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6
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1 import unittest, os
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2 from commons.core.parsing.BlatToGffForBesPaired import BlatToGffForBesPaired
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3
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4
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5 class Test_BlatToGffForBesPaired(unittest.TestCase):
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6
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7
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8 def test_convertBlatObjectToGffLine(self):
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9 blatLine = '315\t20\t0\t0\t3\t10\t2\t9\t+\tMRRE1H001H13FM1\t378\t0\t345\tchr16\t22053297\t21686950\t21687294\t4\t76,185,7,67,\t0,77,263,278,\t21686950,21687026,21687213,21687227,\n'
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10 nbLine = 15
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11 besFastaFileName = '%s/commons/core/parsing/test/besSequences.fasta' % os.environ['REPET_PATH']
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12 self._writeBesSequences(besFastaFileName)
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13 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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14 iBlatToGffForBesPaired._methodName = ''
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15 iBlatToGffForBesPaired._inputFileFasta = besFastaFileName
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16 obsGffLine, obsBesName, obsBesSeq, obsBesType = iBlatToGffForBesPaired.convertBlatObjectToGffLine(blatLine, nbLine)
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17 expGffLine = 'chr16\tBlatToGffForBesPaired\tBES\t21686950\t21687294\t.\t+\t.\tID=MRRE1H001H13FM1;Name=MRRE1H001H13FM1;bes_start=21686950;bes_end=21687294;bes_size=22053297;muscadine_seq=AGACCTACTACGACGTACGATCGATCGACTGCTAGCTAGCTAGGCCTAGCTAGCTAGCTAGCTAGCTAGC\n'
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18 expBesName = 'MRRE1H001H13FM1'
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19 expBesSeq = 'AGACCTACTACGACGTACGATCGATCGACTGCTAGCTAGCTAGGCCTAGCTAGCTAGCTAGCTAGCTAGC'
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20 expBesType = 'FM'
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21 self.assertEquals(expGffLine, obsGffLine)
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22 self.assertEquals(expBesName, obsBesName)
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23 self.assertEquals(expBesSeq, obsBesSeq)
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24 self.assertEquals(expBesType, obsBesType)
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25 os.remove(besFastaFileName)
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26
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27 def test_convertBlatObjectToGffLine_with_methodName(self):
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28 blatLine = '315\t20\t0\t0\t3\t10\t2\t9\t+\tMRRE1H001H13FM1\t378\t0\t345\tchr16\t22053297\t21686950\t21687294\t4\t76,185,7,67,\t0,77,263,278,\t21686950,21687026,21687213,21687227,\n'
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29 nbLine = 15
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30 besFastaFileName = '%s/commons/core/parsing/test/besSequences.fasta' % os.environ['REPET_PATH']
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31 self._writeBesSequences(besFastaFileName)
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32 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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33 iBlatToGffForBesPaired._methodName = 'Test'
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34 iBlatToGffForBesPaired._inputFileFasta = besFastaFileName
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35 obsGffLine, obsBesName, obsBesSeq, obsBesType = iBlatToGffForBesPaired.convertBlatObjectToGffLine(blatLine, nbLine)
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36 expGffLine = 'chr16\tBlatToGffForBesPaired\tTest:BES\t21686950\t21687294\t.\t+\t.\tID=MRRE1H001H13FM1;Name=MRRE1H001H13FM1;bes_start=21686950;bes_end=21687294;bes_size=22053297;muscadine_seq=AGACCTACTACGACGTACGATCGATCGACTGCTAGCTAGCTAGGCCTAGCTAGCTAGCTAGCTAGCTAGC\n'
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37 expBesName = 'MRRE1H001H13FM1'
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38 expBesSeq = 'AGACCTACTACGACGTACGATCGATCGACTGCTAGCTAGCTAGGCCTAGCTAGCTAGCTAGCTAGCTAGC'
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39 expBesType = 'FM'
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40 self.assertEquals(expGffLine, obsGffLine)
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41 self.assertEquals(expBesName, obsBesName)
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42 self.assertEquals(expBesSeq, obsBesSeq)
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43 self.assertEquals(expBesType, obsBesType)
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44 os.remove(besFastaFileName)
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45
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46 def test_getBesName(self):
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47 col9 = 'ID=machin1;Name=machin1;bes_start=21736364;bes_end=21737069;bes_size=22053297\n'
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48 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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49 obsBesName = iBlatToGffForBesPaired.getBesName(col9)
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50 expBesName = 'machin1'
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51 self.assertEquals(expBesName, obsBesName)
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52
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53 def test_checkBesNames_OK(self):
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54 besName1 = 'MRRE1H001H13FM8'
