--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/test/Test_F_CollapseReads.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,92 @@
+import unittest
+import os
+from SMART.Java.Python.CollapseReads import CollapseReads
+from SMART.Java.Python.misc import Utils
+from commons.core.utils.FileUtils import FileUtils
+from SMART.Java.Python.ncList.test.MockFindOverlaps_randomExample import MockFindOverlaps_randomExample_NonOrder
+
+class Test_F_CollapseReads(unittest.TestCase):
+
+    def setUp(self):
+        self._inputFileName = 'inputCR.gff3'
+        self._writeInput(self._inputFileName)
+        self._outputFileName = 'outputCR.gff3'
+        self._expOutputFileName = 'expOutputCR.gff3'
+        
+    def tearDown(self):
+        return
+
+    def test_run_default_option(self):
+        iCR = CollapseReads(0)
+        iCR.setInputFile(self._inputFileName, 'gff3')
+        iCR.setOutputFile(self._outputFileName)
+        iCR.strands = False
+        iCR.collapse()
+        self._writeExp_strand_False(self._expOutputFileName)
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
+            
+    def test_run_strand_option(self):
+        iCR = CollapseReads(0)
+        iCR.setInputFile(self._inputFileName, 'gff3')
+        iCR.setOutputFile(self._outputFileName)
+        iCR.strands = True
+        iCR.collapse()
+        self._writeExp_strand_True(self._expOutputFileName)
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
+        
+    def test_run_asScript_default_option(self):
+        cmd = 'python ../CollapseReads.py -i %s -f gff3 -o %s -v 0' % (self._inputFileName, self._outputFileName)
+        os.system(cmd)
+        self._writeExp_strand_True(self._expOutputFileName)
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))    
+        
+    def test_run_asScript_strand_option(self):
+        cmd = 'python ../CollapseReads.py -i %s -f gff3 -o %s -s -v 0' % (self._inputFileName, self._outputFileName)
+        os.system(cmd)
+        self._writeExp_strand_False(self._expOutputFileName)
+        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))    
+        
+    def test_run_toOrderGff(self):
+        iMRE = MockFindOverlaps_randomExample_NonOrder(self._inputFileName, 'chrom', 10, 1000)    
+        iMRE.write()
+        iCR = CollapseReads(0)
+        iCR.setInputFile(self._inputFileName, 'gff3')
+        iCR.setOutputFile(self._outputFileName)
+        iCR.strands = False
+        iCR.collapse()
+        f = open(self._expOutputFileName, "w")
+        f.close()
+        cmd = 'sort -f -n -k4 -k5.4rn -o %s %s'%(self._expOutputFileName, self._inputFileName)
+        os.system(cmd) 
+
+    def _writeInput(self, fileName):
+        f = open(fileName, 'w')
+        f.write("chr1\ttest\tmatch\t6155418\t6155441\t.\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
+        f.write("chr2\ttest\tmatch\t26303950\t26303981\t.\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
+        f.write("chr3\ttest\tmatch\t28320540\t28320574\t.\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
+        f.write("chr4\ttest\tmatch\t28565007\t28565041\t.\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
+        f.write("chr1\ttest\tmatch\t6155418\t6155441\t.\t+\t.\toccurrence=2;rank=2;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1;ID=test3/1;identity=50;Name=test3/1\n")
+        f.write("chr1\ttest\tmatch\t6155418\t6155441\t.\t-\t.\toccurrence=2;rank=2;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1;ID=test3/1;identity=50;Name=test3/1\n")
+        f.close()
+
+    def _writeExp_strand_False(self, fileName):
+        f = open(fileName, 'w')
+        f.write("""chr1	S-MART	match	6155418	6155441	.	-	.	nbElements=3.000000;ID=test3/1;Name=test3/1--test3/1--test1/1
+chr2	S-MART	match	26303950	26303981	.	+	.	occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1
+chr3	S-MART	match	28320540	28320574	.	+	.	occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1
+chr4	S-MART	match	28565007	28565041	.	+	.	occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1
+""")
+        f.close()
+        
+    def _writeExp_strand_True(self, fileName):
+        f = open(fileName, 'w')
+        f.write("""chr1	S-MART	match	6155418	6155441	.	+	.	nbElements=2.000000;ID=test3/1;Name=test3/1--test1/1
+chr1	S-MART	match	6155418	6155441	.	-	.	occurrence=2;rank=2;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1;ID=test3/1;identity=50;Name=test3/1
+chr2	S-MART	match	26303950	26303981	.	+	.	occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1
+chr3	S-MART	match	28320540	28320574	.	+	.	occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1
+chr4	S-MART	match	28565007	28565041	.	+	.	occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1
+""")
+        f.close()
+        
+if __name__ == "__main__":
+    unittest.main()