annotate Contra/scripts/target_breakdown.py @ 4:9a76d500b049

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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 : 05 October 2011 16:43PM

def target_breakdown(filename, maxRegionSize, targetRegionSize, out_fname):
	from math import ceil

	a	= open(filename)
	output 	= open(out_fname, "w")

	for x in a:
		x 	= x.split()
		chr 	= x[0]
		start 	= int(x[1])
		end	= int(x[2])
		info	= ""
		if (len(x) > 3):
			info	= x[3]
	
		regionSize = end-start

		if regionSize > maxRegionSize:
			seg	= ceil(regionSize/float(targetRegionSize))
			limit	= ceil(regionSize/float(seg))
	
			s_end = start	
			for i in range(int(seg)):
				s_start = s_end
				s_end = int(start + (limit*(i+1)))
				if s_end > end:
					s_end = end
				output.write("\t".join([chr, str(s_start), str(s_end), info+"(SPLIT)"])+"\n")
		else:
			output.write("\t".join([chr, str(start), str(end), info])+"\n")

	output.close()