#!/usr/bin/perl
#
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#
#   qsub_separate_probes.pl
#
#   Program generates a bash script to run with Sun Grid Engine.
#
#   Runs 'separate_all_probes.pl' against all output files 
#   from the previous step in your current directory having names like :
#
#     chr##.xml.#.valid
#
#   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 mega_blast output files are located  (see README for Build 2).
#
#  syntax : [path]/qsub_separate_probes.pl
#
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#
#  First check that executables directory is defined.
#
use Env qw(UPROBE_BIN_DIR);
if (! (-x "$UPROBE_BIN_DIR/separate_all_probes.pl") )
{
  my $ErrMsg = "Error : Did not find 'separate_all_probes.pl'\n ";
  my $ErrMsg = $ErrMsg."  Did you forget to define UPROBE_BIN_DIR ? \n";
  die $ErrMsg."\n";
}
#
#
open (IN,"ls chr*.xml|") || die "Hey - You dont have any probe xml files for me !";
while (<IN>) {
        chop;
        ($chromosome) = ($_ =~ m/chr(.+).xml/);
        $file = $_;
        $stdout = "$file.separate_output";
        $jobname = "Split_$chromosome";
        $bash_script = "chr".$chromosome."_separate.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 yourEmailId\@your.email.domain \n";
        print OUT "# \n";

        print OUT "$UPROBE_BIN_DIR/separate_all_probes.pl -chr $chromosome\n";
        
        close OUT;
        system("qsub $bash_script");

}


##############################################################################
# Start Description
# Run separate_all_probes.pl once for each chromosome represented in XML input files.
# End Description
##############################################################################