Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/sql/test/Test_TablePathAdaptator.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.TablePathAdaptator import TablePathAdaptator |
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36 from commons.core.coord.Path import Path |
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37 from commons.core.coord.Set import Set |
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38 from commons.core.sql.DbMySql import DbMySql |
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39 from commons.core.coord.Range import Range |
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40 from commons.core.coord.PathUtils import PathUtils |
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41 from copy import deepcopy |
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42 |
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43 class Test_TablePathAdaptator( unittest.TestCase ): |
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44 |
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45 def setUp( self ): |
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46 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() ) |
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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 = "dummyPathTable_%s" % ( self._uniqId ) |
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58 self._tpA = TablePathAdaptator( 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._uniqId = None |
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63 self._db.dropTable( self._table ) |
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64 self._db.close() |
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65 self._table = None |
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66 self._tMatchA = None |
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67 os.remove( self._configFileName ) |
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68 self._configFileName = "" |
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69 |
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70 |
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71 ################################################################################## |
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72 ################## Tests for methods in ITableMapAdaptator ####################### |
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73 ################################################################################## |
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74 |
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75 def test_getPathListFromId( self ): |
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76 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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77 pathF = open( pathFileName, "w" ) |
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78 pathF.write( "1\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" ) |
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79 pathF.write( "2\tchr1\t1001\t1006\tTE2\t11\t16\t1e-20\t30\t90.2\n" ) |
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80 pathF.write( "2\tchr1\t1201\t1226\tTE2\t10\t26\t1e-40\t70\t87.2\n" ) |
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81 pathF.close() |
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82 p1 = Path() |
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83 p1.setFromString( "2\tchr1\t1001\t1006\tTE2\t11\t16\t1e-20\t30\t90.2\n" ) |
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84 p2 = Path() |
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85 p2.setFromString( "2\tchr1\t1201\t1226\tTE2\t10\t26\t1e-40\t70\t87.2\n" ) |
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86 lExp = [ p1, p2 ] |
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87 self._db.createTable( self._table, "path", pathFileName ) |
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88 lObs = self._tpA.getPathListFromId( 2 ) |
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89 self.assertEqual( lObs, lExp ) |
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90 os.remove( pathFileName ) |
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91 |
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92 |
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93 def test_getPathListFromIdList_empty_id_list( self ): |
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94 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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95 pathF = open( pathFileName, "w" ) |
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96 pathF.write("1\tchr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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97 pathF.write("2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.2\n") |
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98 pathF.write("3\tchr1\t8\t13\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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99 pathF.close() |
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100 self._db.createTable( self._table, "path", pathFileName ) |
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101 |
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102 expList = [] |
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103 obsList = self._tpA.getPathListFromIdList([]) |
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104 self.assertEquals(expList, obsList) |
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105 |
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106 os.remove( pathFileName ) |
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107 |
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108 |
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109 def test_getPathListFromIdList( self ): |
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110 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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111 pathF = open( pathFileName, "w" ) |
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112 pathF.write("1\tchr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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113 pathF.write("2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.2\n") |
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114 pathF.write("3\tchr1\t8\t13\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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115 pathF.close() |
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116 |
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117 tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") |
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118 p1 = Path() |
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119 p1.setFromTuple(tuple) |
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120 |
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121 tuple = ("2", "chr1","2", "9","TE2","10","13","1e-20","30","90.2") |
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122 p2 = Path() |
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123 p2.setFromTuple(tuple) |
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124 |
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125 tuple = ("3", "chr1","8", "13","TE2","11","17","1e-20","30","90.2") |
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126 p3 = Path() |
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127 p3.setFromTuple(tuple) |
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128 |
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129 self._db.createTable( self._table, "path", pathFileName ) |
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130 lObs = self._tpA.getPathListFromIdList((1, 2, 3)) |
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131 self.assertEquals(3, len(lObs)) |
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132 |
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133 lExp = [p1, p2, p3] |
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134 self.assertEquals(lExp, lObs) |
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135 |
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136 os.remove( pathFileName ) |
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137 |
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138 |
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139 def test_getPathListFromQuery( self ): |
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140 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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141 pathF = open( pathFileName, "w" ) |
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142 pathF.write("1\tchr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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143 pathF.write("2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.2\n") |
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144 pathF.write("3\tchr2\t8\t13\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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145 pathF.close() |
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146 self._db.createTable( self._table, "path", pathFileName ) |
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147 path1 = Path() |
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148 path1.setFromString("1\tchr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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149 path2 = Path() |
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150 path2.setFromString("2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.2\n") |
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151 expList = [ path1, path2 ] |
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152 obsList = self._tpA.getPathListFromQuery("chr1") |
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153 self.assertEquals( expList, obsList ) |
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154 |
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155 os.remove( pathFileName ) |
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156 |
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157 |
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158 def test_getPathListFromQuery_unexisted_query( self ): |
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159 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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160 pathF = open( pathFileName, "w" ) |
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161 pathF.write("1\tchr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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162 pathF.write("2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.2\n") |
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163 pathF.write("3\tchr2\t8\t13\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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164 pathF.close() |
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165 self._db.createTable( self._table, "path", pathFileName ) |
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166 expList = [] |
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167 obsList = self._tpA.getPathListFromQuery("dummy") |
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168 self.assertEquals( expList, obsList ) |
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169 |
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170 os.remove( pathFileName ) |
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171 |
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172 |
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173 def test_getPathListFromSubject( self ): |
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174 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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175 pathF = open( pathFileName, "w" ) |
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176 pathF.write("1\tchr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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177 pathF.write("2\tchr1\t2\t9\tTE3\t10\t13\t1e-20\t30\t90.2\n") |
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178 pathF.write("3\tchr2\t8\t13\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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179 pathF.close() |
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180 self._db.createTable( self._table, "path", pathFileName ) |
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181 path1 = Path() |
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182 path1.setFromString("1\tchr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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183 path3 = Path() |
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184 path3.setFromString("3\tchr2\t8\t13\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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185 expList = [ path1, path3 ] |
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186 obsList = self._tpA.getPathListFromSubject("TE2") |
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187 self.assertEquals( expList, obsList ) |
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188 |
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189 os.remove( pathFileName ) |
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190 |
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191 |
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192 def test_getPathListFromSubject_unexisted_subject( self ): |
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193 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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194 pathF = open( pathFileName, "w" ) |
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195 pathF.write("1\tchr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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196 pathF.write("2\tchr1\t2\t9\tTE3\t10\t13\t1e-20\t30\t90.2\n") |
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197 pathF.write("3\tchr2\t8\t13\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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198 pathF.close() |
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199 self._db.createTable( self._table, "path", pathFileName ) |
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200 expList = [] |
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201 obsList = self._tpA.getPathListFromSubject("dummy") |
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202 self.assertEquals( expList, obsList ) |
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203 |
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204 os.remove( pathFileName ) |
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205 |
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206 |
