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

10 files changed, 0 insertions, 1296 deletions

diff --git a/web/webqtl/textUI/__init__.py b/web/webqtl/textUI/__init__.py
deleted file mode 100755
index e69de29b..00000000
--- a/web/webqtl/textUI/__init__.py
+++ /dev/null
diff --git a/web/webqtl/textUI/cmdClass.py b/web/webqtl/textUI/cmdClass.py
deleted file mode 100755
index e394218e..00000000
--- a/web/webqtl/textUI/cmdClass.py
+++ /dev/null
@@ -1,224 +0,0 @@
-import string
-import os
-import MySQLdb
-
-from base import webqtlConfig
-
-######################################### 
-#      Basic Class
-#########################################
-class cmdClass:
-	def __init__(self,fd):
-		self.contents = []
-		self.accessError = 0
-		self.error = 0
-		self.accessCode = '###Database Code : <a href="%s%s?cmd=help">%s%s?cmd=help</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)
-		self.data = fd.formdata
-		self.cmdID = self.data.getvalue('cmd')
-		self.showurl = self.data.getvalue('url')
-		self.cursor = None
-		self.user_ip = fd.remote_ip
-		
-		try:
-			if not self.openMysql():
-				self.accessError = 1
-				self.contents = ['###Error: Database is not ready']
-				return
-			
-			if not self.accessCount():
-				self.accessError = 1
-				self.contents = ['###Error: You have reached maximum access today ']
-				return
-			self.accessRecord()
-		except:
-			self.accessError = 1
-			self.contents = ['###Error: Database is not ready']
-			return
-
-		
-		self.probeset = self.data.getvalue('probeset')
-		self.database = self.data.getvalue('db')
-		self.probe = self.data.getvalue('probe')
-		
-		self.sourcedata = []
-		
-		
-		try:
-			self.format = self.data.getvalue('format')[:3]
-		except:
-			self.format = 'row'
-		if not self.probeset or not self.database:
-			self.error = 1
-			return
-
-	def openMysql(self):
-		try:
-			# con = MySQLdb.Connect(db='db_webqtl', host = webqtlConfig.MYSQL_SERVER)
-			# Modified by Fan Zhang
-			con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
-			self.cursor = con.cursor()
-			return 1
-		except:
-			return 0
-
-	#XZ, 03/23/2009: The function name is confusing. This function is to get the database type(ProbeSet, Publish, Geno) id.	
-	def getDBId(self,code):
-		self.cursor.execute('SELECT DBType.Name, DBList.FreezeId from DBType, DBList WHERE DBType.Id = DBList.DBTypeId and DBList.code= "%s"' % code)
-		result = self.cursor.fetchall()
-		if not result:
-			return (None, None)
-		else:
-			return result[0]
-
-	#XZ, 03/23/2009: This is to get the inbredset name.
-	def getRISet(self,prefix, DbId):
-		if prefix == 'ProbeSet':
-			self.cursor.execute('SELECT InbredSet.Name from InbredSet, ProbeSetFreeze, ProbeFreeze WHERE ProbeFreeze.InbredSetId = InbredSet.Id and ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId and ProbeSetFreeze.Id = %d' % DbId)
-		else:
-			self.cursor.execute('SELECT InbredSet.Name from %sFreeze, InbredSet WHERE %sFreeze.InbredSetId = InbredSet.Id and %sFreeze.Id = %d' % (prefix, prefix, prefix, DbId))
-		result = self.cursor.fetchall()
-		if result:
-			if result[0][0] == "BXD300":
-				return "BXD"
-			else:
-				return result[0][0]
-		else:
-			return None
-		
-	def accessCount(self):
-		try:
-			user_ip = self.user_ip
-			query = """SELECT count(id) FROM AccessLog WHERE ip_address = %s AND UNIX_TIMESTAMP()-UNIX_TIMESTAMP(accesstime)<86400"""
-			self.cursor.execute(query,user_ip)
-			daycount = self.cursor.fetchall()
-			if daycount:
-				daycount = daycount[0][0]
-				if daycount > webqtlConfig.DAILYMAXIMUM:
-					return 0
-				else:
-					return 1
-			else:
-				return 1
-		except:
-			return 0
-		
-	def accessRecord(self):
-		try:
-			user_ip = self.user_ip
-			self.updMysql()
-			query = """INSERT INTO AccessLog(accesstime,ip_address) values(Now(),%s)""" 
-			self.cursor.execute(query,user_ip)
-			self.openMysql()
-		except:
-			pass
-
-	def __str__(self):
-		text = map(str,self.contents)
-		if self.showurl:
-			text.append('http://%s%s?%s' % (os.environ['HTTP_HOST'],os.environ['SCRIPT_NAME'],os.environ['QUERY_STRING'][:-8]))
-			text += self.sourcedata
-		return string.join(text,'\n')
-
-	def write(self):
-		if self.cursor:
-			self.cursor.close()
-		try:
-			browser = os.environ['HTTP_USER_AGENT']
-			return '<pre>%s</pre>' % str(self)
-		except:
-			return str(self)
-	
-	def write2(self):
-		print str(self)
-	
-	def getTraitData(self, prefix, dbId, probeset, probe = None): 
-		headerDict = {'ProbeSet':'ProbeSetID', 'Publish':'RecordID', 'Geno':'Locus'}
