Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/seq/test/Test_Bioseq.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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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) |
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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 import sys |
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35 from commons.core.seq.Bioseq import Bioseq |
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36 from commons.core.utils.FileUtils import FileUtils |
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37 from commons.core.coord.Map import Map |
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38 |
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39 |
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40 class Test_Bioseq( unittest.TestCase ): |
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41 |
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42 def setUp(self): |
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43 self._bs = Bioseq() |
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44 |
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45 |
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46 def test_isEmpty_True(self): |
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47 self._bs.setHeader( "" ) |
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48 self._bs.setSequence( "" ) |
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49 exp = True |
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50 obs = self._bs.isEmpty() |
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51 self.assertEquals( exp, obs ) |
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52 |
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53 |
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54 def test_isEmpty_False(self): |
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55 self._bs.setHeader( "seq1" ) |
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56 self._bs.setSequence( "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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57 exp = False |
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58 obs = self._bs.isEmpty() |
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59 self.assertEquals( exp, obs ) |
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60 |
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61 |
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62 def test___eq__(self): |
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63 self._bs.setHeader( "seq1" ) |
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64 self._bs.setSequence( "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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65 obs = Bioseq( "seq1", "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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66 self.assertEquals( self._bs, obs ) |
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67 |
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68 |
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69 def test___ne__Header(self): |
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70 self._bs.setHeader( "seq2" ) |
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71 self._bs.setSequence( "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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72 obs = Bioseq( "seq1", "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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73 self.assertNotEquals( self._bs, obs ) |
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74 |
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75 |
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76 def test___ne__Sequence(self): |
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77 self._bs.setHeader( "seq1" ) |
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78 self._bs.setSequence( "GGACGATGCAGCATGCGAATGACGAT" ) |
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79 obs = Bioseq( "seq1", "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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80 self.assertNotEquals( self._bs, obs ) |
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81 |
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82 |
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83 def test_reverse(self): |
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84 self._bs.setHeader( "seq1" ) |
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85 self._bs.setSequence( "TGCGGA" ) |
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86 exp = "AGGCGT" |
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87 self._bs.reverse() |
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88 obs = self._bs.sequence |
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89 self.assertEqual( obs, exp ) |
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90 |
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91 |
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92 def test_complement(self): |
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93 self._bs.setHeader( "seq1" ) |
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94 self._bs.setSequence( "TGCGGA" ) |
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95 exp = "ACGCCT" |
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96 self._bs.complement() |
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97 obs = self._bs.sequence |
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98 self.assertEqual( obs, exp ) |
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99 |
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100 |
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101 def test_complement_with_unknown_symbol(self): |
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102 self._bs.setHeader( "seq1" ) |
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103 self._bs.setSequence( "TGCGGAFMRWTYSKVHDBN" ) |
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104 exp = "ACGCCTNKYWARSMBDHVN" |
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105 self._bs.complement() |
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106 obs = self._bs.sequence |
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107 self.assertEqual( obs, exp ) |
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108 |
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109 |
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110 def test_reverseComplement(self): |
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111 self._bs.setHeader( "seq1" ) |
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112 self._bs.setSequence( "TGCGGA" ) |
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113 exp = "TCCGCA" |
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114 self._bs.reverseComplement() |
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115 obs = self._bs.sequence |
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116 self.assertEqual( obs, exp ) |
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117 |
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118 |
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119 def test_cleanGap(self): |
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120 self._bs.setSequence("-ATTTTGC-AGTC--TTATTCGAG-----GCCATTGCT-") |
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121 exp = "ATTTTGCAGTCTTATTCGAGGCCATTGCT" |
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122 self._bs.cleanGap() |
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123 obs = self._bs.sequence |
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124 self.assertEquals( obs, exp ) |
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125 |
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126 |
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127 def test_copyBioseqInstance(self): |
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128 self._bs.setHeader( "seq" ) |
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129 self._bs.setSequence( "TGCGGA" ) |
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130 obsBioseq = self._bs.copyBioseqInstance() |
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131 self.assertEquals(self._bs, obsBioseq) |
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132 |
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133 |
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134 def test_setFrameInfoOnHeader_without_description(self): |
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135 self._bs.setHeader( "seq" ) |
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136 self._bs.setSequence( "TGCGGA" ) |
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137 phase = -1 |
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138 expHeader = "seq_-1" |
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139 self._bs.setFrameInfoOnHeader(phase) |
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140 self.assertEquals(expHeader, self._bs.header) |
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141 |
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142 |
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143 def test_setFrameInfoOnHeader_with_description(self): |
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144 self._bs.setHeader( "seq description" ) |
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145 self._bs.setSequence( "TGCGGA" ) |
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146 phase = -1 |
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147 expHeader = "seq_-1 description" |
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148 self._bs.setFrameInfoOnHeader(phase) |
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149 self.assertEquals(expHeader, self._bs.header) |
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150 |
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151 |
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152 def test_read(self): |
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153 faFile = open("dummyFaFile.fa", "w") |
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154 faFile.write(">seq1 description1\n") |
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155 faFile.write("ATGCGTCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") |
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156 faFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") |
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157 faFile.close() |
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158 expBioseq = Bioseq() |
