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
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AUTHOR - Sheldon McKay
Email [email protected]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