[Bioperl-l] New code

[Jason Stajich]

On Fri, 28 Dec 2001, Ewan Birney wrote:
> Many thanks Steve.
>
ditto.
>
> Steve has sent a rather more detailed message to me and Jason. We have
> some unpicking to do here as we now have about 4 different "parsing BLAST"
> based on three frameworks. Thankfully this is not as bad as it sounds as
> both Jason and Steve want to move things together into this event based
> parsing system (SearchIO) keepiing all the goodies from previous systems
> (eg, Bio::Tools::Blast).
>
>
> I am feverently hoping that Jason can take point in smoothing all this
> over and figuring out how and where to prune out modules. Jason - are you
> up for this (...please say yes...)
>

What I need to do are things like fold the Bio::Search::HSPI and
Bio::Search::HSP::HSPI into a single interface - need to agree upon silly
things like the methods report_type() vs algorithm() which are just
different names for same things - or just keep both.  Then reimplement
my parsers (blastxml,fasta) with the new objects.  Not too much work I
think.

We'll have to decide on naming convention here - Hit vs Subject as we use
them interchangeably (Steve's stuff uses Hit - but the SimilarityPair and
BPlite nomeclature was subject).

I like Steve's idea to have a specific BlastHSP implementation rather than
trying to make the object generic enough for all types of reports - should
be able to handle HMMer reports here nicely as well.


>
> I think the right thing to do here is wait for Jason's call on the Search
> modules and the first round of pruning and then go for a 0.9.3 developer
> release in earlish Jan (around the 8th say) assumming everything is
> looking good.
>

Seems reasonable.  I will give it a good once through this weekend and see
what can be done.   This assumes that 0.9.1 has gone out?  and we are
skipping 0.9.2 ?

>
>
> At this point I don't want to hear of any other large additions/changes to
> the modules - we are officially in cleaning up/sdmoothing mode for the
> next month. Realistically we are not going to be releasing 1.0 in late Jan
> - it is going to be late Feb or March, but we need to concentrate on
> details not big things from here on in...
>

I've got Roger looking at implementing DB::GenBank Entrez batch fetch
based on Lincoln's Boulder::GenBank code - just got to be reimplemented
with LWP and hooked into the NCBIHelper system.  Hopefully he will have
time and can get that in - no API changes from this.

>
>
> I'd also like the documentation effort ideal to start around 0.9.3 (Peter
> - are you ready for this - does anyone else want to help here?) with
> someone ideally doing an audit about where we need update/improve etc
> documentation. 1.0 is going to need to have good documentation from the
> start not lagging in a 1.1 release or whatever as I suspect we'll have a
> whole set of new people poking it when we release 1.0
>

Here here!  One thing that would help is a checklist when the audits are
done - Wiki was a bit of pain for this in the past - perhaps something
else can be looked at. (webteam how's it going?)

>
>
> For the newbies - I will be writting a Bio::Perl module which will give
> function orientated access to basic bioperl objects to ease the learning
> curve.
>
>
>
>
> But it is looking like a very impressive 1.0 release when it comes!
>

Should have a nice feature list to talk about end of Jan even if no
executeable - really great.

>
>
> ewan
>
>
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>.
> -----------------------------------------------------------------
>


-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu