Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/sql/test/Test_TableSeqAdaptator.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.sql.DbMySql import DbMySql |
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36 from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator |
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37 from commons.core.seq.Bioseq import Bioseq |
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38 from commons.core.coord.Set import Set |
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39 from commons.core.utils.FileUtils import FileUtils |
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40 |
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41 |
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42 class Test_TableSeqAdaptator( unittest.TestCase ): |
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43 |
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44 def setUp( self ): |
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45 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() ) |
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46 self.fileUtils = FileUtils() |
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47 self._configFileName = "dummyConfigFile_%s" % ( self._uniqId ) |
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48 configF = open(self._configFileName, "w" ) |
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49 configF.write( "[repet_env]\n" ) |
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50 configF.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) ) |
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51 configF.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) ) |
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52 configF.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) ) |
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53 configF.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) ) |
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54 configF.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) ) |
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55 configF.close() |
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56 self._db = DbMySql( cfgFileName=self._configFileName ) |
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57 self._table = "dummySeqTable_%s" % ( self._uniqId ) |
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58 self._tsA = TableSeqAdaptator( self._db, self._table ) |
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59 |
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60 |
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61 def tearDown( self ): |
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62 self._db.dropTable( self._table ) |
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63 self._db.close() |
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64 os.remove( self._configFileName ) |
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65 self._configFileName = "" |
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66 |
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67 |
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68 ################################################################################## |
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69 ################## Tests for methods in ITableSeqAdaptator ####################### |
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70 ################################################################################## |
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71 |
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72 def test_insert( self ): |
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73 bs = Bioseq( "seq1", "AGCGATGACGATGCGAGT" ) |
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74 self._db.createTable( self._table, "fasta" ) |
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75 self._tsA.insert( bs ) |
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76 |
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77 expBioseqTuple = (("seq1", "AGCGATGACGATGCGAGT", "seq1", 18L), ) |
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78 |
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79 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
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80 self._db.execute( sqlCmd ) |
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81 obsBioseqTuple = self._db.cursor.fetchall() |
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82 |
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83 self.assertEqual( expBioseqTuple, obsBioseqTuple ) |
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84 |
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85 |
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86 def test_insertList( self ): |
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87 bs1 = Bioseq( "seq1 desc", "AGCGATGACGATGCGAGT" ) |
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88 bs2 = Bioseq( "seq2", "AGCGATGACGATGCGAGT") |
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89 bs3 = Bioseq( "seq3", "GCGATGCAGATGACGGCGGATGC") |
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90 lBioseq = [ bs1, bs2, bs3 ] |
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91 self._db.createTable( self._table, "fasta" ) |
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92 self._tsA.insertList( lBioseq ) |
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93 |
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94 tuple1 = ("seq1", "AGCGATGACGATGCGAGT", "seq1 desc", 18L) |
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95 tuple2 = ("seq2", "AGCGATGACGATGCGAGT", "seq2", 18L) |
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96 tuple3 = ("seq3", "GCGATGCAGATGACGGCGGATGC", "seq3", 23L) |
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97 expBioseqTuple = ( tuple1, tuple2, tuple3 ) |
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98 |
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99 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
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100 self._db.execute( sqlCmd ) |
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101 obsBioseqTuple = self._db.cursor.fetchall() |
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102 |
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103 self.assertEquals(expBioseqTuple, obsBioseqTuple) |
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104 |
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105 |
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106 def test_getAccessionsList(self): |
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107 faFileName = "dummyFaFile_%s" % ( self._uniqId ) |
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108 faF = open( faFileName, "w" ) |
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109 faF.write(">seq1\n") |
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110 faF.write("AGCGATGACGATGCGAGT\n") |
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111 faF.write(">seq2\n") |
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112 faF.write("GCGATGCAGATGACGGCGGATGC\n") |
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113 faF.close() |
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114 self._db.createTable( self._table, "fasta", faFileName ) |
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115 lExp = [ "seq1", "seq2" ] |
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116 lExp.sort() |
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117 lObs = self._tsA.getAccessionsList() |
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118 lObs.sort() |
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119 self.assertEqual( lObs, lExp ) |
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120 os.remove( faFileName ) |
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121 |
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122 |
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123 def test_saveAccessionsListInFastaFile(self): |
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124 expFileName = "dummyFaFile_%s" % ( self._uniqId ) |
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125 expF = open( expFileName, "w" ) |
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126 expF.write(">seq1\n") |
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127 expF.write("AGCGATGACGATGCGAGT\n") |
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128 expF.write(">seq2\n") |
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129 expF.write("GCGATGCAGATGACGGCGGATGC\n") |
