skip first codon when checking if translation from antismash and biop…

…ython match, cds 1 and 2 from test file are manually altered

src/genbank/cds.py

@@ -250,16 +250,21 @@ def parse(
             correct_translation = check_translation(aa_seq, nt_seq, feature)
 
             if not correct_translation:
-                logging.warning(
-                    "CDS (%s, %s) from %s:"
-                    " translation provided by antiSMASH and generated by biopython"
-                    " do not match, consider checking if there is something"
-                    " special with this CDS",
-                    nt_start,
-                    nt_stop,
-                    parent_gbk.path,
+                correct_skip_start_translation = check_translation(
+                    aa_seq[1:], nt_seq[1:], feature
                 )
 
+                if not correct_skip_start_translation:
+                    logging.warning(
+                        "CDS (%s, %s) from %s:"
+                        " translation provided by antiSMASH and generated by biopython"
+                        " do not match, consider checking if there is something"
+                        " special with this CDS",
+                        nt_start,
+                        nt_stop,
+                        parent_gbk.path,
+                    )
+
             cds.aa_seq = aa_seq
             return cds
 

test/genbank/test_cds.py

@@ -1,6 +1,7 @@
 """Contains tests for the CDS class and functions"""
 
 # from python
+import logging
 from pathlib import Path
 from unittest import TestCase
 
@@ -411,3 +412,59 @@ def test_parse_translate_aa_seq_cds_0(self):
         translation = cds_0.aa_seq
 
         self.assertEqual(expected_translation, translation)
+
+    def test_parse_translation_antismash_start_codon_mismatch(self):
+        """Tests whether the aa seq start codon mismatch (antismash vs biopython)
+        in the feature with location: 1537..2157 raises no warnings"""
+
+        parent_gbk_file_path = Path(
+            "test/test_data/valid_gbk_folder/valid_input_region_cds_no_trans.gbk"
+        )
+        parent_gbk = GBK.parse(parent_gbk_file_path, "query")
+
+        feature = SeqFeature(FeatureLocation(1536, 2156, strand=1), type="CDS")
+
+        feature.qualifiers["translation"] = [
+            "MTYRESARTTTRRIPGAVVPVARRIRGVLLAGLRAVGTRIARSPG"
+            "RPVRPQDRAGLGKTHGAVPAGVTVFDDDVPAVTRLDPALLSALRRAATAAADGGVELCV"
+            "NSGWRSPEYQSRLLREAVAKYGSAAAAARWVATPETSIHVAGKAVDIGPPASASWLSEH"
+            "GADYGLCRVYRNEPWHFELRPEAIEHGCPPLYADPSHDPRLRR"
+        ]
+
+        with self.assertLogs(level=logging.INFO) as cm:
+            logging.info("nonsense")
+            CDS.parse(feature, parent_gbk)
+
+        # cm.output a list of strings of all the logs
+        str = " translation provided by antiSMASH and generated by biopython"
+
+        warning = any(str in log for log in cm.output)
+        self.assertEqual(warning, False)
+
+    def test_parse_translation_antismash_larger_mismatch(self):
+        """Tests whether the aa seq start codon mismatch (antismash vs biopython)
+        in the feature with location: 1537..2157 raises a warning"""
+
+        parent_gbk_file_path = Path(
+            "test/test_data/valid_gbk_folder/valid_input_region_cds_no_trans.gbk"
+        )
+        parent_gbk = GBK.parse(parent_gbk_file_path, "query")
+
+        feature = SeqFeature(FeatureLocation(1536, 2156, strand=1), type="CDS")
+
+        feature.qualifiers["translation"] = [
+            "MTYRESARTTTRRIPGAVVPVARRIRGVLLAGLRAVGTRIARSPG"
+            "RPVRPQDRAGLGKTHGAVPAGVTVFDDDVPAVTRLDPALLSALRRAATAAADGGVELCV"
+            "NSGWRSPEYQSRLLREAVAKYGSAAAAARWVATPETSIHVAGKAVDIGPPASASWLSEH"
+            "GADYGLCRVYRNEPWHFELRPEAIEHGCPPLYADPSHDPXXXX"
+        ]
+
+        with self.assertLogs(level=logging.INFO) as cm:
+            logging.info("nonsense")
+            CDS.parse(feature, parent_gbk)
+
+        # cm.output a list of strings of all the logs
+        str = " translation provided by antiSMASH and generated by biopython"
+        warning = any(str in log for log in cm.output)
+
+        self.assertEqual(warning, True)

test/test_data/valid_gbk_folder/valid_input_region_cds_no_trans.gbk

@@ -3847,7 +3847,7 @@ ORIGIN
      1321 tgaggctcag cagttcgaga gcggtgtcgc cgttgcccgc ggtgtccgcc gcgatcgctt
      1381 ccaaacgcag gccgtcgcgg atggcttcgg ccagataggg ctcgtcctcg acgatcagca
      1441 cgcgcatgcc ccgatggtac gagaggccac tacatatcgt cggcatatgg aaaatcgcat
-     1501 acgtgccggc aacacatcgc cgacttgaat ggacacatga cctaccgcga gtcggcccgg
+     1501 acgtgccggc aacacatcgc cgacttgaat ggacacgtga cctaccgcga gtcggcccgg
      1561 acgacgaccc gccggattcc cggcgccgtc gtgccggtgg cccgccggat tcgcggggtc
      1621 cttctcgccg gcctgcgcgc cgtcggcacg aggattgccc ggtcgcccgg tcgcccggtc
      1681 cgcccccagg accgtgccgg cctcggcaag acccacggtg ccgtccccgc cggggtgacg