fix: update tests to filter wildtype transcripts from variant-only assertions

The wildtype transcript yield (ef49d91) causes existing tests to receive
an extra unmodified transcript. Filter with `if t.vars` so variant-only
test logic is unaffected.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: axelwalter

epytope/test/TestGenerator.py

@@ -66,7 +66,8 @@ def test_non_syn_hetero_snp_trans_number(self):
             [self.non_syn_hetero_snp, self.non_frame_shift_del, self.syn_homo_snp]
 
         trans = \
-            [t for t in Generator.generate_transcripts_from_variants(vars_, self.db_adapter, EIdentifierTypes.REFSEQ)]
+            [t for t in Generator.generate_transcripts_from_variants(vars_, self.db_adapter, EIdentifierTypes.REFSEQ)
+             if t.vars]
 
         self.assertTrue(len(trans) == 2**sum(not v.isHomozygous for v in vars_))
 
@@ -85,17 +86,17 @@ def test_simple_incorporation(self):
 
         # INSERTIONS:
         dummy_vars = [var_3]
-        trans = next(Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ))
+        trans = next(t for t in Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ) if t.vars)
         self.assertEqual(str(trans), "AAAAACCTTCCCGGGGG")
 
         # SNPs:
         dummy_vars = [var_1]
-        trans = next(Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ))
+        trans = next(t for t in Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ) if t.vars)
         self.assertEqual(str(trans), "ATAAACCCCCGGGGG")
 
         # DELETIONS:
         dummy_vars = [var_4]
-        trans = next(Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ))
+        trans = next(t for t in Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ) if t.vars)
         self.assertEqual(str(trans), "AAAAAGGGGG")
 
     def test_offset_single(self):
@@ -112,13 +113,13 @@ def test_offset_single(self):
 
         # 1) INS, SNP, DEL
         dummy_vars = [var_3, var_7, var_6]
-        trans = next(Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ))
+        trans = next(t for t in Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ) if t.vars)
 
         self.assertEqual(str(trans), "AAAAACCTTCTGGGG")
 
         # 2.) INS, DEL, INS
         dummy_vars = [var_9, var_4, var_8]
-        trans = next(Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ))
+        trans = next(t for t in Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ) if t.vars)
         self.assertEqual(str(trans), "AATTAAAGGGGGTTT")
 
     def test_heterozygous_variants(self):
@@ -149,7 +150,7 @@ def test_heterozygous_variants(self):
         # 1) INS, SNP, DEL
         dummy_vars = [var_10, var_11, var_12]
         trans_gener = Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ)
-        trans = [t for t in trans_gener]
+        trans = [t for t in trans_gener if t.vars]
 
         trans = list(map(str, trans))
 
@@ -328,7 +329,7 @@ def test_proteins_from_variants(self):
         dummy_vars = [var_10, var_11, var_12]
         exp_prot = set(['KFG', 'KNLG', 'KFPPG', 'KNFPRG', 'GFK', 'GGLK', 'GFPPK', 'GFPPK', 'GGFPQK'])
         prot = set([str(x) for x in Generator.generate_proteins_from_transcripts(
-                           Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ))]
+                           (t for t in Generator.generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ) if t.vars))]
                    )
         self.assertTrue(len(prot-exp_prot) == 0)
         self.assertTrue(len(exp_prot-prot) == 0)

epytope/test/TestProtein.py

@@ -79,7 +79,8 @@ def test3_protein_from_variants(self):
         dummy_vars = [var_10, var_11, var_12]
 
         proteins = []
-        t = list(generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ))
+        t = [trans for trans in generate_transcripts_from_variants(dummy_vars, dummy_db, EIdentifierTypes.REFSEQ)
+             if trans.vars]
         for trans in t:
             # check gene id field:
             print(trans)