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207 def test_insert_QryDirSbjDir( self ): |
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208 path2Insert = Path() |
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209 |
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210 rangeQuery2Insert = Range() |
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211 rangeQuery2Insert.seqname = "chr1" |
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212 rangeQuery2Insert.start = 1 |
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213 rangeQuery2Insert.end = 10 |
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214 |
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215 rangeSubject2Insert = Range() |
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216 rangeSubject2Insert.seqname = "TE2" |
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217 rangeSubject2Insert.start = 11 |
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218 rangeSubject2Insert.end = 17 |
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219 |
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220 path2Insert.range_query = rangeQuery2Insert |
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221 path2Insert.range_subject = rangeSubject2Insert |
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222 |
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223 path2Insert.identity = 90.2 |
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224 path2Insert.score = 30 |
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225 path2Insert.e_value = 1e-20 |
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226 path2Insert.id = 1 |
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227 |
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228 self._db.createTable( self._table, "path" ) |
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229 self._tpA.insert( path2Insert ) |
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230 |
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231 expPathTuple = ((1L, "chr1", 1L, 10L, "TE2", 11L, 17L, 1e-20, 30L, 90.2),) |
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232 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
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233 self._db.execute( sqlCmd ) |
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234 obsPathTuple = self._db.cursor.fetchall() |
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235 |
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236 self.assertEquals(expPathTuple, obsPathTuple) |
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237 |
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238 |
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239 def test_insert_BigEvalue( self ): |
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240 path2Insert = Path() |
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241 |
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242 rangeQuery2Insert = Range() |
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243 rangeQuery2Insert.seqname = "chr1" |
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244 rangeQuery2Insert.start = 1 |
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245 rangeQuery2Insert.end = 10 |
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246 |
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247 rangeSubject2Insert = Range() |
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248 rangeSubject2Insert.seqname = "TE2" |
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249 rangeSubject2Insert.start = 11 |
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250 rangeSubject2Insert.end = 17 |
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251 |
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252 path2Insert.range_query = rangeQuery2Insert |
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253 path2Insert.range_subject = rangeSubject2Insert |
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254 |
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255 path2Insert.identity = 90.2 |
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256 path2Insert.score = 30.0 |
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257 path2Insert.e_value = 1e-300 |
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258 path2Insert.id = 1 |
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259 |
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260 self._db.createTable( self._table, "path" ) |
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261 self._tpA.insert( path2Insert ) |
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262 |
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263 expPathTuple = ((1L, "chr1", 1L, 10L, "TE2", 11L, 17L, 1e-300, 30L, 90.2),) |
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264 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
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265 self._db.execute( sqlCmd ) |
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266 obsPathTuple = self._db.cursor.fetchall() |
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267 |
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268 self.assertEquals(expPathTuple, obsPathTuple) |
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269 |
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270 |
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271 def test_insert_QryRevSbjDir( self ): |
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272 path2Insert = Path() |
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273 |
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274 rangeQuery2Insert = Range() |
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275 rangeQuery2Insert.seqname = "chr1" |
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276 rangeQuery2Insert.start = 10 |
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277 rangeQuery2Insert.end = 1 |
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278 |
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279 rangeSubject2Insert = Range() |
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280 rangeSubject2Insert.seqname = "TE2" |
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281 rangeSubject2Insert.start = 11 |
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282 rangeSubject2Insert.end = 17 |
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283 |
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284 path2Insert.range_query = rangeQuery2Insert |
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285 path2Insert.range_subject = rangeSubject2Insert |
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286 |
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287 path2Insert.identity = 90.2 |
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288 path2Insert.score = 30 |
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289 path2Insert.e_value = 1e-216 |
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290 path2Insert.id = 1 |
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291 |
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292 self._db.createTable( self._table, "path" ) |
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293 self._tpA.insert( path2Insert ) |
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294 |
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295 expPathTuple = ((1L, "chr1", 1L, 10L, "TE2", 17L, 11L, 1e-216, 30L, 90.2),) |
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296 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
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297 self._db.execute( sqlCmd ) |
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298 obsPathTuple = self._db.cursor.fetchall() |
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299 |
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300 self.assertEquals(expPathTuple, obsPathTuple) |
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301 |
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302 |
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303 def test_insertList(self): |
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304 p1 = Path() |
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305 p1.setFromString( "1\tchr1\t1\t10\tTE1\t11\t17\t1e-20\t30\t90.2\n" ) |
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306 p2 = Path() |
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307 p2.setFromString( "2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.2\n" ) |
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308 p3 = Path() |
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309 p3.setFromString( "2\tchr1\t12\t19\tTE2\t15\t22\t1e-10\t40\t94.2\n" ) |
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310 p4 = Path() |
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311 p4.setFromString( "3\tchr2\t8\t13\tTE1\t11\t17\t1e-20\t30\t90.2\n" ) |
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312 lPath = [ p1, p2, p3, p4] |
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313 self._db.createTable( self._table, "path" ) |
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314 self._tpA.insertList(lPath) |
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315 |
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316 tuple1 = (1L, "chr1", 1L, 10L, "TE1", 11L, 17L, 1e-20, 30L, 90.2) |
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317 tuple2 = (2L, "chr1", 2L, 9L, "TE2", 10L, 13L, 1e-20, 30L, 90.2) |
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318 tuple3 = (2L, "chr1", 12L, 19L, "TE2", 15L, 22L, 1e-10, 40L, 94.2) |
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319 tuple4 = (3L, "chr2", 8L, 13L, "TE1", 11L, 17L, 1e-20, 30L, 90.2) |
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320 expPathTuple = ( tuple1, tuple2, tuple3, tuple4) |
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321 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
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322 self._db.execute( sqlCmd ) |
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323 obsPathTuple = self._db.cursor.fetchall() |
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324 |
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325 self.assertEquals(expPathTuple, obsPathTuple) |
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326 |
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327 |
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328 def test_getIdListFromQuery( self ): |
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329 self._db.createTable( self._table, "path" ) |
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330 p1 = Path() |
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331 p1.setFromString( "1\tchr1\t1\t10\tTE1\t11\t17\t1e-20\t30\t90.2\n" ) |
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332 p2a = Path() |
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333 p2a.setFromString( "2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.2\n" ) |
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334 p2b = Path() |
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335 p2b.setFromString( "2\tchr1\t12\t19\tTE2\t15\t22\t1e-10\t40\t94.2\n" ) |
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336 p3 = Path() |
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337 p3.setFromString( "3\tchr2\t8\t13\tTE1\t11\t17\t1e-20\t30\t90.2\n" ) |
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338 for p in [ p1, p2a, p2b, p3 ]: self._tpA.insert( p ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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339 lExp = [ 1, 2 ] |
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340 lObs = self._tpA.getIdListFromQuery( "chr1" ) |
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341 self.assertEqual( lObs, lExp ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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342 |
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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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344 def test_getIdListFromSubject( self ): |
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345 self._db.createTable( self._table, "path" ) |
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346 p1 = Path() |
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347 p1.setFromString( "1\tchr1\t1\t10\tTE1\t11\t17\t1e-20\t30\t90.2\n" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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348 p2a = Path() |
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349 p2a.setFromString( "2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.2\n" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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350 p2b = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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351 p2b.setFromString( "2\tchr1\t12\t19\tTE2\t15\t22\t1e-10\t40\t94.2\n" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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352 p3 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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353 p3.setFromString( "3\tchr2\t8\t13\tTE1\t11\t17\t1e-20\t30\t90.2\n" ) |
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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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354 for p in [ p1, p2a, p2b, p3 ]: self._tpA.insert( p ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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355 lExp = [ 2 ] |
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356 lObs = self._tpA.getIdListFromSubject( "TE2" ) |
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357 self.assertEqual( lObs, lExp ) |
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358 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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359 |
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360 def test_getIdList( self ): |
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361 self._db.createTable( self._table, "path" ) |
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362 p1 = Path() |