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159 expBioseq.header = "seq1 description1" |
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160 expBioseq.sequence = "ATGCGTCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
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161 obsBioseq = Bioseq() |
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162 faFile = open("dummyFaFile.fa", "r") |
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163 obsBioseq.read( faFile ) |
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164 faFile.close() |
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165 os.remove("dummyFaFile.fa") |
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166 self.assertEquals(expBioseq, obsBioseq) |
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167 |
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168 |
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169 def test_read_WithEmptyFile(self): |
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170 faFile = open("dummyFaFile.fa", "w") |
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171 faFile.close() |
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172 expBioseq = Bioseq() |
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173 expBioseq.header = None |
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174 expBioseq.sequence = None |
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175 obsBioseq = Bioseq() |
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176 faFile = open("dummyFaFile.fa", "r") |
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177 obsBioseq.read( faFile ) |
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178 faFile.close() |
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179 os.remove("dummyFaFile.fa") |
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180 self.assertEquals(expBioseq, obsBioseq) |
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181 |
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182 |
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183 def test_read_without_header(self): |
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184 faFile = open("dummyFaFile.fa", "w") |
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185 faFile.write("seq1 description1\n") |
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186 faFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") |
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187 faFile.close() |
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188 expBioseq = Bioseq() |
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189 expBioseq.header = "" |
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190 expBioseq.sequence = "" |
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191 obsBioseq = Bioseq() |
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192 faFile = open("dummyFaFile.fa", "r") |
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193 obsBioseq.read( faFile ) |
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194 faFile.close() |
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195 os.remove("dummyFaFile.fa") |
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196 self.assertEquals(expBioseq, obsBioseq) |
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197 |
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198 |
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199 def test_read_with_two_consecutive_headers(self): |
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200 faFile = open("dummyFaFile.fa", "w") |
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201 faFile.write(">seq1 description1\n") |
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202 faFile.write(">ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") |
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203 faFile.close() |
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204 expBioseq = Bioseq() |
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205 expBioseq.header = "seq1 description1" |
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206 expBioseq.sequence = "" |
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207 obsBioseq = Bioseq() |
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208 faFile = open("dummyFaFile.fa", "r") |
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209 obsBioseq.read( faFile ) |
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210 faFile.close() |
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211 os.remove("dummyFaFile.fa") |
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212 self.assertEquals(expBioseq, obsBioseq) |
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213 |
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214 |
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215 def test_read_withEmptyLines(self): |
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216 faFile = open("dummyFaFile.fa", "w") |
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217 faFile.write("\n") |
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218 faFile.write(">seq1 description1\n") |
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219 faFile.write("ATGCGTCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") |
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220 faFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") |
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221 faFile.write("\n") |
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222 faFile.close() |
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223 |
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224 exp = Bioseq( "seq1 description1", "ATGCGTCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" ) |
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225 |
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226 obs = Bioseq() |
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227 faFile = open("dummyFaFile.fa", "r") |
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228 obs.read( faFile ) |
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229 faFile.close() |
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230 |
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231 os.remove("dummyFaFile.fa") |
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232 |
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233 self.assertEquals( exp, obs ) |
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234 |
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235 def test_read_with_70nt_by_line(self): |
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236 faFile = open("dummyFaFile.fa", "w") |
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237 faFile.write("\n") |
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238 faFile.write(">seq1 description1\n") |
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239 faFile.write("TGTCACATCCTGATTTTCGTTTCAGGATTTATAAATTATTTAATAAATTAATAATAGAATTTATATTAAA\n") |
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240 faFile.write("TGTTTTTTAATTTACAAGTGAAGTTAAATGTGGGAAATAAAATTTCTTAAATCTAAAGCATGGATGGATT\n") |
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241 faFile.write("\n") |
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242 faFile.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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243 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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244 exp = Bioseq( "seq1 description1", "TGTCACATCCTGATTTTCGTTTCAGGATTTATAAATTATTTAATAAATTAATAATAGAATTTATATTAAATGTTTTTTAATTTACAAGTGAAGTTAAATGTGGGAAATAAAATTTCTTAAATCTAAAGCATGGATGGATT" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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245 |
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246 obs = Bioseq() |
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247 faFile = open("dummyFaFile.fa", "r") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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248 obs.read( faFile ) |
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249 faFile.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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250 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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251 os.remove("dummyFaFile.fa") |
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252 |
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253 self.assertEquals( exp, obs ) |
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254 |
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255 def test_appendBioseqInFile(self): |
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256 obsFaFileName = "dummyFaFile.fa" |
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257 obsFaFile = open(obsFaFileName, "w") |
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258 obsFaFile.write(">seq1 description1\n") |
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259 obsFaFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") |
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260 obsFaFile.close() |
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261 |
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262 bioseq = Bioseq() |
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263 bioseq.header = "seq2 description2" |
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264 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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265 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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266 expFaFileName = "dummyFaFile2.fa" |
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267 expFaFile = open(expFaFileName, "w") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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268 expFaFile.write(">seq1 description1\n") |
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269 expFaFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") |
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270 expFaFile.write(">seq2 description2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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271 expFaFile.write("GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") |
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272 expFaFile.write("ATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") |
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273 expFaFile.write("ATAGCAGACGCATATTATATTGCGCG\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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274 expFaFile.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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275 |
