diff SMART/Java/Python/test/Test_F_CombineTags.py @ 31:0ab839023fe4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/test/Test_F_CombineTags.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,109 @@
+import unittest
+import os
+from optparse import OptionParser
+from SMART.Java.Python.structure.Transcript import Transcript
+from commons.core.parsing.ParserChooser import ParserChooser
+from commons.core.parsing.GffParser import GffParser
+from commons.core.writer.Gff3Writer import Gff3Writer
+from SMART.Java.Python.CombineTags import CombineTags
+
+class Test_F_CombineTags(unittest.TestCase):
+
+    def setUp(self):
+        self._inputFileName  = "inputFileTest.gff3"
+        self._outputFileName = "outputFileTest.gff3"
+        self._tag1           = "tag1"
+        self._tag2           = "tag2"
+        self._outputTag      = "outputTag"
+        
+    def tearDown(self):
+        os.remove(self._inputFileName)
+        os.remove(self._outputFileName)
+
+    def test_plus(self):
+        transcript = self._createDummyTranscript()
+        transcript.setTagValue(self._tag1, 1)
+        transcript.setTagValue(self._tag2, 2)
+        self._writeTranscript(transcript)
+        combiner = CombineTags(0)
+        combiner.setInputFile(self._inputFileName, "gff3")
+        combiner.setOutputFile(self._outputFileName)
+        combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
+        combiner.setOperation("plus")
+        combiner.run()
+        self._testOutputTag(3)
+
+    def test_minus(self):
+        transcript = self._createDummyTranscript()
+        transcript.setTagValue(self._tag1, 2)
+        transcript.setTagValue(self._tag2, 1)
+        self._writeTranscript(transcript)
+        combiner = CombineTags(0)
+        combiner.setInputFile(self._inputFileName, "gff3")
+        combiner.setOutputFile(self._outputFileName)
+        combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
+        combiner.setOperation("minus")
+        combiner.run()
+        self._testOutputTag(1)
+
+    def test_times(self):
+        transcript = self._createDummyTranscript()
+        transcript.setTagValue(self._tag1, 6)
+        transcript.setTagValue(self._tag2, 3)
+        self._writeTranscript(transcript)
+        combiner = CombineTags(0)
+        combiner.setInputFile(self._inputFileName, "gff3")
+        combiner.setOutputFile(self._outputFileName)
+        combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
+        combiner.setOperation("times")
+        combiner.run()
+        self._testOutputTag(18)
+
+    def test_div(self):
+        transcript = self._createDummyTranscript()
+        transcript.setTagValue(self._tag1, 6)
+        transcript.setTagValue(self._tag2, 3)
+        self._writeTranscript(transcript)
+        combiner = CombineTags(0)
+        combiner.setInputFile(self._inputFileName, "gff3")
+        combiner.setOutputFile(self._outputFileName)
+        combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
+        combiner.setOperation("div")
+        combiner.run()
+        self._testOutputTag(2)
+
+    def test_default(self):
+        transcript = self._createDummyTranscript()
+        transcript.setTagValue(self._tag1, 1)
+        self._writeTranscript(transcript)
+        combiner = CombineTags(0)
+        combiner.setInputFile(self._inputFileName, "gff3")
+        combiner.setOutputFile(self._outputFileName)
+        combiner.setTags(self._tag1, self._tag2, self._outputTag, 0)
+        combiner.setOperation("plus")
+        combiner.run()
+        self._testOutputTag(0)
+
+    def _createDummyTranscript(self):
+        transcript = Transcript()
+        transcript.setChromosome("chr1")
+        transcript.setName("test1")
+        transcript.setEnd(200)
+        transcript.setStart(100)
+        transcript.setDirection("+")
+        return transcript
+    
+    def _testOutputTag(self, value):
+        parser = GffParser(self._outputFileName, 0)
+        for transcript in parser.getIterator():
+            self.assertEquals(float(transcript.getTagValue(self._outputTag)), value)
+        parser.close()
+
+    def _writeTranscript(self, transcript):
+        f = open(self._inputFileName, "w")
+        f.write(transcript.printGff3("test"))
+        f.close()
+        
+
+if __name__ == "__main__":
+    unittest.main()