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363 p1.setFromString( "1\tchr1\t1\t10\tTE1\t11\t17\t1e-20\t30\t90.2\n" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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364 p2 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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365 p2.setFromString( "2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.2\n" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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366 p3 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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367 p3.setFromString( "2\tchr1\t12\t19\tTE2\t15\t22\t1e-10\t40\t94.2\n" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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368 p4 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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369 p4.setFromString( "3\tchr2\t8\t13\tTE1\t11\t17\t1e-20\t30\t90.2\n" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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370 lPath = [ p1, p2, p3, p4] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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371 self._tpA.insertList(lPath) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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372 expList = [ 1, 2, 3 ] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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373 obsList = self._tpA.getIdList() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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374 self.assertEqual( expList, obsList ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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375 |
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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 def test_getSubjectList( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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378 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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379 pathF = open( pathFileName, "w" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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380 pathF.write("1\tchr1\t1\t10\tTE3\t11\t17\t1e-20\t30\t90.2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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381 pathF.write("2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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382 pathF.write("2\tchr1\t12\t19\tTE2\t15\t22\t1e-10\t40\t94.2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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383 pathF.write("3\tchr2\t8\t13\tTE1\t11\t17\t1e-20\t30\t90.2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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384 pathF.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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385 self._db.createTable( self._table, "path", pathFileName ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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386 expList = [ "TE1", "TE2", "TE3" ] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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387 obsList = self._tpA.getSubjectList() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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388 self.assertEqual( expList, obsList ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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389 os.remove( pathFileName ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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390 |
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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 def test_getSubjectList_empty_table( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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393 self._db.createTable( self._table, "path" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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394 expList = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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395 obsList = self._tpA.getSubjectList() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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396 self.assertEqual( obsList, expList ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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397 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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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_getQueryList( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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400 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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401 pathF = open( pathFileName, "w" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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402 pathF.write("1\tchr1\t1\t10\tTE3\t11\t17\t1e-20\t30\t90.2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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403 pathF.write("2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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404 pathF.write("2\tchr1\t12\t19\tTE2\t15\t22\t1e-10\t40\t94.2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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405 pathF.write("3\tchr2\t8\t13\tTE1\t11\t17\t1e-20\t30\t90.2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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406 pathF.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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407 self._db.createTable( self._table, "path", pathFileName ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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408 expList = [ "chr1", "chr2" ] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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409 obsList = self._tpA.getQueryList() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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410 self.assertEqual( expList, obsList ) |
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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 os.remove( pathFileName ) |
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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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413 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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414 def test_getSubjectListFromQuery( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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415 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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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 pathF = open( pathFileName, "w" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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417 pathF.write("1\tchr1\t1\t10\tTE3\t11\t17\t1e-20\t30\t90.2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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418 pathF.write("2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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419 pathF.write("2\tchr1\t12\t19\tTE2\t15\t22\t1e-10\t40\t94.2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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420 pathF.write("3\tchr2\t8\t13\tTE1\t11\t17\t1e-20\t30\t90.2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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421 pathF.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
422 self._db.createTable( self._table, "path", pathFileName ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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423 expList = [ "TE3", "TE2" ] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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424 obsList = self._tpA.getSubjectListFromQuery( "chr1" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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425 self.assertEqual( expList, obsList ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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426 os.remove( pathFileName ) |
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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 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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429 def test_getSubjectListFromQuery_with_unexisted_query( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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430 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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431 pathF = open( pathFileName, "w" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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432 pathF.write("1\tchr1\t1\t10\tTE3\t11\t17\t1e-20\t30\t90.2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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433 pathF.write("2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
434 pathF.write("2\tchr1\t12\t19\tTE2\t15\t22\t1e-10\t40\t94.2\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
435 pathF.write("3\tchr2\t8\t13\tTE1\t11\t17\t1e-20\t30\t90.2\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
436 pathF.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
437 self._db.createTable( self._table, "path", pathFileName ) |
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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 expList = [] |
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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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|
439 obsList = self._tpA.getSubjectListFromQuery( "chr3" ) |
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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 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
441 os.remove( pathFileName ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
442 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
443 |
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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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444 def test_getListOfAllPaths( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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445 self._db.createTable( self._table, "path" ) |
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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 p1 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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447 p1.setFromString( "1\tchr1\t1\t10\tTE3\t11\t17\t1e-20\t30\t85.2\n" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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448 p2a = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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449 p2a.setFromString( "2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.5\n" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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450 p2b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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451 p2b.setFromString( "2\tchr1\t12\t19\tTE2\t15\t22\t1e-10\t40\t89.5\n" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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452 lPaths = [ p1, p2a, p2b ] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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453 self._tpA.insertList( lPaths ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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454 expList = [ p1, p2a, p2b ] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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455 obsList = self._tpA.getListOfAllPaths() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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456 self.assertEqual( expList, obsList ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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457 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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458 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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459 def test_getListOfAllPaths_empty_table( 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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460 self._db.createTable( self._table, "path" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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461 expList = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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462 obsList = self._tpA.getListOfAllPaths() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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463 self.assertEqual( expList, obsList ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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464 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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465 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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466 def test_getPathListWithDirectQueryDirectSubjectFromQuerySubject( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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467 self._db.createTable( self._table, "path" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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468 p1 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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469 p1.setFromString( "1\tchr1\t1\t100\tTE1\t11\t110\t1e-20\t130\t85.2\n" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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470 p2 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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471 p2.setFromString( "2\tchr2\t1\t100\tTE1\t11\t110\t1e-20\t130\t85.2\n" ) # different query |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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472 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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473 p3.setFromString( "3\tchr1\t1\t100\tTE2\t11\t110\t1e-20\t130\t85.2\n" ) # different subject |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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474 p4 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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475 p4.setFromString( "4\tchr1\t100\t1\tTE1\t11\t110\t1e-20\t130\t85.2\n" ) # query on reverse strand |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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476 p5 = Path() |
