renamed multiply to scale, added support scale command

evolbioinfo · Jan 8, 2018 · d290577 · d290577
1 parent 2bcaefa
commit d290577
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Showing 8 changed files with 109 additions and 25 deletions.
diff --git a/README.md b/README.md
@@ -76,7 +76,7 @@ You may go to the [doc](docs/index.md) for a more detailed documentation of the
 *  annotate:    Annotate internal nodes of a tree with given data
 *  brlen:       Modify branch lengths
     * clear       Clear lengths from input trees
-    * multiply    Multiply lengths from input trees by a given factor
+    * scale       Scale lengths from input trees by a given factor
 	* setmin      Set a min branch length to all branches with length < cutoff
 	* setrand     Assign a random length to edges of input trees
 *  collapse:    Collapse branches of input trees
@@ -127,6 +127,7 @@ You may go to the [doc](docs/index.md) for a more detailed documentation of the
 *  support: Modify branch supports
     * clear       Clear supports from input trees
     * setrand     Assign a random support to edges of input trees
+    * scale       Scale branch supports from input trees by a given factor
 *  stats:       Print statistics about the tree, its edges, its nodes, if it is rooted, and its tips
     * edges
     * nodes

diff --git a/cmd/multiplybrlen.go b/cmd/multiplybrlen.go
@@ -4,16 +4,15 @@ import (
 	"github.com/spf13/cobra"
 
 	"github.com/fredericlemoine/gotree/io"
-	"github.com/fredericlemoine/gotree/tree"
 )
 
-var multiplylengthfactor float64
+var scalelengthfactor float64
 
 // clearlengthCmd represents the clearlength command
-var multiplylengthCmd = &cobra.Command{
-	Use:   "multiply",
-	Short: "Multiply lengths from input trees by a given factor",
-	Long:  `Multiply lengths from input trees by a given factor.`,
+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.`,
 	Run: func(cmd *cobra.Command, args []string) {
 		f := openWriteFile(outtreefile)
 		treefile, treechan := readTrees(intreefile)
@@ -22,18 +21,14 @@ var multiplylengthCmd = &cobra.Command{
 			if tr.Err != nil {
 				io.ExitWithMessage(tr.Err)
 			}
-			for _, e := range tr.Tree.Edges() {
-				if e.Length() != tree.NIL_LENGTH {
-					e.SetLength(e.Length() * multiplylengthfactor)
-				}
-			}
+			tr.Tree.ScaleLengths(scalelengthfactor)
 			f.WriteString(tr.Tree.Newick() + "\n")
 		}
 		f.Close()
 	},
 }
 
 func init() {
-	brlenCmd.AddCommand(multiplylengthCmd)
-	multiplylengthCmd.Flags().Float64VarP(&multiplylengthfactor, "factor", "f", 1.0, "Branch length multiplication factor")
+	brlenCmd.AddCommand(scalelengthCmd)
+	scalelengthCmd.Flags().Float64VarP(&scalelengthfactor, "factor", "f", 1.0, "Branch length scaling factor")
 }
diff --git a/cmd/multiplybrsupport.go b/cmd/multiplybrsupport.go
@@ -0,0 +1,34 @@
+package cmd
+
+import (
+	"github.com/spf13/cobra"
+
+	"github.com/fredericlemoine/gotree/io"
+)
+
+var scalesupportfactor float64
+
+// clearsupportCmd represents the support scale command
+var scalesupportCmd = &cobra.Command{
+	Use:   "scale",
+	Short: "Scale branch supports from input trees by a given factor",
+	Long:  `Scale branch supports from input trees by a given factor.`,
+	Run: func(cmd *cobra.Command, args []string) {
+		f := openWriteFile(outtreefile)
+		treefile, treechan := readTrees(intreefile)
+		defer treefile.Close()
+		for tr := range treechan {
+			if tr.Err != nil {
+				io.ExitWithMessage(tr.Err)
+			}
+			tr.Tree.ScaleSupports(scalesupportfactor)
+			f.WriteString(tr.Tree.Newick() + "\n")
+		}
+		f.Close()
+	},
+}
+
+func init() {
+	supportCmd.AddCommand(scalesupportCmd)
+	scalesupportCmd.Flags().Float64VarP(&scalesupportfactor, "factor", "f", 1.0, "Branch support scaling factor")
+}
diff --git a/docs/commands/brlen.md b/docs/commands/brlen.md
@@ -35,18 +35,18 @@ Global Flags:
   -o, --output string   Cleared tree output file (default "stdout")
 ```
 
-multiply subcommand
+scale subcommand
 ```
 Usage:
-  gotree brlen multiply [flags]
+  gotree brlen scale [flags]
 
 Flags:
-  -f, --factor float   Branch length multiplication factor (default 1)
-  -h, --help           help for multiply
+  -f, --factor float   Branch length scaling factor (default 1)
+  -h, --help           help for scale
 
 Global Flags:
   -i, --input string    Input tree (default "stdin")
-  -o, --output string   Cleared tree output file (default "stdout")
+  -o, --output string   Scaled tree output file (default "stdout")
 ```
 
 setmin subcommand
@@ -143,9 +143,9 @@ Random Tree                          | Min brlen tree
 ![Random Tree](minbrlen_1.svg)       | ![Min brlen tree](minbrlen_2.svg) 
 
 
-4. Multiplying branch lengths by 3.0
+4. Scaling branch lengths by a factor 3.0
 
