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

[Andrew Dalke]

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