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

3 files changed, 0 insertions, 1895 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
-
-
diff --git a/web/webqtl/qtlminer/QTLminer.py b/web/webqtl/qtlminer/QTLminer.py
deleted file mode 100755
index e565cdd7..00000000
--- a/web/webqtl/qtlminer/QTLminer.py
+++ /dev/null
@@ -1,1237 +0,0 @@
-#Note that although this module gets imported a bit, the dict columnNames is never used outside this code.
-#Also note that snpBrowser also defines a columnNames dict; it's different. -KA
-
-from htmlgen import HTMLgen2 as HT
-import os
-import time
-import pyXLWriter as xl
-
-import GeneUtil
-from base.templatePage import templatePage
-from utility import webqtlUtil
-from base import webqtlConfig
-
-
-_scriptfile = "main.py?FormID=qtlminerresult"
-
-#A dictionary that lets us map the html form names "txStart_mm6" -> "Mb Start (mm8)"
-#the first item is the short name (column headers) and the second item is the long name (dropdown list)
-#   [short name, long name, category]
-columnNames = {"GeneSymbol" : ["Gene", "Gene Name", 'gene'], 
-			"GeneDescription" : ["Description", "Gene Description", 'species'],
-#			"probeset" : ["ProbeSet", "ProbeSet", 'gene'],
-#		    "probesetsymbolA" : ["ProbeSet Symbol A", "ProbeSetsymbolA", 'gene'],
-#			"probesetchrA" : ["probesetchrA", "probesetchrA", 'gene'],
-			"hassnp" : ["Has nsSNP", "Has nsSNP", 'gene'],
-			"hasindel" : ["Has indel", "Has indel", 'gene'],
-			"hasexpr" : ["Has expr", "Has expression", 'gene'],
-			"hascis" : ["Has cis", "Has cis regulation", 'gene'],
-			"score" : ["Score", "Score", 'gene'],
-			"meanA" : ["Expression A", "Expression in dataset 1", 'gene'],
-			"meanB" : ["Expression B", "Expression in dataset 2", 'gene'],
-			"meanC" : ["Expression C", "Expression in dataset 3", 'gene'],
-			"probesetcisA" : ["Cis A", "Cis regulation in dataset 1", 'gene'],
-			"probesetcisB" : ["Cis B", "Cis regulation in dataset 2", 'gene'],
-			"probesetcisC" : ["Cis C", "Cis regulation in dataset 3", 'gene'],
-			"probesetA" : ["ProbeSet A", "ProbeSet in dataset 1", 'gene'],
-			"probesetB" : ["ProbeSet B", "ProbeSet in dataset 2", 'gene'],
-			"probesetC" : ["ProbeSet C", "ProbeSet in dataset 3", 'gene'],
-			"goterms" : ["GO biological process", "GO biological process", 'gene'],
-			"pathways" : ["KEGG PathwayIDs", "KEGG PathwayIDs", 'gene'],
-			"pathwaynames" : ["KEGG Pathways", "KEGG Pathways", 'gene'],
-#			"newlrsA" : ["Lrs A", "lrs A", 'gene'],
-#			"probesetchrB" : ["probesetchrB", "probesetchrB", 'gene'],
-#			"newlrsB" : ["lrs B", "lrs B", 'gene'],
-#			"probesetchrC" : ["probesetchrC", "probesetchrC", 'gene'],
-#			"newlrsC" : ["lrs C", "lrs C", 'gene'],
-			'GeneNeighborsCount' : ["Neighbors", "Gene Neighbors", 'gene'], 
-			'GeneNeighborsRange' : ["Neighborhood", "Gene Neighborhood (Mb)", 'gene'], 
-			'GeneNeighborsDensity' : ["Gene Density", "Gene Density (Neighbors/Mb)", 'gene'],  
-			"ProteinID" : ["Prot ID", "Protein ID", 'protein'],
-			"Chromosome" : ["Chr", "Chromosome", 'species'], 
-			"TxStart" : ["Start", "Mb Start", 'species'], 
-			"TxEnd" : ["End", "Mb End", 'species'], 
-			"GeneLength" : ["Length", "Kb Length", 'species'], 
-			"cdsStart" : ["CDS Start", "Mb CDS Start", 'species'], 
-			"cdsEnd" : ["CDS End", "Mb CDS End", 'species'],
-			"exonCount" : ["Num Exons", "Exon Count", 'species'], 
-			"exonStarts" : ["Exon Starts", "Exon Starts", 'species'], 
-			"exonEnds" : ["Exon Ends", "Exon Ends", 'species'], 
-			"Strand" : ["Strand", "Strand", 'species'], 
-			"GeneID" : ["Gene ID", "Gene ID", 'species'],
-			"GenBankID" : ["GenBank", "GenBank ID", 'species'], 
-			"UnigenID" : ["Unigen", "Unigen ID", 'species'],
-			"NM_ID" : ["NM ID", "NM ID", 'species'], 
-			"kgID" : ["kg ID", "kg ID", 'species'],
-			"snpCountall" : ["SNPs", "SNP Count", 'species'], 
-			"snpCountmis": ["nsSNPs all", "nsSNP Count all strains", 'species'], 
-			"snpCountmissel": ["nsSNPs selected", "nsSNP Count selected strains", 'species'], 
-			"snpDensity" : ["SNP Density", "SNP Density", 'species'], 
-			"indelCountBXD" : ["Indels in BXD mice", "Indel Count in BXD mice", 'species'], 
-			"lrs" : ["LRS", "Likelihood Ratio Statistic", 'misc'], 
-			"lod" : ["LOD", "Likelihood Odds Ratio", 'misc'], 
-			"pearson" : ["Pearson", "Pearson Product Moment", 'misc'], 
-			"literature" : ["Lit Corr", "Literature Correlation", 'misc'], 
-	}
-
-###Species Freeze
-speciesFreeze = {'mouse':'mm9', 'rat':'rn3', 'human':'hg19'}
-for key in speciesFreeze.keys():
-	speciesFreeze[speciesFreeze[key]] = key
-
-class QTLminer (templatePage): ###
-	filename = webqtlUtil.genRandStr("Itan_")
-
-	javascript_content = """
-<SCRIPT language="JAVASCRIPT">
-
-function update4(self,form) {
-   self.database='leeg';
-
-}
-
-
-
-	
-</SCRIPT>
-"""	
-	def __init__(self, fd):
-		templatePage.__init__(self, fd)
-		if not self.openMysql():
-			return
-
-		self.species = fd.formdata.getvalue("species", "mouse")
-		try:
-			self.startMb = float(fd.formdata.getvalue("startMb"))
-		except:
-			self.startMb = 173
-		try:
-			self.endMb = float(fd.formdata.getvalue("endMb"))
-		except:
-			self.endMb = self.startMb + 1
-			
-		self.Chr = fd.formdata.getvalue("chromosome", "1")
-
-
-
-######################################################### FOR A 
-		###### species
-		
-		self.cursor.execute("""
-			Select
-				Name, Id from Species
-			Order by
-				Id
-			""" )
-		res = self.cursor.fetchall()
-		self.spA = res
-		self.spAsel = fd.formdata.getvalue("myspeciesA", "mouse")
-
-		if not hasattr(self,"spA"):
-			self.spA = res2
-			self.spAsel = 'mouse'
-
-		###### group
-		
-		self.cursor.execute("""
-			select 
-				distinct InbredSet.Name, InbredSet.FullName
