def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if os.path.isdir(opts.input_path):
multiple_file_upgma(opts.input_path, opts.output_path)
elif os.path.isfile(opts.input_path):
single_file_upgma(opts.input_path, opts.output_path)
else:
print("io error, check input file path")
exit(1)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if os.path.isdir(opts.input_path):
multiple_file_upgma(opts.input_path,opts.output_path)
elif os.path.isfile(opts.input_path):
single_file_upgma(opts.input_path, opts.output_path)
else:
print("io error, check input file path")
exit(1)
def test_single_file_upgma(self):
""" single_file_upgma should throw no errors"""
titles = ["hi", "ho"]
distdata = numpy.array([[0, 0.5], [0.5, 0.0]])
fname = get_tmp_filename(prefix="upgma_", suffix=".txt")
f = open(fname, "w")
self._paths_to_clean_up.append(fname)
f.write(format_distance_matrix(titles, distdata))
f.close()
fname2 = get_tmp_filename(prefix="upgma_", suffix=".txt", result_constructor=str)
self._paths_to_clean_up.append(fname2)
single_file_upgma(fname, fname2)
assert os.path.exists(fname2)
def test_single_file_upgma(self):
""" single_file_upgma should throw no errors"""
titles = ['hi','ho']
distdata = numpy.array([[0,.5],[.5,0.]])
fname = get_tmp_filename(prefix='upgma_',suffix='.txt')
f = open(fname,'w')
self._paths_to_clean_up.append(fname)
f.write(format_distance_matrix(titles, distdata))
f.close()
fname2 = get_tmp_filename(prefix='upgma_',suffix='.txt',
result_constructor=str)
self._paths_to_clean_up.append(fname2)
single_file_upgma(fname,fname2)
assert(os.path.exists(fname2))
def test_single_file_upgma(self):
""" single_file_upgma should throw no errors"""
titles = ['hi','ho']
distdata = numpy.array([[0,.5],[.5,0.]])
fname = get_tmp_filename(prefix='upgma_',suffix='.txt')
f = open(fname,'w')
self._paths_to_clean_up.append(fname)
f.write(format_distance_matrix(titles, distdata))
f.close()
fname2 = get_tmp_filename(prefix='upgma_',suffix='.txt',
result_constructor=str)
self._paths_to_clean_up.append(fname2)
single_file_upgma(fname,fname2)
assert(os.path.exists(fname2))
