soflat - a parser for the Sequence Ontology flat-file format
use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO my $parser = Bio::OntologyIO->new ( -format => "so", # or soflat -defs_file => "/home/czmasek/SO/SO.defs", -file => "/home/czmasek/SO/sofa.ontology" ); my $sofa_ontology = $parser->next_ontology(); my $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" ); my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
Needs Graph.pm from CPAN.
This is essentially a very thin derivation of the dagflat base-parser.
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report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:
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Christian M. Zmasek
Email: czmasek@gnf.org or cmzmasek@yahoo.com
WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/
Address:
Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121
Hilmar Lapp, hlapp at gmx.net
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : $parser = Bio::OntologyIO->new( -format => "go", -defs_file => "/path/to/GO.defs", -files => ["/path/to/component.ontology", "/path/to/function.ontology", "/path/to/process.ontology"] ); Function: Creates a new soflat parser. Returns : A new soflat parser object, implementing L<Bio::OntologyIO>. Args : -defs_file => the name of the file holding the term definitions -files => a single ontology flat file holding the term relationships, or an array ref holding the file names -file => if there is only a single flat file, it may also be specified via the -file parameter -ontology_name => the name of the ontology, defaults to "Gene Ontology" -engine => the L<Bio::Ontology::OntologyEngineI> object to be reused (will be created otherwise); note that every L<Bio::Ontology::OntologyI> will qualify as well since that one inherits from the former.
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.