Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::SeqIO::game::gameWriter -- a class for writing game-XML

SYNOPSIS

         use Bio::SeqIO;

         my $in  = Bio::SeqIO->new( -format => 'genbank',
                                    -file => 'myfile.gbk' );
         my $out = Bio::SeqIO->new( -format => 'game',
                                    -file => 'myfile.xml' );

         # get a sequence object
         my $seq = $in->next_seq;

         #write it in GAME format
         $out->write_seq($seq);

DESCRIPTION

       Bio::SeqIO::game::gameWriter writes GAME-XML (v. 1.2) that is readable by Apollo.  It is
       best not used directly.  It is accessed via Bio::SeqIO.

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 of the bugs and their
       resolution. Bug reports can be submitted via the web:

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

AUTHOR - Sheldon McKay

       Email mckays@cshl.edu

APPENDIX

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

   new
        Title   : new
        Usage   : my $writer = Bio::SeqIO::game::gameWriter->new($seq);
        Function: constructor method for gameWriter
        Returns : a game writer object
        Args    : a Bio::SeqI implementing object
                  optionally, an argument to set map_position to on.
                  ( map => 1 ).  This will create a map_position elemant
                  that will cause the feature coordinates to be remapped to
                  a parent seqeunce.  A sequence name in the format seq:xxx-xxx
                  is expected to determine the offset for the map_position.
                  The default behavior is to have features mapped relative to
                  the sequence contained in the GAME-XML file

   write_to_game
        Title   : write_to_game
        Usage   : $writer->write_to_game
        Function: writes the sequence object to game-XML
        Returns : xml as a multiline string
        Args    : none

   _rearrange_hierarchies
        Title   : _rearrange_hierarchies
        Usage   : $self->_rearrange_hierarchies($seq)
        Function: internal method to rearrange gene containment hierarchies
                  so that snRNA or transposon features contain their genes
                  rather than the other way around
        Returns : nothing
        Args    : a Bio::RichSeq object
        Note    : Not currently used, may be removed

   _write_feature
        Title   : _write_feature
        Usage   : $seld->_write_feature($feat, 1)
        Function: internal method for writing generic features as <annotation> elements
        Returns : nothing
        Args    : a Bio::SeqFeature::Generic object and an optional flag to write a
                  bare feature set with no annotation wrapper

   _write_gene
        Title   : _write_gene
        Usage   : $self->_write_gene($feature)
        Function: internal method for rendering gene containment hierarchies into
                  a nested <annotation> element
        Returns : nothing
        Args    : a nested Bio::SeqFeature::Generic gene feature
        Note    : A nested gene hierarchy (gene->mRNA->CDS->exon) is expected.  If other gene
                  subfeatures occur as level one subfeatures (same level as mRNA subfeats)
                  an attempt will be made to link them to transcripts via the 'standard_name'
                  qualifier

   _check_cds
        Title   : _check_cds
        Usage   : $self->_check_cds($cds, $name)
        Function: internal method to check if the CDS associated with an mRNA is
                  the correct alternative splice variant
        Returns : a Bio::SeqFeature::Generic CDS object
        Args    : the CDS object plus the transcript\'s 'standard_name'
        Note    : this method only works if alternatively spliced transcripts are bound
                  together by a 'standard_name' or 'mRNA' qualifier.  If none is present,
                  we will hope that the exons were derived from a segmented RNA or a CDS
                  with no associated mRNA feature.  Neither of these two cases would be
                  confounded by alternative splice variants.

   _comp_analysis
         Usage:
         Desc :
         Ret  :
         Args :
         Side Effects:
         Example:

   _comp_result
         Usage:
         Desc : recursively render a feature and its subfeatures as
                <result_set> and <result_span> elements
         Ret  : nothing meaningful
         Args : a feature

   _comp_result_span
         Usage: _comp_result_span('foo12',$feature);
         Desc : write GAME XML for a Bio::SeqFeature::Computation feature
                that has no subfeatures
         Ret  : nothing meaningful
         Args : name for this span (some kind of identifier),
                SeqFeature object to put into this span
         Side Effects:
         Example:

   _render_tags
         Usage:
         Desc :
         Ret  :
         Args :
         Side Effects:
         Example:

   _render_output_tags
         Usage:
         Desc : print out <output> elements, with contents
                taken from the SeqFeature::Computation's 'output' tag
         Ret  : array of tag names this did not render
         Args : feature object, list of tag names to maybe render

         In game xml, only <result_span> and <result_set> elements can
         have <output> elements.

