my $serverroot = '/path/to/ensembl';
  my $support = new Bio::EnsEMBL::Utils::ConversionSupport($serverroot);

  # parse common options
  $support->parse_common_options;

  # parse extra options for your script
  $support->parse_extra_options( 'string_opt=s', 'numeric_opt=n' );

  # ask user if he wants to run script with these parameters
  $support->confirm_params;

  # see individual method documentation for more stuff

    my @awords = split /-/, $a;
    my @bwords = split /-/, $b;

    my $anum = $awords[0];
    my $bnum = $bwords[0];

    if ($anum !~ /^[0-9]*$/) {
        if ($bnum !~ /^[0-9]*$/) {
            return $anum cmp $bnum;
        } else {
            return 1;
        }
    }
    if ($bnum !~ /^[0-9]*$/) {
        return -1;
    }

    if ($anum <=> $bnum) {
        return $anum <=> $bnum;
    } else {
        if ($#awords == 0) {
            return -1;
        } elsif ($#bwords == 0) {
            return 1;
        } else {
            return $awords[1] cmp $bwords[1];
        }
    }

	my $self        = shift;
	my $attrib_code = shift;
	my $dbh         = shift;
	my ($attrib_id) = $dbh->selectrow_array(
		qq(select attrib_type_id
           from attrib_type
           where code = ?),
			{},
		($attrib_code)
	);
	if (! $attrib_id) {
		$self->log_warning("There is no attrib_type_id for code $attrib_code, please patch the attrib_table\n");
		exit;
	}
	else {
		return $attrib_id;
	}

  my $self = shift;

  # setter
  if (@_) {
    @{ $self->{'_allowed_params'} } = @_;
  }

  # getter
  if (ref($self->{'_allowed_params'}) eq 'ARRAY') {
    return @{ $self->{'_allowed_params'} };
  } else {
    return ();
  }

    my ($self, @params) = @_;
    my @missing = ();
    foreach my $param (@params) {
        push @missing, $param unless $self->param($param);
    }
    if (@missing) {
        throw("Missing parameters: @missing.\nYou must specify them on the commandline or in your conffile.\n");
    }
    return(1);

    my $self = shift;
    foreach my $param (@_) {
        $self->param($param,
            split (/,/, join (',', $self->param($param))));
    }
    return(1);

  my $self = shift;
  my $num = shift;

  $num = reverse($num);
  $num =~ s/(\d\d\d)(?=\d)(?!\d*\.)/$1,/g;

  return scalar reverse $num;

  my $self = shift;

  # print parameter table
  print "Running script with these parameters:\n\n";
  print $self->list_all_params;

  if ($self->param('host') eq 'ensdb-1-10') {
    # ask user if he wants to proceed
    exit unless $self->user_proceed("**************\n\n You're working on ensdb-1-10! Is that correct and you want to continue ?\n\n**************");
  }
  else {
    # ask user if he wants to proceed
    exit unless $self->user_proceed("Continue?");
  }
  return(1);

    my ($self, $settings) = @_;
    my %param_hash;

    # get all allowed parameters
    if ($settings->{'allowed_params'}) {
        # exclude params explicitly stated
        my %exclude = map { $_ => 1 } @{ $settings->{'exclude'} || [] };
        foreach my $param ($self->allowed_params) {
            unless ($exclude{$param}) {
                my ($first, @rest) = $self->param($param);
                next unless (defined($first));

                if (@rest) {
                    $first = join(",", $first, @rest);
                }
                $param_hash{$param} = $first;
            }
        }

    }

    # replace values
    foreach my $key (keys %{ $settings->{'replace'} || {} }) {
        $param_hash{$key} = $settings->{'replace'}->{$key};
    }

    # create the commandline options string
    my $options_string;
    foreach my $param (keys %param_hash) {
        $options_string .= sprintf("--%s %s ", $param, $param_hash{$param});
    }
    return $options_string;

    return strftime "%Y-%m-%d %T", localtime;

    my $date = strftime "%Y-%m-%d %T", localtime;
    my $mem = `ps -p $$ -o vsz |tail -1`;
    chomp $mem;
    return "[$date, mem $mem]";

   my( $self, $time, $format ) = @_;
  my( $d,$m,$y) = (localtime($time))[3,4,5];
  my %S = ('d'=>sprintf('%02d',$d),'m'=>sprintf('%02d',$m+1),'y'=>$y+1900);
  (my $res = $format ) =~s/%(\w)/$S{$1}/ge;
  return $res;