-				from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze
-			where
-			        InbredSet.SpeciesId= Species.Id and
-				Species.Name='%s' and InbredSet.Name != 'BXD300' and
-				(PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id)
-			order by
-			        InbredSet.Name
-			""" % self.spAsel)
-
-		res = self.cursor.fetchall()
-
-		if not hasattr(self,"grA"):
-			self.grA = res
-			self.grAsel = 'BXD'
-
-		if fd.formdata.getvalue('submitter') == 'a1': 
-			self.grA = res
-			self.grAsel = self.grA[0][0]
-		else:
-			self.grAsel = fd.formdata.getvalue("groupA","BXD")
-
-		###### type
-		
-		self.cursor.execute("""
-			select
-			   distinct Tissue.Name, concat(Tissue.Name, ' mRNA')
-			from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue
-			where
-			   ProbeFreeze.TissueId = Tissue.Id and
-			   ProbeFreeze.InbredSetId = InbredSet.Id and
-			   InbredSet.Name in ('%s') and
-			   ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
-			   ProbeSetFreeze.public > %d
-			order by Tissue.Name
-			""" % (self.grAsel,webqtlConfig.PUBLICTHRESH))
-
-		res = self.cursor.fetchall()
-
-		if not hasattr(self,"tyA"):
-			self.tyA = res
-			self.tyAsel = 'Hippocampus' 
-
-		if fd.formdata.getvalue('submitter') in ['a1','a2'] : 
-			self.tyA = res
-			self.tyAsel = self.tyA[0][0]
-		else:
-			self.tyAsel = fd.formdata.getvalue("typeA","Hippocampus")
-
-		###### database
-
-		self.cursor.execute("""
-		        select
-			   ProbeSetFreeze.Name, ProbeSetFreeze.FullName
-			   from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
-			where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
-			   ProbeFreeze.TissueId = Tissue.Id and
-			   ProbeFreeze.InbredSetId = InbredSet.Id and
-			   InbredSet.Name in ('%s') and Tissue.name = '%s' and
-			   ProbeSetFreeze.public > %d
-			order by ProbeSetFreeze.CreateTime desc
-			""" % (self.grAsel,self.tyAsel,webqtlConfig.PUBLICTHRESH))
-
-		res = self.cursor.fetchall()
-
-		if not hasattr(self,"daA"):
-			self.daA = res
-			self.daAsel = 'HC_M2_0606_P'
-
-		if fd.formdata.getvalue('submitter') in ['a1','a2','a3'] : 
-			self.daA = res
-			self.daAsel = self.daA[0][0]
-		else:
-			self.daAsel = fd.formdata.getvalue("databaseA","HC_M2_0606_P")
-
-
-######################################################### FOR B
-		###### species
-		
-		self.cursor.execute("""
-			Select
-				Name, Id from Species
-			Order by
-				Id
-			""" )
-		res = self.cursor.fetchall()
-		self.spB = res
-		self.spBsel = fd.formdata.getvalue("myspeciesB", "mouse")
-
-		if not hasattr(self,"spB"):
-			self.spB = res
-			self.spBsel = 'mouse'
-
-		###### group
-		
-		self.cursor.execute("""
-			select 
-				distinct InbredSet.Name, InbredSet.FullName
-				from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze
-			where
-			        InbredSet.SpeciesId= Species.Id and
-				Species.Name='%s' and InbredSet.Name != 'BXD300' and
-				(PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id)
-			order by
-			        InbredSet.Name
-			""" % self.spBsel)
-
-		res = self.cursor.fetchall()
-
-		if not hasattr(self,"grB"):
-			self.grB = res
-			self.grBsel = 'CXB'
-
-		if fd.formdata.getvalue('submitter') == 'b1': 
-			self.grB = res
-			self.grBsel = self.grB[0][0]
-		else:
-			self.grBsel = fd.formdata.getvalue("groupB","CXB")
-
-		###### type
-		
-		self.cursor.execute("""
-			select
-			   distinct Tissue.Name, concat(Tissue.Name, ' mRNA')
-			from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue
-			where
-			   ProbeFreeze.TissueId = Tissue.Id and
-			   ProbeFreeze.InbredSetId = InbredSet.Id and
-			   InbredSet.Name in ('%s') and
-			   ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
-			   ProbeSetFreeze.public > %d
-			order by Tissue.Name
-			""" % (self.grBsel,webqtlConfig.PUBLICTHRESH))
-
-		res = self.cursor.fetchall()
-
-		if not hasattr(self,"tyB"):
-			self.tyB = res
-			self.tyBsel = 'Hippocampus' 
-
-		if fd.formdata.getvalue('submitter') in ['b1','b2'] : 
-			self.tyB = res
-			self.tyBsel = self.tyB[0][0]
-		else:
-			self.tyBsel = fd.formdata.getvalue("typeB","Hippocampus")
-
-		###### database
-
-		self.cursor.execute("""
-		        select
-			   ProbeSetFreeze.Name, ProbeSetFreeze.FullName
-			   from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
-			where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
-			   ProbeFreeze.TissueId = Tissue.Id and
-			   ProbeFreeze.InbredSetId = InbredSet.Id and
-			   InbredSet.Name in ('%s') and Tissue.name = '%s' and
-			   ProbeSetFreeze.public > %d
-			order by ProbeSetFreeze.CreateTime desc
-			""" % (self.grBsel,self.tyBsel,webqtlConfig.PUBLICTHRESH))
-
-		res = self.cursor.fetchall()
-
-		if not hasattr(self,"daB"):
-			self.daB = res
-			self.daBsel = 'HC_M2CB_1205_R'
-
-		if fd.formdata.getvalue('submitter') in ['b1','b2','b3'] : 
-			self.daB = res
-			self.daBsel = self.daB[0][0]
-		else:
-			self.daBsel = fd.formdata.getvalue("databaseB","HC_M2CB_1205_R")
-
-
-
-######################################################### FOR C
-		###### species
-	
-		self.cursor.execute("""
-			Select
-				Name, Id from Species
-			Order by
-				Id
-			""" )
-		res = self.cursor.fetchall()
-		self.spC = res
-		self.spCsel = fd.formdata.getvalue("myspeciesC", "mouse")
-
-		if not hasattr(self,"spC"):
-			self.spC = res
-			self.spCsel = 'mouse'
-
-		###### group
-		
-		self.cursor.execute("""
-			select 
-				distinct InbredSet.Name, InbredSet.FullName
-				from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze
-			where
-			        InbredSet.SpeciesId= Species.Id and
-				Species.Name='%s' and InbredSet.Name != 'BXD300' and
-				(PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id)
-			order by
