diff options
Diffstat (limited to 'web/webqtl/genomeGraph/genAllDbResultPage.py')
| -rwxr-xr-x | web/webqtl/genomeGraph/genAllDbResultPage.py | 309 |
1 files changed, 0 insertions, 309 deletions
diff --git a/web/webqtl/genomeGraph/genAllDbResultPage.py b/web/webqtl/genomeGraph/genAllDbResultPage.py deleted file mode 100755 index f0663a7c..00000000 --- a/web/webqtl/genomeGraph/genAllDbResultPage.py +++ /dev/null @@ -1,309 +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 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 |