Remove references to protein

      List of fasta files.

    auto_add_annotations: bool (default False)

      Whether create_dataset will automatically add [CLS] and [SEP] annotations

      to the protein sequences it reads in order to assist tokenization.

      to the sequences it reads in order to assist tokenization.

      Keep False if your FASTA file already includes [CLS] and [SEP] annotations.

    data_dir: str, optional (default None)

      Name of directory where featurized data is stored.

        Uses a fasta_file to create a numpy array of annotated FASTA-format strings 

        """

        sequences = np.array([])

        protein = []

        sequence = []

        header_read = False

        for line in fasta_file:

          # Check if line is a header

          if line.startswith(header_mark): # New header line

            header_read = True

            sequences = _add_sequence(sequences, protein)

            protein = []

          elif header_read == True: # Line contains protein sequence in FASTA format

            sequences = _add_sequence(sequences, sequence)

            sequence = []

          elif header_read == True: # Line contains sequence in FASTA format

            if line[-1:] == '\n': # Check last character in string

              line = line[0:-1] # Remove last character

            protein.append(line)

        sequences = _add_sequence(sequences, protein)

            sequence.append(line)

        sequences = _add_sequence(sequences, sequence)

        return sequences

      def _add_sequence(sequences: np.array, protein: list) -> np.array:

      def _add_sequence(sequences: np.array, sequence: list) -> np.array:

        # Handle empty sequence

        if protein == None or len(protein) <= 0:

          logger.warning("Attempting to add empty protein sequence, returning empty array...")

        if sequence == None or len(sequence) <= 0:

          logger.warning("Attempting to add empty sequence, returning empty array...")

          return np.array([])

        # Annotate start/stop of protein

        # Annotate start/stop of sequence 

        if auto_add_annotations:

          protein.insert(0, "[CLS]")

          protein.append("[SEP]")

        new_sequence = ''.join(protein)

          sequence.insert(0, "[CLS]")

          sequence.append("[SEP]")

        new_sequence = ''.join(sequence)

        return np.append(sequences, new_sequence)

      with open(input_file, 'r') as f: # Read FASTA file