[coriny]

BioPerl has probably got a lot better over the years, I haven't touched it in a long time (5 years+), so my views may be very out of date. I don't really want to get into reviewing Bio* libraries generally :)

There is a general problem I think though, and other people have experienced the same. I've been trying to reason why, but I think it's due to multiple factors. By the time you've managed to get that bit working reliably with BioPerl you could have written it yourself. And it would be faster and use less memory. BioPerl has the problem of trying to solve every case, whereas normally I'm working with a limited subset of possibilities.

So why? I think it's a combination of dodgy, manually hacked inputs (e.g PDB files!), the learning curve, poor backwards compatibility preventing upgrading, and, ah I don't know. Every time it's seemed like a good idea, and yet every time I've ended up abandoning BioPerl. Maybe it's too integrated with itself as a library of functions?

Take parsing a FASTA. By the time I've read the BioPerl documentation, I could have already written that one line split string statement (because I e.g. know in advance the sequence string is always on one line). It's hard to overcome that laziness and make the commitment to learn it and become fluent in it.