def __init__(self, seq, fwd_coded_seq=None, rc_coded_seq=None, include_shape=False):
self.seq = seq
if fwd_coded_seq is None:
fwd_one_hot_coded_seq = one_hot_encode_sequence(seq)
if include_shape:
fwd_coded_shape = code_sequence_shape(seq)
fwd_coded_seq = np.hstack((fwd_one_hot_coded_seq, fwd_coded_shape))
else:
fwd_coded_seq = fwd_one_hot_coded_seq
if rc_coded_seq is None:
rc_seq = reverse_complement(seq)
rc_one_hot_coded_seq = one_hot_encode_sequence(rc_seq)
if include_shape:
rc_coded_shape = code_sequence_shape(rc_seq)
rc_coded_seq = np.hstack((rc_one_hot_coded_seq, rc_coded_shape))
else:
rc_coded_seq = rc_one_hot_coded_seq
self.fwd_coded_seq = fwd_coded_seq
self.rc_coded_seq = rc_coded_seq
def score_binding_sites(self, seq, direction):
"""Score all binding sites in seq.
"""
assert direction in ScoreDirection.__slots__
if isinstance(seq, str):
coded_seq = one_hot_encode_sequence(seq)
elif isinstance(seq, DNASequence):
coded_seq = seq.one_hot_coded_seq
elif isinstance(seq, OneHotCodedDNASeq):
coded_seq = seq
else:
assert False, "Unrecognized sequence type '%s'" % str(type(seq))
return score_coded_seq_with_convolutional_filter(
coded_seq, self.convolutional_filter, direction=direction)
def __init__(self, seq, one_hot_coded_seq=None):
self.seq = seq
if one_hot_coded_seq is None:
one_hot_coded_seq = one_hot_encode_sequence(seq)
self.one_hot_coded_seq = one_hot_coded_seq