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# 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 time
from htmlgen import HTMLgen2 as HT
from base import webqtlConfig
from utility import webqtlUtil
from base.webqtlDataset import webqtlDataset
from base.templatePage import templatePage
#########################################
# Genome Scan PAGE
#########################################
class genAllDbResultPage(templatePage):
def __init__(self,fd):
templatePage.__init__(self,fd)
if not self.openMysql():
return
self.database = fd.formdata.getvalue('database', '')
db = webqtlDataset(self.database, self.cursor)
try:
if db.type != "ProbeSet" or not db.id:
raise DbNameError
except:
print 'Content-type: text/html\n'
heading = "Download Results"
detail = ["Only results of microarray database are available to download."]
self.error(heading=heading,detail=detail)
self.write()
return
#XZ, protect confidential dataset.
userExist = None
self.cursor.execute('SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM ProbeSetFreeze WHERE Name = "%s"' % self.database)
indId, indName, indFullName, indConfid, AuthorisedUsers = self.cursor.fetchall()[0]
if indConfid == 1 and userExist == None:
try:
userExist = self.userName
#for the dataset that confidentiality is 1
#1. 'admin' and 'root' can see all of the dataset
#2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table)
if webqtlConfig.USERDICT[self.privilege] < webqtlConfig.USERDICT['admin']:
if not AuthorisedUsers:
userExist=None
else:
AuthorisedUsersList=AuthorisedUsers.split(',')
if not AuthorisedUsersList.__contains__(self.userName):
userExist=None
except:
pass
if not userExist:
#Error, Confidential Database
heading = "Correlation Table"
detail = ["The %s database you selected is not open to the public at this time, please go back and select other database." % indFullName]
self.error(heading=heading,detail=detail,error="Confidential Database")
return
self.cursor.execute("""
Select
InbredSet.Name
From
ProbeSetFreeze, ProbeFreeze, InbredSet
whERE
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
ProbeFreeze.InbredSetId = InbredSet.Id AND
ProbeSetFreeze.Id = %d
""" % db.id)
thisRISet = self.cursor.fetchone()[0]
if thisRISet =='BXD300':
thisRISet = 'BXD'
#XZ, 06/26/2009: It seems that this query is not neccessary. It doesn't return any result.
#XZ: It seems it is just for test purpose. The next try-except block does the real work.
#XZ: I think it should be deleted to shorten the response time.
#self.cursor.execute("""
# Select
# ProbeSet.Name, ProbeSet.symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSetXRef.Locus,
# ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.additive, ProbeSetXRef.mean
# From
# ProbeSet, ProbeSetXRef
# whERE
# ProbeSetXRef.ProbeSetFreezeId = %d AND
# ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
# ProbeSetXRef.Locus is not NULL
# Order by
# ProbeSet.name_num
# """ % db.id)
filename = os.path.join(webqtlConfig.SECUREDIR, db.name+'.result.xls')
try:
import random234
if random.choice(range(10)) == 0:
raise "ReCalculate"
fp = open(filename, 'rb')
text = fp.read()
fp.close()
except:
self.cursor.execute("Select ProbeSetXRef.ProbeSetId from ProbeSetXRef where ProbeSetFreezeId=%d" % db.id)
ProbeSetIds = self.cursor.fetchall()
self.mouseChrLengthDict, sum = self.readMouseGenome(thisRISet)
if ProbeSetIds:
import reaper
markerGMb = {}
genotype_1 = reaper.Dataset()
genotype_1.read(os.path.join(webqtlConfig.GENODIR, thisRISet + '.geno'))
for chr in genotype_1:
chrlen = self.mouseChrLengthDict[chr.name]
for locus in chr:
markerGMb[locus.name] = [chr.name, locus.Mb, locus.Mb + chrlen]
text = []
text.append(['ProbeSetId', 'Symbol', 'Description', 'Target Description', 'Chr', 'TMb', 'TGMb', 'Locus', 'LRS', 'Additive', 'pvalue', 'markerChr', 'markerMb', 'markerGMb', 'meanExpression'])
ProbeSetIdList = []
for ProbeSetId in ProbeSetIds:
ProbeSetIdList.append(ProbeSetId[0])
if len(ProbeSetIdList)==1000:
ProbeSetIdStr = ','.join(map(str, ProbeSetIdList))
ProbeSetIdList = []
cmd = """
Select
ProbeSet.Name, ProbeSet.symbol, ProbeSet.description,ProbeSet.Probe_Target_Description,ProbeSet.Chr, ProbeSet.Mb,
ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue,
ProbeSetXRef.additive, ProbeSetXRef.mean
From
ProbeSet, ProbeSetXRef
Where
ProbeSetXRef.ProbeSetFreezeId = %s AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
ProbeSetXRef.Locus is not NULL AND
ProbeSet.Id in (%s)
Order by
ProbeSet.name_num
""" % (db.id, ProbeSetIdStr)
self.cursor.execute(cmd)
results = self.cursor.fetchall()
for result in results:
_Id, _symbol, _desc,_targetDesc, _chr, _TMb, _marker, _lrs, _pvalue, _additive, _mean = result
if _marker == "-":
continue
if not _additive:
_additive = ""
try:
_TGMb = _TMb + self.mouseChrLengthDict[string.strip(_chr)]
except:
_TGMb = ""
result2 = [_Id, _symbol, _desc, _targetDesc, _chr, _TMb, _TGMb, _marker, _lrs, _additive, _pvalue]
try:
result2 += markerGMb[_marker]
except:
result2 += ['', '', '']
result2 += [_mean]
text.append(map(str, result2))
#XZ, 06/29/2007: This block is dealing with the last several probesets that fall out of the 1000-probeset block.
