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1 import unittest
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2 import time
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3 from commons.tools.refalign2fasta import *
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4 from commons.core.utils.FileUtils import FileUtils
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5
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6
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7 class Test_refalign2fasta( unittest.TestCase ):
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8
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9
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10 def setUp( self ):
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11 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
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12
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13
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14 def tearDown( self ):
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15 self._uniqId = None
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16
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17
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18 def test_getAlignments( self ):
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19 inFile = "dummyInFile_%s" % ( self._uniqId )
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20 inFileHandler = open( inFile, "w" )
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21 inFileHandler.write( "AAAACTTTT-T\tAAAA-TTTGGT\trefseq::1 chr3 1..10\n" ) # 1 insertion and 1 deletion in the copy + 1 mismatch
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22 inFileHandler.close()
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23 lExp = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ]
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24 lObs = getAlignments( inFile )
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25 self.assertEqual( lExp, lObs )
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26 os.remove( inFile )
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27
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28
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29 def test_getGaps_OneGap( self ):
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30 sequence = "AAAACTTTT-T"
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31 lExp = [ ( 9, 1 ) ]
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32 lObs = getGaps( sequence )
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33 self.assertEqual( lExp, lObs )
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34
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35
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36 def test_getGaps_TwoGaps( self ):
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37 sequence = "AAAA--CTTT-TT"
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38 lExp = [ ( 4, 2 ), ( 8, 1 ) ]
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39 lObs = getGaps( sequence )
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40 self.assertEqual( lExp, lObs )
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41
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42
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43 def test_getGapsOnRefSeq_OneSeq( self ):
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44 lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ]
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45 lExp = [ [ ( 9, 1 ) ] ]
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46 lObs = getGapsOnRefSeq( lAlign )
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47 self.assertEqual( lExp, lObs )
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48
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49
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50 def test_getGapsOnRefSeq_TwoSeq( self ):
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51 lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ]
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52 lAlign.append( ( "AAAA--CTTT-TT", "AAAAGGCTTTGTT", "refseq::2 chr5 1..10" ) )
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53 lExp = [ [ ( 9, 1 ) ] ]
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54 lExp.append( [ ( 4, 2 ), ( 8, 1 ) ] )
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55 lObs = getGapsOnRefSeq( lAlign )
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56 self.assertEqual( lExp, lObs )
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57
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58
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59 def test_insertGap( self ):
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60 sequence = "GGGGAAAGTTG"
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61 start = 5
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62 length = 3
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63 exp = "GGGGA---AAGTTG"
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64 obs = insertGap( sequence, start, length )
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65 self.assertEqual( exp, obs )
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66
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67
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68 def test_insertListGaps( self ):
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69 sequence = "GGGGAAAGTTG"
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70 lGaps =[ ( 5, 3 ), ( 9, 1 ) ]
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71 exp = "GGGGA---AAGT-TG"
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72 obs = insertListGaps( sequence, lGaps )
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73 self.assertEqual( exp, obs )
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74
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75
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76 def test_insertGapsInRefSeq( self ):
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77 lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ]
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78 lAlign.append( ( "AAAA--CTTT-TT", "AAAAGGCTTTGTT", "refseq::2 chr5 1..10" ) )
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79 lGapsOnRefSeqPerAlign = [ [ ( 9, 1 ) ] ]
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80 lGapsOnRefSeqPerAlign.append( [ ( 4, 2 ), ( 8, 1 ) ] )
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81 refseqName = "reference_sequence"
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82 lExp = ( refseqName, "AAAA--CTTT-T-T" )
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83 lObs = insertGapsInRefSeq( lAlign, lGapsOnRefSeqPerAlign, refseqName )
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84 self.assertEqual( lExp, lObs )
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85
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86
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87 def test_insertgap_seq( self ):
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88 # AAAACTTTT-T (refseq)
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89 # AAAA-TTTGGT ( copy 1)
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90 #
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91 # AAAA--CTTT-TT (refseq)
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92 # AAAAGGCTTTGTT (copy 2)
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93 lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ]
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94 lAlign.append( ( "AAAA--CTTT-TT", "AAAAGGCTTTGTT", "refseq::2 chr5 1..10" ) )
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95 lGapsOnRefSeqPerAlign = [ [ ( 9, 1 ) ] ]
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96 lGapsOnRefSeqPerAlign.append( [ ( 4, 2 ), ( 8, 1 ) ] )
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97 lExp = [ ( "refseq::1 chr3 1..10", "AAAA---TTT-GGT" ) ]
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98 lExp.append( ( "refseq::2 chr5 1..10", "AAAAGGCTTTGT-T" ) )
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99 lObs = insertgap_seq( lAlign, lGapsOnRefSeqPerAlign )
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100 self.assertEqual( lExp, lObs )
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101
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102
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103 def test_getSeqWithDeletions( self ):
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104 lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "refseq::1 chr3 1..10" ) ]
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105 lExp = [ ( "refseq::1 chr3 1..10", "AAAA-TTTGT" ) ]
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106 lObs = getSeqWithDeletions( lAlign )
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107 self.assertEqual( lExp, lObs )
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108
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109
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110 def test_saveOnlyWithDeletions( self ):
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111 refseqName = "Dm-B-G54-Map3"
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112 lAlign = [ ( "AAAACTTTT-T", "AAAA-TTTGGT", "Dm-B-G54-Map3::1 chr3 1..10" ) ]
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113 lAlign.append( ( "AAAA--CTTT-TT", "AAAAGGCTTTGTT", "Dm-B-G54-Map3::2 chr5 1..10" ) )
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114
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115 expFile = "dummyExpFile_%s" %( self._uniqId )
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116 expFileHandler = open( expFile, "w" )
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117 expFileHandler.write( ">Dm-B-G54-Map3\n" )
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118 expFileHandler.write( "AAAACTTTTT\n" )
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119 expFileHandler.write( ">Dm-B-G54-Map3::1 chr3 1..10\n" )
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120 expFileHandler.write( "AAAA-TTTGT\n" )
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121 expFileHandler.write( ">Dm-B-G54-Map3::2 chr5 1..10\n" )
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122 expFileHandler.write( "AAAACTTTTT\n" )
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123 expFileHandler.close()
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124
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125 obsFile = "dummyObsFile_%s" % ( self._uniqId )
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126
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127 saveOnlyWithDeletions( lAlign, refseqName, obsFile )
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128
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129 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
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130
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131 for f in [ expFile, obsFile ]:
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132 os.remove( f )
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133
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134 if __name__ == "__main__":
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135 unittest.main() |
