[Biopython-dev] Bio.File

[João Rodrigues]

Hey Peter, all,

Sorry to peek in. I was going over some code lately together with Eric and
he suggested I use Bio.File as it was done in plenty of Bio.*IO modules.

What is this deprecation about then?

Cheers,

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



2011/10/17 Peter Cock <p.j.a.cock at googlemail.com>

> Hi Michiel,
>
> Regarding code using Bio.File, which you asked about
> deprecating last month:
>
> http://lists.open-bio.org/pipermail/biopython-dev/2011-September/009144.html
>
> I objected at the time because I was using it for the
> TogoWS code I was working on,
>
> On Thu, Sep 8, 2011 at 4:25 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> On Wed, Sep 7, 2011 at 3:36 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> >>> If the server could be relied on to always give an
> >>> HTTP error code this wouldn't be needed:
> >>>
> >>>
> https://github.com/peterjc/biopython/blob/togows/Bio/TogoWS/__init__.py
> >>>
> >
> > ...
> >
> > [Some of those TogoWS checks are probably superfluous
> > right now, I'm still polishing the error handling - some of
> > which will rely on TogoWS itself catching more conditions]
>
> I've updated my TogoWS to rely on the HTTP error codes,
> and removed the heuristic error detection which required
> Bio.File for the UndoHandle. That seems to be working fine
> now.
>
> That leaves Bio/SCOP/__init__.py as the only existing or
> imminent code using Bio.File, so if we can sort that out,
> we can deprecate Bio.File as you suggested.
>
> Regards,
>
> Peter
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