Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

1 files changed, 0 insertions, 658 deletions

diff --git a/web/webqtl/qtlminer/GeneUtil.py b/web/webqtl/qtlminer/GeneUtil.py
deleted file mode 100755
index 3ae7f3c0..00000000
--- a/web/webqtl/qtlminer/GeneUtil.py
+++ /dev/null
@@ -1,658 +0,0 @@
-import string
-import os
-
-
-from base import webqtlConfig
-
-
-#Just return a list of dictionaries
-#each dictionary contains sub-dictionary
-def loadGenes(cursor, chrName, diffCol, startMb, endMb, webqtlDb =None, species='mouse'):
-	#cursor.execute("desc GeneList")
-	#results = cursor.fetchall()
-	#fetchFields = map(lambda X:X[0], results)
-	fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd', 
-	'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID', 
-	'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd']
-	
-	##List All Species in the Gene Table
-	speciesDict = {}
-	cursor.execute("select Species.Name, GeneList.SpeciesId from Species, GeneList where \
-			GeneList.SpeciesId = Species.Id group by GeneList.SpeciesId")
-	results = cursor.fetchall()
-	for item in results:
-		speciesDict[item[0]] = item[1]
-	
-	##List current Species and other Species
-	speciesId = speciesDict[species]
-	otherSpecies = map(lambda X: [X, speciesDict[X]], speciesDict.keys())
-	otherSpecies.remove([species, speciesId])
-
-	cursor.execute("""SELECT %s from GeneList 
-						where 
-					SpeciesId = %d AND Chromosome = '%s' AND
-					((TxStart > %f and TxStart <= %f) OR (TxEnd > %f and TxEnd <= %f))
-					order by txStart
-					""" 
-					% (string.join(fetchFields, ", "), speciesId, chrName, startMb, endMb, startMb, endMb))
-	results = cursor.fetchall()
-	GeneList = []
-
-	if results:
-		for result in results:
-			newdict = {}
-			for j, item in enumerate(fetchFields):
-				newdict[item] = result[j]
-			#count SNPs if possible	
-			if diffCol and species=='mouse':
-				cursor.execute("""
-					select 
-						count(*) from BXDSnpPosition
-					where 
-						Chr = '%s' AND Mb >= %2.6f AND Mb < %2.6f AND
-						StrainId1 = %d AND StrainId2 = %d
-				""" % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1]))
-				newdict["snpCount"] = cursor.fetchone()[0]
-				newdict["snpDensity"] = newdict["snpCount"]/(newdict["TxEnd"]-newdict["TxStart"])/1000.0
-			else:
-				newdict["snpDensity"] = newdict["snpCount"] = 0
-			
-			try:
-				newdict['GeneLength'] = 1000.0*(newdict['TxEnd'] - newdict['TxStart'])
-			except:
-				pass
-			
-			#load gene from other Species by the same name
-			for item in otherSpecies:
-				othSpec, othSpecId = item
-				newdict2 = {}
-				
-				cursor.execute("SELECT %s from GeneList where SpeciesId = %d and geneSymbol= '%s' limit 1" % 
-							(string.join(fetchFields, ", "), othSpecId, newdict["GeneSymbol"]))
-				resultsOther = cursor.fetchone()
-				if resultsOther:
-					for j, item in enumerate(fetchFields):
-						newdict2[item] = resultsOther[j]
-							
-					#count SNPs if possible, could be a separate function	
-					if diffCol and othSpec == 'mouse':
-						cursor.execute("""
-							select
-								count(*) from BXDSnpPosition
-							where
-								Chr = '%s' AND Mb >= %2.6f AND Mb < %2.6f AND
-								StrainId1 = %d AND StrainId2 = %d
-							""" % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1]))
-
-
-
-						newdict2["snpCount"] = cursor.fetchone()[0]
-						newdict2["snpDensity"] = newdict2["snpCount"]/(newdict2["TxEnd"]-newdict2["TxStart"])/1000.0
-					else:
-						newdict2["snpDensity"] = newdict2["snpCount"] = 0
-						
-					try:
-						newdict2['GeneLength'] = 1000.0*(newdict2['TxEnd'] - newdict2['TxStart'])
-					except:
-						pass
-						
