Added options --internal / --external to gotree brlen subcommands. ap…

…i has been modified: Tree functions have been updated

cmd/brlen.go

@@ -12,8 +12,11 @@ var brlenCmd = &cobra.Command{
 Set a minimum branch length, or set random branch lengths, or multiply branch lengths by a factor.
 `,
 }
+var brlenexternal, brleninternal bool
 
 func init() {
 	RootCmd.AddCommand(brlenCmd)
 	brlenCmd.PersistentFlags().StringVarP(&intreefile, "input", "i", "stdin", "Input tree")
+	brlenCmd.PersistentFlags().BoolVar(&brlenexternal, "external", true, "Applies to external branches")
+	brlenCmd.PersistentFlags().BoolVar(&brleninternal, "internal", true, "Applies to internal branches")
 }

cmd/brlenset.go

@@ -0,0 +1,64 @@
+package cmd
+
+import (
+	goio "io"
+	"os"
+
+	"github.com/evolbioinfo/gotree/io"
+	"github.com/evolbioinfo/gotree/tree"
+	"github.com/spf13/cobra"
+)
+
+var brlensetlen float64
+
+// minbrlenCmd represents the minbrlen command
+var brlenSetCmd = &cobra.Command{
+	Use:   "set",
+	Short: "Set the given branch length to all branches",
+	Long: `Set the given branch length to all branches
+
+Example of usage:
+
+gotree brlen set -i tree.nw -o out.nw -l 0.001
+if --internal=false is given, it won't apply to internal branches (only external)
+if --external=false is given, it won't apply to external branches (only internal)
+`,
+	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
+			}
+			for _, e := range t.Tree.Edges() {
+				if (e.Right().Tip() && brlenexternal) || (!e.Right().Tip() && brleninternal) {
+					e.SetLength(brlensetlen)
+				}
+			}
+			f.WriteString(t.Tree.Newick() + "\n")
+		}
+		return
+	},
+}
+
+func init() {
+	brlenCmd.AddCommand(brlenSetCmd)
+	brlenSetCmd.Flags().Float64VarP(&brlensetlen, "length", "l", 0.0, "Desired branch length")
+	brlenSetCmd.PersistentFlags().StringVarP(&intreefile, "input", "i", "stdin", "Input tree")
+	brlenSetCmd.PersistentFlags().StringVarP(&outtreefile, "output", "o", "stdout", "Min length output tree file")
+}

cmd/clearlength.go

@@ -13,7 +13,12 @@ import (
 var clearlengthCmd = &cobra.Command{
 	Use:   "clear",
 	Short: "Clear lengths from input trees",
-	Long:  `Clear lengths from input trees.`,
+	Long: `Clear lengths from input trees.
+	
+	if --internal=false is given, it won't apply to internal branches (only external)
+	if --external=false is given, it won't apply to external branches (only internal)
+
+	`,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
 		var f *os.File
 		var treefile goio.Closer
@@ -35,7 +40,7 @@ var clearlengthCmd = &cobra.Command{
 				io.LogError(t.Err)
 				return t.Err
 			}
-			t.Tree.ClearLengths()
+			t.Tree.ClearLengths(brleninternal, brlenexternal)
 			f.WriteString(t.Tree.Newick() + "\n")
 		}
 		return

cmd/minbrlen.go

@@ -17,7 +17,10 @@ var minbrlenCmd = &cobra.Command{
 
 Example of usage:
 
-gotree minbrlen -i tree.nw -o out.nw -l 0.001
+gotree brlen setmin -i tree.nw -o out.nw -l 0.001
+
+if --internal=false is given, it won't apply to internal branches (only external)
+if --external=false is given, it won't apply to external branches (only internal)
 
