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 library? 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? http://www.digicool.com/releases/ExtensionClass/ Konrad, do you know the license? I can't find it. Jeff -- J.W. Bizzaro Phone: 617-552-3905 Boston College mailto:bizzaro at bc.edu Department of Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ --