[Biopython-dev] Interested in a Phenotype Microarray parser?

Marco Galardini marco.galardini at unifi.it
Sat Jan 11 12:49:53 UTC 2014

On 10/01/2014 09:36, Michiel de Hoon wrote:
> Hi Marco,
>> So far the dependencies would be pyYaml (for the yaml/json
>   > parsing, but maybe i could use the stdlib json module) and
>   > numpy/scipy for the extraction of curve parameters. Does
>   > this sound ok?
> It would be better to avoid scipy, as currently it is not used in any Biopython module.
> Same goes for pyYaml; keep in mind that the number of users may decrease if there are more dependencies (and it puts a burden on developers also for testing).
> Numpy should be OK; a quick count suggests that 12 biopython modules are already using it.
Ok, I'll try to remove all this dependencies: if scipy will not be 
included, then most probably also numpy won't be needed. The drawback is 
that it would be difficult to fit the sigmoid functions to the PM curves 
(so the lag, plateau and slope parameters won't be computed).

>>   how about a "phenomics" module?
> In principle that sounds fine to me.
> Best,
> -Michiel.
I'll try to draft a first tentative version and let you know how it goes.


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