Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/sql/test/Test_TableBinPathAdaptator.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 import unittest |
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32 import os |
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33 import time |
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34 from commons.core.sql.TableBinPathAdaptator import TableBinPathAdaptator |
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35 from commons.core.coord.Path import Path |
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36 from commons.core.coord.Set import Set |
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37 from commons.core.sql.DbFactory import DbFactory |
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38 |
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39 class Test_TableBinPathAdaptator( unittest.TestCase ): |
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40 |
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41 def setUp( self ): |
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42 self._uniqId = "%s_%s" % (time.strftime("%Y%m%d%H%M%S") , os.getpid()) |
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43 self._db = DbFactory.createInstance() |
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44 self._table = "dummyPathTable_%s" % self._uniqId |
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45 self._table_idx = "dummyPathTable_%s_idx" % self._uniqId |
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46 |
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47 def tearDown( self ): |
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48 self._db.dropTable(self._table) |
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49 self._db.dropTable(self._table_idx) |
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50 self._db.close() |
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51 |
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52 #TODO: strand ?!? How does it work ? |
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53 def test_insert_QryRevSbjDir( self ): |
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54 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
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55 p1 = Path() |
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56 p1.setFromTuple(tuple) |
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57 |
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58 tuple = ("1", "chr1", "250", "100", "TE1", "11", "17", "1e-18", "20", "87.4") |
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59 p2 = Path() |
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60 p2.setFromTuple(tuple) |
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61 |
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62 tuple = ("2", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
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63 p3 = Path() |
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64 p3.setFromTuple(tuple) |
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65 |
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66 tuple = ("4", "chr5", "140", "251", "TE5", "140", "251", "2e-14", "14", "73.1") |
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67 p4 = Path() |
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68 p4.setFromTuple(tuple) |
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69 |
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70 self._db.createTable( self._table, "path" ) |
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71 self._db.createBinPathTable(self._table, True) |
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72 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
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73 self._tpA.insert(p1) |
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74 self._tpA.insert(p2) |
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75 self._tpA.insert(p3) |
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76 self._tpA.insert(p4) |
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77 |
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78 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
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79 self._db.execute( sqlCmd ) |
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80 obsPathTuple = self._db.cursor.fetchall() |
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81 expPathTuple = ((1, "chr1", 10, 25, "TE1", 11, 17, 1e-18, 20, 87.4), |
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82 (1, "chr1", 100, 250, "TE1", 17, 11, 1e-18, 20, 87.4), |
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83 (2, "chr1", 15, 30, "TE2", 10, 13, 5e-24, 34, 93.1), |
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84 (4, "chr5", 140, 251, "TE5", 140, 251, 2e-14, 14, 73.1),) |
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85 self.assertEquals(expPathTuple, obsPathTuple) |
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86 |
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87 sqlCmd = "SELECT * FROM %s_idx" % ( self._table ) |
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88 self._db.execute( sqlCmd ) |
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89 obsPathTuple = self._db.cursor.fetchall() |
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90 expPathTuple = ((1, 1000000, "chr1", 10, 25, 1), |
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91 (1, 1000000, "chr1", 100, 250, 1), |
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92 (2, 1000000, "chr1", 15, 30, 1), |
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93 (4, 1000000, "chr5", 140, 251, 1),) |
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94 self.assertEquals(expPathTuple, obsPathTuple) |
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95 |
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96 def test_getPathListOverlappingQueryCoord_one_included( self ): |
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97 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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98 pathF = open( pathFileName, "w" ) |
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99 pathF.write("6\tchr1\t950\t1010\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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100 pathF.close() |
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101 |
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102 tuple = ("6", "chr1", "950", "1010", "TE2", "11", "17", "1e-20", "30", "90.2") |
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103 p1 = Path() |
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104 p1.setFromTuple(tuple) |
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105 |
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106 self._db.createTable( self._table, "path", pathFileName ) |
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107 self._db.createBinPathTable(self._table, True) |
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108 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
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109 |
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110 lObs = self._tpA.getPathListOverlappingQueryCoord( "chr1", 900, 1010 ) |
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111 self.assertEquals(1, len(lObs)) |
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112 lExp = [p1] |
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113 self.assertEquals(lExp, lObs) |
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114 |
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115 os.remove( pathFileName ) |
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116 |
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117 def test_getPathListOverlappingQueryCoord_two_overlapped( self ): |
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118 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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119 pathF = open( pathFileName, "w" ) |
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120 pathF.write("6\tchr1\t950\t1500\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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121 pathF.write("7\tchr1\t750\t1000\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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122 pathF.close() |
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123 |
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124 tuple = ("6", "chr1", "950", "1500", "TE2", "11", "17", "1e-20", "30", "90.2") |
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125 p1 = Path() |
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126 p1.setFromTuple(tuple) |
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127 |
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128 tuple = ("7", "chr1", "750", "1000", "TE2", "11", "17", "1e-20", "30", "90.2") |
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129 p2 = Path() |
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130 p2.setFromTuple(tuple) |
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131 |
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132 self._db.createTable( self._table, "path", pathFileName ) |
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133 self._db.createBinPathTable(self._table, True) |
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134 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
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135 |
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136 lObs = self._tpA.getPathListOverlappingQueryCoord( "chr1", 900, 1010 ) |
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137 self.assertEquals(2, len(lObs)) |
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138 lExp = [p1, p2] |
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139 self.assertEquals(lExp, lObs) |
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140 |
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141 os.remove( pathFileName ) |
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142 |
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143 def test_getPathListOverlappingQueryCoord_two_not_overlapped_and_not_included( self ): |
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144 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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145 pathF = open( pathFileName, "w" ) |
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146 pathF.write("6\tchr1\t1050\t1500\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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147 pathF.write("7\tchr1\t750\t800\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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148 pathF.close() |
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149 |
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150 tuple = ("6", "chr1", "1050", "1500", "TE2", "11", "17", "1e-20", "30", "90.2") |
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151 p1 = Path() |
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152 p1.setFromTuple(tuple) |
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153 |
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154 tuple = ("7", "chr1", "750", "800", "TE2", "11", "17", "1e-20", "30", "90.2") |
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155 p2 = Path() |
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156 p2.setFromTuple(tuple) |
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157 |
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158 self._db.createTable( self._table, "path", pathFileName ) |
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159 self._db.createBinPathTable(self._table, True) |
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160 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
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161 |
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162 lObs = self._tpA.getPathListOverlappingQueryCoord( "chr1", 900, 1010 ) |
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163 self.assertEquals(0, len(lObs)) |
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164 lExp = [] |
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165 self.assertEquals(lExp, lObs) |
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166 |
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167 os.remove( pathFileName ) |
