bio::seqio::embldriver(3pm) [debian man page]

Bio::SeqIO::embldriver(3pm)				User Contributed Perl Documentation			       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), "
";

	  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://redmine.open-bio.org/projects/bioperl/

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

perl v5.14.2							    2012-03-02					       Bio::SeqIO::embldriver(3pm)