diff smart_toolShed/SMART/Java/Python/structure/test/Test_SubMapping.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/structure/test/Test_SubMapping.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,292 @@
+import unittest
+from SMART.Java.Python.structure.Interval import Interval
+from SMART.Java.Python.structure.SubMapping import SubMapping
+
+class Test_SubMapping(unittest.TestCase):
+
+    def test__init__(self):
+        expEvalue = 0.00
+        expScore = 0
+        expIdentity = 0.00
+        expTargetInterval = Interval()
+        expQueryInterval = Interval()
+        expQueryRange = expQueryInterval
+        expSubjectRange = expTargetInterval
+        expSize = None
+        expTags = {}
+        
+        iSubMapping = SubMapping()
+        obsQueryRange = iSubMapping.getQueryAsRange()
+        obsSubjectRange = iSubMapping.getSubjectAsRange()
+        obsEvalue = iSubMapping.getEvalue()
+        obsScore = iSubMapping.getScore()
+        obsIdentity = iSubMapping.getIdentity()
+        obsTargetInterval = iSubMapping.getTargetInterval()
+        obsQueryInterval = iSubMapping.getQueryInterval()
+        obsSize = iSubMapping.getSize()
+        obsTags = iSubMapping.getTags()
+        
+        self.assertEquals(expEvalue, obsEvalue)
+        self.assertEquals(expIdentity, obsIdentity)
+        self.assertEquals(expQueryInterval, obsQueryInterval)
+        self.assertEquals(expQueryRange, obsQueryRange)
+        self.assertEquals(expScore, obsScore)
+        self.assertEquals(expSize, obsSize)
+        self.assertEquals(expSubjectRange, obsSubjectRange)
+        self.assertEquals(expTags, obsTags)
+        self.assertEquals(expTargetInterval, obsTargetInterval)
+        
+    def test__init__change_values_by_Interval(self):
+        iSubMapping = SubMapping()
+        
+        expSeqName = ""
+        
+        obsRangeSubject = iSubMapping.range_subject.getSeqname()
+        obsRangeQuery = iSubMapping.range_query.getSeqname()
+        obsIntervalTarget = iSubMapping.getTargetInterval().getChromosome()
+        obsIntervalQuery = iSubMapping.getQueryInterval().getChromosome()
+        
+        self.assertEquals(expSeqName, obsRangeSubject)
+        self.assertEquals(expSeqName, obsRangeQuery)
+        self.assertEquals(expSeqName, obsIntervalTarget)
+        self.assertEquals(expSeqName, obsIntervalQuery)
+        
+        iSubMapping.getTargetInterval().setChromosome("intervalTarget")
+        iSubMapping.getQueryInterval().setChromosome("intervalQuery")
+        
+        expTargetSeqName = "intervalTarget"
+        expQuerySeqName = "intervalQuery"
+        
+        obsRangeSubject = iSubMapping.range_subject.getSeqname()
+        obsRangeQuery = iSubMapping.range_query.getSeqname()
+        obsIntervalTarget = iSubMapping.getTargetInterval().getChromosome()
+        obsIntervalQuery = iSubMapping.getQueryInterval().getChromosome()
+        
+        self.assertEquals(expTargetSeqName, obsRangeSubject)
+        self.assertEquals(expQuerySeqName, obsRangeQuery)
+        self.assertEquals(expTargetSeqName, obsIntervalTarget)
+        self.assertEquals(expQuerySeqName, obsIntervalQuery)
+        
+    def test__init__change_values_by_Align(self):
+        iSubMapping = SubMapping()
+        
+        expSeqName = ""
+        
+        obsRangeSubject = iSubMapping.range_subject.getSeqname()
+        obsRangeQuery = iSubMapping.range_query.getSeqname()
+        obsIntervalTarget = iSubMapping.getTargetInterval().getChromosome()
+        obsIntervalQuery = iSubMapping.getQueryInterval().getChromosome()
+        
+        self.assertEquals(expSeqName, obsRangeSubject)
+        self.assertEquals(expSeqName, obsRangeQuery)
+        self.assertEquals(expSeqName, obsIntervalTarget)
+        self.assertEquals(expSeqName, obsIntervalQuery)
+        
