Upload dna_tokenizer_fast.py

dna_tokenizer_fast.py

@@ -0,0 +1,57 @@
+from transformers import RobertaTokenizerFast
+
+# split the dna seq by len
+# AAGTGGCAGA ----->  AA, GT, GG, CA, GA
+class DNATokenizerFast(RobertaTokenizerFast):
+    def __init__(self, vocab_file=None, merges_file=None, k_mer=2, stride=1,
+        errors="replace",
+        bos_token="<s>",
+        eos_token="</s>",
+        sep_token="</s>",
+        cls_token="<s>",
+        unk_token="<unk>",
+        pad_token="<pad>",
+        mask_token="<mask>",
+        add_prefix_space=False,
+        **kwargs
+    ):
+        self.k_mer = k_mer
+        self.stride = stride
+        self.model_max_length = 1000000
+        super().__init__(
+            vocab_file=vocab_file,
+            merges_file=merges_file,
+            errors=errors,
+            bos_token=bos_token,
+            eos_token=eos_token,
+            unk_token=unk_token,
+            sep_token=sep_token,
+            cls_token=cls_token,
+            pad_token=pad_token,
+            mask_token=mask_token,
+            add_prefix_space=add_prefix_space,
+            **kwargs,
+        )
+
+    def cut_and_encode(self, sequence, add_special_tokens):
+        seq_len = ((int)((len(sequence)-self.k_mer) / self.stride)) * self.stride
+        tokens = [sequence[i:i + self.k_mer] for i in range(0, seq_len + 1, self.stride)]
+        token_ids = [self._convert_token_to_id(token) for token in tokens]
+        if add_special_tokens:
+            token_ids = [self.cls_token_id] + token_ids + [self.eos_token_id]
+        return tokens, token_ids
+
+    def _convert_token_to_id(self, token):
+        index = self._tokenizer.token_to_id(token)
+        if index:
+            return index
+        if token == '':
+            return self.pad_token_id
+        return self.unk_token_id
+
+    def __call__(self, seq_list, add_special_tokens=False):
+        token_ids_list = []
+        for seq in seq_list:
+            _, token_ids = self.cut_and_encode(seq, add_special_tokens)
+            token_ids_list.append(token_ids)
+        return {"input_ids": token_ids_list}