[Bioperl-l] Bioperl Developer snapshot 1.3.02

[Heikki Lehvaslaiho]

   Bioperl developer snap shot  1.3.02
   ---------------------------------


This is the second developer snap shot from the BioPerl CVS head
that will eventually lead to release 1.4.

http://bioperl.org/DIST/current_core_unstable.tar.gz
http://bioperl.org/DIST/bioperl-1.3.02.tar.gz


Last fortnight has been dominated by bug fixing (but more is needed; see
bugzilla). The only new stuff added has been on comparison matrix
modules by Stafan Kirov.

The most important fixes have been tweaks in ontology handling, GFF
histograms, some Bio::Graphics glyphs, feature table output and
Gene/Genomewise parsing. The full list is below.

Enjoy,

	-Heikki




NEW DIRECTORIES and FILES
=========================

Bio::Matrix::PSM
  IO InstanceSite InstanceSiteI Psm PsmHeader 
  PsmHeaderI PsmI SiteMatrix SiteMatrixI 

  Added DNA PSM (Position Scoring Matrix) modules This includes meme,
  mast and transfac parsers

examples/rnai_finder.cgi 
  cgi script for RNAi reagent design


CHANGES
=======

Bio::DB::GFF::Adaptor::dbi 
  fixed bug 1384; histograms not working

Bio::DB::GFF::Feature
bulk_load_gff.PLS fast_load_gff.PLS load_gff.PLS
  fixed overly-promiscuous regexp for detecting FASTA files

Bio::DB::Query::WebQuery 
  quell undef warnings

Bio::DB::WebDBSeqI 
  reset MODVERSION to use Packagewide Version system - change agent
  string to be 'bioperl-Bio_DB_GenBank/1.3' for example

Bio::Graphics::FeatureFile 
  All functionality moved to Bio::DB::GFF->split_group, however still
  see major perf problems, not sure if this is localized to
  FeatureFile or not

Bio::Graphics::Glyph::Factory 
  fixed implementation of user-defined glyph sort routines

Bio::Graphics::Glyph::arrow
Bio::Graphics::Glyph
  partial fix for incorrectly-rendered half-open intervals

Bio::Index::Abstract 
  don't warn if we set verbose to -1

Bio::Location::Simple::to_FTstring()
  was never returning a location of the form "complement(12345)

Bio::Ontology::SimpleGOEngine 
Bio::OntologyIO::dagflat 
Bio::Expression::FeatureGroup 
  allowing an underscore in ontology IDs.  this is necessary to be
  able to parse cjm's OBO_REL relationship ontology, which otherwise
  observes DAG-Edit format

Bio::Ontology::SimpleGOEngine
Bio::OntologyIO::dagflat.pm 
  MPATH ontology doesn't have at least 3 digits in all identifiers

Bio::SearchIO::(chado&chadosxpr)
  removed as redundant

Bio::SeqFeature::Tools::TypeMapper 
  updated type sequence_variant to reflect SO

Bio::SeqIO::chadoxml 
  fix bug of null srcfeature_id for featureloc when srcfeature is not
  given on write_seq() invocation; fix bug of not calling unflattener
  when -seq_so_type is explicitly supplied.

  fixed bug 1532 with regard to filehandle; modified code to eliminate
  warnings when run with 'perl -w'.
  debugging code clean up

Bio::SearchIO::wise 
  was swapping query/target improperly

Bio::Restriction::IO::base 
  fix suggested in bug report #1538, correctly parse negative cut site
  locations

Bio::Tools::Phylo::PAML::Result
  doc fixes

+ several minor fixes to quiet warnings when Test::Harness runs tests
with 'use warnings'


-- 
______ _/      _/_____________________________________________________
      _/      _/                      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
___ _/_/_/_/_/________________________________________________________