-		if prefix == None or dbId == None:
-			return None, None
-		if probe and prefix=='ProbeSet':
-			#XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=98332_at&db=bra08-03MAS5&probe=pm&format=col
-			if string.lower(probe) in ("all","mm","pm"):
-				query = "SELECT Probe.Name from Probe, ProbeSet WHERE Probe.ProbeSetId = ProbeSet.Id and ProbeSet.Name = '%s' order by Probe.Name" % probeset
-				self.cursor.execute(query)
-				allprobes = self.cursor.fetchall()
-				if not allprobes:
-					return None, None
-					
-				fetchprobes = []
-				for item in allprobes:
-					if probe == 'all':
-						fetchprobes.append(item[0])
-					else:		
-						try:
-							taildigit =  int(item[0][-1]) % 2
-							if probe == "pm" and taildigit == 1:
-								fetchprobes.append(item[0])
-							if probe == "mm" and taildigit == 0:
-								fetchprobes.append(item[0])
-						except:
-							pass
-				if not fetchprobes:
-					return None, None
-				#XZ, 03/05/2009: Xiaodong changed Data to ProbeData	
-				query = "SELECT Strain.Name, ProbeData.value, Probe.Name from ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, Strain, Probe, ProbeSet WHERE ProbeSet.Name = '%s' and Probe.ProbeSetId = ProbeSet.Id and ProbeXRef.ProbeId = Probe.Id and ProbeXRef.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Id = %d and ProbeXRef.DataId = ProbeData.Id and ProbeData.StrainId = Strain.Id and Probe.Name in (%s) order by Strain.Id, Probe.Name " % (probeset,dbId, "'" + string.join(fetchprobes, "', '") +"'")
-				self.cursor.execute(query)
-				traitdata = self.cursor.fetchall()
-				if not traitdata:
-					pass
-				else:
-					nfield = len(fetchprobes)
-					heads = [['ProbeSet'] + [probeset]*nfield]
-					heads.append(['probe'] + fetchprobes)
-					posdict = {}
-					i = 0
-					for item in fetchprobes:
-						posdict[item] = i
-						i += 1
-					prevStrain = ''
-					traitdata2 = []
-					i = -1 
-					for item in traitdata:
-						if item[0] != prevStrain:
-							prevStrain = item[0]
-							i += 1
-							traitdata2.append([item[0]] +  [None] * nfield)
-						else:
-							pass
-						traitdata2[i][posdict[item[-1]]+1] = item[1]
-					
-					traitdata = traitdata2
-			#XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=98332_at&db=bra08-03MAS5&probe=119637&format=col
-			else:
-				heads = [('ProbeSetId', probeset), ('ProbeId',probe)]
-				#XZ, 03/05/2009: Xiaodong changed Data to ProbeData
-				query = "SELECT Strain.Name, ProbeData.value from ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, Strain, Probe, ProbeSet WHERE Probe.Name = '%s' and ProbeSet.Name = '%s' and Probe.ProbeSetId = ProbeSet.Id and ProbeXRef.ProbeId = Probe.Id and ProbeXRef.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Id = %d and ProbeXRef.DataId = ProbeData.Id and ProbeData.StrainId = Strain.Id" % (probe,probeset,dbId)
-				#print 'Content-type: text/html\n'
-				self.cursor.execute(query)
-				traitdata = self.cursor.fetchall()
-		#XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=98332_at&db=bra08-03MAS5&format=col
-		elif prefix=='ProbeSet': #XZ: probeset data
-			heads = [(headerDict[prefix], probeset)]
-			query = "SELECT Strain.Name, %sData.value from %sData, Strain, %s, %sXRef WHERE %s.Name = '%s' and %sXRef.%sId = %s.Id and %sXRef.%sFreezeId = %d and  %sXRef.DataId = %sData.Id and %sData.StrainId = Strain.Id order by Strain.Id" % (prefix, prefix, prefix, prefix, prefix, probeset,prefix, prefix, prefix, prefix, prefix, dbId, prefix, prefix, prefix)
-			self.cursor.execute(query)
-			traitdata = self.cursor.fetchall()
-		#XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=10834&db=BXDPublish&format=col
-		elif prefix=='Publish':
-			heads = [(headerDict[prefix], probeset)]
-			#XZ, 03/05/2009: Xiaodong changed Data to PublishData
-			query = "SELECT Strain.Name, PublishData.value from PublishData, Strain, PublishXRef, PublishFreeze WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId and PublishData.Id = PublishXRef.DataId and PublishXRef.Id = %s and PublishFreeze.Id = %d and PublishData.StrainId = Strain.Id" % (probeset, dbId)
-			self.cursor.execute(query)
-			traitdata = self.cursor.fetchall()
-		#XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=get&probeset=rs13475701&db=BXDGeno&format=col
-		else: #XZ: genotype data
-			heads = [(headerDict[prefix], probeset)]
-			RISet = self.getRISet(prefix, dbId)
-			self.cursor.execute("select SpeciesId from InbredSet where Name = '%s'" % RISet)
-			speciesId = self.cursor.fetchone()[0]			