-				newdict['%sGene' % othSpec] = newdict2
-				
-			GeneList.append(newdict)
-
-	return GeneList
-
-
-
-
-
-
-def loadGenesForQTLminer(cursor, chrName, diffCol, startMb, endMb, webqtlDb =None, species='mouse', databaseA='HC_M2_0606_P', databaseB='HC_M2CB_1205_R', databaseC='Illum_LXS_Hipp_loess0807', str1='C57BL/6J', str2='DBA/2J'):
-	#cursor.execute("desc GeneList")
-	#results = cursor.fetchall()
-	#fetchFields = map(lambda X:X[0], results)
-	fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd', 
-	'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID', 
-	'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd']
-	
-	##List All Species in the Gene Table
-	speciesDict = {}
-	cursor.execute("select Species.Name, GeneList.SpeciesId from Species, GeneList where \
-			GeneList.SpeciesId = Species.Id group by GeneList.SpeciesId")
-	results = cursor.fetchall()
-	for item in results:
-		speciesDict[item[0]] = item[1]
-
-
-#		fpText = open(os.path.join(webqtlConfig.TMPDIR, "strains") + str(j) + '.txt','wb')
-#		fpText.write("strain:  '%d'  \n" % thisone  )
-#		fpText.close()
-#		strainids.append(thisone)
-
-
-
-	
-	##List current Species and other Species
-	speciesId = speciesDict[species]
-	otherSpecies = map(lambda X: [X, speciesDict[X]], speciesDict.keys())
-	otherSpecies.remove([species, speciesId])
-
-	cursor.execute("""SELECT %s from GeneList 
-						where 
-					SpeciesId = %d AND Chromosome = '%s' AND
-					((TxStart > %f and TxStart <= %f) OR (TxEnd > %f and TxEnd <= %f))
-					order by txStart
-					""" 
-					% (string.join(fetchFields, ", "), speciesId, chrName, startMb, endMb, startMb, endMb))
-	results = cursor.fetchall()
-	GeneList = []
-	
-	if results:
-		for result in results:
-			newdict = {}
-			for j, item in enumerate(fetchFields):
-				newdict[item] = result[j]
-
-## get pathways
-
-			cursor.execute("""
-			    select 
-					pathway						
-				FROM
-				    kegg.mmuflat
-				where 
-					gene = '%s' 
-				""" % (newdict["GeneID"]) )
-				
-			resAAA = cursor.fetchall()
-			if resAAA:
-				myFields = ['pathways']
-				for j, item in enumerate(myFields):
-					temp = []
-					for k in resAAA:
-						temp.append(k[j])
-					newdict["pathways"] = temp 
-			
-			cursor.execute("""
-			    select 
-					name						
-				FROM
-				    kegg.mmuflat
-				where 
-					gene = '%s' 
-				""" % (newdict["GeneID"]) )
-				
-			resAAA = cursor.fetchall()
-			if resAAA:
-				myFields = ['pathwaynames']
-				for j, item in enumerate(myFields):
-					temp = []
-					for k in resAAA:
-						temp.append(k[j])
-					newdict["pathwaynames"] = temp 
-
-## get GO terms
-
-			cursor.execute("""
-			    SELECT
-				  distinct go.term.name
-				FROM   go.gene_product
-				  INNER JOIN go.dbxref ON (go.gene_product.dbxref_id=go.dbxref.id)
-				  INNER JOIN go.association ON (go.gene_product.id=go.association.gene_product_id)
-				  INNER JOIN go.term ON (go.association.term_id=go.term.id)
-				WHERE
-				  go.dbxref.xref_key = (select mgi from go.genemgi where gene='%s' limit 1)
-				AND
-				  go.dbxref.xref_dbname = 'MGI'
-				AND
-				  go.term.term_type='biological_process'
-				""" % (newdict["GeneID"]) )
-
-			resAAA = cursor.fetchall()
-			if resAAA:
-				myFields = ['goterms']
-				for j, item in enumerate(myFields):
-					temp = []
-					for k in resAAA:
-						temp.append(k[j])
-					newdict["goterms"] = temp 
-			
-
-
-
-
-
-			newdict["snpDensity"] = newdict["snpCount"] = newdict["snpCountall"] = newdict["snpCountmis"] = newdict["snpCountBXD"] = newdict["snpCountmissel"] = 0
-
-			#count SNPs if possible	
-			if diffCol and species=='mouse':
-				cursor.execute("""
-					select 
-						count(*) from BXDSnpPosition
