Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/seq/test/Test_BioseqDB.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 time |
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35 from commons.core.seq.BioseqDB import BioseqDB |
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36 from commons.core.seq.Bioseq import Bioseq |
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37 from commons.core.utils.FileUtils import FileUtils |
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38 from commons.core.coord.Map import Map |
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39 |
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40 |
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41 class Test_BioseqDB( unittest.TestCase ): |
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42 |
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43 def setUp( self ): |
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44 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() ) |
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45 |
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46 |
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47 def tearDown( self ): |
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48 if os._exists("dummyBioseqDB.fa"): |
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49 os.remove("dummyBioseqDB.fa") |
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50 |
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51 |
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52 def test__eq__(self): |
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53 iBioseq1 = Bioseq( "seq1", "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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54 iBioseq2 = Bioseq( "seq2", "GCGATGCGATCGATGCGATAGCA" ) |
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55 expBioseqDB = BioseqDB() |
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56 expBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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57 |
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58 iBioseq3 = Bioseq( "seq1", "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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59 iBioseq4 = Bioseq( "seq2", "GCGATGCGATCGATGCGATAGCA" ) |
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60 obsBioseqDB = BioseqDB() |
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61 obsBioseqDB.setData( [ iBioseq3, iBioseq4 ] ) |
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62 |
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63 self.assertEquals( expBioseqDB, obsBioseqDB ) |
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64 |
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65 |
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66 def test__eq__instances_with_different_header(self): |
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67 iBioseq1 = Bioseq( "seq1", "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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68 iBioseq2 = Bioseq( "seq2", "GCGATGCGATCGATGCGATAGCA" ) |
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69 expBioseqDB = BioseqDB() |
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70 expBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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71 |
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72 iBioseq3 = Bioseq( "seq3", "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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73 iBioseq4 = Bioseq( "seq4", "GCGATGCGATCGATGCGATAGCA" ) |
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74 obsBioseqDB = BioseqDB() |
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75 obsBioseqDB.setData( [ iBioseq3, iBioseq4 ] ) |
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76 |
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77 self.assertNotEquals( expBioseqDB, obsBioseqDB ) |
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78 |
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79 |
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80 def test__eq__instances_with_different_sequences(self): |
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81 iBioseq1 = Bioseq( "seq1", "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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82 iBioseq2 = Bioseq( "seq2", "GCGATGCGATCGATGCGATAGCA" ) |
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83 expBioseqDB = BioseqDB() |
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84 expBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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85 |
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86 iBioseq3 = Bioseq( "seq1", "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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87 iBioseq4 = Bioseq( "seq2", "GCGATGCGATCGATGCGATAGCATATATATATATATATATATATAT" ) |
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88 obsBioseqDB = BioseqDB() |
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89 obsBioseqDB.setData( [ iBioseq3, iBioseq4 ] ) |
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90 |
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91 self.assertNotEquals( expBioseqDB, obsBioseqDB ) |
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92 |
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93 |
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94 def test__eq__instances_with_different_sequences_and_headers(self): |
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95 iBioseq1 = Bioseq( "seq1", "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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96 iBioseq2 = Bioseq( "seq2", "GCGATGCGATCGATGCGATAGCA" ) |
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97 expBioseqDB = BioseqDB() |
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98 expBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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99 |
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100 iBioseq3 = Bioseq( "seq3", "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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101 iBioseq4 = Bioseq( "seq4", "GCGATGCGATCGATGCGATAGCATATATATATATATATATATATAT" ) |
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102 obsBioseqDB = BioseqDB() |
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103 obsBioseqDB.setData( [ iBioseq3, iBioseq4 ] ) |
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104 |
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105 self.assertNotEquals( expBioseqDB, obsBioseqDB ) |
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106 |
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107 |
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108 def test__eq__instances_with_different_sizeOfBioseq(self): |
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109 iBioseq1 = Bioseq( "seq1", "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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110 iBioseq2 = Bioseq( "seq2", "GCGATGCGATCGATGCGATAGCA" ) |
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111 expBioseqDB = BioseqDB() |
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112 expBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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113 |
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114 iBioseq3 = Bioseq( "seq3", "AGCGGACGATGCAGCATGCGAATGACGAT" ) |
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115 obsBioseqDB = BioseqDB() |
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116 obsBioseqDB.setData( [ iBioseq3 ] ) |
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117 |
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118 self.assertNotEquals( expBioseqDB, obsBioseqDB ) |
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119 |
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120 |
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121 def test_setName (self): |
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122 expName = "myDataBank" |
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123 iBioseqDB = BioseqDB() |
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124 self.assertEquals (iBioseqDB.name, "") |
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125 |
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126 iBioseqDB.setName (expName) |
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127 obsName = iBioseqDB.name |
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128 self.assertEquals (expName, obsName) |
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129 |
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130 |
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131 def test_read(self): |
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132 iBioseq1 = Bioseq("consensus1","GAGATGGCTCATGGAGTACCTGCCT") |
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133 iBioseq2 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGC") |
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134 expBioseqDB = BioseqDB() |
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135 expBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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136 |
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137 faFN = "dummyFaFile.fa" |
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138 faF = open( faFN, "w" ) |
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139 faF.write(">consensus1\n") |
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140 faF.write("GAGATGGCTCATGGAGTACCTGCCT\n") |
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141 faF.write(">consensus2\n") |
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142 faF.write("GAGATGGCTCATGGAGTACCGC\n") |
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143 faF.close() |
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144 |
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145 faF = open( faFN, "r" ) |
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146 obsBioseqDB = BioseqDB() |
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147 obsBioseqDB.read( faF ) |
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148 faF.close() |
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149 os.remove( faFN ) |
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150 self.assertEquals( expBioseqDB, obsBioseqDB ) |