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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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477 p5.setFromString( "5\tchr1\t1\t100\tTE1\t110\t11\t1e-20\t130\t85.2\n" ) # subject on reverse strand |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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478 p6 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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479 p6.setFromString( "6\tchr1\t301\t400\tTE1\t11\t110\t1e-20\t130\t85.2\n" ) # further along the query |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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480 for p in [ p1, p2, p3, p4, p5, p6 ]: self._tpA.insert( p ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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481 expList = [ p1, p6 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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482 obsList = self._tpA.getPathListWithDirectQueryDirectSubjectFromQuerySubject( "chr1", "TE1" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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483 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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484 |
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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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485 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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486 def test_getPathListWithDirectQueryReverseSubjectFromQuerySubject( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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487 self._db.createTable( self._table, "path" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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488 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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489 p1.setFromString( "1\tchr1\t1\t100\tTE1\t110\t11\t1e-20\t130\t85.2\n" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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490 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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491 p2.setFromString( "2\tchr2\t1\t100\tTE1\t110\t11\t1e-20\t130\t85.2\n" ) # different query |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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492 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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493 p3.setFromString( "3\tchr1\t1\t100\tTE2\t110\t11\t1e-20\t130\t85.2\n" ) # different subject |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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494 p4 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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495 p4.setFromString( "4\tchr1\t100\t1\tTE1\t110\t11\t1e-20\t130\t85.2\n" ) # query on reverse strand |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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496 p5 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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497 p5.setFromString( "5\tchr1\t1\t100\tTE1\t11\t110\t1e-20\t130\t85.2\n" ) # subject on direct strand |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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498 p6 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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499 p6.setFromString( "6\tchr1\t301\t400\tTE1\t110\t11\t1e-20\t130\t85.2\n" ) # further along the query |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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500 for p in [ p1, p2, p3, p4, p5, p6 ]: self._tpA.insert( p ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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501 lExp = [ p1, p6 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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502 lObs = self._tpA.getPathListWithDirectQueryReverseSubjectFromQuerySubject( "chr1", "TE1" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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503 self.assertEqual( lObs, lExp ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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504 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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505 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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506 def test_isEmpty( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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507 self._db.createTable( self._table, "path" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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508 obs = self._tpA.isEmpty() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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509 self.assertTrue( obs ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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510 p = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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511 p.setFromTuple( ( "1", "qry1", "1", "100", "sbj1", "1", "100", "1e-32", "164", "97.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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512 self._tpA.insert( p ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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513 obs = self._tpA.isEmpty() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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514 self.assertFalse( obs ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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515 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
516 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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517 def test_getNbPathsFromQuery( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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518 self._db.createTable( self._table, "path" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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519 p1a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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520 p1a.setFromTuple( ( "1", "qry1", "1", "100", "sbj1", "1", "100", "1e-32", "164", "97.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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521 p1b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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522 p1b.setFromTuple( ( "1", "qry1", "111", "200", "sbj1", "101", "190", "1e-32", "164", "97.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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523 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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524 p2.setFromTuple( ( "2", "qry1", "2001", "2200", "sbj3", "1", "200", "1e-76", "247", "96.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
525 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
526 p3.setFromTuple( ( "3", "qry2", "1", "350", "sbj1", "1", "350", "1e-43", "624", "98.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
527 lPaths = [ p1a, p1b, p2, p3 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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528 self._tpA.insertList( lPaths ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
529 expNb = 3 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
530 obsNb = self._tpA.getNbPathsFromQuery( "qry1" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
531 self.assertEqual( expNb, obsNb ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
532 |
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 def test_getNbPathsFromQuery_unexisted_query( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
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535 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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536 p1a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
537 p1a.setFromTuple( ( "1", "qry1", "1", "100", "sbj1", "1", "100", "1e-32", "164", "97.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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538 p1b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
539 p1b.setFromTuple( ( "1", "qry1", "111", "200", "sbj1", "101", "190", "1e-32", "164", "97.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
540 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
541 p2.setFromTuple( ( "2", "qry1", "2001", "2200", "sbj3", "1", "200", "1e-76", "247", "96.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
542 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
543 p3.setFromTuple( ( "3", "qry2", "1", "350", "sbj1", "1", "350", "1e-43", "624", "98.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
544 lPaths = [ p1a, p1b, p2, p3 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
545 self._tpA.insertList( lPaths ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
546 expNb = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
547 obsNb = self._tpA.getNbPathsFromQuery( "qry3" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
548 self.assertEqual( expNb, obsNb ) |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
551 def test_getNbPathsFromSubject( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
552 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
553 p1a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
554 p1a.setFromTuple( ( "1", "qry1", "1", "100", "sbj1", "1", "100", "1e-32", "164", "97.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
555 p1b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
556 p1b.setFromTuple( ( "1", "qry1", "111", "200", "sbj1", "101", "190", "1e-32", "164", "97.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
557 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
558 p2.setFromTuple( ( "2", "qry1", "2001", "2200", "sbj3", "1", "200", "1e-76", "247", "96.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
559 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
560 p3.setFromTuple( ( "3", "qry2", "1", "350", "sbj1", "1", "350", "1e-43", "624", "98.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
561 lPaths = [ p1a, p1b, p2, p3 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
562 self._tpA.insertList( lPaths ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
563 expNb = 3 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
564 obsNb = self._tpA.getNbPathsFromSubject( "sbj1" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
565 self.assertEqual( expNb, obsNb ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
566 |
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 def test_getNbPathsFromSubject_unexisted_subject( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
569 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
570 p1a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
571 p1a.setFromTuple( ( "1", "qry1", "1", "100", "sbj1", "1", "100", "1e-32", "164", "97.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
572 p1b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
573 p1b.setFromTuple( ( "1", "qry1", "111", "200", "sbj1", "101", "190", "1e-32", "164", "97.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
574 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
575 p2.setFromTuple( ( "2", "qry1", "2001", "2200", "sbj3", "1", "200", "1e-76", "247", "96.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
576 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
577 p3.setFromTuple( ( "3", "qry2", "1", "350", "sbj1", "1", "350", "1e-43", "624", "98.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
578 lPaths = [ p1a, p1b, p2, p3 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
579 self._tpA.insertList( lPaths ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
580 expNb = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
581 obsNb = self._tpA.getNbPathsFromSubject( "qry1" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
582 self.assertEqual( expNb, obsNb ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
583 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
584 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
585 def test_getNbIds( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
586 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
587 p1a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
588 p1a.setFromTuple( ( "1", "qry1", "1", "100", "sbj1", "1", "100", "1e-32", "164", "97.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
589 p1b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
590 p1b.setFromTuple( ( "1", "qry1", "111", "200", "sbj1", "101", "190", "1e-32", "164", "97.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
591 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
592 p2.setFromTuple( ( "2", "qry1", "2001", "2200", "sbj3", "1", "200", "1e-76", "247", "96.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
593 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
594 p3.setFromTuple( ( "3", "qry2", "1", "350", "sbj1", "1", "350", "1e-43", "624", "98.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
595 for p in [ p1a, p1b, p2, p3 ]: self._tpA.insert( p ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
596 exp = 3 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
597 obs = self._tpA.getNbIds() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
598 self.assertEqual( obs, exp ) |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
601 def test_getNbIdsFromSubject( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
602 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
603 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
604 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
605 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
606 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
607 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj1", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
608 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
609 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
610 expNb = 2 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
611 obsNb = self._tpA.getNbIdsFromSubject( "sbj1" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
612 self.assertEqual( expNb, obsNb ) |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
615 def test_getNbIdsFromSubject_unexisted_subject( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
616 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
617 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
618 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
619 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
620 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
621 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj1", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
622 self._tpA.insert( p2 ) |
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 expNb = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
625 obsNb = self._tpA.getNbIdsFromSubject( "sbj2" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
626 self.assertEqual( expNb, obsNb ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
627 |
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 def test_getNbIdsFromQuery( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
630 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
