diff commons/launcher/tests/Test_F_LaunchRepeatMasker.py @ 31:0ab839023fe4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/tests/Test_F_LaunchRepeatMasker.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,110 @@
+import unittest
+import os
+from commons.core.utils.FileUtils import FileUtils
+from commons.launcher.LaunchRepeatMasker import LaunchRepeatMasker
+
+
+class Test_F_RepeatMasker(unittest.TestCase):
+    
+    def setUp(self):
+        self._queryFastaFileName = "query.fa"
+        self._libFastaFileName = "lib.fa"
+        self._expMaskedQueryFileName = "expMaskedQuery.fa"
+        self._obsMaskedQueryFileName = "%s.masked" % self._queryFastaFileName
+        
+        self._expCatFileName = "expCat.fa"
+        self._obsCatFileName = "%s.cat" % self._queryFastaFileName
+        
+        self._writeInputFastaFiles()
+        self._writeExpMaskedQueryFile()
+        self._writeExpCatFile()
+   
+    def tearDown(self):
+        os.remove(self._queryFastaFileName)
+        os.remove(self._libFastaFileName)
+        os.remove(self._expMaskedQueryFileName)
+        os.remove(self._obsMaskedQueryFileName)
+        os.remove(self._expCatFileName)
+        os.remove(self._obsCatFileName)
+        os.remove("%s.tbl" % self._queryFastaFileName)
+        os.remove("%s.out" % self._queryFastaFileName)
+        os.remove("%s.ori.out" % self._queryFastaFileName)
+        
+    def test_run(self):
+        ilauncher = LaunchRepeatMasker(self._queryFastaFileName, self._libFastaFileName,verbosity=1 )
+        ilauncher.run()
+        self.assertTrue(FileUtils.are2FilesIdentical(self._obsMaskedQueryFileName, self._expMaskedQueryFileName))
+        
+    def test_run_as_script(self):
+        #FIXME : change path to launcher
+        cmd = 'python %s/commons/launcher/LaunchRepeatMasker.py -q %s -l %s' % (os.environ["REPET_PATH"],self._queryFastaFileName, self._libFastaFileName)
+        os.system(cmd)
+        self.assertTrue(FileUtils.are2FilesIdentical(self._obsMaskedQueryFileName, self._expMaskedQueryFileName))
+        
+    def _writeInputFastaFiles(self):
+        InputFile = open(self._queryFastaFileName, 'w')
+        InputFile.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n')
+        InputFile.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAGACCCCGGTTC\n')
+        InputFile.write('GATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTG\n')
+        InputFile.write('GGCTTCCCTGGTGGCTCAGACGGTAAAGAATCCGCCTGCAATGCGGGAGACCTGGGTTCG\n')
+        InputFile.write('ATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGC\n')
+        InputFile.write('CTGGAGAATCCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n')
+        InputFile.write('TCGGACACGACTGAGCGACTAAGCACAGCACAGGTCTTTCCTGCCACTTACCTCCTTCCA\n')
+        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
+        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
+        InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
+        InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
+        InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
+        InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCGACCCTCAGTGGAGGAA\n')
+        InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
+        InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
+        InputFile.write('GGGGAGGGTATAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n')
+        InputFile.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTCCCCCACCAAA\n')
+        InputFile.write('AAAAAAA\n')
+        InputFile.close()
+        
+        InputFile = open(self._libFastaFileName, 'w')
+        InputFile.write('>RefLib\n')
+        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
+        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
+        InputFile.close()
+        
+    def _writeExpMaskedQueryFile(self):
+        f = open(self._expMaskedQueryFileName, 'w')  
+        f.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n')
+        f.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAG\n')
+        f.write('ACCCCGGTTCGATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGC\n')
+        f.write('TACCCACTCCAGTATTCTTGGGCTTCCCTGGTGGCTCAGACGGTAAAGAA\n')
+        f.write('TCCGCCTGCAATGCGGGAGACCTGGGTTCGATCCCTGGGTTGGGAAGATC\n')
+        f.write('CCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGCCTGGAGAATC\n')
+        f.write('CCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n')
+        f.write('TCGGACACGACTGAGCGACTAAGCACAGCACAGGTCTTTCCTGCCACTTA\n')
+        f.write('CCTCCTTCCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n')
+        f.write('NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n')
+        f.write('NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCCTGCGTGGGTTCTCTCCG\n')
+        f.write('GGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGATTGGGGATTA\n')
+        f.write('GGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
+        f.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCC\n')
+        f.write('AGGGTGTACCCTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCC\n')
+        f.write('CGCGACCCTCAGTGGAGGAAGGGCAGCCTGGGTGGCTCAGCGGTTTAGCG\n')
+        f.write('CCTGCCTTTGGCCCAGGGCGTGATCCTGGAGACCCGGGATCGAGTCCCAC\n')
+        f.write('ATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTGGGGGAGGGTA\n')
+        f.write('TAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n')
+        f.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTC\n')
+        f.write('CCCCACCAAAAAAAAAA\n')
+        f.close()
+        
+    def _writeExpCatFile(self):
+        f = open(self._expCatFileName, 'w')  
+        f.write('958 0.00 0.00 0.00 Bovc-tA2:classI:SINE:SINE2/tRNA 361 480 (487) RefLib 1 120 (0) 5\n')
+        f.write('## Total Sequences: 1\n')
+        f.write('## Total Length: 967\n')
+        f.write('## Total NonMask ( excluding >20bp runs of N/X bases ): 967\n')
+        f.write('## Total NonSub ( excluding all non ACGT bases ):967\n')
+        f.write('RepeatMasker version open-3.2.6 , default mode\n')
+        f.write('run with blastp version 2.0MP-WashU\n')
+        f.write('RepBase Update 20080801, RM database version 20080801\n')
+        f.close()
+                       
+if __name__ == "__main__":
+    unittest.main()
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