diff smart_toolShed/commons/core/sql/TableSeqAdaptator.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/commons/core/sql/TableSeqAdaptator.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,185 @@
+# Copyright INRA (Institut National de la Recherche Agronomique)
+# http://www.inra.fr
+# http://urgi.versailles.inra.fr
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use, 
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info". 
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability. 
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or 
+# data to be ensured and,  more generally, to use and operate it in the 
+# same conditions as regards security. 
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+
+import sys
+from commons.core.sql.TableAdaptator import TableAdaptator
+from commons.core.sql.ITableSeqAdaptator import ITableSeqAdaptator
+from commons.core.coord.SetUtils import SetUtils
+from commons.core.seq.Bioseq import Bioseq
+
+
+## Adaptator for a Seq table
+#
+class TableSeqAdaptator( TableAdaptator, ITableSeqAdaptator ):
+    
+    ## Retrieve all the distinct accession names in a list.
+    #
+    # @return lAccessions list of accessions
+    #
+    def getAccessionsList( self ):
+        sqlCmd = "SELECT DISTINCT accession FROM %s;" % ( self._table )
+        lAccessions = self._getStringListWithSQLCmd(sqlCmd)
+        return lAccessions
+    
+    ## Save sequences in a fasta file from a list of accession names.
+    # 
+    # @param lAccessions list of accessions
+    # @param outFileName string Fasta file
+    #
+    def saveAccessionsListInFastaFile( self, lAccessions, outFileName ):
+        outFile = open( outFileName, "w" )
+        for ac in lAccessions:
+            bs = self.getBioseqFromHeader( ac )
+            bs.write(outFile)
+        outFile.close()
+    
+    ## Get a bioseq instance given its header
+    #
+    # @param header string name of the sequence ('accession' field in the 'seq' table) 
+    # @return bioseq instance
+    #
+    def getBioseqFromHeader( self, header ):
+        sqlCmd = "SELECT * FROM %s WHERE accession='%s';" % ( self._table, header )
+        self._iDb.execute( sqlCmd )
+        res = self._iDb.fetchall()
+        return Bioseq( res[0][0], res[0][1] )
+        
+    ## Retrieve the length of a sequence given its name.
+    #
+    # @param accession name of the sequence
+    # @return seqLength integer length of the sequence
+    # 
+    def getSeqLengthFromAccession( self, accession ):
+        sqlCmd = 'SELECT length FROM %s WHERE accession="%s"' % ( self._table, accession )
+        seqLength = self._iDb.getIntegerWithSQLCmd(sqlCmd)
+        return seqLength
+    
+    ## Retrieve the length of a sequence given its description.
+    #
+    # @param description of the sequence
+    # @return seqLength integer length of the sequence
+    # 
+    def getSeqLengthFromDescription( self, description ):
+        sqlCmd = 'SELECT length FROM %s WHERE description="%s"' % ( self._table, description )
+        seqLength = self._iDb.getIntegerWithSQLCmd(sqlCmd)
+        return seqLength
+        
+    ## Retrieve all the accessions with length in a list of tuples
+    #
+    # @return lAccessionLengthTuples list of tuples
+    # 
+    def getAccessionAndLengthList(self):
+        sqlCmd = 'SELECT accession, length FROM %s' % self._table
+        self._iDb.execute(sqlCmd)
+        res = self._iDb.fetchall()
+        lAccessionLengthTuples = []
+        for i in res:
+            lAccessionLengthTuples.append(i)
+        return lAccessionLengthTuples
+    
+    ## get subsequence according to given parameters
+    #
+    # @param accession 
+    # @param start integer 
+    # @param end integer
+    # @return bioseq.sequence string
+    #
+    def getSubSequence( self, accession, start, end ):
+        bs = Bioseq()
+        if start <= 0 or end <= 0:
+            print "ERROR with coordinates start=%i or end=%i" % ( start, end )
+            sys.exit(1)
+            
+        if accession not in self.getAccessionsList():
+            print "ERROR: accession '%s' absent from table '%s'" % ( accession, self._table )
+            sys.exit(1)
+            
+        lengthAccession = self.getSeqLengthFromAccession( accession )
+        if start > lengthAccession or end > lengthAccession:
+            print "ERROR: coordinates start=%i end=%i out of sequence '%s' range (%i bp)" % ( start, end, accession, lengthAccession )
+            sys.exit(1)
+            
+        sqlCmd = "SELECT SUBSTRING(sequence,%i,%i) FROM %s WHERE accession='%s'" % ( min(start,end), abs(end-start)+ 1, self._table, accession )
+        self._iDb.execute( sqlCmd )
+        res = self._iDb.fetchall()
+        bs.setSequence( res[0][0] )
+        if start > end:
+            bs.reverseComplement()
+        return bs.sequence
+    
+    ## get bioseq from given set list
+    #
+    # @param lSets set list of sets 
+    # @return bioseq instance
+    #
+    def getBioseqFromSetList( self, lSets ):
+        header = "%s::%i %s " % ( lSets[0].name, lSets[0].id, lSets[0].seqname )
+        sequence = ""
+        lSortedSets = SetUtils.getSetListSortedByIncreasingMinThenMax( lSets )
+        if not lSets[0].isOnDirectStrand():
+            lSortedSets.reverse()
+        for iSet in lSortedSets:
+            header += "%i..%i," % ( iSet.getStart(), iSet.getEnd() )
+            sequence += self.getSubSequence( iSet.seqname, iSet.getStart(), iSet.getEnd() )
+        return Bioseq( header[:-1], sequence )
+    
+    ## Return True if the given accession is present in the table
+    #
+    def isAccessionInTable( self, name ):
+        sqlCmd = "SELECT accession FROM %s WHERE accession='%s'" % ( self._table, name )
+        self._iDb.execute( sqlCmd )
+        res = self._iDb.fetchall()
+        return bool(res)
+    
+    ## Retrieve all the distinct accession names in a fasta file.
+    #
+    # @param outFileName string Fasta file
+    # 
+    def exportInFastaFile(self, outFileName ):
+        lAccessions = self.getAccessionsList()
+        self.saveAccessionsListInFastaFile( lAccessions, outFileName )
+        
+    def _getStringListWithSQLCmd( self, sqlCmd ):
+        self._iDb.execute(sqlCmd)
+        res = self._iDb.fetchall()
+        lString = []
+        for i in res:
+            lString.append(i[0])
+        return lString
+   
+    def _getTypeAndAttr2Insert(self, bs):
+        type2Insert =  ( "'%s'", "'%s'", "'%s'", "'%i'" ) 
+        attr2Insert =  (bs.header.split()[0], bs.sequence, bs.header, bs.getLength())
+        return type2Insert, attr2Insert
+    
+    def _escapeAntislash(self, obj):
+        pass
+