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

NAME

       Bio::SeqIO::embldriver - EMBL sequence input/output stream

SYNOPSIS

       It is probably best not to use this object directly, but rather go through the SeqIO
       handler system. Go:

           $stream = Bio::SeqIO->new(-file => $filename, -format => 'embldriver');

           while ( (my $seq = $stream->next_seq()) ) {
               # do something with $seq
           }

DESCRIPTION

       This object can transform Bio::Seq objects to and from EMBL flat file databases.

       There is a lot of flexibility here about how to dump things which should be documented
       more fully.

       There should be a common object that this and Genbank share (probably with Swissprot). Too
       much of the magic is identical.

   Optional functions
       _show_dna()
          (output only) shows the dna or not

       _post_sort()
          (output only) provides a sorting func which is applied to the FTHelpers before printing

       _id_generation_func()
          This is function which is called as

             print "ID   ", $func($annseq), "\n";

          To generate the ID line. If it is not there, it generates a sensible ID line using a
          number of tools.

          If you want to output annotations in EMBL format they need to be stored in a
          Bio::Annotation::Collection object which is accessible through the Bio::SeqI interface
          method annotation().

          The following are the names of the keys which are polled from a
          Bio::Annotation::Collection object.

           reference  - Should contain Bio::Annotation::Reference objects
           comment    - Should contain Bio::Annotation::Comment objects
           dblink     - Should contain Bio::Annotation::DBLink objects

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 - Ewan Birney

       Email birney@ebi.ac.uk

APPENDIX

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

   next_seq
        Title   : next_seq
        Usage   : $seq = $stream->next_seq()
        Function: returns the next sequence in the stream
        Returns : Bio::Seq object
        Args    :

   write_seq
        Title   : write_seq
        Usage   : $stream->write_seq($seq)
        Function: writes the $seq object (must be seq) to the stream
        Returns : 1 for success and 0 for error
        Args    : array of 1 to n Bio::SeqI objects

   seqhandler
        Title   : seqhandler
        Usage   : $stream->seqhandler($handler)
        Function: Get/Set the Bio::Seq::HandlerBaseI object
        Returns : Bio::Seq::HandlerBaseI
        Args    : Bio::Seq::HandlerBaseI