-					where 
-						Chr = '%s' AND Mb >= %2.6f AND Mb < %2.6f AND
-						StrainId1 = %d AND StrainId2 = %d
-				""" % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1]))
-				newdict["snpCount"] = cursor.fetchone()[0]
-				newdict["snpDensity"] = newdict["snpCount"]/(newdict["TxEnd"]-newdict["TxStart"])/1000.0
-			else:
-				newdict["snpDensity"] = newdict["snpCount"] = 0
-			
-			try:
-				newdict['GeneLength'] = 1000.0*(newdict['TxEnd'] - newdict['TxStart'])
-			except:
-				pass
-
-
-
-#self.cursor.execute("SELECT geneSymbol, chromosome, txStart, txEnd from GeneList where SpeciesId= 1 and geneSymbol = %s", opt.geneName)
-
-
-
-			
-			## search with gene name... doesnt matter. it changed to start and end position anyway
-			##self.cursor.execute("SELECT geneSymbol, chromosome, txStart, txEnd from GeneList where SpeciesId= 1 and geneSymbol = %s", newdict["GeneSymbol"])
-
-
-			#count SNPs for all strains
-			cursor.execute("""
-			     SELECT 
-				distinct SnpAll.Id
-			     from 
-			        SnpAll 
-			     where 
-			        SpeciesId = '1' and SnpAll.Chromosome = '%s' AND 
-				    SnpAll.Position >= %2.6f and SnpAll.Position < %2.6f AND
-				    SnpAll.Exon='Y'
-				""" % (newdict["Chromosome"], newdict["TxStart"], newdict["TxEnd"]))
-			snpfetch = cursor.fetchall()
-			newdict["snpCountmis"] = len(snpfetch)
-
-## 			# count SNPs for selected strains
-			
-			sql = """SELECT 
-					distinct SnpAll.Id, `%s`, `%s`
-				from 
-					SnpAll, SnpPattern 
-				where 
-					SpeciesId = '1' and SnpAll.Chromosome = '%s' AND 
-					SnpAll.Position >= %2.6f and SnpAll.Position < %2.6f and SnpAll.Id = SnpPattern.SnpId AND 
-					SnpPattern.`%s` != SnpPattern.`%s` AND
-					SnpAll.Exon='Y'
-					""" % (str1, str2, newdict["Chromosome"], newdict["TxStart"], newdict["TxEnd"], str1, str2)
-			cursor.execute(sql)
-			ressnp = cursor.fetchall()
-			newdict["snpCountmissel"] = len(ressnp)
-			newdict["hassnp"] = 'n'
-			if len(ressnp)>0 :
-				newdict["hassnp"]= 'y'
-##          ####################################### NEW NEW NEW
-
-
-
-
-
-
-
-			# count Indels for BXD mice
-			cursor.execute("""
-				SELECT 
-				   distinct IndelAll.Name, IndelAll.Chromosome, IndelAll.SourceId, IndelAll.Mb_start,
-				   IndelAll.Mb_end, IndelAll.Strand, IndelAll.Type, IndelAll.Size, IndelAll.InDelSequence,
-				   SnpSource.Name  
-				from 
-				   SnpSource, IndelAll
-				where 
-				   IndelAll.SpeciesId = '1' and IndelAll.Chromosome = '%s' AND 
-				   IndelAll.Mb_start >= %2.6f and IndelAll.Mb_start < (%2.6f+.0010) AND
-				   SnpSource.Id = IndelAll.SourceId 
-				   order by IndelAll.Mb_start
-				""" % (newdict["Chromosome"], newdict["TxStart"], newdict["TxEnd"]))
-				
-			ressnp = cursor.fetchall()
-			newdict["indelCountBXD"] = len(ressnp)
-			newdict["hasindel"] = 'n'
-			newdict["hasexpr"] = 'n'
-			newdict["hascis"] = 'n'
-			newdict["score"] = 0
-			if len(ressnp)>0 :
-				newdict["hasindel"]= 'y'
-
-## #			cursor.execute("""
-## #				select 
-## #					Name from ProbeSet
-## #				where 
-## #					GeneId = '%s' AND ChipId=4 limit 1
-## #			""" % (newdict["GeneID"]))
-## #			if species=='mouse':
-## #				cursor.execute("""
-## #					select 
-## #						Name from ProbeSet
-## #					where 
-## #						GeneId = '%s' AND ChipId=4
-## #				""" % (newdict["GeneID"]))
-## #				results = cursor.fetchall()
-## #				psets = []
-## #				for item in results:
-## #					psets.append(item)
-## #				newdict["probeset"] = psets 
-## #				
-## #			else:
-## #				newdict["probeset"] = "empty"
-
-
-
-
-			if species=='mouse':
-				cursor.execute("""
-					select 
-						distinct 0,
-						ProbeSet.Name as TNAME,
