diff SMART/Java/Python/test/Test_F_compareOverlapping.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/test/Test_F_compareOverlapping.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,199 @@
+import unittest
+import os, os.path
+from SMART.Java.Python.misc import Utils
+
+SMART_PATH = os.environ["REPET_PATH"] + "/SMART"
+
+class Test_F_compareOverlapping(unittest.TestCase):
+
+    def setUp(self):
+        self._inputFileQuery     = "inputFileTest1.bed"
+        self._inputFileReference = "inputFileTest2.bed"
+        self._inputFileName3     = "inputFileTest3.bed"
+        self._expOutputFileName  = "expOutput.gff3"  
+        self._outputFileName     = "output.gff3"   
+        self._writeInputFileQuery()
+        self._writeInputFileRefence()
+        self._writeInputFile3()  
+        
+    def tearDown(self):
+        for fileName in (self._inputFileQuery, self._inputFileReference, self._inputFileName3, self._expOutputFileName, self._outputFileName):
+            if os.path.exists(fileName):
+                os.remove(fileName)
+
+    def test_runAsScript_withoutOption(self):
+        self._writeOutputFile_withoutOption(self._expOutputFileName) 
+        os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
+            
+    def test_runAsScript_optionNFirstNucleotide(self):
+        self._writeOutputFile_NFirstNucleotide(self._expOutputFileName) 
+        os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -S 200 -s 200 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
+
+    def test_runAsScript_optionNLastNucleotide(self):
+        self._writeOutputFile_NLastNucleotide(self._expOutputFileName) 
+        os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -U 200 -u 200 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
+
+    def test_runAsScript_option_5PrimeExtension(self):
+        self._writeOutputFile_5PrimeExtension(self._expOutputFileName) 
+        os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -E 110 -e 110 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
+
+    def test_runAsScript_option_3PrimeExtension(self):
+        self._writeOutputFile_3PrimeExtension(self._expOutputFileName) 
+        os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -N 110 -n 110 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
+        
+    def test_runAsScript_colinear(self):
+        self._writeOutputFile_colinear(self._expOutputFileName) 
+        os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -c -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
+
+    def test_runAsScript_antisense(self):
+        self._writeOutputFile_antisense(self._expOutputFileName) 
+        os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -a -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
+
+    def test_runAsScript_minOverlap(self):
+        self._writeOutputFile_minOverlap(self._expOutputFileName) 
+        os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -m 51 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileName3, self._outputFileName))
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
+
+    def test_runAsScript_pcOverlap(self):
+        self._writeOutputFile_pcOverlap(self._expOutputFileName) 
+        os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -p 60 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileName3, self._outputFileName))
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
+
+    def test_runAsScript_included(self):
+        self._writeOutputFile_included(self._expOutputFileName) 
+        os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -k -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
+            
+    def test_runAsScript_including(self):
+        self._writeOutputFile_including(self._expOutputFileName) 
+        os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -K -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
+            
+    def test_runAsScript_includeNotOverlap(self):
+        self._writeOutputFile_includeNotOverlap(self._expOutputFileName) 
+        os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -O -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
+
+    def test_runAsScript_exclude(self):
+        self._writeOutputFile_exclude(self._expOutputFileName) 
+        os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -x -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
+              
+    def _writeInputFileQuery(self):
+        f = open(self._inputFileQuery, "w")
+        f.write("arm_X\t1000\t2000\ttest1.1\t1000\t+\t1000\t2000\t0\t1\t1000,\t0,\n")
+        f.write("arm_X\t1000\t2000\ttest1.2\t1000\t-\t1000\t2000\t0\t1\t1000,\t0,\n")
