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GO::IO::OBDXML.3pm

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);

cgi_header

     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'.