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276 bioseq.appendBioseqInFile(obsFaFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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277 self.assertTrue(FileUtils.are2FilesIdentical(expFaFileName, obsFaFileName)) |
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278 os.remove(obsFaFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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279 os.remove(expFaFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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280 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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281 |
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282 def test_writeABioseqInAFastaFile(self): |
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283 obsFaFileName = "dummyFaFile.fa" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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284 obsFaFile = open(obsFaFileName, "w") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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285 obsFaFile.write(">seq1 description1\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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286 obsFaFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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287 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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288 bioseq = Bioseq() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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289 bioseq.header = "seq2 description2" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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290 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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291 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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292 expFaFileName = "dummyFaFile2.fa" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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293 expFaFile = open(expFaFileName, "w") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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294 expFaFile.write(">seq1 description1\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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295 expFaFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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296 expFaFile.write(">seq2 description2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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297 expFaFile.write("GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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298 expFaFile.write("ATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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299 expFaFile.write("ATAGCAGACGCATATTATATTGCGCG\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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300 expFaFile.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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301 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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302 bioseq.writeABioseqInAFastaFile(obsFaFile) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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303 obsFaFile.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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304 self.assertTrue(FileUtils.are2FilesIdentical(expFaFileName, obsFaFileName)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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305 os.remove(obsFaFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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306 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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307 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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308 def test_writeABioseqInAFastaFileWithOtherHeader(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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309 obsFaFileName = "dummyFaFile.fa" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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310 obsFaFile = open(obsFaFileName, "w") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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311 obsFaFile.write(">seq1 description1\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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312 obsFaFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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313 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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314 bioseq = Bioseq() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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315 bioseq.header = "seq2 description2" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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316 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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317 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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318 expFaFileName = "dummyFaFile2.fa" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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319 newHeader = "seq2 New header2" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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320 expFaFile = open(expFaFileName, "w") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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321 expFaFile.write(">seq1 description1\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
322 expFaFile.write("ATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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323 expFaFile.write(">" + newHeader + "\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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324 expFaFile.write("GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
325 expFaFile.write("ATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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326 expFaFile.write("ATAGCAGACGCATATTATATTGCGCG\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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327 expFaFile.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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328 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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329 bioseq.writeABioseqInAFastaFileWithOtherHeader(obsFaFile, newHeader) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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330 obsFaFile.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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331 self.assertTrue(FileUtils.are2FilesIdentical(expFaFileName, obsFaFileName)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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332 os.remove(obsFaFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
333 os.remove(expFaFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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334 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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335 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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336 def test_writeSeqInFasta(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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337 iBs = Bioseq() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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338 iBs.header = "dummySeq" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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339 iBs.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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340 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
341 expFaFile = "dummyExpFile.fa" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
342 expFaFileHandler = open(expFaFile, "w") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
343 expFaFileHandler.write("GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
344 expFaFileHandler.write("ATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
345 expFaFileHandler.write("ATAGCAGACGCATATTATATTGCGCG\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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346 expFaFileHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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347 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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348 obsFaFile = "dummyObsFile.fa" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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349 obsFaFileHandler = open( obsFaFile, "w" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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350 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
351 iBs.writeSeqInFasta( obsFaFileHandler ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
352 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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353 obsFaFileHandler.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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354 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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355 self.assertTrue( FileUtils.are2FilesIdentical( expFaFile, obsFaFile ) ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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356 os.remove(obsFaFile) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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357 os.remove(expFaFile) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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358 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