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168 |
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169 def test_getPathListOverlappingQueryCoord_one_verlapping_and_others_chained( self ): |
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170 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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171 pathF = open( pathFileName, "w" ) |
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172 pathF.write("6\tchr1\t900\t1010\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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173 pathF.write("6\tchr1\t1020\t1030\tTE2\t10\t13\t1e-20\t30\t90.2\n") |
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174 pathF.write("7\tchr1\t950\t999\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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175 pathF.write("7\tchr1\t1020\t1030\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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176 pathF.write("7\tchr5\t8000\t15000\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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177 pathF.close() |
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178 |
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179 tuple = ("6", "chr1", "900", "1010", "TE2", "11", "17", "1e-20", "30", "90.2") |
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180 p1 = Path() |
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181 p1.setFromTuple(tuple) |
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182 |
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183 tuple = ("6", "chr1", "1020", "1030", "TE2", "10", "13", "1e-20", "30", "90.2") |
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184 p2 = Path() |
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185 p2.setFromTuple(tuple) |
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186 |
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187 tuple = ("7", "chr1", "850", "999", "TE2", "11", "17", "1e-20", "30", "90.2") |
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188 p3 = Path() |
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189 p3.setFromTuple(tuple) |
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190 |
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191 tuple = ("7", "chr1", "1020", "1030", "TE2", "11", "17", "1e-20", "30", "90.2") |
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192 p4 = Path() |
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193 p4.setFromTuple(tuple) |
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194 |
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195 tuple = ("7", "chr5", "8000", "15000", "TE2", "11", "17", "1e-20", "30", "90.2") |
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196 p5 = Path() |
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197 p5.setFromTuple(tuple) |
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198 |
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199 self._db.createTable( self._table, "path", pathFileName ) |
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200 self._db.createBinPathTable(self._table, True) |
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201 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
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202 |
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203 lObs = self._tpA.getPathListOverlappingQueryCoord( "chr1", 1000, 1010 ) |
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204 self.assertEquals(1, len(lObs)) |
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205 lExp = [p1] |
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206 self.assertEquals(lExp, lObs) |
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207 |
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208 os.remove( pathFileName ) |
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209 |
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210 def test_getChainListOverlappingQueryCoord_with_all_path_strictly_included_in_the_given_region(self): |
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211 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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212 pathF = open( pathFileName, "w" ) |
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213 pathF.write("1\tchr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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214 pathF.write("2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.2\n") |
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215 pathF.write("3\tchr1\t8\t13\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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216 pathF.write("4\tchr1\t11\t15\tTE2\t15\t19\t1e-10\t25\t80.2\n") |
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217 pathF.write("5\tchr1\t14\t19\tTE1\t1\t6\t1e-15\t45\t98.4\n") |
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218 pathF.close() |
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219 |
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220 tuple = ("1", "chr1", "1", "10", "TE2", "11", "17", "1e-20", "30", "90.2") |
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221 p1 = Path() |
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222 p1.setFromTuple(tuple) |
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223 |
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224 tuple = ("2", "chr1", "2", "9", "TE2", "10", "13", "1e-20", "30", "90.2") |
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225 p2 = Path() |
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226 p2.setFromTuple(tuple) |
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227 |
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228 tuple = ("3", "chr1", "8", "13", "TE2", "11", "17", "1e-20", "30", "90.2") |
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229 p3 = Path() |
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230 p3.setFromTuple(tuple) |
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231 |
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232 tuple = ("4", "chr1", "11", "15", "TE2", "15", "19", "1e-10", "25", "80.2") |
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233 p4 = Path() |
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234 p4.setFromTuple(tuple) |
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235 |
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236 tuple = ("5", "chr1", "14", "19", "TE1", "1", "6", "1e-15", "45", "98.4") |
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237 p5 = Path() |
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238 p5.setFromTuple(tuple) |
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239 |
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240 self._db.createTable( self._table, "path", pathFileName ) |
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241 self._db.createBinPathTable(self._table, True) |
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242 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
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243 lObs = self._tpA.getChainListOverlappingQueryCoord( "chr1", 1, 20 ) |
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244 self.assertEquals(5, len(lObs)) |
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245 |
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246 lExp = [p1, p2, p3, p4, p5] |
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247 self.assertEquals(lExp, lObs) |
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248 |
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249 os.remove( pathFileName ) |
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250 |
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251 def test_getChainListOverlappingQueryCoord_with_2_path_overlapping_the_given_region(self): |
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252 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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253 pathF = open( pathFileName, "w" ) |
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254 pathF.write("1\tchr1\t1\t20\tTE1\t11\t17\t1e-18\t20\t87.4\n") |
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255 pathF.write("2\tchr1\t10\t30\tTE2\t10\t13\t5e-24\t34\t93.1\n") |
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256 pathF.close() |
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257 |
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258 tuple = ("1", "chr1", "1", "20", "TE1", "11", "17", "1e-18", "20", "87.4") |
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259 p1 = Path() |
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260 p1.setFromTuple(tuple) |
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261 |
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262 tuple = ("2", "chr1", "10", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
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263 p2 = Path() |
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264 p2.setFromTuple(tuple) |
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265 |
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266 self._db.createTable( self._table, "path", pathFileName ) |
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267 self._db.createBinPathTable(self._table, True) |
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268 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
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269 lObs = self._tpA.getChainListOverlappingQueryCoord( "chr1", 12, 18 ) |
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270 self.assertEquals(2, len(lObs)) |
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271 |
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272 lExp = [p1, p2] |
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273 self.assertEquals(lExp, lObs) |
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274 |
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275 os.remove( pathFileName ) |
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276 |
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277 def test_getChainListOverlappingQueryCoord_without_path_overlapping_the_given_region(self): |
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278 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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279 pathF = open( pathFileName, "w" ) |
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280 pathF.write("1\tchr1\t1\t20\tTE1\t11\t17\t1e-18\t20\t87.4\n") |
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281 pathF.write("2\tchr1\t10\t30\tTE2\t10\t13\t5e-24\t34\t93.1\n") |
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282 pathF.write("3\tchr5\t45\t50\tTE2\t10\t13\t5e-24\t34\t93.1\n") |
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283 pathF.close() |
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284 |
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285 tuple = ("1", "chr1", "1", "20", "TE1", "11", "17", "1e-18", "20", "87.4") |
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286 p1 = Path() |
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287 p1.setFromTuple(tuple) |
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288 |
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289 tuple = ("2", "chr1", "10", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
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290 p2 = Path() |
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291 p2.setFromTuple(tuple) |
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292 |
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293 tuple = ("3", "chr5", "45", "50", "TE2", "10", "13", "5e-24", "34", "93.1") |
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294 p3 = Path() |
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295 p3.setFromTuple(tuple) |
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296 |
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297 self._db.createTable( self._table, "path", pathFileName ) |
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298 self._db.createBinPathTable(self._table, True) |
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299 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
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300 lObs = self._tpA.getChainListOverlappingQueryCoord( "chr1", 40, 50 ) |
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301 self.assertEquals(0, len(lObs)) |
