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Produce less weird crash on non existing files

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Former-commit-id: 74bb27bd53c685be530632994bd2ba24c1f362e1
This commit is contained in:
Eric Coissac
2023-03-07 17:34:25 +07:00
parent fbfed52508
commit b3922c3896
21 changed files with 147 additions and 32 deletions
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9
cmd/obitools/obiannotate/main.go
View File

@ -2,6 +2,7 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@ -34,7 +35,13 @@ func main() {
_, args := optionParser(os.Args)
sequences, _ := obiconvert.CLIReadBioSequences(args...)
sequences, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)",err)
os.Exit(1)
}
annotator := obiannotate.CLIAnnotationPipeline()
obiconvert.CLIWriteBioSequences(sequences.Pipe(annotator), true)

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

@ -2,6 +2,7 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiclean"
@ -15,7 +16,12 @@ func main() {
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)",err)
os.Exit(1)
}
cleaned := obiclean.IOBIClean(fs)

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

@ -2,6 +2,7 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obicleandb"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@ -14,7 +15,12 @@ func main() {
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)",err)
os.Exit(1)
}
cleaned := obicleandb.ICleanDB(fs)

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

@ -2,6 +2,7 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
@ -15,7 +16,12 @@ func main() {
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)",err)
os.Exit(1)
}
comp := fs.MakeIWorker(obiseq.ReverseComplementWorker(true))
obiconvert.CLIWriteBioSequences(comp, true)

9
cmd/obitools/obiconvert/main.go
View File

@ -2,6 +2,7 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@ -14,7 +15,13 @@ func main() {
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)",err)
os.Exit(1)
}
obiconvert.CLIWriteBioSequences(fs, true)
obiiter.WaitForLastPipe()

9
cmd/obitools/obicount/main.go
View File

@ -3,6 +3,7 @@ package main
import (
"fmt"
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obicount"
@ -33,7 +34,13 @@ func main() {
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)",err)
os.Exit(1)
}
nvariant, nread, nsymbol := fs.Count(true)
if obicount.CLIIsPrintingVariantCount() {

9
cmd/obitools/obicsv/main.go
View File

@ -2,6 +2,7 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@ -14,7 +15,13 @@ func main() {
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)",err)
os.Exit(1)
}
obicsv.CLIWriteCSV(fs, true)
obiiter.WaitForLastPipe()

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

@ -2,6 +2,7 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@ -15,7 +16,12 @@ func main() {
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)",err)
os.Exit(1)
}
obidistribute.DistributeSequence(fs)

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

@ -2,6 +2,7 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@ -34,7 +35,12 @@ func main() {
_, args := optionParser(os.Args)
sequences, _ := obiconvert.CLIReadBioSequences(args...)
sequences, err := obiconvert.CLIReadBioSequences(args...)
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/obimultiplex/main.go
View File

@ -2,6 +2,7 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@ -29,7 +30,12 @@ func main() {
_, args := optionParser(os.Args)
sequences, _ := obiconvert.CLIReadBioSequences(args...)
sequences, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)",err)
os.Exit(1)
}
amplicons, _ := obimultiplex.IExtractBarcode(sequences)
obiconvert.CLIWriteBioSequences(amplicons, true)
amplicons.Wait()

9
cmd/obitools/obipairing/main.go
View File

@ -2,6 +2,7 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@ -30,7 +31,13 @@ func main() {
optionParser := obioptions.GenerateOptionParser(obipairing.OptionSet)
optionParser(os.Args)
pairs, _ := obipairing.CLIPairedSequence()
pairs, err := obipairing.CLIPairedSequence()
if err != nil {
log.Errorf("Cannot open file (%v)",err)
os.Exit(1)
}
paired := obipairing.IAssemblePESequencesBatch(pairs,
obipairing.CLIGapPenality(),
obipairing.CLIDelta(),

9
cmd/obitools/obipcr/main.go
View File

@ -2,6 +2,7 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@ -31,7 +32,13 @@ func main() {
_, args := optionParser(os.Args)
sequences, _ := obiconvert.CLIReadBioSequences(args...)
sequences, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)",err)
os.Exit(1)
}
amplicons, _ := obipcr.PCR(sequences)
obiconvert.CLIWriteBioSequences(amplicons, true)
obiiter.WaitForLastPipe()

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

@ -2,6 +2,7 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@ -15,7 +16,12 @@ func main() {
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)",err)
os.Exit(1)
}
indexed := obirefidx.IndexReferenceDB(fs)
obiconvert.CLIWriteBioSequences(indexed, true)

9
cmd/obitools/obitag/main.go
View File

@ -3,6 +3,7 @@ package main
import (
"fmt"
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@ -33,7 +34,13 @@ func main() {
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)",err)
os.Exit(1)
}
identified := obitag.AssignTaxonomy(fs)
obiconvert.CLIWriteBioSequences(identified, true)

9
cmd/obitools/obiuniq/main.go
View File

@ -2,6 +2,7 @@ package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@ -34,7 +35,13 @@ func main() {
_, args := optionParser(os.Args)
sequences, _ := obiconvert.CLIReadBioSequences(args...)
sequences, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)",err)
os.Exit(1)
}
unique := obiuniq.Unique(sequences)
obiconvert.CLIWriteBioSequences(unique, true)