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.