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302 |
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303 lExp = [] |
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304 self.assertEquals(lExp, lObs) |
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305 |
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306 os.remove( pathFileName ) |
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307 |
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308 def test_getChainListOverlappingQueryCoord_with_inverse_coord(self): |
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309 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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310 pathF = open( pathFileName, "w" ) |
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311 pathF.write("1\tchr1\t2000\t1010\tTE2\t17\t11\t1e-20\t30\t90.2\n") |
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312 pathF.write("2\tchr1\t5000\t3030\tTE2\t13\t10\t1e-20\t30\t90.2\n") |
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313 pathF.close() |
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314 |
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315 tuple = ("1", "chr1", "2000", "1010", "TE2", "17", "11", "1e-20", "30", "90.2") |
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316 p1 = Path() |
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317 p1.setFromTuple(tuple) |
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318 |
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319 tuple = ("2", "chr1", "5000", "3030", "TE2", "13", "10", "1e-20", "30", "90.2") |
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320 p2 = Path() |
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321 p2.setFromTuple(tuple) |
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322 |
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323 self._db.createTable( self._table, "path", pathFileName ) |
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324 self._db.createBinPathTable(self._table, True) |
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325 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
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326 |
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327 lObs = self._tpA.getChainListOverlappingQueryCoord( "chr1", 1000, 1500 ) |
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328 self.assertEquals(1, len(lObs)) |
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329 lExp = [p1] |
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330 self.assertEquals(lExp, lObs) |
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331 |
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332 lObs = self._tpA.getChainListOverlappingQueryCoord( "chr1", 4000, 4510 ) |
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333 self.assertEquals(1, len(lObs)) |
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334 lExp = [p2] |
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335 self.assertEquals(lExp, lObs) |
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336 |
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337 lObs = self._tpA.getChainListOverlappingQueryCoord( "chr1", 1000, 4510 ) |
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338 self.assertEquals(2, len(lObs)) |
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339 lExp = [p1, p2] |
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340 self.assertEquals(lExp, lObs) |
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341 |
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342 os.remove( pathFileName ) |
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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_getChainListOverlappingQueryCoord_with_chain_id_and_coord( self ): |
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345 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
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346 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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347 pathF.write("6\tchr1\t900\t1010\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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348 pathF.write("6\tchr1\t1020\t1030\tTE2\t10\t13\t1e-20\t30\t90.2\n") |
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349 pathF.write("7\tchr1\t950\t999\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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350 pathF.write("7\tchr1\t1020\t1030\tTE2\t11\t17\t1e-20\t30\t90.2\n") |
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351 pathF.write("7\tchr5\t8000\t15000\tTE2\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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352 pathF.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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353 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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354 tuple = ("6", "chr1", "900", "1010", "TE2", "11", "17", "1e-20", "30", "90.2") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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355 p1 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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356 p1.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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357 |
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358 tuple = ("6", "chr1", "1020", "1030", "TE2", "10", "13", "1e-20", "30", "90.2") |
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359 p2 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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360 p2.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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361 |
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362 tuple = ("7", "chr1", "950", "999", "TE2", "11", "17", "1e-20", "30", "90.2") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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363 p3 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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364 p3.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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365 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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366 tuple = ("7", "chr1", "1020", "1030", "TE2", "11", "17", "1e-20", "30", "90.2") |
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367 p4 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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368 p4.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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369 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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370 tuple = ("7", "chr5", "8000", "15000", "TE2", "11", "17", "1e-20", "30", "90.2") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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371 p5 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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372 p5.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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373 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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374 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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375 self._db.createBinPathTable(self._table, True) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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376 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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377 lObs = self._tpA.getChainListOverlappingQueryCoord( "chr1", 1000, 1010 ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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378 self.assertEquals(5, len(lObs)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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379 lExp = [p1, p2, p3, p4, p5] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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380 self.assertEquals(lExp, lObs) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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381 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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382 os.remove( pathFileName ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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383 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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384 def test_getPathListIncludedInQueryCoord_all_included(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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385 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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386 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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387 pathF.write("1\tchr1\t10\t20\tTE1\t11\t17\t1e-18\t20\t87.4\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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388 pathF.write("2\tchr1\t20\t30\tTE2\t10\t13\t5e-24\t34\t93.1\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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389 pathF.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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390 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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391 tuple = ("1", "chr1", "10", "20", "TE1", "11", "17", "1e-18", "20", "87.4") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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392 p1 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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393 p1.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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394 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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395 tuple = ("2", "chr1", "20", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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396 p2 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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397 p2.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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 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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400 self._db.createBinPathTable(self._table, True) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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401 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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402 lObs = self._tpA.getPathListIncludedInQueryCoord( "chr1", 1, 40 ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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403 self.assertEquals(2, len(lObs)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
