--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Contra/scripts/get_chr_length.py	Thu Sep 13 02:31:43 2012 -0400
@@ -0,0 +1,43 @@
+# ----------------------------------------------------------------------#
+# 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()
+
+