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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/test/Test_F_getWigData.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,71 @@
+import unittest
+import os, os.path
+from SMART.Java.Python.misc import Utils
+from SMART.Java.Python.getWigData import *
+
+class Test_F_getWigData(unittest.TestCase):
+
+
+    def setUp(self):
+        self._inputGffFileName = 'inputGff.gff3'
+        self._writeInputGff(self._inputGffFileName)
+        self._inputWigFileName = '../TestFiles/sorted_query_wig.wig'
+        self._expOutFileName = 'expOut.gff3'
+        self._outFileName = 'outGffWig.gff3'
+
+
+    def tearDown(self):
+        os.remove(self._inputGffFileName)
+        os.remove(self._expOutFileName)
+        os.remove(self._outFileName)
+
+
+    def test_getWigData_DefaultOption_asScript(self):
+        cmd = 'python ../getWigData.py -i %s -f gff3 -w %s -t wigValue -o %s -v 0' % (self._inputGffFileName, self._inputWigFileName, self._outFileName)
+        os.system(cmd)
+        self._writeExpDefaultOption(self._expOutFileName)
+        self.assertTrue(Utils.diff(self._expOutFileName, self._outFileName))
+        
+    def test_getWigData_strandsOption(self):
+        cmd = 'python ../getWigData.py -i %s -f gff3 -w %s -t wigValue -o %s -s -v 0' % (self._inputGffFileName, self._inputWigFileName, self._outFileName)
+        os.system(cmd)
+        self._writeExpStransOption(self._expOutFileName)
+        self.assertTrue(Utils.diff(self._expOutFileName, self._outFileName))  
+        
+    
+    def _writeInputGff(self, fileName):
+        f = open(fileName, 'w')
+        f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=query_1;Name=test1.1\n")
+        f.write("chr1\tquery\ttest1.2\t70\t850\t781\t-\t.\tID=query_2;Name=test1.2\n")
+        f.write("chr1\tquery\ttest1.3\t550\t850\t201\t-\t.\tID=query_3;Name=test1.3\n")
+        f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=query_4;Name=test1.4\n")
+        f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=query_5;Name=test1.5\n")
+        f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=query_6;Name=test1.6\n")
+        f.close()
+        
+    def _writeExpDefaultOption(self, fileName):
+        f = open(fileName, 'w')
+        f.write("chr1\tS-MART\ttest1.1\t25\t150\t126\t+\t.\twigValue=1.64285714286;ID=query_1;Name=test1.1\n")
+        f.write("chr1\tS-MART\ttest1.2\t70\t850\t781\t-\t.\twigValue=1.48911651729;ID=query_2;Name=test1.2\n")
+        f.write("chr1\tS-MART\ttest1.3\t550\t850\t201\t-\t.\twigValue=2.0;ID=query_3;Name=test1.3\n")
+        f.write("chr1\tS-MART\ttest1.4\t925\t1025\t101\t+\t.\twigValue=1.0;ID=query_4;Name=test1.4\n")
+        f.write("chr1\tS-MART\ttest1.5\t1201\t1210\t10\t+\t.\twigValue=1.0;ID=query_5;Name=test1.5\n")
+        f.write("chr1\tS-MART\ttest1.6\t1500\t1600\t101\t+\t.\twigValue=1.0;ID=query_6;Name=test1.6\n")
+        f.close()
+        
+    def _writeExpStransOption(self, fileName):
+        f = open(fileName, 'w')
+        f.write("chr1\tS-MART\ttest1.1\t25\t150\t126\t+\t.\twigValue=0.0;ID=query_1;Name=test1.1\n")
+        f.write("chr1\tS-MART\ttest1.2\t70\t850\t781\t-\t.\twigValue=0.0;ID=query_2;Name=test1.2\n")
+        f.write("chr1\tS-MART\ttest1.3\t550\t850\t201\t-\t.\twigValue=0.0;ID=query_3;Name=test1.3\n")
+        f.write("chr1\tS-MART\ttest1.4\t925\t1025\t101\t+\t.\twigValue=0.0;ID=query_4;Name=test1.4\n")
+        f.write("chr1\tS-MART\ttest1.5\t1201\t1210\t10\t+\t.\twigValue=0.0;ID=query_5;Name=test1.5\n")
+        f.write("chr1\tS-MART\ttest1.6\t1500\t1600\t101\t+\t.\twigValue=0.0;ID=query_6;Name=test1.6\n")
+        f.close() 
+        
+    
+        
+
+
+if __name__ == "__main__":
+    unittest.main()