 ```
 gotree generate yuletree -s 10 -l 100 -o outtree.nw
-gotree brlen multiply -f 3.0 -i outtree.nw
+gotree brlen scale -f 3.0 -i outtree.nw
 ```
diff --git a/docs/commands/support.md b/docs/commands/support.md
@@ -34,6 +34,20 @@ Global Flags:
   -o, --output string   Cleared tree output file (default "stdout")
 ```
 
+scale subcommand
+```
+Usage:
+  gotree support scale [flags]
+
+Flags:
+  -f, --factor float   Branch support scaling factor (default 1)
+  -h, --help           help for scale
+
+Global Flags:
+  -i, --input string    Input tree (default "stdin")
+  -o, --output string   Scaled tree output file (default "stdout")
+```
+
 setrand subcommand
 ```
 Usage:
@@ -99,3 +113,15 @@ gotree draw svg -w 200 -H 200  -i outtree2.nw --with-branch-support --support-cu
 Initial random Tree                 | Random Supports
 ------------------------------------|---------------------------------------
 ![Random Tree 1](randsupport_1.svg) | ![Random Supports](randsupport_2.svg)
+
+3. Scaling branch supports by a factor 0.01 (/100 to /1)
+
+```
+echo "((a,b)100,c,d);" | gotree support scale -f 0.01
+```
+
+Should produce:
+```
+((a,b)1,c,d);
+```
+
diff --git a/docs/index.md b/docs/index.md
@@ -38,7 +38,7 @@ Command                                                            | Subcommand
 [annotate](commands/annotate.md) ([api](api/annotate.md))          |                   | Annotates internal nodes of a tree with given data
 [brlen](commands/brlen.md) ([api](api/brlen.md))                   |                   | Modifies branch lengths
 --                                                                 | clear             | Clear lengths from input trees
---                                                                 | multiply          | Multiplies lengths from input trees by a given factor
+--                                                                 | scale             | Scales branch lengths from input trees by a given factor
 --                                                                 | setmin            | Sets a min branch length to all branches with length < cutoff
 --                                                                 | setrand           | Assigns a random length to edges of input trees
 [collapse](commands/collapse.md) ([api](api/collapse.md))          |                   | Collapses/Removes branches of input trees
@@ -88,6 +88,7 @@ Command                                                            | Subcommand
 [subtree](commands/subtree.md) ([api](api/subtree.md))             |                   | Extracts a subtree starting at a given node
 [support](commands/support.md) ([api](api/support.md))             |                   | Modifies branch supports
 --                                                                 | clear             | Clears branch supports from input trees
+--                                                                 | scale             | Scales branch supports from input trees by a given factor
 --                                                                 | setrand           | Assigns a random support to edges of input trees
 [stats](commands/stats.md) ([api](api/stats.md))                   |                   | Prints statistics about the tree, its edges, its nodes, if it is rooted, and its tips
 --                                                                 | edges             | Prints informations about all the edges

diff --git a/test.sh b/test.sh
@@ -35,8 +35,8 @@ gotree generate yuletree -s 10 -n 10 | gotree brlen clear > result
 diff result expected
 rm -f expected result
 
-# gotree brlen multiply
-echo "->gotree brlen multiply"
+# gotree brlen scale
+echo "->gotree brlen scale"
 cat > input.tree <<EOF
 ((Tip4:1,(Tip7:1,Tip2:1):1):1,Tip0:1,((Tip8:1,(Tip9:1,Tip3:1):1):1,((Tip6:1,Tip5:1):1,Tip1:1):1):1);
 (Tip5,Tip0,((Tip6,(Tip7,Tip4)),(Tip2,((Tip8,(Tip9,Tip3)),Tip1))));
@@ -47,10 +47,26 @@ cat > expected <<EOF
 (Tip5,Tip0,((Tip6,(Tip7,Tip4)),(Tip2,((Tip8,(Tip9,Tip3)),Tip1))));
 (Tip6:1.5,Tip0:1.5,((((Tip5:1.5,Tip4:1.5):1.5,((Tip9:1.5,Tip8:1.5),Tip3:1.5):1.5):1.5,(Tip7:1.5,Tip2:1.5):1.5):1.5,Tip1:1.5):1.5);
 EOF
-gotree brlen multiply -i input.tree -f 3.0 > result
+gotree brlen scale -i input.tree -f 3.0 > result
 diff result expected
 rm -f expected result input.tree
 
+# gotree support scale
+echo "->gotree support scale"
+cat > input.tree <<EOF
+((a,b)99,(c,d)50,(e,f)0,g);
+EOF
+cat > expected.1 <<EOF
+((a,b)0.99,(c,d)0.5,(e,f)0,g);
+EOF
+cat > expected.2 <<EOF
+((a,b)198,(c,d)100,(e,f)0,g);
+EOF
+gotree support scale -i input.tree -f 0.01 > result.1
+gotree support scale -i input.tree -f 2 > result.2
+diff result.1 expected.1
+diff result.2 expected.2
+rm -f expected.1 expected.2 result.1 result.2 input.tree
 
 
 # gotree support clear

diff --git a/tree/tree.go b/tree/tree.go
@@ -1413,3 +1413,14 @@ func (t *Tree) ScaleSupports(factor float64) {
 		}
 	}
 }
+
+// Scale branch lengths by a given factor.
+//
+// Does not do anything for branches with a length of NIL_LENGTH
+func (t *Tree) ScaleLengths(factor float64) {
+	for _, e := range t.Edges() {
+		if s := e.Length(); s != NIL_LENGTH {
+			e.SetLength(e.Length() * factor)
+		}
+	}
+}