[BioPython] Biopython hackathon

[Ann Loraine]

I hope you will consider the following two requests as possible
hackathon activities:

(1) If it does not already do this, it would be nice if the blast
"plain text" (non-XML) parser would report the length of the target
("hit") sequence as well as the query. If I recall correctly, the last
time I used the plain text blast parser, I had to measure the length
of the targets by opening up the fasta copy of the blastable database
and reading the lengths one-by-one. My database wasn't very big, so it
wasn't a hassle to do this, but I can foresee situations where this
kludge would fail.

(2) Another request is for a Python interface to the Bio::Db::SQL
database schema described in:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12368253.

The part that seems particularly valuable would be code that to
construct the location-based queries.

My apologies if this already exists -- if yes, please let me know
where I can find it!!

All the best,

Ann Loraine



On 3/14/07, Julius Lucks <lucks at fas.harvard.edu> wrote:
> Hi all,
>
> I was just chatting with Jason Stajich about the openbio hackathon
> that took place a few years ago.  What biopython projects do people
> think would be appropriate for another hackathon in the near future?
> Are there things that have been on the TODO list for a while?  New
> functionality that would benefit from a bunch of us getting together
> in one place (possibly with other openbio projects)?
>
> Cheers,
>
> Julius
>
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