/ 
FAST-1.03
River stage zero No dependents
/ FAST::Bio::SeqIO::embldriver

NAME

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

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

DESCRIPTION

This object can transform FAST::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 FAST::Bio::Annotation::Collection object which is accessible through the FAST::Bio::SeqI interface method annotation().

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

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

seqhandler

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