    my ($self, $database) = shift;
    return $self->{'_dba'}->{$database} || $self->{'_dba'}->{'default'};

    my ($self, $classname) = @_;
    my ($parent_namespace, $module) = $classname =~/^(.*::)(.*)$/ ?
                                        ($1,$2) : ('::', $classname);

    no strict 'refs';
    # return if module has already been imported
    return 1 if $parent_namespace->{$module.'::'} && %{ $parent_namespace->{$module.'::'}||{} };
    
    eval "require $classname";
    throw("Failed to require $classname: $@") if ($@);
    $classname->import();

    return 1;

    my $self = shift;
    $self->{'_error'} = shift if (@_);
    return $self->{'_error'};

  my $self = shift;
  my $aa   = shift or throw("You must supply an attribute adaptor");
  my $sa   = shift or throw("You must supply a slice adaptor");
  my $cs   = shift || 'chromosome';
  my $cv   = shift || 'Otter';
  my $visible_chroms;
  foreach my $chrom ( @{$sa->fetch_all($cs,$cv)} ) {
    my $chrom_name = $chrom->name;
    my $attribs = $aa->fetch_all_by_Slice($chrom,'hidden');
    if ( scalar(@$attribs) > 1 ) {
      $self->log_warning("More than one hidden attribute for chromosome $chrom_name\n");
    }
    elsif ($attribs->[0]->value == 0) {				
      push @$visible_chroms, $chrom;
    }
    elsif ($attribs->[0]->value == 1) {	
      $self->log_verbose("chromosome $chrom_name is hidden\n");	
    }
    else {
      $self->log_warning("No hidden attribute for chromosome $chrom_name\n");
    }
  }
  return $visible_chroms;

    my ($self, $mode, $file) = @_;
    $mode ||= ">";
    my $fh;
    if ($file) {
        open($fh, "$mode", $file) or throw(
            "Unable to open $file for writing: $!");
    } elsif ($mode =~ />/) {
        $fh =\* STDOUT;
    } elsif ($mode =~ /</) {
        $fh =\* STDIN;
    }
    return $fh;

    my $self = shift;
    $self->log("\nAll done. ".$self->warnings." warnings. ");
    if ($self->{'_start_time'}) {
        $self->log("Runtime ");
        my $diff = time - $self->{'_start_time'};
        my $sec = $diff % 60;
        $diff = ($diff - $sec) / 60;
        my $min = $diff % 60;
        my $hours = ($diff - $min) / 60;
        $self->log("${hours}h ${min}min ${sec}sec ");
    }
    $self->log($self->date_and_mem."\n\n");
    return(1);

	my $self        = shift;
	my $attribs     = shift;
	my $id          = shift;
	my $name        = shift;
	my $code        = shift;
	my $value       = shift;
	my $interact    = shift || 0;
	my $table       = shift || 'seq_region_attrib';

	#transiently set interactive parameter to zero
	my $int_before;
	if (! $interact) {
		$int_before = $self->param('interactive');
		$self->param('interactive',0);
	}

	#get any existing value(s) for this attribute
	my $existings = $self->get_attrib_values($attribs,$code);
	
	#add a new attribute if there is none...
	if (! @$existings ) {
		if ($self->user_proceed("Do you want to set $name attrib (code = $code) to value $value ?")) {
			my $r = $self->store_new_attribute($id,$code,$value);
			
			#reset interactive parameter
			$self->param('interactive',$int_before) if (! $interact);
			return $r;
		}
	}
	#...warn and exit if you're trying to update more than one value for the same attribute...
	elsif (scalar @$existings > 1) {
		$self->log_warning("You shouldn't be trying to update multiple attributes with the same code at once ($name:$code,$value), looks like you have duplicate entries in the (seq_region_)attrib table\n");
		exit;
	}

