Bio::GMOD::GenericGenePage::Chado -
my $page = Bio::GMOD::GenericGenePage->new( $gene_identifier ); my $xml = $page->render_xml(); my $html = $page->render_html();
#and then you can print the xml or html in your page
none
none yet
Usage: my $genepage = MyGenePage->new( -id => $gene_identifier ); my $genepage = Bio::GMOD::GenericGenePage::Chado->new( feature_id => $id); Desc : create a new gene page object; overridden from abstract class. Args : -id => $feature_id Ret : a new gene page object Side Effects: Sets feature_id attribute, creates db connection
Usage: my $dbh = $obj->dbh(); Desc: Sets/Gets Chado database handle Args: DBI database handle to set, none to get
Usage: my $feature_id = $obj->feature_id(); Desc: Sets/Gets feature_id Args: Integer to set, none to get
Methods below were overridden from the GenericGenePage abstract implementation.
Usage: my $name = $genepage->name(); Desc : get the string name of this gene Args : none Ret : string gene name, e.g. 'Pax6' Side Effects: none
Usage: my @accessions = $genepage->accessions(); Desc : get a list of local accession values Args : none Ret : a list of local accessions Side Effects: none
Note that these are the accession the is used by the MOD providing the information.
Usage: my $data_provider = $genepage->data_provider(); Desc : The name of the data providing authority (ie, WormBase, SGD, etc) Args : none Ret : string, name of the data provider Side Effects: none
Usage: my @syn = $genepage->synonyms(); Desc : get a list of synonyms for this gene Args : none Ret : list of strings, with the canonical/official/approved gene name first. e.g. ( '1500038E17Rik', 'AEY11', 'Dey', "Dickie's small eye", 'Gsfaey11', 'Pax-6', ) Side Effects: none
Usage: my @locs = $genepage->map_locations() Desc : get a list of known map locations for this gene Args : none Ret : list of map locations, each a hashref as: { map_name => string map name, chromosome => string chromosome name, marker => (optional) associated marker name, position => numerical position on the map, units => map units, either 'cm', for centimorgans, or 'b', for bases } Side Effects: none
Usage: my @terms = $genepage->ontology_terms(); Desc : get a list of ontology terms Args : none Ret : hash-style list as: termname => human-readable description, Side Effects: none Example: my %terms = $genepage->ontology_terms() # and %terms is now ( GO:0016711 => 'F:flavonoid 3'-monooxygenase activity', ... )
Usage: my @dbxrefs = $genepage->dbxrefs(); Desc : get a list of database cross-references for info related to this gene Args : none Ret : list of strings, like type:id e.g. ('PFAM:00012') Side Effects: none
Usage: my @refs = $genepage->lit_refs(); Desc : get a list of literature references for this gene Args : none Ret : list of literature reference identifers, as type:id, like ('PMID:0023423',...) Side Effects: none
Usage: my $summary = $page->summary_text(); Desc : get a text string of plain-English summary text for this gene Args : none Ret : string of summary text Side Effects: none
Usage: my $species_info = $genepage->organism Desc : get a handful of species-related information Args : none Ret : hashref as: { ncbi_taxon_id => ncbi taxon id, (e.g. 3702), binomial => e.g. 'Arabidopsis thaliana', common => e.g. 'Mouse-ear cress', } Side Effects: none
Usage: my @comments = $genepage->comments(); Desc : get a list of comments with types Args : none Ret : a hash of comment=>type, where type is optional (empty string) Side Effects: none
Robert Buels
To install Bio::GMOD::GenericGenePage, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::GMOD::GenericGenePage
CPAN shell
perl -MCPAN -e shell install Bio::GMOD::GenericGenePage
For more information on module installation, please visit the detailed CPAN module installation guide.