--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/tests/Test_LaunchTallymer.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,121 @@
+from commons.core.utils.FileUtils import FileUtils
+import os
+import unittest
+from commons.launcher.LaunchTallymer import ConvertUtils
+
+class Test_ConvertUtils(unittest.TestCase):
+
+    def test_convertTallymerFormatIntoMapFormatAndGenerateData(self):
+        inputFastaFileName = "input.fa"
+        inputTallymerSearchFileName = "input.tallymer"
+        expMapFileName = "exp.map"
+        obsMapFileName = "obs.map"
+        self._writeInputFasta(inputFastaFileName)
+        self._writeInputTallymerSearch(inputTallymerSearchFileName)
+        self._writeExpMap(expMapFileName)
+        
+        expOccNb = 4
+        expDKmer2Occ = {"caagatgcgtaacggccata":1,
+                        "aagatgcgtaacggccatac":1,
+                        "agatgcgtaacggccataca":1,
+                        "gatgcgtaacggccatacat":1}
+        expPlotData = {4379: 17,
+                       4380: 17,
+                       4381: 16,
+                       4382: 16}
+        
+        obsOccNb, obsDKmer2Occ, obsPlotData, obsPlotData2 = ConvertUtils.convertTallymerFormatIntoMapFormatAndGenerateData(inputFastaFileName, inputTallymerSearchFileName, obsMapFileName)
+        
+        self.assertEquals(expOccNb, obsOccNb)
+        self.assertEquals(expDKmer2Occ, obsDKmer2Occ)
+        self.assertEquals(expPlotData, obsPlotData)
+        self.assertTrue(FileUtils.are2FilesIdentical(expMapFileName, obsMapFileName))
+        
+        os.remove(inputFastaFileName)
+        os.remove(inputTallymerSearchFileName)
+        os.remove(expMapFileName)
+        os.remove(obsMapFileName)
+        
+    def test_convertTallymerFormatIntoMapFormatAndGenerateDataMultiFasta(self):
+        inputFastaFileName = "input.fa"
+        inputTallymerSearchFileName = "input.tallymer"
+        expMapFileName = "exp.map"
+        obsMapFileName = "obs.map"
+        self._writeInputMultiFasta(inputFastaFileName)
+        self._writeInputTallymerSearchMultiFasta(inputTallymerSearchFileName)
+        self._writeExpMapMultiFasta(expMapFileName)
+        
+        expOccNb = 6
+        expDKmer2Occ = {"caagatgcgtaacggccata":1,
+                        "aagatgcgtaacggccatac":1,
+                        "agatgcgtaacggccataca":1,
+                        "gatgcgtaacggccatacat":1,
+                        "agatgcgtaacggccataca":2,
+                        "gatgcgtaacggccatacat":2}
+        expPlotData = {4379: 17, 4380: 17, 4381: 16, 4382: 35}
+        
+        obsOccNb, obsDKmer2Occ, obsPlotData, obsPlotData2 = ConvertUtils.convertTallymerFormatIntoMapFormatAndGenerateData(inputFastaFileName, inputTallymerSearchFileName, obsMapFileName)
+        
+        self.assertEquals(expOccNb, obsOccNb)
+        self.assertEquals(expDKmer2Occ, obsDKmer2Occ)
+        self.assertEquals(expPlotData, obsPlotData)
+        self.assertTrue(FileUtils.are2FilesIdentical(expMapFileName, obsMapFileName))
+        
+        os.remove(inputFastaFileName)
+        os.remove(inputTallymerSearchFileName)
+        os.remove(expMapFileName)
+        os.remove(obsMapFileName)
+    
+    def _writeInputTallymerSearch(self, tallymerFormatFileName):
+        with open(tallymerFormatFileName, 'w') as f:
+            f.write("0\t+4378\t17\tcaagatgcgtaacggccata\n")
+            f.write("0\t+4379\t17\taagatgcgtaacggccatac\n")
+            f.write("0\t+4380\t16\tagatgcgtaacggccataca\n")
+            f.write("0\t+4381\t16\tgatgcgtaacggccatacat\n")
+             
+    def _writeInputFasta(self, fastaFileName):
+        with open(fastaFileName, 'w') as f:
+            f.write(">Seq1\n")
+            f.write("caagatgcgtaacggccata\n")
+            f.write("aagatgcgtaacggccatac\n")
+            f.write("agatgcgtaacggccataca\n")
+            f.write("gatgcgtaacggccatacat\n")
+            
+    def _writeExpMap(self, mapFileName):
+        with open(mapFileName, 'w') as f:
+            f.write("caagatgcgtaacggccata_17\tSeq1\t4379\t4399\t17\n")
+            f.write("aagatgcgtaacggccatac_17\tSeq1\t4380\t4400\t17\n")
+            f.write("agatgcgtaacggccataca_16\tSeq1\t4381\t4401\t16\n")
+            f.write("gatgcgtaacggccatacat_16\tSeq1\t4382\t4402\t16\n")
+            
+    def _writeInputTallymerSearchMultiFasta(self, tallymerFormatFileName):
+        with open(tallymerFormatFileName, 'w') as f:
+            f.write("0\t+4378\t17\tcaagatgcgtaacggccata\n")
+            f.write("0\t+4379\t17\taagatgcgtaacggccatac\n")
+            f.write("0\t+4380\t16\tagatgcgtaacggccataca\n")
+            f.write("0\t+4381\t16\tgatgcgtaacggccatacat\n")
+            f.write("1\t+4380\t16\tagatgcgtaacggccataca\n")
+            f.write("1\t+4381\t35\tgatgcgtaacggccatacat\n")
+            
+    def _writeInputMultiFasta(self, fastaFileName):
+        with open(fastaFileName, 'w') as f:
+            f.write(">Seq1\n")
+            f.write("caagatgcgtaacggccata\n")
+            f.write("aagatgcgtaacggccatac\n")
+            f.write("agatgcgtaacggccataca\n")
+            f.write("gatgcgtaacggccatacat\n")
+            f.write(">Seq2\n")
+            f.write("agatgcgtaacggccataca\n")
+            f.write("gatgcgtaacggccatacat\n")
+            
+    def _writeExpMapMultiFasta(self, mapFileName):
+        with open(mapFileName, 'w') as f:
+            f.write("caagatgcgtaacggccata_17\tSeq1\t4379\t4399\t17\n")
+            f.write("aagatgcgtaacggccatac_17\tSeq1\t4380\t4400\t17\n")
+            f.write("agatgcgtaacggccataca_16\tSeq1\t4381\t4401\t16\n")
+            f.write("gatgcgtaacggccatacat_16\tSeq1\t4382\t4402\t16\n")
+            f.write("agatgcgtaacggccataca_16\tSeq2\t4381\t4401\t16\n")
+            f.write("gatgcgtaacggccatacat_35\tSeq2\t4382\t4402\t35\n")
+
+if __name__ == "__main__":
+    unittest.main()
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