From 6ead8b65a08509600a06edf67064a1daecdebc91 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Tue, 31 Jan 2012 12:41:06 +0000
Subject: [PATCH] Unit tests for GI references
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@470 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
tests/test_variantchecker.py | 36 ++++++++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)
diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py
index 1687db66..65d5c45c 100644
--- a/tests/test_variantchecker.py
+++ b/tests/test_variantchecker.py
@@ -460,3 +460,39 @@ class TestVariantchecker():
but we should not crash on it.
"""
check_variant('NC_002128(tagA):c.3del', self.output)
+
+ def test_gi_reference_plain(self):
+ """
+ Test reference sequence notation with GI number.
+ """
+ check_variant('31317229:c.6del', self.output)
+ error_count, _, _ = self.output.Summary()
+ assert_equal(error_count, 0)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ '31317229:n.105del')
+ assert '31317229(FCER1A_v001):c.6del' \
+ in self.output.getOutput('descriptions')
+
+ def test_gi_reference_prefix(self):
+ """
+ Test reference sequence notation with GI number and prefix.
+ """
+ check_variant('GI31317229:c.6del', self.output)
+ error_count, _, _ = self.output.Summary()
+ assert_equal(error_count, 0)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ '31317229:n.105del')
+ assert '31317229(FCER1A_v001):c.6del' \
+ in self.output.getOutput('descriptions')
+
+ def test_gi_reference_prefix_colon(self):
+ """
+ Test reference sequence notation with GI number and prefix with colon.
+ """
+ check_variant('GI:31317229:c.6del', self.output)
+ error_count, _, _ = self.output.Summary()
+ assert_equal(error_count, 0)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ '31317229:n.105del')
+ assert '31317229(FCER1A_v001):c.6del' \
+ in self.output.getOutput('descriptions')
--
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