404 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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405 lExp = [p1, p2] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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406 self.assertEquals(lExp, lObs) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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407 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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408 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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409 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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410 def test_getPathListIncludedInQueryCoord_all_not_included(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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411 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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412 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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413 pathF.write("1\tchr1\t10\t20\tTE1\t11\t17\t1e-18\t20\t87.4\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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414 pathF.write("2\tchr1\t20\t30\tTE2\t10\t13\t5e-24\t34\t93.1\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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415 pathF.write("3\tchr5\t55\t60\tTE2\t10\t13\t5e-24\t34\t93.1\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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416 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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417 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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418 tuple = ("1", "chr1", "10", "20", "TE1", "11", "17", "1e-18", "20", "87.4") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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419 p1 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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420 p1.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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421 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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422 tuple = ("2", "chr1", "20", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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423 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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424 p2.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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425 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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426 tuple = ("3", "chr2", "55", "60", "TE2", "10", "13", "5e-24", "34", "93.1") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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427 p3 = 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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|
428 p3.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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429 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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430 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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431 self._db.createBinPathTable(self._table, True) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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432 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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433 lObs = self._tpA.getPathListIncludedInQueryCoord( "chr1", 50, 70 ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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434 self.assertEquals(0, len(lObs)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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435 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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436 lExp = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
437 self.assertEquals(lExp, lObs) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
438 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
439 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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changeset
|
440 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
441 def test_getPathListIncludedInQueryCoord_all_overlapping(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
442 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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|
443 pathF = open( pathFileName, "w" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
444 pathF.write("1\tchr1\t10\t25\tTE1\t11\t17\t1e-18\t20\t87.4\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
445 pathF.write("2\tchr1\t15\t30\tTE2\t10\t13\t5e-24\t34\t93.1\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
446 pathF.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
447 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
448 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
449 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
450 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
451 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
452 tuple = ("2", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
453 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
454 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
455 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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456 self._db.createTable( self._table, "path", pathFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
457 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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458 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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459 lObs = self._tpA.getPathListIncludedInQueryCoord( "chr1", 13, 22 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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460 self.assertEquals(0, len(lObs)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
461 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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462 lExp = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
463 self.assertEquals(lExp, lObs) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
464 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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465 os.remove( pathFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
466 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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467 def test_getPathListIncludedInQueryCoord_with_one_included_and_one_overlapping(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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468 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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469 pathF = open( pathFileName, "w" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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470 pathF.write("1\tchr1\t10\t25\tTE1\t11\t17\t1e-18\t20\t87.4\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
471 pathF.write("2\tchr1\t15\t30\tTE2\t10\t13\t5e-24\t34\t93.1\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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472 pathF.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
473 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
474 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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475 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
476 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
477 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
478 tuple = ("2", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
479 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
480 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
481 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
482 self._db.createTable( self._table, "path", pathFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
483 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
484 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
485 lObs = self._tpA.getPathListIncludedInQueryCoord( "chr1", 9, 27 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
486 self.assertEquals(1, len(lObs)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
487 lExp = [p1] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
488 self.assertEquals(lExp, lObs) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
489 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
490 os.remove( pathFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
491 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
492 def test_getPathListIncludedInQueryCoord_with_one_included_and_two_chained(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
493 pathFileName = "dummyPathFile_%s" % ( self._uniqId ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
494 pathF = open( pathFileName, "w" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
495 pathF.write("1\tchr1\t10\t25\tTE1\t11\t17\t1e-18\t20\t87.4\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
496 pathF.write("1\tchr1\t100\t250\tTE1\t11\t17\t1e-18\t20\t87.4\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
497 pathF.write("2\tchr1\t15\t30\tTE2\t10\t13\t5e-24\t34\t93.1\n") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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498 pathF.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
499 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
500 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
501 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
502 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
503 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
504 tuple = ("1", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
505 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
506 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
507 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
508 tuple = ("2", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
509 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
510 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
511 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
512 self._db.createTable( self._table, "path", pathFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
513 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
514 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
515 lObs = self._tpA.getPathListIncludedInQueryCoord( "chr1", 9, 27 ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
516 self.assertEquals(1, len(lObs)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
517 lExp = [p1] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
518 self.assertEquals(lExp, lObs) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
519 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
520 os.remove( pathFileName ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
521 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
522 def test_deleteFromId_with_correct_ID(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
523 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
524 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
525 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
526 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
527 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
528 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
529 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
530 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
531 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
532 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
533 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
534 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
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
|
536 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
537 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
538 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
539 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
540 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
541 self._tpA.deleteFromId(3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
542 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
543 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
544 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
545 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
546 expPathTuple = ((1, "chr1", 10, 25, "TE1", 11, 17, 1e-18, 20, 87.4), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
547 (2, "chr1", 100, 250, "TE1", 11, 17, 1e-18, 20, 87.4),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
548 self.assertEquals(expPathTuple, obsPathTuple) |
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 sqlCmd = "SELECT * FROM %s_idx" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
551 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
552 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
553 expPathTuple = ((1, 1000000, "chr1", 10, 25, 1), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
554 (2, 1000000, "chr1", 100, 250, 1),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
555 self.assertEquals(expPathTuple, obsPathTuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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556 |
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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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557 def test_deleteFromId_with_not_exist_ID(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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558 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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559 p1 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
