Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/sql/TableBinSetAdaptator.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 from commons.core.sql.TableSetAdaptator import TableSetAdaptator |
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32 from commons.core.coord.SetUtils import SetUtils |
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33 |
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34 ## Adaptator for Set tables with bin indexes |
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35 # |
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36 class TableBinSetAdaptator(TableSetAdaptator): |
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37 |
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38 ## constructor |
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39 # |
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40 # @param iDb DbMySql instance instance of DbMySql |
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41 # @param tableName string table name (default = "") |
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42 # |
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43 def __init__(self, iDb, tableName = ""): |
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44 TableSetAdaptator.__init__(self, iDb, tableName) |
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45 self._table_idx = "%s_idx" % (self._table) |
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46 |
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47 ## Insert a set instance in a set bin table |
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48 # |
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49 # @param iSet set instance an instance of set object |
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50 # @param delayed boolean an insert delayed or not |
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51 # |
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52 def insASetInSetAndBinTable(self, iSet, delayed = False): |
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53 self.insert(iSet, delayed) |
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54 iSet.seqname = iSet.seqname.replace("\\", "\\\\") |
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55 iSet.name = iSet.name.replace("\\", "\\\\") |
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56 bin = iSet.getBin() |
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57 max = iSet.getMax() |
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58 min = iSet.getMin() |
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59 strand = iSet.isOnDirectStrand() |
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60 sql_prefix = '' |
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61 if delayed: |
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62 sql_prefix = 'INSERT DELAYED INTO ' |
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63 else: |
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64 sql_prefix = 'INSERT INTO ' |
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65 sql_cmd = sql_prefix + '%s VALUES (%d,%f,"%s",%d,%d,%d)'\ |
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66 %(self._table_idx,\ |
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67 iSet.id,\ |
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68 bin,\ |
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69 iSet.seqname,\ |
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70 min,\ |
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71 max,\ |
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72 strand) |
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73 self._iDb.execute(sql_cmd) |
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74 |
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75 ## Delete set corresponding to a given identifier number in set and bin set table |
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76 # @param id integer identifier number |
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77 # @note old name was delSet_from_num |
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78 # |
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79 def deleteFromIdFromSetAndBinTable(self, id): |
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80 self.deleteFromId(id) |
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81 sql_cmd = 'delete from %s where path=%d' % (self._table_idx, id) |
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82 self._iDb.execute(sql_cmd) |
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83 |
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84 ## Delete path corresponding to a given list of identifier number |
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85 # |
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86 # @param lId integer list list of identifier number |
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87 # @note old name was delSet_from_listnum |
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88 # |
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89 def deleteFromListIdFromSetAndBinTable(self, lId): |
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90 if lId != []: |
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91 self.deleteFromIdList(lId) |
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92 sql_cmd = 'delete from %s where path=%d' % (self._table_idx, lId[0]) |
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93 for i in lId[1:]: |
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94 sql_cmd += " or path=%d" % (i) |
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95 self._iDb.execute(sql_cmd) |
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96 |
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97 ## Join two set by changing id number of id1 and id2 path |
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98 # to the least of id1 and id2 |
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99 # |
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100 # @param id1 integer id path number |
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101 # @param id2 integer id path number |
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102 # @return id integer new id |
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103 # @note old name was joinSet |
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104 # |
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105 def joinTwoSetsFromSetAndBinTable(self, id1, id2): |
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106 self.joinTwoSets(id1, id2) |
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107 if id1 < id2: |
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108 new_id = id1 |
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109 old_id = id2 |
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110 else: |
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111 new_id = id2 |
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112 old_id = id1 |
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113 sql_cmd = 'UPDATE %s SET path=%d WHERE path=%d'\ |
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114 % (self._table_idx, new_id, old_id) |
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115 self._iDb.execute(sql_cmd) |
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116 return new_id |
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117 |
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118 ## Get a new id number from set bin table |
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119 # |
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120 def getNewId(self): |
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121 sql_cmd = 'select max(path) from %s;' % (self._table_idx) |
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122 self._iDb.execute(sql_cmd) |
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123 max_id = self._iDb.fetchall()[0][0] |
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124 if max_id != None: |
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125 return int(max_id)+1 |
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126 else: |
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127 return 1 |
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128 |
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129 ## Get a set list instance between start and end parameters |
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130 # using the bin scheme |
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131 # |
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132 # @param seqName reference seq name |
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133 # @param start start coordinate |
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134 # @param end end coordinate |
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135 # @return lSet set list |
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136 # @note old name was getSetList_from_qcoord |
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137 # |
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138 def getSetListFromQueryCoord(self, seqName, start, end): |
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139 |
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140 min_coord = min(start,end) |
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141 max_coord = max(start,end) |
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142 |
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143 sql_cmd = 'select path from %s where contig="%s" and ('\ |
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144 % (self._table + "_idx", seqName) |
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145 for i in xrange(8, 2, -1): |
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146 bin_lvl = pow(10, i) |
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147 if int(start/bin_lvl) == int(end/bin_lvl): |
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148 bin = float(bin_lvl + (int(start / bin_lvl) / 1e10)) |
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149 sql_cmd += 'bin=%f' % (bin) |
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150 else: |
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151 bin1 = float(bin_lvl + (int(start / bin_lvl) / 1e10)) |
