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


import subprocess, shlex

def get_genome(srcFile, genomeOut):
	genome = open(genomeOut, "w")

	args = shlex.split("samtools view -H %s" %(srcFile))
	raw_header = subprocess.Popen(args, stdout = subprocess.PIPE).communicate()[0]
	headers = raw_header.split("\n")

	for header in headers:
		header = header.split("\t")
		if header[0][1:] != "SQ":
			continue

		genome.write(header[1].strip("SN:") + "\t" + header[2].strip("LN:") + "\n")

	genome.close()