NAME
Bio::SeqIO::game::gameWriter -- a class for writing game-XML
SYNOPSIS
my $in = Bio::SeqIO->new( -format => 'genbank',
-file => 'myfile.gbk' );
my $out = Bio::SeqIO->new( -format => 'game',
-file => 'myfile.xml' );
my $seq = $in->next_seq;
$out->write_seq($seq);
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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
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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:
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
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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
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_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
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_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
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_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
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_check_cds
Title : _check_cds
Usage : $self->_check_cds($cds, $name)
Function: internal method to check if the CDS associated with an mRNA is
the correct alternative splice variant
Returns : a Bio::SeqFeature::Generic CDS object
Args : the CDS object plus the transcript\'s 'standard_name'
Note : this method only works if alternatively spliced transcripts are bound
together by a 'standard_name' or 'mRNA' qualifier. If none is present,
we will hope that the exons were derived from a segmented RNA or a CDS
with no associated mRNA feature. Neither of these two cases would be
confounded by alternative splice variants.
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_comp_analysis
Usage:
Desc :
Ret :
Args :
Side Effects:
Example:
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_comp_result
Usage:
Desc : recursively render a feature and its subfeatures as
<result_set> and <result_span> elements
Ret : nothing meaningful
Args : a feature
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_comp_result_span
Usage: _comp_result_span('foo12',$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:
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Usage:
Desc :
Ret :
Args :
Side Effects:
Example:
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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.
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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.
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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.
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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.
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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.
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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.
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_property
Title : _property
Usage : $self->_property($tag => $value);
Function: an internal method to write property XML elements
Returns : nothing
Args : a tag/value pair
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_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
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_xref
Title : _xref
Usage : $self->_xref($value)
Function: an internal method to write db_xref elements
Returns : nothing
Args : a list of strings
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_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
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_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
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_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 };
$self->_element($name, $content, $attributes);
Returns : nothing
Args : the element name and content plus a ref to an attribute hash
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_span
Title : _span
Usage : $self->_span($loc)
Function: an internal method to write the 'span' element
Returns : nothing
Args : a Bio::LocationI-compliant object
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_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
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_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
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