[Biopython] Deprecating BlastTextParser

[Wibowo Arindrarto]

Hi Michiel and Peter,

I've opened a PR to continue this discussion here:
https://github.com/biopython/biopython/pull/1866.

If that is sensible, I'll also update the documentation and then merge it.

With kind regards,
Bow
On Thu, Nov 22, 2018 at 3:34 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> Yes. If we wanted to do so, we could indeed remove the files
> Bio/Blast/NCBIStandalone.py and Bio/ParserSupport.py and
> put their code under Bio/SearchIO/BlastIO/_legacy.py or
> something (leading underscore to indicate private), or
> even inside Bio/SearchIO/BlastIO/blast_text.py itself.
>
> That would be cleaner.
>
> Peter
>
> On Thu, Nov 22, 2018 at 11:23 AM Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> >
> > Then can we move Bio/Blast/NCBIStandalone.py and Bio/ParserSupport.py into Bio.SearchIO ?
> > Or integrate those two modules into Bio.SearchIO.BlastIO.blast_text ?
> > It's confusing to have two deprecated modules at the top level of Bio/*, and remind ourselves each time that actually they should not be removed.
> >
> > Best,
> > -Michiel
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