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diff commons/core/parsing/test/Test_SsrParser.py @ 6:769e306b7933

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Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/test/Test_SsrParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,154 @@
+from commons.core.parsing.SsrParser import SsrParser
+import unittest
+
+
+class Test_SsrParser(unittest.TestCase):
+
+
+    def test_setAttributesFromString(self):
+        ssrLine = "MRRE1H001B07RM1\t1\t2\tta\t19\t153\t190\t734"
+        
+        iSsrParser = SsrParser()
+        iSsrParser.setAttributesFromString(ssrLine)
+        
+        obsBES_name = iSsrParser.getBesName()
+        obsBES_redundancy = iSsrParser.getBesRedundancy()
+        obsSSR_nbNucleotides = iSsrParser.getSsrNbNucleotides()
+        obsSSR_Motif = iSsrParser.getSsrMotif()
+        obsSSR_Motif_number = iSsrParser.getSsrMotifNumber()
+        obsSSR_start = iSsrParser.getSsrStart()
+        obsSSR_end = iSsrParser.getSsrEnd()
+        obsBES_size = iSsrParser.getBesSize()
+        
+        expBES_name = 'MRRE1H001B07RM1'
+        expBES_redundancy = '1'
+        expSSR_nbNucleotides = '2'
+        expSSR_Motif = 'ta'
+        expSSR_Motif_number = '19'
+        expSSR_start = '153'
+        expSSR_end = '190'
+        expBES_size = '734'
+        
+        self.assertEquals(expBES_name, obsBES_name)
+        self.assertEquals(expBES_redundancy, obsBES_redundancy)
+        self.assertEquals(expSSR_nbNucleotides, obsSSR_nbNucleotides)
+        self.assertEquals(expSSR_Motif, obsSSR_Motif)
+        self.assertEquals(expSSR_Motif_number, obsSSR_Motif_number)
+        self.assertEquals(expSSR_start, obsSSR_start)
+        self.assertEquals(expSSR_end, obsSSR_end)
+        self.assertEquals(expBES_size, obsBES_size)
+        
+    def test_setAttributesFromString_empty_BESName(self):
+        ssrLine = "\t1\t2\tta\t19\t153\t190\t734"
+        
+        iSsrParser = SsrParser()
+        iSsrParser.setAttributesFromString(ssrLine)
+        
+        obsBES_name = iSsrParser.getBesName()
+        obsBES_redundancy = iSsrParser.getBesRedundancy()
+        obsSSR_nbNucleotides = iSsrParser.getSsrNbNucleotides()
+        obsSSR_Motif = iSsrParser.getSsrMotif()
+        obsSSR_Motif_number = iSsrParser.getSsrMotifNumber()
+        obsSSR_start = iSsrParser.getSsrStart()
+        obsSSR_end = iSsrParser.getSsrEnd()
+        obsBES_size = iSsrParser.getBesSize()
+        
+        expBES_name = ''
+        expBES_redundancy = ''
+        expSSR_nbNucleotides = ''
+        expSSR_Motif = ''
+        expSSR_Motif_number = ''
+        expSSR_start = ''
+        expSSR_end = ''
+        expBES_size = ''
+        
+        self.assertEquals(expBES_name, obsBES_name)
+        self.assertEquals(expBES_redundancy, obsBES_redundancy)
+        self.assertEquals(expSSR_nbNucleotides, obsSSR_nbNucleotides)
+        self.assertEquals(expSSR_Motif, obsSSR_Motif)
+        self.assertEquals(expSSR_Motif_number, obsSSR_Motif_number)
+        self.assertEquals(expSSR_start, obsSSR_start)
+        self.assertEquals(expSSR_end, obsSSR_end)
+        self.assertEquals(expBES_size, obsBES_size)
+
+    def test_setAttributesFromString_less_than_8_fields(self):
+        ssrLine = "1\t2\tta\t19\t153\t190\t734"
+        
+        iSsrParser = SsrParser()
