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1 # Copyright INRA (Institut National de la Recherche Agronomique)
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30
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31
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32 import sys
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33 from commons.core.sql.TableAdaptator import TableAdaptator
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34 from commons.core.sql.ITableMapAdaptator import ITableMapAdaptator
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35 from commons.core.coord.Map import Map
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36 from commons.core.coord.MapUtils import MapUtils
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37
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38
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39 ## Adaptator for Map table
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40 #
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41 class TableMapAdaptator( TableAdaptator, ITableMapAdaptator ):
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42
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43 ## Give a list of Map instances having a given seq name
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44 #
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45 # @param seqName string seq name
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46 # @return lMap list of instances
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47 #
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48 def getListFromSeqName( self, seqName ):
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49 sqlCmd = "SELECT * FROM %s" % (self._table)
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50 colum2Get, type2Get, attr2Get = self._getTypeColumAttr2Get(seqName)
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51 sqlCmd += " WHERE " + colum2Get
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52 sqlCmd += " = "
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53 sqlCmd = sqlCmd + type2Get
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54 sqlCmd = sqlCmd % "'" + attr2Get + "'"
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55 return self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
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56
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57 ## Give a list of Map instances overlapping a given region
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58 #
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59 # @param query string query name
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60 # @param start integer start coordinate
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61 # @param end integer end coordinate
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62 # @return list map instances
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63 #
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64 def getListOverlappingCoord(self, query, start, end):
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65 sqlCmd = 'select * from %s where chr="%s" and ((start between least(%d,%d) and greatest(%d,%d) or end between least(%d,%d) and greatest(%d,%d)) or (least(start,end)<=least(%d,%d) and greatest(start,end)>=greatest(%d,%d))) ;' % (self._table, query, start, end, start, end, start, end, start, end, start, end, start, end)
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66 return self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
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67
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68 ## Give a list of Map instances having a given sequence name
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69 #
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70 # @param seqName string sequence name
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71 # @return lMap list of instances
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72 #
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73 def getMapListFromSeqName(self, seqName):
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74 lMap = self.getListFromSeqName( seqName )
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75 return lMap
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76
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77 #TODO: Check getListFromSeqName method: uses name instead of seqname
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78 # ## Give a list of Map instances having a given sequence name from list
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79 # #
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80 # # @param lSeqName string sequence name list
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81 # # @return lMap list of instances
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82 # #
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83 # def getMapListFromSeqNameList(self, lSeqName):
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84 # lMap = []
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85 # [lMap.extend(self.getListFromSeqName(seqName)) for seqName in lSeqName]
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86 # return lMap
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87
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88 ## Give a list of Map instances having a given chromosome
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89 #
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90 # @param chr string chromosome
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91 # @return lMap list of instances
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92 #
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93 def getMapListFromChr(self, chr):
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94 sqlCmd = "SELECT * FROM %s WHERE chr='%s'" % (self._table, chr)
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95 lMap = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
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96 return lMap
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97
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98 ## Give a list of the distinct seqName/chr present in the table
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99 #
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100 # @return lDistinctContigNames string list
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101 #
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102 def getSeqNameList(self):
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103 sqlCmd = "SELECT DISTINCT chr FROM %s" % ( self._table )
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104 lDistinctContigNames = self._iDb.getStringListWithSQLCmd(sqlCmd)
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105 return lDistinctContigNames
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106
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107 ## Return a list of Set instances from a given sequence name
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108 #
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109 # @param seqName string sequence name
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110 # @return lSets list of Set instances
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111 #
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112 def getSetListFromSeqName( self, seqName ):
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113 lMaps = self.getListFromSeqName( seqName )
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114 lSets = MapUtils.mapList2SetList( lMaps )
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115 return lSets
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116
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117 ## Give a map instances list overlapping a given region
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118 #
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119 # @param seqName string seq name
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120 # @param start integer start coordinate
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121 # @param end integer end coordinate
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122 # @return lMap list of map instances
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123 #
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124 def getMapListOverlappingCoord(self, seqName, start, end):
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125 lMap = self.getListOverlappingCoord(seqName, start, end)
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126 return lMap
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127
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128 ## Return a list of Set instances overlapping a given sequence
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129 #
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130 # @param seqName string sequence name
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131 # @param start integer start coordinate
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132 # @param end integer end coordinate
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133 # @return lSet list of Set instances
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134 #
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135 def getSetListOverlappingCoord( self, seqName, start, end ):
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136 lMaps = self.getListOverlappingCoord( seqName, start, end )
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137 lSets = MapUtils.mapList2SetList( lMaps )
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138 return lSets
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139
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140 ## Give a dictionary which keys are Map names and values the corresponding Map instances
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141 #
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142 # @return dName2Maps dict which keys are Map names and values the corresponding Map instances
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143 #
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144 def getDictPerName( self ):
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145 dName2Maps = {}
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146 lMaps = self.getListOfAllMaps()
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147 for iMap in lMaps:
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148 if dName2Maps.has_key( iMap.name ):
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149 if iMap == dName2Maps[ iMap.name ]:
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150 continue
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151 else:
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152 msg = "ERROR: in table '%s' two different Map instances have the same name '%s'" % ( self._table, iMap.name )
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153 sys.stderr.write( "%s\n" % ( msg ) )
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154 sys.exit(1)
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155 dName2Maps[ iMap.name ] = iMap
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156 return dName2Maps
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157
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158 ## Return a list of Map instances with all the data contained in the table
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159 #
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160 # @return lMaps list of Map instances
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161 #
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162 def getListOfAllMaps( self ):
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163 sqlCmd = "SELECT * FROM %s" % ( self._table )
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164 lMaps = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
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165 return lMaps
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166
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167 ## Give the end of map as integer
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168 #
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169 # @return end integer the end of map
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170 #
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171 def getEndFromSeqName(self, seqName):
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172 sqlCmd = "SELECT end FROM %s WHERE chr = '%s'" % (self._table, seqName)
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173 end = self._iDb.getIntegerWithSQLCmd(sqlCmd)
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174 return end
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175
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176 def _getInstanceToAdapt(self):
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177 iMap = Map()
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178 return iMap
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179
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180 def _getTypeColumAttr2Get(self, name):
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181 colum2Get = 'name'
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182 type2Get = '%s'
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183 attr2Get = name
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184 return colum2Get, type2Get, attr2Get
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185
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186 def _getTypeAndAttr2Insert(self, map):
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187 type2Insert = ("'%s'","'%s'","'%d'","'%d'")
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188 attr2Insert = (map.name, map.seqname, map.start, map.end)
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189 return type2Insert, attr2Insert
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190
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191 def _escapeAntislash(self, obj):
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192 obj.name = obj.name.replace("\\", "\\\\")
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193 obj.seqname = obj.seqname.replace("\\", "\\\\")
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