	#...or update an attribute with new values...
	else {
		my $existing = $existings->[0];
		if ($existing ne $value) {
			if ($self->user_proceed("Do you want to reset $name attrib (code = $code) from $existing to $value ?")) {
				my $r = $self->update_attribute($id,$code,$value);
				$self->param('interactive',$int_before) if (! $interact);
				push @$r, $existing;
				return $r;
			}
		}
		#...or make no change
		else {
			$self->param('interactive',$int_before) if (! $interact);
			return [];
		}
	}

  my $self    = shift;
  my $attribs = shift;
  my $code    = shift;
  my $value   = shift;
  if (my @atts = grep {$_->code eq $code } @$attribs) {
    my $r = [];
    if ($value) {
      if (my @values = grep {$_->value eq $value} @atts) {
	foreach (@values) {
	  push @$r, $_->value;
	}
	return $r;
      }
      else {
	return [];
      }
    }
    else {
      foreach (@atts) {
	push @$r, $_->value;
      }
      return $r;
    }
  }
  else {
    return [];
  }

    my ($self, $dba, $version,$type,$include_non_reference) = @_;
    $dba ||= $self->dba;
	$type ||= 'toplevel';
    throw("get_chrlength should be passed a Bio::EnsEMBL::DBSQL::DBAdaptor\n")
        unless ($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'));

    my $sa = $dba->get_SliceAdaptor;

    my @chromosomes = map { $_->seq_region_name } 
                            @{ $sa->fetch_all($type, $version,$include_non_reference) };
    my %chr = map { $_ => $sa->fetch_by_region($type, $_, undef, undef, undef, $version)->length } @chromosomes;

    my @wanted = $self->param('chromosomes');
    if (@wanted) {
        # check if user supplied invalid chromosome names
        foreach my $chr (@wanted) {
            my $found = 0;
            foreach my $chr_from_db (keys %chr) {
                if ($chr_from_db eq $chr) {
                    $found = 1;
                    last;
                }
            }
            unless ($found) {
                warning("Didn't find chromosome $chr in database " .
                         $self->param('dbname'));
            }
        }
        
        # filter to requested chromosomes only
        HASH: 
        foreach my $chr_from_db (keys %chr) {
            foreach my $chr (@wanted) {
                if ($chr_from_db eq $chr) {
                    next HASH;
                }
            }
            delete($chr{$chr_from_db});
        }
    }

    return\% chr;

  return qw(
	    conffile
	    dbname
	    host
	    port
	    user
	    pass
	    logpath
	    logfile
	    logappend
	    verbose
	    interactive
	    dry_run
	  );

    my $self = shift;
    my $database = shift or throw("You must provide a database");
    my $prefix = shift || '';
    $self->check_required_params(
        "${prefix}host",
        "${prefix}port",
        "${prefix}user",
        # "${prefix}pass", not required since might be empty
        "${prefix}dbname",
    );

    my %adaptors = (
        core    => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
        ensembl => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
        evega   => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
        otter   => 'Bio::Otter::DBSQL::DBAdaptor',
        vega    => 'Bio::Otter::DBSQL::DBAdaptor',
		compara => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
		loutre  => 'Bio::Vega::DBSQL::DBAdaptor',
    );
    throw("Unknown database: $database") unless $adaptors{$database};

    $self->dynamic_use($adaptors{$database});
    my $dba = $adaptors{$database}->new(
            -host   => $self->param("${prefix}host"),
            -port   => $self->param("${prefix}port"),
            -user   => $self->param("${prefix}user"),
            -pass   => $self->param("${prefix}pass") || '',
            -dbname => $self->param("${prefix}dbname"),
            -group  => $database,
    );
	#can use this approach to get dna from another db
#	my $dna_db = $adaptors{$database}->new(
#			-host => 'otterlive',
#            -port => '3301',
#			-user => $self->param("${prefix}user"),
#			-pass => $self->param("${prefix}pass"),
#            -dbname => 'loutre_human',
#		);
#	$dba->dnadb($dna_db);

    # otherwise explicitely set the dnadb to itself - by default the Registry assumes
    # a group 'core' for this now
    $dba->dnadb($dba);

    $self->{'_dba'}->{$database} = $dba;
    $self->{'_dba'}->{'default'} = $dba unless $self->{'_dba'}->{'default'};
    return $self->{'_dba'}->{$database};

  my $self = shift;
  my $prefix = shift;
 
  $self->check_required_params(
      "${prefix}host",
      "${prefix}port",
      "${prefix}user",
  );

  my $dsn = "DBI:" . ($self->param('driver')||'mysql') .
            ":host=" . $self->param("${prefix}host") .
            ";port=" . $self->param("${prefix}port");

  if ($self->param("${prefix}dbname")) {
    $dsn .= ";dbname=".$self->param("${prefix}dbname");
  }

