[Biopython-dev] Bio.GenBank

[Michiel de Hoon]

Hi Peter,

> I'd have to dig into the code to understand the patch, but
> I presume there is a follow up question coming - can we
> then deprecate Bio.ParserSupport since right now only the
> GenBank and "pending deprecation" plain text BLAST
> parsers use it (plus Compass which you recently fixed)?

Yes. With this patch, the plain text BLAST parser is the last piece of code that uses Bio.ParserSupport.

Best,
--Michiel.


--- On Mon, 9/5/11, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> From: Peter Cock <p.j.a.cock at googlemail.com>
> Subject: Re: [Biopython-dev] Bio.GenBank
> To: "Michiel de Hoon" <mjldehoon at yahoo.com>
> Cc: biopython-dev at biopython.org
> Date: Monday, September 5, 2011, 6:04 AM
> On Sun, Sep 4, 2011 at 7:09 AM,
> Michiel de Hoon <mjldehoon at yahoo.com>
> wrote:
> > Dear all,
> >
> > Currently, Bio/GenBank/__init__.py imports
> Bio.ParserSupport
> > but uses very little of it. Therefore I would like to
> suggest to
> > remove this dependency on ParserSupport from
> > Bio/GenBank/__init__.py. I copied the corresponding
> patch below.
> > Any objections, anybody?
> 
> Hi Michiel,
> 
> I'd have to dig into the code to understand the patch, but
> I presume there is a follow up question coming - can we
> then deprecate Bio.ParserSupport since right now only the
> GenBank and "pending deprecation" plain text BLAST
> parsers use it (plus Compass which you recently fixed)?
> 
> Peter
>