631 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
632 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
633 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
634 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
635 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj2", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
636 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
637 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
638 expNb = 2 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
639 obsNb = self._tpA.getNbIdsFromQuery( "qry1" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
640 self.assertEqual( expNb, obsNb ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
641 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
642 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
643 def test_getNbIdsFromQuery_unexisted_query( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
644 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
645 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
646 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
647 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
648 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
649 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj2", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
650 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
651 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
652 expNb = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
653 obsNb = self._tpA.getNbIdsFromQuery( "qry2" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
654 self.assertEqual( expNb, obsNb ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
655 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
656 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
657 def test_getPathListIncludedInQueryCoord_included( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
658 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
659 p = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
660 p.setFromTuple( ( "1", "qry1", "123", "184", "sbj1", "1", "63", "0.0", "75", "97.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
661 self._tpA.insert( p ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
662 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
663 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj2", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
664 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
665 expList = [ p ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
666 obsList = self._tpA.getPathListIncludedInQueryCoord( "qry1", 100, 200 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
667 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
668 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
669 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
670 def test_getPathListIncludedInQueryCoord_included_start_higher_than_end( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
671 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
672 p = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
673 p.setFromTuple( ( "1", "qry1", "123", "184", "sbj1", "1", "63", "0.0", "75", "97.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
674 self._tpA.insert( p ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
675 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
676 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj2", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
677 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
678 expList = [ p ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
679 obsList = self._tpA.getPathListIncludedInQueryCoord( "qry1", 200, 100 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
680 self.assertEqual( expList, obsList ) |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
683 def test_getPathListIncludedInQueryCoord_overlapping( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
684 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
685 p = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
686 p.setFromTuple( ( "1", "qry1", "83", "184", "sbj1", "1", "103", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
687 self._tpA.insert( p ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
688 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
689 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj2", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
690 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
691 expList = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
692 obsList = self._tpA.getPathListIncludedInQueryCoord( "qry1", 100, 200 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
693 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
694 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
695 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
696 def test_getPathListOverlappingQueryCoord(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
697 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
698 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
699 p1.setFromTuple( ( "1", "qry1", "83", "184", "sbj1", "1", "103", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
700 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
701 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj2", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
702 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
703 p3.setFromTuple( ( "3", "qry1", "1", "350", "sbj1", "1", "350", "1e-43", "624", "98.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
704 lPath = [ p1, p2, p3 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
705 self._tpA.insertList(lPath) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
706 expList = [ p1, p3 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
707 obsList = self._tpA.getPathListOverlappingQueryCoord( "qry1", 100, 200 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
708 self.assertEqual( expList, obsList ) |
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_getPathListOverlappingQueryCoord_no_overlapping_and_start_higher_than_end(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
712 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
713 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
714 p1.setFromTuple( ( "1", "qry1", "83", "184", "sbj1", "1", "103", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
715 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
716 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj2", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
717 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
718 p3.setFromTuple( ( "3", "qry2", "1", "350", "sbj1", "1", "350", "1e-43", "624", "98.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
719 lPath = [ p1, p2, p3 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
720 self._tpA.insertList(lPath) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
721 expList = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
722 obsList = self._tpA.getPathListOverlappingQueryCoord( "qry1", 80, 1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
723 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
724 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
725 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
726 def test_getPathListOverlappingQueryCoord_withChains(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
727 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
728 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
729 p1.setFromTuple( ( "1", "qry1", "83", "184", "sbj1", "1", "103", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
730 p2a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
731 p2a.setFromTuple( ( "2", "qry1", "1", "150", "sbj2", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
732 p2b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
733 p2b.setFromTuple( ( "2", "qry1", "251", "350", "sbj1", "151", "250", "1e-43", "624", "98.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
734 lPath = [ p1, p2a, p2b ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
735 self._tpA.insertList(lPath) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
736 expList = [ p1, p2a ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
737 obsList = self._tpA.getPathListOverlappingQueryCoord( "qry1", 100, 200 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
738 self.assertEqual( expList, obsList ) |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
741 def test_getChainListOverlappingQueryCoord(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
742 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
743 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
744 p1.setFromTuple( ( "1", "qry1", "83", "184", "sbj1", "1", "103", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
745 p2a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
746 p2a.setFromTuple( ( "2", "qry1", "1", "150", "sbj2", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
747 p2b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
748 p2b.setFromTuple( ( "2", "qry1", "251", "350", "sbj1", "151", "250", "1e-43", "624", "98.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
749 lPath = [ p1, p2a, p2b ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
750 self._tpA.insertList(lPath) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
751 expList = [ p1, p2a, p2b ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
752 obsList = self._tpA.getChainListOverlappingQueryCoord( "qry1", 100, 200 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
753 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
754 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
755 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
756 def test_getSetListOverlappingQueryCoord(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
757 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
758 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
759 p1.setFromTuple( ( "1", "qry1", "83", "184", "sbj1", "1", "103", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
760 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
761 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj2", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
762 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
763 p3.setFromTuple( ( "3", "qry1", "1", "350", "sbj2", "1", "350", "1e-43", "624", "98.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
764 lPath = [ p1, p2, p3 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
765 self._tpA.insertList(lPath) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
766 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
767 set1 = Set() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
768 set1.setFromTuple( ( "1", "sbj1", "qry1", "83", "184" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
769 set3 = Set() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
770 set3.setFromTuple( ( "3", "sbj2", "qry1", "1", "350" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
771 expList = [ set1, set3 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
772 obsList = self._tpA.getSetListOverlappingQueryCoord( "qry1", 100, 200 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
773 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
774 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
775 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
776 def test_getSetListOverlappingQueryCoord_no_overlapping_and_start_higher_than_end(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
777 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
778 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
779 p1.setFromTuple( ( "1", "qry1", "83", "184", "sbj1", "1", "103", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
780 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
781 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj2", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
782 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
783 p3.setFromTuple( ( "3", "qry2", "1", "350", "sbj1", "1", "350", "1e-43", "624", "98.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
784 lPath = [ p1, p2, p3 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
785 self._tpA.insertList(lPath) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
786 expList = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
787 obsList = self._tpA.getSetListOverlappingQueryCoord( "qry1", 80, 1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
788 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
789 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
790 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
791 def test_getSetListIncludedInQueryCoord(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
792 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
793 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
794 p1.setFromTuple( ( "1", "qry1", "102", "184", "sbj1", "1", "103", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
795 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
796 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj2", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
797 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
798 p3.setFromTuple( ( "3", "qry1", "1", "350", "sbj2", "1", "350", "1e-43", "624", "98.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
799 lPath = [ p1, p2, p3 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
800 self._tpA.insertList(lPath) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
801 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
802 set1 = Set() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
803 set1.setFromTuple( ( "1", "sbj1", "qry1", "102", "184" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
804 expList = [ set1 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
805 obsList = self._tpA.getSetListIncludedInQueryCoord( "qry1", 100, 200 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
806 self.assertEqual( expList, obsList ) |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
809 def test_getSetListIncludedInQueryCoord_no_including_and_start_higher_than_end(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
810 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
811 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
812 p1.setFromTuple( ( "1", "qry1", "83", "184", "sbj1", "1", "103", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
813 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
814 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj2", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
815 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
816 p3.setFromTuple( ( "3", "qry2", "1", "350", "sbj1", "1", "350", "1e-43", "624", "98.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
817 lPath = [ p1, p2, p3 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
818 self._tpA.insertList(lPath) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
