Added options --root and --tips to collapse brlength, support, and de…

…pth commands #12

cmd/collapsebrlen.go

@@ -10,16 +10,24 @@ import (
 )
 
 var shortbranchesThreshold float64
+var shortbranchesRemoveRoot bool
+var shortbranchesRemoveTips bool
 
 // collapseCmd represents the collapse command
 var collapsebrlenCmd = &cobra.Command{
 	Use:   "length",
 	Short: "Collapse short branches of the input tree",
 	Long: `Collapse short branches of the input tree.
 
-Short branches are defined by a threshold (-l). All branches 
+Short branches are defined by a threshold (-l). All internal branches 
 with length <= threshold are removed.
 
+If --root is given, then it applies also to internal branches connected to the root in the case 
+of rooted trees. This may unroot the tree. In that case, so far the two branches connected to the root are 
+considered independently whereas it may be more useful to consider them as a single bipartition if the 
+tree is going to be unrooted.
+
+If --tips is given, then it applies also to external branches, just by setting their length to 0.0
 `,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
 		var f *os.File
@@ -43,7 +51,7 @@ with length <= threshold are removed.
 				io.LogError(t.Err)
 				return t.Err
 			}
-			t.Tree.CollapseShortBranches(shortbranchesThreshold)
+			t.Tree.CollapseShortBranches(shortbranchesThreshold, shortbranchesRemoveRoot, shortbranchesRemoveTips)
 			f.WriteString(t.Tree.Newick() + "\n")
 		}
 		return
@@ -53,4 +61,6 @@ with length <= threshold are removed.
 func init() {
 	collapseCmd.AddCommand(collapsebrlenCmd)
 	collapsebrlenCmd.Flags().Float64VarP(&shortbranchesThreshold, "length", "l", 0.0, "Length cutoff to collapse branches")
+	collapsebrlenCmd.Flags().BoolVar(&shortbranchesRemoveRoot, "root", false, "Applies also to branches connected to the root (may unroot the tree)")
+	collapsebrlenCmd.Flags().BoolVar(&shortbranchesRemoveTips, "tips", false, "Applies also to tips (keeps a 0.0 length tip)")
 }

cmd/collapsedepth.go

@@ -11,20 +11,26 @@ import (
 
 var maxdepthThreshold int
 var mindepthThreshold int
+var collapseDepthRoot bool
+var collapseDepthTips bool
 
 // collapsedepthCmd represents the collapsedepth command
 var collapsedepthCmd = &cobra.Command{
 	Use:   "depth",
 	Short: "Collapse branches having a given depth",
 	Long: `Collapse branches having a given depth.
 
-Branches having depth (number of taxa on the lightest side of 
-the bipartition) d such that:
+Removes internal branches (not connected to the root in case of rooted trees) 
+having depth (number of taxa on the lightest side of the bipartition) d such that:
 
 min-depth<=d<=max-depth
 
 will be collapsed.
 
+If --root is given, then it applies also to internal branches connected to the root in the case 
+of rooted trees. This may unroot the tree.
+
+If --tips is given, then it applies also to external branches (if min-depth<=1), just by setting their length to 0.0
 `,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
 		var f *os.File
@@ -53,7 +59,7 @@ will be collapsed.
 				return
 			}
 
-			t.Tree.CollapseTopoDepth(mindepthThreshold, maxdepthThreshold)
+			t.Tree.CollapseTopoDepth(mindepthThreshold, maxdepthThreshold, collapseDepthRoot, collapseDepthTips)
 			f.WriteString(t.Tree.Newick() + "\n")
 		}
 		return
@@ -65,4 +71,6 @@ func init() {
 
 	collapsedepthCmd.Flags().IntVarP(&mindepthThreshold, "min-depth", "m", 0, "Min depth cutoff to collapse branches")
 	collapsedepthCmd.Flags().IntVarP(&maxdepthThreshold, "max-depth", "M", 0, "Max Depth cutoff to collapse branches")
+	collapsedepthCmd.Flags().BoolVar(&collapseDepthRoot, "root", false, "Applies also to branches connected to the root (may unroot the tree)")
+	collapsedepthCmd.Flags().BoolVar(&collapseDepthTips, "tips", false, "Applies also to tips (keeps a 0.0 length tip)")
 }

cmd/collapsesupport.go

@@ -10,16 +10,21 @@ import (
 )
 
 var lowSupportThreshold float64
+var supportRemoveRoot bool
 
 // collapsesupportCmd represents the collapsesupport command
 var collapsesupportCmd = &cobra.Command{
 	Use:   "support",
 	Short: "Collapse lowly supported branches of the input tree",
 	Long: `Collapse lowly supported branches of the input tree.
 
