From ea46f42ee640928b92947bfb204c41a482d80937 Mon Sep 17 00:00:00 2001
From: root
Date: Tue, 8 May 2012 18:39:56 -0500
Subject: Add all the source codes into the github.

---
 web/webqtl/intervalAnalyst/GeneUtil.py            | 124 +++++++
 web/webqtl/intervalAnalyst/IntervalAnalystPage.py | 405 ++++++++++++++++++++++
 web/webqtl/intervalAnalyst/__init__.py            |   0
 3 files changed, 529 insertions(+)
 create mode 100755 web/webqtl/intervalAnalyst/GeneUtil.py
 create mode 100755 web/webqtl/intervalAnalyst/IntervalAnalystPage.py
 create mode 100755 web/webqtl/intervalAnalyst/__init__.py

(limited to 'web/webqtl/intervalAnalyst')

diff --git a/web/webqtl/intervalAnalyst/GeneUtil.py b/web/webqtl/intervalAnalyst/GeneUtil.py
new file mode 100755
index 00000000..43008ecf
--- /dev/null
+++ b/web/webqtl/intervalAnalyst/GeneUtil.py
@@ -0,0 +1,124 @@
+# 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
+
+#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
+
+
diff --git a/web/webqtl/intervalAnalyst/IntervalAnalystPage.py b/web/webqtl/intervalAnalyst/IntervalAnalystPage.py
new file mode 100755
index 00000000..ec9aa29c
--- /dev/null
+++ b/web/webqtl/intervalAnalyst/IntervalAnalystPage.py
@@ -0,0 +1,405 @@
+# 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 mod_python import apache, util, Cookie
+import os
+import time
+import pyXLWriter as xl
+
+from htmlgen import HTMLgen2 as HT
+
+import GeneUtil
+from base.templatePage import templatePage
+from utility import webqtlUtil
+from base import webqtlConfig
+
+
+class IntervalAnalystPage(templatePage):
+	filename = webqtlUtil.genRandStr("Itan_")
+
+	_scriptfile = "main.py?FormID=intervalAnalyst"
+
+	#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'],
+			'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'],
+			"snpCount" : ["SNPs", "SNP Count", 'species'], 
+			"snpDensity" : ["SNP Density", "SNP Density", '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
+	
+	def __init__(self, fd):
+
+		templatePage.__init__(self, fd)
+
+		fd.formdata['remote_ip'] = fd.remote_ip
+		if not self.openMysql():
+			return
+		
+		self.species = fd.formdata.getvalue("species", "mouse")
+		try:
+			self.startMb = float(fd.formdata.getvalue("startMb"))
+		except:
+			self.startMb = 10
+		try:
+			self.endMb = float(fd.formdata.getvalue("endMb"))
+		except:
+			self.endMb = self.startMb + 10
+			
+		self.Chr = fd.formdata.getvalue("chromosome", "1")
+		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
+			
+		controlFrm, dispFields = self.genControlForm(fd)
+		geneTable, filename = self.genGeneTable(fd, dispFields)
+		
+		infoTD = HT.TD(width=400, valign= "top")
+		infoTD.append(HT.Paragraph("Interval Analyst : Chr %s" % self.Chr, Class="title"), 
+			HT.Strong("Species : "), self.species.title(), HT.BR(),  
+			HT.Strong("Database : "), "UCSC %s" % self.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)
+		mainTable.append(HT.TR(HT.TD(geneTable, colspan=3)))
+		self.dict['body'] = HT.TD(mainTable)
+		self.dict['title'] = "Interval Analyst"
+		
+	def genGeneTable(self, fd, dispFields):
+		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, self._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.formdata['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 len(column) == 1:
+				headerRow.append(HT.TD(self.columnNames[column[0]][0], Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
+				if self.xls:
+					colTitle = self.columnNames[column[0]][0]
+					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
+					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
+			else:
+				headerRow.append(HT.TD(self.columnNames[column[0]][0], HT.BR(), " (%s)" % self.speciesFreeze[column[1]], 
+					Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1, align="Center"))
+				if self.xls:
+					colTitle = self.columnNames[column[0]][0] + " (%s)" % self.speciesFreeze[column[1]]
+					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
+					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
+				#headerRow.append(HT.TD(self.columnNames[column[0]][0], HT.BR(), 
+				#	"(%s %s)" % (column[1].title(), self.speciesFreeze[column[1]]), 
