| def parse(f, comment="#"): | |
| """ | |
| Parse a file in ``.fasta`` format. | |
| :param f: Input file object | |
| :type f: _io.TextIOWrapper | |
| :param comment: Character used for comments | |
| :type comment: str | |
| :return: names, sequence | |
| :rtype: list[str], list[str] | |
| """ | |
| starter = ">" | |
| empty = "" | |
| if "b" in f.mode: | |
| comment = b"#" | |
| starter = b">" | |
| empty = b"" | |
| names = [] | |
| sequences = [] | |
| name = None | |
| sequence = [] | |
| for line in f: | |
| if line.startswith(comment): | |
| continue | |
| line = line.strip() | |
| if line.startswith(starter): | |
| if name is not None: | |
| names.append(name) | |
| sequences.append(empty.join(sequence)) | |
| name = line[1:] | |
| sequence = [] | |
| else: | |
| sequence.append(line.upper()) | |
| if name is not None: | |
| names.append(name) | |
| sequences.append(empty.join(sequence)) | |
| return names, sequences | |
| def parse_directory(directory, extension=".seq"): | |
| """ | |
| Parse all files in a directory ending with ``extension``. | |
| :param directory: Input directory | |
| :type directory: str | |
| :param extension: Extension of all files to read in | |
| :type extension: str | |
| :return: names, sequence | |
| :rtype: list[str], list[str] | |
| """ | |
| names = [] | |
| sequences = [] | |
| for seqPath in os.listdir(directory): | |
| if seqPath.endswith(extension): | |
| n, s = parse(open(f"{directory}/{seqPath}", "rb")) | |
| names.append(n[0].decode("utf-8").strip()) | |
| sequences.append(s[0].decode("utf-8").strip()) | |
| return names, sequences | |
| def write(nam, seq, f): | |
| """ | |
| Write a file in ``.fasta`` format. | |
| :param nam: List of names | |
| :type nam: list[str] | |
| :param seq: List of sequences | |
| :type seq: list[str] | |
| :param f: Output file object | |
| :type f: _io.TextIOWrapper | |
| """ | |
| for n, s in zip(nam, seq): | |
| f.write(">{}\n".format(n)) | |
| f.write("{}\n".format(s)) | |