-			#XZ, 03/05/2009: Xiaodong changed Data to %sData
-			query = "SELECT Strain.Name, %sData.value from %sData, Strain, %s, %sXRef WHERE %s.SpeciesId=%s and %s.Name = '%s' and %sXRef.%sId = %s.Id and %sXRef.%sFreezeId = %d and  %sXRef.DataId = %sData.Id and %sData.StrainId = Strain.Id order by Strain.Id" % (prefix, prefix, prefix, prefix, prefix, speciesId, prefix, probeset,prefix, prefix, prefix, prefix, prefix, dbId, prefix, prefix, prefix)
-			self.cursor.execute(query)
-			traitdata = self.cursor.fetchall()
-		if traitdata:
-			return traitdata, heads
-		else:
-			return None, None
diff --git a/web/webqtl/textUI/cmdCorrelation.py b/web/webqtl/textUI/cmdCorrelation.py
deleted file mode 100755
index 04595fc5..00000000
--- a/web/webqtl/textUI/cmdCorrelation.py
+++ /dev/null
@@ -1,325 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import os
-import string
-from math import *
-import time
-
-import reaper
-
-from base import webqtlConfig
-from utility import webqtlUtil
-from cmdClass import cmdClass
-
-
-#########################################
-#      Correlation Class
-#########################################
-class cmdCorrelation(cmdClass):
-
-	calFunction = 'webqtlUtil.calCorrelation'
-
-	def __init__(self,fd=None):
-
-		cmdClass.__init__(self,fd)
-
-		if not webqtlConfig.TEXTUI:
-			self.contents.append("Please send your request to http://robot.genenetwork.org")
-			return
-
-
-		self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&searchdb=BXDPublish&return=500&sort=pvalue">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&searchdb=BXDPublish&return=500&sort=pvalue</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
-
-		if self.accessError:
-			return
-			
-		self.searchDB = self.data.getvalue('searchdb')
-		if not self.searchDB or self.error:
-			self.contents.append("###Error: source trait doesn't exist or no target database was given")
-			self.contents.append(self.example)
-			self.contents.append(self.accessCode)
-			return
-		
-		try:
-			self.returnNumber = int(self.data.getvalue('return'))
-		except:
-			self.returnNumber = None
-		
-		self.sort = self.data.getvalue('sort')
-
-		prefix, dbId = self.getDBId(self.database)
-		if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")):
-			self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
-			self.contents.append(self.example)
-			self.contents.append(self.accessCode)
-			return
-		RISet = self.getRISet(prefix, dbId)
-		prefix2, dbId2 = self.getDBId(self.searchDB)
-		if not prefix2 or not dbId2:
-			self.contents.append("###Error: target database doesn't exist.")
-			self.contents.append(self.example)
-			self.contents.append(self.accessCode)
-			return
-		RISet2 = self.getRISet(prefix2, dbId2)
-		if RISet2 != RISet:
-			self.contents.append("###Error: target database has different Mouse InbredSet.")
-			self.contents.append(self.example)
-			self.contents.append(self.accessCode)
-			return
-		
-		traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
-		if not traitdata:
-			self.contents.append("###Error: source trait doesn't exist.")
-			self.contents.append(self.example)
-			self.contents.append(self.accessCode)
-			return
-			
-		StrainNames = []
-		sourceTrait = []
-		StrainIds = []
-
-		#XZ, Jan 27, 2011: Only the strains that are of the same inbredset are used to calculate correlation.
-		for item in traitdata:
-			one_strain_name = item[0]
-			one_strain_value = item[1]
-
-			self.cursor.execute('SELECT Strain.Id from Strain,StrainXRef, InbredSet WHERE Strain.Name="%s" and Strain.Id = StrainXRef.StrainId and StrainXRef.InbredSetId = InbredSet.Id and InbredSet.Name = "%s"' % (one_strain_name, RISet2))
-			Results = self.cursor.fetchall()
-			if Results:
-				StrainIds.append('%d' % Results[0][0])
-				StrainNames.append( one_strain_name )
-				sourceTrait.append( one_strain_value )
-
-		correlationArray = []
-
-		useFastMethod = False
-		if prefix2 == "ProbeSet":
-			DatabaseFileName = self.getFileName( target_db_id=dbId2 )
-			DirectoryList = os.listdir(webqtlConfig.TEXTDIR)  ### List of existing text files.  Used to check if a text file already exists
-			if DatabaseFileName in DirectoryList:
-				useFastMethod = True
-
-		if useFastMethod:
-			datasetFile = open(webqtlConfig.TEXTDIR+DatabaseFileName,'r')
-
-			#XZ, 01/08/2009: read the first line
-			line = datasetFile.readline()
-			dataset_strains = webqtlUtil.readLineCSV(line)[1:]
-
-			#XZ, 01/08/2009: This step is critical. It is necessary for this new method.