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130 expF.close() |
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131 self._db.createTable( self._table, "fasta", expFileName ) |
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132 lAccessions = [ "seq1", "seq2" ] |
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133 obsFileName = "dummyObsFile_%s" % ( self._uniqId ) |
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134 self._tsA.saveAccessionsListInFastaFile( lAccessions, obsFileName ) |
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135 self.assertTrue( self.fileUtils.are2FilesIdentical( obsFileName, expFileName ) ) |
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136 os.remove( expFileName ) |
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137 os.remove( obsFileName ) |
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138 |
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139 def test_exportInFastaFile(self): |
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140 expFileName = "dummyFaFile_%s" % ( self._uniqId ) |
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141 faF = open( expFileName, "w" ) |
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142 faF.write(">seq1\n") |
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143 faF.write("AGCGATGACGATGCGAGT\n") |
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144 faF.write(">seq2\n") |
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145 faF.write("GCGATGCAGATGACGGCGGATGC\n") |
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146 faF.close() |
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147 self._db.createTable( self._table, "fasta", expFileName ) |
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148 obsFileName = "dummyFaFileObs_%s" % ( self._uniqId ) |
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149 self._tsA.exportInFastaFile( obsFileName ) |
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150 self.assertTrue( self.fileUtils.are2FilesIdentical( obsFileName, expFileName ) ) |
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151 os.remove( expFileName ) |
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152 os.remove( obsFileName ) |
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153 |
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154 ################################################################################## |
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155 ########################### Tests for other methods ############################## |
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156 ################################################################################## |
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157 |
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158 def test_insertWithBioseqEmpty( self ): |
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159 bs = Bioseq( "", "" ) |
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160 self._db.createTable( self._table, "fasta" ) |
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161 exp = None |
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162 obs = self._tsA.insert(bs) |
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163 self.assertEqual( exp, obs ) |
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164 |
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165 |
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166 def test_getBioseqFromHeader( self ): |
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167 faFileName = "dummyFaFile_%s" % ( self._uniqId ) |
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168 faF = open( faFileName, "w" ) |
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169 faF.write(">seq1\n") |
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170 faF.write("AGCGATGACGATGCGAGT\n") |
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171 faF.write(">seq2\n") |
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172 faF.write("GCGATGCAGATGACGGCGGATGC\n") |
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173 faF.close() |
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174 self._db.createTable( self._table, "fasta", faFileName ) |
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175 exp = Bioseq( "seq1", "AGCGATGACGATGCGAGT" ) |
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176 obs = self._tsA.getBioseqFromHeader( "seq1" ) |
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177 self.assertEqual( obs, exp ) |
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178 exp = Bioseq( "seq2", "GCGATGCAGATGACGGCGGATGC" ) |
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179 obs = self._tsA.getBioseqFromHeader( "seq2" ) |
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180 self.assertEqual( obs, exp ) |
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181 os.remove( faFileName ) |
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182 |
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183 |
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184 def test_getSeqLengthFromAccession( self ): |
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185 inFileName = "dummyFaFile_%s" % ( self._uniqId ) |
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186 inF = open( inFileName, "w" ) |
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187 inF.write(">seq1\n") |
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188 inF.write("AGCGATGACGATGCGAGT\n") |
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189 inF.write(">seq2\n") |
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190 inF.write("GCGATGCAGATGACGGCGGATGC\n") |
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191 inF.close() |
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192 self._db.createTable( self._table, "fasta", inFileName ) |
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193 exp = 18 |
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194 obs = self._tsA.getSeqLengthFromAccession( "seq1" ) |
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195 self.assertEqual( obs, exp ) |
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196 os.remove( inFileName ) |
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197 |
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198 |
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199 def test_getSeqLengthFromDescription( self ): |
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200 inFileName = "dummyFaFile_%s" % ( self._uniqId ) |
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201 inF = open( inFileName, "w" ) |
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202 inF.write(">seq1 descriptionfield\n") |
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203 inF.write("AGCGATGACGATGCGAGT\n") |
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204 inF.write(">seq2 descriptionfield\n") |
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205 inF.write("GCGATGCAGATGACGGCGGATGC\n") |
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206 inF.close() |
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207 self._db.createTable( self._table, "fasta", inFileName ) |
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208 exp = 18 |
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209 obs = self._tsA.getSeqLengthFromDescription( "seq1 descriptionfield" ) |
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210 self.assertEqual( obs, exp ) |
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211 os.remove( inFileName ) |
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212 |
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213 |
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214 def test_getAccessionAndLengthList( self ): |
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215 inFileName = "dummyFaFile_%s" % ( self._uniqId ) |
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216 inF = open( inFileName, "w" ) |
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217 inF.write(">seq1\n") |
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218 inF.write("AGCGATGACGATGCGAGT\n") |
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219 inF.write(">seq2\n") |
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220 inF.write("GCGATGCAGATGACGGCGGATGC\n") |
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221 inF.close() |
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222 self._db.createTable( self._table, "fasta", inFileName ) |
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223 lSeq1 = ("seq1", 18) |
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224 lSeq2 = ("seq2", 23) |