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359 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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360 def test_subseq(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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361 bioseq = Bioseq() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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362 bioseq.header = "seq1 description1" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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363 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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364 start = 10 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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365 end = 30 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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366 expSubBioseq = Bioseq() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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367 expSubBioseq.header = "seq1 description1 fragment " + str(start) + ".." + str(end) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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368 expSubBioseq.sequence = bioseq.sequence[(start - 1) : end] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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369 obsBioseq = bioseq.subseq(start, end) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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370 self.assertEquals(expSubBioseq, obsBioseq) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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371 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
372 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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373 def test_subseq_no_end(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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374 bioseq = Bioseq() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
375 bioseq.header = "seq1 description1" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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376 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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377 start = 10 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
378 expSubBioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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379 expEnd = len(bioseq.sequence) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
380 expSubBioseq.header = "seq1 description1 fragment " + str(start) + ".." + str(expEnd) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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381 expSubBioseq.sequence = bioseq.sequence[(start - 1) : expEnd] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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382 obsBioseq = bioseq.subseq(start) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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383 self.assertEquals(expSubBioseq, obsBioseq) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
384 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
385 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
386 def test_subseq_start_gt_end(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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387 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
388 bioseq.header = "seq1 description1" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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389 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
390 start = 30 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
391 end = 10 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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392 expSubBioseq = None |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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393 obsBioseq = bioseq.subseq(start, end) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
394 self.assertEquals(expSubBioseq, obsBioseq) |
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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 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
397 def test_subseq_start_eq_end(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
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398 bioseq = Bioseq() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
399 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
400 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
401 start = 10 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
402 end = 10 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
403 expSubBioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
404 expSubBioseq.header = "seq1 description1 fragment " + str(start) + ".." + str(end) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
405 expSubBioseq.sequence = bioseq.sequence[(start - 1) : end] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
406 obsBioseq = bioseq.subseq(start, end) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
407 self.assertEquals(expSubBioseq, obsBioseq) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
408 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
409 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
410 def test_subseq_negative_start(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
411 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
412 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
413 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
414 start = -10 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
415 end = 10 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
416 expSubBioseq = None |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
417 obsBioseq = bioseq.subseq(start, end) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
418 self.assertEquals(expSubBioseq, obsBioseq) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
419 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
420 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
421 def test_getNtFromPosition_1(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
422 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
423 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
424 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
425 expNt = "G" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
426 obsNt = bioseq.getNtFromPosition(1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
427 self.assertEquals(expNt, obsNt) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
428 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
429 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
430 def test_getNtFromPosition_10(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
431 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
432 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
433 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
434 expNt = "C" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
435 obsNt = bioseq.getNtFromPosition(10) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
436 self.assertEquals(expNt, obsNt) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
437 |
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 def test_getNtFromPosition_last(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
440 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
441 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
442 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
443 expNt = "G" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
444 obsNt = bioseq.getNtFromPosition(146) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
445 self.assertEquals(expNt, obsNt) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
446 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
447 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
448 def test_getNtFromPosition_position_outside_range_0(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
449 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
450 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
451 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
452 expNt = None |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
453 obsNt = bioseq.getNtFromPosition(0) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
454 self.assertEquals(expNt, obsNt) |
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_getNtFromPosition_position_outside_range_negative(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
458 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
459 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
460 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
461 expNt = None |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
462 obsNt = bioseq.getNtFromPosition(-10) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
463 self.assertEquals(expNt, obsNt) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
464 |
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 def test_getNtFromPosition_position_outside_range_positive(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
467 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
468 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
469 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
470 expNt = None |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
471 obsNt = bioseq.getNtFromPosition(147) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
472 self.assertEquals(expNt, obsNt) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
473 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
474 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
475 def test_view(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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476 obsFileName = "obsdummy_Bioseq_view" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
477 expFileName = "expDummy_Bioseq_View" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
478 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
479 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
480 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
481 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
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 obsFile = open(obsFileName,"w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
484 expFile = open(expFileName, "w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
485 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
486 expFile.write ( ">seq1 description1\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
487 expFile.write ( "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
488 expFile.write ( "ATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
489 expFile.write ( "ATAGCAGACGCATATTATATTGCGCG\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