819 expList = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
820 obsList = self._tpA.getSetListIncludedInQueryCoord( "qry1", 80, 1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
821 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
822 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
823 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
824 def test_getPathListSortedByQueryCoord( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
825 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
826 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
827 p1.setFromTuple( ( "3", "qry2", "101", "200", "sbj3", "1", "100", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
828 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
829 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
830 p2.setFromTuple( ( "2", "qry1", "151", "500", "sbj1", "1", "350", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
831 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
832 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
833 p3.setFromTuple( ( "1", "qry1", "1", "200", "sbj3", "1", "200", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
834 self._tpA.insert( p3 ) |
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 expList = [ p3, p2, p1 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
837 obsList = self._tpA.getPathListSortedByQueryCoord() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
838 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
839 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
840 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
841 def test_getPathListSortedByQueryCoordFromQuery( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
842 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
843 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
844 p1.setFromTuple( ( "3", "qry2", "101", "200", "sbj3", "1", "100", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
845 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
846 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
847 p2.setFromTuple( ( "2", "qry1", "151", "500", "sbj1", "1", "350", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
848 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
849 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
850 p3.setFromTuple( ( "1", "qry1", "1", "200", "sbj3", "1", "200", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
851 self._tpA.insert( p3 ) |
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 expList = [ p3, p2 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
854 obsList = self._tpA.getPathListSortedByQueryCoordFromQuery( "qry1" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
855 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
856 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
857 def test_getPathListSortedByQueryCoordAndScoreFromQuery( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
858 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
859 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
860 p1.setFromTuple( ( "3", "qry2", "101", "200", "sbj3", "1", "100", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
861 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
862 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
863 p2.setFromTuple( ( "2", "qry1", "151", "500", "sbj1", "1", "350", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
864 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
865 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
866 p3.setFromTuple( ( "1", "qry1", "1", "200", "sbj3", "1", "200", "0.0", "137", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
867 self._tpA.insert( p3 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
868 p4 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
869 p4.setFromTuple( ( "4", "qry1", "1", "200", "sbj3", "1", "200", "0.0", "200", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
870 self._tpA.insert( p4 ) |
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 expList = [ p3, p4, p2 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
873 obsList = self._tpA.getPathListSortedByQueryCoordAndScoreFromQuery( "qry1" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
874 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
875 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
876 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
877 def test_getCumulLengthFromSubject( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
878 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
879 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
880 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
881 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
882 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
883 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj1", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
884 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
885 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
886 exp = 250 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
887 obs = self._tpA.getCumulLengthFromSubject( "sbj1" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
888 self.assertEqual( obs, exp ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
889 |
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 def test_getCumulLengthFromSubject_with_no_subject( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
892 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
893 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
894 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
895 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
896 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
897 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj1", "1", "150", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
898 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
899 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
900 exp = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
901 obs = self._tpA.getCumulLengthFromSubject( "sbj2" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
902 self.assertEqual( obs, exp ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
903 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
904 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
905 def test_getChainLengthListFromSubject( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
906 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
907 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
908 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
909 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
910 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
911 p2.setFromTuple( ( "1", "qry1", "351", "500", "sbj1", "101", "250", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
912 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
913 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
914 p3.setFromTuple( ( "2", "qry1", "801", "900", "sbj1", "1", "100", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
915 self._tpA.insert( p3 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
916 p4 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
917 p4.setFromTuple( ( "3", "qry1", "1900", "1801", "sbj1", "1", "100", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
918 self._tpA.insert( p4 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
919 p5 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
920 p5.setFromTuple( ( "4", "qry1", "1801", "1900", "sbj1", "100", "1", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
921 self._tpA.insert( p5 ) |
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 expList = [ 250, 100, 100, 100 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
924 obsList = self._tpA.getChainLengthListFromSubject( "sbj1" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
925 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
926 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
927 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
928 def test_getChainIdentityListFromSubject( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
929 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
930 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
931 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
932 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
933 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
934 p2.setFromTuple( ( "1", "qry1", "351", "500", "sbj1", "101", "250", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
935 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
936 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
937 p3.setFromTuple( ( "2", "qry1", "801", "900", "sbj1", "1", "100", "0.0", "187", "94.3" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
938 self._tpA.insert( p3 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
939 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
940 idChain1 = ( 98.5*(200-101+1) + 97.2*(500-351+1) ) / float(200-101+1+500-351+1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
941 idChain2 = 94.3*(900-801+1) / float(900-801+1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
942 expList = [ idChain1, idChain2 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
943 obsList = self._tpA.getChainIdentityListFromSubject( "sbj1" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
944 self.assertEqual( expList, obsList ) |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
947 def test_getPathLengthListFromSubject( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
948 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
949 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
950 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
951 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
952 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
953 p2.setFromTuple( ( "1", "qry1", "351", "500", "sbj1", "101", "250", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
954 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
955 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
956 p3.setFromTuple( ( "2", "qry1", "801", "900", "sbj1", "1", "100", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
957 self._tpA.insert( p3 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
958 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
959 expList = [ 100, 150, 100 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
960 obsList = self._tpA.getPathLengthListFromSubject( "sbj1" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
961 self.assertEqual( expList, obsList ) |
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 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
964 def test_getIdListSortedByDecreasingChainLengthFromSubject( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
965 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
966 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
967 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0847", "100", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
968 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
969 p2a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
970 p2a.setFromTuple( ( "2", "qry1", "351", "500", "sbj1", "1", "150", "0.0035", "100", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
971 self._tpA.insert( p2a ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
972 p2b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
973 p2b.setFromTuple( ( "2", "qry1", "551", "700", "sbj1", "151", "300", "0.0098", "100", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
974 self._tpA.insert( p2b ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
975 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
976 p3.setFromTuple( ( "3", "qry2", "541", "800", "sbj1", "1", "260", "0.147", "100", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
977 self._tpA.insert( p3 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
978 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
979 expList = [ 2, 3, 1 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
980 obsList = self._tpA.getIdListSortedByDecreasingChainLengthFromSubject( "sbj1" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
981 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
982 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
983 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
984 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
985 def test_getIdListFromSubjectWhereChainsLongerThanThreshold( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
986 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
987 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
988 p1.setFromTuple( ( "1", "qry1", "1", "100", "sbj1", "1", "100", "0.0847", "100", "97.2" ) ) # 1-fragment copy, long enough |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
989 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
990 p2a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
991 p2a.setFromTuple( ( "2", "qry2", "1", "50", "sbj1", "1", "50", "0.0035", "100", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
992 self._tpA.insert( p2a ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
993 p2b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
994 p2b.setFromTuple( ( "2", "qry2", "101", "150", "sbj1", "51", "100", "0.0098", "100", "97.2" ) ) # 2-fragment copy, long enough |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
995 self._tpA.insert( p2b ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
996 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
997 p3.setFromTuple( ( "3", "qry3", "1", "80", "sbj1", "1", "80", "0.147", "100", "97.2" ) ) # 1-fragment copy, too short |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
998 self._tpA.insert( p3 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
