def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_fp = opts.input_fp
# mapping_fp = opts.mapping_fp
output_prefix = opts.output_prefix
column_name = opts.site_id
# data, headers, _ = parse_mapping_file(open(mapping_fp, 'U'))
lines = open(input_fp, 'U').readlines()
individuals, time_points, data = parse_smp_unifrac_distances(lines)
# write the three output files
fd = open(output_prefix+'individuals.txt', 'w')
fd.writelines([ind+'.'+column_name+'\n' for ind in individuals])
fd.close
fd = open(output_prefix+'time_points.txt', 'w')
fd.writelines('\t'.join(map(str, time_points)))
fd.close()
# the data goes tab separated
fd = open(output_prefix+'data.txt', 'w')
fd.writelines(['\t'.join(map(str, element))+'\n' for element in data])
fd.close()
def test_parse_smp_unifrac_distances(self):
individuals, timepoints, data = parse_smp_unifrac_distances(
FORHEAD_TEST)
expected_individuals = ['CUB000', 'CUB003', 'CUB004', 'CUB007']
expected_timepoints = ['0.5', '1', '2', '3', '4', '5', '6', '7', '8']
expected_data = DATA_MATRIX
self.assertEquals(expected_individuals, individuals)
self.assertEquals(expected_timepoints, timepoints)
self.assertTrue(all((expected_data == data).tolist()))
