Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/sql/TableSeqAdaptator.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.ITableSeqAdaptator import ITableSeqAdaptator |
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35 from commons.core.coord.SetUtils import SetUtils |
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36 from commons.core.seq.Bioseq import Bioseq |
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37 |
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38 |
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39 ## Adaptator for a Seq table |
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40 # |
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41 class TableSeqAdaptator( TableAdaptator, ITableSeqAdaptator ): |
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42 |
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43 ## Retrieve all the distinct accession names in a list. |
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44 # |
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45 # @return lAccessions list of accessions |
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46 # |
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47 def getAccessionsList( self ): |
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48 sqlCmd = "SELECT DISTINCT accession FROM %s;" % ( self._table ) |
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49 lAccessions = self._getStringListWithSQLCmd(sqlCmd) |
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50 return lAccessions |
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51 |
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52 ## Save sequences in a fasta file from a list of accession names. |
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53 # |
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54 # @param lAccessions list of accessions |
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55 # @param outFileName string Fasta file |
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56 # |
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57 def saveAccessionsListInFastaFile( self, lAccessions, outFileName ): |
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58 outFile = open( outFileName, "w" ) |
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59 for ac in lAccessions: |
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60 bs = self.getBioseqFromHeader( ac ) |
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61 bs.write(outFile) |
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62 outFile.close() |
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63 |
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64 ## Get a bioseq instance given its header |
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65 # |
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66 # @param header string name of the sequence ('accession' field in the 'seq' table) |
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67 # @return bioseq instance |
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68 # |
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69 def getBioseqFromHeader( self, header ): |
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70 sqlCmd = "SELECT * FROM %s WHERE accession='%s';" % ( self._table, header ) |
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71 self._iDb.execute( sqlCmd ) |
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72 res = self._iDb.fetchall() |
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73 return Bioseq( res[0][0], res[0][1] ) |
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74 |
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75 ## Retrieve the length of a sequence given its name. |
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76 # |
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77 # @param accession name of the sequence |
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78 # @return seqLength integer length of the sequence |
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79 # |
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80 def getSeqLengthFromAccession( self, accession ): |
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81 sqlCmd = 'SELECT length FROM %s WHERE accession="%s"' % ( self._table, accession ) |
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82 seqLength = self._iDb.getIntegerWithSQLCmd(sqlCmd) |
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83 return seqLength |
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84 |
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85 ## Retrieve the length of a sequence given its description. |
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86 # |
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87 # @param description of the sequence |
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88 # @return seqLength integer length of the sequence |
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89 # |
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90 def getSeqLengthFromDescription( self, description ): |
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91 sqlCmd = 'SELECT length FROM %s WHERE description="%s"' % ( self._table, description ) |
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92 seqLength = self._iDb.getIntegerWithSQLCmd(sqlCmd) |
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93 return seqLength |
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94 |
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95 ## Retrieve all the accessions with length in a list of tuples |
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96 # |
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97 # @return lAccessionLengthTuples list of tuples |
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98 # |
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99 def getAccessionAndLengthList(self): |
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100 sqlCmd = 'SELECT accession, length FROM %s' % self._table |
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101 self._iDb.execute(sqlCmd) |
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102 res = self._iDb.fetchall() |
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103 lAccessionLengthTuples = [] |
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104 for i in res: |
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105 lAccessionLengthTuples.append(i) |
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106 return lAccessionLengthTuples |
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107 |
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108 ## get subsequence according to given parameters |
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109 # |
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110 # @param accession |
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111 # @param start integer |
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112 # @param end integer |
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113 # @return bioseq.sequence string |
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114 # |
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115 def getSubSequence( self, accession, start, end ): |
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116 bs = Bioseq() |
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117 if start <= 0 or end <= 0: |
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118 print "ERROR with coordinates start=%i or end=%i" % ( start, end ) |
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119 sys.exit(1) |
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120 |
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121 if accession not in self.getAccessionsList(): |
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122 print "ERROR: accession '%s' absent from table '%s'" % ( accession, self._table ) |
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123 sys.exit(1) |
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124 |
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125 lengthAccession = self.getSeqLengthFromAccession( accession ) |
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126 if start > lengthAccession or end > lengthAccession: |
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127 print "ERROR: coordinates start=%i end=%i out of sequence '%s' range (%i bp)" % ( start, end, accession, lengthAccession ) |
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128 sys.exit(1) |
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129 |
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130 sqlCmd = "SELECT SUBSTRING(sequence,%i,%i) FROM %s WHERE accession='%s'" % ( min(start,end), abs(end-start)+ 1, self._table, accession ) |
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131 self._iDb.execute( sqlCmd ) |
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132 res = self._iDb.fetchall() |
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133 bs.setSequence( res[0][0] ) |
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134 if start > end: |
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135 bs.reverseComplement() |
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136 return bs.sequence |
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137 |
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138 ## get bioseq from given set list |
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139 # |
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140 # @param lSets set list of sets |
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141 # @return bioseq instance |
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142 # |
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143 def getBioseqFromSetList( self, lSets ): |
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144 header = "%s::%i %s " % ( lSets[0].name, lSets[0].id, lSets[0].seqname ) |
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145 sequence = "" |
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146 lSortedSets = SetUtils.getSetListSortedByIncreasingMinThenMax( lSets ) |
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147 if not lSets[0].isOnDirectStrand(): |
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148 lSortedSets.reverse() |
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149 for iSet in lSortedSets: |
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150 header += "%i..%i," % ( iSet.getStart(), iSet.getEnd() ) |
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151 sequence += self.getSubSequence( iSet.seqname, iSet.getStart(), iSet.getEnd() ) |
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152 return Bioseq( header[:-1], sequence ) |
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153 |
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154 ## Return True if the given accession is present in the table |
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155 # |
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156 def isAccessionInTable( self, name ): |
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157 sqlCmd = "SELECT accession FROM %s WHERE accession='%s'" % ( self._table, name ) |
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158 self._iDb.execute( sqlCmd ) |
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159 res = self._iDb.fetchall() |
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160 return bool(res) |
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161 |
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162 ## Retrieve all the distinct accession names in a fasta file. |
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163 # |
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164 # @param outFileName string Fasta file |
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165 # |
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166 def exportInFastaFile(self, outFileName ): |
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167 lAccessions = self.getAccessionsList() |
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168 self.saveAccessionsListInFastaFile( lAccessions, outFileName ) |
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169 |
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170 def _getStringListWithSQLCmd( self, sqlCmd ): |
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171 self._iDb.execute(sqlCmd) |
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172 res = self._iDb.fetchall() |
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173 lString = [] |
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174 for i in res: |
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175 lString.append(i[0]) |
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176 return lString |
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177 |
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178 def _getTypeAndAttr2Insert(self, bs): |
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179 type2Insert = ( "'%s'", "'%s'", "'%s'", "'%i'" ) |
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180 attr2Insert = (bs.header.split()[0], bs.sequence, bs.header, bs.getLength()) |
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181 return type2Insert, attr2Insert |
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182 |
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183 def _escapeAntislash(self, obj): |
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184 pass |
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185 |