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.