Bio::DB::XEMBL(3)

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

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.

FEEDBACK

  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.

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

  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 email or the web:

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

AUTHOR - Lincoln Stein
Email Lincoln Stein <lstein@cshl.org>

APPENDIX
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.