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55 besName2 = 'MRRE1H001H13RM2'
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56 line = 10
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57 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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58 self.assertTrue(iBlatToGffForBesPaired.checkBesNames(besName1, besName2, line))
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59
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60 def test_checkBesNames_NOK(self):
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61 besName1 = 'MRRE1H001H13FM1'
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62 besName2 = 'TOTORM2'
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63 line = 10
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64 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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65 self.assertFalse(iBlatToGffForBesPaired.checkBesNames(besName1, besName2, line))
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66
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67 def test_checkBesPositions_OK1(self):
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68 tBes1 = ('chr16', 25, 150)
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69 tBes2 = ('chr16', 300, 350)
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70 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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71 self.assertTrue(iBlatToGffForBesPaired.checkBesPositions(tBes1, tBes2))
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72
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73 def test_checkBesPositions_OK2(self):
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74 tBes1 = ('chr16', 300, 350)
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75 tBes2 = ('chr16', 3, 50)
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76 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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77 self.assertTrue(iBlatToGffForBesPaired.checkBesPositions(tBes1, tBes2))
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78
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79 def test_checkBesPositions_NOK1(self):
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80 tBes1 = ('chr16', 25, 150)
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81 tBes2 = ('chr14', 300, 350)
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82 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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83 self.assertFalse(iBlatToGffForBesPaired.checkBesPositions(tBes1, tBes2))
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84
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85 def test_checkBesPositions_NOK2(self):
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86 tBes1 = ('chr16', 25, 300)
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87 tBes2 = ('chr16', 150, 350)
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88 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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89 self.assertFalse(iBlatToGffForBesPaired.checkBesPositions(tBes1, tBes2))
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90
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91 def test_checkBesPositions_NOK3(self):
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92 tBes1 = ('chr16', 25, 300)
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93 tBes2 = ('chr16', 1, 50)
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94 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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95 self.assertFalse(iBlatToGffForBesPaired.checkBesPositions(tBes1, tBes2))
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96
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97 def test_getBacName(self):
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98 besName = 'MRRE1H001H13FM1'
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99 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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100 obsBacName = iBlatToGffForBesPaired.getBacName(besName)
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101 expBacName = 'MRRE1H001H13'
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102 self.assertEquals(expBacName, obsBacName)
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103
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104 def test_getBacPositions_case1(self):
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105 tBes1 = ('chr16', 25, 300)
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106 tBes2 = ('chr16', 1, 50)
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107 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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108 obsStart, obsEnd = iBlatToGffForBesPaired.getBacPositions(tBes1, tBes2)
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109 expStart = 1
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110 expEnd = 300
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111 self.assertEquals(expStart, obsStart)
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112 self.assertEquals(expEnd, obsEnd)
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113
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114 def test_getBacPositions_case2(self):
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115 tBes1 = ('chr16', 1, 300)
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116 tBes2 = ('chr16', 1000, 50000)
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117 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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118 obsStart, obsEnd = iBlatToGffForBesPaired.getBacPositions(tBes1, tBes2)
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119 expStart = 1
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120 expEnd = 50000
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121 self.assertEquals(expStart, obsStart)
