[Biopython-dev] [BioPython] Bio.SCOP.FileIndex

Peter biopython at maubp.freeserve.co.uk
Fri Jun 27 22:06:14 UTC 2008

On Wed, Jun 25, 2008 at 3:04 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Hi everybody,
> When I was modifying Bio.SCOP, I noticed that Bio.SCOP.FileIndex is flawed
> if file reading is done via a buffer (which is often the case in Python).

Are you talking about Bio/SCOP/FileIndex.py?  The whole design seems to be
geared to indexing the position of record in a file - down to the fact
that it takes
as filename rather than a handle. Why does it need "fixing"?

> Before we try to fix this, is anybody actually using Bio.SCOP.FileIndex?
> If not, I think we should deprecate it instead of trying to fix it.

We've deprecated similar functionality in Bio.GenBank, although if I recall
correctly that was because it was using Martel and broke with mxTextTools 3.0,
and therefore fixing it was non-trivial.

If Bio.SCOP.FileIndex is broken, then deprecation seems sensible.


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