-			        InbredSet.Name
-			""" % self.spCsel)
-
-		res = self.cursor.fetchall()
-
-		if not hasattr(self,"grC"):
-			self.grC = res
-			self.grCsel = 'LXS'
-
-		if fd.formdata.getvalue('submitter') == 'c1': 
-			self.grC = res
-			self.grCsel = self.grC[0][0]
-		else:
-			self.grCsel = fd.formdata.getvalue("groupC","LXS")
-
-		###### type
-		
-		self.cursor.execute("""
-			select
-			   distinct Tissue.Name, concat(Tissue.Name, ' mRNA')
-			from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue
-			where
-			   ProbeFreeze.TissueId = Tissue.Id and
-			   ProbeFreeze.InbredSetId = InbredSet.Id and
-			   InbredSet.Name in ('%s') and
-			   ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
-			   ProbeSetFreeze.public > %d
-			order by Tissue.Name
-			""" % (self.grCsel,webqtlConfig.PUBLICTHRESH))
-
-		res = self.cursor.fetchall()
-
-		if not hasattr(self,"tyC"):
-			self.tyC = res
-			self.tyCsel = 'Hippocampus' 
-
-		if fd.formdata.getvalue('submitter') in ['c1','c2'] : 
-			self.tyC = res
-			self.tyCsel = self.tyC[0][0]
-		else:
-			self.tyCsel = fd.formdata.getvalue("typeC","Hippocampus")
-
-		###### database
-		
-
-		self.cursor.execute("""
-		        select
-			   ProbeSetFreeze.Name, ProbeSetFreeze.FullName
-			   from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
-			where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
-			   ProbeFreeze.TissueId = Tissue.Id and
-			   ProbeFreeze.InbredSetId = InbredSet.Id and
-			   InbredSet.Name in ('%s') and Tissue.name = '%s' and
-			   ProbeSetFreeze.public > %d
-			order by ProbeSetFreeze.CreateTime desc
-			""" % (self.grCsel,self.tyCsel,webqtlConfig.PUBLICTHRESH))
-
-		res = self.cursor.fetchall()
-
-		if not hasattr(self,"daC"):
-			self.daC = res
-			self.daCsel = 'Illum_LXS_Hipp_loess0807'
-
-		if fd.formdata.getvalue('submitter') in ['c1','c2','c3'] : 
-			self.daC = res
-			self.daCsel = self.daC[0][0]
-		else:
-			self.daCsel = fd.formdata.getvalue("databaseC","Illum_LXS_Hipp_loess0807")
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-#		self.myspeciesA = fd.formdata.getvalue("myspeciesA", "mouse")
-#		self.groupA = fd.formdata.getvalue("groupA", "BXD")
-#		self.typeA = fd.formdata.getvalue("typeA", "Spleen")
-#		self.databaseA = fd.formdata.getvalue("databaseA", "IoP_SPL_RMA_0509")#
-
-#		self.myspeciesB = fd.formdata.getvalue("myspeciesB", "mouse")
-#		self.groupB = fd.formdata.getvalue("groupB", "BXD")
-#		self.typeB = fd.formdata.getvalue("typeB", "Spleen")
-#		self.databaseB = fd.formdata.getvalue("databaseB", "IoP_SPL_RMA_0509")
-
-		self.xls = fd.formdata.getvalue("xls", "1")
-		try:
-			s1 = int(fd.formdata.getvalue("s1"))
-			s2 = int(fd.formdata.getvalue("s2"))
-			self.diffColDefault = self.diffCol = [s1, s2]
-		except:
-			self.diffColDefault = self.diffCol = []
-			if self.species !=  'mouse':
-				self.diffColDefault = [2, 3]#default is B6 and D2 for other species
-
-
-
-		self.str1 = fd.formdata.getvalue("str1", "C57BL/6J")
-		self.str2 = fd.formdata.getvalue("str2", "DBA/2J")
-		self.sorton = fd.formdata.getvalue("sorton", "Position")
-			
-		controlFrm, dispFields, dispFields2 = self.genControlForm(fd)
-		##		if not fd.formdata.getvalue('submitter') in ['a1','a2','a3''a4'] :
-
-		self.cursor.execute("""select Id from Strain where Name='%s'
-			""" % self.str1 )
-		strain1 = self.cursor.fetchone()[0]
-		self.cursor.execute("""select Id from Strain where Name='%s'
-			""" % self.str2 )
-		strain2 = self.cursor.fetchone()[0]
-		
-		filename=''
-		if fd.formdata.getvalue('submitter') in ['refresh'] or not hasattr(self,"daA"):
-			geneTable, filename = self.genGeneTable(fd, dispFields, strain1, strain2)
-		
-		infoTD = HT.TD(width=400, valign= "top")
-		infoTD.append(HT.Paragraph("QTLminer : Chr %s" % self.Chr, Class="title"), 
-#			HT.Strong("Species : "), self.species.title(), HT.BR(),  
-
-#			HT.Strong("myspeciesA : "), self.myspeciesA, HT.BR(),  
-#			HT.Strong("groupA : "), self.groupA, HT.BR(),  
-#			HT.Strong("typeA : "), self.typeA, HT.BR(),  
-#			HT.Strong("databaseA : "), self.databaseA, HT.BR(),  
-
-#			HT.Strong("myspeciesB : "), self.myspeciesB, HT.BR(),  
-#			HT.Strong("groupB : "), self.groupB, HT.BR(),  
-#			HT.Strong("typeB : "), self.typeB, HT.BR(),  
-#			HT.Strong("databaseB : "), self.databaseB, HT.BR(),  
-
-#			HT.Strong("spAsel : "), self.spAsel, HT.BR(),  
-#			HT.Strong("grAsel : "), self.grAsel, HT.BR(),  
-#			HT.Strong("tyAsel : "), self.tyAsel, HT.BR(),  
-#			HT.Strong("daAsel : "), self.daAsel, HT.BR(),  
-
-#			HT.Strong("spBsel : "), self.spBsel, HT.BR(),  
-#			HT.Strong("grBsel : "), self.grBsel, HT.BR(),  
-#			HT.Strong("tyBsel : "), self.tyBsel, HT.BR(),  
-#			HT.Strong("daBsel : "), self.daBsel, HT.BR(),  
-
-#			HT.Strong("chr : "), self.Chr, HT.BR(),  
-#			HT.Strong("formdata.submitter :"), fd.formdata.getvalue("submitter"), HT.BR(),  
-#			HT.Strong("formdata.myspeciesA : "), fd.formdata.getvalue("myspeciesA"), HT.BR(),  
-#			HT.Strong("formdata.groupA: "), fd.formdata.getvalue("groupA") , HT.BR(),  
-#			HT.Strong("formdata.myspeciesB : "), fd.formdata.getvalue("myspeciesB"), HT.BR(),  
-#			HT.Strong("formdata.groupB: "), fd.formdata.getvalue("groupB") , HT.BR(),  
-#			HT.Strong("formdata.type: "), fd.formdata.getvalue("type") , HT.BR(),  
-#			HT.Strong("formdata.database: "), fd.formdata.getvalue("database") , HT.BR(),  
-#			HT.Strong("Database : "), "UCSC %s" % speciesFreeze[self.species], HT.BR(),  
-			HT.Strong("Range : "), "%2.6f Mb - %2.6f Mb" % (self.startMb, self.endMb), HT.BR(),  
-			)
-
-		if filename:
-			infoTD.append(HT.BR(), HT.BR(), HT.Href(text="Download", url = "/tmp/" + filename, Class="normalsize")
-					, " output in MS excel format.")