+        iSubMapping.range_subject.setSeqName("intervalTarget")
+        iSubMapping.range_query.setSeqName("intervalQuery")
+        
+        expTargetSeqName = "intervalTarget"
+        expQuerySeqName = "intervalQuery"
+        
+        obsRangeSubject = iSubMapping.range_subject.getSeqname()
+        obsRangeQuery = iSubMapping.range_query.getSeqname()
+        obsIntervalTarget = iSubMapping.getTargetInterval().getChromosome()
+        obsIntervalQuery = iSubMapping.getQueryInterval().getChromosome()
+        
+        self.assertEquals(expTargetSeqName, obsRangeSubject)
+        self.assertEquals(expQuerySeqName, obsRangeQuery)
+        self.assertEquals(expTargetSeqName, obsIntervalTarget)
+        self.assertEquals(expQuerySeqName, obsIntervalQuery)
+  
+    def test__eq__(self):
+        iSubMapping1 = SubMapping()
+        iSubMapping1.setQueryName("Query")
+        iSubMapping1.setQueryStart(50)
+        iSubMapping1.setQueryEnd(150)
+        iSubMapping1.setSubjectName("Subject")
+        iSubMapping1.setSubjectStart(100)
+        iSubMapping1.setSubjectEnd(200)
+        iSubMapping1.e_value = 1e-20
+        iSubMapping1.score = 30
+        iSubMapping1.identity = 90.2         
+        iInterval1 = Interval()
+        iInterval1.setChromosome("chromosome1")
+        iInterval1.setStart(0)
+        iInterval1.setEnd(100)
+        iInterval1.setDirection("+")
+        iInterval2 = Interval()
+        iInterval2.setChromosome("chromosome2")
+        iInterval2.setStart(200)
+        iInterval2.setEnd(300)
+        iInterval2.setDirection("+")
+        iSubMapping1.setTargetInterval(iInterval1)
+        iSubMapping1.setQueryInterval(iInterval2)
+        iSubMapping1.setTagValue("name", 50)
+        iSubMapping1.setSize(100)
+        
+        iSubMapping2 = SubMapping()
+        iSubMapping2.setQueryName("Query")
+        iSubMapping2.setQueryStart(50)
+        iSubMapping2.setQueryEnd(150)
+        iSubMapping2.setSubjectName("Subject")
+        iSubMapping2.setSubjectStart(100)
+        iSubMapping2.setSubjectEnd(200)
+        iSubMapping2.e_value = 1e-20
+        iSubMapping2.score = 30
+        iSubMapping2.identity = 90.2 
+        iSubMapping2.setTargetInterval(iInterval1)
+        iSubMapping2.setQueryInterval(iInterval2)
+        iSubMapping2.setTagValue("name", 50)
+        iSubMapping2.setSize(100)
+        self.assertEqual(iSubMapping1, iSubMapping2)
+        
+        
+    def test__eq__withInitialValue(self):
+        iSubMapping1 = SubMapping()
+        iInterval1 = Interval()
+        iInterval2 = Interval()
+        iSubMapping1.setTargetInterval(iInterval1)
+        iSubMapping1.setQueryInterval(iInterval2)
+        iSubMapping1.setTagValue("name", 50)
+        iSubMapping1.setSize(100)
+        
+        iSubMapping2 = SubMapping()
+        iSubMapping2.setTargetInterval(iInterval1)
+        iSubMapping2.setQueryInterval(iInterval2)
+        iSubMapping2.setTagValue("name", 50)
+        iSubMapping2.setSize(100)
+        self.assertEqual(iSubMapping1, iSubMapping2)       
+              
+              
+    def test__init__with_copy(self):
+        iTestSubMapping = SubMapping()
+        iTestSubMapping.setQueryName("Query")
+        iTestSubMapping.setQueryStart(50)
+        iTestSubMapping.setQueryEnd(150)
+        iTestSubMapping.setSubjectName("Subject")
+        iTestSubMapping.setSubjectStart(100)
+        iTestSubMapping.setSubjectEnd(200)
+        iTestSubMapping.e_value = 1e-20
+        iTestSubMapping.score = 30
+        iTestSubMapping.identity = 90.2 
+        
+        iIntervalTarget = Interval()
+        iIntervalTarget.setChromosome("chromosomeTarget")
+        iIntervalTarget.setName("sequenceTarget")
+        iIntervalTarget.setStart(0)
+        iIntervalTarget.setEnd(123)
+        iIntervalTarget.setDirection("+")
+        iIntervalQuery = Interval()
