cn_status = '6' if chr_name not in chr_list: continue rows = reader.get_rows( chr_name ) segment_indices = np.logical_and( rows['position'] >= start, rows['position'] <= stop ) segment_rows = rows[segment_indices] if len( segment_rows ) == 0: continue cncnt_file.add_rows( cn_status, chr_name, segment_rows ) reader.close() cncnt_file.close() if __name__ == "__main__": import sys args = Namespace() args.jcnt_file_name = sys.argv[1] args.cncnt_file_name = sys.argv[2] args.segment_file_name = sys.argv[3] jcnt_to_cncnt( args )