[Biopython-dev] Bio.File

[Peter Cock]

On Mon, Oct 17, 2011 at 5:10 PM, João Rodrigues <anaryin at gmail.com> wrote:
> Hi Peter,
> To be honest, I didn't see much of a point to use the module but for
> consistency's sake.

Michiel's point was [at that time] there was very little useful
code if any in Bio.File, so could we deprecate it?

> I grep'ed Bio.File in my biopython dir and I got a few more modules
> with Bio.File, don't know if you were aware.
>
> Bio/Application/__init__.py:from Bio import File
> Bio/Blast/NCBIStandalone.py:from Bio import File
> Bio/PDB/parse_pdb_header.py:from Bio import File
> Bio/Phylo/_io.py:from Bio import File
> Bio/SCOP/__init__.py:    from Bio import File
>
> Just wanting to clear my doubts about this, thanks!
> Cheers,

Oh - I remember now. We recently added the as_handle
context manager to Bio.File, and that is a useful bit of
functionality of general interest.

At the time I had forgotten about Michiel's suggestion
we deprecate Bio.File, which is unfortunate, but we
can still change this before our next release.

So, should we keep Bio.File for as_handle (even if
everything else in Bio.File is to be deprecated), or
should we move the new as_handle functionality
somewhere else and deprecate all of Bio.File.

Thanks for double checking João,

Peter