 `,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
@@ -43,7 +46,7 @@ gotree minbrlen -i tree.nw -o out.nw -l 0.001
 				return t.Err
 			}
 			for _, e := range t.Tree.Edges() {
-				if e.Length() < cutoff {
+				if ((e.Right().Tip() && brlenexternal) || (!e.Right().Tip() && brleninternal)) && e.Length() < cutoff {
 					e.SetLength(cutoff)
 				}
 			}

cmd/multiplybrlen.go

@@ -15,7 +15,12 @@ var scalelengthfactor float64
 var scalelengthCmd = &cobra.Command{
 	Use:   "scale",
 	Short: "Scale lengths from input trees by a given factor",
-	Long:  `Scale lengths from input trees by a given factor.`,
+	Long: `Scale lengths from input trees by a given factor.
+	
+	if --internal=false is given, it won't apply to internal branches (only external)
+	if --external=false is given, it won't apply to external branches (only internal)
+
+`,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
 		var f *os.File
 		var treefile goio.Closer
@@ -37,7 +42,7 @@ var scalelengthCmd = &cobra.Command{
 				io.LogError(tr.Err)
 				return tr.Err
 			}
-			tr.Tree.ScaleLengths(scalelengthfactor)
+			tr.Tree.ScaleLengths(scalelengthfactor, brleninternal, brlenexternal)
 			f.WriteString(tr.Tree.Newick() + "\n")
 		}
 		return

cmd/randbrlen.go

@@ -28,6 +28,9 @@ Two possibilities for the mean:
 
 2) Otherwise, 'mean' is set to --mean value.
 
+if --internal=false is given, it won't apply to internal branches (only external)
+if --external=false is given, it won't apply to external branches (only internal)
+
 `,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
 		var f *os.File
@@ -58,7 +61,9 @@ Two possibilities for the mean:
 			}
 
 			for _, e := range tr.Tree.Edges() {
-				e.SetLength(gostats.Exp(1.0 / lmean))
+				if (e.Right().Tip() && brlenexternal) || (!e.Right().Tip() && brleninternal) {
+					e.SetLength(gostats.Exp(1.0 / lmean))
+				}
 			}
 			f.WriteString(tr.Tree.Newick() + "\n")
 		}

cmd/roundlengths.go

@@ -25,6 +25,10 @@ if -p 5 is given, precision of 10⁻5 is considered.
 Does not do anything if precision is <=0;
 Takes precision=15 if precision>15.
 
+if --internal=false is given, it won't apply to internal branches (only external)
+if --external=false is given, it won't apply to external branches (only internal)
+
+
 `,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
 		var f *os.File
@@ -47,7 +51,7 @@ Takes precision=15 if precision>15.
 				io.LogError(t.Err)
 				return t.Err
 			}
-			t.Tree.RoundLengths(roundlengthprecision)
+			t.Tree.RoundLengths(roundlengthprecision, brleninternal, brlenexternal)
 			f.WriteString(t.Tree.Newick() + "\n")
 		}
 		return

tests/tree_test.go

@@ -15,7 +15,7 @@ func TestClearLengths(t *testing.T) {
 	if err != nil {
 		t.Error(err)
 	}
-	tr.ClearLengths()
+	tr.ClearLengths(true, true)
 	if tr.Newick() != "(Tip4,Tip0,(Tip3,(Tip2,Tip1)0.8)0.9);" {
 		t.Error(fmt.Sprintf("Tree after clear supports is not valid: %s", tr.Newick()))
 	}
@@ -39,7 +39,7 @@ func TestRoundLengths(t *testing.T) {
 	if err != nil {
 		t.Error(err)
 	}
-	tr.RoundLengths(4)
+	tr.RoundLengths(4, true, true)
 	if tr.Newick() != "(Tip4:0.0001,Tip0:0.0001,(Tip3:0.0001,(Tip2:0.0002,Tip1:0.0002)0.8:0.0003)0.9:0.0004);" {
 		t.Error(fmt.Sprintf("Tree after round supports is not valid: %s", tr.Newick()))
 	}