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.\" ========================================================================
.\"
.IX Title "Bio::SeqIO::chaos 3pm"
.TH Bio::SeqIO::chaos 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
Bio::SeqIO::chaos \- chaos sequence input/output stream
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&    #In general you will not want to use this module directly;
\&    #use the chaosxml format via SeqIO
\&
\&    $outstream = Bio::SeqIO\->new(\-file => $filename,
\&                                 \-format => \*(Aqchaosxml\*(Aq);
\&
\&    while ( my $seq = $instream\->next_seq() ) {
\&       $outstream\->write_seq($seq);
\&    }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is the guts of Bio::SeqIO::chaosxml \- please refer to the
documentation for this module
.PP
\&\fB\s-1CURRENTLY WRITE ONLY\s0\fR
.PP
ChaosXML is an \s-1XML\s0 mapping of the chado relational database; for more
information, see http://www.fruitfly.org/chaos\-xml
.PP
chaos can be represented in various syntaxes \- \s-1XML,\s0 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.
.SS "\s-1USING STAG OBJECTS\s0"
.IX Subsection "USING STAG OBJECTS"
\&\fBnon-standard bioperl stuff you don't necessarily need to know follows\fR
.PP
This module (in write mode) is an \fBevent producer\fR \- it generates \s-1XML\s0
events via the Data::Stag module. If you only care about the final
end-product xml, use Bio::SeqIO::chaosxml
.PP
You can treat the resulting chaos-xml stream as stag \s-1XML\s0 objects;
.PP
.Vb 1
\&    $outstream = Bio::SeqIO\->new(\-file => $filename, \-format => \*(Aqchaos\*(Aq);
\&
\&    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(\*(Aqfeature\*(Aq,
\&                    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]\en",
\&        $feature\->sget_name,
\&        $featureloc\->sget_nbeg,
\&        $featureloc\->sget_end,
\&        $featureloc\->sget_srcfeature_id;
\&    }
.Ve
.SH "MODULES REQUIRED"
.IX Header "MODULES REQUIRED"
Data::Stag
.PP
Downloadable from \s-1CPAN\s0; see also http://stag.sourceforge.net
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Chris Mungall"
.IX Header "AUTHOR - Chris Mungall"
Email cjm@fruitfly.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
.SS "context_namespace"
.IX Subsection "context_namespace"
.Vb 6
\& 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)
.Ve
.PP
IDs will be preceded with the context namespace
.SS "next_seq"
.IX Subsection "next_seq"
.Vb 5
\& Title   : next_seq
\& Usage   : $seq = $stream\->next_seq()
\& Function: returns the next sequence in the stream
\& Returns : Bio::Seq object
\& Args    :
.Ve
.SS "write_seq"
.IX Subsection "write_seq"
.Vb 5
\& 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
.Ve