Package obitools :: Package unit :: Package obitools
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Source Code for Package obitools.unit.obitools

 1  import unittest 
 2   
 3  import obitools 
 4   
5 -class BioseqTest(unittest.TestCase):
6 7 sequenceId = 'id1' 8 sequenceDefinition = 'sequence definition' 9 sequenceQualifier = {'extra':3} 10
11 - def setUp(self):
12 self.bioseq = self.bioseqClass(self.sequenceId, 13 self.sequenceString, 14 self.sequenceDefinition, 15 **self.sequenceQualifier) 16 17 title = self.__doc__.strip() 18 underline = "=" * len(title)
19 20 #print "%s\n%s" % (title,underline) 21
22 - def tearDown(self):
23 pass
24 #print "\n" 25
26 - def testIdAttribute(self):
27 ''' 28 test if id attribute exists 29 ''' 30 self.failUnless(hasattr(self.bioseq, 'id'), 'id missing attribute')
31
32 - def testIdValue(self):
33 ''' 34 test if id attribute value is 'id1' 35 ''' 36 self.failUnlessEqual(self.bioseq.id, 'id1', 37 'identifier is created with good value')
38
39 - def testDefinitionAttribute(self):
40 ''' 41 test if definition attribute exists 42 ''' 43 self.failUnless(hasattr(self.bioseq, 'definition'), 'definition missing attribute')
44
45 - def testSequenceIsLowerCase(self):
46 ''' 47 test if sequence is stored as lower case letter 48 ''' 49 self.failUnlessEqual(str(self.bioseq), 50 str(self.bioseq).lower(), 51 "Sequence is not stored as lower case string")
52
53 - def testSequenceQualifier(self):
54 ''' 55 test if the extra qualifier is present and its value is three. 56 ''' 57 self.failUnlessEqual(self.bioseq['extra'], 58 3, 59 "Sequence qualifier cannot be successfully retrieve")
60
62 self.bioseq['testqualifier']='ok' 63 self.failUnlessEqual(self.bioseq['testqualifier'], 64 'ok', 65 "Sequence qualifier cannot be successfully created")
66 67 68
69 -class NucBioseqTest(BioseqTest):
70 ''' 71 Test obitools.NucSequence class 72 ''' 73 74 bioseqClass = obitools.NucSequence 75 sequenceString = 'AACGT' * 5
76 77
78 -class AABioseqTest(BioseqTest):
79 ''' 80 Test obitools.AASequence class 81 ''' 82 83 bioseqClass = obitools.AASequence 84 sequenceString = 'MLKCVT' * 5
85 86 87 88 89 tests_group = [NucBioseqTest,AABioseqTest] 90