-			_newvals = []
-			for item in dataset_strains:
-				if item in StrainNames:
-					_newvals.append(sourceTrait[StrainNames.index(item)])
-				else:
-					_newvals.append('None')
-
-			nnCorr = len(_newvals)
-
-			
-			for line in datasetFile:
-				traitdata=webqtlUtil.readLineCSV(line)
-				traitdataName = traitdata[0]
-				traitvals = traitdata[1:]
-
-				corr,nOverlap = webqtlUtil.calCorrelationText(traitvals,_newvals,nnCorr)
-				traitinfo = [traitdataName,corr,nOverlap]
-				correlationArray.append( traitinfo )
-
-		#calculate correlation with slow method
-		else:
-			correlationArray = self.calCorrelation(sourceTrait, self.readDB(StrainIds, prefix2, dbId2) )
-
-		correlationArray.sort(self.cmpCorr) #XZ: Do not forget the sort step
-
-		if not self.returnNumber:
-			correlationArray = correlationArray[:100]
-		else:
-			if self.returnNumber < len(correlationArray):
-				correlationArray = correlationArray[:self.returnNumber]
-		NN = len(correlationArray)
-		for i in range(NN):
-			nOverlap = correlationArray[i][-1]
-			corr = correlationArray[i][-2]
-			if nOverlap < 3:
-				corrPValue = 1.0
-			else:
-				if abs(corr) >= 1.0:
-					corrPValue = 0.0
-				else:
-					ZValue = 0.5*log((1.0+corr)/(1.0-corr))
-					ZValue = ZValue*sqrt(nOverlap-3)
-					corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
-			correlationArray[i].append(corrPValue)
-		if self.sort == 'pvalue':
-			correlationArray.sort(self.cmpPValue)
-		
-		if prefix2 == 'Publish':
-			self.contents.append("RecordID\tCorrelation\t#Strains\tp-value")
-		elif  prefix2 == 'Geno':
-			self.contents.append("Locus\tCorrelation\t#Strains\tp-value")
-		else:
-			pass
-
-		if prefix2 == 'Publish' or prefix2 == 'Geno':
-			for item in correlationArray:
-				self.contents.append("%s\t%2.6f\t%d\t%2.6f" % tuple(item))
-		else:
-			id = self.data.getvalue('id')
-			if id == 'yes':					
-				self.contents.append("ProbesetID\tCorrelation\t#Strains\tp-value\tGeneID")
-				for item in correlationArray:
-					query = """SELECT GeneID from %s WHERE Name = '%s'""" % (prefix2,item[0])
-					self.cursor.execute(query)
-					results = self.cursor.fetchall()
-					if not results:
-						item = item + [None]
-					else:
-						item = item + list(results[0])
-					self.contents.append("%s\t%2.6f\t%d\t%2.6f\t%s" % tuple(item))
-			elif id == 'only':					
-				self.contents.append("GenID")
-				for item in correlationArray:
-					query = """SELECT GeneID from %s WHERE Name = '%s'""" % (prefix2,item[0])
-					self.cursor.execute(query)
-					results = self.cursor.fetchall()
-					if not results:
-						self.contents.append('None')
-					else:
-						self.contents.append(results[0][0])
-			else:
-				self.contents.append("ProbesetID\tCorrelation\t#Strains\tp-value")
-				for item in correlationArray:
-					self.contents.append("%s\t%2.6f\t%d\t%2.6f" % tuple(item))
-
-
-
-
-	def getFileName(self, target_db_id):
-
-		query = 'SELECT Id, FullName FROM ProbeSetFreeze WHERE Id = %s' %  target_db_id
-		self.cursor.execute(query)
-		result = self.cursor.fetchone()
-		Id = result[0]
-		FullName = result[1]
-		FullName = FullName.replace(' ','_')
-		FullName = FullName.replace('/','_')
-
-		FileName = 'ProbeSetFreezeId_' + str(Id) + '_FullName_' + FullName + '.txt'
-
-		return FileName
-
-
-	
-	def calCorrelation(self,source,target):
-		allcorrelations = []
-		NN = len(source)
-
-		if len(source) != len(target[0]) - 1:
-			return allcorrelations
-		else:
-			for traitData in target:
-				corr,nOverlap = eval("%s(traitData[1:],source,NN)" % self.calFunction)
-				traitinfo = [traitData[0],corr,nOverlap]				
-				allcorrelations.append(traitinfo)
-
-			return allcorrelations
-	
-	def cmpCorr(self,A,B):
-		try:
-			if abs(A[1]) < abs(B[1]):
-				return 1
-			elif abs(A[1]) == abs(B[1]):
-				return 0
-			else:
-				return -1	
-		except:
-			return 0
-
-	def cmpPValue(self,A,B):
-		try:
-			if A[-1] > B[-1]:
-				return 1
-			elif A[-1] ==  B[-1]:
-				return 0
-			else:
-				return -1	
-		except:
-			return 0
-
-
-        def  readDB(self, StrainIds=[], prefix2='', dbId2=''):
-
-                #retrieve data from target database
-                nnn = len(StrainIds) / 25
-                if len(StrainIds) % 25:
-                        nnn += 1
-                oridata = []
-                for step in range(nnn):
-                        temp = []
-                        StrainIdstep = StrainIds[step*25:min(len(StrainIds), (step+1)*25)]
-                        for item in StrainIdstep:
-                                temp.append('T%s.value' % item)
-                        #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=BXDPublish&return=500&sort=pvalue
-                        if prefix2 == "Publish":
-                                query = "SELECT PublishXRef.Id, "
-                                dataStartPos = 1
-                                query += string.join(temp,', ')
-                                query += ' from (PublishXRef, PublishFreeze)\n'
-                                #XZ, 03/05/2009: Xiaodong changed Data to PublishData
-                                for item in StrainIdstep:
-                                        query += 'left join PublishData as T%s on T%s.Id = PublishXRef.DataId and T%s.StrainId=%s\n' %(item,item,item,item)
-                                query += "WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId and PublishFreeze.Id = %d" % (dbId2, )
-                        #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=HC_M2_1005_M&return=500&sort=pvalue
-                        #XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=BXDGeno&return=500&sort=pvalue
-                        else:
-                                query = "SELECT %s.Name," %  prefix2
-                                query += string.join(temp,', ')
-                                query += ' from (%s, %sXRef, %sFreeze) \n' % (prefix2,prefix2,prefix2)
-                                #XZ, 03/05/2009: Xiaodong changed Data to %sData
-                                for item in StrainIdstep:
-                                        query += 'left join %sData as T%s on T%s.Id = %sXRef.DataId and T%s.StrainId=%s\n' %(prefix2,item,item,prefix2,item,item)
-                                query += "WHERE %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Id = %d  and %s.Id = %sXRef.%sId" % (prefix2, prefix2, prefix2, prefix2, dbId2, prefix2, prefix2, prefix2)
-                        self.cursor.execute(query)
-                        results = self.cursor.fetchall()
-                        if not results:
-                                self.contents.append("###Error: target database doesn't exist.")
