Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/seq/test/Test_BioseqUtils.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 # Copyright INRA (Institut National de la Recherche Agronomique)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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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yufei-luo
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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140
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yufei-luo
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141 def test_translateBioseqListInAllFrames_with_one_item( self ):
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142 bioseq1 = Bioseq()
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yufei-luo
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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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yufei-luo
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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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yufei-luo
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158 expBioseq3.sequence = "WLLVDQFMITMISRRCLVAPTNQQYNASRA*"
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159
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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160 expBioseq4 = Bioseq()
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161 expBioseq4.header = "header1_4 description"
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yufei-luo
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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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yufei-luo
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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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yufei-luo
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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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yufei-luo
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183 bioseq2.sequence = "TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTACGACTAATCAACAATATAATGCGAGTAGAGCTTGA"
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yufei-luo
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184 lBioseq = [bioseq1, bioseq2]
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yufei-luo
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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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yufei-luo
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189 expBioseq1.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
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190
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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191 expBioseq2 = Bioseq()
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yufei-luo
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192 expBioseq2.header = "header1_2 description"
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yufei-luo
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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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yufei-luo
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196 expBioseq3.header = "header1_3 description"
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yufei-luo
parents:
diff changeset
197 expBioseq3.sequence = "WLLVDQFMITMISRRCLVAPTNQQYNASRA*"
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198
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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199 expBioseq4 = Bioseq()
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yufei-luo
parents:
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200 expBioseq4.header = "header1_4 description"
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yufei-luo
parents:
diff changeset
201 expBioseq4.sequence = "SSSTRIILLISRSHETPT*NHCDHKLIN*KP"
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202
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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203 expBioseq5 = Bioseq()
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yufei-luo
parents:
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204 expBioseq5.header = "header1_5 description"
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yufei-luo
parents:
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205 expBioseq5.sequence = "QALLALYC*LVGATRHLREIIVIIN*STRSH"
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206
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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207 expBioseq6 = Bioseq()
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yufei-luo
parents:
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208 expBioseq6.header = "header1_6 description"
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yufei-luo
parents:
diff changeset
209 expBioseq6.sequence = "KLYSHYIVD*SEPRDTYVKSL*S*TDQLEAT"
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210
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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211 expBioseq7 = Bioseq()
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yufei-luo
parents:
diff changeset
212 expBioseq7.header = "header2_1"
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yufei-luo
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diff changeset
213 expBioseq7.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
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214
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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215 expBioseq8 = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
216 expBioseq8.header = "header2_2"
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yufei-luo
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217 expBioseq8.sequence = "VASS*SVYDHNDFT*VSRGYD*STI*CE*SL"
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218
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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219 expBioseq9 = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
220 expBioseq9.header = "header2_3"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
221 expBioseq9.sequence = "WLLVDQFMITMISRRCLVATTNQQYNASRA*"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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222
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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223 expBioseq10 = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
224 expBioseq10.header = "header2_4"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
225 expBioseq10.sequence = "SSSTRIILLISRSHETPT*NHCDHKLIN*KP"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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226
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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227 expBioseq11 = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
228 expBioseq11.header = "header2_5"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
229 expBioseq11.sequence = "QALLALYC*LVVATRHLREIIVIIN*STRSH"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
230
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
231 expBioseq12 = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
232 expBioseq12.header = "header2_6"
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yufei-luo
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diff changeset
233 expBioseq12.sequence = "KLYSHYIVD*S*PRDTYVKSL*S*TDQLEAT"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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234
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
235 expLBioseq = [expBioseq1, expBioseq2, expBioseq3, expBioseq4, expBioseq5, expBioseq6, expBioseq7, expBioseq8, expBioseq9, expBioseq10, expBioseq11, expBioseq12]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
236 self.assertEquals( expLBioseq, obsLBioseq )
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237
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
238
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
239 def test_replaceStopCodonsByXInBioseqList_empty_list( self ):
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yufei-luo
parents:
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240 lBioseq = []
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
241 obsLBioseq = BioseqUtils.replaceStopCodonsByXInBioseqList( lBioseq )
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yufei-luo
parents:
diff changeset
242 expLBioseq = []
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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243 self.assertEquals(obsLBioseq, expLBioseq)
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244
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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245
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
246 def test_replaceStopCodonsByXInBioseqList_without_stop_codon( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
247 bioseq1 = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
248 bioseq1.header = "header1 description"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
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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yufei-luo
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255 bioseq2 = Bioseq()
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yufei-luo
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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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yufei-luo