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122 self.assertEquals(expEnd, obsEnd)
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123
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124 def test_getBacPositions_case3(self):
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125 tBes1 = ('chr16', 300, 25)
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126 tBes2 = ('chr16', 1, 50)
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127 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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128 obsStart, obsEnd = iBlatToGffForBesPaired.getBacPositions(tBes1, tBes2)
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129 expStart = 1
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130 expEnd = 300
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131 self.assertEquals(expStart, obsStart)
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132 self.assertEquals(expEnd, obsEnd)
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133
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134 def test_createGffLineForBac(self):
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135 gffLine1 = 'chr16\tBlatToGffForBesPaired\tBES\t10\t1000\t.\t+\t.\tID=MRRE1H001H13FM1;Name=MRRE1H001H13FM1;bes_start=10;bes_end=1000;bes_size=991;muscadine_seq=ATCGATCGATCGATCGTACGACTGACTCGATCAGCTAGCTAGCTAGCACATCG\n'
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136 nameBes1 = 'MRRE1H001H13FM1'
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137 seqBes1 = 'ATCGATCGATCGATCGTACGACTGACTCGATCAGCTAGCTAGCTAGCACATCG'
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138 typeBes1 = 'FM'
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139 gffLine2 = 'chr16\tBlatToGffForBesPaired\tBES\t2000\t3000\t.\t+\t.\tID=MRRE1H001H13RM2;Name=MRRE1H001H13RM2;bes_start=2000;bes_end=3000;bes_size=1001;muscadine_seq=CAGCTAGCTACGTACGTACGTACGTAGCATCGATCGAT\n'
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140 nameBes2 = 'MRRE1H001H13RM2'
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141 seqBes2 = 'CAGCTAGCTACGTACGTACGTACGTAGCATCGATCGAT'
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142 typeBes2 = 'RM'
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143 line = 2
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144 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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145 iBlatToGffForBesPaired._methodName = ''
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146 obsGffBac = iBlatToGffForBesPaired.createGffLineForBac(gffLine1, nameBes1, seqBes1, typeBes1, gffLine2, nameBes2, seqBes2, typeBes2, line)
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147 expGffBac = 'chr16\tBlatToGffForBesPaired\tBAC\t10\t3000\t.\t.\t.\tID=MRRE1H001H13;Name=MRRE1H001H13;bac_start=10;bac_end=3000;bac_size=2991;besFM_name=MRRE1H001H13FM1;muscadine_besFM_seq=ATCGATCGATCGATCGTACGACTGACTCGATCAGCTAGCTAGCTAGCACATCG;besRM_name=MRRE1H001H13RM2;muscadine_besRM_seq=CAGCTAGCTACGTACGTACGTACGTAGCATCGATCGAT\n'
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148 self.assertEquals(expGffBac, obsGffBac)
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149
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150 def test_createGffLineForBac_with_methodName(self):
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151 gffLine1 = 'chr16\tBlatToGffForBesPaired\tBES\t10\t1000\t.\t+\t.\tID=MRRE1H001H13FM1;Name=MRRE1H001H13FM1;bes_start=10;bes_end=1000;bes_size=991;muscadine_seq=ATCGATCGATCGATCGTACGACTGACTCGATCAGCTAGCTAGCTAGCACATCG\n'
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152 nameBes1 = 'MRRE1H001H13FM1'
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153 seqBes1 = 'ATCGATCGATCGATCGTACGACTGACTCGATCAGCTAGCTAGCTAGCACATCG'
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154 typeBes1 = 'FM'
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155 gffLine2 = 'chr16\tBlatToGffForBesPaired\tBES\t2000\t3000\t.\t+\t.\tID=MRRE1H001H13RM2;Name=MRRE1H001H13RM2;bes_start=2000;bes_end=3000;bes_size=1001;muscadine_seq=CAGCTAGCTACGTACGTACGTACGTAGCATCGATCGAT\n'
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156 nameBes2 = 'MRRE1H001H13RM2'
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157 seqBes2 = 'CAGCTAGCTACGTACGTACGTACGTAGCATCGATCGAT'
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158 typeBes2 = 'RM'
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159 line = 2
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160 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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161 iBlatToGffForBesPaired._methodName = 'Test'
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162 obsGffBac = iBlatToGffForBesPaired.createGffLineForBac(gffLine1, nameBes1, seqBes1, typeBes1, gffLine2, nameBes2, seqBes2, typeBes2, line)
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163 expGffBac = 'chr16\tBlatToGffForBesPaired\tTest:BAC\t10\t3000\t.\t.\t.\tID=MRRE1H001H13;Name=MRRE1H001H13;bac_start=10;bac_end=3000;bac_size=2991;besFM_name=MRRE1H001H13FM1;muscadine_besFM_seq=ATCGATCGATCGATCGTACGACTGACTCGATCAGCTAGCTAGCTAGCACATCG;besRM_name=MRRE1H001H13RM2;muscadine_besRM_seq=CAGCTAGCTACGTACGTACGTACGTAGCATCGATCGAT\n'
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164 self.assertEquals(expGffBac, obsGffBac)
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165
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166 def test_extractBesSequenceFromFastaFileToTmpFile_with_seqInMultipleLines(self):
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167 fastaFileName = '%s/commons/core/parsing/test/sequence.fasta' % os.environ['REPET_PATH']
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168 fastaFile = open(fastaFileName, 'w')
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169 fastaFile.write('>seq1\n')
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170 fastaFile.write('ATCGATCGATCGATCGATACGTCAGCGATCGAT\n')