if ProbeSetIdList:
ProbeSetIdStr = ','.join(map(str, ProbeSetIdList))
cmd = """
Select
ProbeSet.Name, ProbeSet.symbol, ProbeSet.description,ProbeSet.Probe_Target_Description, ProbeSet.Chr, ProbeSet.Mb,
ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue,
ProbeSetXRef.additive, ProbeSetXRef.mean
From
ProbeSet, ProbeSetXRef
Where
ProbeSetXRef.ProbeSetFreezeId = %s AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
ProbeSetXRef.Locus is not NULL AND
ProbeSet.Id in (%s)
Order by
ProbeSet.name_num
""" % (db.id, ProbeSetIdStr)
self.cursor.execute(cmd)
results = self.cursor.fetchall()
for result in results:
_Id, _symbol, _desc, _targetDesc,_chr, _TMb, _marker, _lrs, _pvalue, _additive, _mean = result
if _marker == "-":
continue
if not _additive:
_additive = ""
try:
_TGMb = _TMb + self.mouseChrLengthDict[string.strip(_chr)]
except:
_TGMb = ""
result2 = [_Id, _symbol, _desc,_targetDesc, _chr, _TMb, _TGMb, _marker, _lrs, _additive, _pvalue]
try:
result2 += markerGMb[_marker]
except:
result2 += ['', '', '']
result2 += [_mean]
text.append(map(str, result2))
import pyXLWriter as xl
# Create a new Excel workbook
workbook = xl.Writer(filename)
worksheet = workbook.add_worksheet()
heading = workbook.add_format(align = 'center', bold = 1, size=13, color = 'red')
titleStyle = workbook.add_format(align = 'left', bold = 0, size=14, border = 1, border_color="gray")
worksheet.write([0, 0], "Data source: The GeneNetwork at http://www.genenetwork.org", titleStyle)
worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
worksheet.write([2, 0], "Database : %s" % db.fullname, titleStyle)
worksheet.write([3, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime()), titleStyle)
worksheet.write([4, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime()), titleStyle)
worksheet.write([5, 0], "Status of data ownership: Possibly unpublished data; please see %s/statusandContact.html for details on sources, ownership, and usage of these data." % webqtlConfig.PORTADDR, titleStyle)
table_row_start_index = 7
nrow = table_row_start_index
for row in text:
for ncol, cell in enumerate(row):
if nrow == table_row_start_index:
worksheet.write([nrow, ncol], cell.strip(), heading)
worksheet.set_column([ncol, ncol], 20)
else:
worksheet.write([nrow, ncol], cell.strip())
nrow += 1
worksheet.write([1+nrow, 0], "Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)", titleStyle)
worksheet.write([2+nrow, 0], "PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE", titleStyle)
workbook.close()
fp = open(filename, 'rb')
text = fp.read()
fp.close()
else:
heading = "Download Results"
detail = ["Database calculation is not finished."]
self.error(heading=heading,detail=detail)
return
self.content_type = 'application/xls'
self.content_disposition = 'attachment; filename=%s' % ('export-%s.xls' % time.strftime("%y-%m-%d-%H-%M"))
self.attachment = text
def readMouseGenome(self, RISet):
ldict = {}
lengths = []
sum = 0
#####################################
# Retrieve Chr Length Information
#####################################
self.cursor.execute("""
Select
Chr_Length.Name, Length from Chr_Length, InbredSet
where
Chr_Length.SpeciesId = InbredSet.SpeciesId AND
InbredSet.Name = '%s'
Order by
OrderId
""" % RISet)
lengths = self.cursor.fetchall()
ldict[lengths[0][0]] = 0
prev = lengths[0][1]/1000000.0
sum += lengths[0][1]/1000000.0
for item in lengths[1:]:
ldict[item[0]] = prev
prev += item[1]/1000000.0
sum += item[1]/1000000.0
return ldict, sum
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