Mercurial > repos > yufei-luo > s_mart
view commons/core/sql/TableSetAdaptator.py @ 14:c79b9ae3f65f
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author | m-zytnicki |
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date | Fri, 19 Apr 2013 10:13:11 -0400 |
parents | 769e306b7933 |
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# 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.ITableSetAdaptator import ITableSetAdaptator from commons.core.sql.TableAdaptator import TableAdaptator from commons.core.coord.Set import Set ## Adaptator for a Set table # class TableSetAdaptator( TableAdaptator, ITableSetAdaptator ): ## Give a list of Set instances having a given seq name # # @param seqName string seq name # @return lSet 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 + "'" lSet = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) return lSet ## Give a list of set instances overlapping a given region # # @param query string query name # @param start integer start coordinate # @param end integer end coordinate # @return lSet list of set 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) lSet = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) return lSet #TODO: to test !!! ## Give a list of Set instances overlapping a given region # # @note whole chains are returned, even if only a fragment overlap with the given region # @param query string query name # @param start integer start coordinate # @param end integer end coordinate # @return lSets list of Path instances # def getChainListOverlappingCoord(self, query, start, end): sqlCmd = "select distinct path 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) lIdentifiers = self._iDb.getIntegerListWithSQLCmd(sqlCmd) lSets = self.getSetListFromIdList(lIdentifiers) return lSets ## Give a list of identifier numbers contained in the table # # @return lId integer list # def getIdList(self): sqlCmd = "select distinct path from %s;" % (self._table) lId = self._iDb.getIntegerListWithSQLCmd( sqlCmd ) return lId ## 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 ## Give a list of Set instances having a given seq name # # @param seqName string seq name # @return lSet list of instances # def getSetListFromSeqName( self, seqName): lSets = self.getListFromSeqName(seqName) return lSets ## Give a set instances list with a given identifier number # # @param id integer identifier number # @return lSet list of set instances # def getSetListFromId(self, id): SQLCmd = "select * from %s where path=%d;" % (self._table, id) return self._iDb.getObjectListWithSQLCmd( SQLCmd, self._getInstanceToAdapt ) ## Give a set instances list with a list of identifier numbers # # @param lId integers list identifiers list numbers # @return lSet list of set instances # def getSetListFromIdList(self,lId): lSet = [] if lId == []: return lSet SQLCmd = "select * from %s where path=%d" % (self._table, lId[0]) for i in lId[1:]: SQLCmd += " or path=%d" % (i) SQLCmd += ";" return self._iDb.getObjectListWithSQLCmd( SQLCmd, self._getInstanceToAdapt ) ## 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 ): lSet = self.getListOverlappingCoord( seqName, start, end ) return lSet ## Delete set corresponding to a given identifier number # # @param id integer identifier number # def deleteFromId(self, id): sqlCmd = "delete from %s where path=%d;" % (self._table, id) self._iDb.execute(sqlCmd) ## Delete set corresponding to a given list of identifier number # # @param lId integers list list of identifier number # def deleteFromIdList(self, lId): if lId == []: return sqlCmd = "delete from %s where path=%d" % ( self._table, lId[0] ) for i in lId[1:]: sqlCmd += " or path=%d"%(i) sqlCmd += ";" self._iDb.execute(sqlCmd) ## Join two set by changing id number of id1 and id2 set to the least of id1 and id2 # # @param id1 integer id path number # @param id2 integer id path number # def joinTwoSets(self, id1, id2): if id1 < id2: newId = id1 oldId = id2 else: newId = id2 oldId = id1 sqlCmd = "UPDATE %s SET path=%d WHERE path=%d" % (self._table, newId, oldId) self._iDb.execute(sqlCmd) ## Get a new id number # # @return new_id integer max_id + 1 # def getNewId(self): sqlCmd = "select max(path) from %s;" % (self._table) maxId = self._iDb.getIntegerWithSQLCmd(sqlCmd) newId = int(maxId) + 1 return newId ## Give the data contained in the table as a list of Sets instances # # @return lSets list of set instances # def getListOfAllSets( self ): return self.getListOfAllCoordObject() def _getInstanceToAdapt(self): iSet = Set() return iSet def _getTypeColumAttr2Get(self, contig): colum2Get = 'chr' type2Get = '%s' attr2Get = contig return colum2Get, type2Get, attr2Get def _getTypeAndAttr2Insert(self, set): type2Insert = ("'%d'","'%s'","'%s'","'%d'","'%d'") attr2Insert = (set.id, set.name, set.seqname, set.start, set.end) return type2Insert, attr2Insert def _escapeAntislash(self, obj): obj.name = obj.name.replace("\\", "\\\\") obj.seqname = obj.seqname.replace("\\", "\\\\")