[Pipet Devel] libraries - was more nice interfaces

J.W. Bizzaro bizzaro at bc.edu
Mon Mar 1 05:56:02 EST 1999

Thomas wrote:

> Hej Jeff,
>  > One major part of the Loci Project is to create a "library" of Python modules
>  > (and C wrapped in Python) that handle common sequence and structure
>  > manipulations.  The library for structure is something Konrad will hopefully
>  > contribute, along the line of MMTK.
>  >
>  > If you are writing or rewriting code to manipulate sequences (like reversing or
>  > complementing), the code should become part of this library.
>  >
>  > Tim, a guy we haven't heard from in a while, was going to write code to
>  > convert codons into amino acids.  Tim, this also needs to be in the
>  > library, in Python or Python/C.
> I see ... that would make life easier. How are we going to do this
> practically ? Are we using different namespaces in the library ?

Well, I havent really thought about naming conventions for the libraries.  Since
you are the first to do this, you get the honor of inventing the namespace.  You
can start everything with "locus_", if that is along the line of your question.

> How shold I rewrite the rewrite of my lib ?

Quoting Konrad:

    You *could* write some C-level type and
    inherit from it in a Python class by using the ExtensionClass
    package, but there's no point unless you really want/need to
    provide a generally useful C type.

I think ExtensionClass is great in that the OO paradigm of Python is brought to
the C module.  I would like to see this become standard Python in a future
release.  But is it worth the effort to use a new Python package for the

I think we have to consider though just how much we will be using C to speed
things up in Loci.  Much of what we intend to do will be very
compute-intensive.  So maybe.  Think about it.

Here is the URL?


Konrad, do you know the license?  I can't find it.

J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/

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