[bip] Bioinformatics Programming Language Shootout, Python performance poopoo'd

[Brent Pedersen]

On Feb 5, 2008 12:00 PM, Chris Lasher <chris.lasher at gmail.com> wrote:
> Fourment and Gillings performed a language shootout in the wild west
> of bioinformatics.
>
> http://www.biomedcentral.com/1471-2105/9/82
>
> Python got railed on for performance, particularly in parsing. I feel
> more surprised than perhaps I should. They claim the source code is
> available at the link below, but it doesn't work for me.
>
> http://www.bioinformatics.org/benchmark/
>
> Oh well, I still love the language.
>
> Chris
>
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> biology-in-python mailing list - bip at lists.idyll.org.
>
> See http://bio.scipy.org/ for our Wiki.
>

the code is up now. i just had a brief look, are the authors python users?
my favorite so far is the max()  function in the python  file here:
ftp://ftp.bioinformatics.org/pub/benchmark/python/alignment.py
which has a header of #!/usr/bin/perl

the rest of the stuff looks like a prime candidate for psyco.