[Biopython] Deprecating BlastTextParser

[Michiel de Hoon]

 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
   On Thursday, November 22, 2018, 7:12:25 PM GMT+9, Peter Cock <p.j.a.cock at googlemail.com> wrote:  
 
 So leave the code and its warnings as they are for the time being,
but perhaps stronger wording in the documentation that using
the "blast-text" parser in SearchIO is not encouraged?

i.e. Add a note here?:
https://github.com/biopython/biopython/blob/biopython-172/Bio/SearchIO/__init__.py#L189

And a stronger caveat than "Newer versions may not always work" here?:
https://biopython.org/wiki/SearchIO

Peter
On Thu, Nov 22, 2018 at 9:59 AM Wibowo Arindrarto <bow at bow.web.id> wrote:
>
> Dear Michiel, Peter, and everyone,
>
> I actually prefer to have the text parsing functionality in
> maintenance mode: no addition of new features, but also not removing
> it entirely. We probably can make a few things clearer / more visible
> in our documentation: that this was developed using the text output of
> old BLAST releases and that we will not be adding support or updating
> it to work with text output from new releases.
>
> So far, I have seen only very minor (if any) maintenance work related
> to the text output parser. And I believe it still has its uses in
> those corner cases where one really needs to parse the text output
> from an irreproducible BLAST search. So it seems to me that we would
> be losing more (functionality-wise) by deprecating it, rather than
> keeping it in maintenance mode.
>
> With kind regards,
> Bow
> On Wed, Nov 21, 2018 at 5:25 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
> >
> > Hi Michiel,
> >
> > This is up to Bow really - does he want to continue to support
> > parsing plain text human readable BLAST output in SearchIO?
> >
> > I've not tried the new BLAST+ 2.8.0alpha release, but am not
> > aware of any current problems with the parser - although as
> > you note, the NCBI and parts of our own documentation do
> > not recommend parsing it - and it could easily break with the
> > next BLAST+ release.
> >
> > I agree from a code cleanliness perspective, it would be nice
> > to remove this and Bio/ParserSupport.py as well. Sadly while
> > we've had deprecation warnings in place for direct use of
> > Bio.ParserSupport or Bio.Blast.NCBIStandalone, indirect
> > use via SearchIO has been deliberately handled without
> > a warning.
> >
> > Minor correction: Bio.Blast.NCBIStandalone has got tests in
> > test_NCBITextParser.py, and indirectly via the SearchIO tests.
> > In fact it has a respectable 90% test coverage:
> >
> > https://codecov.io/gh/biopython/biopython/src/master/Bio/Blast/NCBIStandalone.py
> >
> > Likewise for Bio.ParserSupport:
> >
> > https://codecov.io/gh/biopython/biopython/src/master/Bio/ParserSupport.py
> >
> > Peter
> > On Wed, Nov 21, 2018 at 2:54 AM Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> > >
> > > Dear all,
> > >
> > > The blast_text module in Bio.SearchIO.BlastIO contains a parser for plain-text output from Blast.
> > > NCBI and Biopython itself recommend against parsing plain-text Blast output.
> > > As far as I can tell, this module currently has no documentation and no tests.
> > > The module relies on the deprecated module Bio.Blast.NCBIStandalone, which relies on the deprecated module Bio.ParserSupport.
> > >
> > > Can we deprecate Bio.SearchIO.BlastIO.blast_text ?
> > >
> > > Best,
> > > -Michiel
> > >
> > > _______________________________________________
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