-						round(ProbeSetXRef.Mean,1) as TMEAN,
-						round(ProbeSetXRef.LRS,1) as TLRS,
-						ProbeSet.Chr_num as TCHR_NUM,
-						ProbeSet.Mb as TMB,
-						ProbeSet.Symbol as TSYMBOL,
-						ProbeSet.name_num as TNAME_NUM
-						FROM  ProbeSetXRef, ProbeSetFreeze, ProbeSet
-					where 
-						( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,
-						alias,GenbankId,UniGeneId, Probe_Target_Description)
-						AGAINST ('%s' IN BOOLEAN MODE) )
-						and ProbeSet.symbol = '%s'
-						and ProbeSet.Id = ProbeSetXRef.ProbeSetId
-						and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
-						and ProbeSetFreeze.Id = (select Id from ProbeSetFreeze where Name='%s' limit 1)
-				""" % (newdict["GeneSymbol"],newdict["GeneSymbol"],databaseA))
-				resA = cursor.fetchall()
-				
-				if resA:
-					myFields = ['dummyA','probesetA','meanA','newlrsA','probesetchrA','probesetmbA','probesetsymbolA','probesetnamenumA']
-
-#					fpText = open(os.path.join(webqtlConfig.TMPDIR, "res") + '.txt','wb')
-					#fpText.write("newdictgeneid  '%s'  \n" % newdict["GeneId"])
-					for j, item in enumerate(myFields):
-						temp = []
-						for k in resA:
-							#							fpText.write("j: result:  '%s'  \n" % k[j])
-							temp.append(k[j])
-						newdict[item] = temp 
-					#					fpText.close()
-
-
-					# put probesetcisA here
-				
-					cursor.execute("""
-					select 
-						distinct 0,
-						if( (ProbeSet.Chr = Geno.Chr AND ProbeSetXRef.LRS > 10.0000000  and ABS(ProbeSet.Mb-Geno.Mb) < 10.0000000  ) , concat('yes(',round(ProbeSetXRef.LRS,1),')') , 'no') as cis
-						FROM  Geno, ProbeSetXRef, ProbeSetFreeze, ProbeSet
-					where 
-						( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,
-						alias,GenbankId,UniGeneId, Probe_Target_Description)
-						AGAINST ('%s' IN BOOLEAN MODE) )
-						and ProbeSet.symbol = '%s'
-						and ProbeSet.Id = ProbeSetXRef.ProbeSetId
-						and Geno.SpeciesId=1 #XZ: I add this line to speed up query
-						and ProbeSetXRef.Locus = Geno.name
-						and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
-						and ProbeSetFreeze.Id = (select Id from ProbeSetFreeze where Name='%s' limit 1)
-						""" % (newdict["GeneSymbol"],newdict["GeneSymbol"],databaseA))
-
-					resA2 = cursor.fetchall()
-					if resA2:
-						myFields = ['dummyA2','probesetcisA']
-						for j, item in enumerate(myFields):
-							temp = []
-							for k in resA2:
-								#							fpText.write("j: result:  '%s'  \n" % k[j])
-								temp.append(k[j])
-							newdict[item] = temp 
-					else:
-						newdict['probesetcisA'] = ''
-
-
-
-					# specially for this dataset only
-					newdict["hasexpr"] = 'n'
-					if len(newdict["meanA"])>0:
-						for mym in newdict["meanA"]:
-							if mym>8:
-								newdict["hasexpr"] = 'y'
-
-					# specially for this dataset only
-					newdict["hascis"] = 'n'
-					if len(newdict["probesetcisA"])>0:
-						for mym in newdict["probesetcisA"]:
-							if mym != 'no':
-								newdict["hascis"] = 'y'
-			
-			else:
-				myFields = ['dummyA','probesetA,''meanA','newlrsA','probesetchrA','probesetmbA','probesetsymbolA','probesetnamenumA', 'probesetcisA']
-				for j, item in enumerate(myFields):
-					newdict[item] = "--"
-
-				# specially for this dataset only
-				newdict["hasexpr"] = 'n'
-				newdict["hascis"] = 'n'
-				newdict["score"] = 0
-
-##########################  FOR B
-
-			newdict["score"] = 0
-			if newdict["hassnp"] == 'y':
-				newdict["score"] = newdict["score"] + 1					
-			if newdict["hasexpr"] == 'y':
-				newdict["score"] = newdict["score"] + 1					
-			if newdict["hasindel"] == 'y':
-				newdict["score"] = newdict["score"] + 1					
-			if newdict["hascis"] == 'y':