#  warn $dsn;

  my $dbh;
  eval{
    $dbh = DBI->connect($dsn, $self->param("${prefix}user"),
      $self->param("${prefix}pass"), {'RaiseError' => 1, 'PrintError' => 0});
  };

  if (!$dbh || $@ || !$dbh->ping) {
    $self->log_error("Could not connect to db server as user ".
      $self->param("${prefix}user") .
      " using [$dsn] as a locator:\n" . $DBI::errstr . $@);
  }

  $self->{'_dbh'} = $dbh;
  return $self->{'_dbh'};

  my ($self, $dba, $version) = @_;
  $dba ||= $self->dba;
  throw("get_ensembl_chr_mapping should be passed a Bio::EnsEMBL::DBSQL::DBAdaptor\n") unless ($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'));

  my $sa = $dba->get_SliceAdaptor;
  my @chromosomes = map { $_->seq_region_name } 
    @{ $sa->fetch_all('chromosome', $version) };

  my %chrs;
  foreach my $chr (@chromosomes) {
    my $sr = $sa->fetch_by_region('chromosome', $chr, undef, undef, undef, $version);
    my ($ensembl_name_attr) = @{ $sr->get_all_Attributes('ensembl_name') };
    if ($ensembl_name_attr) {
      $chrs{$chr} = $ensembl_name_attr->value;
    } else {
      $chrs{$chr} = $chr;
    }
  }
  return\% chrs;

    my $self = shift;
    $self->check_required_params(qw(
        glovarhost
        glovarport
        glovaruser
        glovarpass
        glovardbname
        oracle_home
        ld_library_path
        glovar_snp_consequence_exp
    ));

    # check for core dbadaptor
    my $core_db = $self->dba;
    unless ($core_db && (ref($core_db) =~ /Bio::.*::DBSQL::DBAdaptor/)) {
        $self->log_error("You have to connect to a core db before you can get a glovar dbadaptor.\n");
        exit;
    }
    
    # setup Oracle environment
    $ENV{'ORACLE_HOME'} = $self->param('oracle_home');
    $ENV{'LD_LIBRARY_PATH'} = $self->param('ld_library_path');

    # connect to Glovar db
    $self->dynamic_use('Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor');
    my $dba = Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor->new(
            -host   => $self->param("glovarhost"),
            -port   => $self->param("glovarport"),
            -user   => $self->param("glovaruser"),
            -pass   => $self->param("glovarpass"),
            -dbname => $self->param("glovardbname"),
            -group  => 'glovar',
    );

    # setup adaptor inter-relationships
    $dba->dnadb($core_db);
    $self->dynamic_use('Bio::EnsEMBL::ExternalData::Glovar::GlovarSNPAdaptor');
    my $glovar_snp_adaptor = $dba->get_GlovarSNPAdaptor;
    $glovar_snp_adaptor->consequence_exp($self->param('glovar_snp_consequence_exp'));
    $core_db->add_ExternalFeatureAdaptor($glovar_snp_adaptor);

    return $dba;

  my ($self,$p) = @_;
  if ($p) {
    return qw(
	      loutrehost=s
	      loutreport=s
	      loutreuser=s
	      loutrepass=s
	      loutredbname=s
	    );
  }
  else {
    return qw(
	      loutrehost
	      loutreport
	      loutreuser
	      loutrepass
	      loutredbname
	    );
  }

  my $self = shift;
  my $aa   = shift or throw("You must supply an attribute adaptor");
  my $sa   = shift or throw("You must supply a slice adaptor");
  my $cs   = shift || 'chromosome';
  my $cv   = shift || 'Otter';
  my $visible_chrom_names;
  foreach my $chrom ( @{$sa->fetch_all($cs,$cv)} ) {
    my $chrom_name = $chrom->seq_region_name;
    my $attribs = $aa->fetch_all_by_Slice($chrom,'hidden');
    if ( scalar(@$attribs) > 1 ) {
      $self->log_warning("More than one hidden attribute for chromosome $chrom_name\n");
    }
    elsif ($attribs->[0]->value == 0) {				
      push @$visible_chrom_names, $chrom_name;
    }
    elsif ($attribs->[0]->value == 1) {	
      $self->log_verbose("chromosome $chrom_name is hidden\n");	
    }
    else {
      $self->log_warning("No hidden attribute for chromosome $chrom_name\n");
    }
  }
  return $visible_chrom_names;