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151 |
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152 |
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153 def test_write(self): |
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154 iBioseq1 = Bioseq("consensus1","GAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCT") |
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155 iBioseq2 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
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156 iBioseqDB = BioseqDB() |
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157 iBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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158 |
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159 expFaFileName = "dummyFaFile.fa" |
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160 expFaFile = open( expFaFileName, "w" ) |
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161 expFaFile.write(">consensus1\n") |
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162 expFaFile.write("GAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCTGAGATGGCTC\n") |
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163 expFaFile.write("ATGGAGTACCTGCCT\n") |
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164 expFaFile.write(">consensus2\n") |
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165 expFaFile.write("GAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAG\n") |
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166 expFaFile.write("TACCGCGAGATGGCTCATGGAGTACCGC\n") |
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167 expFaFile.close() |
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168 |
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169 obsFaFileName = "obsDummyFastaFile.fa" |
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170 obsFaFile = open( obsFaFileName, "w" ) |
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171 iBioseqDB.write( obsFaFile ) |
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172 obsFaFile.close() |
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173 |
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174 self.assertTrue( FileUtils.are2FilesIdentical(expFaFileName, obsFaFileName) ) |
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175 os.remove( expFaFileName ) |
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176 os.remove( obsFaFileName ) |
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177 |
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178 |
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179 def test_save(self): |
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180 iBioseq1 = Bioseq("consensus1","GAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCT") |
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181 iBioseq2 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
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182 iBioseqDB = BioseqDB() |
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183 iBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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184 |
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185 expFaFileName = "dummyFaFile.fa" |
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186 expFaFile = open( expFaFileName, "w" ) |
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187 expFaFile.write(">consensus1\n") |
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188 expFaFile.write("GAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCTGAGATGGCTC\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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189 expFaFile.write("ATGGAGTACCTGCCT\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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190 expFaFile.write(">consensus2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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191 expFaFile.write("GAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAG\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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192 expFaFile.write("TACCGCGAGATGGCTCATGGAGTACCGC\n") |
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193 expFaFile.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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194 |
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195 obsFaFileName = "obsDummyFastaFile.fa" |
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196 iBioseqDB.save( obsFaFileName ) |
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197 |
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198 self.assertTrue( FileUtils.are2FilesIdentical(expFaFileName, obsFaFileName) ) |
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199 os.remove( expFaFileName ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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200 os.remove( obsFaFileName ) |
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201 |
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202 |
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203 def test_load(self): |
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204 iBioseq1 = Bioseq("consensus1","GAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCT") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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205 iBioseq2 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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206 expBioseqDB = BioseqDB() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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207 expBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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208 |
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209 FaFileName = "dummyFaFile.fa" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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210 FaFile = open( FaFileName, "w" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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211 FaFile.write(">consensus1\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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212 FaFile.write("GAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCTGAGATGGCTC\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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213 FaFile.write("ATGGAGTACCTGCCT\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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214 FaFile.write(">consensus2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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215 FaFile.write("GAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAG\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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216 FaFile.write("TACCGCGAGATGGCTCATGGAGTACCGC\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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217 FaFile.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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218 |
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219 obsBioseqDB = BioseqDB() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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220 obsBioseqDB.load( FaFileName ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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221 |
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222 self.assertEquals( expBioseqDB, obsBioseqDB ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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223 os.remove( FaFileName ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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224 |
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225 |
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226 def test_reverse( self ): |
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227 iBioseq1 = Bioseq( "seq1", "ATTG" ) |
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228 iBioseq2 = Bioseq( "seq2", "CGAAT" ) |
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229 expBioseqDB = BioseqDB() |
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230 expBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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231 |
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232 iBioseq3 = Bioseq( "seq1", "GTTA" ) |
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233 iBioseq4 = Bioseq( "seq2", "TAAGC" ) |
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234 obsBioseqDB = BioseqDB() |
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235 obsBioseqDB.setData( [ iBioseq3, iBioseq4 ] ) |
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236 obsBioseqDB.reverse() |
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237 self.assertEquals( expBioseqDB, obsBioseqDB ) |
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238 |
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239 |
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240 def test_complement( self ): |
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241 iBioseq1 = Bioseq( "seq1", "ATTG" ) |
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242 iBioseq2 = Bioseq( "seq2", "CGAAT" ) |
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243 expBioseqDB = BioseqDB() |
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244 expBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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245 |
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246 iBioseq3 = Bioseq( "seq1", "TAAC" ) |
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247 iBioseq4 = Bioseq( "seq2", "GCTTA" ) |
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248 obsBioseqDB = BioseqDB() |
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249 obsBioseqDB.setData( [ iBioseq3, iBioseq4 ] ) |
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250 |
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251 obsBioseqDB.complement() |
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252 self.assertEquals( expBioseqDB, obsBioseqDB ) |
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253 |
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254 |
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255 def test_reverseComplement( self ): |
