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

[Michiel de Hoon]

Hi Bow,

--- On Sun, 1/27/13, Wibowo Arindrarto <w.arindrarto at gmail.com> wrote:
> All of this seems different from Bio.ParserSupport, which
> attempts to be a one-single solution for writing new parsers
> (only parsers). Given the wildly incoherent nature of different
> file output formats, it's not surprising that Bio.ParserSupport's
> code base has to be quite complicated to accommodate all of them.
> Naturally it has many related parts and functions, and understanding
> them all is much harder than to understand the small functions in
> Bio._utils (in my experience).

It's not just Bio.ParserSupport; previously we also had Bio/listfns.py; Bio/mathfns.py; Bio/stringfns.py; their C versions; and Bio/csupport.c. These all contained small utility functions. But in the end we dropped them.

Btw, was Bio._utils ever discussed on the mailing list? If yes, I apologize for missing this discussion and raising these issues now.

Best,

-Michiel.