#!/usr/bin/perl
#
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#   qsub_megablast.pl
#
#   Program generates a bash script to run with Sun Grid Engine.
#
#   Run mega_blast against all probe files in your current directory
#   having names similar to :
#
#     chr##.xml.#
#
#   Use of Sun Grid Engine allows multiple jobs to be generated
#   by this program and SGE queues them and executes each as
#   machine resources are available.
#
#   Command-line Parameters :
#
#       none
#
#  Before running this program you must 'cd' into directory where
#  your probe files are located  (see README for Build 2).
#
#  syntax : [path]/qsub_megablast.pl
#
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#
#
open (IN,"ls *.xml.* |") || die "Hey - You dont have any XML files for me !";
while (<IN>) {
        chop;
        print "Creating file for $_ \n"; 
        ($chromosome, $fractional) = ($_ =~ m/chr(.+).xml.(.+)/);
        $file = $_;
        $base_name = "mega_".$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 be \n";
      # print OUT "#\$ -M yourEmailId\@your.email.domain \n";
        print OUT "# \n";
#
#
        print OUT "/usr/local/genome/ncbi/megablast -t 16 -N2 -W11 -e 0.6 -i $file -o $file.mega_out -d /opt2/local_blastdb/human_april2003/ucscapril2003_ncbi33 -F F -D 3 \n";
        close OUT;
        system("qsub $outname");

}


##############################################################################
# Start Description
# Run mega_blast once for each input file in current directory.
# End Description
##############################################################################