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256 iBioseq1 = Bioseq( "seq1", "ATTG" ) |
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257 iBioseq2 = Bioseq( "seq2", "CGAAT" ) |
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258 expBioseqDB = BioseqDB() |
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259 expBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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260 |
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261 iBioseq3 = Bioseq( "seq1", "CAAT" ) |
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262 iBioseq4 = Bioseq( "seq2", "ATTCG" ) |
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263 obsBioseqDB = BioseqDB() |
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264 obsBioseqDB.setData( [ iBioseq3, iBioseq4 ] ) |
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265 |
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266 obsBioseqDB.reverseComplement() |
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267 self.assertEquals( expBioseqDB, obsBioseqDB ) |
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268 |
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269 |
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270 def test_setData(self): |
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271 iBioseq1 = Bioseq( "seq1", "ATTG" ) |
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272 iBioseq2 = Bioseq( "seq2", "CGAAT" ) |
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273 iBioseq3 = Bioseq( "seq3", "CAAT" ) |
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274 iBioseq4 = Bioseq( "seq4", "ATTCG" ) |
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275 |
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276 lBioseq = [iBioseq1, iBioseq2, iBioseq3, iBioseq4] |
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277 expBioseqDB = BioseqDB() |
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278 expBioseqDB.db = lBioseq |
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279 |
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280 iBioseq5 = Bioseq( "seq1", "ATTG" ) |
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281 iBioseq6 = Bioseq( "seq2", "CGAAT" ) |
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282 iBioseq7 = Bioseq( "seq3", "CAAT" ) |
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283 iBioseq8 = Bioseq( "seq4", "ATTCG" ) |
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284 |
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285 lBioseq2 = [iBioseq5, iBioseq6, iBioseq7, iBioseq8] |
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286 obsBioseqDB = BioseqDB() |
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287 obsBioseqDB.setData(lBioseq2) |
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288 |
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289 self.assertEquals(expBioseqDB, obsBioseqDB) |
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290 |
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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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292 def test_reset( self ): |
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293 iBioseq1 = Bioseq( "seq1", "ATTG" ) |
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294 iBioseq2 = Bioseq( "seq2", "CGAAT" ) |
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295 iBioseq3 = Bioseq( "seq3", "CAAT" ) |
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296 iBioseq4 = Bioseq( "seq4", "ATTCG" ) |
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297 |
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298 lBioseq = [iBioseq1, iBioseq2, iBioseq3, iBioseq4] |
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299 obsBioseqDB = BioseqDB() |
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300 obsBioseqDB.setData(lBioseq) |
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301 obsBioseqDB.reset() |
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302 |
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303 expBioseqDB = BioseqDB() |
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304 |
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305 self.assertEquals(expBioseqDB, obsBioseqDB) |
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306 |
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307 |
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308 def testCleanGap(self): |
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309 iBioseq1 = Bioseq( "seq1", "ATTG" ) |
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310 iBioseq2 = Bioseq( "seq2", "CGAAT" ) |
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311 expBioseqDB = BioseqDB() |
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312 expBioseqDB.setData([iBioseq1, iBioseq2]) |
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313 |
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314 iBioseq3 = Bioseq( "seq1", "AT-----TG" ) |
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315 iBioseq4 = Bioseq( "seq2", "CGAA----T" ) |
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316 |
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317 obsBioseqDB = BioseqDB() |
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318 obsBioseqDB.setData( [ iBioseq3, iBioseq4 ] ) |
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319 obsBioseqDB.cleanGap() |
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320 |
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321 self.assertEquals(expBioseqDB, obsBioseqDB) |
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322 |
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323 |
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324 def testCleanGap_on_empty_db(self): |
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325 expBioseqDB = BioseqDB() |
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326 |
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327 obsBioseqDB = BioseqDB() |
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328 obsBioseqDB.cleanGap() |
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329 |
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330 self.assertEquals(expBioseqDB, obsBioseqDB) |
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331 |
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332 |
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333 def testCleanGap_on_size_one_db(self): |
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334 iBioseq1 = Bioseq( "seq1", "ATTG" ) |
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335 expBioseqDB = BioseqDB() |
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336 expBioseqDB.setData([iBioseq1]) |
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337 |
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338 iBioseq2 = Bioseq( "seq1", "AT-----TG" ) |
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339 obsBioseqDB = BioseqDB() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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340 obsBioseqDB.setData([iBioseq2]) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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341 |
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342 obsBioseqDB.cleanGap() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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343 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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344 self.assertEquals(expBioseqDB, obsBioseqDB) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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345 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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346 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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347 def test_add_to_a_empty_bioseqDB_instance (self): |
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348 sHeader = "embl::AF332402:AF332402 Arabidopsis thaliana clone C00024 (f)" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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349 sHeader += "(At4g29080) mRNA, complete cds." |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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350 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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351 expDictIdx = { sHeader : 0} |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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352 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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353 sHeaderRenamed = "embl-AF332402-AF332402_Arabidopsis_thaliana_clone_C00024_(f)" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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354 sHeaderRenamed += "(At4g29080)_mRNA-_complete_cds." |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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355 expDictIdxRenamed = {sHeaderRenamed : 0} |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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356 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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357 iBioseq1 = Bioseq( sHeader, "ATTG" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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358 obsBioseqDB = BioseqDB() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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359 obsBioseqDB.add(iBioseq1) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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360 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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361 obsDictIdx = obsBioseqDB.idx |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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362 obsDictIdxRenamed = obsBioseqDB.idx_renamed |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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363 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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364 self.assertEquals(expDictIdx,obsDictIdx) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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365 self.assertEquals(expDictIdxRenamed,obsDictIdxRenamed) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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366 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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367 |