    my ($self, $dba) = @_;
    $dba ||= $self->dba;
    my $sql_tmp = "SELECT meta_value FROM meta WHERE meta_key =\' species.classification\' ORDER BY meta_id";
    my $sql = $dba->dbc->add_limit_clause($sql_tmp,2);
    my $sth = $dba->dbc->db_handle->prepare($sql);
    $sth->execute;
    my @sp;
    while (my @row = $sth->fetchrow_array) {
        push @sp, $row[0];
    }
    $sth->finish;
    my $species = join(" ", reverse @sp);
    $self->throw("Could not determine species scientific name from database.")
        unless $species;
    return $species;

    my ($self, $dba) = @_;
    $dba ||= $self->dba;
    my $sql = 'SELECT meta_value FROM meta WHERE meta_key = "species.taxonomy_id"';
    my $sth = $dba->dbc->db_handle->prepare($sql);
    $sth->execute;
    my ($tid) = $sth->fetchrow_array;
    $sth->finish;
    $self->throw("Could not determine taxonomy_id from database.") unless $tid;
    return $tid;

  my $self = shift;
  my $aa   = shift or throw("You must supply an attribute adaptor");
  my $sa   = shift or throw("You must supply a slice adaptor");
  my $cs   = shift || 'chromosome';
  my $cv   = shift || 'Otter';
  my $export_mode = $self->param('release_type');
  my $release = $self->param('vega_release');
  my $names;
  my $chroms  = $self->fetch_non_hidden_slices($aa,$sa,$cs,$cv);
 CHROM:
  foreach my $chrom (@$chroms) {
    my $attribs = $aa->fetch_all_by_Slice($chrom);
    my $vals = $self->get_attrib_values($attribs,'vega_export_mod');
    if (scalar(@$vals > 1)) {
      $self->log_warning ("Multiple attribs for\' vega_export_mod\', please fix before continuing");
      exit;
    }
    next CHROM if (! grep { $_ eq $export_mode} @$vals);
    $vals =  $self->get_attrib_values($attribs,'vega_release',$release);	
    if (scalar(@$vals > 1)) {
      $self->log_warning ("Multiple attribs for\' vega_release\' value = $release , please fix before continuing");
      exit;
    }
    next CHROM if (! grep { $_ eq $release} @$vals);
    my $name = $chrom->seq_region_name;
    if (my @ignored = $self->param('ignore_chr')) {
      next CHROM if (grep {$_ eq $name} @ignored);
    }
    push @{$names}, $name;
  }
  return $names;

    my $self = shift;

    # get a log filehandle
    my $log = $self->log_filehandle;

    # print script name, date, user who is running it
    my $hostname = `hostname`;
    chomp $hostname;
    my $script = "$hostname:$Bin/$Script";
    my $user = `whoami`;
    chomp $user;
    $self->log("Script: $script\nDate: ".$self->date."\nUser: $user\n");

    # print parameters the script is running with
    $self->log("Parameters:\n\n");
    $self->log($self->list_all_params);

    # remember start time
    $self->{'_start_time'} = time;

    return $log;

  my $self = shift;
  my $txt = sprintf "    %-21s%-40s\n", qw(PARAMETER VALUE);
  $txt .= "    " . "-"x71 . "\n";
  $Text::Wrap::colums = 72;
  my @params = $self->allowed_params;
  foreach my $key (@params) {
        my @vals = $self->param($key);
        if (@vals) {
            $txt .= Text::Wrap::wrap( sprintf('   %-21s', $key),
                                      ' 'x24,
                                      join(", ", @vals)
                                    ) . "\n";
        }
    }
    $txt .= "\n";
    return $txt;

    my ($self, $param) = @_;
    my @vals = $self->param($param);
    return unless (@vals);

    my $firstval = $vals[0];
    if (scalar(@vals) == 1 && -e $firstval) {
        # we didn't get a list of values, but a file to read values from
        @vals = ();
        open(IN, $firstval) or throw("Cannot open $firstval for reading: $!");
        while(<IN>){
            chomp;
            push(@vals, $_);
        }
        close(IN);
        $self->param($param, @vals);
    }
    $self->comma_to_list($param);
    return(1);

    my ($self, $txt, $indent) = @_;
    $indent ||= 0;
    
