diff Contra/scripts/convert_targeted_regions.py @ 0:7564f3b1e675

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Contra/scripts/convert_targeted_regions.py	Thu Sep 13 02:31:43 2012 -0400
@@ -0,0 +1,71 @@
+# ----------------------------------------------------------------------#
+# Copyright (c) 2011, Richard Lupat & Jason Li.
+#
+# > Source License <
+# This file is part of CONTRA.
+#
+#    CONTRA is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    CONTRA 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 General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with CONTRA.  If not, see <http://www.gnu.org/licenses/>.
+#
+# 
+#-----------------------------------------------------------------------#
+# Last Updated : 28 Mar 2011 11:00AM
+
+class Target:
+	"""
+	Class for target regions
+	"""
+	
+	population = 0
+
+	def __init__(self):
+		self.id = 0
+		self.gene = "unknown"
+		self.chr = "chr1"
+		self.start = 0
+		self.end = 0
+		self.numberExon = 0
+		self.oriStart = 0
+		self.oriEnd = 0
+
+def convertTarget(target):
+	targets = open(target)
+
+	targetList = []
+
+	count = 0
+	for region in targets:
+		region = region.split()
+		chr = "chr" + region[0].strip("chr")
+		start = region[1]
+		end = region[2]
+		try:
+			gene = region[3]
+		except:
+			gene = "unknown"	
+		count += 1
+
+		aTarget = Target()
+		aTarget.id = count
+		aTarget.gene = gene
+		aTarget.chr  = chr
+		aTarget.start = start
+		aTarget.end = end
+		aTarget.numberExon = 1
+		aTarget.oriStart = start
+		aTarget.oriEnd	 = end
+
+		targetList.append(aTarget)
+
+
+	return targetList