+        f.write("arm_X\t100\t200\ttest1.3\t1000\t+\t100\t200\t0\t1\t100,\t0,\n")
+        f.write("arm_X\t100\t3200\ttest1.4\t1000\t+\t100\t3200\t0\t1\t3100,\t0,\n")
+        f.close()
+        
+    def _writeInputFileRefence(self):
+        f = open(self._inputFileReference, "w")
+        f.write("arm_X\t1000\t2000\ttest2.1\t1000\t+\t1000\t2000\t0\t1\t1000,\t0,\n")
+        f.close()
+        
+    def _writeInputFile3(self):
+        f = open(self._inputFileName3, "w")
+        f.write("arm_X\t1000\t2000\ttest2.1\t1000\t+\t1000\t2000\t0\t1\t1000,\t0,\n")
+        f.write("arm_X\t250\t350\ttest2.2\t1000\t+\t250\t350\t0\t1\t100,\t0,\n")
+        f.write("arm_X\t150\t250\ttest2.3\t1000\t+\t150\t250\t0\t1\t100,\t0,\n")
+        f.close()
+        
+    def _writeOutputFile_withoutOption(self, outputFileName):
+        f = open(outputFileName, "w")
+        f.write("arm_X\tS-MART\ttranscript\t100\t3199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
+        f.close()
+
+    def _writeOutputFile_NFirstNucleotide(self, outputFileName):
+        f = open(outputFileName, "w")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t1199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
+        f.close()  
+        
+    def _writeOutputFile_NLastNucleotide(self, outputFileName):
+        f = open(outputFileName, "w")
+        f.write("arm_X\tS-MART\ttranscript\t1800\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
+        f.close()              
+
+    def _writeOutputFile_5PrimeExtension(self, outputFileName):
+        f = open(outputFileName, "w")
+        f.write("arm_X\tS-MART\ttranscript\t0\t3199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
+        f.write("arm_X\tS-MART\ttranscript\t890\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t2109\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
+        f.close()
+        
+    def _writeOutputFile_3PrimeExtension(self, outputFileName):
+        f = open(outputFileName, "w")
+        f.write("arm_X\tS-MART\ttranscript\t100\t3309\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t2109\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
+        f.write("arm_X\tS-MART\ttranscript\t890\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
+        f.close()   
+        
+    def _writeOutputFile_colinear(self, outputFileName):
+        f = open(outputFileName, "w")
+        f.write("arm_X\tS-MART\ttranscript\t100\t3199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
+        f.close()    
+        
+    def _writeOutputFile_antisense(self, outputFileName):
+        f = open(outputFileName, "w")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
+        f.close()  
+           
+    def _writeOutputFile_minOverlap(self, outputFileName):
+        f = open(outputFileName, "w")
+        f.write("arm_X\tS-MART\ttranscript\t100\t3199\t.\t+\t.\toverlapWith=test2.3,test2.2,test2.1;nbOverlaps=3.000000;ID=test1.4;Name=test1.4\n")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
+        f.close() 
+        
+    def _writeOutputFile_pcOverlap(self, outputFileName):
+        f = open(outputFileName, "w")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
+        f.close() 
+        
+    def _writeOutputFile_includeNotOverlap(self, outputFileName):
+        f = open(outputFileName, "w")
+        f.write("arm_X\tS-MART\ttranscript\t100\t3199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
+        f.write("arm_X\tS-MART\ttranscript\t100\t199\t.\t+\t.\tnbOverlaps=0;ID=test1.3;Name=test1.3\n")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
+        f.close()
+
+    def _writeOutputFile_exclude(self, outputFileName):
+        f = open(outputFileName, "w")
+        f.write("arm_X\tS-MART\ttranscript\t100\t199\t.\t+\t.\tID=test1.3;Name=test1.3\n")
+        f.close()
+        
+    def _writeOutputFile_included(self, outputFileName):
+        f = open(outputFileName, "w")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
+        f.close()
+
+    def _writeOutputFile_including(self, outputFileName):
+        f = open(outputFileName, "w")
+        f.write("arm_X\tS-MART\ttranscript\t100\t3199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
+        f.close()
+
+    def _writeInputFileQuery_withExon(self):
+        f = open(self._inputFileQuery, "w")
+        f.write("arm_X\t1000\t2000\ttest1.1\t1000\t+\t1000\t2000\t0\t1\t1000,\t0,\n")
+        f.write("arm_X\t1000\t2000\ttest1.2\t1000\t-\t1000\t2000\t0\t1\t1000,\t0,\n")
+        f.write("arm_X\t100\t200\ttest1.3\t1000\t+\t100\t200\t0\t1\t100,\t0,\n")
+        f.write("arm_X\t100\t3200\ttest1.4\t1000\t+\t100\t3200\t0\t2\t100,100,\t0,3000,\n")
+        f.close()
+        
+if __name__ == "__main__":
+    unittest.main()