[Biopython-dev] Blast parsers and records

[Sebastian Bassi]

On Sat, May 29, 2010 at 12:23 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> 1) Blast parsers are located in several modules (Bio.Blast.NCBIXML, Bio.Blast.NCBIStandalone, Bio.Blast.ParseBlastTable). I think we should have one read() function and one parse() function under Bio.Blast, with arguments specifying which format the Blast output is in.
>
....

I would add another issue (7). The interface to run the BLAST search
is different. The "clasic" will execute the search while the blast+
one "just" generate the command line and it is up to the programmer to
actually run it (and get the result back to the program).
>From my POV, it is adding 3 lines in my code, but you didn't have to
use subprocess before blast+, so I find this a little inconsistent.