[Bioperl-l] Bioperl Developer snapshot 1.3.04

[Heikki Lehvaslaiho]

   Bioperl Developer snapshot  1.3.04
   ----------------------------------

This is the fourth and last developer snapshot from the BioPerl CVS
head before release 1.4 which is due early next week. Bug fixes are
still welcome, but please do not commit anything you do not have 
time to test well.

http://bioperl.org/DIST/current_core_unstable.tar.gz
http://bioperl.org/DIST/bioperl-1.3.04.tar.gz

Changes since 1.3.04
--------------------

This time I dit not have the time to collect details from all the cvs
commits (maybe that level of detail is not necessary? It is all in
bioperl-guts, anyway.) The highlights are:

* SVG::Graphics fine tuning ; SVG output,

* Bio::Tree major changes plus a new howto. There is a new
  Feature-Annotation howto, too.

* Parse more BLAST statistics and lots of BLAST-related fixes

* Bio::Restriction::Analysis is now fixed and can handle overlapping
  and multiple cuts as well as circular sequences.

* Bio::SearchIO and Bio::AlignIO can quess the incoming format by
  looking ahead into stream, thanks to Bio::Tools::GuessSeqFormat.

* GenBank and EMBL parsers now tolerate words longer than line
  width. Also, they parse non-binomial virus names better into
  Bio::Species objects. EMBL parser now does better roundtrip of
  files.

* New GAME format modules.

* last minute fix: scripts/Bio-DB-GFF/bp_genbank2gff.PLS can now write
  to stdout without depending on mysql.


NEW FILES:

* Bio/OntologyIO/Handlers::InterPro_BioSQL_Handler.pm 
* Bio/Restriction/IO::bairoch.pm 
* Bio/SeqIO::game.pm 
* Bio::Tools::GuessSeqFormat
* doc/howto/sgmlFeature-Annotation.sgml 
* doc/howto/sgm/Trees.sgml 
* examples/biographics/all_glyphs.pl 


Enjoy,

        -Heikki & the rest of the bioperl core team


P.S. The web site was updated over five hours ago when I wrote the
first version of this message which seems to have vanished into a black
hole,


-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________