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# $Id: 15549 2009-02-21 00:48:48Z maj $
# BioPerl module for Bio::DB::Ace
# Please direct questions and support issues to <>
# Cared for by Ewan Birney <>
# Copyright Ewan Birney
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::Ace - Database object interface to ACeDB servers
$db = Bio::DB::Ace->new( -server => '', port => '120000');
$seq = $db->get_Seq_by_id('MUSIGHBA1'); # Unique ID
# or ...
$seq = $db->get_Seq_by_acc('J00522'); # Accession Number
This provides a standard BioPerl database access to Ace, using Lincoln Steins
excellent AcePerl module. You need to download and install the aceperl module from
before this interface will work.
This interface is designed at the moment to work through a aceclient/aceserver
type mechanism
Download the latest aceperl tar file, gunzip/untar and cd into the directory.
This is a standard CPAN-style directory, so if you go
Perl Makefile.PL
<become root>
make install
Then you will have installed Aceperl. Use the PREFIX mechanism to install elsewhere.
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated. - General discussion - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
=head1 AUTHOR - Ewan Birney
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
# Let the code begin...
package Bio::DB::Ace;
use strict;
# Object preamble - inherits from Bio::DB::RandomAccessI
use Bio::Seq;
eval "require Ace;";
if( $@) {
print STDERR "You have not installed\n Read the docs in Bio::DB::Ace for more information about how to do this.\n It is very easy\n\nError message $@";
use base qw(Bio::DB::RandomAccessI);
# new() is inherited from Bio::DB::Abstract
# _initialize is where the heavy stuff will happen when new is called
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($host,$port) = $self->_rearrange([qw(
if( !$host || !$port ) {
$self->throw("Must have a host and port for an acedb server to work");
my $aceobj = Ace->connect(-host => $host,
-port => $port) ||
$self->throw("Could not make acedb object to $host:$port");
return $self;
=head2 get_Seq_by_id
Title : get_Seq_by_id
Usage : $seq = $db->get_Seq_by_id($uid);
Function: Gets a Bio::Seq object by its unique identifier/name
Returns : a Bio::Seq object
Args : $id : the id (as a string) of the desired sequence entry
sub get_Seq_by_id {
my $self = shift;
my $id = shift or $self->throw("Must supply an identifier!\n");
my $ace = $self->_aceobj();
my ($seq,$dna,$out);
$seq = $ace->fetch( 'Sequence' , $id);
# get out the sequence somehow!
$dna = $seq->asDNA();
$dna =~ s/^>.*\n//;
$dna =~ s/\n//g;
$out = Bio::Seq->new( -id => $id, -alphabet => 'Dna', -seq => $dna, -name => "Sequence from Bio::DB::Ace $id");
return $out;
=head2 get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $seq = $db->get_Seq_by_acc($acc);
Function: Gets a Bio::Seq object by its accession number
Returns : a Bio::Seq object
Args : $acc : the accession number of the desired sequence entry
sub get_Seq_by_acc {
my $self = shift;
my $acc = shift or $self->throw("Must supply an accesion number!\n");
return $self->get_Seq_by_id($acc);
=head2 _aceobj
Title : _aceobj
Usage : $ace = $db->_aceobj();
Function: Get/Set on the acedb object
Returns : Ace object
Args : New value of the ace object
sub _aceobj {
my ($self,$arg) = @_;
if( $arg ) {
$self->{'_aceobj'} = $arg;
return $self->{'_aceobj'};