feat(IPVC-2471): fix tests to cover codon_table values

invitae · May 23, 2024 · 445ca1c · 445ca1c
1 parent a739ee4
commit 445ca1c
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Showing 3 changed files with 24 additions and 10 deletions.
diff --git a/tests/data/txinfo.gz b/tests/data/txinfo.gz
diff --git a/tests/test_uta_loading.py b/tests/test_uta_loading.py
@@ -207,6 +207,24 @@ def test_load_txinfo(self):
             },
         )
 
+        transcript.self.session.query(usam.Transcript).filter(usam.Transcript.ac == 'NC_012920.1_09206_09990').one()
+        self.assertEqual(
+            {
+                'ac': transcript.ac,
+                'gene_id': transcript.gene_id,
+                'cds_start_i': transcript.cds_start_i,
+                'cds_end_i': transcript.cds_end_i,
+                'codon_table': transcript.codon_table,
+            },
+            {
+                'ac': 'NC_012920.1_09206_09990',
+                'gene_id': '4514',
+                'cds_start_i': 0,
+                'cds_end_i': 784,
+                'codon_table': 2,
+            },
+        )
+
         exon_set = self.session.query(usam.ExonSet).filter(usam.ExonSet.tx_ac == 'NM_080430.4').one()
         exons = self.session.query(usam.Exon).filter(usam.Exon.exon_set_id == exon_set.exon_set_id).all()
         self.assertEqual(len(exons), 5)

diff --git a/tests/test_uta_parsers_seqrecord.py b/tests/test_uta_parsers_seqrecord.py
@@ -27,6 +27,7 @@ class TestSeqRecordFacade(unittest.TestCase):
             expected_cds_translation="MAESGRPWAQARSAYRASEVLRRGTGRRRDPGPQSNGPGQEDARAPGRMARLRGQLRAEAASRSEVPRLLKLVERAGAG" \
                 "AAGAGERTGAHSRGSVCSVCGEPRGGATYPAGVLEVSERRLQEGLAAVREELGAGIEALRAELRAELDALRALLPPPPSPPARREPRAVPRAAPRGPTLP" \
                 "RTLGTVSALVAASRPADDAPDGPAECGAHRAPARKNHKKMPVPPGAPQGGGD",
+            expected_codon_table=1,
             expected_exons_se_i=[(0, 696)],
         ),
         param(
@@ -49,6 +50,7 @@ class TestSeqRecordFacade(unittest.TestCase):
                 "EDIDECALPTGGHICSYRCINIPGSFQCSCPSSGYRLAPNGRNCQDIDECVTGIHNCSINETCFNIQGGFRCLAFECPENYRRSAATRCERLPCHENREC" \
                 "SKLPLRITYYHLSFPTNIQAPAVVFRMGPSSAVPGDSMQLAITGGNEEGFFTTRKVSPHSGVVALTKPVPEPRDLLLTVKMDLSRHGTVSSFVAKLFIFV" \
                 "SAEL",
+            expected_codon_table=1,
             expected_exons_se_i=[
                 (0, 182),
                 (182, 288),
@@ -80,6 +82,7 @@ class TestSeqRecordFacade(unittest.TestCase):
             expected_cds_product=None,
             expected_cds_protein_id=None,
             expected_cds_translation=None,
+            expected_codon_table=None,
             expected_exons_se_i=[],
         ),
         param(
@@ -95,6 +98,7 @@ class TestSeqRecordFacade(unittest.TestCase):
             expected_cds_product=None,
             expected_cds_protein_id=None,
             expected_cds_translation=None,
+            expected_codon_table=None,
             expected_exons_se_i=[],
         ),
     ])
@@ -112,6 +116,7 @@ def test_seq_record_facade(
         expected_cds_product,
         expected_cds_protein_id,
         expected_cds_translation,
+        expected_codon_table,
         expected_exons_se_i,
     ):
         gbff_file = os.path.join(self.test_data_dir, file_name)
@@ -127,18 +132,9 @@ def test_seq_record_facade(
         assert self.seq_record_facade.cds_product == expected_cds_product
         assert self.seq_record_facade.cds_protein_id == expected_cds_protein_id
         assert self.seq_record_facade.cds_translation == expected_cds_translation
+        assert self.seq_record_facade.codon_table == expected_codon_table
         assert self.seq_record_facade.exons_se_i == expected_exons_se_i
 
-    # @parameterized.expand([    @parameterized.expand([
-    #     param('no genes', features={}),
-    #     param('no genes', features={'gene': []}),
-    #     param('more than one gene', features={'gene': [Mock(), Mock()]}),
-    #     param('more than one CDS', features={'CDS': [Mock(), Mock()]}),
-    # ])
-    # def test_validate_features_by_type_invalid(self, test_name, features):
-    #     with self.assertRaises(SeqRecordFeatureError):
-    #         SeqRecordFacade.validate_features_by_type(features)
-
     @parameterized.expand([
         param("no gene feature", gene_feature_mock={}),
         param("gene feature is None", gene_feature_mock={"gene": None}),