diff options
Diffstat (limited to 'web/webqtl/cmdLine/cmdIntervalMappingPage.py')
| -rwxr-xr-x | web/webqtl/cmdLine/cmdIntervalMappingPage.py | 75 |
1 files changed, 75 insertions, 0 deletions
diff --git a/web/webqtl/cmdLine/cmdIntervalMappingPage.py b/web/webqtl/cmdLine/cmdIntervalMappingPage.py new file mode 100755 index 00000000..8e0a3d92 --- /dev/null +++ b/web/webqtl/cmdLine/cmdIntervalMappingPage.py @@ -0,0 +1,75 @@ +# 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 + |