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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/test/Test_F_plotCoverage.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,39 @@
+import unittest
+import os, glob
+from SMART.Java.Python.plotCoverage import PlotParser
+
+
+class Test_F_PlotCoverage(unittest.TestCase):
+
+    def setUp(self):
+        self.queryFileName  = "queryFile.gff3"
+        self.refFileName    = "refFile.gff3"
+        self.outputFileName = "outputFile"
+         
+    def tearDown(self):
+        for fileRoot in (self.queryFileName, self.refFileName, self.outputFileName):
+            for file in glob.glob("%s*" % (fileRoot)):
+                os.remove(file)
+        os.remove(".RData")
+
+    def test_run_simple(self):
+        handle = open(self.refFileName, "w")
+        handle.write("chr1\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test1;Name=test1")
+        handle.close()
+        handle = open(self.queryFileName, "w")
+        handle.write("chr1\tSMART\tmRNA\t1100\t1200\t.\t+\t.\tID=test2.1;Name=test2.1\n")
+        handle.write("chr1\tSMART\tmRNA\t1300\t1400\t.\t+\t.\tID=test2.2;Name=test2.2\n")
+        handle.close()
+        pp = PlotParser(0)
+        pp.addInput(0, self.queryFileName, "gff3")
+        pp.addInput(1, self.refFileName, "gff3")
+        pp.setLabels("x", "y")
+        pp.setPlotSize(1000, 500)
+        pp.setOutput(self.outputFileName)
+        pp.start()
+        self.assertTrue(os.path.exists("%s_test1_overlap.png" % (self.outputFileName)))
+        self.assertTrue(os.path.exists("%s_test1_coverage.png" % (self.outputFileName)))
+        
+if __name__ == "__main__":
+    unittest.main()
+