diff commons/launcher/tests/Test_F_LaunchBlastclust.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/tests/Test_F_LaunchBlastclust.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,103 @@
+import unittest
+import os
+from commons.launcher.LaunchBlastclust import LaunchBlastclust
+from commons.core.utils.FileUtils import FileUtils
+
+class Test_F_LaunchBlastclust(unittest.TestCase):
+
+    def setUp(self):
+        self._inputFileName = "DmelChr4_LTRharvest_expected_with_default_params.fa"
+        os.symlink("%s/Tools/%s" % (os.environ["REPET_DATA"], self._inputFileName), self._inputFileName)
+        self._outputFileName = "%s_Blastclust.fa" % self._inputFileName
+        self._outBlastclustFileName = "%s_blastclust.txt" % self._inputFileName
+        
+    def tearDown(self):
+        if os.path.exists(self._outputFileName):
+            os.remove(self._outputFileName)
+        if os.path.exists(self._outBlastclustFileName):
+            os.remove(self._outBlastclustFileName)
+        os.remove(self._inputFileName)
+
+    def test_run(self):
+        iLaunchBlastclust = LaunchBlastclust(self._inputFileName, clean = True)
+        iLaunchBlastclust.run()
+        expFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected.fa" % os.environ["REPET_DATA"]
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
+        
+    def test_run_with_tweaked_params(self):
+        iLaunchBlastclust = LaunchBlastclust(self._inputFileName, clean = True)
+        iLaunchBlastclust.setBothSequences("F")
+        iLaunchBlastclust.setIdentityThreshold(0)
+        iLaunchBlastclust.setIsBlastToMap()
+        iLaunchBlastclust.run()
+        
+        faExpFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected_with_tweaked_params.fa" % os.environ["REPET_DATA"]
+        mapExpFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected_with_tweaked_params.map" % os.environ["REPET_DATA"]
+        
+        self.assertTrue(FileUtils.are2FilesIdentical(faExpFileName, self._outputFileName))
+        self.assertTrue(FileUtils.are2FilesIdentical(mapExpFileName, "%s.map" % os.path.splitext(self._outputFileName)[0]))
+        
+        os.remove("%s.map" % os.path.splitext(self._outputFileName)[0])
+      
+    def test_run_with_header_options(self):
+        inFileName = "dummyHeaderForTEdenovo.fa"
+        expFileName = "expDummyHeaderForTEdenovo.fa"
+        self._writeInputFile_header_options(inFileName)
+        self._writeExpFile_header_options(expFileName)
+        obsFileName = "%s_Blastclust.fa" % inFileName
+        
+        iLaunchBlastclust = LaunchBlastclust(inFileName, clean = True)
+        iLaunchBlastclust.setIsHeaderForTEdenovo(True)
+        iLaunchBlastclust.run()
+        
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
+        
+        os.remove(inFileName)
+        os.remove(expFileName)
+        os.remove(obsFileName)
+        os.remove("%s_blastclust.txt" % inFileName)
+          
+    def test_run_as_script(self):
+        cmd = "LaunchBlastclust.py -i %s" % self._inputFileName
+        os.system(cmd)
+        expFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected.fa" % os.environ["REPET_DATA"]
+        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
+        
+    def _writeInputFile_header_options(self, inFileName):
+        f = open(inFileName,"w")
+        f.write(">DTX-incomp_DmelChr4-B-R9-Map3_reversed\n")
+        f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
+        f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
+        f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
+        f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
+        f.write(">DTX-incomp_DmelChr4-B-R10-Map3_reversed\n")
+        f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
+        f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
+        f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
+        f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
+        f.write(">PotentialHostGene-chim_DmelChr4-B-R4-Map5_reversed\n")
+        f.write("TACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTT\n")
+        f.write("TTTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAG\n")
+        f.write("AGCGGAGAGCGCTACAGCGAACAGCTCTTTTCAACGCATAAAGTGATAGCAGACAACTGT\n")
+        f.close()
+        
+    def _writeExpFile_header_options(self, expFileName):
+        f = open(expFileName,"w")
+        f.write(">DTX-incomp_Blc1_DmelChr4-B-R9-Map3_reversed\n")
+        f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
+        f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
+        f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
+        f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
+        f.write(">DTX-incomp_Blc1_DmelChr4-B-R10-Map3_reversed\n")
+        f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
+        f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
+        f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
+        f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
+        f.write(">PotentialHostGene-chim_Blc2_DmelChr4-B-R4-Map5_reversed\n")
+        f.write("TACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTT\n")
+        f.write("TTTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAG\n")
+        f.write("AGCGGAGAGCGCTACAGCGAACAGCTCTTTTCAACGCATAAAGTGATAGCAGACAACTGT\n")
+        f.close()
+        
+if __name__ == "__main__":
+    unittest.main()
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