def parse_ma_file_raw(in_file):
name = "<STR_LIT>"<EOL>index = <NUM_LIT:1><EOL>total = defaultdict(int)<EOL>seq_obj = defaultdict(sequence)<EOL>with open(in_file) as handle_in:<EOL><INDENT>line = handle_in.readline().strip()<EOL>cols = line.split("<STR_LIT:\t>")<EOL>samples = cols[<NUM_LIT:2>:]<EOL>for line in handle_in:<EOL><INDENT>line = line.strip()<EOL>cols = line.split("<STR_LIT:\t>")<EOL>name = int(cols[<NUM_LIT:0>].replace("<STR_LIT>", "<STR_LIT>"))<EOL>seq = cols[<NUM_LIT:1>]<EOL>exp = {}<EOL>for i in range(len(samples)):<EOL><INDENT>exp[samples[i]] = int(cols[i+<NUM_LIT:2>])<EOL>total[samples[i]] += int(cols[i+<NUM_LIT:2>])<EOL><DEDENT>index = index+<NUM_LIT:1><EOL>if name not in seq_obj:<EOL><INDENT>seq_obj[name] = sequence(name)<EOL><DEDENT>seq_obj[name].set_freq(exp)<EOL>seq_obj[name].set_seq(seq)<EOL><DEDENT><DEDENT>seq_obj = _normalize_seqs(seq_obj, total)<EOL>return seq_obj, total, index<EOL>
read seqs.ma file and create dict with
sequence object