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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 import os
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34 from commons.core.seq.Bioseq import Bioseq
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35 from commons.core.seq.BioseqUtils import BioseqUtils
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36 from commons.core.utils.FileUtils import FileUtils
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37
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38
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39 class Test_BioseqUtils( unittest.TestCase ):
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40
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41 def test_translateSequence_one_nt( self ):
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42 bioseq = Bioseq()
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43 bioseq.sequence = "G"
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44 BioseqUtils.translateSequence(bioseq, 1)
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45 expSequence = ""
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46 obsSequence = bioseq.sequence
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47 self.assertEqual(expSequence, obsSequence)
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48
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49
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50 def test_translateSequence_frame1( self ):
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51 bioseq = Bioseq()
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52 bioseq.sequence = "NGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTCCGACTAATCAACAATATAATGCGAGTAGAGCTTGA"
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53 BioseqUtils.translateSequence(bioseq, 1)
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54 expSequence = "XGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
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55 obsSequence = bioseq.sequence
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56 self.assertEqual(expSequence, obsSequence)
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57
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58
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59 def test_translateSequence_frame2( self ):
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60 bioseq = Bioseq()
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61 bioseq.sequence = "NGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTCCGACTAATCAACAATATAATGCGAGTAGAGCTTGA"
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62 BioseqUtils.translateSequence(bioseq, 2)
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63 expSequence = "VASS*SVYDHNDFT*VSRGSD*STI*CE*SL"
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64 obsSequence = bioseq.sequence
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65 self.assertEqual(expSequence, obsSequence)
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66
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67
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68 def test_translateSequence_frame3( self ):
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69 bioseq = Bioseq()
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70 bioseq.sequence = "NGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTCCGACTAATCAACAATATAATGCGAGTAGAGCTTGA"
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71 BioseqUtils.translateSequence(bioseq, 3)
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72 expSequence = "WLLVDQFMITMISRRCLVAPTNQQYNASRA*"
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73 obsSequence = bioseq.sequence
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74 self.assertEqual(expSequence, obsSequence)
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75
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76
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77 def test_setFrameInfoOnHeader(self):
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78 bioseq = Bioseq()
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79 bioseq.header = "header1 description1 description2"
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80 BioseqUtils.setFrameInfoOnHeader(bioseq,1)
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81 expHeader = "header1_1 description1 description2"
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82 obsHeader = bioseq.header
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83 self.assertEquals(expHeader,obsHeader)
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84
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85
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86 def test_setFrameInfoOnHeader_header_without_space(self):
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87 bioseq = Bioseq()
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88 bioseq.header = "header"
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89 BioseqUtils.setFrameInfoOnHeader(bioseq,1)
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90 expHeader = "header_1"
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91 obsHeader = bioseq.header
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92 self.assertEquals(expHeader, obsHeader)
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93
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94
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95 def test_TranslateInAllFrame( self ):
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96 bioseq = Bioseq()
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97 bioseq.header = "header1"
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98 bioseq.sequence = "TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTCCGACTAATCAACAATATAATGCGAGTAGAGCTTGA"
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99
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100 bioseq1 = Bioseq()
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101 bioseq1.header = "header1_1"
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102 bioseq1.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
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103 bioseq2 = Bioseq()
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104 bioseq2.header = "header1_2"
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105 bioseq2.sequence = "VASS*SVYDHNDFT*VSRGSD*STI*CE*SL"
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106 bioseq3 = Bioseq()
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107 bioseq3.header = "header1_3"
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108 bioseq3.sequence = "WLLVDQFMITMISRRCLVAPTNQQYNASRA*"
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109 bioseq4 = Bioseq()
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110 bioseq4.header = "header1_4"
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111 bioseq4.sequence = "SSSTRIILLISRSHETPT*NHCDHKLIN*KP"
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112 bioseq5 = Bioseq()
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113 bioseq5.header = "header1_5"
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114 bioseq5.sequence = "QALLALYC*LVGATRHLREIIVIIN*STRSH"
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115 bioseq6 = Bioseq()
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116 bioseq6.header = "header1_6"
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117 bioseq6.sequence = "KLYSHYIVD*SEPRDTYVKSL*S*TDQLEAT"
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118
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119 expLBioseq = [bioseq1, bioseq2, bioseq3, bioseq4, bioseq5, bioseq6]
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120 obsLBioseq = BioseqUtils.translateInAllFrame(bioseq)