-
-   		mainTable = HT.TableLite(HT.TR(infoTD, HT.TD(controlFrm, Class="doubleBorder", width=400), HT.TD("&nbsp;", width="")), cellpadding=10)
-
-		if fd.formdata.getvalue('submitter') in ['refresh'] or not hasattr(self,"daA"):
-			mainTable.append(HT.TR(HT.TD(geneTable, colspan=3)))
-
-		self.dict['body'] = HT.TD(mainTable)
-		self.dict['title'] = "QTLminer"
-		
-		self.cursor.close();
-		
-	def genGeneTable(self, fd, dispFields, strain1, strain2):
-	
-		filename = ""
-		if self.xls:
-			#import pyXLWriter as xl
-			filename = "IntAn_Chr%s_%2.6f-%2.6f" % (self.Chr, self.startMb, self.endMb)
-			filename += ".xls"
-			
-			# Create a new Excel workbook
-			workbook = xl.Writer(os.path.join(webqtlConfig.TMPDIR, filename))
-			worksheet = workbook.add_worksheet()
-			titleStyle = workbook.add_format(align = 'left', bold = 0, size=18, border = 1, border_color="gray")
-			headingStyle = workbook.add_format(align = 'center', bold = 1, size=13, fg_color = 0x1E, color="white", border = 1, border_color="gray")
-			
-			##Write title Info
-			worksheet.write([0, 0], "GeneNetwork Interval Analyst Table", titleStyle)
-			worksheet.write([1, 0], "%s%s" % (webqtlConfig.PORTADDR, os.path.join(webqtlConfig.CGIDIR, _scriptfile)))
-			#
-			worksheet.write([2, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime()))
-			worksheet.write([3, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime()))
-			worksheet.write([4, 0], "Search by : %s" % fd.remote_ip)
-			worksheet.write([5, 0], "view region : Chr %s %2.6f - %2.6f Mb" % (self.Chr, self.startMb, self.endMb))
-			nTitleRow = 7
-			
-		geneTable = HT.TableLite(Class="collap", cellpadding=5)
-		headerRow = HT.TR(HT.TD(" ", Class="fs13 fwb ffl b1 cw cbrb", width="1"))
-		if self.xls:
-			worksheet.write([nTitleRow, 0], "Index", headingStyle)
-			
-		for ncol, column in enumerate(dispFields):
-			if column[0]=='meanA':
-				headerRow.append(HT.TD("Expression in" , HT.BR(), self.grAsel, HT.BR(), self.tyAsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
-				if self.xls:
-					colTitle = columnNames[column[0]][0]
-					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
-					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-			elif column[0]=='meanB':
-				headerRow.append(HT.TD("Expression in" , HT.BR(), self.grBsel, HT.BR(), self.tyBsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
-				if self.xls:
-					colTitle = columnNames[column[0]][0]
-					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
-					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-			elif column[0]=='meanC':
-				headerRow.append(HT.TD("Expression in" , HT.BR(), self.grCsel, HT.BR(), self.tyCsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
-				if self.xls:
-					colTitle = columnNames[column[0]][0]
-					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
-					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-			elif column[0]=='probesetcisA':
-				headerRow.append(HT.TD("Cis regulated in" , HT.BR(), self.grAsel, HT.BR(), self.tyAsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
-				if self.xls:
-					colTitle = columnNames[column[0]][0]
-					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
-					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-			elif column[0]=='probesetcisB':
-				headerRow.append(HT.TD("Cis regulated in" , HT.BR(), self.grBsel, HT.BR(), self.tyBsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
-				if self.xls:
-					colTitle = columnNames[column[0]][0]
-					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
-					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-			elif column[0]=='probesetcisC':
-				headerRow.append(HT.TD("Cis regulated in" , HT.BR(), self.grCsel, HT.BR(), self.tyCsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
-				if self.xls:
-					colTitle = columnNames[column[0]][0]
-					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
-					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-			elif column[0]=='probesetA':
-				headerRow.append(HT.TD("Probeset in" , HT.BR(), self.grAsel, HT.BR(), self.tyAsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
-				if self.xls:
-					colTitle = columnNames[column[0]][0]
-					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
-					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-			elif column[0]=='probesetB':
-				headerRow.append(HT.TD("Probeset in" , HT.BR(), self.grBsel, HT.BR(), self.tyBsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
-				if self.xls:
-					colTitle = columnNames[column[0]][0]
-					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
-					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-			elif column[0]=='probesetC':
-				headerRow.append(HT.TD("Probeset in" , HT.BR(), self.grCsel, HT.BR(), self.tyCsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
-				if self.xls:
-					colTitle = columnNames[column[0]][0]
-					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
-					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-			elif column[0]=='hasexpr':
-				headerRow.append(HT.TD("Has expression in" , HT.BR(), self.grAsel, HT.BR(), self.tyAsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
-				if self.xls:
-					colTitle = columnNames[column[0]][0]
-					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
-					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-			elif column[0]=='hascis':
-				headerRow.append(HT.TD("Cis regulated in" , HT.BR(), self.grAsel, HT.BR(), self.tyAsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
-				if self.xls:
-					colTitle = columnNames[column[0]][0]
-					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
-					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-			elif column[0]=='snpCountmis':
-				headerRow.append(HT.TD("nsSNPs" , HT.BR(), "all strains", HT.BR(), "  ", Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
-				if self.xls:
-					colTitle = columnNames[column[0]][0]
-					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
-					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-			elif column[0]=='snpCountmissel':
-				headerRow.append(HT.TD("nsSNPs" , HT.BR(), self.str1, " vs", HT.BR(), self.str2, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
-				if self.xls:
-					colTitle = columnNames[column[0]][0]
-					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
-					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-
-
-
-
-			elif len(column) == 1:
-				# header 
-				headerRow.append(HT.TD(columnNames[column[0]][0], Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
-				if self.xls:
-					colTitle = columnNames[column[0]][0]
