#! /usr/bin/env python
"""
    reroot.py -i <infile> -o <outfile> -g <outgroups>

    <infile>  contains just a tree in newick format
    <outfile> will contain the rerooted tree
    <outgroups> comma separated list of taxa in outgroup
"""
import sys
import os
import getopt

def usage():
    sys.exit("usage: " + sys.argv[0] + __doc__)

if __name__ == '__main__':
    print "here in main"
    fp = os.path.abspath(sys.argv[0])
    cipres_bin = os.path.dirname(fp)
    cipres_root = os.path.dirname(cipres_bin)
    cipres_cp_jar_path = os.path.join(cipres_root, "lib", "cipres", "cipres-classpath.jar")

    infile=''
    outfile=''
    outgroups=''
    try:
        opts, args = getopt.getopt(sys.argv[1:], "i:o:g:")
    except getopt.GetoptError:
        usage()
    for opt, arg in opts:
        if opt in ("-i"):
            infile = arg
        if opt in ("-o"):
            outfile = arg
        if opt in ("-g"):
            outgroups = arg

    preargs = [ "java", 
                "-ea",
                "-Dinfile=%s" % infile,
                "-Doutfile=%s" % outfile,
                "-Doutgroups=%s" % outgroups
              ]
    postargs = [
        "-classpath",
        cipres_cp_jar_path,
        "org.cipres.util.tree.UTree"
        ]
    args = preargs +  postargs
    print args
    os.execvp("java", args)