Bioperl: Re: Bioperl-guts: 06 - pre release 2.

[Steve Chervitz]

Ewan Birney writes:
 > 
 > 
 > The second pre release of the 06 series is out for people to download
 > and test/break/complain about. It is at
 > 
 > ftp://bio.perl.org/pub/birney
 > 
 > bioperl-06pre2.tar.gz
 > 
 > 
 > This pre-release includes new modules 
 > 
 >   SeqStats - protein and DNA molecular weight functions 
 >              Peter Schattner
 > 
 >   CodonTable - Codon Table translations and reverse translation
 >                for all known codon tables. 
 >                Heikki Lehvaslaiho
 > 
 > Many thanks to both of these authors
 > 
 > 
 > In addition I have split out the Root Object system to allow better
 > integration with non-perl based systems, fixed minor errors. Steve
 > Chervitz has provided a number of fixes to the BLAST parsing modules.

Ooops! Not all of my Blast module fixes are in. Also, I want to add
the retrieve_blast.pl helper script. I'll commit shortly, so if you're
planning to do lots of blast testing, wait till the next pre-release,
which should be soon.

I also fixed up the examples/seq scripts to be SeqIO-compliant (these
are in pre2).

 > 
 > We have 144 tests in the test suite, all of which pass.

:-)

 > I have the following things left to do before the stable branch
 > can be put in:
 > 
 > a) see whether I can make the BLAST HSP objects compliant to
 > the new Bio::SeqFeatureI interface, making the BLAST parser
 > play well with the new sequence object.

Ideally, you'll also want to make the BLAST Sbjct object (i.e., a hit) 
compliant to SeqFeatureI. It's natural to think of a database hit 
as a feature on a sequence that contains child features (HSPs). When
your looking at a bunch of HSPs, it's important to know which ones
belong to the same hit. 

Regarding the Blast parser, let me know if you have questions.

Cheers,

Steve Chervitz
sac@neomorphic.com


 > b) map all the seqio function read/writes to the ->_readline
 > syntax from lincoln's new seqio.pm base class.
 > 
 > c) fixing the Bio::DB to be more biocorba ready
 > 
 > c) find more bugs and squash them before the branch.
 > 
 > 
 > **YOU** can help with c) by downloading the code and attempting
 > to run your existing scripts and/or writing new ones which
 > make the system not behave how you want it to...
 > 
 > 
 > -----------------------------------------------------------------
 > Ewan Birney. Mobile: +44 (0)7970 151230
 > <birney@ebi.ac.uk>
 > -----------------------------------------------------------------
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