-					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
-					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-			else:
-				# header 
-				headerRow.append(HT.TD(columnNames[column[0]][0], HT.BR(), " (%s)" % speciesFreeze[column[1]], 
-					Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1, align="Center"))
-				if self.xls:
-					colTitle = columnNames[column[0]][0] + " (%s)" % speciesFreeze[column[1]]
-					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
-					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-				#headerRow.append(HT.TD(columnNames[column[0]][0], HT.BR(), 
-				#	"(%s %s)" % (column[1].title(), speciesFreeze[column[1]]), 
-				#	Class="colorBlue", NOWRAP=1, align="Center"))
-		geneTable.append(headerRow)
-
-		geneColnul = GeneUtil.loadGenesForQTLminer(self.cursor, self.Chr, self.diffColDefault, self.startMb, self.endMb, species=self.species, databaseA=self.daAsel, databaseB=self.daBsel, databaseC=self.daCsel, str1=self.str1, str2=self.str2)
-		
-		# scores = []
-		# for gIndex, theGO in enumerate(geneCol):
-		# 	keyValue = ""
-		#	fieldName = 'score'
-		# 	if theGO.has_key(fieldName):
-		# 		keyValue = theGO[fieldName]
-		# 	scores.append(keyValue)
-
-		sort_on = "TxStart"
-		myrev = False
-		if self.sorton == "Score":
-			sort_on = "score"
-			myrev = True
-		geneColeen = [(dict_[sort_on], dict_) for dict_ in geneColnul]
-		geneColeen.sort(reverse=myrev)
-		geneCol = [dict_ for (key, dict_) in geneColeen]
-					
-
-
-		for gIndex, theGO in enumerate(geneCol):
-			geneRow = HT.TR(HT.TD(gIndex+1, Class="fs12 fwn b1", align="right"))
-			if self.xls:
-				nTitleRow += 1
-				worksheet.write([nTitleRow, 0], gIndex + 1)
-				
-			for ncol, column in enumerate(dispFields):
-				if len(column) == 1 or column[1]== self.species:
-					keyValue = ""
-					fieldName = column[0]
-					curSpecies = self.species
-					curGO = theGO
-					if theGO.has_key(fieldName):
-						keyValue = theGO[fieldName]
-				else:
-					fieldName , othSpec = column
-					curSpecies = othSpec
-					subGO = '%sGene' % othSpec
-					keyValue = ""
-					curGO = theGO[subGO]
-					if theGO[subGO].has_key(fieldName):
-						keyValue = theGO[subGO][fieldName]
-				
-				if self.xls:
-					worksheet.write([nTitleRow, ncol+1], keyValue)
-				geneRow.append(self.formatTD(keyValue, fieldName, curSpecies, curGO, strain1, strain2))
-					
-			geneTable.append(geneRow)
-			
-		if self.xls:
-			workbook.close()
-		return geneTable, filename
-	
-	def formatTD(self, keyValue, fieldName, Species, theGO, strain1, strain2):
-		if keyValue is None:
-			keyValue = ""
-		if keyValue != "":
-			if fieldName in ("exonStarts", "exonEnds"):
-				keyValue = string.replace(keyValue, ',', ' ')
-				return HT.TD(HT.Span(keyValue, Class="code", Id="green"), width=350, Class="fs12 fwn b1")
-			elif fieldName in ("GeneDescription"):
-				if keyValue == "---":
-					keyValue = ""
-				return HT.TD(keyValue, Class="fs12 fwn b1", width=300)
-			elif fieldName in ("GeneSymbol"):
-				webqtlLink = HT.Href("./%s/%s?cmd=sch&gene=%s&alias=1&species=%s" % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, keyValue, Species), 		
-					HT.Image("/images/webqtl_search.gif", border=0, valign="top"), target="_blank")
-				if theGO['GeneID']:
-					geneSymbolLink = HT.Href(webqtlConfig.NCBI_LOCUSID % theGO['GeneID'], keyValue, Class="normalsize", target="_blank")
-				else:
-					geneSymbolLink = keyValue
-				return HT.TD(webqtlLink, geneSymbolLink, Class="fs12 fwn b1",NOWRAP=1)
-			elif fieldName == 'UnigenID':
-				try:
-					gurl = HT.Href(webqtlConfig.UNIGEN_ID % tuple(string.split(keyValue,'.')[:2]), keyValue, Class="normalsize", target="_blank")
-				except:
-					gurl = keyValue
-				return HT.TD(gurl, Class="fs12 fwn b1",NOWRAP=1)
-			elif fieldName in ("exonCount", "Chromosome"):
-				return HT.TD(keyValue, Class="fs12 fwn b1",align="right")
-			elif fieldName in ("snpCount"):
-				return HT.TD(keyValue, Class="fs12 fwn b1",NOWRAP=1)
-			elif fieldName in ("snpCountmis"):
-				snpString = HT.Href(url="%s?FormID=SnpBrowserResultPage&submitStatus=1&chr=%s&start=%s&end=%s&domain=Exon&variant=SNP" % (os.path.join(webqtlConfig.CGIDIR, 'main.py'),theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"] ), text=theGO["snpCountmis"], target="_blank", Class="normalsize")
-				return HT.TD(snpString, Class="fs12 fwn b1",NOWRAP=1)
-			elif fieldName in ("snpCountmissel"):
-				snpString = HT.Href(url="%s?FormID=SnpBrowserResultPage&submitStatus=1&chr=%s&start=%s&end=%s&domain=Exon&variant=SNP&customStrain=1&diffAlleles=1&chosenStrains=%s,%s" % (os.path.join(webqtlConfig.CGIDIR, 'main.py'),theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"], self.str1, self.str2 ), text=theGO["snpCountmissel"], target="_blank", Class="normalsize")
-				return HT.TD(snpString, Class="fs12 fwn b1",NOWRAP=1)
-
-
-#				if keyValue:
-#					snpString = HT.Href(url="%s?chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (os.path.join(webqtlConfig.CGIDIR, 'snpBrowser.py'), theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"], theGO["GeneSymbol"], self.diffColDefault[0], self.diffColDefault[1]), text=theGO["snpCount"], target="_blank", Class="normalsize")
-#				else:
-#					snpString = keyValue
-#				return HT.TD(snpString, Class="fs12 fwn b1",align="right")
-			elif fieldName in ("snpDensity", "GeneLength"):
-				if keyValue: keyValue = "%2.3f" % keyValue
-				else: keyValue = ""
-				return HT.TD(keyValue, Class="fs12 fwn b1",align="right")
-			elif fieldName in ("TxStart", "TxEnd"):
-				return HT.TD("%2.6f" % keyValue, Class="fs12 fwn b1",align="right")
-			elif fieldName in ("score"):
-				return HT.TD("%1d" % keyValue, Class="fs12 fwn b1",align="right")
-			elif fieldName in ("pathways", "pathwaynames", "goterms"):
-				html = HT.Paragraph(Class="fs12 fwn b1")
-				for kk in keyValue:
-					html.append(kk,HT.BR())
-				return HT.TD(html, Class="fs12 fwn b1",align="right",NOWRAP=1)
-			elif fieldName in ("probesetA", "probesetB", "probesetC"):
-				html = HT.Paragraph(Class="fs12 fwn b1")
-				for kk in keyValue:
-					html.append(kk,HT.BR())
-				return HT.TD(html, Class="fs12 fwn b1",align="right")
-			elif fieldName in ("probesetsymbolA"):
-				html = HT.Paragraph(Class="fs12 fwn b1")
-				for kk in keyValue:
-					html.append(kk,HT.BR())
-				return HT.TD(html, Class="fs12 fwn b1",align="right")
-			elif fieldName in ("meanA", "meanB", "meanC"):
-				html = HT.Paragraph(Class="fs12 fwn b1")
-				for kk in keyValue:
-					html.append(str(round(kk,1)),HT.BR())
-				return HT.TD(html, Class="fs12 fwn b1",align="right")
