--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Contra/scripts/vcf_out.py	Thu Sep 13 02:31:43 2012 -0400
@@ -0,0 +1,64 @@
+# ----------------------------------------------------------------------#
+# 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 : 09 Apr 2011 11:00AM
+
+def vcf_out(inF, outF):
+	import math
+	f = file.readlines(open(inF))
+	vcf = open(outF, "w")
+
+	#header
+	vcf.write("##fileformat=VCFv4.0\n")
+	vcf.write("##reference=1000GenomesPilot-NCBI36\n")
+	vcf.write('##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"\n')
+	vcf.write('##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"\n')
+	vcf.write('##ALT=<ID=CNV,Description="Copy number variable region"\n')
+	vcf.write("#CHROM \tPOS \tID \tREF \tALT \tQUAL \tFILTER \tINFO\n")
+
+	count = 0 
+	while count < len(f):
+		if (count % 2 == 0):
+			region = f[count].strip(">\n")
+			region = region.split(":")
+			chr = region[0]
+
+			adjPVal = float(region[2])
+			if adjPVal <= 0:
+				adjPVal = 0
+			else:
+				adjPVal = -10 * math.log(adjPVal, 10)
+			adjPVal = str(round(adjPVal,3))		
+			region[1] = region[1].split("-")
+			start = region[1][0]
+			end = region[1][1]
+		else:
+			ref = f[count].strip("\n")
+			vcf.write(chr +"\t"+ start + "\t" + "." + "\t" + ref + "\t")
+			vcf.write("<CNV>" + "\t" + adjPVal + "\t" + "PASS" + "\t")
+			vcf.write("SVTYPE=CNV;END="+ end + "\n")
+		count += 1		
+
+	vcf.close()
+	
+
+
+