[Biopython-dev] Bio.File

[João Rodrigues]

Hey Peter,


> For just the one little function, maybe not. I suspect we may want
> more "File related" things like this for Python 3, what with text vs
> binary handles and so on, in which case keeping Bio/File.py is
> sensible.
>

What kind of "things" are we talking about here? Could they be anticipated?


>
> It may be short, but duplicating this function all over the place
> seems like a very bad idea. I think we should just be vigilant in
> making sure it is used uniformly wherever we want to accept
> either a handle or a filename. Perhaps some of the historically
> handle-only parsers should start using it now?
>

Duplicating is not a beautiful solution I must agree, but keeping a module
and adding an import statement in every parser for only 5 lines isn't
neither.

I suggest we keep Bio.File, deprecating all the other functions, and
meanwhile look at which changes we could include due to Py3.