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

Uploaded

# ----------------------------------------------------------------------#
# 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 get_libsize(bedgraph_file):
	bedgraph = open(bedgraph_file)
	libsize = 0
	for line in bedgraph:
		line	= line.split()
		chr	= line[0]
		start	= int(line[1])
		end	= int(line[2])
		cov	= float(line[3])
		#cov	= int(line[3])
		
		libsize += (end-start)*cov

	bedgraph.close()
	return int(libsize)