obitools/obitools4
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Add a first version of obitag the successor of ecotag

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This commit is contained in:
Eric Coissac
2022-10-26 13:16:56 +02:00
parent e17d1fbca6
commit 8aa323dad5
17 changed files with 884 additions and 5 deletions
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22
cmd/obitools/obirefidx/main.go Normal file
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package main
import (
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obirefidx"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
)
func main() {
optionParser := obioptions.GenerateOptionParser(obirefidx.OptionSet)
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequencesBatch(args...)
indexed := obirefidx.IndexReferenceDB(fs)
written, _ := obiconvert.WriteBioSequencesBatch(indexed, false)
written.Consume()
}

21
cmd/obitools/obitag/main.go Normal file
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package main
import (
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obitag"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
)
func main() {
optionParser := obioptions.GenerateOptionParser(obitag.OptionSet)
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequencesBatch(args...)
identified := obitag.AssignTaxonomy(fs)
obiconvert.WriteBioSequencesBatch(identified, true)
}