diff SMART/Java/Python/ncList/test/Test_F_FileSorter.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/ncList/test/Test_F_FileSorter.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,84 @@
+import os
+import unittest
+import struct
+from SMART.Java.Python.misc import Utils
+from SMART.Java.Python.ncList.FileSorter import FileSorter
+from SMART.Java.Python.structure.Transcript import Transcript
+from commons.core.writer.Gff3Writer import Gff3Writer
+from commons.core.parsing.GffParser import GffParser
+from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle
+
+
+class Test_F_FileSorter(unittest.TestCase):
+
+    def setUp(self):
+        self._inputGff3FileName = 'inputFile.gff3'
+        self._outputFileName    = 'outputFile.pkl'
+        
+    def tearDown(self):
+        return
+        for fileName in (self._inputGff3FileName, self._sortedFileName, self._expHFileName, self._expLFileName, self._obsHFileName, self._obsLFileName, self._addressFileName):
+            if os.path.exists(fileName):
+                os.remove(fileName)
+        
+    def test_unique(self):
+        transcript = self._createTranscript("chr1", 100, 200, "test1.1")
+        parser     = self._writeAndSortAndParse([transcript])
+        self.assertEquals(parser.getNbTranscripts(), 1)
+        for transcript in parser.getIterator():
+            self._checkTranscript(transcript, "chr1", 100, 200, "test1.1")
+            
+    def test_simple(self):
+        transcript1 = self._createTranscript("chr1", 300, 400, "test1.1")
+        transcript2 = self._createTranscript("chr1", 100, 200, "test1.2")
+        parser = self._writeAndSortAndParse([transcript1, transcript2])
+        self.assertEquals(parser.getNbTranscripts(), 2)
+        for cpt, transcript in enumerate(parser.getIterator()):
+            if cpt == 0:
+                self._checkTranscript(transcript, "chr1", 100, 200, "test1.2")
+            else:
+                self._checkTranscript(transcript, "chr1", 300, 400, "test1.1")
+
+    def test_same_start(self):
+        transcript1 = self._createTranscript("chr1", 100, 200, "test1.1")
+        transcript2 = self._createTranscript("chr1", 100, 300, "test1.2")
+        parser = self._writeAndSortAndParse([transcript1, transcript2])
+        self.assertEquals(parser.getNbTranscripts(), 2)
+        for cpt, transcript in enumerate(parser.getIterator()):
+            if cpt == 0:
+                self._checkTranscript(transcript, "chr1", 100, 300, "test1.2")
+            else:
+                self._checkTranscript(transcript, "chr1", 100, 200, "test1.1")
+
+    def _writeAndSortAndParse(self, transcripts):
+        writer = Gff3Writer(self._inputGff3FileName, 0)
+        for transcript in transcripts:
+            writer.addTranscript(transcript)
+        writer.close()
+        parser = GffParser(self._inputGff3FileName, 0)
+        fs = FileSorter(parser, 0)
+        fs.setOutputFileName(self._outputFileName)
+        fs.sort()
+        parser = NCListFileUnpickle(self._outputFileName, 0)
+        return parser
+
+    def _createTranscript(self, chromosome, start, end, name):
+        transcript = Transcript()
+        transcript.setChromosome(chromosome)
+        transcript.setStart(start)
+        transcript.setEnd(end)
+        transcript.setDirection("+")
+        transcript.setName(name)
+        return transcript
+
+    def _checkTranscript(self, transcript, chromosome, start, end, name):
+        self.assertEquals(transcript.getChromosome(), chromosome)
+        self.assertEquals(transcript.getStart(),      start)
+        self.assertEquals(transcript.getEnd(),        end)
+        self.assertEquals(transcript.getDirection(),  1)
+        self.assertEquals(transcript.getName(),       name)
+        
+            
+if __name__ == "__main__":
+    unittest.main()
+