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authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/webqtl/cmdLine/cmdIntervalMappingPage.py
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
Diffstat (limited to 'web/webqtl/cmdLine/cmdIntervalMappingPage.py')
-rwxr-xr-xweb/webqtl/cmdLine/cmdIntervalMappingPage.py75
1 files changed, 75 insertions, 0 deletions
diff --git a/web/webqtl/cmdLine/cmdIntervalMappingPage.py b/web/webqtl/cmdLine/cmdIntervalMappingPage.py
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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
+