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1 # Copyright INRA (Institut National de la Recherche Agronomique)
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30
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31
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32 import unittest
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33 from SMART.Java.Python.structure.Sequence import Sequence
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34
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35
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36 class Test_Sequence(unittest.TestCase):
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37
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38 def setUp(self):
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39 self._bs = Sequence()
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40 self._bs1 = Sequence()
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41
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42 def test_getSize(self):
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43 self._bs.setName("sequence1")
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44 self._bs.setSequence("AGCGGACGATGCAGCATGCGAATGACGATA")
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45 obsSize = self._bs.getSize()
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46 expSize = 30
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47 self.assertEquals( expSize, obsSize )
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48
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49 def test_concatenate(self):
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50 self._bs.setName("sequence")
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51 self._bs.setSequence("GATGTGCAGACTTTTCACGCAGGACTACATCACTGT")
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52 self._bs.setQuality("WWWVVVWPWWWVWWWWVVVVKVPWWVVWVWUUQUTQ")
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53 self._bs1.setName("sequence1")
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54 self._bs1.setSequence("GGAAACATATGCACATAAACGTTGAAATCATGCTTA")
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55 self._bs1.setQuality("WWWWWWWWWWWWWWWWWVWWVWWVWWWWWWUUUUUU")
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56 self._bs.concatenate(self._bs1)
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57 expSeq = "GATGTGCAGACTTTTCACGCAGGACTACATCACTGTGGAAACATATGCACATAAACGTTGAAATCATGCTTA"
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58 expQal = "WWWVVVWPWWWVWWWWVVVVKVPWWVVWVWUUQUTQWWWWWWWWWWWWWWWWWVWWVWWVWWWWWWUUUUUU"
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59 self.assertEquals(expSeq, self._bs.getSequence())
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60 self.assertEquals(expQal, self._bs.getQuality())
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61
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62 def test_reverseComplement(self):
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63 self._bs.setName("seq1")
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64 self._bs.setSequence("TACGGC")
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65 exp = "GCCGTA"
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66 self._bs.reverseComplement()
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67 obs = self._bs.getSequence()
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68 self.assertEquals(exp, obs)
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69
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70 def test_containsAmbiguousNucleotides(self):
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71 self._bs.setName("seq1")
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72 self._bs.setSequence("WCGTUacgtu")
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73 self.assertTrue (self._bs.containsAmbiguousNucleotides())
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74
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75 def test_shrinkToFirstNucleotides(self):
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76 self._bs.setName("seq1")
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77 self._bs.setSequence("WCGTUacgtu")
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78 self._bs.shrinkToFirstNucleotides(3)
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79 expSeq = "WCG"
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80 self.assertEquals(expSeq, self._bs.getSequence())
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81
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82 def test_shrinkToLastNucleotides(self):
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83 self._bs.setName("seq1")
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84 self._bs.setSequence("WCGTUacgtu")
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85 self._bs.shrinkToLastNucleotides(5)
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86 expSeq = "acgtu"
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87 self.assertEquals(expSeq, self._bs.getSequence())
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88
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89 if __name__ == "__main__":
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90 unittest.main()
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