NAME¶
GO::IO::OBDXML - dump GO terms as xml
SYNOPSIS¶
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();
DESCRIPTION¶
Utility class to dump GO terms as OBD XML. Currently you just call
start_ducument, then draw_term for each term, then end_document.
new¶
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.
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.
start_graph¶
Usage - $xml_out->start_graph;
Returns - None
Args - None
start_graph opens a new graph segment.
end_document¶
Usage - $xml_out->end_document;
Call this when done.
end_graph¶
Usage - $xml_out->end_graph;
Call this when done a graph segment.
draw_node_graph¶
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'.
draw_term¶
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'.