comparison smart_toolShed/commons/core/sql/TableMapAdaptator.py @ 0:e0f8dcca02ed

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

0:e0f8dcca02ed

# Copyright INRA (Institut National de la Recherche Agronomique)
# http://www.inra.fr
# http://urgi.versailles.inra.fr
#
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#
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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("\\", "\\\\")