[Biopython] Deprecating BlastTextParser

[Peter Cock]

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
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython