obitools/obitools4
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Add obiminion first version

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Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d
This commit is contained in:
Eric Coissac
2024-05-14 08:16:12 +02:00
parent 9e63013bc2
commit 017030bcce
24 changed files with 1599 additions and 469 deletions
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33
cmd/obitools/obiminion/main.go Normal file
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@ -0,0 +1,33 @@
package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiminion"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
)
func main() {
optionParser := obioptions.GenerateOptionParser(obiminion.OptionSet)
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
cleaned := obiminion.CLIOBIMinion(fs)
obiconvert.CLIWriteBioSequences(cleaned, true)
obiiter.WaitForLastPipe()
}

2
cmd/obitools/obiuniq/main.go
View File

@ -43,7 +43,7 @@ func main() {
os.Exit(1)
}
unique := obiuniq.Unique(sequences)
unique := obiuniq.CLIUnique(sequences)
obiconvert.CLIWriteBioSequences(unique, true)
obiiter.WaitForLastPipe()