Merge pull request #196 from medema-group/hotfix/cds-warn

move CDS warning to debug
medema-group · Oct 21, 2024 · 4f9dd28 · 4f9dd28
2 parents 3b7d91b + f51d952
commit 4f9dd28
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/big_scape/genbank/cds.py b/big_scape/genbank/cds.py
@@ -251,11 +251,11 @@ def parse(
                 not correct_translation
                 and not parent_gbk.source_type == SOURCE_TYPE.MIBIG
             ):
-                logging.warning(
+                logging.debug(
                     "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",
+                    " do not match, likely due to fuzzy starts/ends."
+                    " Consider checking if there is something special with this CDS",
                     nt_start,
                     nt_stop,
                     parent_gbk.path,

diff --git a/test/genbank/test_cds.py b/test/genbank/test_cds.py
@@ -542,7 +542,7 @@ def test_parse_translation_antismash_larger_mismatch(self):
             "GADYGLCRVYRNEPWHFELRPEAIEHGCPPLYADPSHDPXXXX"
         ]
 
-        with self.assertLogs(level=logging.INFO) as cm:
+        with self.assertLogs(level=logging.DEBUG) as cm:
             logging.info("nonsense")
             CDS.parse(feature, parent_gbk)