indent a fragment of a newick to make it easier to grab a subtree - does not correctly parse labels (so quoted parens and commas cause problems)

indent-newick-frag.py

#!/usr/bin/env python
from StringIO import StringIO
import sys

out = sys.stdout
def get_indented(x, indent):
    start_indent = indent
    written_something = False
    out = StringIO()
    for letter in x:
        if letter == '(':
            if written_something and not prev_comma:
                out.write('\n' + '  '*indent)
            out.write('(')
            indent += 1
        elif letter == ')':
            indent -= 1
            if indent < 0:
                return get_indented(x, start_indent + 1)
            out.write('\n' + '  '*indent + ')')
        elif letter == ',':
            out.write(',\n' + '  '*indent)
        else:
            out.write(letter)
        written_something = True
        prev_comma = letter == ','
    out.write('\n')
    return out.getvalue()

if len(sys.argv) == 1:
    for line in sys.stdin:
        ls = line.strip()
        out.write(get_indented(ls, 0))
else:
    for arg in sys.argv[1:]:
        out.write(get_indented(arg, 0))