From 1dcd441d4e931909007f06a60c9e285c994699b0 Mon Sep 17 00:00:00 2001
From: K D Ahlquist <6993450+kdahlo@users.noreply.github.com>
Date: Tue, 4 Apr 2023 11:39:27 -0400
Subject: [PATCH] Added support and testing for MNPs

---
 spliceai/utils.py         | 13 +++++++++----
 tests/test_delta_score.py | 14 ++++++++++++++
 2 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/spliceai/utils.py b/spliceai/utils.py
index 991afd1..3237fa7 100644
--- a/spliceai/utils.py
+++ b/spliceai/utils.py
@@ -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)
@@ -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])
 
diff --git a/tests/test_delta_score.py b/tests/test_delta_score.py
index 4630095..5560aee 100755
--- a/tests/test_delta_score.py
+++ b/tests/test_delta_score.py
@@ -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'])