From bd3ce1d1cd45f4e89754fe1ce25e9d07adc6edf0 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 25 Feb 2013 12:24:26 +0000
Subject: [PATCH] Warning on non-adjacent exons in transcript reference
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@671 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
mutalyzer/GenRecord.py | 9 +++++++++
tests/test_variantchecker.py | 18 ++++++++++++++++++
2 files changed, 27 insertions(+)
diff --git a/mutalyzer/GenRecord.py b/mutalyzer/GenRecord.py
index cd2eace4..05f40be5 100644
--- a/mutalyzer/GenRecord.py
+++ b/mutalyzer/GenRecord.py
@@ -511,6 +511,15 @@ class GenRecord() :
for j in i.transcriptList :
if not j.mRNA :
usableExonList = self.__checkExonList(j.exon, j.CDS)
+ if self.record.molType == 'n' and j.exon:
+ if not all(p1 + 1 == p2 for p1, p2 in
+ util.grouper(j.exon.positionList[1:-1])):
+ code = 'WEXON_ANNOTATION' if j.current else 'WEXON_ANNOTATION_OTHER'
+ self.__output.addMessage(__file__, 2, code,
+ "Exons for gene %s, transcript variant %s were "
+ "found not to be adjacent. This signifies a "
+ "possible problem in the annotation of the "
+ "reference sequence." % (i.name, j.name))
if not j.exon or not usableExonList :
if self.record.molType == 'g' :
code = 'WNOMRNA' if j.current else 'WNOMRNA_OTHER'
diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py
index 4ef4dab5..b4fc0a50 100644
--- a/tests/test_variantchecker.py
+++ b/tests/test_variantchecker.py
@@ -829,3 +829,21 @@ class TestVariantchecker():
wnomrna = self.output.getMessagesWithErrorCode('WNOMRNA')
wnomrna_other = self.output.getMessagesWithErrorCode('WNOMRNA_OTHER')
assert len(wnomrna) == len(wnomrna_other) == 1
+
+ def test_mrna_ref_adjacent_exons_warn(self):
+ """
+ Warning for mRNA reference where exons are not adjacent.
+
+ In L41870.1 exon 15 ends on 1558 and 16 starts on 1636.
+ """
+ check_variant('L41870.1:c.1del', self.output)
+ w_exon_annotation = self.output.getMessagesWithErrorCode('WEXON_ANNOTATION')
+ assert len(w_exon_annotation) == 1
+
+ def test_mrna_ref_adjacent_exons_no_warn(self):
+ """
+ No warning for mRNA reference where exons are adjacent.
+ """
+ check_variant('NM_133378.3:c.1del', self.output)
+ w_exon_annotation = self.output.getMessagesWithErrorCode('WEXON_ANNOTATION')
+ assert len(w_exon_annotation) == 0
--
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