From 5706caed72773a2abc83194326b1aa903a84ac0a Mon Sep 17 00:00:00 2001 From: Andrey Prjibelski Date: Wed, 21 Feb 2024 17:58:31 +0200 Subject: [PATCH] add log message --- isoquant.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/isoquant.py b/isoquant.py index 03b8bb64..5064d954 100755 --- a/isoquant.py +++ b/isoquant.py @@ -683,6 +683,7 @@ def run_pipeline(args): # convert GTF/GFF if needed if args.genedb and not args.genedb.lower().endswith('db'): + logger.info("Checking input gene annotation") gtf_is_correct, corrected_gtf, out_fname = check_gtf_duplicates(args.genedb) if not gtf_is_correct: new_gtf_path = os.path.join(args.output, out_fname) @@ -692,6 +693,8 @@ def run_pipeline(args): "An attempt to correct this GTF was made, the result is written to %s" % new_gtf_path) logger.error("Provide a correct GTF by fixing the original input GTF or checking the corrected one.") exit(-3) + else: + logger.info("Gene annotation seems to be correct") args.genedb = convert_gtf_to_db(args) # map reads if fastqs are provided