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

[Paulo Nuin]

Hi all

I am running pylint on the code and getting some evaluation.

Currently the alignment.py scored -10.16/10, mainly because of 
indentation issues and lack of spaces between operators.
NJ.py scored -7.66/10
parse.py scored -6.10/10
readFasta.py scored -7.00/10

Of course this test just measures the "Pythonic" level of the code, but 
it does not check the code itself for quality.

Cheers

Paulo



Andrew Dalke wrote:
> 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
>
>
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython