Amended so that only really padded transcripts are padded

EI-CoreBioinformatics · Oct 1, 2018 · 3f1d60c · 3f1d60c
1 parent 069e25a
commit 3f1d60c
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Showing 2 changed files with 9 additions and 2 deletions.
diff --git a/Mikado/loci/locus.py b/Mikado/loci/locus.py
@@ -894,6 +894,7 @@ def expand_transcript(transcript, new_start, new_end, fai, logger):
         transcript.load_orfs(new_orfs)
 
     # Now finalize again
-    transcript.attributes["padded"] = True
+    if upstream > 0 or downstream > 0:
+        transcript.attributes["padded"] = True
     transcript.finalize()
     return transcript
diff --git a/Mikado/tests/locus_tester.py b/Mikado/tests/locus_tester.py
@@ -1934,16 +1934,22 @@ def test_padding(self):
                 locus.json_conf["pick"]["alternative_splicing"]["ts_max_splices"] = max_splice
                 locus.pad_transcripts()
 
-                if pad_distance == 1000:
+                if pad_distance != 200:
                     self.assertEqual(locus["mikado.44G2.1"].end, locus["mikado.44G2.2"].end)
+                    self.assertTrue(locus["mikado.44G2.2"].attributes["padded"])
+                else:
+                    self.assertFalse(locus["mikado.44G2.1"].attributes.get("padded", False))
 
                 self.assertEqual(locus["mikado.44G2.3"].end, locus["mikado.44G2.2"].end)
                 self.assertEqual(locus["mikado.44G2.4"].end, locus["mikado.44G2.2"].end)
 
                 if locus.ts_max_splices == 5:
                     self.assertEqual(locus["mikado.44G2.4"].end, locus["mikado.44G2.5"].end)
+                    self.assertTrue(locus["mikado.44G2.1"].attributes.get("padded", False))
                 else:
                     self.assertNotEqual(locus["mikado.44G2.4"].end, locus["mikado.44G2.5"].end)
+                    self.assertFalse(locus["mikado.44G2.1"].attributes.get("padded", False))
+
                 for transcript in locus:
                     self.assertGreater(locus[transcript].combined_cds_length, 0)
                     self.assertEqual(locus[transcript].combined_cds_start, cds_coordinates[transcript][0])