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368 def test_add_to_a_size_one_bioseqDB_instance (self): |
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369 sHeader1 = "embl::AF332402:AF332402 Arabidopsis thaliana clone C00024 (f)" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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370 sHeader1 += "(At4g29080) mRNA, complete cds." |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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371 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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372 sHeader2 = "embl::AF332503:AF332402 Arabidopsis thaliana clone C00024 (f)" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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373 sHeader2 += "(At4g29080) mRNA, complete cds." |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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374 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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375 expDictIdx = { sHeader1 : 0, sHeader2 : 1} |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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376 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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377 sHeaderRenamed1 = "embl-AF332402-AF332402_Arabidopsis_thaliana_clone_C00024_(f)" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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378 sHeaderRenamed1 += "(At4g29080)_mRNA-_complete_cds." |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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379 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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380 sHeaderRenamed2 = "embl-AF332503-AF332402_Arabidopsis_thaliana_clone_C00024_(f)" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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381 sHeaderRenamed2 += "(At4g29080)_mRNA-_complete_cds." |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
382 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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383 expDictIdxRenamed = {sHeaderRenamed1 : 0, sHeaderRenamed2 : 1} |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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384 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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385 iBioseq1 = Bioseq( sHeader1, "ATTG" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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386 iBioseq2 = Bioseq( sHeader2, "ATTG" ) |
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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 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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388 obsBioseqDB = BioseqDB() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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389 obsBioseqDB.setData([ iBioseq1]) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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390 obsBioseqDB.add(iBioseq2) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
391 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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392 obsDictIdx = obsBioseqDB.idx |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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393 obsDictIdxRenamed = obsBioseqDB.idx_renamed |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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394 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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395 self.assertEquals(expDictIdx,obsDictIdx) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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396 self.assertEquals(expDictIdxRenamed,obsDictIdxRenamed) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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397 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
398 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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399 def test_add_to_a_size_two_bioseqDB_instance (self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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400 sHeader1 = "embl::AF332402:AF332402 Arabidopsis thaliana clone C00024 (f)" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
401 sHeader1 += "(At4g29080) mRNA, complete cds." |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
402 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
403 sHeader2 = "embl::AF332503:AF332402 Arabidopsis thaliana clone C00024 (f)" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
404 sHeader2 += "(At4g29080) mRNA, complete cds." |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
405 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
406 sHeader3 = "embl::AF332604:AF332402 Arabidopsis thaliana clone C00024 (f)" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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407 sHeader3 += "(At4g29080) mRNA, complete cds." |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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408 expDictIdx = { sHeader1 : 0, sHeader2 : 1, sHeader3 : 2} |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
409 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
410 sHeaderRenamed1 = "embl-AF332402-AF332402_Arabidopsis_thaliana_clone_C00024_(f)" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
411 sHeaderRenamed1 += "(At4g29080)_mRNA-_complete_cds." |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
412 |
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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
|
413 sHeaderRenamed2 = "embl-AF332503-AF332402_Arabidopsis_thaliana_clone_C00024_(f)" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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414 sHeaderRenamed2 += "(At4g29080)_mRNA-_complete_cds." |
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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
|
415 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
416 sHeaderRenamed3 = "embl-AF332604-AF332402_Arabidopsis_thaliana_clone_C00024_(f)" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
417 sHeaderRenamed3 += "(At4g29080)_mRNA-_complete_cds." |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
418 expDictIdxRenamed = {sHeaderRenamed1 : 0, sHeaderRenamed2 : 1, sHeaderRenamed3 :2} |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
419 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
420 iBioseq1 = Bioseq( sHeader1, "ATTG" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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421 iBioseq2 = Bioseq( sHeader2, "ATTG" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
422 iBioseq3 = Bioseq( sHeader3, "ATTG" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
423 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
424 obsBioseqDB = BioseqDB() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
425 obsBioseqDB.setData([ iBioseq1, iBioseq2 ]) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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426 obsBioseqDB.add(iBioseq3) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
427 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
428 obsDictIdx = obsBioseqDB.idx |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
429 obsDictIdxRenamed = obsBioseqDB.idx_renamed |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
430 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
431 self.assertEquals(expDictIdx,obsDictIdx) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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432 self.assertEquals(expDictIdxRenamed,obsDictIdxRenamed) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
433 |
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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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|
434 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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435 def test__getitem__(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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436 iBioseq1 = Bioseq("seq1","ATTG") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
437 iBioseq2 = Bioseq("seq2","CGAAT") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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438 iBioseqDB = BioseqDB() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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439 iBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
440 expBioseq = Bioseq("seq2","CGAAT") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
441 obsBioseq = iBioseqDB[1] |
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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
|
442 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
443 self.assertEquals(expBioseq, obsBioseq) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
444 |
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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
|
445 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
446 def test_getSize(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
447 expSize = 4 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
448 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
449 iBioseq1 = Bioseq( "seq1", "ATTG" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
450 iBioseq2 = Bioseq( "seq2", "CGAAT" ) |
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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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|
451 iBioseq3 = Bioseq( "seq3", "AT-----TG" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
452 iBioseq4 = Bioseq( "seq4", "CGAA----T" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
453 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
454 obsBioseqDB = BioseqDB() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
455 obsBioseqDB.setData( [iBioseq1, iBioseq2 , iBioseq3, iBioseq4 ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
