Merge branch 'master' into dev

cmd/collapsebrname.go

@@ -0,0 +1,102 @@
+package cmd
+
+import (
+	"fmt"
+	goio "io"
+	"os"
+
+	"github.com/evolbioinfo/gotree/io"
+	"github.com/evolbioinfo/gotree/tree"
+	"github.com/spf13/cobra"
+)
+
+var brnamefile string
+var brid bool
+
+// collapseCmd represents the collapse command
+var collapsebrnameCmd = &cobra.Command{
+	Use:   "name",
+	Short: "Collapse branches having given name or ID",
+	Long: `Collapse branches having given name or ID.
+
+	Names (or ID) are defined in an input file (-b)
+
+	If an external branch name/id is given, then does not do anything.
+`,
+	RunE: func(cmd *cobra.Command, args []string) (err error) {
+		var f *os.File
+		var treefile goio.Closer
+		var treechan <-chan tree.Trees
+		var brnames []string
+		var brids []int
+		var toremove []*tree.Edge
+
+		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()
+
+		if brid {
+
+			if brids, err = parseIntFile(brnamefile); err != nil {
+				io.LogError(err)
+				return
+			}
+		} else {
+			if brnames, err = parseStringFile(brnamefile); err != nil {
+				io.LogError(err)
+				return
+			}
+		}
+
+		for t := range treechan {
+			if t.Err != nil {
+				io.LogError(t.Err)
+				return t.Err
+			}
+			t.Tree.ReinitIndexes()
+			alledges := t.Tree.Edges()
+			if brid {
+				for _, i := range brids {
+					if i < 0 || i >= len(alledges) {
+						err = fmt.Errorf("branch index is not in the tree (<0 or >#branches)")
+						io.LogError(err)
+						return
+					}
+					toremove = append(toremove, alledges[i])
+				}
+			} else {
+				for _, n := range brnames {
+					found := false
+					for _, e := range alledges {
+						if e.Name(t.Tree.Rooted()) == n {
+							toremove = append(toremove, e)
+							found = true
+						}
+					}
+					if !found {
+						err = fmt.Errorf("branch name %s not found in the tree", n)
+						io.LogError(err)
+						return
+					}
+				}
+			}
+			t.Tree.RemoveEdges(true, false, toremove...)
+			f.WriteString(t.Tree.Newick() + "\n")
+		}
+		return
+	},
+}
+
+func init() {
+	collapseCmd.AddCommand(collapsebrnameCmd)
+	collapsebrnameCmd.Flags().StringVarP(&brnamefile, "brfile", "b", "none", "File with one branch name/id per line")
+	collapsebrnameCmd.Flags().BoolVar(&brid, "id", false, "Input file contains branch ids (otherwise, branch names)")
+}

cmd/root.go

@@ -178,28 +178,61 @@ func readTree(infile string) (t *tree.Tree, err error) {
 	return
 }
 
-func parseTipsFile(file string) (tips []string, err error) {
+// Parse a file with one string per line
+func parseStringFile(file string) (s []string, err error) {
+	var ifilereader *bufio.Reader
+	var ifile goio.Closer
+	var line string
+	var err2 error
 
-	var treereader *bufio.Reader
-	var treefile goio.Closer
+	s = make([]string, 0, 100)
+
+	if ifile, ifilereader, err = utils.GetReader(file); err == nil {
+		line, err2 = Readln(ifilereader)
+		for err2 == nil {
+			for _, name := range strings.Split(line, ",") {
+				s = append(s, name)
+			}
+			line, err2 = Readln(ifilereader)
+		}
+		ifile.Close()
+	}
+	return
+}
+
+// Parse a file with one int per line
+func parseIntFile(file string) (islice []int, err error) {
+	var ifilereader *bufio.Reader
+	var ifile goio.Closer
 	var line string
 	var err2 error
+	var tempi int
 
-	tips = make([]string, 0, 100)
+	islice = make([]int, 0, 100)
 
-	if treefile, treereader, err = utils.GetReader(file); err == nil {
-		line, err2 = Readln(treereader)
+	if ifile, ifilereader, err = utils.GetReader(file); err == nil {
+		line, err2 = Readln(ifilereader)
 		for err2 == nil {
 			for _, name := range strings.Split(line, ",") {
-				tips = append(tips, name)
+
+				if tempi, err = strconv.Atoi(name); err != nil {
+					return
+				}
+				islice = append(islice, tempi)
 			}
-			line, err2 = Readln(treereader)
+			line, err2 = Readln(ifilereader)
 		}
-		treefile.Close()
+		ifile.Close()
 	}
 	return
 }
 
+// Parse a file with one tip name per line
+func parseTipsFile(file string) (tips []string, err error) {
+	tips, err = parseStringFile(file)
+	return
+}
+
 func readMapFile(file string, revert bool) (map[string]string, error) {
 	outmap := make(map[string]string, 0)
 	var mapfile *os.File

test.sh

@@ -315,6 +315,35 @@ ${GOTREE} generate yuletree --seed 10 | ${GOTREE} collapse depth -m 2 -M 2 | ${G
 diff -q -b result expected
 rm -f expected result
 
+# gotree collapse id
+echo "->gotree collapse id/name"
+cat > input <<EOF
+((Tip4,Tip7,Tip2),Tip0,((Tip8,Tip9,Tip3),(Tip1,Tip6,Tip5)));
+EOF
+cat > expected <<EOF
+(Tip0,Tip4,Tip7,Tip2,Tip8,Tip9,Tip3,Tip1,Tip6,Tip5);
+EOF
+cat > expected2 <<EOF
+(Tip0,Tip4,Tip7,Tip2,(Tip1,Tip6,Tip5),Tip8,Tip9,Tip3);
+EOF
+cat > br <<EOF
+0
+5
+6
+10
+EOF
+cat > br2 <<EOF
+0
+5
+6
+EOF
+
+${GOTREE} collapse name -i input --id -b br > result
+diff -q -b result expected
+${GOTREE} collapse name -i input --id -b br2 > result
+diff -q -b result expected2
+rm -f input expected result br br2 expected2
+
 # gotree collapse single
 echo "->gotree collapse single"
 cat > test_input <<EOF