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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/test/Test_F_mergeTranscriptLists.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,92 @@
+import unittest
+import os, os.path, glob
+from SMART.Java.Python.structure.Transcript import Transcript
+from SMART.Java.Python.mergeTranscriptLists import MergeLists
+from commons.core.writer.Gff3Writer import Gff3Writer
+from commons.core.parsing.GffParser import GffParser
+
+class Test_F_mergeTranscriptLists(unittest.TestCase):
+
+    def setUp(self):
+        self.queryFileName     = "testQuery.gff3"
+        self.referenceFileName = "testReference.gff3"
+        self.outputFileName    = "testOutput.gff3"
+         
+    def tearDown(self):
+        for fileRoot in (self.queryFileName, self.referenceFileName, self.outputFileName):
+            for file in glob.glob("%s*" % (fileRoot)):
+                os.remove(file)
+        for file in glob.glob("tmp_*.gff3"):
+            os.remove(file)
+
+    def test_run_simple(self):
+        reference1 = self._createTranscript("chr1", 1000, 2000, "+", "ref1")
+        reference2 = self._createTranscript("chr1", 3000, 4000, "+", "ref2")
+        reference3 = self._createTranscript("chr1", 5000, 6000, "+", "ref3")
+        writer = Gff3Writer(self.referenceFileName, 0)
+        writer.addTranscript(reference1)
+        writer.addTranscript(reference2)
+        writer.addTranscript(reference3)
+        writer.close()
+        query1 = self._createTranscript("chr1", 1500, 3500, "+", "query1")
+        writer = Gff3Writer(self.queryFileName, 0)
+        writer.addTranscript(query1)
+        writer.close()
+        ml = MergeLists(0)
+        ml.setInputFileName(self.queryFileName, 'gff3', 0)
+        ml.setInputFileName(self.referenceFileName, 'gff3', 1)
+        ml.setOutputFileName(self.outputFileName)
+        ml.run()
+        parser = GffParser(self.outputFileName)
+        self.assertEqual(parser.getNbTranscripts(), 1)
+        for transcript in parser.getIterator():
+            self._checkTranscript(transcript, "chr1", 1000, 4000, "+", None)
+
+    def test_run_simple_aggregate(self):
+        reference1 = self._createTranscript("chr1", 1000, 2000, "+", "ref1")
+        reference2 = self._createTranscript("chr1", 3000, 4000, "+", "ref2")
+        reference3 = self._createTranscript("chr1", 5000, 6000, "+", "ref3")
+        writer = Gff3Writer(self.referenceFileName, 0)
+        writer.addTranscript(reference1)
+        writer.addTranscript(reference2)
+        writer.addTranscript(reference3)
+        writer.close()
+        query1 = self._createTranscript("chr1", 1500, 3500, "+", "query1")
+        writer = Gff3Writer(self.queryFileName, 0)
+        writer.addTranscript(query1)
+        writer.close()
+        ml = MergeLists(0)
+        ml.setInputFileName(self.queryFileName, 'gff3', 0)
+        ml.setInputFileName(self.referenceFileName, 'gff3', 1)
+        ml.setOutputFileName(self.outputFileName)
+        ml.setAggregate(True)
+        ml.run()
+        parser = GffParser(self.outputFileName)
+        self.assertEqual(parser.getNbTranscripts(), 2)
+        for cpt, transcript in enumerate(parser.getIterator()):
+            if cpt == 0:
+                self._checkTranscript(transcript, "chr1", 1000, 4000, "+", None)
+            else:
+                self._checkTranscript(transcript, "chr1", 5000, 6000, "+", None)
+
+    def _createTranscript(self, chromosome, start, end, strand, name):
+        transcript = Transcript()
+        transcript.setChromosome(chromosome)
+        transcript.setStart(start)
+        transcript.setEnd(end)
+        transcript.setDirection(strand)
+        transcript.setName(name)
+        return transcript
+
+    def _checkTranscript(self, transcript, chromosome, start, end, strand, name):
+        self.assertEqual(transcript.getChromosome(), chromosome)
+        self.assertEqual(transcript.getStart(), start)
+        self.assertEqual(transcript.getEnd(), end)
+        self.assertEqual(transcript.getStrand(), strand)
+        if name != None:
+            self.assertEqual(transcript.getName(), name)
+
+        
+if __name__ == "__main__":
+    unittest.main()
+