    # strip off leading linebreaks so that indenting doesn't break
    $txt =~ s/^(\n*)//;
    
    $txt = $1."    "x$indent . $txt;
    my $fh = $self->{'_log_filehandle'};
    throw("Unable to obtain log filehandle") unless $fh;
    print $fh "$txt";
    return(1);

    my ($self, $txt, $indent) = @_;
    $txt = "ERROR: ".$txt;
    $self->log($txt, $indent);
    $self->log("Exiting.\n");
    exit;

    my ($self, $mode) = @_;
    $mode ||= '>';
    $mode = '>>' if ($self->param('logappend'));
    my $fh =\* STDERR;
    if (my $logfile = $self->param('logfile')) {
        if (my $logpath = $self->param('logpath')) {
            unless (-e $logpath) {
                system("mkdir $logpath") == 0 or
                    $self->log_error("Can't create log dir $logpath: $!\n");
            }
            $logfile = "$logpath/$logfile";
        }
        open($fh, "$mode", $logfile) or throw(
            "Unable to open $logfile for writing: $!");
    }
    $self->{'_log_filehandle'} = $fh;
    return $self->{'_log_filehandle'};

    my ($self, $txt, $indent) = @_;
    
    # append timestamp and memory usage to log text
    $txt =~ s/(\n*)$//;
    $txt .= " ".$self->date_and_mem.$1;
    
    $self->log($txt, $indent);
    return(1);

    my ($self, $txt, $indent) = @_;

    return(0) unless $self->param('verbose');

    $self->log($txt, $indent);
    return(1);

    my ($self, $txt, $indent, $break) = @_;
    $txt = "WARNING: " . $txt;
	$txt = "\n$txt" if ($break);
    $self->log($txt, $indent);
    $self->{'_warnings'}++;
    return(1);

    my $mem = `ps -p $$ -o vsz |tail -1`;
    chomp $mem;
    return $mem;

  my $class = shift;
  (my $serverroot = shift) or throw("You must supply a serverroot.");
  my $self = {
    '_serverroot'   => $serverroot,
    '_param'        => { interactive => 1 },
    '_warnings'     => 0,
  };
  bless ($self, $class);
  return $self;

    my $self = shift;
    my $name = shift or throw("You must supply a parameter name");

    # setter
    if (@_) {
        if (scalar(@_) == 1) {
            # single value
            $self->{'_param'}->{$name} = shift;
        } else {
            # list of values
            undef $self->{'_param'}->{$name};
            @{ $self->{'_param'}->{$name} } = @_;
        }
    }

    # getter
    if (ref($self->{'_param'}->{$name}) eq 'ARRAY') {
        # list parameter
        return @{ $self->{'_param'}->{$name} };
    } elsif (defined($self->{'_param'}->{$name})) {
        # single-value parameter
        return $self->{'_param'}->{$name};
    } else {
        return ();
    }

  my $self = shift;

  # read commandline options
  my %h;
  Getopt::Long::Configure("pass_through");
  &GetOptions(\% h,
	       'dbname|db_name=s',
	       'host|dbhost|db_host=s',
	       'port|dbport|db_port=n',
	       'user|dbuser|db_user=s',
	       'pass|dbpass|db_pass=s',
	       'conffile|conf=s',
	       'logfile|log=s',
	       'logpath=s',
	       'logappend|log_append=s',
	       'verbose|v=s',
	       'interactive|i=s',
	       'dry_run|dry|n=s',
	       'help|h|?',
	     );

  # reads config file
  my $conffile = $h{'conffile'} || $self->serverroot . "/sanger-plugins/vega/conf/ini-files/Conversion.ini";
  $conffile = abs_path($conffile);
  if (-e $conffile) {
    open(CONF, $conffile) or throw( 
      "Unable to open configuration file $conffile for reading: $!");
    my $serverroot = $self->serverroot;
    while (<CONF>) {
      chomp;

      # remove comments
      s/^[#;].*//;
      s/\s+[;].*$//;

      # read options into internal parameter datastructure, removing whitespace
      next unless (/(\w\S*)\s*=\s*(\S*)\s*/);
      my $name = $1;
      my $val = $2;
      if ($val =~ /\$SERVERROOT/) {
	$val =~ s/\$SERVERROOT/$serverroot/g;
	$val = abs_path($val);
      }
      $self->param($name, $val);
    }
    $self->param('conffile', $conffile);
  } elsif ($conffile) {
    warning("Unable to open configuration file $conffile for reading: $!");
  }