560 p1.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
561 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
562 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
563 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
564 p2.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
565 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
566 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
567 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
568 p3.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
569 |
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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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570 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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571 self._db.createBinPathTable(self._table, True) |
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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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|
572 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
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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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573 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
|
574 self._tpA.insert(p2) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
575 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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576 self._tpA.deleteFromId(4) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
577 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
578 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
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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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|
579 self._db.execute( sqlCmd ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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580 obsPathTuple = self._db.cursor.fetchall() |
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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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581 expPathTuple = ((1, "chr1", 10, 25, "TE1", 11, 17, 1e-18, 20, 87.4), |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
582 (2, "chr1", 100, 250, "TE1", 11, 17, 1e-18, 20, 87.4), |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
583 (3, "chr1", 15, 30, "TE2", 10, 13, 5e-24, 34, 93.1),) |
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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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|
584 self.assertEquals(expPathTuple, obsPathTuple) |
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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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585 |
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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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|
586 sqlCmd = "SELECT * FROM %s_idx" % ( self._table ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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587 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
588 obsPathTuple = self._db.cursor.fetchall() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
589 expPathTuple = ((1, 1000000, "chr1", 10, 25, 1), |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
590 (2, 1000000, "chr1", 100, 250, 1), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
591 (3, 1000000, "chr1", 15, 30, 1),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
592 self.assertEquals(expPathTuple, obsPathTuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
593 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
594 def test_deleteFromId_with_multiple_ID(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
595 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
596 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
597 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
598 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
599 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
600 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
601 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
602 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
603 tuple = ("2", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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604 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
605 p3.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
606 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
607 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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608 self._db.createBinPathTable(self._table, True) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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609 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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610 self._tpA.insert(p1) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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611 self._tpA.insert(p2) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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612 self._tpA.insert(p3) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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613 self._tpA.deleteFromId(2) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
614 |
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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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|
615 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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616 self._db.execute( sqlCmd ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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617 obsPathTuple = self._db.cursor.fetchall() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
618 expPathTuple = ((1, "chr1", 10, 25, "TE1", 11, 17, 1e-18, 20, 87.4),) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
619 self.assertEquals(expPathTuple, obsPathTuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
620 |
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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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|
621 sqlCmd = "SELECT * FROM %s_idx" % ( self._table ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
622 self._db.execute( sqlCmd ) |
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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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|
623 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
624 expPathTuple = ((1, 1000000, "chr1", 10, 25, 1),) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
625 self.assertEquals(expPathTuple, obsPathTuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
626 |
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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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|
627 def test_deleteFromIdList(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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628 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
629 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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changeset
|
630 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
631 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
632 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
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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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|
633 p2 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
634 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
635 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
636 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
637 p3 = Path() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
638 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
639 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
640 self._db.createTable( self._table, "path" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
641 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
642 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
643 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
644 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
645 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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646 lNumToRemove = [2, 3] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
647 self._tpA.deleteFromIdList(lNumToRemove) |
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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
|
648 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
649 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
650 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
651 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
652 expPathTuple = ((1, "chr1", 10, 25, "TE1", 11, 17, 1e-18, 20, 87.4),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
653 self.assertEquals(expPathTuple, obsPathTuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
654 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
655 sqlCmd = "SELECT * FROM %s_idx" % ( self._table ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
656 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
657 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
658 expPathTuple = ((1, 1000000, "chr1", 10, 25, 1),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
659 self.assertEquals(expPathTuple, obsPathTuple) |
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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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|
660 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
661 def test_deleteFromIdList_with_empty_list(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
662 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
663 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
664 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
665 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
666 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
667 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
668 p2.setFromTuple(tuple) |
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 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
671 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
672 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
673 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
674 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
|
675 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
676 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
677 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
678 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
679 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
680 lNumToRemove = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
681 self._tpA.deleteFromIdList(lNumToRemove) |
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 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
684 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
685 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
686 expPathTuple = ((1, "chr1", 10, 25, "TE1", 11, 17, 1e-18, 20, 87.4), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
687 (2, "chr1", 100, 250, "TE1", 11, 17, 1e-18, 20, 87.4), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
688 (3, "chr1", 15, 30, "TE2", 10, 13, 5e-24, 34, 93.1),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
689 self.assertEquals(expPathTuple, obsPathTuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
690 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
691 sqlCmd = "SELECT * FROM %s_idx" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
692 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
693 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
694 expPathTuple = ((1, 1000000, "chr1", 10, 25, 1), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
695 (2, 1000000, "chr1", 100, 250, 1), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
696 (3, 1000000, "chr1", 15, 30, 1),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
697 self.assertEquals(expPathTuple, obsPathTuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
698 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
699 def test_deleteFromIdList_with_list_of_existing_and_not_existing_ID(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
700 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
701 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
702 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
703 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
704 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
705 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
706 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
707 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
708 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
709 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
710 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
711 |
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 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
714 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
715 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
716 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
717 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
718 lNumToRemove = [3, 4] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
719 self._tpA.deleteFromIdList(lNumToRemove) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
720 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
721 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
722 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
723 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
724 expPathTuple = ((1, "chr1", 10, 25, "TE1", 11, 17, 1e-18, 20, 87.4), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
725 (2, "chr1", 100, 250, "TE1", 11, 17, 1e-18, 20, 87.4),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
726 self.assertEquals(expPathTuple, obsPathTuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
727 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
728 sqlCmd = "SELECT * FROM %s_idx" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
729 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
730 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
731 expPathTuple = ((1, 1000000, "chr1", 10, 25, 1), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
732 (2, 1000000, "chr1", 100, 250, 1),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
733 self.assertEquals(expPathTuple, obsPathTuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
734 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
735 def test_deleteFromIdList_with_multiple_ID_on_BinPathTable(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
736 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
737 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
738 p1.setFromTuple(tuple) |
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 tuple = ("3", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
741 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
742 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
743 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
744 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
745 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
746 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
747 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
748 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
|
749 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
750 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
751 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
752 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
753 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
754 lNumToRemove = [3] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
755 self._tpA.deleteFromIdList(lNumToRemove) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
756 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
757 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
758 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
759 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
760 expPathTuple = ((1, "chr1", 10, 25, "TE1", 11, 17, 1e-18, 20, 87.4),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
761 self.assertEquals(expPathTuple, obsPathTuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
762 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
763 sqlCmd = "SELECT * FROM %s_idx" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
764 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
765 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
766 expPathTuple = ((1, 1000000, "chr1", 10, 25, 1),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
767 self.assertEquals(expPathTuple, obsPathTuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
768 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
769 def test_joinTwoPaths_with_min_and_max_existing_IDs(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
770 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
771 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
772 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
773 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
774 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
775 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
776 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
777 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
778 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
779 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
780 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
781 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
782 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
|
783 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
784 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
785 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
786 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
787 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
788 expNewId = 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
789 obsNewId = self._tpA.joinTwoPaths(1, 2) |
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 self.assertEquals(expNewId, obsNewId) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
792 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
793 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
794 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
795 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
796 expPathTuple = ((1, "chr1", 10, 25, "TE1", 11, 17, 1e-18, 20, 87.4), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
797 (1, "chr1", 100, 250, "TE1", 11, 17, 1e-18, 20, 87.4), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
798 (3, "chr1", 15, 30, "TE2", 10, 13, 5e-24, 34, 93.1),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
799 self.assertEquals(expPathTuple, obsPathTuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
800 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
801 sqlCmd = "SELECT * FROM %s_idx" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
802 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
803 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
804 expPathTuple = ((1, 1000000, "chr1", 10, 25, 1), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
805 (1, 1000000, "chr1", 100, 250, 1), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
806 (3, 1000000, "chr1", 15, 30, 1),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
807 self.assertEquals(expPathTuple, obsPathTuple) |
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_joinTwoPaths_with_min_ID_not_existing_and_max_ID_existing(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
810 tuple = ("4", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
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(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
813 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
814 tuple = ("5", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
815 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
816 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
817 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
818 tuple = ("6", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
819 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
820 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
821 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
822 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
|
823 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
824 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
825 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
826 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
827 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
828 expNewId = 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
829 obsNewId = self._tpA.joinTwoPaths(1, 5) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
830 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
831 self.assertEquals(expNewId, obsNewId) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
832 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
833 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
834 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
835 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
836 expPathTuple = ((4, "chr1", 10, 25, "TE1", 11, 17, 1e-18, 20, 87.4), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
837 (1, "chr1", 100, 250, "TE1", 11, 17, 1e-18, 20, 87.4), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
838 (6, "chr1", 15, 30, "TE2", 10, 13, 5e-24, 34, 93.1),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
839 self.assertEquals(expPathTuple, obsPathTuple) |
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 sqlCmd = "SELECT * FROM %s_idx" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
842 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
843 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
844 expPathTuple = ((4, 1000000, "chr1", 10, 25, 1), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
845 (1, 1000000, "chr1", 100, 250, 1), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
846 (6, 1000000, "chr1", 15, 30, 1),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
847 self.assertEquals(expPathTuple, obsPathTuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
848 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
849 def test_joinTwoPaths_with_min_ID_existing_and_max_ID_not_existing(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
850 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
851 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
852 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
853 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
854 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
855 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
856 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
857 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
858 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
859 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
860 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
861 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
862 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
|
863 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
864 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
865 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
866 self._tpA.insert(p2) |
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 expNewId = 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
869 obsNewId = self._tpA.joinTwoPaths(1, 5) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
870 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
871 self.assertEquals(expNewId, obsNewId) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
872 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
873 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
874 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
875 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
876 expPathTuple = ((1, "chr1", 10, 25, "TE1", 11, 17, 1e-18, 20, 87.4), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
877 (2, "chr1", 100, 250, "TE1", 11, 17, 1e-18, 20, 87.4), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
878 (3, "chr1", 15, 30, "TE2", 10, 13, 5e-24, 34, 93.1),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
879 self.assertEquals(expPathTuple, obsPathTuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
880 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
881 sqlCmd = "SELECT * FROM %s_idx" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