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121
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122 self.assertEquals(expLBioseq, obsLBioseq)
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123
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124
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125 def test_replaceStopCodonsByX( self ):
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126 bioseq = Bioseq()
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127 bioseq.sequence = "VASS*SVYDHNDFT*VSRGSD*STI*CE*SL"
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128 BioseqUtils.replaceStopCodonsByX(bioseq)
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129 expSequence = "VASSXSVYDHNDFTXVSRGSDXSTIXCEXSL"
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130 obsSequence = bioseq.sequence
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131 self.assertEquals(expSequence, obsSequence)
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132
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133
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134 def test_translateBioseqListInAllFrames_with_empty_list( self ):
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135 lBioseq = []
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136 obsLBioseq = BioseqUtils.translateBioseqListInAllFrames( lBioseq )
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137 expLBioseq = []
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138 self.assertEquals( expLBioseq, obsLBioseq )
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139
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140
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141 def test_translateBioseqListInAllFrames_with_one_item( self ):
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142 bioseq1 = Bioseq()
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143 bioseq1.header = "header1 description"
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144 bioseq1.sequence = "TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTCCGACTAATCAACAATATAATGCGAGTAGAGCTTGA"
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145 lBioseq = [bioseq1]
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146 obsLBioseq = BioseqUtils.translateBioseqListInAllFrames( lBioseq )
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147
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148 expBioseq1 = Bioseq()
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149 expBioseq1.header = "header1_1 description"
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150 expBioseq1.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
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151
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152 expBioseq2 = Bioseq()
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153 expBioseq2.header = "header1_2 description"
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154 expBioseq2.sequence = "VASS*SVYDHNDFT*VSRGSD*STI*CE*SL"
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155
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156 expBioseq3 = Bioseq()
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157 expBioseq3.header = "header1_3 description"
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158 expBioseq3.sequence = "WLLVDQFMITMISRRCLVAPTNQQYNASRA*"
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159
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160 expBioseq4 = Bioseq()
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161 expBioseq4.header = "header1_4 description"
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162 expBioseq4.sequence = "SSSTRIILLISRSHETPT*NHCDHKLIN*KP"
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163
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164 expBioseq5 = Bioseq()
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165 expBioseq5.header = "header1_5 description"
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166 expBioseq5.sequence = "QALLALYC*LVGATRHLREIIVIIN*STRSH"
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167
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168 expBioseq6 = Bioseq()
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169 expBioseq6.header = "header1_6 description"
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170 expBioseq6.sequence = "KLYSHYIVD*SEPRDTYVKSL*S*TDQLEAT"
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171
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172 expLBioseq = [expBioseq1, expBioseq2, expBioseq3, expBioseq4, expBioseq5, expBioseq6]
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173
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174 self.assertEquals( expLBioseq, obsLBioseq )
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175
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176
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177 def test_translateBioseqListInAllFrames( self ):
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178 bioseq1 = Bioseq()
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179 bioseq1.header = "header1 description"
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180 bioseq1.sequence = "TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTCCGACTAATCAACAATATAATGCGAGTAGAGCTTGA"
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181 bioseq2 = Bioseq()
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182 bioseq2.header = "header2"
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183 bioseq2.sequence = "TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTACGACTAATCAACAATATAATGCGAGTAGAGCTTGA"
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184 lBioseq = [bioseq1, bioseq2]
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185 obsLBioseq = BioseqUtils.translateBioseqListInAllFrames( lBioseq )
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186
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187 expBioseq1 = Bioseq()
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188 expBioseq1.header = "header1_1 description"
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189 expBioseq1.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
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190
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191 expBioseq2 = Bioseq()
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192 expBioseq2.header = "header1_2 description"
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193 expBioseq2.sequence = "VASS*SVYDHNDFT*VSRGSD*STI*CE*SL"
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194
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195 expBioseq3 = Bioseq()
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196 expBioseq3.header = "header1_3 description"
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197 expBioseq3.sequence = "WLLVDQFMITMISRRCLVAPTNQQYNASRA*"
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198
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199 expBioseq4 = Bioseq()
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200 expBioseq4.header = "header1_4 description"
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201 expBioseq4.sequence = "SSSTRIILLISRSHETPT*NHCDHKLIN*KP"
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202
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203 expBioseq5 = Bioseq()
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204 expBioseq5.header = "header1_5 description"
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205 expBioseq5.sequence = "QALLALYC*LVGATRHLREIIVIIN*STRSH"
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206
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207 expBioseq6 = Bioseq()
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208 expBioseq6.header = "header1_6 description"
