forked from evolbioinfo/gotree
/
clearlength.go
48 lines (42 loc) · 1.05 KB
/
clearlength.go
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package cmd
import (
goio "io"
"os"
"github.com/evolbioinfo/gotree/io"
"github.com/evolbioinfo/gotree/tree"
"github.com/spf13/cobra"
)
// clearlengthCmd represents the clearlength command
var clearlengthCmd = &cobra.Command{
Use: "clear",
Short: "Clear lengths from input trees",
Long: `Clear lengths from input trees.`,
RunE: func(cmd *cobra.Command, args []string) (err error) {
var f *os.File
var treefile goio.Closer
var treechan <-chan tree.Trees
if f, err = openWriteFile(outtreefile); err != nil {
io.LogError(err)
return
}
defer closeWriteFile(f, outtreefile)
if treefile, treechan, err = readTrees(intreefile); err != nil {
io.LogError(err)
return
}
defer treefile.Close()
for t := range treechan {
if t.Err != nil {
io.LogError(t.Err)
return t.Err
}
t.Tree.ClearLengths()
f.WriteString(t.Tree.Newick() + "\n")
}
return
},
}
func init() {
brlenCmd.AddCommand(clearlengthCmd)
clearlengthCmd.PersistentFlags().StringVarP(&outtreefile, "output", "o", "stdout", "Cleared tree output file")
}