[Bioperl-announce-l] Release Announcement: Bioperl 1.2.3
jason at cgt.duhs.duke.edu
Wed Sep 17 23:22:39 EDT 2003
On behalf of the Bioperl developers, I am pleased to announce the release
of Bioperl 1.2.3. This is the set of Core libraries which constitutes
Bioperl and covers areas like Sequence file parsing, Sequence Feature
representations, Database access to flatfile and webbased sequence
thadatabases, Alignment parsing and manipulation, parsing of and data
representation of output from a majority of standard bioinformatics tools,
and many more features.
This release constitutes several major bugfixes from the 1.2.2 release
earlier this summer and provides some new minor functionality
improvements. This release is intended to be compatible with code
which has been programmed using the API in the 1.2.x series of releases.
The release is available as always from
As well as from mirrors generously provided by Don Gilbert at Indiana
MD5 signatures for the release files
HTML-ized documentation for the release is available from the
documentation website http://doc.bioperl.org/
The Generic Genome Browser (www.gmod.org) which depends on bioperl will
likely release a new version which will utilize features in bioperl 1.2.3.
This is coordinated by Lincoln Stein and Scott Cain. Code is available
from the project site at http://www.gmod.org.
We plan to release a new version of bioperl-run in the coming week.
bioperl-run is a package of perl module wrappers around many applications
common to bioinformatics analyses. Shawn Hoon is responsible for
overseeing this release. Previous and future releases are available at
http://bioperl.org/DIST/ and in CPAN and as always from our CVS
A brand new package bioperl-microarray will be released this week as well,
version 0.1. This is a project headed by Allen Day and he will be
announcing a code release shortly. The code will be available from CPAN,
http://bioperl.org/DIST, and http://cvs.open-bio.org/.
Another recent project which has not been released yet, but should be out
this fall is bioperl-pedigree. This will include codes for parsing and
representing pedigree data and will interface with genotype parsing and
representations already part of the Bioperl Core. This package is
overseen by Jason Stajich. Code is available from our CVS repository and
will be available at http://bioperl.org/DIST.
The hard work of many people has gone into this release, please see
AUTHORS file for a complete list of individuals who have contributed to
We would especially like to thank those who have provided bug reports and
feedback about the modules to help us improve them. We would like to
welcome several new developers who have joined us recently to provide code
improvements and implementations of new areas for Bioperl.
We intend to focus our energy on the next set of developer's releases in
the Fall of 2003 which will be numbered 1.3.x and will lead to the next
stable release 1.4 in 2004.
We encourage new and old developers to be part of the development cycle as
well as users to provide feedback and bug reports.
Bugs should be reported at our bug tracking site
A synopsis of changes from the Changes file
1.2.3 Stable release update
o Bug #1475 - Fix and add speedup to spliced_seq for remote location
o Bug #1477 - Sel --> Sec abbreviation fixed
o Fix bug #1487 where paring in-between locations when
end < start caused the FTLocationFactory logic to fail.
o Fix bug #1489 which was not dealing with keywords as an
arrayref properly (this is fixed on the main trunk because
keywords returns a string and the array is accessible via
o Bio::Tree::Tree memory leak (bug #1480) fixed
Added a new initialization option -nodelete which
won't try and cleanup the containing nodes if this
o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
this was only present on the branch for the 1.2.1 and 1.2.2 series
- Also merged main trunk changes to the branch which make
newick -> nhx round tripping more effective (storing branch
length and bootstrap values in same locate for NodeNHX and Node
implementations.) Fixes to TreeIO parsing for labeled internal
also required small changes to TreeIO::nhx. Improved
tests for this module as well.
- Fixed bugs in BLAST parsing which couldn't parse NCBI
gapped blast properly (was losing hit significance values due to
the extra unexpeted column).
- Parsing of blastcl3 (netblast from NCBI) now can handle case of
integer overflow (# of letters in nt seq dbs is > MAX_INT)
although doesn't try to correct it - will get the negative
number for you. Added a test for this as well.
- Fixed HMMER parsing bug which prevented parsing when a hmmpfam
report has no top-level family classification scores but does have
scores and alignments for individual domains.
- Parsing FASTA reports where ungapped percent ID is < 10 and the
regular expression to match the line was missing the possibility of
an extra space. This is rare, which is why we probably did not
catch it before.
- BLAST parsing picks up more of the statistics/parameter fields
at the bottom of reports. Still not fully complete.
- SearchIO::Writer::HTMLResultWriter and TextResultWriter
were fixed to include many improvements and added flexiblity
in outputting the files. Bug #1495 was also fixed in the process.
- Update for GFF3 compatibility.
- Added scripts for importing from UCSC and GenBank.
- Added a 1.2003 version number.
- Updated tutorial.
- Added a 1.2003 version number.
o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
properly writing keywords out.
- Fixed bug/enhancement #1513 where dates of
the form D-MMM-YYYY were not parsed. Even though this is
invalid format we can handle it - and also cleanup the date
string so it is properly formatted.
- Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
and written with Genbank format. Similarly bug #1515 is fixed to
parse in the ORIGIN text.
o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
to specify the ID type, one of (accession accession.version
display primary). See Bio::SeqIO::preferred_id_type method
documentation for more information.
o Unigene parsing updated to handle file format changes by NCBI
Jason Stajich on behalf of the Bioperl developers.
jason at cgt.mc.duke.edu
More information about the Bioperl-announce-l