[Bioperl-announce-l] Bioperl 1.0.2 Released
Mon, 15 Jul 2002 19:59:01 -0400 (EDT)
I am pleased to announce the release of Bioperl 1.0.2 a bug fix release
which corrects several issues in the previous release. This release is
API compliant with the 1.0 branch so all scripts which have been written
for modules in the 1.0 or 1.0.1 releases should also work with this
As per usual you can obtain the release from the usual channels, primarily
our server at
Additionally Windows ActiveState Perl users can use the PPM utillity
PPM> set repository Bioperl http://bioperl.org/DIST/
PPM> search bioperl (this will show you what are the available
PPM> install bioperl (will install the default version
The package will be released onto CPAN and will be available from your
local CPAN mirror in the next few days depending on the synchronization
This release contains 413 modules and over 169k lines of code and
represents the work of dozens of developers.
Some notable problems with IRIX and Makefiles have been reported for this
release series because of the number of modules in our distribution.
Please see the PLATFORMS file for information on workarounds.
I would also like to encourage any user, will little or lots of experience
with the toolkit to help us gauge the project's use throughout industry
and academia by participating in the user survey [Yes you Bioperl
developers too - there's a Question just for you!]. This is available at
http://bioperl.org/survey.html or from the toolbar at the lefthand side of
the project website http://bioperl.org.
This release represents the last release on the 1.0 series. The
developers have begun work 1.1 developer/preview releases which will lead
to the next stable Bioperl release 1.2 which we expect to release in the
late Fall of 2002. Expect the first 1.1 release by the beginning of
Please note that because of the expected changeover for NCBI Entrez URLs
at the end of 2002, some modules (Bio::DB::GenBank, Bio::DB::GenPept) will
not work after 2002. The necessary fixes have already been applied and
tested on the 1.1 branch and will be available in the 1.2 release.
We expect a number of major components to be added to the toolkit in the
coming months and encourage any user interested in specific functionality
being added to the toolkit to join the mailing list discussion.
The Changes for 1.0.2 are appended below.
Jason Stajich on behalf of the Bioperl developers. Please see the
AUTHORS file in the distribution for a complete list of individuals who
made this release possible.
1.0.2 Bug fix release
o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
in this release will not work after December 2002 when NCBI
shuts off the old Entrez cgi scripts. We have already fixed
on our main development branch and the functionality will be
available in the next stable bioperl release (1.2) slated for
o Numerous parsing bugs in Bio::SearchIO::fasta found through
testset by Robin Emig. These were fixed as was the get_aln
method in Bio::Search::HSP::GenericHSP to handle the extra
context sequence that is provided with a FastA alignment.
o Migrating differences between Bio::Search::XX::BlastXX to
Bio::Search::XX::GenericXX objects. This included mechanism
to retrieve whole list of HSPs from Hits and whole list of Hits from
Results in addition to the current next_XX iterator methods that
are available. Added seq_inds() method to GenericHSP which identifies
indexes in the query or hit sequences where conserved,identical,gaps,
or mismatch residues are located (adapted from Steve Chervitz's
implementation in BlastHSP).
o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
o Bio::Graphics glyph set improved and extended for GBrowse release
o Bio::Tree::Tree get_nodes implementation improvement thanks
to Howard Ross notice performance problem when writing out
o Bio::Location::Fuzzy::new named parameter -loc_type became
-location_type, Bio::Location::Simple::new named parameter
-seqid becamse -seq_id.
o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
was mis-detecting that gaps should be placed at the beginning of
the alignment when the best alignment starts internally in the
jason at cgt.mc.duke.edu