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        print "\n";
        print "grep -w -f $current_found $sto > $next_sto\n";
        print "$stock2fasta $next_sto > $next_fasta\n";
        print "\n";
        print "\n";
    }

    return;
}

sub get_full_path_for_executable {
    my $exe       = shift;
    my $config    = shift;
    my $full_path = $config->{executables}->{$exe} || die "Path for executable '$exe' not found in configuration file";
    return $full_path;
}

sub filenames {
    my $basename = shift;
    my $round    = shift;

    return (
        $round => {
            cm    => "${basename}_rnd$round.cm",
            tab   => "${basename}_rnd$round.tab",
            found => "${basename}_rnd${round}_clusters_found.txt",
            sto   => "${basename}_rnd$round.sto",
            aln   => "${basename}_rnd${round}_aln.cm",
            fasta => "${basename}_rnd${round}.fasta",
        },
    );
}

#
#=============================================================================

1;    

#Documentation-----------------------------------------------------------------------------

=pod

=head1 SYNOPSIS

    covarianceSearchScripts --cm rna.cm --fasta rna.fasta --sto rna.sto [--rounds 10] [--config cluster.cfg]

=head1 DESCRIPTION

=head1 SUBROUTINES/METHODS

=head1 DIAGNOSTICS

=head1 CONFIGURATION AND ENVIRONMENT

=head1 DEPENDENCIES

=head1 INCOMPATIBILITIES

    None known

=head1 BUGS AND LIMITATIONS

     There are no known bugs in this module.
     Please report problems to molecules <at> cpan <dot> org.
     Patches are welcome.

=head1 SEE ALSO

=head1 ACKNOWLEDGEMENTS