Bio::DB::XEMBL(3pm)

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

  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";
  }

Allows the dynamic retrieval of Bio::Seq objects from the XEMBL database. See Bio::Seq for details.
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Email Lincoln Stein <[email protected]> The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
get_Seq_by_id

 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

get_Stream_by_batch

  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.

get_Seq_by_acc

 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

get_Seq_by_version

 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

endpoint

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

new_from_registry

 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

The following registry-configuration tags are recognized:

  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

NOTE: Since this info is supposed to be coming from WSDL, the location is currently ignored.