882 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
883 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
884 expPathTuple = ((1, 1000000, "chr1", 10, 25, 1), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
885 (2, 1000000, "chr1", 100, 250, 1), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
886 (3, 1000000, "chr1", 15, 30, 1),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
887 self.assertEquals(expPathTuple, obsPathTuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
888 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
889 def test_joinTwoPaths_with_min_and_max_not_existing_IDs(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
890 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
891 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
892 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
893 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
894 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
895 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
896 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
897 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
898 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
899 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
900 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
901 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
902 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
|
903 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
904 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
905 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
906 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
907 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
908 expNewId = 4 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
909 obsNewId = self._tpA.joinTwoPaths(4, 5) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
910 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
911 self.assertEquals(expNewId, obsNewId) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
912 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
913 sqlCmd = "SELECT * FROM %s" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
914 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
915 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
916 expPathTuple = ((1, "chr1", 10, 25, "TE1", 11, 17, 1e-18, 20, 87.4), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
917 (2, "chr1", 100, 250, "TE1", 11, 17, 1e-18, 20, 87.4), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
918 (3, "chr1", 15, 30, "TE2", 10, 13, 5e-24, 34, 93.1),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
919 self.assertEquals(expPathTuple, obsPathTuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
920 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
921 sqlCmd = "SELECT * FROM %s_idx" % ( self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
922 self._db.execute( sqlCmd ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
923 obsPathTuple = self._db.cursor.fetchall() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
924 expPathTuple = ((1, 1000000, "chr1", 10, 25, 1), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
925 (2, 1000000, "chr1", 100, 250, 1), |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
926 (3, 1000000, "chr1", 15, 30, 1),) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
927 self.assertEquals(expPathTuple, obsPathTuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
928 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
929 def test_getNewId(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
930 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
931 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
932 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
933 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
934 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
935 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
936 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
937 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
938 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
939 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
940 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
941 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
942 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
|
943 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
944 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
945 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
946 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
947 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
948 expNewId = 4 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
949 obsNewId = self._tpA.getNewId() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
950 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
951 self.assertEquals(expNewId, obsNewId) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
952 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
953 def test_getNewId_with_empty_path_table(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
954 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
|
955 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
956 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
957 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
958 expNewId = 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
959 obsNewId = self._tpA.getNewId() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
960 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
961 self.assertEquals(expNewId, obsNewId) |
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 def test_getSetListIncludedInQueryCoord_one_included(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
964 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
965 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
966 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
967 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
968 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
969 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
970 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
971 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
972 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
973 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
974 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
975 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
976 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
|
977 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
978 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
979 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
980 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
981 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
982 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
983 s2 = Set() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
984 s2.setFromTuple(("2","TE1","chr1","100","250")) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
985 expLSet = [s2] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
986 obsLSet = self._tpA.getSetListIncludedInQueryCoord('chr1', 95, 300) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
987 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
988 self.assertEquals(expLSet, obsLSet) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
989 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
990 def test_getSetListIncludedInQueryCoord_one_overlapping(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
991 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
992 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
993 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
994 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
995 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
996 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
997 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
998 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
999 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1000 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1001 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1002 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1003 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
|
1004 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1005 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1006 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1007 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1008 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1009 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1010 expLSet = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1011 obsLSet = self._tpA.getSetListIncludedInQueryCoord('chr1', 150, 200) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1012 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1013 self.assertEquals(expLSet, obsLSet) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1014 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1015 def test_getSetListIncludedInQueryCoord_with_no_result(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1016 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1017 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1018 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1019 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1020 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1021 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1022 p2.setFromTuple(tuple) |
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 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1025 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1026 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1027 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1028 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
|
1029 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1030 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1031 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1032 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1033 self._tpA.insert(p3) |
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 expLSet = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1036 obsLSet = self._tpA.getSetListIncludedInQueryCoord('chr1', 5000, 6000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1037 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1038 self.assertEquals(expLSet, obsLSet) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1039 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1040 def test_getSetListIncludedInQueryCoord_one_included_and_two_chain(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1041 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1042 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1043 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1044 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1045 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1046 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1047 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1048 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1049 tuple = ("2", "chr1", "1000", "2500", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1050 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1051 p3.setFromTuple(tuple) |
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 tuple = ("3", "chr1", "50", "150", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1054 p4 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1055 p4.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1056 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1057 tuple = ("4", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1058 p5 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1059 p5.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1060 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1061 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
|
1062 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1063 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1064 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1065 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1066 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1067 self._tpA.insert(p4) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1068 self._tpA.insert(p5) |