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171 fastaFile.write('TACGTACGTACGATCGATCGATCGATCGATCGG\n')
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172 fastaFile.write('TACGTACGTACGATCGACGATCGATGCCGATCG\n')
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173 fastaFile.write('ATCGAC\n')
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174 fastaFile.write('>seq2\n')
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175 fastaFile.write('GTCTAGCTAGCTATATCTGACTGACGCGACGGT\n')
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176 fastaFile.write('CATGCTAGCTAGCACTGTACAGCTATCGATGCT\n')
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177 fastaFile.write('ACTGACACTGTACGTAC\n')
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178 fastaFile.write('>seq3\n')
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179 fastaFile.write('ACTCGATCGATCG\n')
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180 fastaFile.close()
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181
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182 seqName = 'seq1'
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183 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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184 iBlatToGffForBesPaired._inputFileFasta = fastaFileName
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185 obsSeq = iBlatToGffForBesPaired.extractBesSequenceFromFastaFile(seqName, 5)
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186 expSeq = 'ATCGATCGATCGATCGATACGTCAGCGATCGATTACGTACGTACGATCGATCGATCGATCGATCGGTACGTACGTACGATCGACGATCGATGCCGATCGATCGAC'
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187 self.assertEquals(expSeq, obsSeq)
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188 os.remove(fastaFileName)
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189
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190 def test_extractBesSequenceFromFastaFileToTmpFile_with_seqInUniqueLines(self):
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191 fastaFileName = '%s/commons/core/parsing/test/sequence.fasta' % os.environ['REPET_PATH']
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192 fastaFile = open(fastaFileName, 'w')
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193 fastaFile.write('>seq1\n')
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194 fastaFile.write('ATCGATCGATCGATCGATACGTCAGCGATCGAT\n')
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195 fastaFile.write('TACGTACGTACGATCGATCGATCGATCGATCGG\n')
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196 fastaFile.write('TACGTACGTACGATCGACGATCGATGCCGATCG\n')
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197 fastaFile.write('ATCGAC\n')
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198 fastaFile.write('>seq2\n')
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199 fastaFile.write('GTCTAGCTAGCTATATCTGACTGACGCGACGGT\n')
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200 fastaFile.write('CATGCTAGCTAGCACTGTACAGCTATCGATGCT\n')
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201 fastaFile.write('ACTGACACTGTACGTAC\n')
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202 fastaFile.write('>seq3\n')
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203 fastaFile.write('ACTCGATCGATCG\n')
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204 fastaFile.close()
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205
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206 seqName = 'seq3'
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207 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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208 iBlatToGffForBesPaired._inputFileFasta = fastaFileName
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209 obsSeq = iBlatToGffForBesPaired.extractBesSequenceFromFastaFile(seqName, 5)
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210 expSeq = 'ACTCGATCGATCG'
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211 self.assertEquals(expSeq, obsSeq)
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212 os.remove(fastaFileName)
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213
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214 def test_extractBesSequenceFromFastaFileToTmpFile_without_seqInThisFastaFile(self):
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215 fastaFileName = '%s/commons/core/parsing/test/sequence.fasta' % os.environ['REPET_PATH']
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216 fastaFile = open(fastaFileName, 'w')
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217 fastaFile.write('>seq1\n')
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218 fastaFile.write('ATCGATCGATCGATCGATACGTCAGCGATCGAT\n')
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219 fastaFile.write('TACGTACGTACGATCGATCGATCGATCGATCGG\n')
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220 fastaFile.write('TACGTACGTACGATCGACGATCGATGCCGATCG\n')
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221 fastaFile.write('ATCGAC\n')
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222 fastaFile.write('>seq2\n')
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223 fastaFile.write('GTCTAGCTAGCTATATCTGACTGACGCGACGGT\n')
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224 fastaFile.write('CATGCTAGCTAGCACTGTACAGCTATCGATGCT\n')
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225 fastaFile.write('ACTGACACTGTACGTAC\n')
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226 fastaFile.write('>seq3\n')
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227 fastaFile.write('ACTCGATCGATCG\n')
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228 fastaFile.close()
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229
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230 seqName = 'seq4'
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231 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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232 iBlatToGffForBesPaired._inputFileFasta = fastaFileName
