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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 from commons.core.coord.Range import getIdx
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32 from commons.core.sql.TablePathAdaptator import TablePathAdaptator
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33 from commons.core.coord.PathUtils import PathUtils
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34
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35 ## Bin Adaptator for a path table.
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36 #
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37 class TableBinPathAdaptator(TablePathAdaptator):
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38
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39
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40 ## Constructor
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41 #
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42 # @param db db instance
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43 # @param tableName string table name (default = "")
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44 #
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45 def __init__(self, db, tableName = ""):
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46 TablePathAdaptator.__init__(self, db, tableName)
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47 self._table_idx = "%s_idx" % (self._table)
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48
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49 ## Insert a path instance
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50 #
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51 # @param path a path instance
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52 # @param delayed boolean indicating if the insert must be delayed (default = false)
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53 #
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54 def insert( self, path, delayed = False ):
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55 TablePathAdaptator.insert(self, path, delayed)
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56 self._escapeAntislash(path)
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57 idx = path.range_query.findIdx()
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58 max = path.range_query.getMax()
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59 min = path.range_query.getMin()
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60 strand = path.range_query.isOnDirectStrand()
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61 if delayed:
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62 sql_cmd = 'INSERT DELAYED INTO %s VALUES (%d,%d,"%s",%d,%d,%d)'\
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63 % (self._table_idx,\
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64 path.id,\
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65 idx,\
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66 path.range_query.seqname,\
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67 min,\
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68 max,\
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69 strand)
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70 else:
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71 sql_cmd = 'INSERT INTO %s VALUES (%d,%d,"%s",%d,%d,%d)'\
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72 % (self._table_idx,\
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73 path.id,\
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74 idx,\
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75 path.range_query.seqname,\
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76 min,\
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77 max,\
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78 strand)
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79
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80 self._iDb.execute(sql_cmd)
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81
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82 ## Return a path instances list included in a given region using the bin scheme
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83 #
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84 # @param contig string contig name
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85 # @param start integer start coordinate
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86 # @param end integer end coordinate
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87 # @return lOutPath a path instances list
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88 #
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89 def getPathListIncludedInQueryCoord(self, contig, start, end):
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90 min_coord = min(start, end)
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91 max_coord = max(start, end)
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92 lpath = self.getChainListOverlappingQueryCoord(contig, start, end)
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93 lOutPath = []
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94 for i in lpath:
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95 if i.range_query.getMin() > min_coord and \
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96 i.range_query.getMax() < max_coord:
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97 lOutPath.append(i)
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98
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99 return lOutPath
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100
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101 ## Return a path instances list overlapping (and included) in a given region using the bin scheme
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102 #
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103 # @param contig string contig name
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104 # @param start integer start coordinate
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105 # @param end integer end coordinate
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106 # @return lOutPath a path instances list
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107 #
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108 def getPathListOverlappingQueryCoord(self, contig, start, end):
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109 min_coord = min(start, end)
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110 max_coord = max(start, end)
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111 lpath = self.getChainListOverlappingQueryCoord(contig, start, end)
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112 lOutPath = []
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113 for i in lpath:
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114 if ((i.range_query.getMin() <= min_coord and i.range_query.getMax() >= min_coord) or \
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115 (i.range_query.getMin() >= min_coord and i.range_query.getMin() <= max_coord) or \
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116 (i.range_query.getMin() <= min_coord and i.range_query.getMax() >= max_coord) or \
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117 (i.range_query.getMin() >= min_coord and i.range_query.getMax() <= max_coord)) and \
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118 (i.range_query.getSeqname() == contig):
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119 lOutPath.append(i)
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120
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121 return lOutPath
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122
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123 ## Return a path instances list chain (by Id and Coord in chr) list overlapping a given region using the bin scheme
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124 #
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125 # @param contig string contig name
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126 # @param start integer start coordinate
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127 # @param end integer end coordinate
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128 # @return lpath a path instances list
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129 #
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130 def getChainListOverlappingQueryCoord(self, contig, start, end):
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131 min_coord = min(start, end)
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132 max_coord = max(start, end)
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133 sql_cmd = 'select distinct path from %s where contig="%s" and ('\
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134 % (self._table + "_idx", contig)
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135
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136 for bin_lvl in xrange(6, 2, -1):
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137 if getIdx(start,bin_lvl) == getIdx(end, bin_lvl):
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138 idx = getIdx(start, bin_lvl)
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139 sql_cmd += 'idx=%d' % (idx)
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140 else:
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141 idx1 = getIdx(min_coord, bin_lvl)
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142 idx2 = getIdx(max_coord, bin_lvl)
