Why so much prejudice against Perl on Hacker News??!!
I should know, because I shared the same biased views until I had a job which required quick iterations of complicated computation of a large dataset with limited hardware. I never had really used perl before that, but when it started to save me literally weeks of work I came to love it.
There's a tool for every job.
I think I didn't like Perl before because the code looked hard to understand. But since then I found out first hand one can do shitty C or Python too.
Sorry, I just had to suffer some Perl plus Bash and Makefiles big-ball-of-mud at work. Just makes you disgruntled. (We're re-writing that piece in Haskell.)
I don't know how other Perl programs fare. Probably better. Though the syntax makes you cry. And treating things like lists of lists as an advanced topic, that's needs something special like `references'. Did I mention how functions get their parameters? The interpolation in strings can be handy, though.
And I agree about the possibility of bad code in Python and C. (I have some Python nightmare at hand, too.)
Well, bioinformaticians are far from uniform in terms of language usage (my mentor staunchly defends his use of VB6, for instance...), but this link shows people using Python for structural bioinformatics as early as 2001: http://mgl.scripps.edu/people/sanner/html/talks/PSB2001talk....