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233 obsSeq = iBlatToGffForBesPaired.extractBesSequenceFromFastaFile(seqName, 5)
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234 expSeq = 'NA'
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235 self.assertEquals(expSeq, obsSeq)
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236 os.remove(fastaFileName)
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237
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238 def test_getBesFmAndRmNamesAndSequences_case1(self):
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239 nameBes1 = 'MRRE1H0072T1FM1'
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240 seqBes1 = 'TACGTCAGCTGATCGACATCGATCGATCGATCGATCGATCGTC'
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241 typeBes1 = 'FM'
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242 nameBes2 = 'MRRE1H0072T1RM3'
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243 seqBes2 = 'GCGCAGCGCGACTGACTTGACTATCGGCGACGCGACGATCGATCGATCGATC'
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244 typeBes2 = 'RM'
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245 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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246 obsNameBesFM, obsSeqBesFM, obsNameBesRM, obsSeqBesRM = iBlatToGffForBesPaired.getBesFmAndRmNamesAndSequences(nameBes1, seqBes1, typeBes1, nameBes2, seqBes2, typeBes2)
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247 expNameBesFM = 'MRRE1H0072T1FM1'
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248 expNameBesRM = 'MRRE1H0072T1RM3'
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249 expSeqBesFM = 'TACGTCAGCTGATCGACATCGATCGATCGATCGATCGATCGTC'
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250 expSeqBesRM = 'GCGCAGCGCGACTGACTTGACTATCGGCGACGCGACGATCGATCGATCGATC'
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251 self.assertEquals(expNameBesFM, obsNameBesFM)
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252 self.assertEquals(expNameBesRM, obsNameBesRM)
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253 self.assertEquals(expSeqBesFM, obsSeqBesFM)
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254 self.assertEquals(expSeqBesRM, obsSeqBesRM)
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255
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256 def test_getBesFmAndRmNamesAndSequences_case2(self):
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257 nameBes1 = 'MRRE1H0072T1RM1'
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258 seqBes1 = 'TACGTCAGCTGATCGACATCGATCGATCGATCGATCGATCGTC'
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259 typeBes1 = 'RM'
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260 nameBes2 = 'MRRE1H0072T1FM3'
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261 seqBes2 = 'GCGCAGCGCGACTGACTTGACTATCGGCGACGCGACGATCGATCGATCGATC'
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262 typeBes2 = 'FM'
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263 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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264 obsNameBesFM, obsSeqBesFM, obsNameBesRM, obsSeqBesRM = iBlatToGffForBesPaired.getBesFmAndRmNamesAndSequences(nameBes1, seqBes1, typeBes1, nameBes2, seqBes2, typeBes2)
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265 expNameBesFM = 'MRRE1H0072T1FM3'
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266 expNameBesRM = 'MRRE1H0072T1RM1'
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267 expSeqBesFM = 'GCGCAGCGCGACTGACTTGACTATCGGCGACGCGACGATCGATCGATCGATC'
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268 expSeqBesRM = 'TACGTCAGCTGATCGACATCGATCGATCGATCGATCGATCGTC'
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269 self.assertEquals(expNameBesFM, obsNameBesFM)
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270 self.assertEquals(expNameBesRM, obsNameBesRM)
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271 self.assertEquals(expSeqBesFM, obsSeqBesFM)
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272 self.assertEquals(expSeqBesRM, obsSeqBesRM)
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273
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274 def _writeBesSequences(self, fileName):
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275 file = open(fileName, 'w')
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276 file.write('>MRRE1H001H13RM1\n')
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277 file.write('ATACGTACGTACGTCAGTACGACTACGTACGTACGTACGTCGTAC\n')
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278 file.write('TACGTCAGCATCGTACGTACGTACGTCGTGCTGGCTAGCTGACGA\n')
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279 file.write('ATCGATCGATCGATCGACATCGTACG\n')
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280 file.write('>MRRE1H001H13FM1\n')
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281 file.write('AGACCTACTACGACGTACGATCGATCGACTGCTAGCTAGCTAGGC\n')
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282 file.write('CTAGCTAGCTAGCTAGCTAGCTAGC\n')
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283 file.write('>MRRE2H007A13FM3\n')
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284 file.write('TCAGCTAGCTGACTGACATCGCTAGCTAGCTAGCTAGCTAGCTAG\n')
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285 file.write('TACGCAGCTACGGGGCATCGACTAAAAAAAAAAACCCACGACTGG\n')
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286 file.write('CTAGCTAGCTAGCTAGCTAGCTACGTCGATCGATCGACTGTTGCC\n')
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287 file.write('TCAGCTACTGACTGATCGATCGACTACGTACGTACGTAC\n')
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288 file.close()
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289
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290
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291 if __name__ == "__main__":
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292 unittest.main() |
