def __init__(self, read_file, known_sequence_type=None):
self.read_file = read_file<EOL>self.known_sequence_type = known_sequence_type<EOL>
New object from a read file.

        read_file: str
            path to input reads
        sequence_type: str:
            PROTEIN_SEQUENCE_TYPE, NUCLEOTIDE_SEQUENCE_TYPE or None
            Whether input is nucleotide, amino acid, or should be guessed by
        peeking at the input sequence file.