NAME

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

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 is the guts of Bio::SeqIO::chaosxml - please refer to the documentation for this
       module

       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 be represented in various syntaxes - XML, S-Expressions or indented text. You
       should see the relevant SeqIO file. You will probably want to use Bio::SeqIO::chaosxml,
       which is a wrapper to this module.

   USING STAG OBJECTS
       non-standard bioperl stuff you don't necessarily need to know follows

       This module (in write mode) is an event producer - it generates XML events via the
       Data::Stag module. If you only care about the final end-product xml, use
       Bio::SeqIO::chaosxml

       You can treat the resulting chaos-xml stream as stag XML objects;

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

           while ( my $seq = $instream->next_seq() ) {
              $outstream->write_seq($seq);
           }
           my $chaos = $outstream->handler->stag;
           # stag provides get/set methods for xml elements
           # (these are chaos objects, not bioperl objects)
           my @features = $chaos->get_feature;
           my @feature_relationships = $chaos->get_feature_relationships;
           # stag objects can be queried with functional-programming
           # style queries
           my @features_in_range =
             $chaos->where('feature',
                           sub {
                                my $featureloc = shift->get_featureloc;
                                $featureloc->strand == 1 &&
                                $featureloc->nbeg > 10000 &&
                                $featureloc->nend < 20000;
                           });
           foreach my $feature (@features_in_range) {
             my $featureloc = $feature->get_featureloc;
             printf "%s [%d->%d on %s]\n",
               $feature->sget_name,
               $featureloc->sget_nbeg,
               $featureloc->sget_end,
               $featureloc->sget_srcfeature_id;
           }

MODULES REQUIRED

       Data::Stag

       Downloadable from CPAN; see also http://stag.sourceforge.net

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 - Chris Mungall

       Email cjm@fruitfly.org

APPENDIX

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

   context_namespace
        Title   : context_namespace
        Usage   : $obj->context_namespace($newval)
        Function:
        Example :
        Returns : value of context_namespace (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

       IDs will be preceded with the context namespace

   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    : Bio::Seq