#!/usr/bin/perl
#
# Program to generate a command file for use
# with the shell or Sun Grid Engine. In this case
# we want to Blast all of the Fasta files (extension
# of .fa ) in the current directory. Since we are
# going to let SGE/qsub handle it we can submit them
# all it once and let them queue up until all are done.
# This could be used to kick off the blast of thousands
# of files
#
open (IN,"ls chr*.xml|") || die "Hey - You dont have any MegaBlast output files for me !";
while (<IN>) {
        chop;
        ($chromosome) = ($_ =~ m/chr(.+).xml/);
        $file = $_;
        $stdout = "$file.seperate_output";
        $jobname = "Split_$chromosome";
        $bash_script = "chr".$chromosome."_seperate.bash";
        print "Creating $bash_script\n";
        open(OUT,"> $bash_script");

        print OUT "#!/bin/bash \n";
        print OUT "#\$ -N $jobname \n";
        print OUT "#\$ -S /bin/bash \n";
        print OUT "#\$ -o $stdout \n";
        print OUT "#\$ -cwd \n";
        print OUT "#\$ -m e \n";
        print OUT "#\$ -M bcarlson\@genetics.emory.edu \n";
        print OUT "# \n";


        print OUT "/home/bcarlson/bin/seperate_all_probes.pl -chr $chromosome\n";
        
        close OUT;
        system("qsub $bash_script");
       

}