Summary

Bio::DB::XEMBL - Database object interface for XEMBL entry retrieval

Package variables

Included modules

Inherit

Bio::DB::RandomAccessI

Synopsis

  use Bio::DB::XEMBL;

  $embl = new Bio::DB::XEMBL;

  # remember that XEMBL_ID does not equal GenBank_ID!
  $seq = $embl->get_Seq_by_id('BUM'); # EMBL ID
 	print "cloneid is ", $seq->id, "\n";

  # or changeing to accession number and Fasta format ...
  $seq = $embl->get_Seq_by_acc('J02231'); # XEMBL ACC
 	print "cloneid is ", $seq->id, "\n";

  # especially when using versions, you better be prepared
  # in not getting what what want
  eval {
      $seq = $embl->get_Seq_by_version('J02231.1'); # XEMBL VERSION
  };
  print "cloneid is ", $seq->id, "\n" unless $@;

  my $seqio = $embl->get_Stream_by_batch(['U83300','U83301','U83302']);
  while( my $clone =  $seqio->next_seq ) {
 	print "cloneid is ", $clone->id, "\n";
  }

Description

Allows the dynamic retrieval of Bio::Seq objects from the XEMBL
database. See Bio::Seq for details.

Methods

Methods description

 Title   : get_Seq_by_id
 Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
 Function: Gets a Bio::Seq object by its name
 Returns : a Bio::Seq object
 Args    : the id (as a string) of a sequence
 Throws  : "id does not exist" exception

  Title   : get_Stream_by_batch
  Usage   : $seq = $db->get_Stream_by_batch($ref);
  Function: Retrieves Seq objects from XEMBL 'en masse', rather than one
            at a time. Currently this is not particularly efficient, as
            it loads the entire result into memory and parses it.
  Example :
  Returns : a Bio::SeqIO stream object
  Args    : $ref : an array reference containing a list of unique 
            ids/accession numbers.

 Title   : get_Seq_by_acc
 Usage   : $seq = $db->get_Seq_by_acc('X77802');
 Function: Gets a Bio::Seq object by accession number
 Returns : A Bio::Seq object
 Args    : accession number (as a string)
 Throws  : "acc does not exist" exception

 Title   : get_Seq_by_version
 Usage   : $seq = $db->get_Seq_by_version('X77802.1');
 Function: Gets a Bio::Seq object by sequence version
 Returns : A Bio::Seq object
 Args    : accession.version (as a string)
 Throws  : "acc.version does not exist" exception

 Title   : endpoint
 Usage   : $endpoint = $db->endpoint([$endpoint])
 Function: Gets/sets endpoint for SOAP connection
 Returns : old endpoint
 Args    : new endpoint(optional)

 Title   : new_from_registry
 Usage   : $db = Bio::DB::XEMBL->new_from_registry(%config)
 Function: creates a new Bio::DB::XEMBL object in a Bio::DB::Registry-
           compatible fashion
 Returns : new Bio::DB::XEMBL
 Args    : provided by the registry, see below
 Status  : Public

  location     Endpoint for the XEMBL service.  Currently the only
               known valid endpoint is 
               http://www.ebi.ac.uk:80/cgi-bin/xembl/XEMBL-SOAP.pl

Methods code

sub new {

    my ($class, @args ) = @_;
    my $self = $class->SUPER::new(@args);
    my $endpoint = $self->_rearrange([qw(ENDPOINT)]);
    $endpoint ||= DEFAULT_ENDPOINT;
    $self->endpoint($endpoint);
    return $self;

}

sub get_Seq_by_id {

   my ($self,@args) = @_;
   my $seqio = $self->get_Stream_by_batch([@args]);
   return $seqio->next_seq;

}

sub get_Stream_by_batch {

  my ($self, $ids) = @_;
  $self->throw("expected an array ref, but got $ids")
    unless ref($ids) eq 'ARRAY';
  my @args = @$ids;

  my $endpoint = $self->endpoint;
  my $som = SOAP::Lite
    ->uri('http://www.ebi.ac.uk/XEMBL')
    ->proxy($endpoint)
    ->getNucSeq(SOAP::Data->name(format=>'bsml'),
		SOAP::Data->name(ids=>"@args"));
  if ($som->fault) {
    $self->throw($som->faultstring);
  }
  my $result = $som->result;
  my($fh,$filename) = tempfile(File::Spec->tmpdir . '/bsmlXXXXXX',SUFFIX=>'.bsml');
  print $fh $result;
  close $fh;
  my $seqio = Bio::SeqIO->new(-file=>$filename,-format=>'bsml');
  unlink $filename;
  $seqio;

}

sub get_Seq_by_acc {

   my ($self,@args) = @_;
   return $self->get_Seq_by_id(@args);

}

sub get_Seq_by_version {

   my ($self,@args) = @_;
   return $self->get_Seq_by_id(@args);

}

sub endpoint {

  my $self = shift;
  my $d = $self->{endpoint};
  $self->{endpoint} = shift if @_;
  $d;

}

sub new_from_registry {

    my ($self,%config) =  @_;
    my $location = $config{'location'} or $self->throw('Location must be specified.');
    my $index    = $self->new(-endpoint => $location);

}

General documentation

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/wiki/Mailing_lists  - 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 the
web:

  http://bugzilla.open-bio.org/

Email Lincoln Stein <lstein@cshl.org>

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