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18
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1 import unittest, os, os.path
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2 from SMART.Java.Python.misc import Utils
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3 SMART_PATH = os.environ["REPET_PATH"] + "/SMART"
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4
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5 class Test_F_trimSequences(unittest.TestCase):
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6
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7 def setUp(self):
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8 self._expOutputFileName = "expOutputFile.fasta"
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9 self._obsOutputFileName = "obsOutputFile.mfa"
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10 self._inputFileName = "inputFile.fasta"
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11
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12 def tearDown(self):
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13 for fileName in (self._expOutputFileName, self._obsOutputFileName, self._inputFileName):
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14 if os.path.exists(fileName):
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15 os.remove(fileName)
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16
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17 def test_simple(self):
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18 expOutputFile = open(self._expOutputFileName, "w")
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19 expOutputFile.write(">sequence1\nTTGCATAGCGCTACGTA\n")
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20 expOutputFile.close()
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21 inputFile = open(self._inputFileName, "w")
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22 inputFile.write(">sequence1\nAGCTCGGGTATTGCATAGCGCTACGTACCCTTTATATC\n")
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23 inputFile.close()
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24 os.system("python %s/Java/Python/trimSequences.py -i %s -f fasta -3 CCCTTTATATC -5 AGCTCGGGTA -o %s -v 0" % (SMART_PATH, self._inputFileName, self._obsOutputFileName))
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25 self.assertTrue(Utils.diff(self._expOutputFileName, self._obsOutputFileName))
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26
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27 if __name__ == "__main__":
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28 unittest.main()
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