From 93f98553824cd519ea3f6fe9f19d528f451a3e39 Mon Sep 17 00:00:00 2001 From: Luca Venturini Date: Tue, 9 Oct 2018 23:52:00 +0100 Subject: [PATCH] Fix for the logging messages --- Mikado/loci/locus.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/Mikado/loci/locus.py b/Mikado/loci/locus.py index 24a684e63..906ed0802 100644 --- a/Mikado/loci/locus.py +++ b/Mikado/loci/locus.py @@ -930,11 +930,13 @@ def expand_transcript(transcript, new_start, new_end, fai, logger): # Now check that we have a valid expansion if backup.is_coding and not transcript.is_coding: # Something has gone wrong. Just return the original transcript. - logger.warning("Padding %s would lead to an invalid CDS. Aborting.") + logger.info("Padding %s would lead to an invalid CDS. Aborting.", + transcript.id) return backup elif ((backup.strand == "-" and backup.combined_cds_end < transcript.combined_cds_end) or (backup.combined_cds_end > transcript.combined_cds_end)): - logger.warning("Padding %s would lead to an in-frame stop codon. Aborting.") + logger.info("Padding %s would lead to an in-frame stop codon. Aborting.", + transcript.id) return backup return transcript