999 p4a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1000 p4a.setFromTuple( ( "4", "qry4", "1", "30", "sbj1", "1", "30", "0.0035", "100", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1001 self._tpA.insert( p4a ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1002 p4b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1003 p4b.setFromTuple( ( "4", "qry4", "101", "150", "sbj1", "31", "80", "0.0098", "100", "97.2" ) ) # 2-fragment copy, too short |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1004 self._tpA.insert( p4b ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1005 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1006 exp = [ 1, 2 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1007 obs = self._tpA.getIdListFromSubjectWhereChainsLongerThanThreshold( "sbj1", 90 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1008 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1009 self.assertEqual( exp, obs ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1010 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1011 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1012 def test_getSetListFromQuery(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1013 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1014 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1015 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1016 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1017 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1018 p2.setFromTuple( ( "1", "qry1", "351", "500", "sbj1", "101", "250", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1019 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1020 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1021 p3.setFromTuple( ( "2", "qry1", "801", "900", "sbj1", "1", "100", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1022 self._tpA.insert( p3 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1023 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1024 set1 = Set() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1025 set1.setFromTuple( ( "1", "sbj1", "qry1", "101", "200" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1026 set2 = Set() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1027 set2.setFromTuple( ( "1", "sbj1", "qry1", "351", "500" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1028 set3 = Set() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1029 set3.setFromTuple( ( "2", "sbj1", "qry1", "801", "900" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1030 expList = [set1, set2, set3] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1031 obsList = self._tpA.getSetListFromQuery("qry1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1032 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1033 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1034 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1035 def test_deleteFromId(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1036 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1037 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1038 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1039 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1040 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1041 p2.setFromTuple( ( "1", "qry1", "351", "500", "sbj1", "101", "250", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1042 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1043 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1044 p3.setFromTuple( ( "2", "qry1", "801", "900", "sbj1", "1", "100", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1045 self._tpA.insert( p3 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1046 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1047 self._tpA.deleteFromId(2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1048 expList = [p1, p2] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1049 obsList = self._tpA.getListOfAllPaths() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1050 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1051 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1052 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1053 def test_deleteFromPath(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1054 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1055 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1056 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1057 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1058 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1059 p2.setFromTuple( ( "1", "qry1", "351", "500", "sbj1", "101", "250", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1060 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1061 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1062 p3.setFromTuple( ( "2", "qry1", "801", "900", "sbj1", "1", "100", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1063 self._tpA.insert( p3 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1064 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1065 self._tpA.deleteFromPath(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1066 expList = [p1, p2] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1067 obsList = self._tpA.getListOfAllPaths() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1068 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1069 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1070 def test_deleteFromPath_two_lines_to_delete(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1071 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1072 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1073 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1074 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1075 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1076 p2.setFromTuple( ( "1", "qry1", "351", "500", "sbj1", "101", "250", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1077 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1078 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1079 p3.setFromTuple( ( "2", "qry1", "801", "900", "sbj1", "1", "100", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1080 self._tpA.insert( p3 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1081 p4 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1082 p4.setFromTuple( ( "2", "qry1", "801", "900", "sbj1", "1", "100", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1083 self._tpA.insert( p4 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1084 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1085 self._tpA.deleteFromPath(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1086 expList = [p1, p2] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1087 obsList = self._tpA.getListOfAllPaths() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1088 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1089 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1090 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1091 def test_deleteFromIdList(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1092 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1093 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1094 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1095 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1096 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1097 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj1", "101", "250", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1098 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1099 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1100 p3.setFromTuple( ( "3", "qry1", "801", "900", "sbj1", "1", "100", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1101 self._tpA.insert( p3 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1102 lId = [ 1, 2 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1103 self._tpA.deleteFromIdList(lId) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1104 expList = [ p3 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1105 obsList = self._tpA.getListOfAllPaths() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1106 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1107 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1108 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1109 def test_joinTwoPaths(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1110 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1111 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1112 idPath1 = 5 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1113 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1114 p1.setFromTuple( ( "5", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1115 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1116 idPath2 = 2 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1117 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1118 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj1", "101", "250", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1119 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1120 lPath = [ p1, p2 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1121 self._tpA.insertList( lPath ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1122 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1123 self._tpA.joinTwoPaths(idPath1, idPath2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1124 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1125 expP1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1126 expP1.setFromTuple( ( "2", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1127 expP2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1128 expP2.setFromTuple( ( "2", "qry1", "351", "500", "sbj1", "101", "250", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1129 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1130 expList = [ expP1, expP2 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1131 obsList = self._tpA.getListOfAllPaths() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1132 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1133 self.assertEqual( expList, obsList) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1134 self._db.dropTable(self._table) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1135 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1136 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1137 def test_joinTwoPaths_with_id1_inferior_at_id2(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1138 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1139 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1140 idPath1 = 5 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1141 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1142 p1.setFromTuple( ( "5", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1143 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1144 idPath2 = 2 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1145 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1146 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj1", "101", "250", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1147 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1148 lPath = [ p1, p2 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1149 self._tpA.insertList( lPath ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1150 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1151 self._tpA.joinTwoPaths(idPath2, idPath1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1152 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1153 expP1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1154 expP1.setFromTuple( ( "2", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1155 expP2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1156 expP2.setFromTuple( ( "2", "qry1", "351", "500", "sbj1", "101", "250", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1157 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1158 expList = [ expP1, expP2 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1159 obsList = self._tpA.getListOfAllPaths() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1160 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1161 self.assertEqual( expList, obsList) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1162 self._db.dropTable(self._table) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1163 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1164 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1165 def test_getNewId(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1166 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1167 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1168 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0", "137", "98.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1169 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1170 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1171 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj1", "101", "250", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1172 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1173 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1174 p3.setFromTuple( ( "3", "qry1", "801", "900", "sbj1", "1", "100", "0.0", "187", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1175 self._tpA.insert( p3 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1176 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1177 expId = 4 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1178 obsId = self._tpA.getNewId() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1179 self.assertEqual( expId, obsId) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1180 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1181 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1182 def test_getNewId_path_null(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1183 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1184 expId = 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1185 obsId = self._tpA.getNewId() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1186 self.assertEqual( expId, obsId) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1187 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1188 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1189 def test_getListOfChainsSortedByAscIdentityFromQuery( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1190 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1191 p1a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1192 p1a.setFromTuple( ( "1", "qry1", "11", "100", "sbj1", "1", "90", "0.0", "132", "96.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1193 p2a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1194 p2a.setFromTuple( ( "2", "qry1", "101", "120", "sbj2", "1", "20", "0.0", "36", "98.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1195 p1b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1196 p1b.setFromTuple( ( "1", "qry1", "121", "200", "sbj1", "91", "170", "0.0", "117", "96.5" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1197 p2b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1198 p2b.setFromTuple( ( "2", "qry1", "201", "800", "sbj2", "21", "620", "0.0", "856", "93.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1199 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1200 p3.setFromTuple( ( "3", "qry2", "1", "1000", "sbj1", "1", "1000", "1e-120", "900", "100.