  # override configured parameter with commandline options
  map { $self->param($_, $h{$_}) } keys %h;
  return(1);

  my ($self, @params) = @_;
  Getopt::Long::Configure("no_pass_through");
  eval {
    # catch warnings to pass to $self->error
    local $SIG{__WARN__} = sub { die @_; };
    &GetOptions(\%{ $self->{'_param'} }, @params);
  };
  $self->error($@) if $@;
  return(1);

    my ($self, $text) = @_;

    if ($self->param('interactive')) {
        print "$text\n" if $text;
        my $input = <>;
        chomp $input;
        return $input;
    }

  my $self = shift;
  foreach my $param (qw(dbname host port user pass)) {
    $self->{'_param'}{$param} = undef;
  }

    my $self = shift;
    $self->{'_serverroot'} = shift if (@_);
    return $self->{'_serverroot'};

    my ($self, $chr_hashref) = @_;
    $chr_hashref = $self->get_chrlength unless ($chr_hashref);
    throw("You have to pass a hashref of your chromosomes")
        unless ($chr_hashref and ref($chr_hashref) eq 'HASH');
    return (sort _by_chr_num keys %$chr_hashref);

    my $self = shift;
    $self->{'_species'} = shift if (@_);
    # get species name from database if not set
    unless ($self->{'_species'}) {
        $self->{'_species'} = join('_',
            split(/ /, $self->get_species_scientific_name));
    }
    return $self->{'_species'};

    my $self = shift;
    my $cutoff = shift || 5000000;
    
    my $slice_adaptor = $self->dba->get_SliceAdaptor;
    my $top_slices;
    if ($self->param('chromosomes')) {
        foreach my $chr ($self->param('chromosomes')) {
            push @{ $top_slices }, $slice_adaptor->fetch_by_region('chromosome', $chr);
        }
    } else {
        $top_slices = $slice_adaptor->fetch_all('chromosome');
    }

    my ($big_chr, $small_chr, $min_big_chr, $min_small_chr);
    foreach my $slice (@{ $top_slices }) {
        if ($slice->length < $cutoff) {
            if (! $min_small_chr or ($min_small_chr > $slice->length)) {
                $min_small_chr = $slice->length;
            }
            # push small chromosomes onto $small_chr
            push @{ $small_chr }, $slice;
        }
        if (! $min_big_chr or ($min_big_chr > $slice->length) && $slice->length > $cutoff) {
            $min_big_chr = $slice->length;
        }
        # push _all_ chromosomes onto $big_chr
        push @{ $big_chr }, $slice;
    }

    my $chr_slices;
    $chr_slices->{int($min_big_chr/150)} = $big_chr if $min_big_chr;
    $chr_slices->{int($min_small_chr/150)} = $small_chr if $min_small_chr;

    return $chr_slices;

	my $self         = shift;
	my $sr_id        = shift;
	my $attrib_code  = shift;
	my $attrib_value = shift || '';
	my $table        = shift || 'seq_region_attrib';

	#get database handle
	my $dbh = $self->get_dbconnection('loutre');
	#get attrib_type_id for this particular attribute
	my $attrib_id = $self->_get_attrib_id($attrib_code,$dbh);
	#store
	my $r = $dbh->do(
		qq(insert into $table
           values (?,?,?)),
        {},
		($sr_id,$attrib_id,$attrib_value)
	);
	return ['Stored',$r];

	my $self = shift;
	my $sr_id = shift;
	my $attrib_code  = shift;
	my $attrib_value = shift;
	my $table        = shift || 'seq_region_attrib';
	my $dbh = $self->get_dbconnection('loutre');
	my $attrib_id = $self->_get_attrib_id($attrib_code,$dbh);
	#update
	my $r = $dbh->do(
		qq(update $table
           set value = ?
           where seq_region_id = $sr_id
           and attrib_type_id = $attrib_id),
        {},
		($attrib_value)
	);
	return ['Updated',$r];
}

1;

    my $self = shift;
    exit unless $self->user_proceed("Continue?");

    my ($self, $text) = @_;

    if ($self->param('interactive')) {
        print "$text\n" if $text;
        print "[y/N] ";
        my $input = lc(<>);
        chomp $input;
        unless ($input eq 'y') {
            print "Skipping.\n";
            return(0);
        }
    }

    return(1);

    my $self = shift;
    return $self->{'_warnings'};

  Copyright (c) 1999-2009 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    /info/about/code_licence.html

  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.

  Example     : print $support->format_time($gene->modifed_date) . "\n";
  Description : Prints timestamps from the database
  Return type : String - nicely formatted time stamp
  Exceptions  : none
  Caller      : general