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Summary

Bio::DB::Ace - Database object interface to ACeDB servers

Package variables

Included modules

Inherit

Bio::DB::RandomAccessI

Synopsis

    $db = Bio::DB::Ace->new( -server => 'myace.server.com', port => '120000');

    $seq = $db->get_Seq_by_id('MUSIGHBA1'); # Unique ID

    # or ...

    $seq = $db->get_Seq_by_acc('J00522'); # Accession Number

Description

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

  http://stein.cshl.org/AcePerl/

before this interface will work.
This interface is designed at the moment to work through a aceclient/aceserver
type mechanism

Methods

Methods description

  Title   : _aceobj
  Usage   : $ace = $db->_aceobj();
  Function: Get/Set on the acedb object 
  Returns : Ace object
  Args    : New value of the ace object

  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

 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

Methods code

BEGIN {

   eval {
    require Ace;
  };
  if( $@) {
    print STDERR "You have not installed Ace.pm.\n Read the docs in Bio::DB::Ace for more information about how to do this.\n It is very easy\n\nError message $@";

}

sub _aceobj {

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

  if( $arg ) {
    $self->{'_aceobj'} = $arg;
  } 

  return $self->{'_aceobj'};
}

1;

}

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);

}

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, -type => 'Dna', -seq => $dna, -name => "Sequence from Bio::DB::Ace $id");
  return $out;

}

sub new {

  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  my ($host,$port) = $self->_rearrange([qw(
					 HOST
					 PORT
					 )],
				     @args,
				     );

  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");

  $self->_aceobj($aceobj);


  return $self;

}

General documentation

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
  make
  <become root>
  make install

Then you will have installed Aceperl. Use the PREFIX mechanism to install elsewhere.

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.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Email birney@sanger.ac.uk

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _