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GO::IO::go_assoc.3pm

NAME

   GO::IO::go_assoc - dump GO terms as OBD 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 $ga_out = GO::IO::go_assoc->new(-output=>$out);
     $ga_out->write_term($term);
 
 

OR:

     my $apph = GO::AppHandle->connect(-d=>$go, -dbhost=>$dbhost);
     my $graph = $apph->get_node_graph(-acc=>00003677, -depth=>2);
     my $out = new FileHandle(">-");
 
     my $ga_out = GO::IO::go_assoc->new(-output=>$out);
     $ga_out->write_graph($graph);
 
 

DESCRIPTION

Utility class to dump GO terms as OBD XML. Currently, you just call start_document, write_term for each term, then end_document.

new

     Usage   - my $ga_out = new GO::IO::go_assoc(-output=>$out);
     Returns - Output emitter.
     Args    - Output FileHandle
 
 

Initializes the writer object. To write to standard out, do:

my $out = new FileHandle(``>-''); my $ga_out = new GO::IO::go_assoc($out);

cgi_header

     Usage   - $ga_out->cgi_header;
     Returns - None
     Args    - None
 
 

cgi_header prints the ``Content-type: text/plain'' statement. If creating a CGI script, you should call this before further action.

write_graph

     Usage   - $ga_out->write_graph(-graph=>$graph);
     Returns - None
     Args    -graph=>$graph,
             -deep=>1 or 0,           # optional, default 0.
             -qualifier=>1 or 0,      # optional, default 1.
             -with=>1 or 0,           # optional, default 1.
             -object_name=>1 or 0,    # optional, default 1.
             -object_synonym=>1 or 0, # optional, default 1.
 
 

write_term_list

     Usage   - $ga_out->write_term_list();
     Returns - None
     Args    -term_listref=>$term_listref,
             -deep=>1 or 0,           # optional, default 0.
             -qualifier=>1 or 0,      # optional, default 1.
             -with=>1 or 0,           # optional, default 1.
             -object_name=>1 or 0,    # optional, default 1.
             -object_synonym=>1 or 0, # optional, default 1.
 
 

write_term

     Usage   - $ga_out->write_term();
     Returns - None
     Args    -term=>$term,
             -deep=>1 or 0,           # optional, default 0.
             -qualifier=>1 or 0,      # optional, default 1.
             -with=>1 or 0,           # optional, default 1.
             -object_name=>1 or 0,    # optional, default 1.
             -object_synonym=>1 or 0, # optional, default 1.