490 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
491 stdoutRef = sys.stdout |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
492 sys.stdout = obsFile |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
493 bioseq.view() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
494 obsFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
495 expFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
496 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
497 sys.stdout = stdoutRef |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
498 os.remove ( obsFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
499 os.remove ( expFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
500 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
501 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
502 def test_view_with_l(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
503 obsFileName = "obsdummy_Bioseq_view" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
504 expFileName = "expDummy_Bioseq_View" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
505 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
506 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
507 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
508 obsFile = open(obsFileName,"w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
509 expFile = open(expFileName, "w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
510 expFile.write ( ">seq1 description1\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
511 expFile.write ( "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
512 expFile.write ( "ATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTAT\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
513 stdoutRef = sys.stdout |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
514 sys.stdout = obsFile |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
515 bioseq.view(120) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
516 obsFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
517 expFile.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
518 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
519 sys.stdout = stdoutRef |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
520 os.remove ( obsFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
521 os.remove ( expFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
522 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
523 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
524 def test_getLength(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
525 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
526 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
527 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
528 expLength = 146 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
529 obsLength = bioseq.getLength() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
530 self.assertEquals(expLength, obsLength) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
531 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
532 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
533 def test_getLength_empty_seq(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
534 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
535 expLength = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
536 obsLength = bioseq.getLength() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
537 self.assertEquals(expLength, obsLength) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
538 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
539 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
540 def test_getLength_WithoutN(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
541 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
542 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
543 bioseq.sequence = "GCGANCGCTGCTTTATTAAGCGCTAGATGNNNNNNNNNNNNNNNCGACGCTGCATTTATTAAGCGCTAGCGATTATANNNNNNNNNTAGCAGACGCATATTATATTGCGCGATGCGACGCTGCTTTATTANAGCGCTAGCGNNATTATATAGCANGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
544 expLength = 146 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
545 obsLength = bioseq.getLength(False) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
546 self.assertEquals(expLength, obsLength) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
547 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
548 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
549 def test_getLength_WithoutN_empty_seq(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
550 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
551 expLength = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
552 obsLength = bioseq.getLength(False) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
553 self.assertEquals(expLength, obsLength) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
554 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
555 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
556 def test_countNt(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
557 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
558 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
559 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
560 expCount = 3 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
561 obsCount = bioseq.countNt('N') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
562 self.assertEquals(expCount, obsCount) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
563 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
564 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
565 def test_countNt_withCharacterNotExisting(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
566 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
567 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
568 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
569 expCount = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
570 obsCount = bioseq.countNt('W') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
571 self.assertEquals(expCount, obsCount) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
572 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
573 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
574 def test_countAllNt(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
575 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
576 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
577 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
578 dExpCount = {'A': 34, 'C': 31, 'T': 43, 'G': 35, 'N': 3} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
579 dObsCount = bioseq.countAllNt() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
580 self.assertEquals(dExpCount, dObsCount) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
581 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
582 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
583 def test_occ_word_size_1(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
584 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
585 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
586 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
587 dExpOccWord = {'A': 34, 'C': 31, 'T': 43, 'G': 35} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
588 ExpNbWord = 143 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
589 dObsOccWord, ObsNbWord = bioseq.occ_word(1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
590 self.assertEquals(dExpOccWord, dObsOccWord) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
591 self.assertEquals(ExpNbWord, ObsNbWord) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
592 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
593 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
594 def test_occ_word_size_0(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
595 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
596 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
597 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
598 dExpOccWord = {} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
599 ExpNbWord = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
600 dObsOccWord, ObsNbWord = bioseq.occ_word(0) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
601 self.assertEquals(dExpOccWord, dObsOccWord) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
602 self.assertEquals(ExpNbWord, ObsNbWord) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
603 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
604 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
605 def test_occ_word_size_n(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
606 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
607 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
608 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
609 dExpOccWord = {'ACC': 0, 'ATG': 2, 'AAG': 3, 'AAA': 0, 'ATC': 0, 'AAC': 0, 'ATA': 8, 'AGG': 0, 'CCT': 0, 'CTC': 0, 'AGC': 8, 'ACA': 0, 'AGA': 2, 'CAT': 3, 'AAT': 0, 'ATT': 9, 'CTG': 3, 'CTA': 3, 'ACT': 0, 'CAC': 0, 'ACG': 2, 'CAA': 0, 'AGT': 0, 'CAG': 2, 'CCG': 0, 'CCC': 0, 'CTT': 3, 'TAT': 13, 'GGT': 0, 'TGT': 0, 'CGA': 3, 'CCA': 0, 'TCT': 0, 'GAT': 3, 'CGG': 0, 'TTT': 3, 'TGC': 7, 'GGG': 0, 'TAG': 5, 'GGA': 0, 'TAA': 3, 'GGC': 0, 'TAC': 0, 'TTC': 0, 'TCG': 0, 'TTA': 10, 'TTG': 2, 'TCC': 0, 'GAA': 0, 'TGG': 0, 'GCA': 5, 'GTA': 0, 'GCC': 0, 'GTC': 0, 'GCG': 12, 'GTG': 0, 'GAG': 0, 'GTT': 0, 'GCT': 9, 'TGA': 0, 'GAC': 2, 'CGT': 0, 'TCA': 0, 'CGC': 10} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
610 ExpNbWord = 135 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
611 dObsOccWord, ObsNbWord = bioseq.occ_word(3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
612 self.assertEquals(dExpOccWord, dObsOccWord) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
613 self.assertEquals(ExpNbWord, ObsNbWord) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
614 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
615 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
616 def test_freq_word_size_1(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
617 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
618 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
619 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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620 dExpFreqWord = {'A': 0.23776223776223776, 'C': 0.21678321678321677, 'T': 0.30069930069930068, 'G': 0.24475524475524477} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
621 dObsFreqWord = bioseq.freq_word(1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
622 self.assertEquals(dExpFreqWord, dObsFreqWord) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
