From c2d67551482de92f3f223571f7793b45437ff332 Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Mon, 23 Dec 2013 14:31:30 +0100
Subject: [PATCH] Loosen error severity when CDS cannot be translated
---
mutalyzer/variantchecker.py | 43 ++++++++++++++++++++++---------------
1 file changed, 26 insertions(+), 17 deletions(-)
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index ce41a4aa..d71bd5f7 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -1766,35 +1766,44 @@ def check_variant(description, output):
if not len(cds_original) % 3:
try:
# FIXME this is a bit of a rancid fix.
- protein_original = cds_original.translate(table=transcript.txTable,
- cds=True,
- to_stop=True)
+ protein_original = cds_original.translate(
+ table=transcript.txTable, cds=True, to_stop=True)
except Bio.Data.CodonTable.TranslationError:
- output.addMessage(__file__, 4, "ETRANS", "Original " \
- "CDS could not be translated.")
- return
- protein_variant = cds_variant.translate(table=transcript.txTable,
- to_stop=True)
- try:
- cds_length = util.cds_length(
- mutator.shift_sites(transcript.CDS.positionList))
- transcript.proteinDescription = util.protein_description(
- cds_length, protein_original, protein_variant)[0]
- except IndexError:
- # Todo: Probably CDS start was hit by removal of exon...
+ if transcript.current:
+ output.addMessage(
+ __file__, 2, "WTRANS",
+ "Original CDS could not be translated in gene "
+ "%s, transcript variant %s (selected)."
+ % (gene.name, transcript.name))
+ else:
+ output.addMessage(
+ __file__, 2, "WTRANS_OTHER",
+ "Original CDS could not be translated in gene "
+ "%s, transcript variant %s."
+ % (gene.name, transcript.name))
transcript.proteinDescription = 'p.?'
+ else:
+ protein_variant = cds_variant.translate(
+ table=transcript.txTable, to_stop=True)
+ try:
+ cds_length = util.cds_length(
+ mutator.shift_sites(transcript.CDS.positionList))
+ transcript.proteinDescription = util.protein_description(
+ cds_length, protein_original, protein_variant)[0]
+ except IndexError:
+ # Todo: Probably CDS start was hit by removal of exon..
+ transcript.proteinDescription = 'p.?'
else:
if transcript.current:
output.addMessage(__file__, 2, "WCDS", "CDS length is " \
"not a multiple of three in gene %s, transcript " \
"variant %s (selected)." % (gene.name, transcript.name))
- transcript.proteinDescription = 'p.?'
else:
output.addMessage(__file__, 2, "WCDS_OTHER", "CDS length is " \
"not a multiple of three in gene %s, transcript " \
"variant %s." % (gene.name, transcript.name))
- transcript.proteinDescription = 'p.?'
+ transcript.proteinDescription = 'p.?'
reference = output.getOutput('reference')[-1]
if ';' in record.record.description:
--
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