def test_score_from_transcript(self, mock_structure):
mock_structure.return_value = 10
mock_frame = MagicMock(siRNA1='acgt')
offtarget = 5
regexp = 5
result = score.score_from_transcript(
mock_frame, 'original_frame', 'frame_ss', offtarget, regexp
)
self.assertEqual(result['structure'], mock_structure())
self.assertEqual(result['offtarget'], 30)
self.assertEqual(result['regexp'], 25)
self.assertEqual(
result['all'],
mock_structure() + 30 + 25
)
def shmir_from_fasta(siRNA, offtarget, regexp, original_frames, prefix):
siRNA2 = reverse_complement(siRNA)
frames = adjusted_frames(siRNA, siRNA2, 0, 0, deepcopy(original_frames)) # we do not have shifts here
shmirs = [frame.template() for frame in frames]
with allow_join_result():
foldings = group(fold.s(shmir, prefix=prefix).set(queue="subtasks") for shmir in shmirs).apply_async().get()
results = []
iter_frames = izip(frames, original_frames, foldings)
for frame, original_frame, folding in iter_frames:
score = score_from_transcript(frame, original_frame, folding["ss"], offtarget, regexp)
if validate_transcript_by_score(score):
results.append({"score": score, "frame": frame, "folding": folding, "found_sequence": siRNA})
return results
