#!/usr/bin/perl

# Description:
#
# Program to generate a command file for use
# with the shell or Sun Grid Engine. In this case
# it is invoking find_bad_mega_fasta.pl, which 
# is used to get the megablast output for all probes
# in a fasta formatted file file, except the probes that core dump megablast. 
# 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.
# 
# Usage:

open (IN,"ls chr*.xml.* |") || die "Hey - You dont have any Bad fractional files for me !";
while (<IN>) {
        chop;
        print "Creating file for $_ \n"; 
        ($chromosome, $fractional) = ($_ =~ m/chr(.+).xml.(.+)/);
        $file = $_;
        $base_name = "find_".$chromosome."_".$fractional;
        $stdout = "$base_name.out";
        my $jobname = $base_name;
        my $outname= "$base_name.bash";
        open(OUT,"> $outname");

        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/find_bad_mega_fasta.pl -f $file \n";
        close OUT;
        system("qsub $outname");

}