Bio::SeqIO::game::gameWriter -- a class for writing game-XML
# insert sample code here
# Description goes here
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/MailList.shtml - About the mailing lists
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 email or the web:
bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/
Email smckay@bcgsc.bc.ca
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
Title : _rearrange Usage : $self->_rearrange($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
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
Title : _write_gene Usage : $self->_write_gene($feature) Function: internal method for rendering gene containment hierarchies into an 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
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' 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 confused by alternative splice variants.
Title : _feature_set_tags Usage : $self->_feature_set_tags($feature) Function: an internal method to handle tag/value attributes for a feature set element Returns : nothing Args : a Bio::SeqFeatureI-compliant object
Title : _property Usage : $self->_property($tag => $value); Function: an internal method to write property XML elements Returns : nothing Args : a tag/value pair
Title : _tags Usage : $self->_tags($feat) Function: an internal method to intercept GO terms and db_xrefs and handle generic tag/value pairs for a gene Returns : nothing Args : a Bio::SeqFeatureI-compliant object
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
Title : _xref Usage : $self->_xref($value) Function: an internal method to write db_xref elements Returns : nothing Args : a list of strings
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
Title : _seq_relationship Usage : $self->_seq_relationship($type, $loc) Function: an internal method to handle feature_span sequence relationships Returns : nothing Args : feature type and a Bio::LocationI-compliant object
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
Title : _span Usage : $self->_span($loc) Function: an internal method to write the 'span' element Returns : nothing Args : a Bio::LocationI-compliant object
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
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
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.