aboutsummaryrefslogtreecommitdiff
path: root/web/webqtl/genomeGraph/genAllDbResultPage.py
diff options
context:
space:
mode:
authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/webqtl/genomeGraph/genAllDbResultPage.py
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
Diffstat (limited to 'web/webqtl/genomeGraph/genAllDbResultPage.py')
-rwxr-xr-xweb/webqtl/genomeGraph/genAllDbResultPage.py309
1 files changed, 309 insertions, 0 deletions
diff --git a/web/webqtl/genomeGraph/genAllDbResultPage.py b/web/webqtl/genomeGraph/genAllDbResultPage.py
new file mode 100755
index 00000000..f0663a7c
--- /dev/null
+++ b/web/webqtl/genomeGraph/genAllDbResultPage.py
@@ -0,0 +1,309 @@
+# 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