bugfix (456143d7) · Commits · 钟慕尧 / deepchem

deepchem/molnet/dnasim.py

+23 −19

Original line number	Diff line number	Diff line
		@@ -35,6 +35,7 @@ def simple_motif_embedding(motif_name, seq_length, num_seqs, GC_fraction):
		embedding_arr: 1darray
		Array of embedding objects.
		"""
		import simdna
		from simdna import synthetic
		if motif_name is None:
		embedders = []
		@@ -72,6 +73,7 @@ def motif_density(motif_name,
		"""
		Returns sequences with motif density, along with embeddings array.
		"""
		import simdna
		from simdna import synthetic
		loaded_motifs = synthetic.LoadedEncodeMotifs(
		simdna.ENCODE_MOTIFS_PATH, pseudocountProb=0.001)
		@@ -260,6 +262,7 @@ def simulate_multi_motif_embedding(motif_names, seq_length, min_num_motifs,
		Array of embedding objects.
		"""

		import simdna
		from simdna import synthetic
		loaded_motifs = synthetic.LoadedEncodeMotifs(
		simdna.ENCODE_MOTIFS_PATH, pseudocountProb=0.001)
		@@ -369,6 +372,7 @@ def simulate_heterodimer_grammar(motif1, motif2, seq_length, min_spacing,
		embedding_arr: list
		List of embedding objects.
		"""
		import simdna
		from simdna import synthetic
		loaded_motifs = synthetic.LoadedEncodeMotifs(
		simdna.ENCODE_MOTIFS_PATH, pseudocountProb=0.001)