From 1b7c9c03d64eade893b5cfd715376810b2ba6ebd Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Tue, 21 Feb 2012 13:36:25 +0000
Subject: [PATCH] Fix del with deleted sequence length as argument
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@488 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
mutalyzer/variantchecker.py | 2 +-
tests/test_variantchecker.py | 62 ++++++++++++++++++++++++++++++++++++
2 files changed, 63 insertions(+), 1 deletion(-)
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index d7e3472b..8591757b 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -149,7 +149,7 @@ def _check_argument(argument, reference, first, last, output):
# If it is a digit (3_9del7 for example), the digit must be equal to
# the length of the given range.
length = int(argument)
- interval = first - last + 1
+ interval = last - first + 1
if length != interval:
output.addMessage(__file__, 3, 'EARGLEN',
'The length (%i) differed from that of the ' \
diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py
index f5ae5034..a078ec89 100644
--- a/tests/test_variantchecker.py
+++ b/tests/test_variantchecker.py
@@ -527,3 +527,65 @@ class TestVariantchecker():
'UD_127955523176:g.=')
assert 'UD_127955523176(DMD_v001):c.=' \
in self.output.getOutput('descriptions')
+
+ def test_deletion_with_sequence_forward_genomic(self):
+ """
+ Specify the deleted sequence in a deletion.
+ """
+ check_variant('AL449423.14:g.65471_65472delTC', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'AL449423.14:g.65471_65472del')
+ assert 'AL449423.14(CDKN2A_v001):c.98_99del' \
+ in self.output.getOutput('descriptions')
+
+ def test_deletion_with_length_forward_genomic(self):
+ """
+ Specify the deleted sequence length in a deletion.
+ """
+ check_variant('AL449423.14:g.65471_65472del2', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'AL449423.14:g.65471_65472del')
+ assert 'AL449423.14(CDKN2A_v001):c.98_99del' \
+ in self.output.getOutput('descriptions')
+
+ def test_deletion_with_sequence_reverse_coding(self):
+ """
+ Specify the deleted sequence in a deletion on the reverse strand.
+ """
+ check_variant('AL449423.14(CDKN2A_v001):c.161_163delTGG', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'AL449423.14:g.61937_61939del')
+ assert 'AL449423.14(CDKN2A_v001):c.161_163del' \
+ in self.output.getOutput('descriptions')
+
+ def test_deletion_with_length_reverse_coding(self):
+ """
+ Specify the deleted sequence length in a deletion on the reverse strand.
+ """
+ check_variant('AL449423.14(CDKN2A_v001):c.161_163del3', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'AL449423.14:g.61937_61939del')
+ assert 'AL449423.14(CDKN2A_v001):c.161_163del' \
+ in self.output.getOutput('descriptions')
+
+ def test_deletion_with_sequence_reverse_ng_coding(self):
+ """
+ Specify the deleted sequence in a deletion on the reverse strand
+ using a genomic reference.
+ """
+ check_variant('NG_008939.1:c.155_157delAAC', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5206_5208del')
+ assert 'NG_008939.1(PCCB_v001):c.155_157del' \
+ in self.output.getOutput('descriptions')
+
+ def test_deletion_with_length_reverse_ng_coding(self):
+ """
+ Specify the deleted sequence length in a deletion on the reverse strand
+ using a genomic reference.
+ """
+ check_variant('NG_008939.1:c.155_157del3', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5206_5208del')
+ assert 'NG_008939.1(PCCB_v001):c.155_157del' \
+ in self.output.getOutput('descriptions')
--
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