Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/sql/TableMapAdaptator.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 # Copyright INRA (Institut National de la Recherche Agronomique) |
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2 # http://www.inra.fr |
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3 # http://urgi.versailles.inra.fr |
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4 # |
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5 # This software is governed by the CeCILL license under French law and |
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6 # abiding by the rules of distribution of free software. You can use, |
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7 # modify and/ or redistribute the software under the terms of the CeCILL |
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8 # license as circulated by CEA, CNRS and INRIA at the following URL |
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9 # "http://www.cecill.info". |
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10 # |
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11 # As a counterpart to the access to the source code and rights to copy, |
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12 # modify and redistribute granted by the license, users are provided only |
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13 # with a limited warranty and the software's author, the holder of the |
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14 # economic rights, and the successive licensors have only limited |
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15 # liability. |
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16 # |
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17 # In this respect, the user's attention is drawn to the risks associated |
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18 # with loading, using, modifying and/or developing or reproducing the |
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19 # software by the user in light of its specific status of free software, |
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20 # that may mean that it is complicated to manipulate, and that also |
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21 # therefore means that it is reserved for developers and experienced |
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22 # professionals having in-depth computer knowledge. Users are therefore |
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23 # encouraged to load and test the software's suitability as regards their |
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24 # requirements in conditions enabling the security of their systems and/or |
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25 # data to be ensured and, more generally, to use and operate it in the |
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26 # same conditions as regards security. |
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27 # |
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28 # The fact that you are presently reading this means that you have had |
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29 # knowledge of the CeCILL license and that you accept its terms. |
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30 |
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31 |
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32 import 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("\\", "\\\\") |