[BioPython] [bip] Bioinformatics Programming Language Shootout, Python performance poopoo'd
Paulo Nuin
nuin at genedrift.org
Wed Feb 6 16:07:41 UTC 2008
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
>
>
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