456 obsSize = obsBioseqDB.getSize() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
457 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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458 self.assertEquals(expSize,obsSize) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
459 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
460 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
461 def test_getSize_emptyDB(self): |
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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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462 expSize = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
463 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
464 obsBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
465 obsSize = obsBioseqDB.getSize() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
466 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
467 self.assertEquals(expSize,obsSize) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
468 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
469 |
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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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470 def test_getLength(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
471 iBioseq1 = Bioseq("consensus1","GAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
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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472 iBioseq2 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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473 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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474 iBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
475 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
476 expLength = 163 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
477 obsLength = iBioseqDB.getLength() |
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 self.assertEquals( expLength, obsLength) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
480 |
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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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481 def test_getListOfSequencesLength(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
482 iBioseq1 = Bioseq("consensus1","GAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
483 iBioseq2 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
484 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
485 iBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
486 lLength = iBioseqDB.getListOfSequencesLength() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
487 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
488 expLLengh = [75, 88] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
489 self.assertEquals( expLLengh, lLength ) |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
492 def test_getHeaderList( 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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493 lExpHeader = ["seq1", "seq2"] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
494 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
495 iBioseq1 = Bioseq( "seq1", "ATTG" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
496 iBioseq2 = Bioseq( "seq2", "CGAAT" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
497 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
498 obsBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
499 obsBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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 lObsHeader = obsBioseqDB.getHeaderList() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
502 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
503 self.assertEquals( lExpHeader, lObsHeader ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
504 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
505 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
506 def test_getSequencesList( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
507 lExpSeqs = ["ATGC", "AATTCCGG"] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
508 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
509 iBioseq1 = Bioseq("seq1", "ATGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
510 iBioseq2 = Bioseq("seq2", "AATTCCGG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
511 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
512 obsBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
513 obsBioseqDB.setData([iBioseq1, iBioseq2]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
514 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
515 lObsSeqs = obsBioseqDB.getSequencesList() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
516 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
517 self.assertEquals(lExpSeqs, lObsSeqs) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
518 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
519 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
520 def test_fetch( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
521 ibioseq1 = Bioseq( "seq1", "ATTG" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
522 ibioseq2 = Bioseq( "seq2", "CGAAT" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
523 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
524 iBioseqDB.setData( [ ibioseq1, ibioseq2 ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
525 expBioseq = ibioseq1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
526 obsBioseq = iBioseqDB.fetch( "seq1" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
527 self.assertEquals( expBioseq, obsBioseq ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
528 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
529 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
530 def test_getBioseqByRenamedHeader( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
531 Header1 = "embl::AF332402:AF332402 Arabidopsis thaliana clone C00024 (f)" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
532 Header1 += "(At4g29080) mRNA, complete cds." |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
533 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
534 Header2 = "embl::AF332503:AF332402 Arabidopsis thaliana clone C00024 (f)" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
535 Header2 += "(At4g29080) mRNA, complete cds." |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
536 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
537 Header3 = "embl::AF332604:AF332402 Arabidopsis thaliana clone C00024 (f)" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
538 Header3 += "(At4g29080) mRNA, complete cds." |
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 HeaderRenamed2 = "embl-AF332503-AF332402_Arabidopsis_thaliana_clone_C00024_(f)" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
541 HeaderRenamed2 += "(At4g29080)_mRNA-_complete_cds." |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
542 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
543 ibioseq1 = Bioseq( Header1, "ATTG" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
544 ibioseq2 = Bioseq( Header2, "CGAAT" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
545 ibioseq3 = Bioseq( Header3, "TGCGAAT" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
546 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
547 iBioseqDB.setData( [ ibioseq1, ibioseq2, ibioseq3 ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
548 expBioseq = ibioseq2 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
549 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
550 obsBioseq = iBioseqDB.getBioseqByRenamedHeader( HeaderRenamed2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
551 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
552 self.assertEquals( expBioseq, obsBioseq ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
553 |
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 def test_init_with_the_parm_name( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
556 iBioseq1 = Bioseq("seq1","ATTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
557 iBioseq2 = Bioseq("seq2","CGAAT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
558 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
559 expBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
560 fastaFilename = "dummyBioseqDB.fa" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
561 f = open(fastaFilename, "w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
562 f.write(">seq1\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
563 f.write("ATTG\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
564 f.write(">seq2\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
565 f.write("CGAAT\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
566 f.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
567 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
568 obsBioseqDB = BioseqDB(fastaFilename) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
569 os.remove(fastaFilename) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
570 self.assertEquals( expBioseqDB, obsBioseqDB ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
571 |
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 def test_countNt(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
574 iBioseq1 = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
575 iBioseq1.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
576 iBioseq1.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
577 iBioseq2 = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
578 iBioseq2.header = "seq2 description2" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
579 iBioseq2.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
580 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
581 iBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
582 expCount = 6 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
583 obsCount = iBioseqDB.countNt('N') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
584 self.assertEquals(expCount, obsCount) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
585 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
586 def test_countNt_lowercase(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
587 iBioseq1 = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
588 iBioseq1.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
