Add all the source codes into the github.

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
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+++ 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
+