- logger.info("Loading %s", quantification)
- with open(quantification, 'rt') as instream:
- output_headers.append(os.path.basename(quantification))
- headers = instream.readline().split('\t')
- try:
- column_to_use = headers.index(column_name)
- except ValueError as e:
- raise RuntimeError(
- 'Error: {} is not one of the column headers {}'.format(
- args.column, headers))
-
- for line in instream:
- columns = line.split('\t')
- key = columns[0]
- matrix.setdefault(key, []).append(columns[column_to_use])
+ name = basename(getattr(quantification, 'name', quantification))
+ logger.info("Loading %s", name)
+ table = pandas.read_csv(quantification, index_col=0, sep='\t')
+ columns[name] = table[column_name]
+
+ matrix = pandas.DataFrame(columns, columns=columns.keys())