-			elif fieldName in ("hassnp", "hasindel", "hasexpr","hascis"):
-				html = HT.Paragraph(Class="fs12 fwn b1")
-				for kk in keyValue:
-					html.append(kk,HT.BR())
-				return HT.TD(html, Class="fs12 fwn b1",align="right")
-			elif fieldName in ("newlrsA", "newlrsB", "newlrsC"):
-				html = HT.Paragraph(Class="fs12 fwn b1")
-				for kk in keyValue:
-					html.append(str(round(kk,1)),HT.BR())
-				return HT.TD(html, Class="fs12 fwn b1",align="right")
-			elif fieldName in ("probesetcisA", "probesetcisB", "probesetcisC"):
-				html = HT.Paragraph(Class="fs12 fwn b1")
-				for kk in keyValue:
-					html.append(kk,HT.BR())
-#					if kk==0:
-#						html.append('no',HT.BR())
-#					if kk==1:
-#						html.append('yes',HT.BR())
-				return HT.TD(html, Class="fs12 fwn b1",align="right")
-			else:
-				return HT.TD(keyValue, Class="fs12 fwn b1",NOWRAP=1)
-		else:
-			return HT.TD(keyValue, Class="fs12 fwn b1",NOWRAP=1,align="right")
-
-#	def getStrainNameList(self, strain_data):
-#	      return strain_data[1:]
-	def getStrainNamePair(self):
-		strainNamePair=[]
-		query ='SELECT * FROM SnpPattern limit 1'
-		self.cursor.execute(query)
-		num_fields = len(self.cursor.description)
-		field_names = [i[0] for i in self.cursor.description]
-		strainsNameList=field_names[1:]
-		for index, name in enumerate(strainsNameList):
-			strainNamePair.append((name,name))
-		return strainNamePair
-				
-	def genControlForm(self, fd):
-		##desc GeneList
-		self.cursor.execute("Desc GeneList")
-		GeneListFields = self.cursor.fetchall()
-		GeneListFields = map(lambda X: X[0], GeneListFields)
-		
-		#group columns by category--used for creating the dropdown list of possible columns
-		categories = {}
-		for item in columnNames.keys():
-			category = columnNames[item]
-			if category[-1] not in categories.keys():
-				categories[category[-1]] = [item ]
-			else:
-				categories[category[-1]] = categories[category[-1]]+[item]
-	
-		##List All Species in the Gene Table
-		speciesDict = {}
-		self.cursor.execute("select Species.Name, GeneList.SpeciesId from Species, GeneList where \
-			GeneList.SpeciesId = Species.Id group by GeneList.SpeciesId order by Species.Id")
-		results = self.cursor.fetchall()
-		speciesField = categories.pop('species', [])
-		categoriesOrder = ['gene', 'protein']
-		for item in results:
-			specName, specId = item
-			categoriesOrder.append(specName)
-			speciesDict[specName] = specId
-			AppliedField = []
-			for item2 in speciesField:
-				if item2 in GeneListFields:
-					self.cursor.execute("select %s from GeneList where SpeciesId = %d and %s is not NULL limit 1 " % (item2, specId, item2))
-					columnApply = self.cursor.fetchone()
-					if not columnApply:
-						continue
-				elif specName != 'mouse' and item2 in ('snpCount', 'snpDensity'):
-					continue
-				else:
-					pass
-				AppliedField.append(item2)
-			categories[specName] = AppliedField
-			
-		categoriesOrder += ['misc']
-
-		s1_data = self.getStrainNamePair()
-		self.allStrainNames = s1_data[1:]
-
-
-		
-		############################################################
-		## Create the list of possible columns for the dropdown list
-		############################################################
-		allColumnsList = HT.Select(name="allColumns", Class="snpBrowserDropBox")#onChange="addToList(this.form.allColumns.options[this.form.allColumns.selectedIndex].text, this.form.allColumns.options[this.form.allColumns.selectedIndex].value, this.form.columns)")
-		
-		for category in categoriesOrder:
-			allFields = categories[category]
-			if allFields:
-				geneOpt = HT.Optgroup(label=category.title())
-				for item in allFields:
-					if category in speciesFreeze.keys():
-						geneOpt.append(("%s (%s %s)" % (columnNames[item][1], category.title(), speciesFreeze[category]), 
-							"%s__%s" % (item, speciesFreeze[category])))
-					else:
-						geneOpt.append((columnNames[item][1], item))
-				geneOpt.sort()
-				allColumnsList.append(geneOpt)
-
-		allColumnsList2 = HT.Select(name="allColumns2", Class="snpBrowserDropBox")
-		for item in self.allStrainNames:
-			allColumnsList2.append(item)
-		
-		######################################
-		## Create the list of selected columns
-		######################################
-		
-		#cols contains the value of all the selected columns
-		submitCols = cols = fd.formdata.getvalue("columns", "default")
-		
-		if cols == "default":
-			if self.species=="mouse":  #these are the same columns that are shown on intervalPage.py
-				cols = ['GeneSymbol', 'GeneDescription', 'goterms', 'pathwaynames', 'Chromosome', 'TxStart', 'snpCountmis', 'snpCountmissel', 'meanA', 'meanB', 'meanC', 'probesetcisA','probesetcisB','probesetcisC', 'probesetA','probesetB','probesetC', 'indelCountBXD','hassnp','hasindel','hasexpr','hascis','score']
-			elif self.species=="rat":
-				cols = ['GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'GeneLength', 'Strand', 'GeneID', 'UnigenID']
-			else:
-				#should not happen
-				cols = []
-		else:
-			if type(cols)==type(""):
-				cols = [cols]
-			
-		colsLst = []
-		dispFields = []
-		for column in cols:
-			if submitCols == "default" and column not in ('GeneSymbol') and (column in GeneListFields or column in speciesField):
-				colsLst.append(("%s (%s %s)" % (columnNames[column][1], self.species.title(), speciesFreeze[self.species]), 
-							"%s__%s" % (column, speciesFreeze[self.species])))
-				dispFields.append([column, self.species])
-			else:
-				column2 = column.split("__")
-				if len(column2) == 1:
-					colsLst.append((columnNames[column2[0]][1], column))
-					dispFields.append([column])
-				else:
-					thisSpecies = speciesFreeze[column2[1]]
-					colsLst.append(("%s (%s %s)" % (columnNames[column2[0]][1], thisSpecies.title(), column2[1]), 
-							column))
-					dispFields.append((column2[0], thisSpecies))
-		selectedColumnsList = HT.Select(name="columns", Class="snpBrowserSelectBox", multiple="true", data=colsLst, size=6)
-
-
-
-		######### now for the strains!!!!!!
-
-		#cols contains the value of all the selected columns
-		submitCols2 = cols2 = fd.formdata.getvalue("columns2", "default")
-		
-		if cols2 == "default":
-			if self.species=="mouse":  #these are the same columns that are shown on intervalPage.py
-				cols2 = ['C57BL/6J', 'DBA/2J',]
-			else:
-				#should not happen
-				cols2 = []
-		else:
-			if type(cols2)==type(""):
-				cols2 = [cols2]
-			
-		colsLst2 = []
-		dispFields2 = []
-		for column2 in cols2:
-#			if submitCols2 == "default" and (column in GeneListFields or column in speciesField):
-#				colsLst2.append(("%s (%s %s)" % (columnNames[column][1], self.species.title(), speciesFreeze[self.species]), 
