Bio::OntologyIO::obo(3pm) User Contributed Perl Documentation Bio::OntologyIO::obo(3pm)
NAME
Bio::OntologyIO::obo - a parser for OBO flat-file format from Gene Ontology Consortium
SYNOPSIS
use Bio::OntologyIO;
# do not use directly -- use via Bio::OntologyIO
my $parser = Bio::OntologyIO->new
( -format => "obo",
-file => "gene_ontology.obo");
while(my $ont = $parser->next_ontology()) {
print "read ontology ",$ont->name()," with ",
scalar($ont->get_root_terms)," root terms, and ",
scalar($ont->get_all_terms)," total terms, and ",
scalar($ont->get_leaf_terms)," leaf terms
";
}
DESCRIPTION
Needs Graph.pm from CPAN.
FEEDBACK
Mailing Lists
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 lists Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
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 Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR
Sohel Merchant
Email: s-merchant@northwestern.edu
Address:
Northwestern University
Center for Genetic Medicine (CGM), dictyBase
Suite 1206,
676 St. Clair st
Chicago IL 60611
CONTRIBUTOR
Hilmar Lapp, hlapp at gmx.net
Chris Mungall, cjm at fruitfly.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : $parser = Bio::OntologyIO->new(
-format => "obo",
-file => "gene_ontology.obo");
Function: Creates a new dagflat parser.
Returns : A new dagflat parser object, implementing Bio::OntologyIO.
Args : -file => a single ontology flat file holding the
terms, descriptions and relationships
-ontology_name => the name of the ontology; if not specified the
parser will assign the name of the ontology as the
default-namespace header value from the OBO file.
-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.
See Bio::OntologyIO.
ontology_name
Title : ontology_name
Usage : $obj->ontology_name($newval)
Function: Get/set the name of the ontology parsed by this module.
Example :
Returns : value of ontology_name (a scalar)
Args : on set, new value (a scalar or undef, optional)
parse
Title : parse()
Usage : $parser->parse();
Function: Parses the files set with "new" or with methods
defs_file and _flat_files.
Normally you should not need to call this method as it will
be called automatically upon the first call to
next_ontology().
Returns : Bio::Ontology::OntologyEngineI
Args :
next_ontology
Title : next_ontology
Usage :
Function: Get the next available ontology from the parser. This is the
method prescribed by Bio::OntologyIO.
Example :
Returns : An object implementing Bio::Ontology::OntologyI, and nothing if
there is no more ontology in the input.
Args :
close
Title : close
Usage :
Function: Closes this ontology stream and associated file handles.
Clients should call this method especially when they write
ontologies.
We need to override this here in order to close the file
handle for the term definitions file.
Example :
Returns : none
Args : none
perl v5.14.2 2012-03-02 Bio::OntologyIO::obo(3pm)