Merge pull request #10 from simpsonlab/add_scorpio_to_summary

Fixed pangolin note tag
simpsonlab · Jun 10, 2021 · 32ae56b · 32ae56b
2 parents d98fda2 + 28b6260
commit 32ae56b
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/ncov/parser/Lineage.py b/ncov/parser/Lineage.py
@@ -45,8 +45,10 @@ def get_notes(self, row):
             alt = re.sub(';', '', n_dict[4])
             ref = re.sub(';', '', n_dict[7])
             amb = n_dict[-1]
-            return '/'.join([alt, ref, amb])
-            #return n.replace(" ", "_")
+            tag = 'alt/ref/amb:'
+            value = '/'.join([alt, ref, amb])
+            return ''.join([tag, value])
+
 
     def get_scorpio_call(self, row):
         """

diff --git a/tests/test_Lineage.py b/tests/test_Lineage.py
@@ -12,7 +12,7 @@ class LineageTest(unittest.TestCase):
     def test_create_lineage_dictionary(self):
         lineage_dict = test_lineage.create_lineage_dictionary()
         self.assertEqual(lineage_dict['sampleA']['lineage'], 'B.1.1.7')
-        self.assertEqual(lineage_dict['sampleA']['notes'], '18/3/0')
+        self.assertEqual(lineage_dict['sampleA']['notes'], 'alt/ref/amb:18/3/0')
         self.assertEqual(lineage_dict['sampleB']['lineage'], 'B.1.1.7')
         self.assertEqual(lineage_dict['sampleC']['lineage'], 'B.1.1.7')
         self.assertEqual(lineage_dict['sampleC']['scorpio_call'], 'cB.1.1.7')