+				#	Class="colorBlue", NOWRAP=1, align="Center"))
+		geneTable.append(headerRow)
+		
+		geneCol = GeneUtil.loadGenes(self.cursor, self.Chr, self.diffColDefault, self.startMb, self.endMb, species=self.species)
+		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))
+					
+			geneTable.append(geneRow)
+			
+		if self.xls:
+			workbook.close()
+		return geneTable, filename
+	
+	def formatTD(self, keyValue, fieldName, Species, theGO):
+		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?cmd=sch&gene=%s&alias=1&species=%s" % (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"):
+				if keyValue:
+					snpString = HT.Href(url="%s&chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (os.path.join(webqtlConfig.CGIDIR, 'main.py?FormID=snpBrowser'), 
+							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")
+			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 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 self.columnNames.keys():
+			category = self.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']
+		
+		############################################################
+		## Create the list of possible columns for the dropdown list
+		############################################################
+		allColumnsList = HT.Select(name="allColumns", Class="snpBrowserDropBox")
+		
+		for category in categoriesOrder:
+			allFields = categories[category]
+			if allFields:
+				geneOpt = HT.Optgroup(label=category.title())
+				for item in allFields:
+					if category in self.speciesFreeze.keys():
+						geneOpt.append(("%s (%s %s)" % (self.columnNames[item][1], category.title(), self.speciesFreeze[category]), 
+							"%s__%s" % (item, self.speciesFreeze[category])))
+					else:
+						geneOpt.append((self.columnNames[item][1], item))
+				geneOpt.sort()
+				allColumnsList.append(geneOpt)
+		
+		######################################
+		## 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', 'Chromosome', 'TxStart', 'Strand', 'GeneLength', 'GeneID', 'NM_ID', 'snpCount', 'snpDensity']
+			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)" % (self.columnNames[column][1], self.species.title(), self.speciesFreeze[self.species]), 
+							"%s__%s" % (column, self.speciesFreeze[self.species])))
+				dispFields.append([column, self.species])
+			else:
+				column2 = column.split("__")
+				if len(column2) == 1:
+					colsLst.append((self.columnNames[column2[0]][1], column))
+					dispFields.append([column])
+				else:
+					thisSpecies = self.speciesFreeze[column2[1]]
+					colsLst.append(("%s (%s %s)" % (self.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)
+		
+		##########################
+        ## Create the columns form
+		##########################		
+		columnsForm = HT.Form(name="columnsForm", submit=HT.Input(type='hidden'), cgi=os.path.join(webqtlConfig.CGIDIR, self._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))	
+		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)")
+		removeButton = HT.Input(type="button", name="remove", value="Remove", Class="button", onClick="removeFromList(this.form.columns.selectedIndex, this.form.columns)")
+		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="Refresh", Class="button", onClick="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)
+
+		innerColumnsTable = HT.TableLite(border=0, Class="collap", cellpadding = 2)
+		innerColumnsTable.append(HT.TR(HT.TD(selectedColumnsList)),
+					 HT.TR(HT.TD(clearButton, removeButton, upButton, downButton)))
+		columnsTable = HT.TableLite(border=0, cellpadding=2, cellspacing=0)
+		columnsTable.append(HT.TR(HT.TD(HT.Font("Chr: ", size=-1)),
+					  HT.TD(selectChrBox, submitButton)),
+				    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("Show: ", size=-1)),
+					  HT.TD(allColumnsList, addButton)),
+				    HT.TR(HT.TD(""),
+					  HT.TD(innerColumnsTable)))
+		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
diff --git a/web/webqtl/intervalAnalyst/__init__.py b/web/webqtl/intervalAnalyst/__init__.py
new file mode 100755
index 00000000..e69de29b
-- 
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