[Biopython-dev] HMMER (+ BLAT) wrappers

[Wibowo Arindrarto]

On Wed, May 2, 2012 at 4:50 PM, Chris Mitchell <chris.mit7 at gmail.com> wrote:
> Hey Bow,
>
> I think it would be better to have an option to send the query to the local
> server should one be running as opposed to wrapping a gfServer that would be
> local for the duration of a given python process.  This would allow for
> cases where someone has their BLAT queries split up in a script and not
> incur the loading time for the database multiple times.  The
> gfServer/gfQuery setup is also rather a pain to use from my experience (it's
> all relative paths).  I also think using the -pslx output would be a better
> default since -psl doesn't provide you with the sequence alignments.
>
> Chris
>

Hi Chris,

You are talking about 'gfServer query ...' right? That does make
gfServer usable enough to be wrapped. Thanks for pointing that out ~ I
overlooked that gfServer can also do queries. I admit that the current
BLAT wrapper is very minimum, but like I said, it shouldn't take that
much time to write wrappers for the rest of the executables in the
suite :).

As for the file format, I actually prefer leaving the options as it is
(i.e. the program's default) to keep surprises minimum to users (even
though I agree that the pslx output is more informative).

Bow