-Lowly supported branches are defined by a threshold (-s). All branches 
-with support < threshold are removed.
-`,
+Lowly supported branches are defined by a threshold (-s). All internal branches 
+with support < threshold and that are not connected to the root in case of rooted tree
+ are removed.
+
+ If --root is given, then it applies also to internal branches connected to the root in the case 
+ of rooted trees. This may unroot the tree.
+ `,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
 		var f *os.File
 		var treefile goio.Closer
@@ -38,7 +43,7 @@ with support < threshold are removed.
 				io.LogError(t.Err)
 				return t.Err
 			}
-			t.Tree.CollapseLowSupport(lowSupportThreshold)
+			t.Tree.CollapseLowSupport(lowSupportThreshold, supportRemoveRoot)
 			f.WriteString(t.Tree.Newick() + "\n")
 		}
 		return
@@ -48,4 +53,6 @@ with support < threshold are removed.
 func init() {
 	collapseCmd.AddCommand(collapsesupportCmd)
 	collapsesupportCmd.Flags().Float64VarP(&lowSupportThreshold, "support", "s", 0.0, "Support cutoff to collapse branches")
+	collapsesupportCmd.Flags().BoolVar(&supportRemoveRoot, "root", false, "Applies also to branches connected to the root (may unroot the tree)")
+
 }