-                                self.contents.append(self.example)
-                                self.contents.append(self.accessCode)
-                                return
-                        oridata.append(results)
-
-                datasize = len(oridata[0])
-                targetTrait = []
-                for j in range(datasize):
-                        traitdata = list(oridata[0][j])
-                        for i in range(1,nnn):
-                                traitdata += list(oridata[i][j][1:])
-                        targetTrait.append(traitdata)
-
-                return targetTrait
-			
diff --git a/web/webqtl/textUI/cmdGeno.py b/web/webqtl/textUI/cmdGeno.py
deleted file mode 100755
index 8dd0f924..00000000
--- a/web/webqtl/textUI/cmdGeno.py
+++ /dev/null
@@ -1,118 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import string
-import os
-
-import reaper
-
-from base import webqtlConfig
-from cmdClass import cmdClass
-
-#########################################
-#      Geno Class
-#########################################
-class cmdGeno(cmdClass):
-
-	def __init__(self,fd=None):
-
-		cmdClass.__init__(self,fd)
-
-		if not webqtlConfig.TEXTUI:
-			self.contents.append("Please send your request to http://robot.genenetwork.org")
-			return
-
-		if self.accessError:
-			return
-		self.error = 0
-		self.RISet = None
-		self.chr = None
-		self.dataset = None
-		self.strainList = []
-		try:
-			self.RISet = self.data.getvalue('riset')
-			if not self.RISet:
-				raise ValueError
-		except:
-			self.error = 1
-			self.contents.append('###Example : http://www.genenetwork.org%s%s?cmd=%s&riset=BXD&chr=1' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID))
-			return
-		try:
-			self.format = self.data.getvalue('format')[:3]
-		except:
-			self.format = 'row'
-
-		try:
-			self.dataset = reaper.Dataset()
-			try:
-				self.dataset.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno'))
-			except:
-				self.dataset.read(os.path.join(webqtlConfig.GENODIR, self.RISet.upper() + '.geno'))
-			self.strainList = list(self.dataset.prgy)
-		except:
-			self.error = 1
-			#traceback.print_exc()	
-			self.contents.append('###The name of RISet is incorrect')
-			return
-
-		try:
-			self.chr = self.data.getvalue('chr')
-			if self.chr:
-				if self.chr == 'X' or self.chr == 'x':
-					self.chr = '20'
-				self.chr = int(self.chr)
-		except:
-			pass
-		
-		self.readGeno()
-
-	def  readGeno(self):
-		try:
-			table = [['Chr'] + ['Locus'] + self.strainList]
-			if self.chr:
-				chr = self.dataset[self.chr-1]
-				for locus in chr:
-					items = string.split(string.join(locus.genotext, " "))
-					items = [chr.name] + [locus.name] + items
-					table += [items]
-			else:
-				for chr in self.dataset:
-					for locus in chr:
-						items = string.split(string.join(locus.genotext, " "))
-						items = [chr.name] + [locus.name] + items
-						table += [items]
-			if self.format == 'col':
-				table = [[r[col] for r in table] for col in range(1, len(table[0]))]
-				table[0][0] = 'Line'
-			lines = string.join(map(lambda x: string.join(x, '\t'), table), '\n')
-			self.contents.append(lines)
-		except:	
-			self.contents =['###Error: Read file error or name of chromosome is incorrect']
-			#traceback.print_exc()	
-			return
-
-		
-			
diff --git a/web/webqtl/textUI/cmdGet.py b/web/webqtl/textUI/cmdGet.py
deleted file mode 100755
index a11c97a3..00000000
--- a/web/webqtl/textUI/cmdGet.py
+++ /dev/null
@@ -1,86 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import string
-
-from base import webqtlConfig
-from cmdClass import cmdClass
-
-#########################################
-#      Get trait value Class
-#########################################
-class cmdGet(cmdClass):
-	def __init__(self,fd=None):
-
-		cmdClass.__init__(self,fd)
-
-		if not webqtlConfig.TEXTUI:
-			self.contents.append("Please send your request to http://robot.genenetwork.org")
-			return
-
-		self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&db=bra03-03Mas5&probe=all">%s%s?cmd=%s&probeset=100001_at&db=bra03-03Mas5&probe=all</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
-		if self.accessError:
-			return
-		if not self.error:
-			self.readDB()
-		else:
-			self.contents.append(self.example)
-			self.contents.append(self.accessCode)
-
-	def  readDB(self):
-		prefix, dbId = self.getDBId(self.database)
-		
-		traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
-		try:	
-			if not traitdata:
-				raise ValueError
-			traitdata = heads + list(traitdata)
-			if self.format == 'col':
-				self.formatCols(traitdata)
-			else:
-				self.formatRows(traitdata)
-		except:
-			self.contents.append('Error: no record was found')
-			self.contents.append(self.accessCode)
-			return
-
-	def formatCols(self, traitdata):
-		for item in traitdata:
-			lines = []
-			for item2 in item:
-				lines.append(item2)
-			lines = string.join(map(str,lines), '\t')
-			self.contents.append(lines)
-			
-	def formatRows(self, traitdata):
-		for i in range(len(traitdata[0])):
-			lines = []
-			for j in range(len(traitdata)):
-				lines.append(traitdata[j][i])
-			lines = string.join(map(str,lines), '\t')
-			self.contents.append(lines)
-
-			
diff --git a/web/webqtl/textUI/cmdHelp.py b/web/webqtl/textUI/cmdHelp.py
deleted file mode 100755
index 754ff5b5..00000000
--- a/web/webqtl/textUI/cmdHelp.py
+++ /dev/null
@@ -1,105 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import string
-
-from base import webqtlConfig
-from base.admin import ADMIN_tissue_alias
-from cmdClass import cmdClass
-
-#########################################
-#      Help Class
-#########################################
-
-#XZ, 03/23/2009: There are several issues need attention.
