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some cleanning on the new tools

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Former-commit-id: f265a3910d2872c56af81c9b873669f2cb627781
This commit is contained in:
Eric Coissac
2024-07-11 10:46:11 +02:00
parent c7ed47e110
commit 42c5881ddc
5 changed files with 99 additions and 17 deletions
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8
cmd/obitools/obicleandb/main.go
View File

@ -5,6 +5,7 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicleandb"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
@ -12,6 +13,8 @@ import (
)
func main() {
obioptions.SetBatchSize(10)
optionParser := obioptions.GenerateOptionParser(obicleandb.OptionSet)
_, args := optionParser(os.Args)
@ -25,5 +28,8 @@ func main() {
cleaned := obicleandb.ICleanDB(fs)
obiconvert.CLIWriteBioSequences(cleaned, true)
toconsume, _ := obiconvert.CLIWriteBioSequences(cleaned, false)
toconsume.Consume()
obiiter.WaitForLastPipe()
}

36
cmd/obitools/obidemerge/main.go Normal file
View File

@ -0,0 +1,36 @@
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/obidemerge"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
)
func main() {
obioptions.SetStrictReadWorker(2)
obioptions.SetStrictWriteWorker(2)
optionParser := obioptions.GenerateOptionParser(obidemerge.OptionSet)
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
demerged := obidemerge.CLIDemergeSequences(fs)
obiconvert.CLIWriteBioSequences(demerged, true)
obiiter.WaitForLastPipe()
}

36
cmd/obitools/obijoin/main.go Normal file
View File

@ -0,0 +1,36 @@
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/obijoin"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
)
func main() {
obioptions.SetStrictReadWorker(2)
obioptions.SetStrictWriteWorker(2)
optionParser := obioptions.GenerateOptionParser(obijoin.OptionSet)
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
joined := obijoin.CLIJoinSequences(fs)
obiconvert.CLIWriteBioSequences(joined, true)
obiiter.WaitForLastPipe()
}