annotate Contra/scripts/convert_targeted_regions.py @ 17:1db7b15823ca

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# ----------------------------------------------------------------------#
# 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