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Bio::SeqIO::embldriver.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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 teh Bio::Seq::HandlerBaseI object
  Returns : Bio::Seq::HandlerBaseI 
  Args    : Bio::Seq::HandlerBaseI