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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
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