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209 expBioseq6.sequence = "KLYSHYIVD*SEPRDTYVKSL*S*TDQLEAT"
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210
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211 expBioseq7 = Bioseq()
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212 expBioseq7.header = "header2_1"
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213 expBioseq7.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
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214
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215 expBioseq8 = Bioseq()
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216 expBioseq8.header = "header2_2"
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217 expBioseq8.sequence = "VASS*SVYDHNDFT*VSRGYD*STI*CE*SL"
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218
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219 expBioseq9 = Bioseq()
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220 expBioseq9.header = "header2_3"
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221 expBioseq9.sequence = "WLLVDQFMITMISRRCLVATTNQQYNASRA*"
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222
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223 expBioseq10 = Bioseq()
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224 expBioseq10.header = "header2_4"
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225 expBioseq10.sequence = "SSSTRIILLISRSHETPT*NHCDHKLIN*KP"
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226
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227 expBioseq11 = Bioseq()
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228 expBioseq11.header = "header2_5"
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229 expBioseq11.sequence = "QALLALYC*LVVATRHLREIIVIIN*STRSH"
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230
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231 expBioseq12 = Bioseq()
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232 expBioseq12.header = "header2_6"
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233 expBioseq12.sequence = "KLYSHYIVD*S*PRDTYVKSL*S*TDQLEAT"
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234
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235 expLBioseq = [expBioseq1, expBioseq2, expBioseq3, expBioseq4, expBioseq5, expBioseq6, expBioseq7, expBioseq8, expBioseq9, expBioseq10, expBioseq11, expBioseq12]
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236 self.assertEquals( expLBioseq, obsLBioseq )
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237
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238
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239 def test_replaceStopCodonsByXInBioseqList_empty_list( self ):
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240 lBioseq = []
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241 obsLBioseq = BioseqUtils.replaceStopCodonsByXInBioseqList( lBioseq )
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242 expLBioseq = []
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243 self.assertEquals(obsLBioseq, expLBioseq)
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244
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245
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246 def test_replaceStopCodonsByXInBioseqList_without_stop_codon( self ):
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247 bioseq1 = Bioseq()
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248 bioseq1.header = "header1 description"
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249 bioseq1.sequence = "CGFLISLSQFHVGVSWLRLINNIMRVEL"
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250
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251 lBioseq = [bioseq1]
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252
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253 obsLBioseq = BioseqUtils.replaceStopCodonsByXInBioseqList( lBioseq )
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254
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255 bioseq2 = Bioseq()
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256 bioseq2.header = "header1 description"
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257 bioseq2.sequence = "CGFLISLSQFHVGVSWLRLINNIMRVEL"
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258
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259 expLBioseq = [bioseq2]
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260
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261 self.assertEquals(obsLBioseq, expLBioseq)
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262
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263
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264 def test_replaceStopCodonsByXInBioseqList( self ):
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265 bioseq1 = Bioseq()
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266 bioseq1.header = "header1 description"
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267 bioseq1.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
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268
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269 bioseq2 = Bioseq()
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270 bioseq2.header = "header2"
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271 bioseq2.sequence = "VASS*SVYDHNDFT*VSRGSD*STI*CE*SL"
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272
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273 lBioseq = [bioseq1, bioseq2]
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274
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275 obsLBioseq = BioseqUtils.replaceStopCodonsByXInBioseqList( lBioseq )
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276
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277 bioseq3 = Bioseq()
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278 bioseq3.header = "header1 description"
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279 bioseq3.sequence = "CGFXLISLXSQXFHVGVSWLRLINNIMRVEL"
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280
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281 bioseq4 = Bioseq()
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282 bioseq4.header = "header2"
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283 bioseq4.sequence = "VASSXSVYDHNDFTXVSRGSDXSTIXCEXSL"
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284
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285 expLBioseq = [bioseq3, bioseq4]
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286
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287 self.assertEquals(obsLBioseq, expLBioseq)
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288
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289
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290 def test_writeBioseqListIntoFastaFile(self):
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291 obsFileName = "dummyWrittenFastaFile.fa"
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292
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293 bioseq1 = Bioseq()
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294 bioseq1.header = "header1 description"
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295 bioseq1.sequence = "TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTCCGACTAATCAACAATATAATGCGAGTAGAGCTTGA"
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296 bioseq2 = Bioseq()
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297 bioseq2.header = "header2"
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298 bioseq2.sequence = "TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTACGACTAATCAACAATATAATGCGAGTAGAGCTTGA"
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299
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300 lBioseq = [bioseq1, bioseq2]
