refeditor: tools/refeditor/vcf2genotypes.py comparison

add vcf2genotypes and test-data

author	superyuan <shuaiyuan.emory@gmail.com>
date	Mon, 30 Jun 2014 10:49:54 -0400
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-:9259f2939357
+:85bdf226b67b
+# Filename: vcf2genotypes.py
+# Author: Shuai Yuan
+# Version: 06/29/2012
+#
+# This script is a wrapper for vcf2genotypes
+#
+#  vcf2genotypes is launched based on these inputs:
+#  -i		input VCF file
+#  -p		target individual
+#  -o		output genotypes file
+import sys
+import os
+import re
+import string
+import commands
+from tempfile import NamedTemporaryFile
+# This function is exceedingly useful, perhaps package for reuse?
+def getopts(argv):
+opts = {}
+while argv:
+	if argv[0][0] == '-':
+	    opts[argv[0]] = argv[1]
+	    argv = argv[2:]
+	else:
+	    argv = argv[1:]
+return opts
+def main():
+args = sys.argv[1:]
+try:
+	opts = getopts(args)
+except IndexError:
+	print "Usage:"
+	return 0
+vcf = opts.get("-i")
+if vcf == None:
+print "No input VCF file specified."
+return -1
+individual = opts.get("-p")
+if individual == None:
+print "No valid individual specified."
+return -2
+outputfile = opts.get("-o")
+if outputfile == None:
+print "No output file specified."
+return -6
+# All inputs have been specified at this point, now validate.
+#generate command
+commandline = "vcf2genotypes %s  %s >  %s " % (vcf, individual, outputfile)
+#run
+errorcode, stdout = commands.getstatusoutput(commandline)
+#return error code
+return errorcode
+if __name__ == "__main__":
+main()

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