-#							"%s__%s" % (column, speciesFreeze[self.species])))
-#				dispFields.append([column, self.species])
-#			else:
-#				column2 = column.split("__")
-#				if len(column2) == 1:
-			colsLst2.append((column2, column2))
-			dispFields2.append([column2])
-		selectedColumnsList2 = HT.Select(name="columns2", Class="snpBrowserSelectBox", multiple="true", data=colsLst2, size=6)
-
-		######### now for the sorton
-
-		#cols contains the value of all the selected columns
-		submitCols3 = cols3 = fd.formdata.getvalue("columns3", "default")
-		
-		if cols3 == "default":
-			if self.species=="mouse":  #these are the same columns that are shown on intervalPage.py
-				cols3 = ['Position', 'Score',]
-			else:
-				#should not happen
-				cols3 = []
-		else:
-			if type(cols3)==type(""):
-				cols3 = [cols3]
-			
-		colsLst3 = []
-		dispFields3 = []
-		for column3 in cols3:
-			colsLst3.append((column3, column3))
-			dispFields3.append([column3])
-		selectedColumnsList3 = HT.Select(name="columns3", Class="snpBrowserSelectBox", multiple="true", data=colsLst3, size=6)
-
-
-
-
-		
-		##########################
-        ## Create the columns form
-		##########################		
-		columnsForm = HT.Form(name="columnsForm", submit=HT.Input(type='hidden'), cgi=os.path.join(webqtlConfig.CGIDIR, _scriptfile), enctype="multipart/form-data")
-		columnsForm.append(HT.Input(type="hidden", name="fromdatabase", value= fd.formdata.getvalue("fromdatabase", "unknown")))
-		columnsForm.append(HT.Input(type="hidden", name="species", value=self.species))	
-		columnsForm.append(HT.Input(type="hidden", name="submitter", value="empty"))	
-		if self.diffCol:
-			columnsForm.append(HT.Input(type="hidden", name="s1", value=self.diffCol[0]))
-			columnsForm.append(HT.Input(type="hidden", name="s2", value=self.diffCol[1]))
-		startBox = HT.Input(type="text", name="startMb", value=self.startMb, size=10)
-		endBox = HT.Input(type="text", name="endMb", value=self.endMb, size=10)
-		addButton = HT.Input(type="button", name="add", value="Add", Class="button", onClick="addToList(this.form.allColumns.options[this.form.allColumns.selectedIndex].text, this.form.allColumns.options[this.form.allColumns.selectedIndex].value, this.form.columns)")
-#		addButton2 = HT.Input(type="button", name="add", value="Add", Class="button", onClick="addToList(this.form.allColumns2.options[this.form.allColumns2.selectedIndex].text, this.form.allColumns2.options[this.form.allColumns2.selectedIndex].value, this.form.columns2)")
-		removeButton = HT.Input(type="button", name="remove", value="Remove", Class="button", onClick="removeFromList(this.form.columns.selectedIndex, this.form.columns)")
-#		removeButton2 = HT.Input(type="button", name="remove", value="Remove", Class="button", onClick="removeFromList(this.form.columns2.selectedIndex, this.form.columns2)")
-		upButton = HT.Input(type="button", name="up", value="Up", Class="button", onClick="swapOptions(this.form.columns.selectedIndex, this.form.columns.selectedIndex-1, this.form.columns)")
-		downButton = HT.Input(type="button", name="down", value="Down", Class="button", onClick="swapOptions(this.form.columns.selectedIndex, this.form.columns.selectedIndex+1, this.form.columns)")
-		clearButton = HT.Input(type="button", name="clear", value="Clear", Class="button", onClick="deleteAllElements(this.form.columns)")		
-		submitButton = HT.Input(type="submit", value="Analyze QTL interval", Class="button", onClick="Javascript:this.form.submitter.value='refresh';selectAllElements(this.form.columns)")		
-
-
-		selectChrBox = HT.Select(name="chromosome")
-		self.cursor.execute("""
-			Select
-				Chr_Length.Name, Length from Chr_Length, Species
-			where
-				Chr_Length.SpeciesId = Species.Id AND
-				Species.Name = '%s' 
-			Order by
-				Chr_Length.OrderId
-			""" % self.species)
-		
-		results = self.cursor.fetchall()
-		for chrInfo in results:
-			selectChrBox.append((chrInfo[0], chrInfo[0]))
-		selectChrBox.selected.append(self.Chr)
-
-############################################ 2 strain boxes
-
-		selectstr1 = HT.Select(name="str1")
-		for item in self.allStrainNames:
-			selectstr1.append(item[0])
-		selectstr1.selected.append(self.str1)
-
-		selectstr2 = HT.Select(name="str2")
-		for item in self.allStrainNames:
-			selectstr2.append(item[0])
-		selectstr2.selected.append(self.str2)
-
-############################################ select sort on
-
-		selectsorton = HT.Select(name="sorton")
-		selectsorton.append('Position')
-		selectsorton.append('Score')
-		selectsorton.selected.append('Position')
-
-
-############################################
-		selectSpeciesBoxA = HT.Select(name="myspeciesA",onChange="Javascript:this.form.submitter.value='s2';submit();")
-		for speciesInfo in self.spA:
-			name = ''
-			if speciesInfo[0]=='mouse':
-				name='Mouse'
-			elif speciesInfo[0]=='rat':
-				name='Rat'
-			elif speciesInfo[0]=='arabidopsis':
-				name='Arabidopsis thaliana'
-			elif speciesInfo[0]=='human':
-				name='Human'
-			elif speciesInfo[0]=='barley':
-				name='Barley'
-			elif speciesInfo[0]=='drosophila':
-				name='Drosophila'
-			elif speciesInfo[0]=='macaque monkey':
-				name='Macaque Monkey'
-
-			selectSpeciesBoxA.append((name, speciesInfo[0]))
-		selectSpeciesBoxA.selected.append(self.spAsel)
-
-		selectGroupBoxA = HT.Select(name="groupA",onChange="Javascript:this.form.submitter.value='a2';submit();")
-		for groupInfo in self.grA:
-			selectGroupBoxA.append((groupInfo[1], groupInfo[0]))
-		selectGroupBoxA.selected.append(self.grAsel)
-
-		selectTypeBoxA = HT.Select(name="typeA",onChange="Javascript:this.form.submitter.value='a3';submit();")
-		for typeInfo in self.tyA:
-			selectTypeBoxA.append((typeInfo[0] + ' mRNA', typeInfo[0]))
-		selectTypeBoxA.selected.append(self.tyAsel)
-
-		selectDatabaseBoxA = HT.Select(name="databaseA",onChange="Javascript:this.form.submitter.value='a4';submit();")
-		for databaseInfo in self.daA:
-			selectDatabaseBoxA.append((databaseInfo[1], databaseInfo[0]))
-		selectDatabaseBoxA.selected.append(self.daAsel)
-
-#############################
-############################################
-		selectSpeciesBoxB = HT.Select(name="myspeciesB",onChange="Javascript:this.form.submitter.value='b1';submit();")
-		for speciesInfo in self.spB:
-			name = ''
-			if speciesInfo[0]=='mouse':
-				name='Mouse'
-			elif speciesInfo[0]=='rat':
-				name='Rat'
-			elif speciesInfo[0]=='arabidopsis':
-				name='Arabidopsis thaliana'
-			elif speciesInfo[0]=='human':
-				name='Human'
-			elif speciesInfo[0]=='barley':
-				name='Barley'
-			elif speciesInfo[0]=='drosophila':
-				name='Drosophila'