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301
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302 BioseqUtils.writeBioseqListIntoFastaFile( lBioseq, obsFileName )
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303
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304 expFileName = "dummyFastaFile.fa"
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305 f = open(expFileName, "w")
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306 f.write(">header1 description\n")
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307 f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTC\n")
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308 f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA\n")
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309 f.write(">header2\n")
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310 f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTA\n")
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311 f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA\n")
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312 f.close()
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313
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314 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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315
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316 os.remove(expFileName)
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317 os.remove(obsFileName)
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318
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319
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320 def test_extractBioseqListFromFastaFile( self ):
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321 fileName = "dummyFastaFile.fa"
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322 f = open(fileName,"w")
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323 f.write(">header1_1 description1\n")
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324 f.write("CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL\n")
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325 f.write(">header1_2 description2\n")
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326 f.write("VASS*SVYDHNDFT*VSRGSD*STI*CE*SL\n")
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327 f.write(">header1_3 description3\n")
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328 f.write("CWLLVDQFMITMISRRCLVAPTNQQYNASRA*\n")
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329 f.close()
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330
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331 bioseq1 = Bioseq()
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332 bioseq1.header = "header1_1 description1"
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333 bioseq1.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
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334 bioseq2 = Bioseq()
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335 bioseq2.header = "header1_2 description2"
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336 bioseq2.sequence = "VASS*SVYDHNDFT*VSRGSD*STI*CE*SL"
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337 bioseq3 = Bioseq()
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338 bioseq3.header = "header1_3 description3"
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339 bioseq3.sequence = "CWLLVDQFMITMISRRCLVAPTNQQYNASRA*"
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340
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341 expLBioseq = [bioseq1, bioseq2, bioseq3]
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342
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343 obsLBioseq = BioseqUtils.extractBioseqListFromFastaFile( fileName )
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344 self.assertEquals(expLBioseq , obsLBioseq)
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345
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346 os.remove( fileName )
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347
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348
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349 def test_extractBioseqListFromFastaFile_empty_seq( self ):
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350 fileName = "dummyFastaFile.fa"
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351 f = open(fileName,"w")
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352 f.write(">header1_1 description1\n")
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353 f.close()
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354
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355 bioseq1 = Bioseq()
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356 bioseq1.header = "header1_1 description1"
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357 bioseq1.sequence = ""
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358 expLBioseq = [bioseq1]
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359
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360 obsLBioseq = BioseqUtils.extractBioseqListFromFastaFile( fileName )
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361 self.assertEquals(expLBioseq , obsLBioseq)
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362
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363 os.remove( fileName )
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364
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365
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366 def test_extractBioseqListFromFastaFile_empty_file( self ):
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367 fileName = "dummyFastaFile.fa"
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368
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369 f = open(fileName,"w")
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370 f.close()
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371
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372 expLBioseq = []
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373
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374 obsLBioseq = BioseqUtils.extractBioseqListFromFastaFile( fileName )
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375 self.assertEquals(expLBioseq , obsLBioseq)
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376
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377 os.remove( fileName )
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378
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379
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380 def test_getSeqLengthWithSeqName ( self ):
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381 bioseq1 = Bioseq()
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382 bioseq1.header = "header1 description"
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383 bioseq1.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
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384
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385 bioseq2 = Bioseq()
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386 bioseq2.header = "header2"
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387 bioseq2.sequence = "ATGCGTGCGTAAATGCGTATGCGTATGCGTTCGCGAATGCGTGT"
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388
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389 lBioseq = [bioseq1, bioseq2]
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390
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391 obsLength = BioseqUtils.getSeqLengthWithSeqName(lBioseq, "header1 description")
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392 expLength = 31
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393
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394 self.assertEquals( expLength, obsLength)
