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Summary

Bio::SeqIO::chaosxml - chaosxml sequence input/output stream

Package variables

Included modules

Inherit

Bio::SeqIO::chaos

Synopsis

    #In general you will not want to use this module directly;
    #use the chaosxml format via SeqIO

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

    while ( my $seq = $instream->next_seq() ) {
       $outstream->write_seq($seq);
    }

Description

This object can transform Bio::Seq objects to and from chaos files.
CURRENTLY WRITE ONLY
ChaosXML is an XML mapping of the chado relational database; for more
information, see http://www.fruitfly.org/chaos-xml
Chaos can have other syntaxes than XML (eg S-Expressions, Indented text)
See Bio::SeqIO::chaos for a full description

Methods

Methods description

None available.

Methods code

sub default_handler_class {

    return Data::Stag->getformathandler('xml');
}

1;

}

General documentation

!!!!!!!!!!!CHADO AND CHAOS USE INTERBASE COORDINATES!!!!!!!!!!!!!!!!

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

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.

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/

Email cjm@fruitfly.org

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