Reference

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'.

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