| GO::IO::OBDXML(3pm) | User Contributed Perl Documentation | GO::IO::OBDXML(3pm) |
GO::IO::OBDXML - dump GO terms as xml
my $apph = GO::AppHandle->connect(-d=>$go, -dbhost=>$dbhost);
my $term = $apph->get_term({acc=>00003677});
#### ">-" is STDOUT
my $out = new FileHandle(">-");
my $xml_out = GO::IO::OBDXML->new(-output=>$out);
$xml_out->start_document();
$xml_out->draw_term($term);
$xml_out->end_document();
OR:
my $apph = GO::AppHandle->connect(-d=>$go, -dbhost=>$dbhost);
my $term = $apph->get_node_graph(-acc=>00003677, -depth=>2);
my $out = new FileHandle(">-");
my $xml_out = GO::IO::OBDXML(-output=>$out);
$xml_out->start_document();
$xml_out->draw_graph($term, 3677);
$xml_out->end_document();
Utility class to dump GO terms as OBD XML. Currently you just call start_ducument, then draw_term for each term, then end_document.
Usage - my $xml_out = GO::IO::OBDXML->new(-output=>$out);
Returns - None
Args - Output FileHandle
Initializes the writer object. To write to standard out, do:
my $out = new FileHandle(">-"); my $xml_out = new GO::IO::OBDXML(-output=>$out);
Usage - $xml_out->cgi_header;
Returns - None
Args - None
cgi_header prints the "Content-type: text/xml" statement. If creating a CGI script, you should call this before start_document.
Usage - $xml_out->start_document;
Returns - None
Args - None
start_document takes care of the fiddly bits like xml declarations, namespaces, etc. It draws the initial tags and leaves the document ready to add go:term nodes.
Usage - $xml_out->start_graph;
Returns - None
Args - None
start_graph opens a new graph segment.
Usage - $xml_out->end_document;
Call this when done.
Usage - $xml_out->end_graph;
Call this when done a graph segment.
Usage - $xml_out->draw_node_graph(-graph=>$graph);
Returns - None
Args -graph=>$graph,
-show_associations=>'yes' or 'no', # optional, default 'yes'.
-show_terms=>'yes' or 'no', # optional, default 'yes'.
-show_xrefs=>'yes' or 'no', # optional, default 'yes'.
-show_evidence=>'yes' or 'no', # optional, default 'yes'.
Usage - $xml_out->draw_term();
Returns - None
Args -term=>$term,
-graph=>$graph, # optional
-show_associations=>'yes' or 'no', # optional, default 'yes'.
-show_terms=>'yes' or 'no', # optional, default 'yes'.
-show_xrefs=>'yes' or 'no', # optional, default 'yes'.
-show_evidence=>'yes' or 'no', # optional, default 'yes'.
| 2021-01-09 | perl v5.32.0 |