589 iBioseq1.sequence = "gcgncgctgctttattaagcgctagcatgcgncgctgctttattaagcgctagcgattatatagcagacgcatattatattgcgcgatgcgncgctgctttattaagcgctagcgattatatagcagacgcatattatattgcgcg" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
590 iBioseq2 = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
591 iBioseq2.header = "seq2 description2" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
592 iBioseq2.sequence = "gcgncgctgctttattaagcgctagcatgcgncgctgctttattaagcgctagcgattatatagcagacgcatattatattgcgcgatgcgncgctgctttattaagcgctagcgattatatagcagacgcatattatattgcgcg" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
593 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
594 iBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
595 expCount = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
596 obsCount = iBioseqDB.countNt('N') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
597 self.assertEquals(expCount, obsCount) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
598 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
599 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
600 def test_countNt_withCharacterNotExisting(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
601 iBioseq1 = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
602 iBioseq1.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
603 iBioseq1.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
604 iBioseq2 = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
605 iBioseq2.header = "seq2 description2" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
606 iBioseq2.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
607 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
608 iBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
609 expCount = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
610 obsCount = iBioseqDB.countNt('W') |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
611 self.assertEquals(expCount, obsCount) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
612 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
613 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
614 def test_countAllNt(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
615 iBioseq1 = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
616 iBioseq1.header = "seq1 description1" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
617 iBioseq1.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
618 iBioseq2 = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
619 iBioseq2.header = "seq2 description2" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
620 iBioseq2.sequence = "GCGNCGCTGCTTTATTAAGCGCTAGCATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCGATGCGNCGCTGCTTTATTAAGCGCTAGCGATTATATAGCAGACGCATATTATATTGCGCG" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
621 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
622 iBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
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 dExpCount = {'A': 68, 'C': 62, 'T': 86, 'G': 70, 'N': 6} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
625 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
626 dObsCount = iBioseqDB.countAllNt() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
627 self.assertEquals(dExpCount, dObsCount) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
628 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
629 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
630 def test_extractPart(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
631 iBioseq1 = Bioseq("consensus1","GAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
632 iBioseq2 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGCGAGACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
633 iBioseq3 = Bioseq("consensus3","GAGATGGCTCATGGAGTACCTGCCTTGCATGACTGCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
634 iBioseq4 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
635 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
636 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
637 iBioseqDB.setData( [ iBioseq1, iBioseq2, iBioseq3, iBioseq4 ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
638 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
639 iBioseq5 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGCGAGACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
640 iBioseq6 = Bioseq("consensus3","GAGATGGCTCATGGAGTACCTGCCTTGCATGACTGCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACCTGCCT") |
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 expSubBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
643 expSubBioseqDB.setData( [ iBioseq5, iBioseq6 ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
644 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
645 obsSubBioseqDB = iBioseqDB.extractPart (1, 2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
646 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
647 self.assertEquals(expSubBioseqDB, obsSubBioseqDB) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
648 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
649 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
650 def test_bestLength(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
651 iBioseq1 = Bioseq("consensus1","GAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
652 iBioseq2 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGCGAGACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
653 iBioseq3 = Bioseq("consensus3","GAGATGGCTCATGGAGTACC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
654 iBioseq4 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
655 iBioseq5 = Bioseq("consensus5","TGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
656 iBioseq6 = Bioseq("consensus6","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
657 iBioseq7 = Bioseq("consensus7","TGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
658 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
659 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
660 iBioseqDB.setData( [ iBioseq1, iBioseq2, iBioseq3, iBioseq4, iBioseq5, iBioseq6 , iBioseq7] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
661 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
662 iBioseq8 = Bioseq("consensus1","GAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
663 iBioseq9 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGCGAGACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
664 iBioseq10 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
665 iBioseq11 = Bioseq("consensus6","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
666 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
667 expBioseqDB.setData( [ iBioseq8, iBioseq9, iBioseq10, iBioseq11] ) |
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 obsBioseqDB = iBioseqDB.bestLength (4) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
670 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
671 self.assertEquals(expBioseqDB, obsBioseqDB) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
672 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
673 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
674 def test_bestLength_with_a_none_sequence_include(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
675 iBioseq1 = Bioseq("consensus1", None) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
676 iBioseq2 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGCGAGACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
677 iBioseq3 = Bioseq("consensus3","GAGATGGCTCATGGAGTACC") |
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 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
680 iBioseqDB.setData( [ iBioseq1, iBioseq2, iBioseq3] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
681 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
682 iBioseq4 = Bioseq("consensus1", None) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
683 iBioseq5 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGCGAGACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
684 iBioseq6 = Bioseq("consensus3","GAGATGGCTCATGGAGTACC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
685 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
686 expBioseqDB.setData( [ iBioseq4, iBioseq5, iBioseq6] ) |
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 obsBioseqDB = iBioseqDB.bestLength (3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
689 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
690 self.assertEquals(expBioseqDB, obsBioseqDB) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
691 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
692 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
693 def test_bestLength_with_a_none_sequence_not_include(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
694 iBioseq1 = Bioseq("consensus1", None) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
695 iBioseq2 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGCGAGACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
696 iBioseq3 = Bioseq("consensus3","GAGATGGCTCATGGAGTACC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
697 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
698 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
699 iBioseqDB.setData( [ iBioseq1, iBioseq2, iBioseq3] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
700 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
701 iBioseq5 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGCGAGACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
702 iBioseq6 = Bioseq("consensus3","GAGATGGCTCATGGAGTACC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
703 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
704 expBioseqDB.setData( [ iBioseq5, iBioseq6] ) |
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 obsBioseqDB = iBioseqDB.bestLength (2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
707 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
708 self.assertEquals(expBioseqDB, obsBioseqDB) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
709 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
710 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
711 def test_bestLength_number_of_bioseq_requiered_gt_BioseqDB_size(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
712 iBioseq1 = Bioseq("consensus1","GAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
713 iBioseq2 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGCGAGACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
714 iBioseq3 = Bioseq("consensus3","GAGATGGCTCATGGAGTACC") |
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 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