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259 expLBioseq = [bioseq2]
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260
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yufei-luo
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261 self.assertEquals(obsLBioseq, expLBioseq)
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262
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yufei-luo
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263
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yufei-luo
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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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yufei-luo
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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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yufei-luo
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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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yufei-luo
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298 bioseq2.sequence = "TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTACGACTAATCAACAATATAATGCGAGTAGAGCTTGA"
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299
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yufei-luo
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300 lBioseq = [bioseq1, bioseq2]
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301
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yufei-luo
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302 BioseqUtils.writeBioseqListIntoFastaFile( lBioseq, obsFileName )
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303
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yufei-luo
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304 expFileName = "dummyFastaFile.fa"
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yufei-luo
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305 f = open(expFileName, "w")
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yufei-luo
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306 f.write(">header1 description\n")
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yufei-luo
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diff changeset
307 f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTC\n")
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yufei-luo
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308 f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA\n")
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yufei-luo
parents:
diff changeset
309 f.write(">header2\n")
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yufei-luo
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diff changeset
310 f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTA\n")
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yufei-luo
parents:
diff changeset
311 f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA\n")
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yufei-luo
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diff changeset
312 f.close()
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313
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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314 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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315
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yufei-luo
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316 os.remove(expFileName)
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yufei-luo
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diff changeset
317 os.remove(obsFileName)
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318
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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319
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yufei-luo
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320 def test_extractBioseqListFromFastaFile( self ):
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321 fileName = "dummyFastaFile.fa"
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yufei-luo
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322 f = open(fileName,"w")
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yufei-luo
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diff changeset
323 f.write(">header1_1 description1\n")
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yufei-luo
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324 f.write("CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL\n")
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yufei-luo
parents:
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325 f.write(">header1_2 description2\n")
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yufei-luo
parents:
diff changeset
326 f.write("VASS*SVYDHNDFT*VSRGSD*STI*CE*SL\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
327 f.write(">header1_3 description3\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
328 f.write("CWLLVDQFMITMISRRCLVAPTNQQYNASRA*\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
329 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
330
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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331 bioseq1 = Bioseq()
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yufei-luo
parents:
diff changeset
332 bioseq1.header = "header1_1 description1"
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yufei-luo
parents:
diff changeset
333 bioseq1.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
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yufei-luo
parents:
diff changeset
334 bioseq2 = Bioseq()
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yufei-luo
parents:
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335 bioseq2.header = "header1_2 description2"
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yufei-luo
parents:
diff changeset
336 bioseq2.sequence = "VASS*SVYDHNDFT*VSRGSD*STI*CE*SL"
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yufei-luo
parents:
diff changeset
337 bioseq3 = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
338 bioseq3.header = "header1_3 description3"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
339 bioseq3.sequence = "CWLLVDQFMITMISRRCLVAPTNQQYNASRA*"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
340
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
341 expLBioseq = [bioseq1, bioseq2, bioseq3]
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342
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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343 obsLBioseq = BioseqUtils.extractBioseqListFromFastaFile( fileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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344 self.assertEquals(expLBioseq , obsLBioseq)
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345
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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346 os.remove( fileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
347
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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348
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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349 def test_extractBioseqListFromFastaFile_empty_seq( self ):
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350 fileName = "dummyFastaFile.fa"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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351 f = open(fileName,"w")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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352 f.write(">header1_1 description1\n")
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yufei-luo
parents:
diff changeset
353 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
354
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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355 bioseq1 = Bioseq()
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yufei-luo
parents:
diff changeset
356 bioseq1.header = "header1_1 description1"
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yufei-luo
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357 bioseq1.sequence = ""
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
358 expLBioseq = [bioseq1]
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yufei-luo
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diff changeset
359
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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360 obsLBioseq = BioseqUtils.extractBioseqListFromFastaFile( fileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
361 self.assertEquals(expLBioseq , obsLBioseq)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
362
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
363 os.remove( fileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
364
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
365
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
366 def test_extractBioseqListFromFastaFile_empty_file( self ):
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yufei-luo
parents:
diff changeset
367 fileName = "dummyFastaFile.fa"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
368
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
369 f = open(fileName,"w")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
370 f.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
371
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
372 expLBioseq = []
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
373
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
374 obsLBioseq = BioseqUtils.extractBioseqListFromFastaFile( fileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
