def load_file(file_name):
'''Load tree, leaf DNA strings from file.'''
f = open(file_name, 'rb')
t = rt.read_newick_str(f.readline().strip())
aug_tree(t)
d_leaf = ['' for _ in xrange(t.num_nodes)]
for record in FastaIterator(f): d_leaf[t.node_index[record.id]] = record.seq
return t, d_leaf
def rsub(file_name):
'''Main driver to solve this problem.'''
f = open(file_name, 'rb')
t = rt.read_newick_str(f.readline().strip())
s = dict((record.name, record.seq) for record in FastaIterator(f))
# print s
for i in xrange(len(next(s.itervalues()))):
# print '-' * 70
# print 'i', i
# print '-' * 70
si = dict((k, v[i]) for k, v in s.iteritems())
for node, letter in reversing_subs(t, si):
print '%s %s %d %s->%s->%s' % (node[0], node[1], i + 1, letter[1], letter[0], letter[1])
def sptd(f):
'''Main driver to solve this problem.'''
lines = ro.read_lines(f)
return rt.dist_split(rt.read_newick_str(lines[1]), rt.read_newick_str(lines[2]), lines[0].split())