623 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
624 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
625 def test_freq_word_size_0(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
626 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
627 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
628 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
629 dExpFreqWord = {} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
630 dObsFreqWord = bioseq.freq_word(0) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
631 self.assertEquals(dExpFreqWord, dObsFreqWord) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
632 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
633 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
634 def test_freq_word_size_n(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
635 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
636 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
637 bioseq.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
638 dExpFreqWord = {'ACC': 0.0, 'ATG': 0.014814814814814815, 'AAG': 0.022222222222222223, 'AAA': 0.0, 'ATC': 0.0, 'AAC': 0.0, 'ATA': 0.059259259259259262, 'AGG': 0.0, 'CCT': 0.0, 'CTC': 0.0, 'AGC': 0.059259259259259262, 'ACA': 0.0, 'AGA': 0.014814814814814815, 'CAT': 0.022222222222222223, 'AAT': 0.0, 'ATT': 0.066666666666666666, 'CTG': 0.022222222222222223, 'CTA': 0.022222222222222223, 'ACT': 0.0, 'CAC': 0.0, 'ACG': 0.014814814814814815, 'CAA': 0.0, 'AGT': 0.0, 'CAG': 0.014814814814814815, 'CCG': 0.0, 'CCC': 0.0, 'TAT': 0.096296296296296297, 'GGT': 0.0, 'TGT': 0.0, 'CGA': 0.022222222222222223, 'CCA': 0.0, 'TCT': 0.0, 'GAT': 0.022222222222222223, 'CGG': 0.0, 'CTT': 0.022222222222222223, 'TGC': 0.05185185185185185, 'GGG': 0.0, 'TAG': 0.037037037037037035, 'GGA': 0.0, 'TAA': 0.022222222222222223, 'GGC': 0.0, 'TAC': 0.0, 'TTC': 0.0, 'TCG': 0.0, 'TTT': 0.022222222222222223, 'TTG': 0.014814814814814815, 'TCC': 0.0, 'GAA': 0.0, 'TGG': 0.0, 'GCA': 0.037037037037037035, 'GTA': 0.0, 'GCC': 0.0, 'GTC': 0.0, 'TGA': 0.0, 'GCG': 0.088888888888888892, 'GTG': 0.0, 'GAG': 0.0, 'GTT': 0.0, 'GCT': 0.066666666666666666, 'TTA': 0.07407407407407407, 'GAC': 0.014814814814814815, 'CGT': 0.0, 'TCA': 0.0, 'CGC': 0.07407407407407407} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
639 dObsFreqWord = bioseq.freq_word(3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
640 self.assertEquals(dExpFreqWord, dObsFreqWord) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
641 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
642 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
643 def test_findORF_no_ORF_in_sequence (self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
644 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
645 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
646 bioseq.sequence = "GCGNCGCTGCTTTATT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
647 expORF = {0:[],1:[],2:[]} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
648 obsORF = bioseq.findORF() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
649 self.assertEquals (expORF,obsORF) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
650 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
651 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
652 def test_findORF_one_ORF_in_first_phase(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
653 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
654 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
655 bioseq.sequence = "TAAGCGNCGCTGCTTTATT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
656 expORF = {0:[0],1:[],2:[]} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
657 obsORF = bioseq.findORF() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
658 self.assertEquals (expORF,obsORF) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
659 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
660 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
661 def test_findORF_three_ORF_in_first_phase(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
662 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
663 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
664 bioseq.sequence = "TAAGCGTAGNCGTGACTGCTTTATT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
665 expORF = {0:[0,6,12],1:[],2:[]} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
666 obsORF = bioseq.findORF() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
667 self.assertEquals (expORF,obsORF) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
668 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
669 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
670 def test_findORF_two_ORF_in_first_phase_one_ORF_in_second_phase(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
671 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
672 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
673 bioseq.sequence = "TAAGTAGAGNCGTGACTGCTTTATT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
674 expORF = {0:[0,12],1:[4],2:[]} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
675 obsORF = bioseq.findORF() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
676 self.assertEquals (expORF,obsORF) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
677 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
678 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
679 def test_findORF_two_ORF_in_first_phase_three_ORF_in_second_phase(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
680 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
681 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
682 bioseq.sequence = "TAAGTAGAGNCGTGACTGATAGTATT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
683 expORF = {0:[0,12],1:[4,16,19],2:[]} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
684 obsORF = bioseq.findORF() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
685 self.assertEquals (expORF,obsORF) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
686 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
687 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
688 def test_findORF_one_ORF_in_second_phase_three_ORF_in_third_phase(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
689 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
690 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
691 bioseq.sequence = "AATATTAGTGGAGTAGTTGATGATTTT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
692 expORF = {0:[], 1:[13], 2:[5,17,20]} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
693 obsORF = bioseq.findORF() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
694 self.assertEquals (expORF,obsORF) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
695 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
696 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
697 def test_findORF_three_ORF_in_second_phase_one_ORF_in_third_phase(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
698 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
699 bioseq.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
700 bioseq.sequence = "TTTGAAGTGGAGGAGTTGATGATTTTAAT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
701 expORF = {0:[], 1:[16, 19, 25], 2:[2]} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
702 obsORF = bioseq.findORF() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
703 self.assertEquals (expORF,obsORF) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
704 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
705 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
706 def test_upCase(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
707 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
708 bioseq.header = "seq description" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
709 bioseq.sequence = "taattcggcct" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
710 expSeq = "TAATTCGGCCT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
711 bioseq.upCase() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
712 obsSeq = bioseq.sequence |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
713 self.assertEquals( expSeq, obsSeq ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
714 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
715 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
716 def test_lowCase(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
717 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
718 bioseq.header = "seq description" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
719 bioseq.sequence = "TAATTCGGCCT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
720 expSeq = "taattcggcct" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
721 bioseq.lowCase() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
722 obsSeq = bioseq.sequence |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
723 self.assertEquals( expSeq, obsSeq ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
724 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
725 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
726 def test_getClusterID(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
727 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
728 bioseq.header = "MbQ58Gr2Cl0 chunk1 {Fragment} 74091..74624" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
729 bioseq.sequence = "TAATTCGGCCT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
730 expID = "0" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
731 obsID = bioseq.getClusterID() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
732 self.assertEquals( expID, obsID ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
733 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
734 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
735 def test_getGroupID(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
736 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
737 bioseq.header = "MbQ58Gr2Cl0 chunk1 {Fragment} 74091..74624" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
738 bioseq.sequence = "TAATTCGGCCT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
739 expID = "2" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
740 obsID = bioseq.getGroupID() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
741 self.assertEquals( expID, obsID ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
742 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
743 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
744 def test_getHeaderFullSeq(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
745 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
746 bioseq.header = "MbQ58Gr2Cl0 chunk1 {Fragment} 74091..74624" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
