diff options
Diffstat (limited to 'wqflask/dbFunction/webqtlDatabaseFunction.py')
| -rwxr-xr-x | wqflask/dbFunction/webqtlDatabaseFunction.py | 293 |
1 files changed, 146 insertions, 147 deletions
diff --git a/wqflask/dbFunction/webqtlDatabaseFunction.py b/wqflask/dbFunction/webqtlDatabaseFunction.py index 772e0526..7e33da3f 100755 --- a/wqflask/dbFunction/webqtlDatabaseFunction.py +++ b/wqflask/dbFunction/webqtlDatabaseFunction.py @@ -26,7 +26,7 @@ #webqtlDatabaseFunction.py # -#This file consists of various database related functions; the names are generally self-explanatory. +#This file consists of various database related functions; the names are generally self-explanatory. import MySQLdb import string @@ -49,63 +49,63 @@ def getCursor(): ########################################################################### #input: cursor, groupName (string) #output: mappingMethodId (int) info, value will be Null or else -#function: retrieve mappingMethodId info from InbredSet table -########################################################################### +#function: retrieve mappingMethodId info from InbredSet table +########################################################################### def getMappingMethod(cursor=None, groupName=None): - cursor.execute("select MappingMethodId from InbredSet where Name= '%s'" % groupName) - mappingMethodId = cursor.fetchone()[0] - return mappingMethodId + cursor.execute("select MappingMethodId from InbredSet where Name= '%s'" % groupName) + mappingMethodId = cursor.fetchone()[0] + return mappingMethodId ########################################################################### #input: cursor, inbredSetId (int), strainId (int) -#output: isMappingId (bull) info, value will be 0,1,2 or else, 0 or Null means -# "can not do mapping", >0 means "can do mapping", >1 means "there exsists +#output: isMappingId (bull) info, value will be 0,1,2 or else, 0 or Null means +# "can not do mapping", >0 means "can do mapping", >1 means "there exsists # redundant data, user needs to choose one to do mapping function" -#function: retrieve isMappingId info from StrainXRef table -########################################################################### - -def isMapping(cursor=None, inbredSetId=None, strainId=None): - cursor.execute("select IsMapping from StrainXRef where InbredSetId='%d' and StrainId = '%d'" %(inbredSetId, strainId)) - isMappingId = cursor.fetchone()[0] - return isMappingId +#function: retrieve isMappingId info from StrainXRef table +########################################################################### + +def isMapping(cursor=None, inbredSetId=None, strainId=None): + cursor.execute("select IsMapping from StrainXRef where InbredSetId='%d' and StrainId = '%d'" %(inbredSetId, strainId)) + isMappingId = cursor.fetchone()[0] + return isMappingId ########################################################################### #input: cursor, groupName (string) #output: all species data info (array), value will be Null or else -#function: retrieve all species info from Species table -########################################################################### +#function: retrieve all species info from Species table +########################################################################### def getAllSpecies(cursor=None): - cursor.execute("select Id, Name, MenuName, FullName, TaxonomyId,OrderId from Species Order by OrderId") - allSpecies = cursor.fetchall() - return allSpecies + cursor.execute("select Id, Name, MenuName, FullName, TaxonomyId,OrderId from Species Order by OrderId") + allSpecies = cursor.fetchall() + return allSpecies ########################################################################### #input: cursor, RISet (string) #output: specie's name (string), value will be None or else -#function: retrieve specie's name info based on RISet -########################################################################### +#function: retrieve specie's name info based on RISet +########################################################################### def retrieveSpecies(cursor=None, RISet=None): - try: - cursor.execute("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % RISet) - return cursor.fetchone()[0] - except: - return None + try: + cursor.execute("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % RISet) + return cursor.fetchone()[0] + except: + return None ########################################################################### #input: cursor, RISet (string) #output: specie's Id (string), value will be None or else -#function: retrieve specie's Id info based on RISet -########################################################################### - +#function: retrieve specie's Id info based on RISet +########################################################################### + def retrieveSpeciesId(cursor=None, RISet=None): - try: - cursor.execute("select SpeciesId from InbredSet where Name = '%s'" % RISet) - return cursor.fetchone()[0] - except: - return None + try: + cursor.execute("select SpeciesId from InbredSet where Name = '%s'" % RISet) + return cursor.fetchone()[0] + except: + return None ########################################################################### # input: cursor @@ -118,24 +118,24 @@ def retrieveSpeciesId(cursor=None, RISet=None): ########################################################################### def getTissueDataSet(cursor=None): - tissProbeSetFreezeIdList=[] - nameList =[] - fullNameList = [] - - query = "select Id,Name,FullName from TissueProbeSetFreeze; " - try: - cursor.execute(query) - result = cursor.fetchall() - - for row in result: - tissProbeSetFreezeIdList.append(row[0]) - nameList.append(row[1]) - fullNameList.append(row[2]) - except: - return None - - return tissProbeSetFreezeIdList,nameList,fullNameList - + tissProbeSetFreezeIdList=[] + nameList =[] + fullNameList = [] + + query = "select Id,Name,FullName from TissueProbeSetFreeze; " + try: + cursor.execute(query) + result = cursor.fetchall() + + for row in result: + tissProbeSetFreezeIdList.append(row[0]) + nameList.append(row[1]) + fullNameList.append(row[2]) + except: + return None + + return tissProbeSetFreezeIdList,nameList,fullNameList + ########################################################################### # input: cursor,GeneSymbol (string), and TissueProbeSetFreezeId (string) # output: geneId (string), dataId (string) @@ -143,42 +143,42 @@ def getTissueDataSet(cursor=None): ########################################################################### def getGeneIdDataIdForTissueBySymbol(cursor=None, GeneSymbol=None, TissueProbeSetFreezeId= 0): - query ="select GeneId, DataId from TissueProbeSetXRef where Symbol = '%s' and TissueProbeSetFreezeId=%s order by Mean desc" %(GeneSymbol,TissueProbeSetFreezeId) - try: - cursor.execute(query) - result = cursor.fetchone() - geneId = result[0] - dataId = result[1] - except: - geneId = 0 - dataId = 0 - - return geneId,dataId + query ="select GeneId, DataId from TissueProbeSetXRef where Symbol = '%s' and TissueProbeSetFreezeId=%s order by Mean desc" %(GeneSymbol,TissueProbeSetFreezeId) + try: + cursor.execute(query) + result = cursor.fetchone() + geneId = result[0] + dataId = result[1] + except: + geneId = 0 + dataId = 0 + + return geneId,dataId ########################################################################### # input: cursor, TissueProbeSetFreezeId (int) # output: chipId (int) -# function: retrieve chipId from TissueProbeFreeze table +# function: retrieve chipId from TissueProbeFreeze table ########################################################################### def getChipIdByTissueProbeSetFreezeId(cursor=None, TissueProbeSetFreezeId=None): - query = "select TissueProbeFreezeId from TissueProbeSetFreeze where Id =%s" % TissueProbeSetFreezeId - try: - cursor.execute(query) - result = cursor.fetchone() - TissueProbeFreezeId = result[0] - except: - TissueProbeFreezeId =0 - - query1 = "select ChipId from TissueProbeFreeze where Id =%s" % TissueProbeFreezeId - try: - cursor.execute(query1) - result1 = cursor.fetchone() - chipId = result1[0] - except: - chipId =0 - - return chipId + query = "select TissueProbeFreezeId from TissueProbeSetFreeze where Id =%s" % TissueProbeSetFreezeId + try: + cursor.execute(query) + result = cursor.fetchone() + TissueProbeFreezeId = result[0] + except: + TissueProbeFreezeId =0 + + query1 = "select ChipId from TissueProbeFreeze where Id =%s" % TissueProbeFreezeId + try: + cursor.execute(query1) + result1 = cursor.fetchone() + chipId = result1[0] + except: + chipId =0 + + return chipId ########################################################################### # input: cursor, TissueProbeSetFreezeId (int) @@ -186,80 +186,79 @@ def getChipIdByTissueProbeSetFreezeId(cursor=None, TissueProbeSetFreezeId=None): # function: retrieve how many tissue used in the specific dataset based on