+        iIntervalQuery.setChromosome("chromosomeQuery")
+        iIntervalQuery.setName("sequenceQuery")
+        iIntervalQuery.setStart(200)
+        iIntervalQuery.setEnd(323)
+        iIntervalQuery.setDirection("+")    
+        
+        iTestSubMapping.setQueryInterval(iIntervalTarget)
+        iTestSubMapping.setTargetInterval(iIntervalQuery)
+        iTestSubMapping.setTagValue("identity", 50)
+        iTestSubMapping.setSize(10)
+        
+        iSubMappingWithCopy = SubMapping(iTestSubMapping)
+        self.assertEquals(iSubMappingWithCopy, iTestSubMapping)        
+
+      
+    def test_copy(self):
+        iSubMapping = SubMapping()
+        iSubMapping.setQueryName("Query")
+        iSubMapping.setQueryStart(50)
+        iSubMapping.setQueryEnd(150)
+        iSubMapping.setSubjectName("Subject")
+        iSubMapping.setSubjectStart(100)
+        iSubMapping.setSubjectEnd(200)
+        iSubMapping.e_value = 1e-20
+        iSubMapping.score = 30
+        iSubMapping.identity = 90.2 
+               
+        iInterval1 = Interval()
+        iInterval1.setChromosome("chromosome1")
+        iInterval1.setName("sequence1")
+        iInterval1.setStart(0)
+        iInterval1.setEnd(123)
+        iInterval1.setDirection("+")
+        iInterval2 = Interval()
+        iInterval2.setChromosome("chromosome2")
+        iInterval2.setName("sequence2")
+        iInterval2.setStart(200)
+        iInterval2.setEnd(300)     
+        iInterval2.setDirection("+")           
+        iSubMapping.setQueryInterval(iInterval1)
+        iSubMapping.setTargetInterval(iInterval2)
+        iSubMapping.setTagValue("identity", 50)
+        iSubMapping.setSize(10)
+
+        iSubMappingCopy = SubMapping()
+        iSubMappingCopy.copy(iSubMapping)
+        self.assertEqual(iSubMappingCopy, iSubMapping)
+        
+        
+    def test_setTags(self):
+        iSubMapping = SubMapping()
+        iSubMapping.getQueryInterval().setSize(50)
+        iSubMapping.getTargetInterval().setSize(2)
+        iSubMapping.setTagValue("identity", 50)
+        iSubMapping.setSize(10)
+        
+        expQueryIntervalSize = 50
+        expTargetIntervalSize = 2
+        expTags = {"identity" : 50,
+                   "nbMismatches" : 5}
+        
+        obsTags = iSubMapping.getTags()
+        self.assertEquals(expTags, obsTags)
+        
+        
+    def test_setIdentity(self):
+        iSubMapping = SubMapping()        
+        iSubMapping.setIdentity(10)
+        expIdentity = 10
+        expTags = {"identity": 10}
+        
+        obsIdentity = iSubMapping.getIdentity()
+        obsTags = iSubMapping.getTags()
+        
+        self.assertEquals(expIdentity,obsIdentity)
+        self.assertEquals(expTags,obsTags)
+        
+        
+    def test_setIdentity_with_size(self):
+        iSubMapping = SubMapping()        
+        iSubMapping.setSize(10)
+        iSubMapping.setIdentity(50)
+        
+        expIdentity = 50
+        expTags = {"identity" : 50,
+                   "nbMismatches" : 5}
+        
+        obsIdentity = iSubMapping.getIdentity()
+        obsTags = iSubMapping.getTags()
+        
+        self.assertEquals(expIdentity,obsIdentity)
+        self.assertEquals(expTags,obsTags)
+        
+        
+    def test_setIdentity_with_sizeAndMismatchTag(self):
+        iSubMapping = SubMapping()        
+        iSubMapping.setSize(10)
+        iSubMapping.setTagValue("nbMismatches", 8)
+        iSubMapping.setIdentity(50)
+        
+        expIdentity = 50
+        expTags = {"identity" : 50,
+                   "nbMismatches" : 8}
+        
+        obsIdentity = iSubMapping.getIdentity()
+        obsTags = iSubMapping.getTags()
+        
+        self.assertEquals(expIdentity,obsIdentity)
+        self.assertEquals(expTags,obsTags)
+        
+        
+if __name__ == "__main__":
+    unittest.main()