From d094cf4d4a398f9e270c6eed43c13bd177a21204 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Wed, 23 Nov 2011 14:44:24 +0000
Subject: [PATCH] Fix reverse complement of number parameter in position
converter
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@420 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
mutalyzer/mapping.py | 10 ++++++++--
tests/test_mapping.py | 10 ++++++++++
2 files changed, 18 insertions(+), 2 deletions(-)
diff --git a/mutalyzer/mapping.py b/mutalyzer/mapping.py
index 584541f5..d772f4b2 100644
--- a/mutalyzer/mapping.py
+++ b/mutalyzer/mapping.py
@@ -581,8 +581,14 @@ class Converter(object) :
if revc :
# todo: if var.Arg1 is unicode, this crashes
- arg1 = reverse_complement(var.Arg1 or "") #imported from Bio.Seq
- arg2 = reverse_complement(var.Arg2 or "")
+ try:
+ arg1 = str(int(var.Arg1))
+ except ValueError:
+ arg1 = reverse_complement(var.Arg1 or "")
+ try:
+ arg2 = str(int(var.Arg2))
+ except ValueError:
+ arg2 = reverse_complement(var.Arg2 or "")
#if
else :
arg1 = var.Arg1
diff --git a/tests/test_mapping.py b/tests/test_mapping.py
index 5c7b38c6..3180d521 100644
--- a/tests/test_mapping.py
+++ b/tests/test_mapping.py
@@ -50,3 +50,13 @@ class TestConverter():
assert_equal(genomic, 'NC_000006.11:g.32006291C>T')
coding = converter.chrom2c(genomic, 'list')
assert 'NM_000500.5:c.92C>T' in coding
+
+ def test_converter_del_length_reverse(self):
+ """
+ Position converter on deletion (denoted by length) on transcripts
+ located on the reverse strand.
+ """
+ converter = self._converter('hg19')
+ coding = converter.chrom2c('NC_000022.10:g.51016285_51017117del123456789', 'list')
+ assert 'NM_001145134.1:c.-138-u21_60del123456789' in coding
+ assert 'NR_021492.1:c.1-u5170_1-u4338del123456789' in coding
--
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