obitools/obitools4
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Patch a bug on writing to stdout, and add clearer error on openning data files

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This commit is contained in:
Eric Coissac
2024-08-13 09:45:28 +02:00
parent bdb96dda94
commit 31bfc88eb9
43 changed files with 1654 additions and 696 deletions
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8
cmd/obitools/obiannotate/main.go
View File

@ -3,8 +3,6 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
@ -37,11 +35,7 @@ func main() {
_, args := optionParser(os.Args)
sequences, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
annotator := obiannotate.CLIAnnotationPipeline()
obiconvert.CLIWriteBioSequences(sequences.Pipe(annotator), true)

8
cmd/obitools/obiclean/main.go
View File

@ -3,8 +3,6 @@ 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/obiclean"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
@ -18,11 +16,7 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
cleaned := obiclean.CLIOBIClean(fs)

8
cmd/obitools/obicleandb/main.go
View File

@ -3,8 +3,6 @@ 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/obicleandb"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
@ -20,11 +18,7 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
cleaned := obicleandb.ICleanDB(fs)

8
cmd/obitools/obicomplement/main.go
View File

@ -3,8 +3,6 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
@ -18,11 +16,7 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
comp := fs.MakeIWorker(obiseq.ReverseComplementWorker(true), true)
obiconvert.CLIWriteBioSequences(comp, true)

8
cmd/obitools/obiconsensus/main.go
View File

@ -3,8 +3,6 @@ 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/obiconsensus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
@ -18,11 +16,7 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
cleaned := obiconsensus.CLIOBIMinion(fs)

8
cmd/obitools/obiconvert/main.go
View File

@ -3,8 +3,6 @@ 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"
@ -20,11 +18,7 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
obiconvert.CLIWriteBioSequences(fs, true)

8
cmd/obitools/obicount/main.go
View File

@ -4,8 +4,6 @@ import (
"fmt"
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicount"
@ -37,11 +35,7 @@ func main() {
obioptions.SetStrictReadWorker(min(4, obioptions.CLIParallelWorkers()))
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
nvariant, nread, nsymbol := fs.Count(true)

8
cmd/obitools/obicsv/main.go
View File

@ -3,8 +3,6 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
@ -17,11 +15,7 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
obicsv.CLIWriteCSV(fs, true)

8
cmd/obitools/obidemerge/main.go
View File

@ -3,8 +3,6 @@ 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"
@ -21,11 +19,7 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
demerged := obidemerge.CLIDemergeSequences(fs)

8
cmd/obitools/obidistribute/main.go
View File

@ -3,8 +3,6 @@ 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/obidistribute"
@ -18,11 +16,7 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
obidistribute.CLIDistributeSequence(fs)

7
cmd/obitools/obigrep/main.go
View File

@ -3,8 +3,6 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
@ -37,11 +35,8 @@ func main() {
_, args := optionParser(os.Args)
sequences, err := obiconvert.CLIReadBioSequences(args...)
obiconvert.OpenSequenceDataErrorMessage(args, err)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
selected := obigrep.CLIFilterSequence(sequences)
obiconvert.CLIWriteBioSequences(selected, true)
obiiter.WaitForLastPipe()

8
cmd/obitools/obijoin/main.go
View File

@ -3,8 +3,6 @@ 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"
@ -21,11 +19,7 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
joined := obijoin.CLIJoinSequences(fs)

50
cmd/obitools/obikmermatch/main.go Normal file
View File

@ -0,0 +1,50 @@
package main
import (
"os"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obikmersim"
)
func main() {
defer obiseq.LogBioSeqStatus()
// go tool pprof -http=":8000" ./obipairing ./cpu.pprof
// f, err := os.Create("cpu.pprof")
// if err != nil {
// log.Fatal(err)
// }
// pprof.StartCPUProfile(f)
// defer pprof.StopCPUProfile()
// go tool trace cpu.trace
// ftrace, err := os.Create("cpu.trace")
// if err != nil {
// log.Fatal(err)
// }
// trace.Start(ftrace)
// defer trace.Stop()
optionParser := obioptions.GenerateOptionParser(obikmersim.MatchOptionSet)
_, args := optionParser(os.Args)
var err error
sequences := obiiter.NilIBioSequence
if !obikmersim.CLISelf() {
sequences, err = obiconvert.CLIReadBioSequences(args...)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
selected := obikmersim.CLIAlignSequences(sequences)
obiconvert.CLIWriteBioSequences(selected, true)
obiiter.WaitForLastPipe()
}

