From f143415d8627b4bb8a85bfd834fcbc1781645d4b Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 20 Feb 2012 12:18:21 +0000
Subject: [PATCH] Unit tests for describe module
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@483 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
extras/soap-tools/describe.py | 0
mutalyzer/describe.py | 5 ++-
tests/test_describe.py | 63 +++++++++++++++++++++++++++++++++++
tests/test_website.py | 11 ++++++
4 files changed, 78 insertions(+), 1 deletion(-)
mode change 100644 => 100755 extras/soap-tools/describe.py
create mode 100644 tests/test_describe.py
diff --git a/extras/soap-tools/describe.py b/extras/soap-tools/describe.py
old mode 100644
new mode 100755
diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index 4198444f..6ee458c9 100644
--- a/mutalyzer/describe.py
+++ b/mutalyzer/describe.py
@@ -13,6 +13,7 @@ from mutalyzer.util import palinsnoop, roll
def LCSMatrix(s1, s2) :
"""
+ Todo: Not yet in use.
"""
y_max = len(s1) + 1
@@ -36,6 +37,8 @@ def findMax(M, x1, x2, y1, y2) :
N = describe.LCSMatrix("banaan", "na")
describe.findMax(M, 1, 7, 2, 4)
+
+ Todo: Not yet in use.
"""
longest, x_longest, y_longest = 0, 0, 0
@@ -424,7 +427,7 @@ def describeDNA(original, mutated) :
lcs = len(longest_common_suffix(s1[lcp:], s2[lcp:]))
s1_end = len(s1) - lcs
s2_end = len(s2) - lcs
-
+
M = LCSMatrix(s1, s2)
return DNA_description(M, s1, s2, lcp, s1_end, lcp, s2_end)
diff --git a/tests/test_describe.py b/tests/test_describe.py
new file mode 100644
index 00000000..4653d91a
--- /dev/null
+++ b/tests/test_describe.py
@@ -0,0 +1,63 @@
+"""
+Tests for the mutalyzer.describe module.
+"""
+
+
+#import logging; logging.basicConfig()
+import os
+from nose.tools import *
+
+import mutalyzer
+from mutalyzer import describe
+
+
+class TestDescribe():
+ """
+ Test the mytalyzer.describe module.
+ """
+
+ def setUp(self):
+ """
+ Nothing.
+ """
+ pass
+
+ def test1(self):
+ """
+ Test 1.
+ """
+ result = describe.describeDNA(
+ 'ATGATGATCAGATACAGTGTGATACAGGTAGTTAGACAA',
+ 'ATGATTTGATCAGATACATGTGATACCGGTAGTTAGGACAA')
+ description = describe.alleleDescription(result)
+ assert_equal(description, '[5_6insTT;17del;26A>C;35dup]')
+
+ def test2(self):
+ """
+ Test 2.
+ """
+ result = describe.describeDNA(
+ 'TAAGCACCAGGAGTCCATGAAGAAGATGGCTCCTGCCATGGAATCCCCTACTCTACTGTG',
+ 'TAAGCACCAGGAGTCCATGAAGAAGCTGGATCCTCCCATGGAATCCCCTACTCTACTGTG')
+ description = describe.alleleDescription(result)
+ assert_equal(description, '[26A>C;30C>A;35G>C]')
+
+ def test3(self):
+ """
+ Test 3.
+ """
+ result = describe.describeDNA(
+ 'TAAGCACCAGGAGTCCATGAAGAAGATGGCTCCTGCCATGGAATCCCCTACTCTA',
+ 'TAAGCACCAGGAGTCCATGAAGAAGCCATGTCCTGCCATGGAATCCCCTACTCTA')
+ description = describe.alleleDescription(result)
+ assert_equal(description, '[26_29inv;30C>G]')
+
+ def test4(self):
+ """
+ Test 4.
+ """
+ result = describe.describeDNA(
+ 'TAAGCACCAGGAGTCCATGAAGAAGATGGCTCCTGCCATGGAATCCCCTACTCTA',
+ 'TAAGCACCAGGAGTCCATGAAGAAGCCATGTCCTGCCATGAATCCCCTACTCTA')
+ description = describe.alleleDescription(result)
+ assert_equal(description, '[26_29inv;30C>G;41del]')
diff --git a/tests/test_website.py b/tests/test_website.py
index b899afc6..77ffac5d 100644
--- a/tests/test_website.py
+++ b/tests/test_website.py
@@ -117,6 +117,17 @@ class TestWSGI():
href = '/' + href
self.app.get(href)
+ def test_description_extractor(self):
+ """
+ Submit the variant description extractor.
+ """
+ r = self.app.get('/descriptionExtract')
+ form = r.forms[0]
+ form['referenceSeq'] = 'ATGATGATCAGATACAGTGTGATACAGGTAGTTAGACAA'
+ form['variantSeq'] = 'ATGATTTGATCAGATACATGTGATACCGGTAGTTAGGACAA'
+ r = form.submit()
+ r.mustcontain('g.[5_6insTT;17del;26A>C;35dup]')
+
def test_checksyntax_valid(self):
"""
Submit the check syntax form with a valid variant.
--
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