747 bioseq.sequence = "TAATTCGGCCT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
748 expHeader = "chunk1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
749 obsHeader = bioseq.getHeaderFullSeq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
750 self.assertEquals( expHeader, obsHeader ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
751 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
752 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
753 def test_getFragStrand_plus_strand(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
754 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
755 bioseq.header = "MbQ58Gr2Cl0 chunk1 {Fragment} 74091..74624" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
756 bioseq.sequence = "TAATTCGGCCT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
757 expStrand = '+' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
758 obsStrand = bioseq.getFragStrand() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
759 self.assertEquals(expStrand, obsStrand) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
760 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
761 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
762 def test_getFragStrand_minus_strand(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
763 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
764 bioseq.header = "MbQ58Gr2Cl0 chunk1 {Fragment} 74624..74091" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
765 bioseq.sequence = "TAATTCGGCCT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
766 expStrand = '-' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
767 obsStrand = bioseq.getFragStrand() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
768 self.assertEquals(expStrand, obsStrand) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
769 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
770 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
771 def test_getATGCNFromIUPAC_A(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
772 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
773 expNucl = 'A' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
774 obsNucl = bioseq.getATGCNFromIUPAC('A') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
775 self.assertEquals(expNucl, obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
776 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
777 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
778 def test_getATGCNFromIUPAC_T(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
779 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
780 expNucl = 'T' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
781 obsNucl = bioseq.getATGCNFromIUPAC('T') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
782 self.assertEquals(expNucl, obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
783 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
784 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
785 def test_getATGCNFromIUPAC_C(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
786 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
787 expNucl = 'C' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
788 obsNucl = bioseq.getATGCNFromIUPAC('C') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
789 self.assertEquals(expNucl, obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
790 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
791 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
792 def test_getATGCNFromIUPAC_G(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
793 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
794 expNucl = 'G' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
795 obsNucl = bioseq.getATGCNFromIUPAC('G') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
796 self.assertEquals(expNucl, obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
797 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
798 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
799 def test_getATGCNFromIUPAC_N(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
800 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
801 expNucl = 'N' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
802 obsNucl = bioseq.getATGCNFromIUPAC('N') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
803 self.assertEquals(expNucl, obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
804 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
805 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
806 def test_getATGCNFromIUPAC_U(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
807 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
808 expNucl = 'T' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
809 obsNucl = bioseq.getATGCNFromIUPAC('U') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
810 self.assertEquals(expNucl, obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
811 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
812 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
813 def test_getATGCNFromIUPAC_R(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
814 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
815 expNucl1 = 'A' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
816 expNucl2 = 'G' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
817 obsNucl = bioseq.getATGCNFromIUPAC('R') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
818 self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
819 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
820 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
821 def test_getATGCNFromIUPAC_Y(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
822 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
823 expNucl1 = 'C' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
824 expNucl2 = 'T' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
825 obsNucl = bioseq.getATGCNFromIUPAC('Y') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
826 self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
827 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
828 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
829 def test_getATGCNFromIUPAC_M(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
830 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
831 expNucl1 = 'C' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
832 expNucl2 = 'A' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
833 obsNucl = bioseq.getATGCNFromIUPAC('M') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
834 self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
835 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
836 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
837 def test_getATGCNFromIUPAC_K(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
838 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
839 expNucl1 = 'T' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
840 expNucl2 = 'G' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
841 obsNucl = bioseq.getATGCNFromIUPAC('K') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
842 self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
843 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
844 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
845 def test_getATGCNFromIUPAC_W(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
846 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
847 expNucl1 = 'T' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
848 expNucl2 = 'A' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
849 obsNucl = bioseq.getATGCNFromIUPAC('W') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
850 self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
851 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
852 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
853 def test_getATGCNFromIUPAC_S(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
854 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
855 expNucl1 = 'C' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
856 expNucl2 = 'G' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
857 obsNucl = bioseq.getATGCNFromIUPAC('S') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
858 self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
859 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
860 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
861 def test_getATGCNFromIUPAC_B(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
862 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
863 expNucl1 = 'C' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
864 expNucl2 = 'T' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
865 expNucl3 = 'G' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
866 obsNucl = bioseq.getATGCNFromIUPAC('B') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
867 self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl or expNucl3 == obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
868 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
869 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
870 def test_getATGCNFromIUPAC_D(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
871 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
872 expNucl1 = 'A' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
873 expNucl2 = 'T' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
874 expNucl3 = 'G' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
875 obsNucl = bioseq.getATGCNFromIUPAC('D') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
876 self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl or expNucl3 == obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
877 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
878 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
879 def test_getATGCNFromIUPAC_H(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
880 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
881 expNucl1 = 'C' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
882 expNucl2 = 'T' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
883 expNucl3 = 'A' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
884 obsNucl = bioseq.getATGCNFromIUPAC('H') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
885 self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl or expNucl3 == obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
886 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
887 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
888 def test_getATGCNFromIUPAC_V(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
889 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
