Added options --rm-quotes and --add-quotes to gotree rename #9

cmd/rename.go

@@ -14,6 +14,8 @@ var autorename bool
 var autorenamelength int
 var renameInternalNodes bool
 var renameTips bool
+var removeQuotes bool
+var addQuotes bool
 var renameRegex string
 var renameReplaceBy string
 
@@ -63,6 +65,9 @@ var renameCmd = &cobra.Command{
   this will replace all matches of 'Tip(\d+)' with 'Leaf$1', with $1 being the matched string 
   inside ().
 
+* If --add-quotes is specified, then output names will be surrounded by ''
+
+* If --rm-quotes is specified, starting or ending quotes are removed.
 
 Warning: If after this rename, several tips/nodes have the same name, subsequent commands may 
 fail.
@@ -91,7 +96,12 @@ If --internal is specified, then internal nodes are renamed;
 			return
 		}
 
-		if !autorename && !setregex {
+		if autorename || setregex || removeQuotes || addQuotes {
+			if autorenamelength < 5 {
+				autorenamelength = 5
+			}
+			namemap = make(map[string]string)
+		} else {
 			// Read map file
 			if mapfile == "none" {
 				err = errors.New("map file is not given")
@@ -103,11 +113,6 @@ If --internal is specified, then internal nodes are renamed;
 				io.LogError(err)
 				return
 			}
-		} else {
-			if autorenamelength < 5 {
-				autorenamelength = 5
-			}
-			namemap = make(map[string]string)
 		}
 
 		if f, err = openWriteFile(outtreefile); err != nil {
@@ -140,6 +145,16 @@ If --internal is specified, then internal nodes are renamed;
 					io.LogError(err)
 					return
 				}
+			} else if addQuotes {
+				if err = tr.Tree.AddQuotes(renameInternalNodes, renameTips, namemap); err != nil {
+					io.LogError(err)
+					return
+				}
+			} else if removeQuotes {
+				if err = tr.Tree.RemoveQuotes(renameInternalNodes, renameTips, namemap); err != nil {
+					io.LogError(err)
+					return
+				}
 			} else {
 				if err = tr.Tree.Rename(namemap); err != nil {
 					io.LogError(err)
@@ -150,7 +165,7 @@ If --internal is specified, then internal nodes are renamed;
 			f.WriteString(tr.Tree.Newick() + "\n")
 		}
 
-		if (autorename || setregex) && mapfile != "none" {
+		if (autorename || setregex || removeQuotes || addQuotes) && mapfile != "none" {
 			if err = writeNameMap(namemap, mapfile); err != nil {
 				io.LogError(err)
 				return
@@ -166,6 +181,8 @@ func init() {
 	renameCmd.Flags().StringVarP(&intreefile, "input", "i", "stdin", "Input tree")
 	renameCmd.Flags().BoolVar(&renameInternalNodes, "internal", false, "Internal nodes are taken into account")
 	renameCmd.Flags().BoolVar(&renameTips, "tips", true, "Tips are taken into account (--tips=false to cancel)")
+	renameCmd.Flags().BoolVar(&addQuotes, "add-quotes", false, "Add quotes arround tip/node names")
+	renameCmd.Flags().BoolVar(&removeQuotes, "rm-quotes", false, "Remove quotes arround tip/node names (priority over --rm-quotes)")
 	renameCmd.Flags().StringVarP(&mapfile, "map", "m", "none", "Tip name map file")
 	renameCmd.Flags().StringVarP(&renameRegex, "regexp", "e", "none", "Regexp to get matching tip/node names")
 	renameCmd.Flags().StringVarP(&renameReplaceBy, "replace", "b", "none", "String replacement to the given regexp")

docs/commands/rename.md

@@ -5,21 +5,27 @@
 ### rename
 This command renames tips and/or internal nodes of input trees. Several possibilities:
 
-*  An existing map file is given (`-m`), and must be tab separated with columns:
+*  Default: An existing map file is given (`-m`), and must be tab separated with columns:
    1) Current name of the tip
    2) Desired new name of the tip
 
   - If `--revert` is specified then it is the other way
   - If a tip name does not appear in the map file, it will not be renamed. 
   - If a name that does not exist appears in the map file, it will not throw an error.
 
+Then, by order of priority:
+
 * The `-a` option is given. In this case, tips and/or internal nodes are renamed using automatically generated identifiers of length 10 (or of length `--length`).
   - Correspondance between old names and new generated names is written in the map file given with `-m`. 
   - In this mode, `--revert` has no effect.
   - `--length`  allows to customize length of generated id. Length is set to 5 if given length is less that 5.
   - If several trees in input have different tip names, a new identifier is still generated for each tip name that has never been seen (already seen names are associated to the same new name).
 
