Bio::OntologyIO
InterProParser
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Summary
Bio::OntologyIO::InterProParser - Parser for InterPro xml files.
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# don't use this module directly - use Bio::OntologyIO with instead
my $ipp = Bio::OntologyIO->new( -format => 'interpro',
-file => 't/data/interpro.xml',
-ontology_engine => 'simple' );
Description
Use InterProParser to parse InterPro files in xml format. Typical
use is the interpro.xml file published by EBI. The xml records
should follow the format described in interpro.dtd, although the dtd
file is not needed, and the XML file will not be validated against it.
Methods
Methods description
Title : parse
Usage :
Function: Performs the actual parsing.
Example : $ipp->parse();
Returns :
Args : |
Title : next_ontology
Usage : $ipp->next_ontology()
Function: Parses the input file and returns the next InterPro ontology
available.
Usually there will be only one ontology returned from an
InterPro XML input.
Example : $ipp->next_ontology();
Returns : Returns the ontology as a Bio::Ontology::OntologyEngineI
compliant object.
Args :
See Bio::Ontology::OntologyEngineI. |
Title : _is_parsed
Usage : $obj->_is_parsed($newval)
Function:
Example :
Returns : value of _is_parsed (a scalar)
Args : on set, new value (a scalar or undef, optional) |
Title : secondary_accessions_map
Usage : $obj->secondary_accessions_map()
Function: This method is merely for convenience, and one should
normally use the InterProTerm secondary_ids method to
access the secondary accessions.
Example : $map = $interpro_parser->secondary_accessions_map;
Returns : Reference to a hash that maps InterPro identifier to an
array reference of secondary accessions following the
InterPro xml schema.
Args : Empty hash reference |
Methods code
sub _initialize
{ my $self = shift;
$self->SUPER::_initialize(@_);
my ($eng,$eng_type,$name) =
$self->_rearrange([qw(ENGINE
ONTOLOGY_ENGINE
ONTOLOGY_NAME)
], @_);
my $ip_h = Bio::OntologyIO::Handlers::InterProHandler->new(
-ontology_name => $name);
if(! $eng) {
$eng_type = 'simple' unless $eng_type;
if(lc($eng_type) eq 'simple') {
$eng = Bio::Ontology::SimpleOntologyEngine->new();
} else {
$self->throw("ontology engine type '$eng_type' ".
"not implemented yet");
}
}
if($eng->isa("Bio::Ontology::OntologyI")) {
$ip_h->ontology($eng);
$eng = $eng->engine() if $eng->can('engine');
}
$self->{_ontology_engine} = $eng;
$ip_h->ontology_engine($eng);
$self->{_parser} = XML::Parser::PerlSAX->new( Handler => $ip_h );
$self->{_interpro_handler} = $ip_h;
$self->term_factory(Bio::Ontology::TermFactory->new(
-type => "Bio::Ontology::InterProTerm"))
unless $self->term_factory();
$ip_h->term_factory($self->term_factory());} | sub parse
{ my $self = shift;
my $ret;
if ($self->file()) {
$ret = $self->{_parser}->parse( Source => {
SystemId => $self->file() } );
} elsif ($self->_fh()) {
$ret = $self->{_parser}->parse( Source => {
ByteStream => $self->_fh() } );
} else {
$ret = undef;
$self->throw("Only filenames and filehandles are understood here.\n");
}
$self->_is_parsed(1);
return $ret;} | sub next_ontology
{ my $self = shift;
$self->parse() unless $self->_is_parsed();
if(exists($self->{'_ontology_engine'})) {
my $ont = $self->{_interpro_handler}->ontology();
delete $self->{_ontology_engine};
return $ont;
}
return; } | sub _is_parsed
{ my $self = shift;
return $self->{'_is_parsed'} = shift if @_;
return $self->{'_is_parsed'};} | sub secondary_accessions_map
{ my ($self) = @_;
return $self->{_interpro_handler}->{secondary_accessions_map};
}
1;} | General documentation
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
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.
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 - Peter Dimitrov | Top |
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Title : new
Usage :
Function: Initializes objects needed for parsing.
Example : $ipp = Bio::OntologyIO::InterProParser->new(
-file => 't/data/interpro.xml',
-ontology_engine => 'simple' )
Returns : Object of class Bio::OntologyIO::InterProParser.
Args :
-file - file name
-ontology_engine - type of ontology engine. Should satisfy the
OntologyEngine interface requirements. Currently
the only option is 'simple'. In the future
Graph.pm based engine will be added to the
choices.