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152 bin2 = float(bin_lvl + (int(end /bin_lvl) / 1e10)) |
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153 sql_cmd += 'bin between %f and %f' % (bin1, bin2) |
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154 if bin_lvl != 1000: |
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155 sql_cmd += " or " |
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156 |
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157 sql_cmd += ") and min<=%d and max>=%d" % (max_coord, min_coord); |
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158 self._iDb.execute(sql_cmd) |
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159 res = self._iDb.fetchall() |
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160 lId = [] |
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161 for i in res: |
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162 lId.append(int(i[0])) |
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163 lSet = self.getSetListFromIdList(lId) |
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164 return lSet |
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165 |
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166 ## Get a set list instances strictly included between start and end parameters |
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167 # using the bin scheme |
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168 # |
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169 # @param seqName reference seq name |
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170 # @param start start coordinate |
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171 # @param end end coordinate |
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172 # @return lSet set list |
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173 # @note old name was getInSetList_from_qcoord |
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174 # @warning the implementation has been changed : I added the two first lines |
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175 # |
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176 def getSetListStrictlyIncludedInQueryCoord(self, contig, start, end): |
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177 min_coord = min(start,end) |
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178 max_coord = max(start,end) |
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179 lSet = self.getSetListFromQueryCoord(contig, start, end) |
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180 lSetStrictlyIncluded = [] |
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181 for iSet in lSet: |
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182 if iSet.getMin() > min_coord and \ |
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183 iSet.getMax() < max_coord: |
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184 lSetStrictlyIncluded.append(iSet) |
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185 |
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186 return lSetStrictlyIncluded |
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187 |
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188 ## Get a list of the identifier Id contained in the table bin |
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189 # |
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190 # @return lId list of int list of identifier |
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191 # @note old name was getSet_num |
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192 # |
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193 def getIdList(self): |
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194 sql_cmd = 'select distinct path from %s;' % (self._table_idx) |
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195 self._iDb.execute(sql_cmd) |
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196 res = self._iDb.fetchall() |
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197 lId = [] |
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198 for t in res: |
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199 lId.append(int(t[0])) |
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200 return lId |
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201 |
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202 ## Get a list of the query sequence name contained in the table bin |
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203 # |
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204 # @return lSeqName list of string list of query sequence name |
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205 # @note old name was getContig_name |
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206 # |
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207 def getSeqNameList(self): |
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208 sql_cmd = 'select distinct contig from %s;' % (self._table_idx) |
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209 self._iDb.execute(sql_cmd) |
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210 res = self._iDb.fetchall() |
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211 lSeqName = [] |
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212 for t in res: |
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213 lSeqName.append(t[0]) |
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214 return lSeqName |
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215 |
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216 ## Insert a Set list with the same new identifier in the table bin and set |
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217 # |
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218 # @note old name was insAddSetList |
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219 # |
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220 def insertListInSetAndBinTable(self, lSets, delayed = False): |
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221 id = self.getNewId() |
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222 SetUtils.changeIdInList( lSets, id ) |
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223 for iSet in lSets: |
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224 self.insASetInSetAndBinTable(iSet, delayed) |
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225 |
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226 ## Insert a set list instances In table Bin and Set and merge all overlapping sets |
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227 # |
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228 # @param lSets reference seq name |
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229 # @note old name was insMergeSetList |
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230 # |
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231 def insertListInSetAndBinTableAndMergeAllSets(self, lSets): |
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232 min, max = SetUtils.getListBoundaries(lSets) |
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233 oldLSet = self.getSetListFromQueryCoord(lSets[0].seqname, min, max) |
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234 oldQueryhash = SetUtils.getDictOfListsWithIdAsKey(oldLSet) |
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235 qhash = SetUtils.getDictOfListsWithIdAsKey(lSets) |
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236 for lNewSetById in qhash.values(): |
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237 found = False |
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238 for currentId, oldLsetById in oldQueryhash.items(): |
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239 if SetUtils.areSetsOverlappingBetweenLists(lNewSetById, oldLsetById): |
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240 oldLsetById.extend(lNewSetById) |
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241 oldLsetById = SetUtils.mergeSetsInList(oldLsetById) |
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242 self.deleteFromIdFromSetAndBinTable(currentId) |
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243 found = True |
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244 if not found: |
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245 self.insertListInSetAndBinTable(lNewSetById) |
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246 else: |
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247 id = self.getNewId() |
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248 SetUtils.changeIdInList(oldLsetById, id) |
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249 self.insertListInSetAndBinTable(oldLsetById) |
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250 |
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251 ## Insert a set list instances In table Bin and Set after removing all overlaps between database and lSets |
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252 # |
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253 # @param lSets reference seq name |
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254 # @note old name was insDiffSetList |
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255 # |
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256 def insertListInSetAndBinTableAndRemoveOverlaps(self, lSets): |
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257 min, max = SetUtils.getListBoundaries(lSets) |
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258 oldLSet = self.getSetListFromQueryCoord(lSets[0].seqname, min, max) |
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259 oldQueryHash = SetUtils.getDictOfListsWithIdAsKey(oldLSet) |
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260 newQueryHash = SetUtils.getDictOfListsWithIdAsKey(lSets) |
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261 for lNewSetById in newQueryHash.values(): |
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262 for lOldSetById in oldQueryHash.values(): |
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263 if SetUtils.areSetsOverlappingBetweenLists(lNewSetById, lOldSetById): |
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264 lNewSetById = SetUtils.getListOfSetWithoutOverlappingBetweenTwoListOfSet(lOldSetById, lNewSetById) |
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265 self.insertListInSetAndBinTable(lNewSetById) |