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225 lExp = [lSeq1,lSeq2] |
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226 lObs = self._tsA.getAccessionAndLengthList() |
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227 self.assertEqual( lObs, lExp ) |
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228 os.remove( inFileName ) |
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229 |
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230 |
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231 def test_getSeqLengthFromAccessionWithSingleQuote( self ): |
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232 inFileName = "dummyFaFile_%s" % ( self._uniqId ) |
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233 inF = open( inFileName, "w" ) |
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234 inF.write(">seq1'\n") |
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235 inF.write("AGCGATGACGATGCGAGT\n") |
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236 inF.write(">seq2\n") |
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237 inF.write("GCGATGCAGATGACGGCGGATGC\n") |
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238 inF.close() |
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239 self._db.createTable( self._table, "fasta", inFileName ) |
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240 exp = 18 |
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241 obs = self._tsA.getSeqLengthFromAccession( "seq1'" ) |
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242 self.assertEqual( obs, exp ) |
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243 os.remove( inFileName ) |
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244 |
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245 |
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246 def test_getSubSequence_directStrand( self ): |
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247 self._db.createTable( self._table, "seq" ) |
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248 chr = Bioseq() |
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249 chr.setHeader( "chr2" ) |
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250 chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" ) |
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251 self._tsA.insert( chr ) |
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252 exp = "TTTGGG" |
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253 obs = self._tsA.getSubSequence( "chr2", 13, 18 ) |
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254 self.assertEqual( exp, obs ) |
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255 |
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256 |
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257 def test_getSubSequence_reverseStrand( self ): |
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258 self._db.createTable( self._table, "seq" ) |
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259 chr = Bioseq() |
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260 chr.setHeader( "chr2" ) |
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261 chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" ) |
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262 self._tsA.insert( chr ) |
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263 exp = "CCCAAA" |
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264 obs = self._tsA.getSubSequence( "chr2", 18, 13 ) |
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265 self.assertEqual( exp, obs ) |
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266 |
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267 |
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268 def test_getBioseqFromSetList_directStrand( self ): |
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269 self._db.createTable( self._table, "seq" ) |
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270 chr = Bioseq() |
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271 chr.setHeader( "chr2" ) |
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272 chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" ) |
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273 self._tsA.insert( chr ) |
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274 lSets = [] |
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275 lSets.append( Set( 3, "Dm-B-G600-Map3_classI-LTR-incomp", "chr2", 1, 10 ) ) |
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276 lSets.append( Set( 3, "Dm-B-G600-Map3_classI-LTR-incomp", "chr2", 16, 25 ) ) |
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277 exp = Bioseq( "Dm-B-G600-Map3_classI-LTR-incomp::3 chr2 1..10,16..25", "AAAAAAAAAAGGGGGGGGGG" ) |
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278 obs = self._tsA.getBioseqFromSetList( lSets ) |
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279 self.assertEqual( exp, obs ) |
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280 |
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281 |
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282 def test_getBioseqFromSetList_reverseStrand( self ): |
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283 self._db.createTable( self._table, "seq" ) |
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284 chr = Bioseq() |
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285 chr.setHeader( "chr2" ) |
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286 chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" ) |
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287 self._tsA.insert( chr ) |
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288 lSets = [] |
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289 lSets.append( Set( 3, "Dm-B-G600-Map3_classI-LTR-incomp", "chr2", 10, 1 ) ) |
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290 lSets.append( Set( 3, "Dm-B-G600-Map3_classI-LTR-incomp", "chr2", 25, 16 ) ) |
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291 exp = Bioseq( "Dm-B-G600-Map3_classI-LTR-incomp::3 chr2 25..16,10..1", "CCCCCCCCCCTTTTTTTTTT" ) |
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292 obs = self._tsA.getBioseqFromSetList( lSets ) |
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293 self.assertEqual( exp, obs ) |
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294 |
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295 |
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296 def test_isAccessionInTable_true( self ): |
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297 self._db.createTable( self._table, "seq" ) |
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298 chr = Bioseq() |
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299 chr.setHeader( "chr2" ) |
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300 chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" ) |
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301 self._tsA.insert( chr ) |
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302 |
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303 obs = self._tsA.isAccessionInTable( "chr2" ) |
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304 self.assertTrue( obs ) |
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305 |
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306 |
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307 def test_isAccessionInTable_false( self ): |
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308 self._db.createTable( self._table, "seq" ) |
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309 chr = Bioseq() |
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310 chr.setHeader( "chr2" ) |
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311 chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" ) |
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312 self._tsA.insert( chr ) |
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313 |
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314 obs = self._tsA.isAccessionInTable( "chr1" ) |
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315 self.assertFalse( obs ) |
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316 |
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317 |
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318 test_suite = unittest.TestSuite() |
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319 test_suite.addTest( unittest.makeSuite( Test_TableSeqAdaptator ) ) |
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320 if __name__ == "__main__": |
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321 unittest.TextTestRunner(verbosity=2).run( test_suite ) |