+        iSsrParser.setAttributesFromString(ssrLine)
+        
+        obsBES_name = iSsrParser.getBesName()
+        obsBES_redundancy = iSsrParser.getBesRedundancy()
+        obsSSR_nbNucleotides = iSsrParser.getSsrNbNucleotides()
+        obsSSR_Motif = iSsrParser.getSsrMotif()
+        obsSSR_Motif_number = iSsrParser.getSsrMotifNumber()
+        obsSSR_start = iSsrParser.getSsrStart()
+        obsSSR_end = iSsrParser.getSsrEnd()
+        obsBES_size = iSsrParser.getBesSize()
+        
+        expBES_name = ''
+        expBES_redundancy = ''
+        expSSR_nbNucleotides = ''
+        expSSR_Motif = ''
+        expSSR_Motif_number = ''
+        expSSR_start = ''
+        expSSR_end = ''
+        expBES_size = ''
+        
+        self.assertEquals(expBES_name, obsBES_name)
+        self.assertEquals(expBES_redundancy, obsBES_redundancy)
+        self.assertEquals(expSSR_nbNucleotides, obsSSR_nbNucleotides)
+        self.assertEquals(expSSR_Motif, obsSSR_Motif)
+        self.assertEquals(expSSR_Motif_number, obsSSR_Motif_number)
+        self.assertEquals(expSSR_start, obsSSR_start)
+        self.assertEquals(expSSR_end, obsSSR_end)
+        self.assertEquals(expBES_size, obsBES_size)
+        
+    def test_setAttributes(self):
+        lResults = ['MRRE1H001B07RM1','1','2','ta','19','153','190','734']
+        lineNumber = 1
+        
+        iSsrParser = SsrParser()
+        iSsrParser.setAttributes(lResults, lineNumber)
+        
+        obsBES_name = iSsrParser.getBesName()
+        obsBES_redundancy = iSsrParser.getBesRedundancy()
+        obsSSR_nbNucleotides = iSsrParser.getSsrNbNucleotides()
+        obsSSR_Motif = iSsrParser.getSsrMotif()
+        obsSSR_Motif_number = iSsrParser.getSsrMotifNumber()
+        obsSSR_start = iSsrParser.getSsrStart()
+        obsSSR_end = iSsrParser.getSsrEnd()
+        obsBES_size = iSsrParser.getBesSize()
+        
+        expBES_name = 'MRRE1H001B07RM1'
+        expBES_redundancy = '1'
+        expSSR_nbNucleotides = '2'
+        expSSR_Motif = 'ta'
+        expSSR_Motif_number = '19'
+        expSSR_start = '153'
+        expSSR_end = '190'
+        expBES_size = '734'
+        
+        self.assertEquals(expBES_name, obsBES_name)
+        self.assertEquals(expBES_redundancy, obsBES_redundancy)
+        self.assertEquals(expSSR_nbNucleotides, obsSSR_nbNucleotides)
+        self.assertEquals(expSSR_Motif, obsSSR_Motif)
+        self.assertEquals(expSSR_Motif_number, obsSSR_Motif_number)
+        self.assertEquals(expSSR_start, obsSSR_start)
+        self.assertEquals(expSSR_end, obsSSR_end)
+        self.assertEquals(expBES_size, obsBES_size)
+        
+    def test_eq_Equals(self):
+        SsrParser1 = SsrParser('MRRE1H001A12RM1', '1', '4', 'ttta', '6', '272', '295', '724')
+        SsrParser2 = SsrParser('MRRE1H001A12RM1', '1', '4', 'ttta', '6', '272', '295', '724')
+        
+        self.assertTrue(SsrParser1 == SsrParser2)
+        
+    def test_eq_NotEquals(self):
+        SsrParser1 = SsrParser('MRRE1H001A12RM1', '1', '4', 'ttta', '6', '272', '295', '724')
+        SsrParser2 = SsrParser('MRRE1H001A12RM3', '1', '5', 'ttta', '6', '272', '295', '852')
+        
+        self.assertFalse(SsrParser1 == SsrParser2)
+
+if __name__ == "__main__":
+    unittest.main()
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