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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/test/Test_F_getWigProfile.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,65 @@
+import unittest
+import os, glob
+from SMART.Java.Python.getWigProfile import GetWigProfile
+
+
+class Test_F_GetWigProfile(unittest.TestCase):
+
+    def setUp(self):
+        self.transcriptFileName = "transcriptFile.gff3"
+        self.wigFileName        = "file.wig"
+        self.outputFileName     = "outputFile.png"
+         
+    def tearDown(self):
+        for fileRoot in (self.transcriptFileName, self.wigFileName, self.outputFileName):
+            for file in glob.glob("%s*" % (fileRoot)):
+                os.remove(file)
+        os.system("rm .RData .chr1.index ")
+
+    def test_run_simple(self):
+        handle = open(self.transcriptFileName, "w")
+        handle.write("chr1\tSMART\tmRNA\t10\t20\t.\t+\t.\tID=test1;Name=test1")
+        handle.close()
+        handle = open(self.wigFileName, "w")
+        handle.write("variableStep chrom=chr1\n")
+        handle.write("1 1\n")
+        handle.write("2 1\n")
+        handle.write("3 1\n")
+        handle.write("4 1\n")
+        handle.write("5 1\n")
+        handle.write("6 1\n")
+        handle.write("7 1\n")
+        handle.write("8 1\n")
+        handle.write("9 1\n")
+        handle.write("10 1\n")
+        handle.write("11 2\n")
+        handle.write("12 3\n")
+        handle.write("13 4\n")
+        handle.write("14 5\n")
+        handle.write("15 5\n")
+        handle.write("16 5\n")
+        handle.write("17 5\n")
+        handle.write("18 5\n")
+        handle.write("19 5\n")
+        handle.write("20 5\n")
+        handle.write("21 1\n")
+        handle.write("21 1\n")
+        handle.close()
+        wigProfile = GetWigProfile(0)
+        wigProfile.strands        = False
+        wigProfile.inputFileName  = self.transcriptFileName
+        wigProfile.inputFormat    = "gff3"
+        wigProfile.wig            = self.wigFileName
+        wigProfile.nbPoints       = 11
+        wigProfile.distance       = 1
+        wigProfile.smoothenForce  = None
+        wigProfile.log            = False
+        wigProfile.outputFileName = self.outputFileName
+        wigProfile.readTranscripts()
+        wigProfile.smoothen()
+        wigProfile.plot()
+        self.assertTrue(os.path.exists(self.outputFileName))
+        
+if __name__ == "__main__":
+    unittest.main()
+