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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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75
pkg/obitools/obicsv/obicsv.go
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@@ -3,59 +3,78 @@ package obicsv
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
"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"
)
func CLIWriteCSV(iterator obiiter.IBioSequence,
terminalAction bool, filenames ...string) (obiiter.IBioSequence, error) {
func CLIWriteSequenceCSV(iterator obiiter.IBioSequence,
terminalAction bool, filenames ...string) *ICSVRecord {
if obiconvert.CLIProgressBar() {
iterator = iterator.Speed("Writing CSV")
}
var newIter obiiter.IBioSequence
opts := make([]obiformats.WithOption, 0, 10)
opts := make([]WithOption, 0, 10)
nworkers := obioptions.CLIParallelWorkers() / 4
if nworkers < 2 {
nworkers = 2
}
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsCompressed(obiconvert.CLICompressed()))
opts = append(opts, OptionsParallelWorkers(nworkers))
opts = append(opts, OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, OptionsCompressed(obiconvert.CLICompressed()))
opts = append(opts, obiformats.CSVId(CLIPrintId()),
obiformats.CSVCount(CLIPrintCount()),
obiformats.CSVTaxon(CLIPrintTaxon()),
obiformats.CSVDefinition(CLIPrintDefinition()),
obiformats.CSVKeys(CLIToBeKeptAttributes()),
obiformats.CSVSequence(CLIPrintSequence()),
obiformats.CSVAutoColumn(CLIAutoColumns()),
opts = append(opts, CSVId(CLIPrintId()),
CSVCount(CLIPrintCount()),
CSVTaxon(CLIPrintTaxon()),
CSVDefinition(CLIPrintDefinition()),
CSVKeys(CLIToBeKeptAttributes()),
CSVSequence(CLIPrintSequence()),
CSVAutoColumn(CLIAutoColumns()),
)
var err error
csvIter := NewCSVSequenceIterator(iterator, opts...)
newIter := CLICSVWriter(csvIter, terminalAction, opts...)
if len(filenames) == 0 {
newIter, err = obiformats.WriteCSVToStdout(iterator, opts...)
} else {
newIter, err = obiformats.WriteCSVToFile(iterator, filenames[0], opts...)
return newIter
}
func CLICSVWriter(iterator *ICSVRecord,
terminalAction bool,
options ...WithOption) *ICSVRecord {
var err error
var newIter *ICSVRecord
if obiconvert.CLIOutPutFileName() != "-" {
options = append(options, OptionFileName(obiconvert.CLIOutPutFileName()))
}
if err != nil {
log.Fatalf("Write file error: %v", err)
return obiiter.NilIBioSequence, err
opt := MakeOptions(options)
if opt.FileName() != "-" {
newIter, err = WriteCSVToFile(iterator, opt.FileName(), options...)
if err != nil {
log.Fatalf("Cannot write to file : %+v", err)
}
} else {
newIter, err = WriteCSVToStdout(iterator, options...)
if err != nil {
log.Fatalf("Cannot write to stdout : %+v", err)
}
}
if terminalAction {
newIter.Recycle()
return obiiter.NilIBioSequence, nil
newIter.Consume()
return nil
}
return newIter, nil
return newIter
}