58
cmd/obitools/obikmersimcount/main.go Normal file
View File

@ -0,0 +1,58 @@
package main
import (
"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/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obikmersim"
)
func main() {
defer obiseq.LogBioSeqStatus()
// go tool pprof -http=":8000" ./obipairing ./cpu.pprof
// f, err := os.Create("cpu.pprof")
// if err != nil {
// log.Fatal(err)
// }
// pprof.StartCPUProfile(f)
// defer pprof.StopCPUProfile()
// go tool trace cpu.trace
// ftrace, err := os.Create("cpu.trace")
// if err != nil {
// log.Fatal(err)
// }
// trace.Start(ftrace)
// defer trace.Stop()
optionParser := obioptions.GenerateOptionParser(obikmersim.CountOptionSet)
_, args := optionParser(os.Args)
var err error
sequences := obiiter.NilIBioSequence
if !obikmersim.CLISelf() {
sequences, err = obiconvert.CLIReadBioSequences(args...)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
selected := obikmersim.CLILookForSharedKmers(sequences)
topull, err := obiconvert.CLIWriteBioSequences(selected, false)
if err == nil {
log.Panic(err)
}
topull.Consume()
obiiter.WaitForLastPipe()
}

8
cmd/obitools/obilandmark/main.go
View File

@ -3,8 +3,6 @@ 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/obilandmark"
@ -18,11 +16,7 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
indexed := obilandmark.CLISelectLandmarkSequences(fs)

8
cmd/obitools/obimatrix/main.go
View File

@ -4,8 +4,6 @@ import (
"fmt"
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
@ -39,11 +37,7 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
matrix := obimatrix.IMatrix(fs)

7
cmd/obitools/obimicrosat/main.go
View File

@ -3,8 +3,6 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
@ -37,11 +35,8 @@ func main() {
_, args := optionParser(os.Args)
sequences, err := obiconvert.CLIReadBioSequences(args...)
obiconvert.OpenSequenceDataErrorMessage(args, err)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
selected := obimicrosat.CLIAnnotateMicrosat(sequences)
obiconvert.CLIWriteBioSequences(selected, true)
obiiter.WaitForLastPipe()

5
cmd/obitools/obimultiplex/main.go
View File

@ -43,11 +43,8 @@ func main() {
}
sequences, err := obiconvert.CLIReadBioSequences(args...)
obiconvert.OpenSequenceDataErrorMessage(args, err)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
amplicons, _ := obimultiplex.IExtractBarcode(sequences)
obiconvert.CLIWriteBioSequences(amplicons, true)
amplicons.Wait()

8
cmd/obitools/obipcr/main.go
View File

@ -3,8 +3,6 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
@ -35,11 +33,7 @@ func main() {
_, args := optionParser(os.Args)
sequences, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
amplicons, _ := obipcr.CLIPCR(sequences)
obiconvert.CLIWriteBioSequences(amplicons, true)

8
cmd/obitools/obireffamidx/main.go
View File

@ -3,8 +3,6 @@ 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/obirefidx"
@ -18,11 +16,7 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
indexed := obirefidx.IndexFamilyDB(fs)

7
cmd/obitools/obirefidx/main.go
View File

@ -3,8 +3,6 @@ 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/obirefidx"
@ -18,11 +16,8 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
obiconvert.OpenSequenceDataErrorMessage(args, err)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
indexed := obirefidx.IndexReferenceDB(fs)
obiconvert.CLIWriteBioSequences(indexed, true)

8
cmd/obitools/obiscript/main.go
View File

@ -4,8 +4,6 @@ import (
"fmt"
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
@ -43,11 +41,7 @@ func main() {
}
sequences, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
annotator := obiscript.CLIScriptPipeline()
obiconvert.CLIWriteBioSequences(sequences.Pipe(annotator), true)

8
cmd/obitools/obisplit/main.go
View File

@ -4,8 +4,6 @@ import (
"fmt"
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
@ -43,11 +41,7 @@ func main() {
}
sequences, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
annotator := obisplit.CLISlitPipeline()
obiconvert.CLIWriteBioSequences(sequences.Pipe(annotator), true)

7
cmd/obitools/obisummary/main.go
View File

@ -5,7 +5,6 @@ import (
"fmt"
"os"
log "github.com/sirupsen/logrus"
"gopkg.in/yaml.v3"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
@ -39,11 +38,7 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
summary := obisummary.ISummary(fs, obisummary.CLIMapSummary())

6
cmd/obitools/obitag/main.go
View File

@ -42,11 +42,7 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
taxo, error := obifind.CLILoadSelectedTaxonomy()
if error != nil {

6
cmd/obitools/obitag2/main.go
View File

@ -43,11 +43,7 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
taxo, error := obifind.CLILoadSelectedTaxonomy()
if error != nil {

8
cmd/obitools/obiuniq/main.go
View File

@ -3,8 +3,6 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
@ -37,11 +35,7 @@ func main() {
_, args := optionParser(os.Args)
sequences, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
obiconvert.OpenSequenceDataErrorMessage(args, err)
unique := obiuniq.CLIUnique(sequences)
obiconvert.CLIWriteBioSequences(unique, true)