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| # Copyright 2021 AlQuraishi Laboratory | |
| # Copyright 2021 DeepMind Technologies Limited | |
| # | |
| # Licensed under the Apache License, Version 2.0 (the "License"); | |
| # you may not use this file except in compliance with the License. | |
| # You may obtain a copy of the License at | |
| # | |
| # http://www.apache.org/licenses/LICENSE-2.0 | |
| # | |
| # Unless required by applicable law or agreed to in writing, software | |
| # distributed under the License is distributed on an "AS IS" BASIS, | |
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
| # See the License for the specific language governing permissions and | |
| # limitations under the License. | |
| """Functions for parsing various file formats.""" | |
| import collections | |
| import dataclasses | |
| import itertools | |
| import re | |
| import string | |
| from typing import Dict, Iterable, List, Optional, Sequence, Tuple, Set | |
| def parse_fasta(fasta_string: str) -> Tuple[Sequence[str], Sequence[str]]: | |
| """Parses FASTA string and returns list of strings with amino-acid sequences. | |
| Arguments: | |
| fasta_string: The string contents of a FASTA file. | |
| Returns: | |
| A tuple of two lists: | |
| * A list of sequences. | |
| * A list of sequence descriptions taken from the comment lines. In the | |
| same order as the sequences. | |
| """ | |
| sequences = [] | |
| descriptions = [] | |
| index = -1 | |
| for line in fasta_string.splitlines(): | |
| line = line.strip() | |
| if line.startswith(">"): | |
| index += 1 | |
| descriptions.append(line[1:]) # Remove the '>' at the beginning. | |
| sequences.append("") | |
| continue | |
| elif line.startswith("#"): | |
| continue | |
| elif not line: | |
| continue # Skip blank lines. | |
| sequences[index] += line | |
| return sequences, descriptions | |