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

[Colosimo, Marc E.]

<rant>
What is biology in python or more to the point why is there yet another
mailing list (Web site?) for biology in python?

>From looking at their archive messages:

1. Need to establish python/biology community.....

Isn't that what BioPython is? If not, why not?

I'll also point out that there is "CoreBio" a python toolkit for
writing computational biology applications
<http://code.google.com/p/corebio/>

I don't want to subscribe to another mailing list, install another
suite of code, keep track of another Web site.
</rant> 

-----Original Message-----
From: biopython-bounces at lists.open-bio.org
[mailto:biopython-bounces at lists.open-bio.org] On Behalf Of Andrew Dalke
Sent: Wednesday, February 06, 2008 6:04 AM
To: biopython at lists.open-bio.org
Cc: biology-in-python at lists.idyll.org
Subject: Re: [BioPython] [bip] Bioinformatics Programming Language
Shootout,Python performance poopoo'd

On Feb 6, 2008, at 11:44 AM, Peter wrote:
> Am I right in thinking the authors have not made any of their sample
> input files available?  In the case of the multi GB Blast file, this
> is perhaps justified.  Also I didn't see any timing script.

the alignment programs contain the test data.

the fasta parser and blast parser do not contain test data.  The lack  
of data is not justified as having a 9GB file adds little to the  
comparison over having a 9 MB file as it should scale linearly.  It  
does show that the parsers can handle large files, but big whoop.   
And the test is unaffected by having a 9MB file duplicated 1,000 times.

the neighbor-joining code contains no test data

There's no timing script.

				Andrew
				dalke at dalkescientific.com


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