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395
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396
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397 def test_getSeqLengthWithSeqName_second_item ( self ):
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398 bioseq1 = Bioseq()
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399 bioseq1.header = "header1 description"
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400 bioseq1.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
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401
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402 bioseq2 = Bioseq()
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403 bioseq2.header = "header2"
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404 bioseq2.sequence = "ATGCGTGCGTAAATGCGTATGCGTATGCGTTCGCGAATGCGTGT"
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405
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406 lBioseq = [bioseq1, bioseq2]
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407
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408 obsLength = BioseqUtils.getSeqLengthWithSeqName(lBioseq, "header2")
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409 expLength = 44
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410
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411 self.assertEquals( expLength, obsLength)
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412
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413
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414 def test_getSeqLengthWithSeqName_empty_list ( self ):
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415 lBioseq = []
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416
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417 obsLength = BioseqUtils.getSeqLengthWithSeqName(lBioseq, "header2")
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418 expLength = 0
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419
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420 self.assertEquals( expLength, obsLength)
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421
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422
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423 def test_getSeqLengthWithSeqName_empty_sequence ( self ):
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424 bioseq1 = Bioseq()
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425 bioseq1.header = "header1 description"
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426 bioseq1.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
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427
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428 bioseq2 = Bioseq()
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429 bioseq2.header = "header2"
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430 bioseq2.sequence = ""
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431
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432 lBioseq = [bioseq1, bioseq2]
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433
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434 obsLength = BioseqUtils.getSeqLengthWithSeqName(lBioseq, "header2")
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435 expLength = 0
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436
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437 self.assertEquals( expLength, obsLength)
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438
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439
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440 def test_getSeqLengthWithSeqName_sequence_unknown ( self ):
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441 bioseq1 = Bioseq()
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442 bioseq1.header = "header1 description"
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443 bioseq1.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
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444
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445 bioseq2 = Bioseq()
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446 bioseq2.header = "header2"
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447 bioseq2.sequence = "ATGCGTGCGTAAATGCGTATGCGTATGCGTTCGCGAATGCGTGT"
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448
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449 lBioseq = [bioseq1, bioseq2]
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450
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451 obsLength = BioseqUtils.getSeqLengthWithSeqName(lBioseq, "header3")
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452 expLength = 0
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453
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454 self.assertEquals( expLength, obsLength)
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455
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456
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457 def test_getLengthPerSeqFromFile( self ):
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458 inFile = "dummyInFile"
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459 inFileHandler = open( inFile, "w" )
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460 inFileHandler.write( ">seq1\nAGCGATGCAGCTA\n" )
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461 inFileHandler.write( ">seq2\nGCGATGCGCATCGACGCGA\n" )
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462 inFileHandler.close()
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463
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|
464 dExp = { "seq1": 13, "seq2": 19 }
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465
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466 dObs = BioseqUtils.getLengthPerSeqFromFile( inFile )
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467
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468 self.assertEqual( dExp, dObs )
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469
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470 os.remove( inFile )
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471
|
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472
|
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|
473 def test_getBioseqListSortedByDecreasingLength( self ):
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|
474 lBioseqs = [ Bioseq( "TE2", "ACC" ),
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|
475 Bioseq( "TE3", "TA" ),
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|
476 Bioseq( "TE1", "AGCG" ) ]
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|
477 lExp = [ Bioseq( "TE1", "AGCG" ),
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|
478 Bioseq( "TE2", "ACC" ),
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|
479 Bioseq( "TE3", "TA" ) ]
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|
|
480 lObs = BioseqUtils.getBioseqListSortedByDecreasingLength( lBioseqs )
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|
|
481 self.assertEquals( lExp, lObs )
|
|
|
482
|
|
|
483
|
|
|
484 def test_getBioseqListSortedByDecreasingLengthWithoutGaps( self ):
|
|
|
485 lBioseqs = [ Bioseq( "TE2", "-ACC-" ),
|
|
|
486 Bioseq( "TE3", "TA---" ),
|
|
|
487 Bioseq( "TE1", "-AGCG" ) ]
|
|
|
488 lExp = [ Bioseq( "TE1", "-AGCG" ),
|
|
|
489 Bioseq( "TE2", "-ACC-" ),
|
|
|
490 Bioseq( "TE3", "TA---" ) ]
|
|
|
491 lObs = BioseqUtils.getBioseqListSortedByDecreasingLengthWithoutGaps( lBioseqs )
|
|
|
492 self.assertEquals( lExp, lObs )
|
|
|
493
|
|
|
494
|
|
|
495 test_suite = unittest.TestSuite()
|
|
|
496 test_suite.addTest( unittest.makeSuite( Test_BioseqUtils ) )
|
|
|
497 if __name__ == "__main__":
|
|
|
498 unittest.TextTestRunner(verbosity=2).run( test_suite )
|