docs/commands/collapse.md

@@ -3,7 +3,7 @@
 ## Commands
 
 ### collapse
-This command removes branches from a set of input trees. Three subcommands :
+This command removes branches from a set of input trees.  They apply only to internal branches, and not to branches connected to the root (for rooted trees). Three subcommands :
 * `gotree collapse length`  will remove branches whose length is less than or equal to the specified length;
 * `gotree collapse support` will remove branches whose support is less than the specified support;
 * `gotree collapse depth` will remove branches whose depth is between (or equal to) given min and max depths. Here, depth is defined as the number of taxa on the lightest side of the branch.
@@ -17,6 +17,9 @@ This command removes branches from a set of input trees. Three subcommands :
             t2          t2
 ```
 
+- If option `--tips` is given, length of tips matching the threshold will be set to 0.0 (for `depth` and `length` commands).
+- If option `--root` is given, branches connected to the root (in the case of rooted trees) and matching the threshold will be removed (for `depth`, `length`, and `support` commands). Resulting tree may be unrooted. Also, so far the two branches connected to the root are considered independently whereas it may be more useful to consider them as a single bipartition if the tree is going to be unrooted.
+
 #### Usage
 
 General command

test.sh

@@ -245,6 +245,32 @@ ${GOTREE} generate yuletree --seed 10 | ${GOTREE} collapse length -l 0.05 | ${GO
 diff -q -b result expected
 rm -f expected result
 
+echo "->gotree collapse support root + tips"
+cat > expected <<EOF
+(A:1,B:1,C:1,D:1);
+EOF
+echo "((A:1,B:1)0.2:1,(C:1,D:1)0.1:1);" | ${GOTREE} collapse support -s 1 --root > result
+diff -q -b result expected
+rm -f expected result
+
+
+echo "->gotree collapse length root + tips"
+cat > expected <<EOF
+(A:0,B:0,C:0,D:0);
+EOF
+echo "((A:1,B:1)0.2:1,(C:1,D:1)0.1:1);" | ${GOTREE} collapse length  -l 2 --root --tips > result
+diff -q -b result expected
+rm -f expected result
+
+
+echo "->gotree collapse depth root + tips"
+cat > expected <<EOF
+(A:0,B:0,C:0,D:0);
+EOF
+echo "((A:1,B:1)0.2:1,(C:1,D:1)0.1:1);" | ${GOTREE} collapse depth  -m 0 -M 10 --root --tips > result
+diff -q -b result expected
+rm -f expected result
+
 
 # gotree collapse support
 echo "->gotree collapse support"

tests/collapse_test.go

@@ -2,9 +2,10 @@ package tests
 
 import (
 	"fmt"
-	"github.com/evolbioinfo/gotree/io/newick"
 	"strings"
 	"testing"
+
+	"github.com/evolbioinfo/gotree/io/newick"
 )
 
 var treestring string = "(Tip2:1.00000,Node0:1.0000,((Tip7:1.00000,((Tip9:1.00000,Tip6:1.0000):1.0000,(Tip5:1.00000,Tip3:1.0000):1.0000):1.00):1.00,(Tip4:1.00000,(Tip8:1.00000,Tip1:1.000):0.126):0.127):0.125);"
@@ -25,7 +26,7 @@ func TestCollapse(t *testing.T) {
 		t.Error(fmt.Sprintf("The sum of branch lengths before collapse is not  (%f)", sumlen))
 	}
 
-	tree.CollapseShortBranches(0.126)
+	tree.CollapseShortBranches(0.126, false, false)
 	edges = tree.Edges()
 	sumlen = tree.SumBranchLengths()
 
@@ -38,6 +39,100 @@ func TestCollapse(t *testing.T) {
 	}
 }
 
+var treestring3 string = "((A:1,B:1)0.2:1,(C:1,D:1)0.1:1);"
+
+func TestCollapse2(t *testing.T) {
+	tree, err2 := newick.NewParser(strings.NewReader(treestring3)).Parse()
+
+	if err2 != nil {
+		t.Error(err2)
+	}
+
+	edges := tree.Edges()
+	sumlen := tree.SumBranchLengths()
+	if len(edges) != 6 {
+		t.Error(fmt.Sprintf("The number of edges before collapse is not 6 (%d)", len(edges)))
+	}
+	if sumlen != 6 {
+		t.Error(fmt.Sprintf("The sum of branch lengths before collapse is not 6 (%f)", sumlen))
+	}
+
+	tree.CollapseShortBranches(2, true, true)
+	edges = tree.Edges()
+	sumlen = tree.SumBranchLengths()
+
+	if len(edges) != 4 {
+		t.Error(fmt.Sprintf("The number of edges after collapse is not 4 (%d)", len(edges)))
+	}
+
+	if sumlen != 0 {
+		t.Error(fmt.Sprintf("The sum of branch lengths after collapse is not 0 (%f)", sumlen))
+	}
+}
+
+func TestCollapse3(t *testing.T) {
+	tree, err2 := newick.NewParser(strings.NewReader(treestring3)).Parse()
+
+	if err2 != nil {
+		t.Error(err2)
+	}
+
+	edges := tree.Edges()
+	sumlen := tree.SumBranchLengths()
+	if len(edges) != 6 {
+		t.Error(fmt.Sprintf("The number of edges before collapse is not 6 (%d)", len(edges)))
+	}
+	if sumlen != 6 {
+		t.Error(fmt.Sprintf("The sum of branch lengths before collapse is not 6 (%f)", sumlen))
+	}
+
+	tree.CollapseLowSupport(0.5, true)
+	edges = tree.Edges()
+	sumlen = tree.SumBranchLengths()
+
+	if len(edges) != 4 {
+		t.Error(fmt.Sprintf("The number of edges after collapse is not 4 (%d)", len(edges)))
+	}
+
+	if sumlen != 4 {
+		t.Error(fmt.Sprintf("The sum of branch lengths after collapse is not 4 (%f)", sumlen))
+	}
+}
+
+func TestCollapse5(t *testing.T) {
+	tree, err2 := newick.NewParser(strings.NewReader(treestring3)).Parse()
+	if err2 != nil {
+		t.Error(err2)
+	}
+
+	if err2 = tree.ReinitIndexes(); err2 != nil {
+		t.Error(err2)
+	}
+
+	edges := tree.Edges()
+	sumlen := tree.SumBranchLengths()
+	if len(edges) != 6 {
+		t.Error(fmt.Sprintf("The number of edges before collapse is not 6 (%d)", len(edges)))
+	}
+	if sumlen != 6 {
+		t.Error(fmt.Sprintf("The sum of branch lengths before collapse is not 6 (%f)", sumlen))
+	}
+
+	if err2 = tree.CollapseTopoDepth(0, 10, true, true); err2 != nil {
+		t.Error(err2)
+	}
+	edges = tree.Edges()
+	sumlen = tree.SumBranchLengths()
+
+	if len(edges) != 4 {
+		t.Error(fmt.Sprintf("The number of edges after collapse is not 4 (%d)", len(edges)))
+	}
+
+	if sumlen != 0 {
+		t.Error(fmt.Sprintf("The sum of branch lengths after collapse is not 0 (%f)", sumlen))
+	}
+}
+
 var treestring2 string = "(A:1,(B:1):1,C:1);"
 
 func TestCollapseSingle(t *testing.T) {

tests/tree_test.go

@@ -82,7 +82,7 @@ func TestCollapseDepth(t *testing.T) {
 		t.Error(err)
 	}
 
-	if err = tr.CollapseTopoDepth(2, 3); err != nil {
+	if err = tr.CollapseTopoDepth(2, 3, false, false); err != nil {
 		t.Error(err)
 	}
 	if tr.Newick() != "(Tip4,Tip0,Tip3,Tip2,Tip1);" {
@@ -96,7 +96,7 @@ func TestCollapseLength(t *testing.T) {
 	if err != nil {
 		t.Error(err)
 	}
-	tr.CollapseShortBranches(0.01)
+	tr.CollapseShortBranches(0.01, false, false)
 	if tr.Newick() != "(Tip4:0.1,Tip0:0.1,(Tip3:0.1,Tip2:0.2,Tip1:0.2):0.4);" {
 		t.Error(fmt.Sprintf("Tree after collapse lengths is not valid: %s", tr.Newick()))
 	}
@@ -108,7 +108,7 @@ func TestCollapseSupport(t *testing.T) {
 	if err != nil {
 		t.Error(err)
 	}
-	tr.CollapseLowSupport(0.7)
+	tr.CollapseLowSupport(0.7, false)
 	if tr.Newick() != "(Tip4,Tip0,(Tip3,Tip2,Tip1)0.9);" {
 		t.Error(fmt.Sprintf("Tree after collapse support is not valid: %s", tr.Newick()))
 	}