   _render_tags_as_properties
         Usage:
         Desc :
         Ret  : empty array
         Args : feature object, array of tag names
         Side Effects:
         Example:

         In game xml, <annotation>, <computational_analysis>,
         and <feature_set> elements can have properties.

   _render_comment_tags
         Usage:
         Desc :
         Ret  : names of tags that were not comment tags
         Args : feature object, tag names available for us to render
         Side Effects: writes XML
         Example:

         In game xml, <annotation> and <feature_set> elements can
         have comments.

   _render_date_tags
         Usage:
         Desc :
         Ret  : names of tags that were not date tags
         Args : feature, list of tag names available for us to render
         Side Effects: writes XML for <date> elements
         Example:

         In game xml, <annotation>, <computational_analysis>,
         <transaction>, <comment>, and <feature_set> elements
         can have <date>s.

   _render_dbxref_tags
         Desc : look for xref tags and render them if they are there
         Ret  : tag names that we didn't render
         Args : feature object, list of tag names to render
         Side Effects: writes a <dbxref> element if a tag with name
                       matching /xref$/i is present

         In game xml, <annotation> and <seq> elements can have dbxrefs.

   _render_target_tags
         Usage:
         Desc : process any 'Target' tags that would indicate a sequence alignment subject
         Ret  : array of tag names that we didn't render
         Args : feature object
         Side Effects: writes a <seq_relationship> of type 'subject' if it finds
                       any properly formed tags named 'Target'
         Example:

         In game xml, <result_span>, <feature_span>, and <result_set> can have
         <seq_relationship>s.  <result_set> can only have one, a 'query' relation.

   _property
        Title   : _property
        Usage   : $self->_property($tag => $value);
        Function: an internal method to write property XML elements
        Returns : nothing
        Args    : a tag/value pair

   _unflatten_attribute
        Title   : _unflatten_attribute
        Usage   : $self->_unflatten_attribute($name, $value)
        Function: an internal method to unflatten and write comment or evidence elements
        Returns : nothing
        Args    : a list of strings

   _xref
        Title   : _xref
        Usage   : $self->_xref($value)
        Function: an internal method to write db_xref elements
        Returns : nothing
        Args    : a list of strings

   _feature_span
        Title   : _feature_span
        Usage   : $self->_feature_span($name, $type, $loc)
        Function: an internal method to write a feature_span element
                 (the actual feature with coordinates)
        Returns : nothing
        Args    : a feature name and Bio::SeqFeatureI-compliant object

   _seq_relationship
        Title   : _seq_relationship
        Usage   : $self->_seq_relationship($type, $loc)
        Function: an internal method to handle feature_span sequence relationships
        Returns : nothing
        Args    : feature type, a Bio::LocationI-compliant object,
                  (optional) sequence name (defaults to the query seq)
                  and (optional) alignment string

   _element
        Title   : _element
        Usage   : $self->_element($name, $chars, $atts)
        Function: an internal method to generate 'generic' XML elements
        Example :
        my $name = 'foo';
        my $content = 'bar';
        my $attributes = { baz => 1 };
        # print the element
        $self->_element($name, $content, $attributes);
        Returns : nothing
        Args    : the element name and content plus a ref to an attribute hash

   _span
        Title   : _span
        Usage   : $self->_span($loc)
        Function: an internal method to write the 'span' element
        Returns : nothing
        Args    : a Bio::LocationI-compliant object

   _seq
        Title   : _seq
        Usage   : $self->_seq($seq, $dna)
        Function: an internal method to print the 'sequence' element
        Returns : nothing
        Args    : and Bio::SeqI-compliant object and a reference to an attribute  hash

   _find_name
        Title   : _find_name
        Usage   : my $name = $self->_find_name($feature)
        Function: an internal method to look for a gene name
        Returns : a string
        Args    : a Bio::SeqFeatureI-compliant object