890 expNucl1 = 'C' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
891 expNucl2 = 'A' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
892 expNucl3 = 'G' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
893 obsNucl = bioseq.getATGCNFromIUPAC('V') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
894 self.assertTrue(expNucl1 == obsNucl or expNucl2 == obsNucl or expNucl3 == obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
895 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
896 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
897 def test_getATGCNFromIUPAC_Z(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
898 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
899 expNucl = 'N' |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
900 obsNucl = bioseq.getATGCNFromIUPAC('Z') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
901 self.assertEquals(expNucl, obsNucl) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
902 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
903 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
904 def test_partialIUPAC(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
905 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
906 bioseq.sequence = "ATGCNRATGCN" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
907 expSequence1 = "ATGCNAATGCN" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
908 expSequence2 = "ATGCNGATGCN" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
909 bioseq.partialIUPAC() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
910 obsSequence = bioseq.sequence |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
911 self.assertTrue(expSequence1 == obsSequence or expSequence2 == obsSequence) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
912 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
913 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
914 def test_checkEOF(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
915 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
916 bioseq.sequence = "ATGCNRATGCN\rATGCAAT\rTATA\r" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
917 bioseq.checkEOF() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
918 obsSequence = bioseq.sequence |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
919 expSequence = "ATGCNRATGCNATGCAATTATA" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
920 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
921 self.assertEquals(expSequence, obsSequence) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
922 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
923 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
924 def test_getLMapWhithoutGap(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
925 iBioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
926 iBioseq.header = "header" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
927 iBioseq.sequence = "ATGC-RA-GCT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
928 obsLMap = iBioseq.getLMapWhithoutGap() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
929 expLMap = [Map( "header_subSeq1", "header", 1, 4 ), Map( "header_subSeq2", "header", 6, 7 ), Map( "header_subSeq3", "header", 9, 11 )] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
930 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
931 self.assertEquals(expLMap, obsLMap) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
932 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
933 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
934 def test_getLMapWhithoutGap_seqStartsWithGap(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
935 iBioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
936 iBioseq.header = "header" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
937 iBioseq.sequence = "-TGC-RA-GCT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
938 obsLMap = iBioseq.getLMapWhithoutGap() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
939 expLMap = [Map( "header_subSeq1", "header", 2, 4 ), Map( "header_subSeq2", "header", 6, 7 ), Map( "header_subSeq3", "header", 9, 11 )] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
940 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
941 self.assertEquals(expLMap, obsLMap) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
942 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
943 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
944 def test_getLMapWhithoutGap_seqEndsWithGap(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
945 iBioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
946 iBioseq.header = "header" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
947 iBioseq.sequence = "ATGC-RA-GC-" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
948 obsLMap = iBioseq.getLMapWhithoutGap() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
949 expLMap = [Map( "header_subSeq1", "header", 1, 4 ), Map( "header_subSeq2", "header", 6, 7 ), Map( "header_subSeq3", "header", 9, 10 )] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
950 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
951 self.assertEquals(expLMap, obsLMap) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
952 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
953 def test_getGCpercentage_onlyATGC( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
954 iBs = Bioseq( "seq", "TGCAGCT" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
955 exp = 100 * 4 / 7.0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
956 obs = iBs.getGCpercentage() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
957 self.assertEqual( exp, obs ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
958 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
959 def test_getGCpercentageInSequenceWithoutCountNInLength( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
960 iBs = Bioseq( "seq", "TGCAGCTNNNNN" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
961 exp = 100 * 4 / 7.0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
962 obs = iBs.getGCpercentageInSequenceWithoutCountNInLength() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
963 self.assertEqual( exp, obs ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
964 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
965 def test_get5PrimeFlank(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
966 bs = Bioseq( "line1", "AACTTTCCAGAA" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
967 position = 7 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
968 obsFlank = bs.get5PrimeFlank(position, 3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
969 expFlank = "TTT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
970 self.assertEquals(expFlank, obsFlank) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
971 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
972 def test_get5PrimeFlank_flank_length_truncated(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
973 bs = Bioseq( "line1", "AACTTTCCAGAA" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
974 position = 7 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
975 obsFlank = bs.get5PrimeFlank(position, 15) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
976 expFlank = "AACTTT" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
977 self.assertEquals(expFlank, obsFlank) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
978 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
979 def test_get5PrimeFlank_flank_of_first_base(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
980 bs = Bioseq( "line1", "AACTTTCCAGAA" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
981 position = 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
982 obsFlank = bs.get5PrimeFlank(position, 15) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
983 expFlank = "" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
984 self.assertEquals(expFlank, obsFlank) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
985 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
986 def test_get3PrimeFlank(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
987 bs = Bioseq( "line1", "AACTTTCCAGAA" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
988 position = 7 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
989 obsFlank = bs.get3PrimeFlank(position, 3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
990 expFlank = "CAG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
991 self.assertEquals(expFlank, obsFlank) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
992 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
993 def test_get3PrimeFlank_flank_length_truncated(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
994 bs = Bioseq( "line1", "AACTTTCCAGAA" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
995 position = 7 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
996 obsFlank = bs.get3PrimeFlank(position, 15) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
997 expFlank = "CAGAA" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
998 self.assertEquals(expFlank, obsFlank) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
999 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1000 def test_get3PrimeFlank_flank_of_last_base(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1001 bs = Bioseq( "line1", "AACTTTCCAGAA" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1002 position = 12 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1003 obsFlank = bs.get3PrimeFlank(position, 15) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1004 expFlank = "" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1005 self.assertEquals(expFlank, obsFlank) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1006 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1007 def test_get3PrimeFlank_polymLength_different_of_1(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1008 bs = Bioseq( "line1", "AACTTTCCAGAA" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1009 position = 7 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1010 obsFlank = bs.get3PrimeFlank(position, 3, 2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1011 expFlank = "AGA" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1012 self.assertEquals(expFlank, obsFlank) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1013 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1014 test_suite = unittest.TestSuite() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1015 test_suite.addTest( unittest.makeSuite( Test_Bioseq ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1016 if __name__ == "__main__": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1017 unittest.TextTestRunner(verbosity=2).run( test_suite ) |