diff smart_toolShed/commons/core/sql/TableMatchAdaptator.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/TableMatchAdaptator.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,100 @@
+# 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.
+
+
+from commons.core.sql.TableAdaptator import TableAdaptator
+from commons.core.sql.ITableMatchAdaptator import ITableMatchAdaptator
+from commons.core.coord.Match import Match
+
+## Adaptator for Match table
+#
+class TableMatchAdaptator( TableAdaptator, ITableMatchAdaptator ):
+        
+    ## Give a list of Match instances given a query name
+    #
+    # @param query string sequence name
+    # @return lMatches list of Match instances
+    #
+    def getMatchListFromQuery( self, query ):
+        sqlCmd = "SELECT * FROM %s WHERE query_name='%s';" % ( self._table, query )
+        return self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
+    
+    ## Give a list of Match instances having the same identifier
+    #
+    # @param id integer identifier number
+    # @return lMatch a list of Match instances
+    #
+    def getMatchListFromId( self, id ):
+        sqlCmd = "SELECT * FROM %s WHERE path='%d';" % ( self._table, id )
+        lMatch = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
+        return lMatch
+    
+    ## Give a list of Match instances according to the given list of identifier numbers
+    #
+    # @param lId integer list 
+    # @return lMatch a list of Match instances
+    # 
+    def getMatchListFromIdList( self, lId ):
+        lMatch=[]
+        if lId == []:
+            return lMatch
+        sqlCmd = "select * from %s where path=%d" % (self._table, lId[0])
+        for i in lId[1:]:
+            sqlCmd += " or path=%d" % (i)
+        sqlCmd += ";"
+        lMatch = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
+        return lMatch
+    
+    ## Give the data contained in the table as a list of Match instances
+    #
+    # @return lMatchs list of match instances
+    #
+    def getListOfAllMatches( self ):
+        sqlCmd = "SELECT * FROM %s" % ( self._table )
+        lMatches = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
+        return lMatches    
+    
+    def _getInstanceToAdapt(self):
+        iMatch = Match()
+        return iMatch
+    
+    def _getTypeAndAttr2Insert(self, match):
+        type2Insert = ("'%s'","'%d'","'%d'","'%d'","'%f'","'%f'","'%s'","'%d'","'%d'","'%d'","'%f'","'%g'","'%d'","'%f'","'%d'")
+        attr2Insert = ( match.range_query.seqname, match.range_query.start, \
+                        match.range_query.end, match.query_length, match.query_length_perc, \
+                        match.match_length_perc, match.range_subject.seqname, match.range_subject.start,\
+                        match.range_subject.end, match.subject_length, match.subject_length_perc, \
+                        match.e_value, match.score, match.identity, \
+                        match.id)
+        return type2Insert, attr2Insert
+    
+    def _escapeAntislash(self, obj):
+        obj.range_query.seqname = obj.range_query.seqname.replace("\\", "\\\\")
+        obj.range_subject.seqname = obj.range_subject.seqname.replace("\\", "\\\\")