NOTE:We are planning on significant code refactoring for these modules for the 1.7 release. See the code refactor page for upcoming plans.
Bio::FeatureIO is a handler module for the formats in the FeatureIO set (e.g. Bio::FeatureIO::gff).
It previously was the officially sanctioned way of getting at the format objects. As the prior implementation was not completed and has several issues, we are in the midst of reimplementing these modules in a separate project. Please note that further development on these modules should be actively discussed on the mailing list or IRC.
The Bio::FeatureIO system, like the other IO systems BioPerl, can be thought of like biological file handles. They are attached to filehandles with smart formatting rules (eg, GFF format, or BED format) and can either read or write feature objects (Bio::SeqFeature objects, or more correctly, Bio::FeatureHolderI implementing objects, of which Bio::SeqFeature is one such object). If you want to know what to do with a Bio::SeqFeatureI object, read Bio::SeqFeatureI.