Added options --tips and --internal to gotree labels #13

README.md

@@ -39,9 +39,13 @@ root            +---------------- 2
 
 ```
 
-$ echo "(1,(2,(3,4,5,6)polytomy)internal)root;" | gotree labels
+```
+$ echo "(1,(2,(3,4,5,6)polytomy)internal)root;" | gotree labels --internal --tips
+root
 1
+internal
 2
+polytomy
 3
 4
 5

cmd/labels.go

@@ -10,6 +10,9 @@ import (
 	"github.com/spf13/cobra"
 )
 
+var labelsNodes bool
+var labelsTips bool
+
 // labelsCmd represents the labels command
 var labelsCmd = &cobra.Command{
 	Use:   "labels",
@@ -44,14 +47,19 @@ If several trees are given in the input file, labels of all trees are listed.
 				io.LogError(t.Err)
 				return t.Err
 			}
-			for _, n := range t.Tree.Tips() {
-				f.WriteString(fmt.Sprintln(n.Name()))
+			for _, n := range t.Tree.Nodes() {
+				if (n.Tip() && labelsTips) || (!n.Tip() && labelsNodes && n.Name() != "") {
+					f.WriteString(fmt.Sprintln(n.Name()))
+
+				}
 			}
 		}
 		return
 	},
 }
 
 func init() {
+	labelsCmd.Flags().BoolVar(&labelsNodes, "internal", false, "Internal node labels are listed")
+	labelsCmd.Flags().BoolVar(&labelsTips, "tips", true, "Tip labels are listed (--tips=false to cancel)")
 	RootCmd.AddCommand(labelsCmd)
 }

docs/commands/labels.md

@@ -21,7 +21,9 @@ Usage:
   gotree labels [flags]
 
 Flags:
-  -h, --help   help for labels
+  -h, --help       help for labels
+      --internal   Internal node labels are listed
+      --tips       Tip labels are listed (--tips=false to cancel) (default true)
 
 Global Flags:
       --format string   Input tree format (newick, nexus, or phyloxml) (default "newick")
@@ -46,3 +48,27 @@ Tip5
 Tip1
 ```
 
+* List all tips and internal nodes labels 
+
+```
+echo "(1,(2,(3,4,5,6)polytomy)internal)root;" | gotree labels --internal
+root
+1
+internal
+2
+polytomy
+3
+4
+5
+6
+```
+
+
+* List only internal node labels 
+
+```
+echo "(1,(2,(3,4,5,6)polytomy)internal)root;" | gotree labels --tips=false --internal
+root
+internal
+polytomy
+```

docs/index.md

@@ -78,7 +78,7 @@ Command                                                            | Subcommand
 --                                                                 | topologies        | Generates all possible tree topologies
 --                                                                 | uniformtree       | Randomly generates uniform trees
 --                                                                 | yuletree          | Randomly generates Yule-Harding trees
-[labels](commands/labels.md) ([api](api/labels.md))                |                   | Lists labels of tree tips
+[labels](commands/labels.md)                                       |                   | Lists labels of tree tips
 [matrix](commands/matrix.md) ([api](api/matrix.md))                |                   | Prints distance matrix associated to the input tree
 [merge](commands/merge.md) ([api](api/merge.md))                   |                   | Merges two rooted trees
 [nni](commands/nni.md) ([api](api/nni.md))                   |                   | Generates all NNI neighbors from a given tree

test.sh

@@ -954,6 +954,24 @@ ${GOTREE} generate yuletree --seed 10 -n 2 | ${GOTREE} labels > result
 diff -q -b expected result
 rm -f expected result
 
+
+echo "->gotree internal labels"
+cat > expected <<EOF
+root
+1
+internal
+2
+polytomy
+3
+4
+5
+6
+EOF
+
+echo "(1,(2,(3,4,5,6)polytomy)internal)root;" | ${GOTREE} labels --internal > result
+diff -q -b expected result
+rm -f expected result
+
 echo "->gotree unroot"
 cat > expected <<EOF
 ((Tip9,Tip2),(Tip3,((((Tip8,Tip6),Tip5),Tip4),Tip1)),(Tip7,Tip0));