-			elif speciesInfo[0]=='macaque monkey':
-				name='Macaque Monkey'
-
-			selectSpeciesBoxB.append((name, speciesInfo[0]))			
-		selectSpeciesBoxB.selected.append(self.spBsel)
-
-		selectGroupBoxB = HT.Select(name="groupB",onChange="Javascript:this.form.submitter.value='b2';submit();")
-		for groupInfo in self.grB:
-			selectGroupBoxB.append((groupInfo[1], groupInfo[0]))
-		selectGroupBoxB.selected.append(self.grBsel)
-
-		selectTypeBoxB = HT.Select(name="typeB",onChange="Javascript:this.form.submitter.value='b3';submit();")
-		for typeInfo in self.tyB:
-			selectTypeBoxB.append((typeInfo[0] + ' mRNA', typeInfo[0]))
-		selectTypeBoxB.selected.append(self.tyBsel)
-
-		selectDatabaseBoxB = HT.Select(name="databaseB",onChange="Javascript:this.form.submitter.value='b4';submit();")
-		for databaseInfo in self.daB:
-			selectDatabaseBoxB.append((databaseInfo[1], databaseInfo[0]))
-		selectDatabaseBoxB.selected.append(self.daBsel)
-
-############################################
-#############################
-############################################
-		selectSpeciesBoxC = HT.Select(name="myspeciesC",onChange="Javascript:this.form.submitter.value='c1';submit();")
-		for speciesInfo in self.spC:
-			name = ''
-			if speciesInfo[0]=='mouse':
-				name='Mouse'
-			elif speciesInfo[0]=='rat':
-				name='Rat'
-			elif speciesInfo[0]=='arabidopsis':
-				name='Arabidopsis thaliana'
-			elif speciesInfo[0]=='human':
-				name='Human'
-			elif speciesInfo[0]=='barley':
-				name='Barley'
-			elif speciesInfo[0]=='drosophila':
-				name='Drosophila'
-			elif speciesInfo[0]=='macaque monkey':
-				name='Macaque Monkey'
-
-			selectSpeciesBoxC.append((name, speciesInfo[0]))			
-		selectSpeciesBoxC.selected.append(self.spCsel)
-
-		selectGroupBoxC = HT.Select(name="groupC",onChange="Javascript:this.form.submitter.value='c2';submit();")
-		for groupInfo in self.grC:
-			selectGroupBoxC.append((groupInfo[1], groupInfo[0]))
-		selectGroupBoxC.selected.append(self.grCsel)
-
-		selectTypeBoxC = HT.Select(name="typeC",onChange="Javascript:this.form.submitter.value='c3';submit();")
-		for typeInfo in self.tyC:
-			selectTypeBoxC.append((typeInfo[0] + ' mRNA', typeInfo[0]))
-		selectTypeBoxC.selected.append(self.tyCsel)
-
-		selectDatabaseBoxC = HT.Select(name="databaseC",onChange="Javascript:this.form.submitter.value='c4';submit();")
-		for databaseInfo in self.daC:
-			selectDatabaseBoxC.append((databaseInfo[1], databaseInfo[0]))
-		selectDatabaseBoxC.selected.append(self.daCsel)
-
-############################################
-
-
-
-
-#############################
-
-
-		
-
-		innerColumnsTable = HT.TableLite(border=0, Class="collap", cellpadding = 2)
-		innerColumnsTable.append(HT.TR(HT.TD(selectedColumnsList)),
-					 HT.TR(HT.TD(clearButton, removeButton, upButton, downButton)))
-#		innerColumnsTable2 = HT.TableLite(border=0, Class="collap", cellpadding = 2)
-#		innerColumnsTable2.append(HT.TR(HT.TD(selectedColumnsList2)),
-#					 HT.TR(HT.TD(removeButton2)))
-		columnsTable = HT.TableLite(border=0, cellpadding=2, cellspacing=0)
-		columnsTable.append(
-				    HT.TR(HT.TD(HT.Font("&nbsp;")),
-					  HT.TD(HT.Strong("Select the QTL interval"))),
-					HT.TR(HT.TD(HT.Font("Chr: ", size=-1)),
-					  HT.TD(selectChrBox)),
-				    HT.TR(HT.TD(HT.Font("View: ", size=-1)),
-					  HT.TD(startBox, HT.Font("Mb to ", size=-1), endBox, HT.Font("Mb", size=-1))),
-				    HT.TR(HT.TD(HT.Font("&nbsp;", size=-1)),
-					  HT.TD("&nbsp;")),
-				    HT.TR(HT.TD(HT.Font("&nbsp;")),
-					  HT.TD(HT.Strong("Select two mouse strains for inclusion of nsSNP count"))),
-				    HT.TR(HT.TD(HT.Font("Strains: ", size=-1)),
-					  HT.TD(selectstr1,selectstr2)),
-				    HT.TR(HT.TD(HT.Font("&nbsp;", size=-1)),
-					  HT.TD("&nbsp;")),
-				    HT.TR(HT.TD(HT.Font("&nbsp;")),
-					  HT.TD(HT.Strong("Select 3 datasets for inclusion of expression and cis-activity data"))),
-				    HT.TR(HT.TD(HT.Font("&nbsp;", size=-1)),
-					  HT.TD("&nbsp;")),
-				    HT.TR(HT.TD("&nbsp;"),
-					  HT.TD(HT.Font("Dataset 1", size=-1))),
-				    HT.TR(HT.TD(HT.Font("Species: ", size=-1)),
-					  HT.TD(selectSpeciesBoxA)),
-				    HT.TR(HT.TD(HT.Font("Group: ", size=-1)),
-					  HT.TD(selectGroupBoxA)),
-				    HT.TR(HT.TD(HT.Font("Type: ", size=-1)),
-					  HT.TD(selectTypeBoxA)),
-				    HT.TR(HT.TD(HT.Font("Database: ", size=-1)),
-					  HT.TD(selectDatabaseBoxA)),
-				    HT.TR(HT.TD(HT.Font("&nbsp;", size=-1)),
-					  HT.TD("&nbsp;")),
-				    HT.TR(HT.TD("&nbsp;"),
-					  HT.TD(HT.Font("Dataset 2", size=-1))),
-				    HT.TR(HT.TD(HT.Font("Species: ", size=-1)),
-					  HT.TD(selectSpeciesBoxB)),
-				    HT.TR(HT.TD(HT.Font("Group: ", size=-1)),
-					  HT.TD(selectGroupBoxB)),
-				    HT.TR(HT.TD(HT.Font("Type: ", size=-1)),
-					  HT.TD(selectTypeBoxB)),
-				    HT.TR(HT.TD(HT.Font("Database: ", size=-1)),
-					  HT.TD(selectDatabaseBoxB)),
-				    HT.TR(HT.TD(HT.Font("&nbsp;", size=-1)),
-					  HT.TD("&nbsp;")),
-				    HT.TR(HT.TD("&nbsp;"),
-					  HT.TD(HT.Font("Dataset 3", size=-1))),
-				    HT.TR(HT.TD(HT.Font("Species: ", size=-1)),
-					  HT.TD(selectSpeciesBoxC)),	
-				    HT.TR(HT.TD(HT.Font("Group: ", size=-1)),
-					  HT.TD(selectGroupBoxC)),
-					HT.TR(HT.TD(HT.Font("Type: ", size=-1)),
-					  HT.TD(selectTypeBoxC)),
-				    HT.TR(HT.TD(HT.Font("Database: ", size=-1)),
-					  HT.TD(selectDatabaseBoxC)),
-#				    HT.TR(HT.TD(""),
-#					  HT.TD(innerColumnsTable2)),
-				    HT.TR(HT.TD(HT.Font("&nbsp;", size=-1)),
-					  HT.TD("&nbsp;")),
-				    HT.TR(HT.TD(HT.Font("&nbsp;")),
-					  HT.TD(HT.Strong("Optionally, choose additional data to display"))),
-				    HT.TR(HT.TD(HT.Font("Show: ", size=-1)),
-					  HT.TD(allColumnsList, addButton)),
-				    HT.TR(HT.TD(HT.Font("Selected:",size=-1)),
-					  HT.TD(innerColumnsTable)),
-				    HT.TR(HT.TD(HT.Font("&nbsp;", size=-1)),
-					  HT.TD("&nbsp;")),
-				    HT.TR(HT.TD(HT.Font("Sort by: ", size=-1)),
-					  HT.TD(selectsorton)),
-				    HT.TR(HT.TD(HT.Font("&nbsp;", size=-1)),
-					  HT.TD("&nbsp;")),
-				    HT.TR(HT.TD(HT.Font("&nbsp;", size=-1)),
-					  HT.TD(submitButton)),
-				    
-				    )
-		columnsForm.append(columnsTable)
-		#columnsForm.append(HT.Input(type="hidden", name="sort", value=diffCol),
-		#		   HT.Input(type="hidden", name="identification", value=identification),
-		#		   HT.Input(type="hidden", name="traitInfo", value=traitInfo))
-		
-		return columnsForm, dispFields, dispFields2
diff --git a/web/webqtl/qtlminer/__init__.py b/web/webqtl/qtlminer/__init__.py
deleted file mode 100755
index e69de29b..00000000
--- a/web/webqtl/qtlminer/__init__.py
+++ /dev/null