Bio OntologyIO
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Summary
Bio::OntologyIO - Parser factory for Ontology formats
Package variables
Privates (from "my" definitions)
%format_driver_map = ( "go" => "goflat", "so" => "soflat", "interpro" => "InterProParser", "interprosax" => "Handlers::InterPro_BioSQL_Handler", "evoc" => "simplehierarchy", "obo" => "obo" )
Inherit
Bio::Root::IO Bio::Root::Root
Synopsis
    use Bio::OntologyIO;
my $parser = Bio::OntologyIO->new(-format => "go", -file=> $file); while(my $ont = $parser->next_ontology()) { print "read ontology ",$ont->name()," with ", scalar($ont->get_root_terms)," root terms, and ", scalar($ont->get_leaf_terms)," leaf terms\n"; }
Description
This is the parser factory for different ontology sources and
formats. Conceptually, it is very similar to Bio::SeqIO, but the
difference is that the chunk of data returned as an object is an
entire ontology.
Methods
newDescriptionCode
_initialize
No description
Code
next_ontologyDescriptionCode
term_factoryDescriptionCode
_load_format_moduleDescriptionCode
DESTROY
No description
Code
_map_format
No description
Code
unescape
No description
Code
Methods description
newcode    nextTop
 Title   : new
Usage : my $parser = Bio::OntologyIO->new(-format => 'go', @args);
Function: Returns a stream of ontologies opened on the specified input
for the specified format.
Returns : An ontology parser (an instance of Bio::OntologyIO) initialized
for the specified format.
Args : Named parameters. Common parameters are
-format - the format of the input; the following are presently supported: goflat: DAG-Edit Gene Ontology flat files go : synonymous to goflat soflat: DAG-Edit Sequence Ontology flat files so : synonymous to soflat simplehierarchy: text format with one term per line and indentation giving the hierarchy evoc : synonymous to simplehierarchy interpro: InterPro XML interprosax: InterPro XML - this is actually not a Bio::OntologyIO compliant parser; instead it persists terms as they are encountered. Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler
obo : OBO format style from Gene Ontology Consortium
-file - the file holding the data
-fh - the stream providing the data (-file and -fh are
mutually exclusive)
-ontology_name - the name of the ontology
-engine - the Bio::Ontology::OntologyEngineI object
to be reused (will be created otherwise); note
that every Bio::Ontology::OntologyI will
qualify as well since that one inherits from the
former.
-term_factory - the ontology term factory to use. Provide a
value only if you know what you are doing.
DAG-Edit flat file parsers will usually also accept the following parameters. -defs_file - the name of the file holding the term definitions -files - an array ref holding the file names (for GO, there will usually be 3 files: component.ontology, function.ontology, process.ontology) Other parameters are specific to the parsers.
next_ontologycodeprevnextTop
 Title   : next_ontology
Usage : $ont = $stream->next_ontology()
Function: Reads the next ontology object from the stream and returns it.
Returns : a Bio::Ontology::OntologyI compliant object, or undef at the
end of the stream
Args : none
term_factorycodeprevnextTop
 Title   : term_factory
Usage : $obj->term_factory($newval)
Function: Get/set the ontology term factory to use.
As a user of this module it is not necessary to call this method as there will be default. In order to change the default, the easiest way is to instantiate Bio::Ontology::TermFactory with the proper -type
argument. Most if not all parsers will actually use this
very implementation, so even easier than the aforementioned
way is to simply call
$ontio->term_factory->type("Bio::Ontology::MyTerm").
Example : Returns : value of term_factory (a Bio::Factory::ObjectFactoryI object) Args : on set, new value (a Bio::Factory::ObjectFactoryI object, optional)
_load_format_modulecodeprevnextTop
 Title   : _load_format_module
Usage : *INTERNAL OntologyIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
Methods code
newdescriptionprevnextTop
sub new {
    my ($caller,@args) = @_;
    my $class = ref($caller) || $caller;
    # or do we want to call SUPER on an object if $caller is an
# object?
if( $class =~ /Bio::OntologyIO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
my $format = $class->_map_format($param{'-format'}); # normalize capitalization
return unless( $class->_load_format_module($format) ); return "Bio::OntologyIO::$format"->new(@args); }
}
_initializedescriptionprevnextTop
sub _initialize {
    my($self, @args) = @_;

    # initialize factories etc
my ($eng,$fact,$ontname) = $self->_rearrange([qw(TERM_FACTORY) ], @args); # term object factory
$self->term_factory($fact) if $fact; # initialize the Bio::Root::IO part
$self->_initialize_io(@args);
}
next_ontologydescriptionprevnextTop
sub next_ontology {
    shift->throw_not_implemented();
}
term_factorydescriptionprevnextTop
sub term_factory {
    my $self = shift;

    return $self->{'term_factory'} = shift if @_;
    return $self->{'term_factory'};
}
_load_format_moduledescriptionprevnextTop
sub _load_format_module {
    my ($self, $format) = @_;
    my $module = "Bio::OntologyIO::" . $format;
    my $ok;

    eval {
        $ok = $self->_load_module($module);
    };
    if ( $@ ) {
        print STDERR <<END;
$self: $format cannot be found
Exception $@
For more information about the OntologyIO system please see the docs.
This includes ways of checking for formats at compile time, not run time
END
} return $ok;
}
DESTROYdescriptionprevnextTop
sub DESTROY {
    my $self = shift;

    $self->close();
}
_map_formatdescriptionprevnextTop
sub _map_format {
    my $self = shift;
    my $format = shift;
    my $mod;

    if($format) {
        $mod = $format_driver_map{lc($format)};
        $mod = lc($format) unless $mod;
    } else {
        $self->throw("unable to guess ontology format, specify -format");
    }
    return $mod;
}
unescapedescriptionprevnextTop
sub unescape {
  my( $self, $ref ) = @_;
  $ref =~ s/&lt\\;/\</g;
  $ref =~ s/&gt\\;/\>/g;
  $ref =~ s/&pct\\;/\%/g;
  $ref =~ s/\\n/\n/g;
  $ref =~ s/\\t/\t/g;
  return $ref;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar LappTop
Email hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
formatTop
 Title   : format
Usage : $format = $parser->format()
Function: Get the ontology format
Returns : ontology format
Args : none
Private MethodsTop
  Some of these are actually 'protected' in OO speak, which means you
may or will want to utilize them in a derived ontology parser, but
you should not call them from outside.