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

1 files changed, 0 insertions, 405 deletions

diff --git a/web/webqtl/intervalAnalyst/IntervalAnalystPage.py b/web/webqtl/intervalAnalyst/IntervalAnalystPage.py
deleted file mode 100755
index ec9aa29c..00000000
--- a/web/webqtl/intervalAnalyst/IntervalAnalystPage.py
+++ /dev/null
@@ -1,405 +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 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(" ", 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