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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
from base.templatePage import templatePage
from utility import webqtlUtil
from base.webqtlTrait import webqtlTrait
from base import webqtlConfig
import multitrait
# XZ, 09/09/2008: After adding several traits to collection, click "Compare Correlates" button,
# XZ, 09/09/2008: This class will generate what you see.
# XZ, 09/09/2008: This class just collect the input, then pass them to multitrait.py
#########################################
# Multiple Correlation Page
#########################################
class MultipleCorrelationPage(templatePage):
def __init__(self,fd):
templatePage.__init__(self, fd)
if not self.openMysql():
return
if not fd.genotype:
fd.readData()
self.searchResult = fd.formdata.getvalue('searchResult')
if not self.searchResult:
heading = 'Compare Correlates'
detail = ['You need to select at least two traits in order to generate correlation matrix.']
self.error(heading=heading,detail=detail)
print 'Content-type: text/html\n'
self.write()
return
if type("1") == type(self.searchResult):
self.searchResult = [self.searchResult]
if self.searchResult:
if len(self.searchResult) > 100:
heading = 'Compare Correlates'
detail = ['In order to display Compare Correlates properly, Do not select more than %d traits for Compare Correlates.' % 100]
self.error(heading=heading,detail=detail)
print 'Content-type: text/html\n'
self.write()
return
else:
pass
traitList = []
for item in self.searchResult:
thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
thisTrait.retrieveInfo()
traitList.append(thisTrait)
else:
heading = 'Compare Correlates'
detail = [HT.Font('Error : ',color='red'),HT.Font('Error occurs while retrieving data from database.',color='black')]
self.error(heading=heading,detail=detail)
print 'Content-type: text/html\n'
self.write()
return
##########
filename= webqtlUtil.genRandStr("mult_")
fp = open(webqtlConfig.IMGDIR+filename, 'wb')
fp.write('%s\n' % fd.RISet)
for thisTrait in traitList:
fp.write("%s,%s,%s\n" % (thisTrait.db.type,thisTrait.db.id,thisTrait.name))
fp.close()
fd.formdata["filename"] = filename
params = {"filename":filename, "targetDatabase":"",
"threshold":0.5, "subsetSize":10,
"correlation":"pearson", "subsetCount":10,
"firstRun":"1"}
results = []
txtOutputFileName = ""
self.dict['body'] = multitrait.TraitCorrelationPage(fd, params, self.cursor, traitList, results,
fd.RISet,txtOutputFileName).dict['body']
self.dict['title'] = 'Compare Correlates'
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