLIWriteSequenceCSV(fs, true)
obiiter.WaitForLastPipe()

52
cmd/obitools/obifind/main.go
View File

@ -1,9 +1,10 @@
package main
import (
"fmt"
"log"
"os"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obifind"
@ -14,13 +15,7 @@ func main() {
_, args := optionParser(os.Args)
//prof, _ := os.Create("obifind.prof")
//pprof.StartCPUProfile(prof)
restrictions, err := obifind.ITaxonRestrictions()
if err != nil {
fmt.Printf("%+v", err)
}
var iterator *obitax.ITaxon
switch {
case obifind.CLIRequestsPathForTaxid() != "NA":
@ -28,34 +23,45 @@ func main() {
taxon := obitax.DefaultTaxonomy().Taxon(obifind.CLIRequestsPathForTaxid())
if taxon == nil {
fmt.Printf("%+v", err)
log.Fatalf("Cannot identify the requested taxon: %s",
obifind.CLIRequestsPathForTaxid())
}
s := taxon.Path()
if err != nil {
fmt.Printf("%+v", err)
if s == nil {
log.Fatalf("Cannot extract taxonomic path describing %s", taxon.String())
}
obifind.TaxonWriter(s.Iterator(),
fmt.Sprintf("path:%s", taxon.String()))
iterator = s.Iterator()
if obifind.CLIWithQuery() {
iterator = iterator.AddMetadata("query", taxon.String())
}
case len(args) == 0:
taxonomy := obitax.DefaultTaxonomy()
obifind.TaxonWriter(restrictions(taxonomy.Iterator()), "")
iterator = obitax.DefaultTaxonomy().Iterator()
default:
matcher, err := obifind.ITaxonNameMatcher()
iters := make([]*obitax.ITaxon, len(args))
if err != nil {
fmt.Printf("%+v", err)
for i, pat := range args {
ii := obitax.DefaultTaxonomy().IFilterOnName(pat, obifind.CLIFixedPattern(), true)
if obifind.CLIWithQuery() {
ii = ii.AddMetadata("query", pat)
}
iters[i] = ii
}
for _, pattern := range args {
s := restrictions(matcher(pattern))
obifind.TaxonWriter(s, pattern)
iterator = iters[0]
if len(iters) > 1 {
iterator = iterator.Concat(iters[1:]...)
}
}
//pprof.StopCPUProfile()
iterator = obifind.CLITaxonRestrictions(iterator)
obifind.CLICSVTaxaWriter(iterator, true)
obiiter.WaitForLastPipe()
}