717 iBioseqDB.setData( [ iBioseq1, iBioseq2, iBioseq3] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
718 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
719 iBioseq4 = Bioseq("consensus1","GAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
720 iBioseq5 = Bioseq("consensus2","GAGATGGCTCATGGAGTACCGCGAGACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
721 iBioseq6 = Bioseq("consensus3","GAGATGGCTCATGGAGTACC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
722 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
723 expBioseqDB.setData( [ iBioseq4, iBioseq5, iBioseq6] ) |
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 obsBioseqDB = iBioseqDB.bestLength (15) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
726 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
727 self.assertEquals(expBioseqDB, obsBioseqDB) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
728 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
729 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
730 def test_extractPatternOfFile(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
731 fastaFilename = "dummyBioseqDB.fa" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
732 f = open(fastaFilename, "w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
733 f.write(">consensus1\nGAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACC\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
734 f.write(">consensus2\nGAGATGGCTCATGGAGTACCGCGAGACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
735 f.write(">consensus3\nGAGATGGCTCATGGAGTACC\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
736 f.write(">consensus4\nGAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
737 f.write(">consensus11\nTGCCTGAGATGGCTCATGGAGTACCTGCCTTGCCTTGCATGACTGCATGGAGTACCTGCCTGTGCCTGATGGCTCATGGAGTACCTGCCT\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
738 f.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
739 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
740 iBioseq1 = Bioseq("consensus1","GAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
741 iBioseq2 = Bioseq("consensus11","TGCCTGAGATGGCTCATGGAGTACCTGCCTTGCCTTGCATGACTGCATGGAGTACCTGCCTGTGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
742 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
743 expBioseqDB.setData( [ iBioseq1, iBioseq2] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
744 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
745 obsBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
746 obsBioseqDB.extractPatternOfFile("consensus1+" , fastaFilename) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
747 os.remove(fastaFilename) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
748 self.assertEquals(expBioseqDB, obsBioseqDB) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
749 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
750 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
751 def test_extractPatternOfFile_WithNoExistingPattern(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
752 fastaFilename = "dummyBioseqDB.fa" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
753 f = open(fastaFilename, "w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
754 f.write(">consensus1\nGAGATGGCTCATGGAGTACCTGCCTGAGATGGCTCATGGAGTACC\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
755 f.write(">consensus2\nGAGATGGCTCATGGAGTACCGCGAGACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
756 f.write(">consensus3\nGAGATGGCTCATGGAGTACC\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
757 f.write(">consensus4\nGAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
758 f.write(">consensus11\nTGCCTGAGATGGCTCATGGAGTACCTGCCTTGCCTTGCATGACTGCATGGAGTACCTGCCTGTGCCTGATGGCTCATGGAGTACCTGCCT\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
759 f.close() |
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 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
762 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
763 obsBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
764 obsBioseqDB.extractPatternOfFile("NoExistingPattern" , fastaFilename) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
765 os.remove(fastaFilename) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
766 self.assertEquals(expBioseqDB, obsBioseqDB) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
767 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
768 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
769 def test_getByPattern (self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
770 iBioseq1 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
771 iBioseq2 = Bioseq("consensus1","TGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
772 iBioseq3 = Bioseq("consensus6","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
773 iBioseq4 = Bioseq("consensus11","TGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
774 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
775 iBioseqDB.setData( [ iBioseq1, iBioseq2, iBioseq3, iBioseq4] ) |
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 iBioseq5 = Bioseq("consensus1","TGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
778 iBioseq6 = Bioseq("consensus11","TGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
779 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
780 expBioseqDB.setData( [ iBioseq5, iBioseq6] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
781 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
782 obsBioseqDB = iBioseqDB.getByPattern("consensus1+") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
783 self.assertEquals(expBioseqDB, obsBioseqDB) |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
786 def test_getByPattern_with_no_existing_pattern (self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
787 iBioseq1 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
788 iBioseq2 = Bioseq("consensus1","TGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
789 iBioseq3 = Bioseq("consensus6","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
790 iBioseq4 = Bioseq("consensus11","TGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
791 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
792 iBioseqDB.setData( [ iBioseq1, iBioseq2, iBioseq3, iBioseq4] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
793 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
794 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
795 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
796 obsBioseqDB = iBioseqDB.getByPattern("noExistingPattern+") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
797 self.assertEquals(expBioseqDB, obsBioseqDB) |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
800 def test_getDiffFromPattern (self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
801 iBioseq1 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
802 iBioseq2 = Bioseq("consensus1","TGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
803 iBioseq3 = Bioseq("consensus6","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
804 iBioseq4 = Bioseq("consensus11","TGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
805 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
806 iBioseqDB.setData( [ iBioseq1, iBioseq2, iBioseq3, iBioseq4] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
807 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
808 iBioseq5 = Bioseq("consensus1","TGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
809 iBioseq6 = Bioseq("consensus11","TGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
810 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
811 expBioseqDB.setData( [ iBioseq5, iBioseq6] ) |
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 obsBioseqDB = iBioseqDB.getDiffFromPattern("consensus[4|6]") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
814 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
815 self.assertEquals(expBioseqDB, obsBioseqDB) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
816 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
817 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
818 def test_getDiffFromPattern_with_no_existing_pattern (self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
819 iBioseq1 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
820 iBioseq2 = Bioseq("consensus1","TGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
821 iBioseq3 = Bioseq("consensus6","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
822 iBioseq4 = Bioseq("consensus11","TGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
823 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
824 iBioseqDB.setData( [ iBioseq1, iBioseq2, iBioseq3, iBioseq4] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
825 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
826 iBioseq5 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
827 iBioseq6 = Bioseq("consensus1","TGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
828 iBioseq7 = Bioseq("consensus6","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
829 iBioseq8 = Bioseq("consensus11","TGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
830 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
831 expBioseqDB.setData( [ iBioseq5, iBioseq6, iBioseq7, iBioseq8] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
832 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
833 obsBioseqDB = iBioseqDB.getDiffFromPattern("noExistingPattern+") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
834 self.assertEquals(expBioseqDB, obsBioseqDB) |
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_rmByPattern (self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
838 iBioseq1 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
839 iBioseq2 = Bioseq("consensus1","TGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
840 iBioseq3 = Bioseq("consensus6","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
841 iBioseq4 = Bioseq("consensus11","TGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
842 obsBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
843 obsBioseqDB.setData( [ iBioseq1, iBioseq2, iBioseq3, iBioseq4] ) |
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 iBioseq5 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
846 iBioseq6 = Bioseq("consensus6","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
847 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
848 expBioseqDB.setData( [ iBioseq5, iBioseq6 ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