-#1. Some probeset datasets are not added into DBList.
-#2. Do NOT show confidential datasets. 
-#3. Get rid of ADMIN_tissue_alias. We should use info from database instead.
-
-class cmdHelp(cmdClass):
-	def __init__(self,fd=None):
-
-		cmdClass.__init__(self,fd)
-
-		if not webqtlConfig.TEXTUI:
-			self.contents.append("Please send your request to http://robot.genenetwork.org")
-			return
-
-
-		machineParse = self.data.getvalue('parse')
-		topic = self.data.getvalue('topic')
-		if topic:
-			topic = topic.lower()
-			if topic == 'tissue':
-				self.contents.append("%s%s|          %s" %("Tissue", ' '*(50-len("Tissue")), "Tissue Abbreviations"))
-				self.contents.append("%s%s| %s" %("", ' '*50, "(Separated by space, case insensitive)"))
-				self.contents.append("%s|%s" %('_'*50, '_'*40))
-			
-				keys = ADMIN_tissue_alias.keys()
-				keys.sort()
-				for key in keys:
-					self.contents.append("%s%s|   %s" % (key , ' '*(50-len(key)),  string.join(ADMIN_tissue_alias[key], "  ")))
-					self.contents.append("%s|%s" %('_'*50, '_'*40))
-			else:	
-				pass
-		else:
-			self.contents = ["#Use database code table below to access data", "#For machine parse friendly output please use",
-					     "#http://www.genenetwork.org%s%s?cmd=help&parse=machine" % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)]
-			self.cursor.execute("""(SELECT DBType.Name, DBList.FreezeId, DBList.Code, ProbeSetFreeze.CreateTime as Time
-						from ProbeSetFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and 
-						DBType.Name = 'ProbeSet' and DBList.FreezeId = ProbeSetFreeze.Id  and 
-						ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime ,DBList.Name, DBList.Id) 
-						UNION 
-						(SELECT DBType.Name, DBList.FreezeId, DBList.Code, PublishFreeze.CreateTime as Time
-						from PublishFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and 
-						DBType.Name = 'Publish' and DBList.FreezeId = PublishFreeze.Id order by 
-						PublishFreeze.CreateTime ,DBList.Name, DBList.Id) 
-						UNION
-						(SELECT DBType.Name, DBList.FreezeId, DBList.Code, GenoFreeze.CreateTime 
-						from GenoFreeze, DBType, DBList WHERE DBType.Id = DBList.DBTypeId and 
-						DBType.Name = 'Geno' and DBList.FreezeId = GenoFreeze.Id order by 
-						GenoFreeze.CreateTime ,DBList.Name, DBList.Id)""" % webqtlConfig.PUBLICTHRESH)
-			dbs = self.cursor.fetchall()
-			if machineParse =="machine":
-				pass
-			else:
-				self.contents.append("\n")
-				self.contents.append("%s%s|          %s" %("Database_Name", ' '*(50-len("Database_Name")), "Database_Access_Code_Name"))
-				self.contents.append("%s|%s" %('_'*50, '_'*40))
-			for dbInfo in dbs:
-				self.cursor.execute('SELECT FullName from %sFreeze WHERE Id = %d and public > %d' % (dbInfo[0], dbInfo[1],webqtlConfig.PUBLICTHRESH))
-				results = self.cursor.fetchall()
-				if not results:
-					pass
-				else:
-					if machineParse =="machine":
-						self.contents.append(results[0][0]+ ',' +dbInfo[2])
-					else:
-						self.contents.append("%s%s|          %s" %(results[0][0], ' '*(50-len(results[0][0])), dbInfo[2]))
-						self.contents.append("%s|%s" %('_'*50, '_'*40))
-	
-
-			
diff --git a/web/webqtl/textUI/cmdInterval.py b/web/webqtl/textUI/cmdInterval.py
deleted file mode 100755
index 0b97c7c3..00000000
--- a/web/webqtl/textUI/cmdInterval.py
+++ /dev/null
@@ -1,174 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import string
-import os
-
-import reaper
-
-from base import webqtlConfig
-from cmdClass import cmdClass
-		
-#########################################
-#      Interval Mapping Class
-#########################################
-class cmdInterval(cmdClass):
-
-	def __init__(self,fd=None):
-
-		cmdClass.__init__(self,fd)
-
-		if not webqtlConfig.TEXTUI:
-			self.contents.append("Please send your request to http://robot.genenetwork.org")
-			return
-
-
-		self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=pos&return=100&chr=12">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=pos&return=100&chr=12</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
-		if self.accessError:
-			return
-		self.sort = None
-		self.step = 0.01
-		self.peak = 1
-		self.chr = None
-		self.sort = None
-		self.returnnumber = 20
-		if self.error:
-			self.error = 1
-			self.contents.append(self.example)
-			return
-		else:
-			try:
-				self.sort = self.data.getvalue('sort')
-				if string.lower(self.sort) == 'pos':
-					self.sort = 'pos'
-				else:
-					self.sort = 'lrs'
-			except:
-				self.sort = None
