[Bioperl-l] bioperl 1.5.1 release

Jason Stajich jason.stajich at duke.edu
Thu Oct 13 21:00:38 EDT 2005

I am EXTREMELY pleased to announce the release of Bioperl 1.5.1.




MD5sums are here for those who like that sort of thing:

This release represents a developer release which has been thoroughly  
tested and is very much a warm up for a bioperl 1.6.0 release.

This release replaces bioperl 1.5.0 which had several bugs that made  
it incompatible with several bioperl-1.4.0 scripts.  The current  
release should reverse these incompatibilities as well fix several  
outstanding bugs (See Changelog below and Changes file in the  
distribution for more information.  We also re-sync things with the  
NCBI RemoteBlast server so the SearchIO blast parser and RemoteBlast  
client so this should work now.

This has been tested on the latest Gbrowse candidate and it all works  

Please see the HOWTO documents provided in doc/howto/pdf or on the  
website http://bioperl.org/HOWTOs/ for information on using the  
modules as well as the API documentation http://doc.bioperl.org.  The  
code from this release is currently provided as an ever updating link  
under the bioperl-live and bioperl-run and bioperl-ext links under  
the Active Code link.  We will make another doc package for the 1.6  

I am also releasing bioperl-run, bioperl-ext packages labeled with  
the 1.5.1 version as these should all be used in sync.
I have not released bioperl-db (bioperl BioSQL implementation) at  
this time but I expect with Hilmar's help we will do that release in  
the next few weeks.

Some thank yous:
Heikki Lehvaslaiho and Brian Osborne for many helpful last minute bug  
fixes, POD fixes, and generally finding and keeping things  
consistent.  Brian also was instrumental in getting the Docbook to  
work properly and converting us over to XML from my initial SGML  
template.  I also want to thank several new developers who have  
pitched in lately to both help with the details and give big picture  
views on things: Albert Villa, Stefan Kirov, George Hartzell. Thanks  
to Koen van der Drift for providing the OSX port of bioperl on fink  
and to George and Mauricio for working to support bioperl on  
freebsd.  I hope the linux aficionados will also continue to help put  
RPMs up for the toolkit.  Also thanks to Sean Davis, Barry Moore, and  
Marc Logghe who have been extremely helpful at answering questions on  
the list.  We are grateful to all the bug-reports that have come in  
as well this has continued to make this a more robust and tested  

Would you like to see your name in lights (or at least in the thank  
you above; I'm sure this email is forwarded around the world...=)?   
Consider helping out the development team.  We need help adding  
information to the FAQ.   If you read the mailing list YOU can help  
with the FAQ distilling the various Q & A on the list into useful  
questions in the FAQ.

On behalf of Bioperl developers,
Jason Stajich

I have appended the Change log from Bioperl core compents below
1.5.1 Developer release

     o Major problem with how Annotations were written out with
       Bio::Seq is fixed by reverting to old behavior for
       Bio::Annotation objects.

     o Bio::SeqIO

      - genbank.pm
        * bug #1871; REFLOOP' parsing loop, I changed the pattern to
          expect at l east 9 spaces at the beginning of a line to
          indicate line wrapping.

        * Treat multi-line SOURCE sections correctly, this defect broke
          both common_name() and classification()

        * parse swissprot fields in genpept file

        * parse WGS genbank records

      - embl.pm
         * Changed regexp for ID line. The capturing parentheses are
           the same, the difference is an optional repeated-not-semi-
           colon expression following the captured \S+. This means the
           regexp works when the division looks like /PRO;/ or when the
           division looks like /ANG ;/ - the latter is from EMBL

         * fix ID line parsing: the molecule string can have spaces in
           it. Like: "genomic DNA"

      - swiss.pm: bugs  #1727, #1734

      - entrezgene.pm
         * Added parser for entrezgene ASN1 (text format) files.
           Uses Bio::ASN1::EntrezGene as a low level parser (get it  
from CPAN)

     o Bio::AlignIO

      -  maf.pm coordinate problem fixed

     o Bio::Taxonomy and Bio::DB::Taxonomy

      - Parse NCBI XML now so that nearly all the taxonomy up-and-down
        can be done via Web without downloading all the sequence.
     o Bio::Tools::Run::RemoteBlast supports more options and complies
       to changes to the NCBI interface. It is reccomended that you
       retrieve the data in XML instead of plain-text BLAST report to
       insure proper parsing and retrieval of all information as NCBI
       fully expects to change things in the future.
     o Bio::Tree and Bio::TreeIO

       - Fixes so that re-rooting a tree works properly

       - Writing out nhx format from a newick/nexus file will  
properly output
         bootstrap information.  The use must move the internal node  
labels over
         to bootstraps.
          for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
       - Nexus parsing is much more flexible now, does not care about

       - Cladogram drawing module in Bio::Tree::Draw

       - Node height and depth now properly calculated

       - fix tree pruning algorithm so that node with 1 child gets  

     o Graphics tweaks.  Glyph::xyplot improved.  Many other small- 
medium sized
       bugs and improvements were added, see Gbrowse mailing list for  
most of

     o Bio::DB::GFF partially supports GFF3.  See information about
       gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.

     o Better location parsing in Bio::Factory::FTLocationFactory -
       this is part of the engine for parsing EMBL/GenBank feature table
       locations.  Nested join/order-by/complement are allowed now

     o Bio::PrimarySeqI->translate now takes named parameters

     o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
       reconstruction) is now supported.  Parsing different models and
       branch specific parametes are now supported.

     o Bio::Factory::FTLocationFactory - parse hierarchical locations
       (joins of joins)

     o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
       for getter/setter functions

     o Bio::SearchIO

       - blast bug #1739; match scientific notation in score
         and possible e+ values

       - blast.pm reads more WU-BLAST parameters and parameters, match
         a full database pathname,

       - Handle NCBI WEB and newer BLAST formats specifically
         (Query|Sbjct:) match in alignment blocks can now be (Query| 

       - psl off-by-one error fixed

       - exonerate parsing much improved, CIGAR and VULGAR can be parsed
         and HSPs can be constructed from them.

       - HSPs query/hit now have a seqdesc field filled out (this was
         always available via $hit->description and

       - hmmer.pm can parse -A0 hmmpfam files

       - Writer::GbrowseGFF more customizeable.

     o Bio::Tools::Hmmpfam
       make e-value default score displayed in gff, rather than raw  
       allow parse of multiple records

Jason Stajich
Duke University

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