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1201 for p in [ p1a, p2a, p1b, p2b, p3 ]: self._tpA.insert( p ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1202 lPaths1 = [ p1a, p1b ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1203 lPaths2 = [ p2a, p2b ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1204 expList = [ lPaths2, lPaths1 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1205 obsList = self._tpA.getListOfChainsSortedByAscIdentityFromQuery( "qry1" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1206 for lPaths in expList: PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lPaths ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1207 for lPaths in obsList: PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lPaths ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1208 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1209 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1210 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1211 def test_getPathListSortedByIncreasingEvalueFromQuery( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1212 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1213 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1214 p1.setFromTuple( ( "1", "qry1", "101", "200", "sbj1", "1", "100", "0.0847", "100", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1215 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1216 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1217 p2.setFromTuple( ( "2", "qry1", "351", "500", "sbj2", "1", "150", "0.0035", "100", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1218 self._tpA.insert( p2 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1219 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1220 p3.setFromTuple( ( "3", "qry2", "541", "800", "sbj3", "1", "260", "0.147", "100", "97.2" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1221 self._tpA.insert( p3 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1222 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1223 expList = [ p2, p1 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1224 obsList = self._tpA.getPathListSortedByIncreasingEvalueFromQuery( "qry1" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1225 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1226 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1227 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1228 def test_path2PathRange_QryDirSbjDir( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1229 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1230 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1231 p1.setFromTuple( ( "1", "chr1", "1", "10", "TE3", "11", "17", "1e-20", "30", "85.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1232 p2a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1233 p2a.setFromTuple( ( "2", "chr2", "1", "100", "TE2", "10", "109", "1e-20", "163", "92.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1234 p2b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1235 p2b.setFromTuple( ( "2", "chr2", "201", "250", "TE2", "151", "200", "1e-10", "75", "88.7" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1236 for p in [ p1, p2a, p2b ]: self._tpA.insert( p ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1237 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1238 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1239 p2.setFromTuple( ( "2", "chr2", "1", "250", "TE2", "10", "200", "1e-20", "238", "90.96" ) ) # 'merge' p2a and p2b |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1240 expList = [ p1, p2 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1241 obsTable = self._tpA.path2PathRange() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1242 self._tpA._table = obsTable |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1243 obsList = self._tpA.getListOfAllPaths() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1244 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1245 self._db.dropTable( obsTable ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1246 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1247 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1248 def test_path2PathRange_QryDirSbjRev( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1249 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1250 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1251 p1.setFromTuple( ( "1", "chr1", "1", "10", "TE3", "11", "17", "1e-20", "30", "85.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1252 p2a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1253 p2a.setFromTuple( ( "2", "chr2", "1", "100", "TE2", "109", "10", "1e-20", "163", "92.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1254 p2b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1255 p2b.setFromTuple( ( "2", "chr2", "201", "250", "TE2", "200", "151", "1e-10", "75", "88.7" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1256 for p in [ p1, p2a, p2b ]: self._tpA.insert( p ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1257 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1258 p2.setFromTuple( ( "2", "chr2", "1", "250", "TE2", "200", "10", "1e-20", "238", "90.96" ) ) # 'merge' p2a and p2b |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1259 expList = [ p1, p2 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1260 obsTable = self._tpA.path2PathRange() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1261 self._tpA._table = obsTable |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1262 obsList = self._tpA.getListOfAllPaths() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1263 self.assertEqual( obsList, expList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1264 self._db.dropTable( obsTable ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1265 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1266 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1267 ################################################################################### |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1268 ############################ Tests for other methods ############################## |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1269 ################################################################################### |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1270 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1271 def test_path2PathRangeFromQuery_QryDirSbjDir( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1272 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1273 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1274 p1.setFromTuple( ( "1", "chr1", "1", "10", "TE3", "11", "17", "1e-20", "30", "85.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1275 p2a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1276 p2a.setFromTuple( ( "2", "chr2", "1", "100", "TE2", "10", "109", "1e-20", "163", "92.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1277 p2b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1278 p2b.setFromTuple( ( "2", "chr2", "201", "250", "TE2", "151", "200", "1e-10", "75", "88.7" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1279 for p in [ p1, p2a, p2b ]: self._tpA.insert( p ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1280 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1281 p2.setFromTuple( ( "2", "chr2", "1", "250", "TE2", "10", "200", "1e-20", "238", "90.96" ) ) # 'merge' p2a and p2b |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1282 expList = [ p2 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1283 obsTable = self._tpA._path2PathRangeFromQuery( "chr2" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1284 self._tpA._table = obsTable |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1285 obsList = self._tpA.getListOfAllPaths() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1286 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1287 self._db.dropTable( obsTable ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1288 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1289 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1290 def test_path2PathRangeFromQuery_QryDirSbjRev( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1291 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1292 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1293 p1.setFromTuple( ( "1", "chr1", "1", "10", "TE3", "11", "17", "1e-20", "30", "85.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1294 p2a = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1295 p2a.setFromTuple( ( "2", "chr2", "1", "100", "TE2", "109", "10", "1e-20", "163", "92.1" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1296 p2b = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1297 p2b.setFromTuple( ( "2", "chr2", "201", "250", "TE2", "200", "151", "1e-10", "75", "88.7" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1298 for p in [ p1, p2a, p2b ]: self._tpA.insert( p ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1299 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1300 p2.setFromTuple( ( "2", "chr2", "1", "250", "TE2", "200", "10", "1e-20", "238", "90.96" ) ) # 'merge' p2a and p2b |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1301 expList = [ p2 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1302 obsTable = self._tpA._path2PathRangeFromQuery( "chr2" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1303 self._tpA._table = obsTable |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1304 obsList = self._tpA.getListOfAllPaths() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1305 self.assertEqual( obsList, expList ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1306 self._db.dropTable( obsTable ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1307 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1308 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1309 def test_getNbOccurrences( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1310 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1311 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1312 p1.setFromTuple( ( "1", "chr1", "1", "10", "TE3", "11", "17", "1e-20", "30", "85.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1313 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1314 exp = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1315 obs = self._tpA.getNbOccurrences( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1316 self.assertEquals( exp, obs ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1317 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1318 self._tpA.insert( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1319 exp = 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1320 obs = self._tpA.getNbOccurrences( p1 ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1321 self.assertEquals( exp, obs ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1322 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1323 self._tpA.insert( p1 ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1324 exp = 2 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1325 obs = self._tpA.getNbOccurrences( p1 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1326 self.assertEquals( exp, obs ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1327 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1328 def test_getListOfUniqueOccPath(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1329 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1330 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1331 p1.setFromTuple( ( "1", "chr1", "1", "10", "TE3", "11", "17", "1e-20", "30", "85.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1332 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1333 p2.setFromTuple( ( "1", "chr1", "1", "10", "TE3", "11", "17", "1e-20", "30", "85.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1334 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1335 p3.setFromTuple( ( "1", "chr1", "2", "10", "TE3", "11", "17", "1e-20", "30", "85.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1336 p4 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1337 p4.setFromTuple( ( "2", "chr2", "2", "11", "TE4", "10", "18", "1e-30", "40", "95.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1338 lPath = [p1,p2,p3,p4] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1339 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1340 expListPath = deepcopy([p1,p3,p4]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1341 obsListUniquePath = self._tpA.getListOfUniqueOccPath(lPath) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1342 self.assertEquals( expListPath, obsListUniquePath ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1343 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1344 def test_getListOfUniqueOccPath_empty_list(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1345 expListPath = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1346 obsListUniquePath = self._tpA.getListOfUniqueOccPath([]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1347 self.assertEquals( expListPath, obsListUniquePath ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1348 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1349 def test_getListOfUniqueOccPath_one_item(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1350 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1351 p1.setFromTuple( ( "1", "chr1", "1", "10", "TE3", "11", "17", "1e-20", "30", "85.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1352 expListPath = deepcopy([p1]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1353 obsListUniquePath = self._tpA.getListOfUniqueOccPath([p1]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1354 self.assertEquals( expListPath, obsListUniquePath ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1355 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1356 def test_getListOfUniqueOccPath_unsorted_list(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1357 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1358 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1359 p1.setFromTuple( ( "1", "chr1", "1", "10", "TE3", "11", "17", "1e-20", "30", "85.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1360 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1361 p3.setFromTuple( ( "1", "chr1", "3", "10", "TE3", "11", "17", "1e-20", "30", "85.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1362 p4 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1363 p4.setFromTuple( ( "2", "chr2", "2", "11", "TE4", "10", "18", "1e-30", "40", "95.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1364 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1365 p2.setFromTuple( ( "1", "chr1", "1", "10", "TE3", "11", "17", "1e-20", "30", "85.0" ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1366 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1367 lPath = [p1,p3,p4,p2] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1368 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1369 expListPath = deepcopy([p1,p3,p4]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1370 obsListUniquePath = self._tpA.getListOfUniqueOccPath(lPath) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1371 self.assertEquals( expListPath, obsListUniquePath ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1372 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1373 test_suite = unittest.TestSuite() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1374 test_suite.addTest( unittest.makeSuite( Test_TablePathAdaptator ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1375 if __name__ == "__main__": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1376 unittest.TextTestRunner(verbosity=2).run( test_suite ) |