Path 3

  return seq_one_hot_encode(np.array(sequences), letters)

def encode_sequence(fname, letters='ATCGN', file_type="fasta"):

    # TODO: if None, then get from the filename

    sequences = []

    for seq in SeqIO.parse(fname, file_type):

        sequences.append(str(seq.seq).upper())

    return seq_one_hot_encode(np.array(sequences), letters)

# This could just be ambiguous_dna_letters, but that would be much higher dim.

class IUPACUnambiguousDNAWithN(Alphabet):

    letters = unambiguous_dna_letters + "N"