Unit tests for describe module

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@483 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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)

tests/test_describe.py

+"""
+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]')

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.