Bioperl: 06 - pre release 2.

[Ewan Birney]

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.


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.

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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