def test_build_tree_from_alignment(self):
"""Clearcut should return a tree built from the passed alignment"""
tree_short = build_tree_from_alignment(build_tree_seqs_short,\
moltype=DNA)
num_seqs = flatten(build_tree_seqs_short).count('>')
self.assertEqual(len(tree_short.tips()), num_seqs)
tree_long = build_tree_from_alignment(build_tree_seqs_long, moltype=DNA)
seq_names = []
for line in build_tree_seqs_long.split('\n'):
if line.startswith('>'):
seq_names.append(line[1:])
for node in tree_long.tips():
if node.Name not in seq_names:
self.fail()
#repeat with best_tree = True
tree_long = build_tree_from_alignment(build_tree_seqs_long,\
best_tree=True,\
moltype=DNA)
seq_names = []
for line in build_tree_seqs_long.split('\n'):
if line.startswith('>'):
seq_names.append(line[1:])
for node in tree_long.tips():
if node.Name not in seq_names:
self.fail()
#build_tree_from_alignment should raise DataError when constructing
# an Alignment from unaligned sequences. Clearcut only allows aligned
# or a distance matrix as input.
self.assertRaises(DataError,build_tree_from_alignment,\
build_tree_seqs_unaligned,DNA)
def test_build_tree_from_alignment(self):
"""Clearcut should return a tree built from the passed alignment"""
tree_short = build_tree_from_alignment(build_tree_seqs_short,\
moltype=DNA)
num_seqs = flatten(build_tree_seqs_short).count('>')
self.assertEqual(len(tree_short.tips()), num_seqs)
tree_long = build_tree_from_alignment(build_tree_seqs_long,
moltype=DNA)
seq_names = []
for line in build_tree_seqs_long.split('\n'):
if line.startswith('>'):
seq_names.append(line[1:])
for node in tree_long.tips():
if node.Name not in seq_names:
self.fail()
#repeat with best_tree = True
tree_long = build_tree_from_alignment(build_tree_seqs_long,\
best_tree=True,\
moltype=DNA)
seq_names = []
for line in build_tree_seqs_long.split('\n'):
if line.startswith('>'):
seq_names.append(line[1:])
for node in tree_long.tips():
if node.Name not in seq_names:
self.fail()
#build_tree_from_alignment should raise DataError when constructing
# an Alignment from unaligned sequences. Clearcut only allows aligned
# or a distance matrix as input.
self.assertRaises(DataError,build_tree_from_alignment,\
build_tree_seqs_unaligned,DNA)