def score_from_transcript(
frame, original_frame, frame_ss, offtarget, regexp
):
"""
Function which count score from transcript.
Args:
frame: backbone object
original_frame: sh-miR object
frame_ss: file from mfold
offtarget: Number of transcripts
regexp: Number of regular expression
Returns:
Dict of scores for: frame, offtarget, regexp and all together.
"""
structure_points = score_structure(frame, frame_ss, original_frame)
offtarget_points = score_offtarget(offtarget)
regexp_points = score_regexp(regexp)
thermostability_points = score_thermostability(frame)
return {
'structure': structure_points,
'offtarget': offtarget_points,
'regexp': regexp_points,
'thermostability': thermostability_points,
'all': (
structure_points + offtarget_points +
regexp_points + thermostability_points
)
}
def test_score_structure(self, mock_parse_ss, mock_parse_score):
mock_parse_ss.return_value = 'acgtacgt'
mock_parse_score.return_value = 4.0, [('a', 1), ('c', 4)]
frame = MagicMock()
original_frame = MagicMock()
original_frame.flanks5_s = 'acgt'
original_frame.miRNA_s = 'cgta'
original_frame.loop_s = 'aacc'
original_frame.flanks3_s = 'acg'
original_frame.miRNA_a = 'aa'
frame.flanks5_s = 'acg'
frame.siRNA1 = 'ac'
frame.loop_s = 'a'
frame.siRNA2 = 'c'
frame.flanks3_s = 'a'
result = score_structure(frame, 'folding_file', original_frame)
self.assertEqual(result, 250)
def score_from_sirna(frame, original_frame, folding_file):
"""Function for getting score from siRNA.
Args:
frame_tuple: Tuple of frame
original_frame: sh-miR object
folding_file: folded structure from mfold
Returns:
tuple of score of frame, homogeneity and strands
"""
structure = score_structure(frame, folding_file, original_frame)
homogeneity = score_homogeneity(frame)
same_ends = score_two_same_strands(frame.siRNA1, original_frame)
return {
'structure': structure,
'homogeneity': homogeneity,
'same_ends': same_ends,
'all': structure + homogeneity + same_ends
}