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 s2 = Set() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1071 s2.setFromTuple(("2","TE1","chr1","100","250")) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1072 expLSet = [s2] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1073 obsLSet = self._tpA.getSetListIncludedInQueryCoord('chr1', 95, 300) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1074 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1075 self.assertEquals(expLSet, obsLSet) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1076 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1077 def test_getSetListOverlappingQueryCoord_one_included(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1078 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1079 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1080 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1081 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1082 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1083 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1084 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1085 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1086 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1087 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1088 p3.setFromTuple(tuple) |
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 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
|
1091 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1092 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1093 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1094 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1095 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1096 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1097 s2 = Set() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1098 s2.setFromTuple(("2","TE1","chr1","100","250")) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1099 expLSet = [s2] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1100 obsLSet = self._tpA.getSetListOverlappingQueryCoord('chr1', 95, 300) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1101 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1102 self.assertEquals(expLSet, obsLSet) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1103 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1104 def test_getSetListOverlappingQueryCoord_one_overlapping(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1105 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1106 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1107 p1.setFromTuple(tuple) |
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 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1110 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1111 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1112 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1113 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1114 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1115 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1116 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1117 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
|
1118 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1119 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1120 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1121 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1122 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1123 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1124 s2 = Set() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1125 s2.setFromTuple(("2","TE1","chr1","100","250")) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1126 expLSet = [s2] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1127 obsLSet = self._tpA.getSetListOverlappingQueryCoord('chr1', 150, 200) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1128 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1129 self.assertEquals(expLSet, obsLSet) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1130 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1131 def test_getSetListOverlappingQueryCoord_with_no_result(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1132 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1133 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1134 p1.setFromTuple(tuple) |
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 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1137 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1138 p2.setFromTuple(tuple) |
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 tuple = ("3", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1141 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1142 p3.setFromTuple(tuple) |
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 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
|
1145 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1146 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1147 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1148 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1149 self._tpA.insert(p3) |
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 expLSet = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1152 obsLSet = self._tpA.getSetListOverlappingQueryCoord('chr1', 5000, 6000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1153 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1154 self.assertEquals(expLSet, obsLSet) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1155 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1156 def test_getSetListOverlappingQueryCoord_one_included_and_two_chain(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1157 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1158 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1159 p1.setFromTuple(tuple) |
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 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1162 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1163 p2.setFromTuple(tuple) |
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 tuple = ("2", "chr1", "1000", "2500", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1166 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1167 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1168 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1169 tuple = ("3", "chr1", "50", "150", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1170 p4 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1171 p4.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1172 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1173 tuple = ("4", "chr1", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1174 p5 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1175 p5.setFromTuple(tuple) |
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 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
|
1178 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1179 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1180 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1181 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1182 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1183 self._tpA.insert(p4) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1184 self._tpA.insert(p5) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1185 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1186 s2 = Set() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1187 s2.setFromTuple(("2","TE1","chr1","100","250")) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1188 s4 = Set() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1189 s4.setFromTuple(("3","TE1","chr1","50","150")) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1190 expLSet = [s2, s4] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1191 obsLSet = self._tpA.getSetListOverlappingQueryCoord('chr1', 95, 300) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1192 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1193 self.assertEquals(expLSet, obsLSet) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1194 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1195 def test_getIdList( self ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1196 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1197 p1.setFromString( "1\tchr1\t1\t10\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
changeset
|
1198 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1199 p2.setFromString( "2\tchr1\t2\t9\tTE2\t10\t13\t1e-20\t30\t90.2\n" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1200 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1201 p3.setFromString( "2\tchr1\t12\t19\tTE2\t15\t22\t1e-10\t40\t94.2\n" ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1202 p4 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1203 p4.setFromString( "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
changeset
|
1204 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1205 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
|
1206 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1207 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1208 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1209 lPath = [ p1, p2, p3, p4] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1210 self._tpA.insertList(lPath) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1211 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1212 expList = [ 1, 2, 3 ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1213 obsList = self._tpA.getIdList() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1214 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1215 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1216 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1217 def test_getQueryList(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1218 tuple = ("1", "chr1", "10", "25", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1219 p1 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1220 p1.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1221 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1222 tuple = ("2", "chr1", "100", "250", "TE1", "11", "17", "1e-18", "20", "87.4") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1223 p2 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1224 p2.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1225 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1226 tuple = ("3", "chr2", "15", "30", "TE2", "10", "13", "5e-24", "34", "93.1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1227 p3 = Path() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1228 p3.setFromTuple(tuple) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1229 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
1230 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
|
1231 self._db.createBinPathTable(self._table, True) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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1232 self._tpA = TableBinPathAdaptator( self._db, self._table ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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1233 self._tpA.insert(p1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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1234 self._tpA.insert(p2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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1235 self._tpA.insert(p3) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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1236 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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1237 expList = [ "chr1", "chr2" ] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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1238 obsList = self._tpA.getQueryList() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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1239 self.assertEqual( expList, obsList ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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1240 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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1241 test_suite = unittest.TestSuite() |
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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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1242 test_suite.addTest( unittest.makeSuite( Test_TableBinPathAdaptator ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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1243 if __name__ == '__main__': |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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1244 unittest.TextTestRunner(verbosity=2).run( test_suite ) |