-				newdict["score"] = newdict["score"] + 1					
-							
-							
-					
-			if species=='mouse':
-				cursor.execute("""
-					select 
-						distinct 0,
-						ProbeSet.Name as TNAME,
-						round(ProbeSetXRef.Mean,1) as TMEAN,
-						round(ProbeSetXRef.LRS,1) as TLRS,
-						ProbeSet.Chr_num as TCHR_NUM,
-						ProbeSet.Mb as TMB,
-						ProbeSet.Symbol as TSYMBOL,
-						ProbeSet.name_num as TNAME_NUM
-						FROM  ProbeSetXRef, ProbeSetFreeze, ProbeSet
-					where 
-						( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,
-						alias,GenbankId,UniGeneId, Probe_Target_Description)
-						AGAINST ('%s' IN BOOLEAN MODE) )
-						and ProbeSet.symbol = '%s'
-						and ProbeSet.Id = ProbeSetXRef.ProbeSetId
-						and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
-						and ProbeSetFreeze.Id = (select Id from ProbeSetFreeze where Name='%s' limit 1)
-				""" % (newdict["GeneSymbol"],newdict["GeneSymbol"],databaseB))
-
-				resB = cursor.fetchall()
-				if resB:
-					myFields = ['dummyB','probesetB','meanB','newlrsB','probesetchrB','probesetmbB','probesetsymbolB','probesetnamenumB']
-
-#					fpText = open(os.path.join(webqtlConfig.TMPDIR, "res") + '.txt','wb')
-					#fpText.write("newdictgeneid  '%s'  \n" % newdict["GeneId"])
-					for j, item in enumerate(myFields):
-						temp = []
-						for k in resB:
-							#							fpText.write("j: result:  '%s'  \n" % k[j])
-							temp.append(k[j])
-						newdict[item] = temp 
-					#					fpText.close()
-
-
-					# put probesetcisB here
-					cursor.execute("""
-					select 
-						distinct 0,
-						if( (ProbeSet.Chr = Geno.Chr AND ProbeSetXRef.LRS > 10.0000000  and ABS(ProbeSet.Mb-Geno.Mb) < 10.0000000  ) , concat('yes(',round(ProbeSetXRef.LRS,1),')') , 'no') as cis
-						FROM  Geno, ProbeSetXRef, ProbeSetFreeze, ProbeSet
-					where 
-						( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,
-						alias,GenbankId,UniGeneId, Probe_Target_Description)
-						AGAINST ('%s' IN BOOLEAN MODE) )
-						and ProbeSet.symbol = '%s'
-						and ProbeSet.Id = ProbeSetXRef.ProbeSetId
-						and Geno.SpeciesId=1 #XZ: I add this line to speed up query
-						and ProbeSetXRef.Locus = Geno.name
-						and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
-						and ProbeSetFreeze.Id = (select Id from ProbeSetFreeze where Name='%s' limit 1)
-						""" % (newdict["GeneSymbol"],newdict["GeneSymbol"],databaseB))
-
-					resB2 = cursor.fetchall()
-					if resB2:
-						myFields = ['dummyB2','probesetcisB']
-						for j, item in enumerate(myFields):
-							temp = []
-							for k in resB2:
-								#							fpText.write("j: result:  '%s'  \n" % k[j])
-								temp.append(k[j])
-							newdict[item] = temp 
-					else:
-						newdict['probesetcisB'] = ''
-
-				
-			else:
-				myFields = ['dummyB','probesetB,''meanB','newlrsB','probesetchrB','probesetmbB','probesetsymbolB','probesetnamenumB', 'probesetcisB']
-				for j, item in enumerate(myFields):
-					newdict[item] = "--"
-
-
-
-##########################
-
-
-##########################  FOR C
-
-					
-			if species=='mouse':
-				cursor.execute("""
-					select 
-						distinct 0,
-						ProbeSet.Name as TNAME,
-						round(ProbeSetXRef.Mean,1) as TMEAN,
-						round(ProbeSetXRef.LRS,1) as TLRS,
-						ProbeSet.Chr_num as TCHR_NUM,
-						ProbeSet.Mb as TMB,
-						ProbeSet.Symbol as TSYMBOL,
-						ProbeSet.name_num as TNAME_NUM
-						FROM  ProbeSetXRef, ProbeSetFreeze, ProbeSet
-					where 
-						( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,
-						alias,GenbankId,UniGeneId, Probe_Target_Description)
-						AGAINST ('%s' IN BOOLEAN MODE) )
-						and ProbeSet.symbol = '%s'
