NAME

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

SYNOPSIS

  use Bio::DB::EMBL;

  $embl = Bio::DB::EMBL->new();

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

  # or changeing to accession number and Fasta format ...
  $embl->request_format('fasta');
  $seq = $embl->get_Seq_by_acc('J02231'); # EMBL 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'); # EMBL VERSION
  };
  print "cloneid is ", $seq->id, "\n" unless $@;

  # or ... best when downloading very large files, prevents
  # keeping all of the file in memory

  # also don't want features, just sequence so let's save bandwidth
  # and request Fasta sequence
  $embl = Bio::DB::EMBL->new(-retrievaltype => 'tempfile' ,
                            -format => 'fasta');
  my $seqio = $embl->get_Stream_by_id(['AC013798', 'AC021953'] );
  while( my $clone =  $seqio->next_seq ) {
        print "cloneid is ", $clone->id, "\n";
  }

DESCRIPTION

Allows the dynamic retrieval of sequence objects Bio::Seq from the EMBL database using the dbfetch script at EBI: <http://www.ebi.ac.uk/Tools/dbfetch/dbfetch>.

In order to make changes transparent we have host type (currently only ebi) and location (defaults to ebi) separated out. This allows later additions of more servers in different geographical locations.

The functionality of this module is inherited from Bio::DB::DBFetch which implements Bio::DB::WebDBSeqI.

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://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

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.

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 web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Heikki Lehvaslaiho

Email Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>

APPENDIX

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

new

 Title   : new
 Usage   : $gb = Bio::DB::GenBank->new(@options)
 Function: Creates a new genbank handle
 Returns : New genbank handle
 Args    : -delay   number of seconds to delay between fetches (3s)

NOTE: There are other options that are used internally.