| GO::IO::ObanOwl(3pm) | User Contributed Perl Documentation | GO::IO::ObanOwl(3pm) |
GO::IO::ObanOwl - 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 $xml_out = GO::IO::XML->new(-output=>$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 $xml_out = GO::IO::XML(-output=>$out);
$xml_out->start_document();
$xml_out->draw_node_graph($term, 3677);
$xml_out->end_document();
Utility class to dump GO terms as xml. Currently you just call start_ducument, then draw_term for each term, then end_document.
If there's a need I'll add draw_node_graph, draw_node_list, etc.
Usage - my $xml_out = GO::IO::XML->new(-output=>$out);
Returns - None
Args - Output FileHandle
Initializes the writer object. To write to standard out, do:
my $out = new FileHandle(">-"); my $xml_out = new GO::IO::XML(-output=>$out);
Usage - $xml_out->xml_header;
Returns - None
Args - None
start_document prints the "Content-type: text/xml" statement. If creating a cgi script, you should call this before start_document.
Usage - $xml_out->start_document(-timestamp=>$time);
Returns - None
Args - optional: timestamp string, pre-formatted
start_ducument 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->end_document();
Call this when done.
Usage - $xml_out->draw_node_graph(-graph=>$graph);
Returns - None
Args -graph=>$node_graph,
-focus=>$acc, ## optional
-show_associations=>"yes" or "no" ## optional
Usage - $xml_out->draw_term();
Returns - None
Args -term=>$term,
-graph=>$graph,
-is_focus=>"yes" or "no", ## optional
-show_associations=>"yes" or "no", ## optional
-show_terms=>"yes" or "no", ## optional, just draws associations
sub characters
This is simply a wrapper to XML::Writer->characters which strips out any non-ascii characters.
sub dataElement
This is simply a wrapper to XML::Writer->dataElement which strips out any non-ascii characters.
| 2021-01-09 | perl v5.32.0 |