Provided by: libbio-perl-perl_1.7.8-1_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

perl v5.32.1                                       2021-08-15                        Bio::SeqIO::embldriver(3pm)