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1 import unittest
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2 import time
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3 import os
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4 from commons.core.utils.FileUtils import FileUtils
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5 from commons.tools.OrientSequences import OrientSequences
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6
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7
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8 class Test_OrientSequences( unittest.TestCase ):
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9
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10 def setUp( self ):
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11 self._i = OrientSequences ()
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12 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
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13
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14
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15 def tearDown( self ):
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16 self._i = None
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17 self._uniqId = None
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18
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19
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20 def test_parseMummerOutput( self ):
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21 inFileName = "dummyInFile_%s" % ( self._uniqId )
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22 inF = open( inFileName, "w" )
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23 inF.write( "> seq1\n" )
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24 inF.write( " seq2 20 1 20\n" )
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25 inF.write( "> seq1 Reverse\n" )
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26 inF.write( " seq2 100 1 100\n" )
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27 inF.write( " seq2 450 400 50\n" )
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28 inF.close()
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29 dExp = { "direct": 1, "reverse": 2 }
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30 self._i._verbose = 0
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31 dObs = self._i.parseMummerOutput( inFileName, "seq1", "seq2" )
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32 self.assertEqual( dObs, dExp )
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33 os.remove( inFileName )
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34
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35
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36 def test_getSequencesToReverseFromMatrix_2seq( self ):
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37 lNewHeaders = [ "seq1", "seq2" ]
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38 dMatrix = { "1_vs_2": { "direct": 1, "reverse": 2 } }
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39 lExp = [ "seq2" ]
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40 self._i._verbose = 0
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41 lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders )
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42 lExp.sort()
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43 lObs.sort()
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44 self.assertEqual( lObs, lExp )
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45
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46
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47 def test_getSequencesToReverseFromMatrix_3seq( self ):
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48 lNewHeaders = [ "seq1", "seq2", "seq3" ]
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49 dMatrix = { "1_vs_2": { "direct": 1, "reverse": 10 },
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50 "1_vs_3": { "direct": 10, "reverse": 1 },
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51 "2_vs_3": { "direct": 1, "reverse": 10 } }
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52 lExp = [ "seq2" ]
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53 self._i._verbose = 0
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54 lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders )
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55 lExp.sort()
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56 lObs.sort()
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57 self.assertEqual( lExp, lObs )
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58
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59
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60 def test_getSequencesToReverseFromMatrix_4seq( self ):
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61 lNewHeaders = [ "seq1", "seq2", "seq3", "seq4" ]
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62 dMatrix = { "1_vs_2": { "direct": 10, "reverse": 1 },
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63 "1_vs_3": { "direct": 1, "reverse": 10 },
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64 "1_vs_4": { "direct": 1, "reverse": 10 },
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65 "2_vs_3": { "direct": 1, "reverse": 10 },
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66 "2_vs_4": { "direct": 1, "reverse": 10 },
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67 "3_vs_4": { "direct": 1, "reverse": 2 } }
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68 lExp = [ "seq3", "seq4" ]
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69 self._i._verbose = 0
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70 lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders )
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71 lExp.sort()
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72 lObs.sort()
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73 self.assertEqual( lExp, lObs )
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74
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75
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76 def test_orientInputSequences( self ):
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77 lSeqToOrient = [ "seq1" ]
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78 tmpFileName = "dummyInFile_%s" % ( self._uniqId )
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79 tmpF = open( tmpFileName, "w" )
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80 tmpF.write( ">seq1\n" )
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81 tmpF.write( "ATGCGGTGCATG\n" )
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82 tmpF.write( ">seq2\n" )
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83 tmpF.write( "GGCGAAGTGAAA\n" )
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84 tmpF.close()
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85 expFileName = "dummyExpFile_%s" % ( self._uniqId )
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86 expF = open( expFileName, "w" )
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87 expF.write( ">seq1 re-oriented\n" )
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88 expF.write( "CATGCACCGCAT\n" )
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89 expF.write( ">seq2\n" )
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90 expF.write( "GGCGAAGTGAAA\n" )
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91 expF.close()
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92 obsFileName = "dummyObsFile_%s" % ( self._uniqId )
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93 self._i._verbose = 0
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94 self._i._outFileName = obsFileName
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95 self._i.orientInputSequences( lSeqToOrient, tmpFileName )
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96 self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
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97 for f in [ tmpFileName, expFileName, obsFileName ]:
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98 os.remove( f )
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99
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100 if __name__ == "__main__":
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101 unittest.main() |