From 7a0862acf86689fead1935adb348706547fb9134 Mon Sep 17 00:00:00 2001 From: nlouwen Date: Fri, 18 Oct 2024 16:02:31 +0200 Subject: [PATCH 1/2] move CDS warning to debug --- big_scape/genbank/cds.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/big_scape/genbank/cds.py b/big_scape/genbank/cds.py index 7fa691db..752845c6 100644 --- 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, From f51d95202cb02868bf27c5da189ed1bce828fa49 Mon Sep 17 00:00:00 2001 From: nlouwen Date: Mon, 21 Oct 2024 09:43:30 +0200 Subject: [PATCH 2/2] fix test --- test/genbank/test_cds.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/genbank/test_cds.py b/test/genbank/test_cds.py index 13e0cc76..b4d5c9e7 100644 --- 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)