Add all the source codes into the github.

1 files changed, 118 insertions, 0 deletions

diff --git a/web/webqtl/textUI/cmdGeno.py b/web/webqtl/textUI/cmdGeno.py
new file mode 100755
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+++ b/web/webqtl/textUI/cmdGeno.py
@@ -0,0 +1,118 @@
+# 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 string
+import os
+
+import reaper
+
+from base import webqtlConfig
+from cmdClass import cmdClass
+
+#########################################
+#      Geno Class
+#########################################
+class cmdGeno(cmdClass):
+
+	def __init__(self,fd=None):
+
+		cmdClass.__init__(self,fd)
+
+		if not webqtlConfig.TEXTUI:
+			self.contents.append("Please send your request to http://robot.genenetwork.org")
+			return
+
+		if self.accessError:
+			return
+		self.error = 0
+		self.RISet = None
+		self.chr = None
+		self.dataset = None
+		self.strainList = []
+		try:
+			self.RISet = self.data.getvalue('riset')
+			if not self.RISet:
+				raise ValueError
+		except:
+			self.error = 1
+			self.contents.append('###Example : http://www.genenetwork.org%s%s?cmd=%s&riset=BXD&chr=1' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID))
+			return
+		try:
+			self.format = self.data.getvalue('format')[:3]
+		except:
+			self.format = 'row'
+
+		try:
+			self.dataset = reaper.Dataset()
+			try:
+				self.dataset.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno'))
+			except:
+				self.dataset.read(os.path.join(webqtlConfig.GENODIR, self.RISet.upper() + '.geno'))
+			self.strainList = list(self.dataset.prgy)
+		except:
+			self.error = 1
+			#traceback.print_exc()	
+			self.contents.append('###The name of RISet is incorrect')
+			return
+
+		try:
+			self.chr = self.data.getvalue('chr')
+			if self.chr:
+				if self.chr == 'X' or self.chr == 'x':
+					self.chr = '20'
+				self.chr = int(self.chr)
+		except:
+			pass
+		
+		self.readGeno()
+
+	def  readGeno(self):
+		try:
+			table = [['Chr'] + ['Locus'] + self.strainList]
+			if self.chr:
+				chr = self.dataset[self.chr-1]
+				for locus in chr:
+					items = string.split(string.join(locus.genotext, " "))
+					items = [chr.name] + [locus.name] + items
+					table += [items]
+			else:
+				for chr in self.dataset:
+					for locus in chr:
+						items = string.split(string.join(locus.genotext, " "))
+						items = [chr.name] + [locus.name] + items
+						table += [items]
+			if self.format == 'col':
+				table = [[r[col] for r in table] for col in range(1, len(table[0]))]
+				table[0][0] = 'Line'
+			lines = string.join(map(lambda x: string.join(x, '\t'), table), '\n')
+			self.contents.append(lines)
+		except:	
+			self.contents =['###Error: Read file error or name of chromosome is incorrect']
+			#traceback.print_exc()	
+			return
+
+		
+