375 self.assertEquals(expLBioseq , obsLBioseq)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
376
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
377 os.remove( fileName )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
378
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
379
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
380 def test_getSeqLengthWithSeqName ( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
381 bioseq1 = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
382 bioseq1.header = "header1 description"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
383 bioseq1.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
384
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
385 bioseq2 = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
386 bioseq2.header = "header2"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
387 bioseq2.sequence = "ATGCGTGCGTAAATGCGTATGCGTATGCGTTCGCGAATGCGTGT"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
388
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
389 lBioseq = [bioseq1, bioseq2]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
390
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
391 obsLength = BioseqUtils.getSeqLengthWithSeqName(lBioseq, "header1 description")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
392 expLength = 31
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
393
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
394 self.assertEquals( expLength, obsLength)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
395
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
396
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
397 def test_getSeqLengthWithSeqName_second_item ( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
398 bioseq1 = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
399 bioseq1.header = "header1 description"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
400 bioseq1.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
401
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
402 bioseq2 = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
403 bioseq2.header = "header2"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
404 bioseq2.sequence = "ATGCGTGCGTAAATGCGTATGCGTATGCGTTCGCGAATGCGTGT"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
405
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
406 lBioseq = [bioseq1, bioseq2]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
407
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
408 obsLength = BioseqUtils.getSeqLengthWithSeqName(lBioseq, "header2")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
409 expLength = 44
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
410
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
411 self.assertEquals( expLength, obsLength)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
412
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
413
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
414 def test_getSeqLengthWithSeqName_empty_list ( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
415 lBioseq = []
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
416
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
417 obsLength = BioseqUtils.getSeqLengthWithSeqName(lBioseq, "header2")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
418 expLength = 0
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
419
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
420 self.assertEquals( expLength, obsLength)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
421
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
422
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
423 def test_getSeqLengthWithSeqName_empty_sequence ( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
424 bioseq1 = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
425 bioseq1.header = "header1 description"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
426 bioseq1.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
427
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
428 bioseq2 = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
429 bioseq2.header = "header2"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
430 bioseq2.sequence = ""
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
431
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
432 lBioseq = [bioseq1, bioseq2]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
433
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
434 obsLength = BioseqUtils.getSeqLengthWithSeqName(lBioseq, "header2")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
435 expLength = 0
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
436
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
437 self.assertEquals( expLength, obsLength)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
438
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
439
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
440 def test_getSeqLengthWithSeqName_sequence_unknown ( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
441 bioseq1 = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
442 bioseq1.header = "header1 description"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
443 bioseq1.sequence = "CGF*LISL*SQ*FHVGVSWLRLINNIMRVEL"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
444
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
445 bioseq2 = Bioseq()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
446 bioseq2.header = "header2"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
447 bioseq2.sequence = "ATGCGTGCGTAAATGCGTATGCGTATGCGTTCGCGAATGCGTGT"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
448
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
449 lBioseq = [bioseq1, bioseq2]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
450
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
451 obsLength = BioseqUtils.getSeqLengthWithSeqName(lBioseq, "header3")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
452 expLength = 0
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
453
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
454 self.assertEquals( expLength, obsLength)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
455
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
456
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
457 def test_getLengthPerSeqFromFile( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
458 inFile = "dummyInFile"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
459 inFileHandler = open( inFile, "w" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
460 inFileHandler.write( ">seq1\nAGCGATGCAGCTA\n" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
461 inFileHandler.write( ">seq2\nGCGATGCGCATCGACGCGA\n" )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
462 inFileHandler.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
463
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
464 dExp = { "seq1": 13, "seq2": 19 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
465
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
466 dObs = BioseqUtils.getLengthPerSeqFromFile( inFile )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
467
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
468 self.assertEqual( dExp, dObs )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
469
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
470 os.remove( inFile )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
471
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
472
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
473 def test_getBioseqListSortedByDecreasingLength( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
474 lBioseqs = [ Bioseq( "TE2", "ACC" ),
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
475 Bioseq( "TE3", "TA" ),
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
476 Bioseq( "TE1", "AGCG" ) ]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
477 lExp = [ Bioseq( "TE1", "AGCG" ),
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
478 Bioseq( "TE2", "ACC" ),
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
479 Bioseq( "TE3", "TA" ) ]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
480 lObs = BioseqUtils.getBioseqListSortedByDecreasingLength( lBioseqs )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
481 self.assertEquals( lExp, lObs )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
482
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
483
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
484 def test_getBioseqListSortedByDecreasingLengthWithoutGaps( self ):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
485 lBioseqs = [ Bioseq( "TE2", "-ACC-" ),
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
486 Bioseq( "TE3", "TA---" ),
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
487 Bioseq( "TE1", "-AGCG" ) ]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
488 lExp = [ Bioseq( "TE1", "-AGCG" ),
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
489 Bioseq( "TE2", "-ACC-" ),
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
490 Bioseq( "TE3", "TA---" ) ]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
491 lObs = BioseqUtils.getBioseqListSortedByDecreasingLengthWithoutGaps( lBioseqs )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
492 self.assertEquals( lExp, lObs )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
493
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
494
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
495 test_suite = unittest.TestSuite()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
496 test_suite.addTest( unittest.makeSuite( Test_BioseqUtils ) )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
497 if __name__ == "__main__":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
498 unittest.TextTestRunner(verbosity=2).run( test_suite )