Welcome to obogaf::parser’s documentation!

obogaf::parser is a perl5 module designed to handle GO and HPO obo file and their gene annotation file (gaf file). However, all the obogaf::parser subroutines can be safely used to parse any obo file listed in OBO foundry and any gene annotation file structured as those shown in GOA website and HPO website – basically a csv file using tab as separator).

Subroutines contained in obogaf::parser:

• build_edges: extract edges from an obo file;
• build_subonto: extract edges for a specific subontology domain;
• make_stat: make basic statistic on a graph;
• get_parents_or_children_list: build parents or children list for each node of the graph;
• obo_filter: prune obo file relatively to a set of given ontology terms;
• gene2biofun: build the annotations list from a gaf file;
• map_OBOterm_between_release: map ontology terms between releases;

To call an obogaf::parser subroutine you must preface the subroutine’s name with the name of the library (obogaf::parser) and double colon (::): obogaf::parser::subroutine-to-call. See examples in Tutorial section for more details.