def test_call_correct_alignment(self):
"""CogentTreeBuilder: output expected alignment file
"""
p = CogentTreeBuilder({'Module': cogent.app.fasttree})
log_fp = get_tmp_filename(\
prefix='CogentTreeBuilderTests_',suffix='.log')
self._paths_to_clean_up.append(log_fp)
actual = p(result_path=None, aln_path=self.input_fp, log_path=log_fp)
expected = tree
#note: lines in diff order w/ diff versions
self.assertEqual(str(actual), expected)
def test_call_correct_alignment(self):
"""CogentTreeBuilder: output expected alignment file
"""
p = CogentTreeBuilder({'Module': bfillings.fasttree})
fd, log_fp = mkstemp(prefix='CogentTreeBuilderTests_', suffix='.log')
close(fd)
self._paths_to_clean_up.append(log_fp)
actual = p(result_path=None, aln_path=self.input_fp, log_path=log_fp)
actual = str(actual)
# note: order of inputs to FastTree can have very minor effect
# on the distances, so we need to compare against a couple of trees
# to avoid failures on different archs
self.assertTrue(actual == tree or actual == tree2)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if not (opts.tree_method in tree_method_constructors
or opts.tree_method in tree_module_names):
option_parser.error(
'Invalid alignment method: %s.\nValid choices are: %s' %
(opts.tree_method, ' '.join(tree_method_constructors.keys() +
tree_module_names.keys())))
try:
tree_builder_constructor =\
tree_method_constructors[opts.tree_method]
tree_builder_type = 'Constructor'
params = {}
tree_builder = tree_builder_constructor(params)
except KeyError:
tree_builder = CogentTreeBuilder({
'Module':
tree_module_names[opts.tree_method],
'Method':
opts.tree_method
})
tree_builder_type = 'Cogent'
input_seqs_filepath = opts.input_fp
result_path = opts.result_fp
if not result_path: # empty or None
fpath, ext = splitext(input_seqs_filepath) # fpath omits extension
result_path = fpath + ".tre"
open(result_path, 'w').close() # touch
log_path = opts.log_fp
if log_path is not None:
open(log_path, 'w').close()
if tree_builder_type == 'Constructor':
tree_builder(input_seqs_filepath,
result_path=result_path,
log_path=log_path,
failure_path=failure_path)
elif tree_builder_type == 'Cogent':
tree_builder(result_path,
aln_path=input_seqs_filepath,
log_path=log_path,
root_method=opts.root_method)
