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bio::ontologyio::handlers::interpro_biosql_handler(3pm) [debian man page]

Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler(3pm) User Contributed Perl DocumentationBio::OntologyIO::Handlers::InterPro_BioSQL_Handler(3pm)

NAME
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler - parse an InterPro XML file and persist the resulting terms to a Biosql database SYNOPSIS
# see load_interpro.pl in bioperl-db/scripts/biosql/ DESCRIPTION
This module is for parsing an InterPro XML file and persist the resulting terms to a Biosql database as soon as the term is complete as signaled by the appropriate xml tag. This parser takes advantage of SAX, a stream-based XML parser technology, to keep the used memory as small as possible. The alternative parser for InterPro, module InterProHandler, builds up the entire ontology in memory, which given the size of the latest InterPro releases requires a huge amount of memory. This module takes the following non-standard arguments upon instantiation. -db the adaptor factory as returned by a call to Bio::DB::BioDB->new() -version the InterPro version (not available as property!) -term_factory the object factory to use for creating terms Note that there are two alternatives for how to persist the terms and relationships to the database. The default is using the adaptor factory passed as -db or set as a property to create persistent objects and store them in the database. The alternative is to specify a term persistence and a relationship persistence handler; if one or both have been set, the respective handler will be called with each term and relationship that is to be stored. See properties persist_term_handler and persist_relationship_handler. AUTHOR
Juguang Xiao, juguang@tll.org.sg Contributors Hilmar Lapp, hlapp at gmx.net APPENDIX The rest of the documentation details each of the object methods. Interal methods are usually preceded with a _ term_factory 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 L<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) db Title : db Usage : $obj->db($newval) Function: Sets or retrieves the database adaptor factory. The adaptor factory is a Bio::DB::DBAdaptorI compliant object and will be used to obtain the persistence adaptors necessary to serialize terms and relationships to the database. Usually, you will obtain such an object from a call to Bio::DB::BioDB. You *must* set this property before starting the parse. Note that this property is immutable once set, except that you may set it to undef. Therefore, be careful not to set to undef before setting the desired real value. Example : Returns : value of db (a Bio::DB::DBAdaptorI compliant object) Args : on set, new value (a Bio::DB::DBAdaptorI compliant object or undef, optional) persist_term_handler Title : persist_term_handler Usage : $obj->persist_term_handler($handler,@args) Function: Sets or retrieves the persistence handler for terms along with the constant set of arguments to be passed to the handler. If set, the first argument will be treated as a closure and be called for each term to persist to the database. The term will be passed as a named parameter (-term), followed by the other arguments passed to this setter. Note that this allows one to pass an arbitrary configuration to the handler. If not set, terms will be persisted along with their relationships using the respective persistence adaptor returned by the adaptor factory (see property db). Example : Returns : an array reference with the values passed on set, or an empty array if never set Args : On set, an array of values. The first value is the handler as a closure; all other values will be passed to the handler as constant argument. persist_relationship_handler Title : persist_relationship_handler Usage : $obj->persist_relationship_handler($handler,@args) Function: Sets or retrieves the persistence handler for relationships along with the constant set of arguments to be passed to the handler. If set, the first argument will be treated as a closure and be called for each relationship to persist to the database. The relationship will be passed as a named parameter (-rel), followed by the other arguments passed to this setter. Note that this allows one to pass an arbitrary configuration to the handler. If not set, relationships will be persisted along with their relationships using the respective persistence adaptor returned by the adaptor factory (see property db). Example : Returns : an array reference with the values passed on set, or an empty array if never set Args : On set, an array of values. The first value is the handler as a closure; all other values will be passed to the handler as constant argument. _persist_term Title : _persist_term Usage : Function: Persists a term to the database, using either a previously set persistence handler, or the adaptor factory directly. Example : Returns : Args : the ontology term to persist _persist_relationship Title : _persist_relationship Usage : Function: Persists a relationship to the database, using either a previously set persistence handler, or the adaptor factory directly. Example : Returns : Args : the term relationship to persist _persist_ontology Title : _persist_ontology Usage : Function: Perists the ontology itself to the database, by either inserting or updating it. Note that this will only create or update the ontology as an entity, not any of its terms, relationships, or relationship types. Example : Returns : the ontology as a peristent object with primary key Args : the ontology to persist as a Bio::Ontology::OntologyI compliant object perl v5.14.2 2012-03-02 Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler(3pm)
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