-						and ProbeSet.Id = ProbeSetXRef.ProbeSetId
-						and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
-						and ProbeSetFreeze.Id = (select Id from ProbeSetFreeze where Name='%s' limit 1)
-				""" % (newdict["GeneSymbol"],newdict["GeneSymbol"],databaseC))
-
-				resC = cursor.fetchall()
-				if resC:
-					myFields = ['dummyC','probesetC','meanC','newlrsC','probesetchrC','probesetmbC','probesetsymbolC','probesetnamenumC']
-
-#					fpText = open(os.path.join(webqtlConfig.TMPDIR, "res") + '.txt','wb')
-					#fpText.write("newdictgeneid  '%s'  \n" % newdict["GeneId"])
-					for j, item in enumerate(myFields):
-						temp = []
-						for k in resC:
-							#							fpText.write("j: result:  '%s'  \n" % k[j])
-							temp.append(k[j])
-						newdict[item] = temp 
-					#					fpText.close()
-
-
-					# put probesetcisC here
-					cursor.execute("""
-					select 
-						distinct 0,
-						if( (ProbeSet.Chr = Geno.Chr AND ProbeSetXRef.LRS > 10.0000000  and ABS(ProbeSet.Mb-Geno.Mb) < 10.0000000  ) , concat('yes(',round(ProbeSetXRef.LRS,1),')') , 'no') as cis
-						FROM  Geno, ProbeSetXRef, ProbeSetFreeze, ProbeSet
-					where 
-						( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,
-						alias,GenbankId,UniGeneId, Probe_Target_Description)
-						AGAINST ('%s' IN BOOLEAN MODE) )
-						and ProbeSet.symbol = '%s'
-						and ProbeSet.Id = ProbeSetXRef.ProbeSetId
-						and Geno.SpeciesId=1 #XZ: I add this line to speed up query
-						and ProbeSetXRef.Locus = Geno.name
-						and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
-						and ProbeSetFreeze.Id = (select Id from ProbeSetFreeze where Name='%s' limit 1)
-						""" % (newdict["GeneSymbol"],newdict["GeneSymbol"],databaseC))
-
-					resC2 = cursor.fetchall()
-					if resC2:
-						myFields = ['dummyC2','probesetcisC']
-						for j, item in enumerate(myFields):
-							temp = []
-							for k in resC2:
-								#							fpText.write("j: result:  '%s'  \n" % k[j])
-								temp.append(k[j])
-							newdict[item] = temp 
-					else:
-						newdict['probesetcisC'] = ''
-
-			else:
-				myFields = ['dummyC','probesetC,''meanC','newlrsC','probesetchrC','probesetmbC','probesetsymbolC','probesetnamenumC', 'probesetcisC']
-				for j, item in enumerate(myFields):
-					newdict[item] = "--"
-
-
-			             
-			
-			
-
-
-			
-			#load gene from other Species by the same name
-			
-			
-			for item in otherSpecies:
-				othSpec, othSpecId = item
-				newdict2 = {}
-				
-				cursor.execute("SELECT %s from GeneList where SpeciesId = %d and geneSymbol= '%s' limit 1" % 
-							(string.join(fetchFields, ", "), othSpecId, newdict["GeneSymbol"]))
-				resultsOther = cursor.fetchone()
-				if resultsOther:
-					for j, item in enumerate(fetchFields):
-						newdict2[item] = resultsOther[j]
-							
-					#count SNPs if possible, could be a separate function	
-					if diffCol and othSpec == 'mouse':
-						cursor.execute("""
-							select
-								count(*) from BXDSnpPosition
-							where
-								Chr = '%s' AND Mb >= %2.6f AND Mb < %2.6f AND
-								StrainId1 = %d AND StrainId2 = %d
-							""" % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1]))
-
-
-						newdict2["snpCount"] = cursor.fetchone()[0]
-						newdict2["snpDensity"] = newdict2["snpCount"]/(newdict2["TxEnd"]-newdict2["TxStart"])/1000.0
-					else:
-						newdict2["snpDensity"] = newdict2["snpCount"] = 0
-						
-					try:
-						newdict2['GeneLength'] = 1000.0*(newdict2['TxEnd'] - newdict2['TxStart'])
-					except:
-						pass
-						
-				newdict['%sGene' % othSpec] = newdict2
-
-			#newdict['RUDI']='hallo allemaal'
-				
-			GeneList.append(newdict)
-
-					
-	return GeneList
-
-