TissueProbeSetFreezeId ########################################################################### def getTissueCountByTissueProbeSetFreezeId(cursor=None, TissueProbeSetFreezeId=None): - query1 ="select DataId from TissueProbeSetXRef where TissueProbeSetFreezeId =%s limit 1" % TissueProbeSetFreezeId - try: - cursor.execute(query1) - result1 = cursor.fetchone() - DataId = result1[0] - - query2 =" select count(*) from TissueProbeSetData where Id=%s" % DataId - try: - cursor.execute(query2) - result2 = cursor.fetchone() - TissueCount = result2[0] - except: - TissueCount =0 - except: - TissueCount =0 - - return TissueCount - + query1 ="select DataId from TissueProbeSetXRef where TissueProbeSetFreezeId =%s limit 1" % TissueProbeSetFreezeId + try: + cursor.execute(query1) + result1 = cursor.fetchone() + DataId = result1[0] + + query2 =" select count(*) from TissueProbeSetData where Id=%s" % DataId + try: + cursor.execute(query2) + result2 = cursor.fetchone() + TissueCount = result2[0] + except: + TissueCount =0 + except: + TissueCount =0 + + return TissueCount + ########################################################################### # input: cursor, TissueProbeSetFreezeId (int) # output: DatasetName(string),DatasetFullName(string) # function: retrieve DatasetName, DatasetFullName based on TissueProbeSetFreezeId ########################################################################### def getDatasetNamesByTissueProbeSetFreezeId(cursor=None, TissueProbeSetFreezeId=None): - query ="select Name, FullName from TissueProbeSetFreeze where Id=%s" % TissueProbeSetFreezeId - try: - cursor.execute(query) - result = cursor.fetchone() - DatasetName = result[0] - DatasetFullName =result[1] - except: - DatasetName =None - DatasetFullName =None - - return DatasetName, DatasetFullName - + query ="select Name, FullName from TissueProbeSetFreeze where Id=%s" % TissueProbeSetFreezeId + try: + cursor.execute(query) + result = cursor.fetchone() + DatasetName = result[0] + DatasetFullName =result[1] + except: + DatasetName =None + DatasetFullName =None + + return DatasetName, DatasetFullName + ########################################################################### # input: cursor, geneIdLst (list) # output: geneIdSymbolPair(dict),key is geneId, value is geneSymbol # function: retrieve GeneId, GeneSymbol based on geneId List -########################################################################### +########################################################################### def getGeneIdSymbolPairByGeneId(cursor=None, geneIdLst =None): - geneIdSymbolPair={} - for geneId in geneIdLst: - geneIdSymbolPair[geneId]=None - - query ="select GeneId,GeneSymbol from GeneList where GeneId in (%s)" % string.join(geneIdLst, ", ") - try: - cursor.execute(query) - results = cursor.fetchall() - for item in results: - geneId =item[0] - geneSymbol =item[1] - geneIdSymbolPair[geneId]=geneSymbol - except: - geneIdSymbolPair=None - - return geneIdSymbolPair - - + geneIdSymbolPair={} + for geneId in geneIdLst: + geneIdSymbolPair[geneId]=None + + query ="select GeneId,GeneSymbol from GeneList where GeneId in (%s)" % string.join(geneIdLst, ", ") + try: + cursor.execute(query) + results = cursor.fetchall() + for item in results: + geneId =item[0] + geneSymbol =item[1] + geneIdSymbolPair[geneId]=geneSymbol + except: + geneIdSymbolPair=None + + return geneIdSymbolPair + + def updateTissueProbesetXRefByProbesetId(cursor=None, probesetId=None): - query ="select Symbol,GeneId,Chr,Mb,description, Probe_Target_Description from ProbeSet where Id =%s"%probesetId - try: - cursor.execute(query) - result =cursor.fetchone() - - updateQuery =''' - Update TissueProbeSetXRef - Set Symbol='%s',GeneId='%s', Chr='%s', Mb='%s', description ='%s',Probe_Target_Description='%s' - where ProbesetId=%s - '''%(result[0],result[1],result[2],result[3],result[4],result[5],probesetId) - - cursor.execute(updateQuery) - - except: - return None -
\ No newline at end of file + query ="select Symbol,GeneId,Chr,Mb,description, Probe_Target_Description from ProbeSet where Id =%s"%probesetId + try: + cursor.execute(query) + result =cursor.fetchone() + + updateQuery =''' + Update TissueProbeSetXRef + Set Symbol='%s',GeneId='%s', Chr='%s', Mb='%s', description ='%s',Probe_Target_Description='%s' + where ProbesetId=%s + '''%(result[0],result[1],result[2],result[3],result[4],result[5],probesetId) + + cursor.execute(updateQuery) + + except: + return None |