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143 sql_cmd += 'idx between %d and %d' % (idx1, idx2)
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144 if bin_lvl > 3:
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145 sql_cmd += " or "
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146
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147 sql_cmd += ") and min<=%d and max>=%d;" % (max_coord, min_coord)
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148
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149
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150 self._iDb.execute(sql_cmd)
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151 res = self._iDb.fetchall()
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152 lnum = []
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153 for i in res:
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154 lnum.append( int(i[0]) )
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155 lpath = self.getPathListFromIdList(lnum)
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156 return lpath
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157
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158 ## Delete path corresponding to a given identifier number
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159 #
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160 # @param num integer identifier number
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161 #
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162 def deleteFromId(self, num):
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163 TablePathAdaptator.deleteFromId(self, num)
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164 sqlCmd='delete from %s where path=%d;' % (self._table_idx, num)
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165 self._iDb.execute(sqlCmd)
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166
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167 ## Delete path corresponding to a given list of identifier number
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168 #
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169 # @param lNum list list of integer identifier number
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170 #
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171 def deleteFromIdList(self, lNum):
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172 if lNum == []:
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173 return
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174 TablePathAdaptator.deleteFromIdList(self, lNum)
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175 sqlCmd = 'delete from %s where path=%d' % (self._table_idx, lNum[0])
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176 for i in lNum[1:]:
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177 sqlCmd += " or path=%d" % (i)
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178 sqlCmd += ";"
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179 self._iDb.execute(sqlCmd)
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180
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181 ## Join two path by changing id number of id1 and id2 path to the least of id1 and id2
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182 #
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183 # @param id1 integer id path number
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184 # @param id2 integer id path number
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185 # @return newId integer minimum of id1 id2
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186 # @note this method modify the ID even if this one not existing in the path table
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187 #
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188 def joinTwoPaths(self, id1, id2):
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189 TablePathAdaptator.joinTwoPaths(self, id1, id2)
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190 if id1 < id2:
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191 newId = id1
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192 oldId = id2
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193 else:
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194 newId = id2
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195 oldId = id1
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196 sqlCmd = 'UPDATE %s SET path=%d WHERE path=%d' % (self._table_idx, newId, oldId)
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197 self._iDb.execute(sqlCmd)
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198 return newId
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199
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200 ## Get a new id number
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201 #
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202 # @return newId integer max Id in path table + 1
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203 #
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204 def getNewId(self):
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205 sqlCmd = 'select max(path) from %s;' % (self._table_idx)
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206 self._iDb.execute(sqlCmd)
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207 maxId = self._iDb.fetchall()[0][0]
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208 if maxId == None:
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209 maxId = 0
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210 newId = int(maxId) + 1
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211 return newId
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212
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213 ## Give a list of Set instances included in a given region
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214 #
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215 # @param query string query name
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216 # @param start integer start coordinate
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217 # @param end integer end coordinate
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218 # @return lSet list of Set instances
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219 #
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220 def getSetListIncludedInQueryCoord(self, query, start, end):
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221 lPath=self.getPathListIncludedInQueryCoord(query, start, end)
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222 lSet = PathUtils.getSetListFromQueries(lPath)
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223 return lSet
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224
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225 ## Give a list of Set instances overlapping a given region
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226 #
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227 # @param query string query name
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228 # @param start integer start coordinate
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229 # @param end integer end coordinate
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230 # @return lSet list of Set instances
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231 #
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232 def getSetListOverlappingQueryCoord(self, query, start, end):
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233 lPath = self.getPathListOverlappingQueryCoord(query, start, end)
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234 lSet = PathUtils.getSetListFromQueries(lPath)
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235 return lSet
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236
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237 ## Give a list of identifiers contained in the table
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238 #
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239 # @return lId integer list
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240 #
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241 def getIdList(self):
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242 sqlCmd = "SELECT DISTINCT path from %s;" % (self._table_idx)
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243 lId = self._iDb.getIntegerListWithSQLCmd( sqlCmd )
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244 return lId
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245
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246 ## Give a list of the distinct query names present in the table
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247 #
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248 # @return lDistinctQueryNames string list
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249 #
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250 def getQueryList(self):
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251 lDistinctQueryNames = self._getDistinctTypeNamesList("query")
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252 return lDistinctQueryNames
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253
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254 def _getDistinctTypeNamesList( self, type ):
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255 sqlCmd = "SELECT DISTINCT contig FROM %s" % ( self._table_idx )
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256 lDistinctTypeNames = self._iDb.getStringListWithSQLCmd(sqlCmd)
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257 return lDistinctTypeNames |
