def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
mapping_fp = opts.input_fp
categories = opts.categories
header_names = opts.categories_header_names
output_fp = opts.output_fp
if len(categories) != len(header_names):
option_parser.error('This shouldnt be happening what are you doing?')
data, headers, _ = parse_mapping_file(open(mapping_fp, 'U'))
headers, data = apply_operation_on_mapping_file_columns(headers, data,
categories, header_names)
# for j in range(0,len(categories)):
# headers.append(header_names[j])
# for k, line in enumerate(data):
# temp = 0.0
# indices = map(lambda x: headers.index(x), categories[j].split(','))
# for index in indices:
# temp = temp + float(line[index])
# data[k].append('%f' % temp)
lines = format_mapping_file(headers, data)
fd = open(output_fp, 'w')
fd.writelines(lines)
fd.close()
def test_apply_operation_on_mapping_file_columns(self):
# test a sum
new_headers, new_data = apply_operation_on_mapping_file_columns(
self.headers, self.data, ['A,B', 'A,A', 'C,D'], ['first', 'second',
'third'])
self.assertEquals(new_headers, ['SampleID', 'Treatment', 'Info', 'A',
'B', 'C', 'D', 'Description', 'first', 'second', 'third'])
self.assertEquals(new_data, RESULTING_MAPPING_FILE)
