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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/test/Test_F_RestrictFromCoverage.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,133 @@
+import unittest
+import os, os.path
+from optparse import OptionParser
+from SMART.Java.Python.misc import Utils
+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.RestrictFromCoverage import RestrictFromCoverage
+
+REFERENCE = 0
+QUERY     = 1
+
+class Test_F_Clusterize(unittest.TestCase):
+
+    def setUp(self):
+        self._queryFileName     = "testQuery.gff3"
+        self._refFileName       = "testRef.gff3"
+        self._outputFileName    = "output.gff3"
+        self._parsers           = {QUERY: Gff3Writer(self._queryFileName, 0), REFERENCE: Gff3Writer(self._refFileName, 0)}
+        self._writeQuery()
+        
+    def tearDown(self):
+        for file in (self._queryFileName, self._refFileName, self._outputFileName):
+            if os.path.exists(file):
+                os.remove(file)
+
+    def _writeQuery(self):
+        self._addTranscript(QUERY, 1, 1000, 2000, "+")
+        self._parsers[QUERY].close()
+
+    def _writeReferences(self, values):
+        for value in values:
+            self._addTranscript(REFERENCE, value["cpt"], value["start"], value["end"], value["strand"])
+        self._parsers[REFERENCE].close()
+
+    def _addTranscript(self, type, cpt, start, end, strand):
+        t = Transcript()
+        t.setChromosome("chr1")
+        t.setName("test%d" % (cpt))
+        t.setStart(start)
+        t.setEnd(end)
+        t.setDirection(strand)
+        self._parsers[type].addTranscript(t)
+
+    def _checkTranscript(self, transcript, start, end, strand):
+        self.assertEquals(transcript.getStart(),     start)
+        self.assertEquals(transcript.getEnd(),       end)
+        self.assertEquals(transcript.getDirection(), strand)
+
+    def _startTool(self, minNucleotides = None, maxNucleotides = None, minPercent = None, maxPercent = None, minOverlap = None, maxOverlap = None, strands = False):
+        rfc = RestrictFromCoverage(0)
+        rfc.setInputFileName(self._queryFileName, "gff3", QUERY)
+        rfc.setInputFileName(self._refFileName,   "gff3", REFERENCE)
+        rfc.setOutputFileName(self._outputFileName)
+        rfc.setNbNucleotides(minNucleotides, maxNucleotides)
+        rfc.setPercent(minPercent, maxPercent)
+        rfc.setOverlap(minOverlap, maxOverlap)
+        rfc.setStrands(strands)
+        rfc.run()
+        return GffParser(self._outputFileName, 0)
+
+    def test_simple(self):
+        self._writeReferences([{"cpt": 1, "start": 1000, "end": 2000, "strand": "+"}])
+        parser = self._startTool()
+        self.assertEquals(parser.getNbTranscripts(), 1)
+        for transcript in parser.getIterator():
+            self._checkTranscript(transcript, 1000, 2000, 1)
+
+    def test_nbOverlapsMin_pos(self):
+        self._writeReferences([{"cpt": 1, "start": 1000, "end": 2000, "strand": "+"}, {"cpt": 2, "start": 1000, "end": 2000, "strand": "+"}])
+        parser = self._startTool(1, None, None, None, 2)
+        self.assertEquals(parser.getNbTranscripts(), 1)
+        for transcript in parser.getIterator():
+            self._checkTranscript(transcript, 1000, 2000, 1)
+
+    def test_nbOverlapsMin_neg(self):
+        self._writeReferences([{"cpt": 1, "start": 1000, "end": 2000, "strand": "+"}])
+        parser = self._startTool(1, None, None, None, 2)
+        self.assertEquals(parser.getNbTranscripts(), 0)
+
+    def test_nbOverlapsMax_pos(self):
+        self._writeReferences([{"cpt": 1, "start": 1000, "end": 2000, "strand": "+"}])
+        parser = self._startTool(1, None, None, None, None, 1)
+        self.assertEquals(parser.getNbTranscripts(), 1)
+        for transcript in parser.getIterator():
+            self._checkTranscript(transcript, 1000, 2000, 1)
+
+    def test_nbOverlapsMax_neg(self):
+        self._writeReferences([{"cpt": 1, "start": 1000, "end": 2000, "strand": "+"}, {"cpt": 2, "start": 1000, "end": 2000, "strand": "+"}])
+        parser = self._startTool(1, None, None, None, None, 1)
+        self.assertEquals(parser.getNbTranscripts(), 0)
+
+    def test_nbNucleotidesMin_pos(self):
+        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1100, "strand": "+"}])
+        parser = self._startTool(100, None, None, None, 1)
+        self.assertEquals(parser.getNbTranscripts(), 1)
+        for transcript in parser.getIterator():
+            self._checkTranscript(transcript, 1000, 2000, 1)
+
+    def test_nbNucleotidesMin_neg(self):
+        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1100, "strand": "+"}])
+        parser = self._startTool(200, None, None, None, 1)
+        self.assertEquals(parser.getNbTranscripts(), 0)
+
+    def test_PercentMin_pos(self):
+        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1500, "strand": "+"}])
+        parser = self._startTool(None, None, 50, None, 1)
+        self.assertEquals(parser.getNbTranscripts(), 1)
+        for transcript in parser.getIterator():
+            self._checkTranscript(transcript, 1000, 2000, 1)
+
+    def test_PercentMin_neg(self):
+        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1500, "strand": "+"}])
+        parser = self._startTool(None, None, 100, None, 1)
+        self.assertEquals(parser.getNbTranscripts(), 0)
+
+    def test_NoStrand_neg(self):
+        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1500, "strand": "-"}])
+        parser = self._startTool(1, None, None, None, 1)
+        self.assertEquals(parser.getNbTranscripts(), 1)
+
+    def test_strand_pos(self):
+        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1500, "strand": "+"}])
+        parser = self._startTool(1, None, None, None, 1, None, True)
+        self.assertEquals(parser.getNbTranscripts(), 1)
+
+    def test_strand_neg(self):
+        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1500, "strand": "-"}])
+        parser = self._startTool(1, None, None, None, 1, None, True)
+        self.assertEquals(parser.getNbTranscripts(), 0)
+
+if __name__ == "__main__":
+    unittest.main()