-			
-			try:
-				self.returnnumber = int(self.data.getvalue('return'))
-			except:
-				self.returnnumber = 20
-			try:	
-				self.chr = self.data.getvalue('chr')
-			except:
-				self.chr = None
-				
-			self.readDB()
-
-	def  readDB(self):
-		prefix, dbId = self.getDBId(self.database)
-		if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")):
-			self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
-			self.contents.append(self.example)
-			self.contents.append(self.accessCode)
-			return
-		RISet = self.getRISet(prefix, dbId)
-		traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
-		if not traitdata:
-			self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
-			self.contents.append(self.example)
-			self.contents.append(self.accessCode)
-			return
-			
-		dataset0 = reaper.Dataset()
-		dataset0.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno'))
-		strainList = list(dataset0.prgy)
-		dataset = dataset0.addinterval()
-		if self.chr != None:
-			for _chr in dataset:
-				if string.lower(_chr.name) ==  string.lower(self.chr):
-					dataset.chromosome = [_chr]
-					break
-		
-		strains = []
-		trait = []
-		_prgy = dataset.prgy
-		for item in traitdata:
-			if item[0] in _prgy:
-				strains.append(item[0])	
-				trait.append(item[1])
-
-		qtlscan = dataset.regression(strains, trait)
-		LRS = dataset.permutation(strains, trait)
-		nperm = len(LRS)
-		
-		#print inter1[0]
-		returnPeak = []
-		nqtl = len(qtlscan)
-		if self.peak:
-			for i in range(nqtl):
-				if i == 0 or qtlscan[i].locus.chr != qtlscan[i-1].locus.chr:
-					if qtlscan[i].lrs < qtlscan[i+1].lrs:
-						continue
-				elif i == nqtl-1 or qtlscan[i].locus.chr != qtlscan[i+1].locus.chr:
-					if qtlscan[i].lrs < qtlscan[i-1].lrs:
-						continue
-				else:
-					if qtlscan[i].lrs < qtlscan[i+1].lrs or qtlscan[i].lrs < qtlscan[i-1].lrs:
-						continue
-				returnPeak.append(qtlscan[i])
-		else:
-			returnPeak = qtlscan[:]
-			
-		if returnPeak:
-			self.contents.append("Locus\tLRS\tChr\tAdditive\tp-value\tcM") 
-			qtlresult = []
-			for item in returnPeak:
-				p_value = reaper.pvalue(item.lrs,LRS)
-				qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value, item.locus.cM))
-			if self.sort == 'lrs':
-				qtlresult.sort(self.cmpLRS2)
-			for item in qtlresult:
-				self.contents.append("%s\t%2.4f\t%s\t%2.4f\t%1.4f\t%s" % item)
-		else:
-			self.contents.append("###Error: Error occurs while regression.")
-			return
-	
-	def cmpPValue(self,A,B):
-		try:
-			if A[-1] > B[-1]:
-				return 1
-			elif A[-1] ==  B[-1]:
-				return 0
-			else:
-				return -1	
-		except:
-			return 0
-
-	def cmpLRS2(self,A,B):
-		try:
-			if A[1] < B[1]:
-				return 1
-			elif A[1] == B[1]:
-				return 0
-			else:
-				return -1	
-		except:
-			return 0
-
-			
diff --git a/web/webqtl/textUI/cmdMap.py b/web/webqtl/textUI/cmdMap.py
deleted file mode 100755
index 1fbff5a5..00000000
--- a/web/webqtl/textUI/cmdMap.py
+++ /dev/null
@@ -1,144 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import string
-import os
-
-import reaper
-
-from base import webqtlConfig
-from cmdClass import cmdClass
-
-
-#########################################
-#      Mapping Class
-#########################################
-class cmdMap(cmdClass):
-
-	def __init__(self,fd=None):
-
-		cmdClass.__init__(self,fd)
-
-		if not webqtlConfig.TEXTUI:
-			self.contents.append("Please send your request to http://robot.genenetwork.org")
-			return
-
-		self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=lrs&return=20">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=lrs&return=20</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
-		if self.accessError:
-			return
-		try:
-			self.returnnumber = int(self.data.getvalue('return'))
-		except:
-			self.returnnumber = None
-		
-		if self.error:
-			self.contents.append(self.example)
-			self.contents.append(self.accessCode)
-		else:
-			self.sort = self.data.getvalue('sort')
-			self.readDB()
-		
-	def  readDB(self):
-		prefix, dbId = self.getDBId(self.database)
-		if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")):
-			self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
-			self.contents.append(self.example)
-			self.contents.append(self.accessCode)
-			return
-		RISet = self.getRISet(prefix, dbId)
-		traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
-		if not traitdata:
-			self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
-			self.contents.append(self.example)
-			self.contents.append(self.accessCode)
