Provided by: libbio-perl-perl_1.7.2-3_all bug

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.

   Bio::DB::WebDBSeqI methods
       Overriding WebDBSeqI method to help newbies to retrieve sequences.  EMBL database is all
       too often passed RefSeq accessions. This redirects those calls. See Bio::DB::RefSeq.

   get_Stream_by_acc
         Title   : get_Stream_by_acc
         Usage   : $seq = $db->get_Seq_by_acc([$acc1, $acc2]);
         Function: Gets a series of Seq objects by accession numbers
         Returns : a Bio::SeqIO stream object
         Args    : $ref : a reference to an array of accession numbers for
                          the desired sequence entries
         Note    : For GenBank, this just calls the same code for get_Stream_by_id()

   _check_id
         Title   : _check_id
         Usage   :
         Function:
         Returns : A Bio::DB::RefSeq reference or throws
         Args    : $id(s), $string