-* The `-e` (`--regexp`) and `-b` (`--replace`) is given, then it will replace matching strings in tip/node names by string given by `-b`. It takes advantages of the golang regexp machinery, i.e. it is possible to specify capturing groups and refering to it in the replacement string, for instance: `gotree rename -i tree.nh --regexp 'Tip(\d+)' --replace 'Leaf$1' -m map.txt`  will replace all matches of `Tip(\d+)` with `Leaf$1`, $1 being the matched string inside the capturing group `()`.
+* The `-e` (`--regexp`) and `-b` (`--replace`) options are given, then it will replace matching strings in tip/node names by string given by `-b`. It takes advantages of the golang regexp machinery, i.e. it is possible to specify capturing groups and refering to it in the replacement string, for instance: `gotree rename -i tree.nh --regexp 'Tip(\d+)' --replace 'Leaf$1' -m map.txt`  will replace all matches of `Tip(\d+)` with `Leaf$1`, $1 being the matched string inside the capturing group `()`.
+
+* `--add-quotes` is specified, then output names will be surrounded by single quotes. It replaces starting/ending double quotes by single quotes.
+
+* `--rm-quotes` is specified, then starting or ending single/double quotes are removed.
 
 
 Other informations:
@@ -35,6 +41,7 @@ Usage:
   gotree rename [flags]
 
 Flags:
+  --add-quotes       Add quotes arround tip/node names
   -a, --auto             Renames automatically tips with auto generated id of length 10.
   -h, --help             help for rename
   -i, --input string     Input tree (default "stdin")
@@ -45,6 +52,7 @@ Flags:
   -e, --regexp string    Regexp to get matching tip/node names (default "none")
   -b, --replace string   String replacement to the given regexp (default "none")
   -r, --revert           Revert orientation of map file
+      --rm-quotes        Remove quotes arround tip/node names (priority over --rm-quotes)
       --tips             Tips are taken into account (--tips=false to cancel) (default true)
 
 Global Flags:

tree/tree.go

@@ -1492,6 +1492,84 @@ func (t *Tree) RenameRegexp(internals, tips bool, regex, replace string, namemap
 	return nil
 }
 
+// RemoveQuotes removes potential single and double quotes surrounding tip and/or internal node names
+//
+// internals: Remove quotes at internal nodes names
+// tips: Remove quotes at tips names
+func (t *Tree) RemoveQuotes(internals, tips bool, namemap map[string]string) error {
+	for _, n := range t.Nodes() {
+		if (tips && n.Tip()) || (internals && !n.Tip()) {
+			name := n.Name()
+			first := name[0]
+			last := name[len(name)-1]
+			firstpos := 0
+			lastpos := len(name)
+			if first == '\'' || first == '"' {
+				firstpos = 1
+			}
+			if last == '\'' || last == '"' {
+				lastpos = lastpos - 1
+			}
+			newname := name[firstpos:lastpos]
+			n.SetName(newname)
+			namemap[name] = newname
+		}
+	}
+	// After we update bitsets if any, and node indexes
+	//t.ReinitIndexes()
+	if err := t.UpdateTipIndex(); err != nil {
+		return err
+	}
+	// err := t.ClearBitSets()
+	// if err != nil {
+	// 	return err
+	// }
+	// t.UpdateBitSet()
+	return nil
+}
+
+// AddQuotes adds quotes arround tip and/or internal node names.
+//
+// If a single quote is already present at the beginning or at the end, it
+// leaves it unchanged.
+//
+// If a double quote is already present at the bebinning or at the end, it
+// is replaced by a single quote
+//
+// internals: Adds quotes at internal nodes
+// tips: Adds quotes at tips
+func (t *Tree) AddQuotes(internals, tips bool, namemap map[string]string) error {
+	for _, n := range t.Nodes() {
+		if (tips && n.Tip()) || (internals && !n.Tip()) {
+			name := n.Name()
+			first := name[0]
+			last := name[len(name)-1]
+			firstpos := 0
+			lastpos := len(name)
+			if first == '\'' || first == '"' {
+				firstpos = 1
+			}
+			if last == '\'' || last == '"' {
+				lastpos = lastpos - 1
+			}
+			newname := fmt.Sprintf("'%s'", name[firstpos:lastpos])
+			n.SetName(newname)
+			namemap[name] = newname
+		}
+	}
+	// After we update bitsets if any, and node indexes
+	//t.ReinitIndexes()
+	if err := t.UpdateTipIndex(); err != nil {
+		return err
+	}
+	// err := t.ClearBitSets()
+	// if err != nil {
+	// 	return err
+	// }
+	// t.UpdateBitSet()
+	return nil
+}
+
 // Clone the given node, copy attributes of the given
 // node into a new node
 func (t *Tree) CopyNode(n *Node) *Node {
@@ -1559,7 +1637,7 @@ func (t *Tree) copyTreeRecur(copytree *Tree, copynode, node *Node, edge *Edge) {
 	}
 }
 
-// Assumes that the tree is rooted.
+// SubTree Assumes that the tree is rooted.
 //
 // Otherwise, will consider the pseudo root
 // defined by the initial newick file
@@ -1576,7 +1654,7 @@ func (t *Tree) SubTree(n *Node) *Tree {
 	return (subtree)
 }
 
-// Merges Two rooted trees t and t2 in t by adding a new root node with two children
+// Merge merges Two rooted trees t and t2 in t by adding a new root node with two children
 // Corresponding to the roots of the 2 trees.
 //
 // If one of the tree is not rooted, returns an error.
@@ -1616,7 +1694,7 @@ func (t *Tree) Merge(t2 *Tree) error {
 	return nil
 }
 
-// Returns the deepest edge of the tree (considered unrooted)
+// DeepestEdge returns the deepest edge of the tree (considered unrooted)
 // in terms of number of tips on the light side of it.
 //
 // It does not use bitsets, thus they may be uninitialized.