Add all the source codes into the github.

3 files changed, 1895 insertions, 0 deletions

diff --git a/web/webqtl/qtlminer/GeneUtil.py b/web/webqtl/qtlminer/GeneUtil.py
new file mode 100755
index 00000000..3ae7f3c0
--- /dev/null
+++ b/web/webqtl/qtlminer/GeneUtil.py
@@ -0,0 +1,658 @@
+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
new file mode 100755
index 00000000..e565cdd7
--- /dev/null
+++ b/web/webqtl/qtlminer/QTLminer.py
@@ -0,0 +1,1237 @@
+#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
new file mode 100755
index 00000000..e69de29b
--- /dev/null
+++ b/web/webqtl/qtlminer/__init__.py