-			return
-			
-		dataset = reaper.Dataset()
-		dataset.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno'))
-		strainList = list(dataset.prgy)
-		
-		strains = []
-		trait = []
-		_prgy = dataset.prgy
-		for item in traitdata:
-			if item[0] in _prgy:
-				strains.append(item[0])	
-				trait.append(item[1])
-		
-		qtlscan = dataset.regression(strains, trait)
-		LRS = dataset.permutation(strains, trait)
-		nperm = len(LRS)	
-		if qtlscan:
-			self.contents.append("Locus\tLRS\tChr\tAdditive\tp-value") 
-			qtlresult = []
-			if self.returnnumber:
-				self.returnnumber = min(self.returnnumber,len(qtlscan))
-				if self.sort == 'lrs':
-					qtlscan.sort(self.cmpLRS)
-					for item in qtlscan[:self.returnnumber]:
-						p_value = reaper.pvalue(item.lrs,LRS)	
-						qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value))
-				else:#sort by position
-					qtlscan2 = qtlscan[:]
-					qtlscan2.sort(self.cmpLRS)
-					LRSthresh = qtlscan2[self.returnnumber].lrs
-					for item in qtlscan:
-						if item.lrs >= LRSthresh:
-							p_value = reaper.pvalue(item.lrs,LRS)	
-							qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value))
-			else:
-				for item in qtlscan:
-					p_value = reaper.pvalue(item.lrs,LRS)
-					qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value))
-				if self.sort == 'lrs':
-					qtlresult.sort(self.cmpLRS2)
-			for item in qtlresult:
-				self.contents.append("%s\t%2.5f\t%s\t%2.5f\t%1.5f" % item)
-		else:
-			self.contents.append("###Error: Error occurs while regression.")
-			return
-			
-	def cmpLRS(self,A,B):
-		try:
-			if A.lrs < B.lrs:
-				return 1
-			elif A.lrs == B.lrs:
-				return 0
-			else:
-				return -1	
-		except:
-			return 0
-
-	def cmpLRS2(self,A,B):
-		try:
-			if A[1] < B[1]:
-				return 1
-			elif A[1] == B[1]:
-				return 0
-			else:
-				return -1	
-		except:
-			return 0
diff --git a/web/webqtl/textUI/cmdSearchGene.py b/web/webqtl/textUI/cmdSearchGene.py
deleted file mode 100755
index c2c71815..00000000
--- a/web/webqtl/textUI/cmdSearchGene.py
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import string
-
-from cmdClass import cmdClass
-from search.TextSearchPage import TextSearchPage
-
-######################################### 
-#      Search Gene Symbol PAGE
-#########################################
-class cmdSearchGene(cmdClass):
-	def __init__(self,fd):
-		#example
-		cmdClass.__init__(self,fd)
-		self.page = None
-		self.text = ""
-		fd.geneName = fd.formdata.getvalue('gene')
-		fd.returnFmt = fd.formdata.getvalue('format', 'html')
-		if fd.geneName:
-			fd.geneName = string.strip(fd.geneName)
-		fd.refseq = fd.formdata.getvalue('refseq')
-		if fd.refseq:
-			fd.refseq = string.strip(fd.refseq)
-		fd.genbankid = fd.formdata.getvalue('genbankid')
-		if fd.genbankid:
-			fd.genbankid = string.strip(fd.genbankid)
-		fd.geneid = fd.formdata.getvalue('geneid')
-		if fd.geneid:
-			fd.geneid = string.strip(fd.geneid)
-		if 1:
-			if not (fd.geneName or fd.refseq or fd.genbankid or fd.geneid):
-				raise "ValueError"
-			fd.searchAlias = fd.formdata.getvalue('alias')
-			if fd.searchAlias != '1':
-				fd.searchAlias = None
-			self.page = TextSearchPage(fd)
-			if fd.returnFmt != 'text':
-				pass
-			else:
-				self.text = self.page.output
-				self.page = None
-		elif "ValueError":
-			self.text = "You need to submit a Gene name, a Refseq ID, or a GenBank ID"
-		else:
-			self.text = "Error occurs while searching the database"
-			
diff --git a/web/webqtl/textUI/cmdShowEditing.py b/web/webqtl/textUI/cmdShowEditing.py
deleted file mode 100755
index 918e83a7..00000000
--- a/web/webqtl/textUI/cmdShowEditing.py
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-from cmdClass import cmdClass
-from showTrait.ShowTraitPage import ShowTraitPage
-
-
-######################################### 
-#      SHOW DATA-EDITING PAGE
-#########################################
-class cmdShowEditing(cmdClass):
-	def __init__(self,fd):
-		###example = http://www.webqtl.org/cgi-bin/beta/WebQTL?cmd=snp&chr=1&start=0&end=21345677
-		cmdClass.__init__(self,fd)
-		self.page = None
-		prefix, dbId = self.getDBId(self.database)
-		try:
-			if not prefix or not dbId:
-				raise ValueError
-			self.cursor.execute('SELECT Name from %sFreeze WHERE Id=%d' % (prefix, dbId))
-			database = self.cursor.fetchall()[0][0]
-			traitInfos = (database,self.probeset,self.probe)
-			self.page = ShowTraitPage(fd,traitInfos)
-			#self = page
-		except:
-			print "Database Name Incorrect"
-