tokenization_caduceus.py

"""Character tokenizer for Hugging Face.

"""

from typing import List, Optional, Dict, Sequence, Tuple

from transformers import PreTrainedTokenizer


class CaduceusTokenizer(PreTrainedTokenizer):
    model_input_names = ["input_ids"]

    def __init__(self,
                 model_max_length: int,
                 characters: Sequence[str] = ("A", "C", "G", "T", "N"),
                 complement_map=None,
                 bos_token="[BOS]",
                 eos_token="[SEP]",
                 sep_token="[SEP]",
                 cls_token="[CLS]",
                 pad_token="[PAD]",
                 mask_token="[MASK]",
                 unk_token="[UNK]",
                 **kwargs):
        """Character tokenizer for Hugging Face transformers.

        Adapted from https://huggingface.co/LongSafari/hyenadna-tiny-1k-seqlen-hf/blob/main/tokenization_hyena.py
        Args:
            model_max_length (int): Model maximum sequence length.
            characters (Sequence[str]): List of desired characters. Any character which
                is not included in this list will be replaced by a special token called
                [UNK] with id=6. Following is a list of the special tokens with
                their corresponding ids:
                    "[CLS]": 0
                    "[SEP]": 1
                    "[BOS]": 2
                    "[MASK]": 3
                    "[PAD]": 4
                    "[RESERVED]": 5
                    "[UNK]": 6
                an id (starting at 7) will be assigned to each character.
            complement_map (Optional[Dict[str, str]]): Dictionary with string complements for each character.
        """
        if complement_map is None:
            complement_map = {"A": "T", "C": "G", "G": "C", "T": "A"}
        self.characters = characters
        self.model_max_length = model_max_length

        self._vocab_str_to_int = {
            "[CLS]": 0,
            "[SEP]": 1,
            "[BOS]": 2,
            "[MASK]": 3,
            "[PAD]": 4,
            "[RESERVED]": 5,
            "[UNK]": 6,
            **{ch: i + 7 for i, ch in enumerate(self.characters)},
        }
        self._vocab_int_to_str = {v: k for k, v in self._vocab_str_to_int.items()}
        add_prefix_space = kwargs.pop("add_prefix_space", False)
        padding_side = kwargs.pop("padding_side", "left")

        self._complement_map = {}
        for k, v in self._vocab_str_to_int.items():
            complement_id = self._vocab_str_to_int[complement_map[k]] if k in complement_map.keys() else v
            self._complement_map[self._vocab_str_to_int[k]] = complement_id

        super().__init__(
            bos_token=bos_token,
            eos_token=eos_token,
            sep_token=sep_token,
            cls_token=cls_token,
            pad_token=pad_token,
            mask_token=mask_token,
            unk_token=unk_token,
            add_prefix_space=add_prefix_space,
            model_max_length=model_max_length,
            padding_side=padding_side,
            **kwargs,
        )

    @property
    def vocab_size(self) -> int:
        return len(self._vocab_str_to_int)

    @property
    def complement_map(self) -> Dict[int, int]:
        return self._complement_map

    def _tokenize(self, text: str, **kwargs) -> List[str]:
        return list(text.upper())  # Convert all base pairs to uppercase

    def _convert_token_to_id(self, token: str) -> int:
        return self._vocab_str_to_int.get(token, self._vocab_str_to_int["[UNK]"])

    def _convert_id_to_token(self, index: int) -> str:
        return self._vocab_int_to_str[index]

    def convert_tokens_to_string(self, tokens):
        return "".join(tokens)  # Note: this operation has lost info about which base pairs were originally lowercase

    def get_special_tokens_mask(
        self,
        token_ids_0: List[int],
        token_ids_1: Optional[List[int]] = None,
        already_has_special_tokens: bool = False,
    ) -> List[int]:
        if already_has_special_tokens:
            return super().get_special_tokens_mask(
                token_ids_0=token_ids_0,
                token_ids_1=token_ids_1,
                already_has_special_tokens=True,
            )

        result = ([0] * len(token_ids_0)) + [1]
        if token_ids_1 is not None:
            result += ([0] * len(token_ids_1)) + [1]
        return result

    def build_inputs_with_special_tokens(
        self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None
    ) -> List[int]:
        sep = [self.sep_token_id]
        # cls = [self.cls_token_id]
        result = token_ids_0 + sep
        if token_ids_1 is not None:
            result += token_ids_1 + sep
        return result

    def get_vocab(self) -> Dict[str, int]:
        return self._vocab_str_to_int

    # Fixed vocabulary with no vocab file
    def save_vocabulary(self, save_directory: str, filename_prefix: Optional[str] = None) -> Tuple:
        return ()