diff commons/core/sql/TableMapAdaptator.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/sql/TableMapAdaptator.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,193 @@
+# 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.ITableMapAdaptator import ITableMapAdaptator
+from commons.core.coord.Map import Map
+from commons.core.coord.MapUtils import MapUtils
+
+
+## Adaptator for Map table
+#
+class TableMapAdaptator( TableAdaptator, ITableMapAdaptator ):
+            
+    ## Give a list of Map instances having a given seq name
+    #
+    # @param seqName string seq name
+    # @return lMap list of instances
+    #
+    def getListFromSeqName( self, seqName ):
+        sqlCmd = "SELECT * FROM %s" % (self._table)
+        colum2Get, type2Get, attr2Get = self._getTypeColumAttr2Get(seqName)
+        sqlCmd += " WHERE " + colum2Get
+        sqlCmd += " = "
+        sqlCmd = sqlCmd + type2Get
+        sqlCmd = sqlCmd % "'" + attr2Get + "'"
+        return self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
+        
+    ## Give a list of Map instances overlapping a given region
+    #
+    # @param query string query name
+    # @param start integer start coordinate
+    # @param end integer end coordinate
+    # @return list map instances
+    #
+    def getListOverlappingCoord(self, query, start, end):
+        sqlCmd = 'select * from %s where chr="%s" and ((start between least(%d,%d) and greatest(%d,%d) or end between least(%d,%d) and greatest(%d,%d)) or (least(start,end)<=least(%d,%d) and greatest(start,end)>=greatest(%d,%d)))  ;' % (self._table, query, start, end, start, end, start, end, start, end, start, end, start, end)
+        return self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
+    
+    ## Give a list of Map instances having a given sequence name
+    #
+    # @param seqName string sequence name
+    # @return lMap list of instances
+    #
+    def getMapListFromSeqName(self, seqName):
+        lMap = self.getListFromSeqName( seqName )
+        return lMap
+    
+#TODO: Check getListFromSeqName method: uses name instead of seqname
+#    ## Give a list of Map instances having a given sequence name from list
+#    #
+#    # @param lSeqName string sequence name list
+#    # @return lMap list of instances
+#    #
+#    def getMapListFromSeqNameList(self, lSeqName):
+#        lMap = []
+#        [lMap.extend(self.getListFromSeqName(seqName)) for seqName in lSeqName]
+#        return lMap
+    
+    ## Give a list of Map instances having a given chromosome
+    #
+    # @param chr string chromosome
+    # @return lMap list of instances
+    #
+    def getMapListFromChr(self, chr):
+        sqlCmd = "SELECT * FROM %s WHERE chr='%s'" % (self._table, chr)
+        lMap = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
+        return lMap
+
+    ## Give a list of the distinct seqName/chr present in the table
+    #
+    # @return lDistinctContigNames string list
+    #
+    def getSeqNameList(self):
+        sqlCmd = "SELECT DISTINCT chr FROM %s" % ( self._table )
+        lDistinctContigNames = self._iDb.getStringListWithSQLCmd(sqlCmd)
+        return lDistinctContigNames
+    
+    ## Return a list of Set instances from a given sequence name
+    #
+    # @param seqName string sequence name
+    # @return lSets list of Set instances
+    # 
+    def getSetListFromSeqName( self, seqName ):
+        lMaps = self.getListFromSeqName( seqName )
+        lSets = MapUtils.mapList2SetList( lMaps )
+        return lSets
+    
+    ## Give a map instances list overlapping a given region
+    #
+    # @param seqName string seq name
+    # @param start integer start coordinate
+    # @param end integer end coordinate
+    # @return lMap list of map instances
+    #
+    def getMapListOverlappingCoord(self, seqName, start, end):
+        lMap = self.getListOverlappingCoord(seqName, start, end)
+        return lMap
+    
+    ## Return a list of Set instances overlapping a given sequence
+    #   
+    # @param seqName string sequence name
+    # @param start integer start coordinate
+    # @param end integer end coordinate
+    # @return lSet list of Set instances
+    #
+    def getSetListOverlappingCoord( self, seqName, start, end ):
+        lMaps = self.getListOverlappingCoord( seqName, start, end )
+        lSets = MapUtils.mapList2SetList( lMaps )
+        return lSets
+    
+    ## Give a dictionary which keys are Map names and values the corresponding Map instances
+    #
+    # @return dName2Maps dict which keys are Map names and values the corresponding Map instances
+    #
+    def getDictPerName( self ):
+        dName2Maps = {}
+        lMaps = self.getListOfAllMaps()
+        for iMap in lMaps:
+            if dName2Maps.has_key( iMap.name ):
+                if iMap == dName2Maps[ iMap.name ]:
+                    continue
+                else:
+                    msg = "ERROR: in table '%s' two different Map instances have the same name '%s'" % ( self._table, iMap.name )
+                    sys.stderr.write( "%s\n" % ( msg ) )
+                    sys.exit(1)
+            dName2Maps[ iMap.name ] = iMap
+        return dName2Maps
+    
+    ## Return a list of Map instances with all the data contained in the table
+    #
+    # @return lMaps list of Map instances
+    #
+    def getListOfAllMaps( self ):
+        sqlCmd = "SELECT * FROM %s" % ( self._table )
+        lMaps = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
+        return lMaps
+    
+    ## Give the end of map as integer
+    #
+    # @return end integer the end of map 
+    #
+    def getEndFromSeqName(self, seqName):
+        sqlCmd = "SELECT end FROM %s WHERE chr = '%s'" % (self._table, seqName)
+        end = self._iDb.getIntegerWithSQLCmd(sqlCmd)
+        return end
+    
+    def _getInstanceToAdapt(self):
+        iMap = Map()
+        return iMap
+
+    def _getTypeColumAttr2Get(self, name):
+        colum2Get = 'name'
+        type2Get = '%s'
+        attr2Get = name
+        return colum2Get, type2Get, attr2Get
+    
+    def _getTypeAndAttr2Insert(self, map):
+        type2Insert = ("'%s'","'%s'","'%d'","'%d'")
+        attr2Insert = (map.name, map.seqname, map.start, map.end)
+        return type2Insert, attr2Insert
+
+    def _escapeAntislash(self, obj):
+        obj.name = obj.name.replace("\\", "\\\\")
+        obj.seqname = obj.seqname.replace("\\", "\\\\")