Added OneHotFeaturizer default and made edit to return shape (09c4e526) · Commits · 钟慕尧 / deepchem

deepchem/data/data_loader.py

+3 −2

Original line number	Diff line number	Diff line
		@@ -17,6 +17,7 @@ from deepchem.utils.data_utils import load_image_files, load_csv_files, load_jso
		from deepchem.utils.genomics_utils import encode_bio_sequence
		from deepchem.feat import UserDefinedFeaturizer, Featurizer
		from deepchem.data import Dataset, DiskDataset, NumpyDataset, ImageDataset
		from deepchem.feat.molecule_featurizers import OneHotFeaturizer

		from more-itertools import peekable

		@@ -877,7 +878,7 @@ class FASTALoader(DataLoader):
		learning tasks.
		"""

		def __init__(self, featurizer: Featurizer):
		def __init__(self, featurizer: Featurizer = OneHotFeaturizer()):
		self.user_specified_features = None
		if isinstance(featurizer, UserDefinedFeaturizer):
		self.user_specified_features = featurizer.feature_fields
		@@ -916,7 +917,7 @@ class FASTALoader(DataLoader):
		sequences = np.array([])
		for input_file in input_files:
		np.append(sequences, _read_file(input_file))
		yield self.featurizer(sequences)
		yield self.featurizer(sequences), None, None, ids # TODO discuss shape
		"""
		X = encode_bio_sequence(input_file)
		ids = np.ones(len(X))