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

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/test/Test_CrossSsrAndBesMappedByBlatToGff.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,70 @@
+from commons.core.parsing.CrossSsrAndBesMappedByBlatToGff import CrossSsrAndBesMappedByBlatToGff
+from commons.core.parsing.SsrParser import SsrParser
+
+import unittest
+import os
+
+
+class Test_CrossSsrAndBesMappedByBlatToGff(unittest.TestCase):
+
+
+    def test_createDictOfSsrParser(self):
+        obsDictSsrParser = {}
+        
+        ssrFileName = 'input_SSR_Resuts.tab'
+        SSRFile = open(ssrFileName, 'w')
+        SSRFile.write('BES_name\tBES_redundancy\tSSR_di/tri/tetranucleotide\tSSR_Motif\tSSR_Motif_number\tSSR_start\tSSR_end\tBES_size\n')
+        SSRFile.write('MRRE1H001A12RM1\t1\t4\tttta\t6\t272\t295\t724\n')
+        SSRFile.write('MRRE1H001B01RM1\t1\t3\taat\t8\t264\t287\t683\n')
+        SSRFile.write('MRRE1H001B07RM1\t1\t2\tta\t19\t153\t190\t734\n')
+        SSRFile.write('MRRE1H001B07RM1\t2\t2\taata\t25\t83\t90\t734\n')
+        SSRFile.close()
+        
+        iCrossSsrAndBesMappedByBlatToGff = CrossSsrAndBesMappedByBlatToGff()
+        iCrossSsrAndBesMappedByBlatToGff._inputFileSSR = ssrFileName
+        obsDictSsrParser = iCrossSsrAndBesMappedByBlatToGff.createDictOfSsrParser(obsDictSsrParser)
+        
+        SsrParser1 = SsrParser('MRRE1H001A12RM1', '1', '4', 'ttta', '6', '272', '295', '724')
+        SsrParser2 = SsrParser('MRRE1H001B01RM1', '1', '3', 'aat', '8', '264', '287', '683')
+        SsrParser3 = SsrParser('MRRE1H001B07RM1', '1', '2', 'ta', '19', '153', '190', '734')
+        SsrParser4 = SsrParser('MRRE1H001B07RM1', '2', '2', 'aata', '25', '83', '90', '734')
+        
+        expDictSsrParser = {
+                         'MRRE1H001A12RM1': [SsrParser1], 
+                         'MRRE1H001B01RM1': [SsrParser2],
+                         'MRRE1H001B07RM1': [SsrParser3, SsrParser4]
+                        }
+        
+        self.assertEquals(expDictSsrParser, obsDictSsrParser)
+        os.remove(ssrFileName)
+        
+    def test_convertSSRPositionsToBlatPositions_strand_FW(self):
+        ssrPos = 75
+        blatPosStart = 10501475
+        blatPosEnd = 10501985
+        strand = '+'
+        iCrossSsrAndBesMappedByBlatToGff = CrossSsrAndBesMappedByBlatToGff()
+        obsNewPos = iCrossSsrAndBesMappedByBlatToGff.convertSSRPositionsToChromPositions(ssrPos, blatPosStart, blatPosEnd, strand)
+        expNewPos = 10501549
+        self.assertEquals(expNewPos, obsNewPos)
+        
+    def test_convertSSRPositionsToBlatPositions_strand_RV(self):
+        ssrPos = 75
+        blatPosStart = 10501475
+        blatPosEnd = 10501985
+        strand = '-'
+        iCrossSsrAndBesMappedByBlatToGff = CrossSsrAndBesMappedByBlatToGff()
+        obsNewPos = iCrossSsrAndBesMappedByBlatToGff.convertSSRPositionsToChromPositions(ssrPos, blatPosStart, blatPosEnd, strand)
+        expNewPos = 10501911
+        self.assertEquals(expNewPos, obsNewPos)
+        
+    def test_getSsrMotif(self):
+        ssrMotif = 'atg'
+        ssrNbMotif = 4
+        iCrossSsrAndBesMappedByBlatToGff = CrossSsrAndBesMappedByBlatToGff()
+        obsSsrSeq = iCrossSsrAndBesMappedByBlatToGff.getSsrSeq(ssrMotif, ssrNbMotif)
+        expSsrSeq = 'atgatgatgatg'
+        self.assertEquals(expSsrSeq, obsSsrSeq)
+
+if __name__ == "__main__":
+    unittest.main()
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