849 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
850 obsBioseqDB.rmByPattern("consensus1+") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
851 self.assertEquals(expBioseqDB, obsBioseqDB) |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
854 def test_rmByPattern_with_no_existing_pattern (self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
855 iBioseq1 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
856 iBioseq2 = Bioseq("consensus1","TGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
857 iBioseq3 = Bioseq("consensus6","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
858 iBioseq4 = Bioseq("consensus11","TGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
859 obsBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
860 obsBioseqDB.setData( [ iBioseq1, iBioseq2, iBioseq3, iBioseq4] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
861 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
862 iBioseq5 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
863 iBioseq6 = Bioseq("consensus1","TGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
864 iBioseq7 = Bioseq("consensus6","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
865 iBioseq8 = Bioseq("consensus11","TGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
866 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
867 expBioseqDB.setData( [ iBioseq5, iBioseq6, iBioseq7, iBioseq8 ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
868 obsBioseqDB.rmByPattern("noExistingPattern+") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
869 self.assertEquals(expBioseqDB, obsBioseqDB) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
870 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
871 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
872 def test_addBioseqFromABioseqDBIfHeaderContainPattern (self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
873 iBioseq1 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
874 iBioseq2 = Bioseq("consensus1","TGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
875 iBioseq3 = Bioseq("consensus7","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
876 iBioseq4 = Bioseq("consensus11","TGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
877 obsBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
878 obsBioseqDB.setData( [ iBioseq1, iBioseq2, iBioseq3, iBioseq4] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
879 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
880 iBioseq5 = Bioseq("Sequence4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
881 iBioseq6 = Bioseq("consensus6","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
882 inBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
883 inBioseqDB.setData( [ iBioseq5, iBioseq6 ]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
884 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
885 iBioseq7 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
886 iBioseq8 = Bioseq("consensus1","TGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
887 iBioseq9 = Bioseq("consensus7","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
888 iBioseq10 = Bioseq("consensus11","TGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
889 iBioseq11 = Bioseq("consensus6","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
890 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
891 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
892 expBioseqDB.setData( [ iBioseq7, iBioseq8, iBioseq9, iBioseq10, iBioseq11] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
893 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
894 obsBioseqDB.addBioseqFromABioseqDBIfHeaderContainPattern("consensus.*", inBioseqDB) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
895 self.assertEquals(expBioseqDB, obsBioseqDB) |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
898 def test_addBioseqFromABioseqDBIfHeaderContainPattern_with_no_existing_pattern (self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
899 iBioseq1 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
900 iBioseq2 = Bioseq("consensus1","TGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
901 iBioseq3 = Bioseq("consensus7","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
902 iBioseq4 = Bioseq("consensus11","TGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
903 obsBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
904 obsBioseqDB.setData( [ iBioseq1, iBioseq2, iBioseq3, iBioseq4] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
905 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
906 iBioseq5 = Bioseq("Sequence4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
907 iBioseq6 = Bioseq("consensus6","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
908 inBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
909 inBioseqDB.setData( [ iBioseq5, iBioseq6 ]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
910 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
911 iBioseq7 = Bioseq("consensus4","GAGATGGCTCATGGAGTACCGCGAGTGCGGTACCTATGGCCCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGCGAGATGGCTCATGGAGTACCGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
912 iBioseq8 = Bioseq("consensus1","TGCCTGAGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
913 iBioseq9 = Bioseq("consensus7","TGCCTTGCATGACTGCATGGAGTACCTGCCTG") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
914 iBioseq10 = Bioseq("consensus11","TGCCTGATGGCTCATGGAGTACCTGCCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
915 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
916 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
917 expBioseqDB.setData( [ iBioseq7, iBioseq8, iBioseq9, iBioseq10] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
918 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
919 obsBioseqDB.addBioseqFromABioseqDBIfHeaderContainPattern("noExistingPattern", inBioseqDB) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
920 self.assertEquals(expBioseqDB, obsBioseqDB) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
921 |
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 def test_upCase (self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
924 iBioseq1 = Bioseq("consensus4","atgacGatgca") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
925 iBioseq2 = Bioseq("consensus1","atgcgaT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
926 obsBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
927 obsBioseqDB.setData( [ iBioseq1, iBioseq2 ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
928 iBioseq3 = Bioseq("consensus4","ATGACGATGCA") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
929 iBioseq4 = Bioseq("consensus1","ATGCGAT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
930 expBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
931 expBioseqDB.setData( [ iBioseq3, iBioseq4 ] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
932 obsBioseqDB.upCase() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
933 self.assertEquals(expBioseqDB, obsBioseqDB) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
934 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
935 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
936 def test_getMap(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
937 iBioseq1 = Bioseq("header1","ATGC-RA-GCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
938 iBioseq2 = Bioseq("header2","-TGC-RA-GCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
939 iBioseq3 = Bioseq("header3","ATGC-RA-GC-") |
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 iAlignedBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
942 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) |
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 obsDict = iAlignedBioseqDB.getDictOfLMapsWithoutGaps() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
945 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
946 expLMap1 = [Map( "header1_subSeq1", "header1", 1, 4 ), Map( "header1_subSeq2", "header1", 6, 7 ), Map( "header1_subSeq3", "header1", 9, 11 )] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
947 expLMap2 = [Map( "header2_subSeq1", "header2", 2, 4 ), Map( "header2_subSeq2", "header2", 6, 7 ), Map( "header2_subSeq3", "header2", 9, 11 )] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
948 expLMap3 = [Map( "header3_subSeq1", "header3", 1, 4 ), Map( "header3_subSeq2", "header3", 6, 7 ), Map( "header3_subSeq3", "header3", 9, 10 )] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
949 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
950 expDict = { |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
951 "header1": expLMap1, |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
952 "header2": expLMap2, |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
953 "header3": expLMap3 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
954 } |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
955 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
956 self.assertEquals(expDict, obsDict) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
957 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
958 def test_getSeqLengthByListOfName(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
959 iBioseq1 = Bioseq("header1","ATGC-RA-GCT") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
960 iBioseq2 = Bioseq("header2","-TGC-RAR") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
961 iBioseq3 = Bioseq("header3","ATGC") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
962 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
963 iBioseqDB = BioseqDB() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
964 iBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
965 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
966 expList = [11, 4] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
967 obsList = iBioseqDB.getSeqLengthByListOfName(["header1", "header3"]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
968 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
969 self.assertEquals( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
970 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
971 test_suite = unittest.TestSuite() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
972 test_suite.addTest( unittest.makeSuite( Test_BioseqDB ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
973 if __name__ == "__main__": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
974 unittest.TextTestRunner(verbosity=2).run( test_suite ) |