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Adds the command obimultiplex

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This commit is contained in:
Eric Coissac
2022-02-01 17:31:28 +01:00
parent 76d9309508
commit 8dbda68746
13 changed files with 688 additions and 79 deletions
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6
pkg/obitools/obiconvert/sequence_reader.go
View File

@@ -81,14 +81,14 @@ func ReadBioSequencesBatch(filenames ...string) (obiseq.IBioSequenceBatch, error
opts = append(opts, obiformats.OptionsFastSeqHeaderParser(obiformats.ParseGuessedFastSeqHeader))
}
nworkers := obioptions.ParallelWorkers() / 4
nworkers := obioptions.CLIParallelWorkers() / 4
if nworkers < 2 {
nworkers = 2
}
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBufferSize(obioptions.BufferSize()))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.BatchSize()))
opts = append(opts, obiformats.OptionsBufferSize(obioptions.CLIBufferSize()))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsQualityShift(InputQualityShift()))

12
pkg/obitools/obiconvert/sequence_writer.go
View File

@@ -24,14 +24,14 @@ func WriteBioSequences(iterator obiseq.IBioSequence, filenames ...string) error
opts = append(opts, obiformats.OptionsFastSeqHeaderFormat(obiformats.FormatFastSeqJsonHeader))
}
nworkers := obioptions.ParallelWorkers() / 4
nworkers := obioptions.CLIParallelWorkers() / 4
if nworkers < 2 {
nworkers = 2
}
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBufferSize(obioptions.BufferSize()))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.BatchSize()))
opts = append(opts, obiformats.OptionsBufferSize(obioptions.CLIBufferSize()))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsQualityShift(OutputQualityShift()))
@@ -84,14 +84,14 @@ func WriteBioSequencesBatch(iterator obiseq.IBioSequenceBatch,
opts = append(opts, obiformats.OptionsFastSeqHeaderFormat(obiformats.FormatFastSeqJsonHeader))
}
nworkers := obioptions.ParallelWorkers() / 4
nworkers := obioptions.CLIParallelWorkers() / 4
if nworkers < 2 {
nworkers = 2
}
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBufferSize(obioptions.BufferSize()))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.BatchSize()))
opts = append(opts, obiformats.OptionsBufferSize(obioptions.CLIBufferSize()))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsQualityShift(OutputQualityShift()))

76
pkg/obitools/obimultiplex/options.go
View File

@@ -1 +1,77 @@
package obimultiplex
import (
"fmt"
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obingslibrary"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"github.com/DavidGamba/go-getoptions"
)
var _NGSFilterFile = ""
var _UnidentifiedFile = ""
var _AllowedMismatch = int(2)
var _ConservedError = false
// PCROptionSet defines every options related to a simulated PCR.
//
// The function adds to a CLI every options proposed to the user
// to tune the parametters of the PCR simulation algorithm.
//
// Parameters
//
// - option : is a pointer to a getoptions.GetOpt instance normaly
// produced by the
func MultiplexOptionSet(options *getoptions.GetOpt) {
options.StringVar(&_NGSFilterFile, "tag-list", _NGSFilterFile,
options.Alias("t"),
options.Required("You must provide a tag list file following the NGSFilter format"),
options.Description("File name of the NGSFilter file describing PCRs."))
options.BoolVar(&_ConservedError, "keep-errors", _ConservedError,
options.Description("Prints symbol counts."))
options.StringVar(&_UnidentifiedFile, "unidentified", _UnidentifiedFile,
options.Alias("u"),
options.Description("Filename used to store the sequences unassigned to any sample."))
options.IntVar(&_AllowedMismatch, "allowed-mismatches", _AllowedMismatch,
options.Alias("e"),
options.Description("Used to specify the number of errors allowed for matching primers."))
}
func OptionSet(options *getoptions.GetOpt) {
obiconvert.OptionSet(options)
MultiplexOptionSet(options)
}
func CLIAllowedMismatch() int {
return _AllowedMismatch
}
func CLIUnidentifiedFileName() string {
return _UnidentifiedFile
}
func CLIConservedErrors() bool {
return _UnidentifiedFile != "" || _ConservedError
}
func CLINGSFIlter() (obingslibrary.NGSLibrary, error) {
file, err := os.Open(_NGSFilterFile)
if err != nil {
return nil, fmt.Errorf("open file error: %v", err)
}
ngsfiler, err := obiformats.ReadNGSFilter(file)
if err != nil {
return nil, fmt.Errorf("NGSfilter reading file error: %v", err)
}
return ngsfiler, nil
}