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Added support and testing for MNPs #119

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13 changes: 9 additions & 4 deletions spliceai/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -135,10 +135,6 @@ def get_delta_scores(record, ann, dist_var, mask):
if '<' in record.alts[j] or '>' in record.alts[j]:
continue

if len(record.ref) > 1 and len(record.alts[j]) > 1:
delta_scores.append("{}|{}|.|.|.|.|.|.|.|.".format(record.alts[j], genes[i]))
continue

dist_ann = ann.get_pos_data(idxs[i], record.pos)
pad_size = [max(wid//2+dist_ann[0], 0), max(wid//2-dist_ann[1], 0)]
ref_len = len(record.ref)
Expand Down Expand Up @@ -174,6 +170,15 @@ def get_delta_scores(record, ann, dist_var, mask):
np.max(y_alt[:, cov//2:cov//2+alt_len], axis=1)[:, None, :],
y_alt[:, cov//2+alt_len:]],
axis=1)
#MNP handling
elif ref_len > 1 and alt_len > 1:
zblock = np.zeros((1,ref_len-1,3))
y_alt = np.concatenate([
y_alt[:, :cov//2],
np.max(y_alt[:, cov//2:cov//2+alt_len], axis=1)[:, None, :],
zblock,
y_alt[:, cov//2+alt_len:]],
axis=1)

y = np.concatenate([y_ref, y_alt])

Expand Down
14 changes: 14 additions & 0 deletions tests/test_delta_score.py
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Expand Up @@ -44,3 +44,17 @@ def test_get_delta_score_donor(self):
self.assertEqual(scores, ['T|TUBB8|0.01|0.18|0.15|0.62|-2|110|-190|0'])
scores = get_delta_scores(record, self.ann_without_prefix, 500, 0)
self.assertEqual(scores, ['T|TUBB8|0.01|0.18|0.15|0.62|-2|110|-190|0'])

def test_get_delta_score_mnp(self):

record = Record('10', 94077, 'ACT', ['CCT'])
scores = get_delta_scores(record, self.ann, 50, 0)
self.assertEqual(scores, ['CCT|TUBB8|0.07|0.27|0.00|0.01|0|-23|19|-22'])
scores = get_delta_scores(record, self.ann_without_prefix, 50, 0)
self.assertEqual(scores, ['CCT|TUBB8|0.07|0.27|0.00|0.01|0|-23|19|-22'])

record = Record('10', 94555, 'CGA', ['TGA'])
scores = get_delta_scores(record, self.ann, 50, 0)
self.assertEqual(scores, ['TGA|TUBB8|0.01|0.00|0.11|0.62|-2|-6|-23|0'])
scores = get_delta_scores(record, self.ann_without_prefix, 50, 0)
self.assertEqual(scores, ['TGA|TUBB8|0.01|0.00|0.11|0.62|-2|-6|-23|0'])