make sequences a local-er var (1eb26651) · Commits · 钟慕尧 / deepchem

deepchem/data/data_loader.py

+4 −4

Original line number	Diff line number	Diff line
		@@ -924,7 +924,6 @@ class FASTALoader(DataLoader):
		yield X, None, None, ids # TODO discuss shape

		def _read_file(input_file: str, auto_add_annotations: bool=False):
		sequences = np.array([])
		"""
		Convert the FASTA file to a numpy array of FASTA-format strings.
		"""
		@@ -932,20 +931,21 @@ class FASTALoader(DataLoader):
		"""
		Uses a fasta_file to create a numpy array of annotated FASTA-format strings
		"""
		sequences = np.array([])
		protein = []
		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(protein)
		sequences = _add_sequence(sequences, protein)
		protein = []
		elif header_read == True: # Line contains protein sequence in FASTA format
		protein.append(line)
		sequences = _add_sequence(protein)
		sequences = _add_sequence(sequences, protein)
		return sequences

		def _add_sequence(protein: list) -> np.array:
		def _add_sequence(sequences: np.array, protein: list) -> np.array:
		if protein == None or len(protein) <= 0:
		logger.warning("Attempting to add empty protein sequence, returning empty array...")
		return np.array([])