[Biopython-dev] Deprecating Bio.ParserSupport, Bio.Blast.NCBIStandalone

[Peter Cock]

On Fri, Jan 11, 2013 at 12:36 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Hi everybody,
>
> Bio.ParserSupport has had a PendingDeprecationWarning since Biopython
> 1.59, so we may consider upgrading this to a BiopythonDeprecationWarning in
> Biopython 1.61 before removing Bio.ParserSupport. The only tricky point is
> that then we would also have to upgrade the PendingDeprecationWarning in
> Bio/Blast/NCBIStandalone.py to a BiopythonDeprecationWarning, as that code
> relies on Bio.ParserSupport. Bio.Blast.NCBIStandalone has had this
> PendingDeprecationWarning since Biopython release 1.56.
>
> Any objections? This may help giving Bow's Bio.SearchIO module some more
> prominence.

Bow's SearchIO is using Bio.Blast.NCBIStandalone to handle plain text,
https://github.com/biopython/biopython/blob/master/Bio/SearchIO/BlastIO/blast_text.py

We'd discussed a new parser targeting just the plain text from BLAST+
(and if not too different maybe the final legacy BLAST release), which
should be less diverse that the current range of BLAST quirks built up
over the years.

> On a related point, the fact that we are deprecating Bio.ParserSupport
> (which was a painful process) suggests that having a new module Bio._utils
> with a set of generic utility functions is not a good idea.

That's why Bio._utils is a private module - we can drop/change/etc
this without worrying about breaking other people's code. The issue
with Bio.ParserSupport is it was a public API.

Regards,

Peter