What are BioPerl's weaknesses?
(Note: this is a repost due to some of the beta-ness of the site).
BioPerl is a commonly-used toolkit for bioinformatics, but it does have it's share of problems. As educated_foo has pointed out, it can be slow, documentation is spotty for some modules, classes can be overly complex in some cases, and there are interface issues. And, for simple formats like FASTA it's probably overkill if you are just parsing data. Not to mention the monolithic nature of the beast; I think it's over 1000 modules now.
We in the BioPerl community haven't heard much about these issues from users. What (specifically) bugs you about BioPerl? What could be improved? In other words, what are it's weaknesses? Specifics would be nice.
(Just for some balance, I'll blog about some of BioPerl's strengths at a later point)
Rattling off a couple, from educated_foo and myself:
- Make it less monolithic. Break up 'core' into more manageable bits.
- Simplify classes.
- Better tests?
- Maybe a BioPerl Manual? (we do have HOWTOs that could work as starter material...)
- Moose? Some of those interfaces fit nicely into Roles...
- Allow parsers to return simple data structures (hash refs?) as well as objects.
- Re-evaluate interface? educated_foo mentioned problems, but specifics would be nice.