def encode_fasta_sequence(fname):
"""
Loads fasta file and returns an array of one-hot sequences.
Parameters
----------
fname: str
Filename of fasta file.
Returns
-------
np.ndarray: Shape (N_sequences, 5, sequence_length, 1).
"""
warnings.warn(
"This Function has been deprecated and now resides in deepchem.utils.genomics_utils",
DeprecationWarning)
return encode_sequence(fname)
def encode_bio_sequence(fname, file_type="fasta", letters="ATCGN"):
"""
Loads a sequence file and returns an array of one-hot sequences.
Parameters
----------
fname: str
Filename of fasta file.
file_type: str
The type of file encoding to process, e.g. fasta or fastq, this
is passed to Biopython.SeqIO.parse.
letters: str
The set of letters that the sequences consist of, e.g. ATCG.
Returns
-------
np.ndarray: Shape (N_sequences, N_letters, sequence_length, 1).
"""
warnings.warn(
"This Function has been deprecated and now resides in deepchem.utils.genomics_utils ",
DeprecationWarning)
return encode_sequence(fname, file_type=file_type, letters=letters)