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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
cmd/obitools/obimultiplex/main.go
View File

@ -5,7 +5,7 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obipcr"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obimultiplex"
)
func main() {
@ -24,11 +24,11 @@ func main() {
// trace.Start(ftrace)
// defer trace.Stop()
optionParser := obioptions.GenerateOptionParser(obipcr.OptionSet)
optionParser := obioptions.GenerateOptionParser(obimultiplex.OptionSet)
_, args, _ := optionParser(os.Args)
sequences, _ := obiconvert.ReadBioSequencesBatch(args...)
amplicons, _ := obipcr.PCR(sequences)
amplicons, _ := obimultiplex.IExtractBarcodeBatches(sequences)
obiconvert.WriteBioSequencesBatch(amplicons, true)
}

2
cmd/obitools/obipairing/main.go
View File

@ -39,7 +39,7 @@ func main() {
obipairing.MinOverlap(),
obipairing.MinIdentity(),
obipairing.WithStats(),
obioptions.ParallelWorkers(),
obioptions.CLIParallelWorkers(),
)
obiconvert.WriteBioSequencesBatch(paired, true)
}

13
cmd/test/main.go
View File

@ -52,7 +52,18 @@ func main() {
file, _ := os.Open("sample/wolf_diet_ngsfilter.txt")
xxx, _ := obiformats.ReadNGSFilter(file)
xxx.Compile(2)
fmt.Printf("%v\n==================\n", xxx)
fmt.Println(xxx)
for pp, m := range xxx {
fmt.Printf("%v %v\n", pp, *m)
}
seqfile, _ := obiformats.ReadFastSeqFromFile("xxxx.fastq")
for seqfile.Next() {
seq := seqfile.Get()
barcode, _ := xxx.ExtractBarcode(seq, true)
fmt.Println(obiformats.FormatFasta(barcode, obiformats.FormatFastSeqOBIHeader))
}
}