Bioinformatics

[ETLMaster]

Hi all,
I'm getting myself into bioinformatics and I find that perl is the language of choice for parsing sequences and the like. I would like to use Ruby for this, but I'm just worried at the performance compared to Perl. It seems some unofficial benchmarks say that Ruby is 2-3x slower than Perl.
What do you guys think?

 

[stillflame]

I've never seen proof that ruby is slower than perl in a general sense. I do know that the regex engine is a bit slower (like 10-15%), but not massively. There are, just like in perl, some things which are slower than you would think they would be, but, as in perl, there are almost always work-arounds. Ruby's C-API is also very easy to use, and so any speed critical parts of your own applications can be written in C. "If you think you're too small to make a difference, try spending a night in a closed tent with a mosquito."

 

[tty0]

Hi there,
Try taking a similar approach to the one used when producing bioperl and recode any functions directly into the compiler. As this takes any speed difference out.

Cheers


'mi casa es su casa'
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