#!/usr/bin/env python

import os
import sys
import getopt
import exceptions

if not os.environ.has_key( "REPET_PATH" ):
    print "ERROR: no environment variable REPET_PATH"
    sys.exit(1)
sys.path.append( os.environ["REPET_PATH"] )

from pyRepet.launcher.programLauncher import programLauncher


def help():
    print
    print "usage: ",sys.argv[0],"[ options ]"
    print "options:"
    print "     -h: this help"
    print "     -i: name of the input file (format='fasta')"
    print "     -P: parameters"
    print "     -o: name of the output file (format='aligned fasta', default='inFileName'+fa_aln)"
    print "     -c: clean"
    print "     -v: verbosity level (default=0/1)"
    print


def main():

    inFileName = ""
    parameters = ""
    outFileName = ""
    clean = False
    verbose = 0
    
    try:
        opts, args = getopt.getopt(sys.argv[1:],"hi:P:o:cv:")
    except getopt.GetoptError, err:
        print str(err); help(); sys.exit(1)
    for o,a in opts:
        if o == "-h":
            help(); sys.exit(0)
        elif o == "-i":
            inFileName = a
        elif o == "-P":
            parameters = a
        elif o == "-o":
            outFileName = a
        elif o == "-c":
            clean = True
        elif o == "-v":
            verbose = "yes"
            
    if inFileName == "" and parameters == "":
        print "ERROR: missing compulsory options"
        help()
        sys.exit(1)
        
    if outFileName == "":
        outFileName = "%s.fa_aln" % ( inFileName )
        
    if verbose > 0:
        print "START %s" % (sys.argv[0].split("/")[-1])
        sys.stdout.flush()
        
    pL = programLauncher( inFileName )
    pL.launchTcoffee( outFileName, parameters )
    
    if verbose > 0:
        print "END %s" % (sys.argv[0].split("/")[-1])
        sys.stdout.flush()
    
    return 0


if __name__ == "__main__":
    main()