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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Chris Mungall

Email [email protected]

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