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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 os
from base import webqtlConfig
from base.templatePage import templatePage
from utility import webqtlUtil
#########################################
# Interval Mapping Page
#########################################
class cmdIntervalMappingPage(templatePage):
def __init__(self,fd):
templatePage.__init__(self, fd)
wtext = "Mapping "
try:
selectedChr = int(fd.formdata.getvalue('chromosomes')) + 1
if selectedChr < 1:
raise "ValueError"
if selectedChr == 21 or (selectedChr == 20 and fd.RISet != 'HXBBXH'):
selectedChr = 'X'
wtext += 'chromosome %s ' % selectedChr
except:
wtext += 'whole genome '
perm = 0
if fd.formdata.getvalue('permCheck'):
perm = 1
wtext += 'with %d permutation tests ' % fd.nperm
boot = 0
if fd.formdata.getvalue('bootCheck'):
boot = 1
if perm:
wtext += 'and %d bootstrap tests ' % fd.nboot
else:
wtext += 'with %d bootstrap tests ' % fd.nboot
if boot == 0 and perm == 0:
wtext += "without permutation or bootstrap tests"
filename = self.session("Interval Mapping", wtext)
webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session'))
url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename)
os.system("%s %swebqtlCmdLine.py interval %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename))
self.redirection = url
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