Question: Let's say I have an input file where each line contains the path from the root (A) to a leaf

```
echo "A\tB\tC\nA\tB\tD\nA\tE" > lines.txt
A   B   C
A   B   D
A   E

```

How can I easily generate the resulting tree?: `(A(B(C,D),E))` 

I'd like to use GNU tools (awk, sed, etc.) because they tend to work better with large files, but an R script would also work. The R input would be:

```
# lines <- lapply(readLines("lines.txt"), strsplit, " +")
lines <- list(list(c("A", "B", "C")), list(c("A", "B", "D")), list(c("A","E")))

```

Answer: 
Why do it the easy way, if you can use Bourne Shell script instead? Note, this is not even Bash, this is plain old Bourne shell, without arrays...

```
#!/bin/sh
#
# A B C
# A B D
# A E
#
# "" vs "A B C"         -> 0->3, ident 0        -> -0+3 -> "(A(B(C"
# "A B C" vs "A B D"    -> 3->3, ident 2        -> -1+1 -> ",D"
# "A B D" vs "A E"      -> 3->2, ident 1        -> -2+1 -> "),E"
# "A E" vs. endc        -> 2->0, ident 0        -> -2+0 -> "))"
#
# Result: (A(B(C,D),E))
#
# Input stream is a path per line, path segments separated with spaces.

process_line () {
    local line2="$@"
    n2=$#
    set -- $line1
    n1=$#

    s=
    if [ $n2 = 0 ]; then                # last line (empty)
        for s1 in $line1; do
            s="$s)"
        done
    else
        sep=
        remainder=false

        for s2 in $line2; do
            if ! $remainder; then
                if [ "$1" != $s2 ]; then
                    remainder=true
                    if [ $# = 0 ]; then # only children
                        sep='('
                    else                # sibling to an existing element
                        sep=,
                        shift
                        for s1 in $@; do
                            s="$s)"
                        done
                    fi
                fi
            fi

            if $remainder; then         # Process remainder as mismatch
                s="$s$sep$s2"
                sep='('
            fi

            shift                       # remove the first element of line1
        done
    fi

    result="$result$s"
}

result=
line1=
(
    cat - \
    | sed -e 's/[[:space:]]\+/ /' \
    | sed -e '/^$/d' \
    | sort -u
    echo ''                             # last line marker
) | while read line2; do
        process_line $line2
        line1="$line2"

        test -n "$line2" \
            || echo $result
    done

```

This produces the correct answer for two different files (`l.sh` is the shell version, `l.pl` the version in Perl):

```
% for i in l l1; do cat $i; ./l.sh < $i; ./l.pl < $i; echo; done
A
A B
A B C D
A B E F
A G H
A G H I
(A(B(C(D),E(F)),G(H(I))))
(A(B(C(D),E(F)),G(H(I))))

A B C
A B D
A E
(A(B(C,D),E))
(A(B(C,D),E))

```

Hoohah!
Okay, so I think I got it:

```
# input
lines <- c(list(c("A", "B", "C")), list(c("A", "B", "D")), list(c("A","E")))

# generate children
generate_children <- function(lines){
    children <- list()
    for (line in lines) {
        for (index in 1:(length(line)-1)){
            parent <- line[index]
            next_child <- line[index + 1]
            if (is.null(children[[parent]])){
                children[[parent]] <- next_child
            } else {
                if (next_child %notin% children[[parent]]){
                    children[[parent]] <- c(children[[parent]], next_child)
                }
            }
        }
    }
    children
}

expand_children <- function(current_parent, children){
    if (current_parent %in% names(children)){
        expanded_children <- sapply(children[[current_parent]], function(current_child){
            expand_children(current_child, children)
        }, USE.NAMES = FALSE)
        output <- setNames(list(expanded_children), current_parent)
    } else {
        output <- current_parent
    }
    output
}

children <- generate_children(lines)
root <- names(children)[1]
tree <- expand_children(root, children)
dput(tree)
# structure(list(A = structure(list(B = c("C", "D"), "E"), .Names = c("B",""))), .Names = "A")

```

Is there a simpler answer?