$Id: Changes,v 1.11.2.1 2001/03/02 18:31:25 jason Exp $
Revision history for Bioperl core modules
0.7 Large number of changes, including refactoring of the
Object system, new parsers, new functionality and
all round better system. Highlights are:
o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
Bio::Root::IO for I/O and file/handle capabilities.
o Imported BPlite modules from Ian Korf for BLAST
parsing. This is considered the supported BLAST parser;
Bio::Tools::Blast.pm will eventually phase out due to lack of support.
o Improved Sequence Feature model. Added complete location
modelling (with fuzzy and compound locations). See
Bio::LocationI and the modules under Bio/Location. Added
support in Genbank/EMBL format parsing to completely parse
feature tables for complex locations.
o Moved special support for databanks etc to specialized modules under
Bio/Seq/. One of these supports very large sequences through
a temporary file as a backend.
o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
CDS retrieval and exon shuffling.
o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
DB/GDB (the latter has platform-specific limitations).
o New analysis parser framework for HT sequence annotation (see
Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
o New Alignment IO framework
o New Index modules (Swissprot)
o New modules for running Blast within perl
(Bio::Tools::Run::StandAloneBlast). Added modules for running
Multiple Sequence Alignment tools ClustalW and TCoffee
(Bio::Tools::Run::Alignment).
o New Cookbook-style tutorial (see bptutorial.pl). Improved
documentation across the package.
o Much improved cross platform support. Many known incompatibilities
have been fixed; however, NT and Mac do not work across the entire
setup (see PLATFORMS).
o Many bug fixes, code restructuring, etc. Overall stability and
maintainability benefit a lot.
o A total of 957 automatic tests
0.6.2
There are very few functionality changes but a large
number of software improvements/bug fixes across the package.
o The EMBL/GenBank parsing are improved.
o The Swissprot reading is improved. Swissprot writing
is disabled as it doesn't work at all. This needs to
wait for 0.7 release
o BLAST reports with no hits are correctly parsed.
o Several other bugs of the BLAST parser (regular expressions, ...)
fixed.
o Old syntax calls have been replaced with more modern syntax
o Modules that did not work at all, in particular the Sim4
set have been removed
o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
have improved compliance with interface specs and documentation
o Mailing list documentation updated throughout the distribution
o Most minor bug fixes have happened.
o The scripts in /examples now work and have the modern syntax
rather than the deprecated syntax
0.6.1 Sun April 2 2000
o Sequences can have Sequence Features attached to them
- The sequence features can be read from or written to
EMBL and GenBank style flat files
o Objects for Annotation, including References (but not
full medline abstracts), Database links and Comments are
provided
o A Species object to represent nodes on a taxonomy tree
is provided
o The ability to parse HMMER and Sim4 output has been added
o The Blast parsing has been improved, with better PSI-BLAST
support and better overall behaviour.
o Flat file indexed databases provide both random access
and sequential access to their component sequences.
o A CodonTable object has been written with all known
CodonTables accessible.
o A number of new lightweight analysis tools have been
added, such as molecular weight determination.
The 0.6 release also has improved software engineering
o The sequence objects have been rewritten, providing more
maintainable and easier to implement objects. These
objects are backwardly compatible with the 0.05.1 objects
o Many objects are defined in terms of interfaces and then
a Perl implementation has been provided. The interfaces
are found in the 'I' files (module names ending in 'I').
This means that it is possible to wrap C/CORBA/SQL access
as true "bioperl" objects, compatible with the rest of
bioperl.
o The SeqIO system has been overhauled to provide better
processing and perl-like automatic interpretation of <>
over arguments.
o Many more tests have been added (a total of 172 automatic
tests are now run before release).
0.05.1 Tue Jun 29 05:30:44 1999
- Central distribution now requires Perl 5.004. This was
done to get around 5.003-based problems in Bio/Index/*
and SimpleAlign.
- Various bug fixes in the Bio::Tools::Blast modules
including better exception handling and PSI-Blast
support. See Bio/Tools/Blast/CHANGES for more.
- Fixed the Parse mechanism in Seq.pm to use readseq.
Follow the instructions in README for how to install
it (basically, you have to edit Parse.pm).
- Improved documentation of Seq.pm, indicating where
objects are returned and where strings are returned.
- Fixed uninitialized warnings in Bio::Root::Object.pm
and Bio::Tools::SeqPattern.pm.
- Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
0.05 Sun Apr 25 01:14:11 1999
- Bio::Tools::Blast modules have less memory problems
and faster parsing. Webblast uses LWP and supports
more functionality. See Bio/Tools/Blast/CHANGES for more.
- The Bio::SeqIO system has been started, moving the
sequence reformatting code out of the sequence object
- The Bio::Index:: system has been started, providing
generic index capabilities and specifically works for
Fasta formatted databases and EMBL .dat formatted
databases
- The Bio::DB:: system started, providing access to
databases, both via flat file + index (see above) and
via http to NCBI
- The scripts/ directory, where industrial strength scripts
are put has been started.
- Many changes - a better distribution all round.
0.04.4 Wed Feb 17 02:20:13 1999
- Bug fixes in the Bio::Tools::Blast modules and postclient.pl
(see Bio::Tools::Blast::CHANGES).
- Fixed a bug in Bio::Tools::Fasta::num_seqs().
- Beefed up the t/Fasta.t test script.
- Small fix in Bio::Seq::type() (now always returns a string).
- Changed Bio::Root::Utilities::get_newline_char() to
get_newline() since it could return more than one char.
- Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
- Changed default timeout to 20 seconds (was 3).
- Moved lengthy modification notes to the bottom of some files.
- Fixed SimpleAlign write_fasta bug.
- Beefed up SimpleAlign.t test
0.04.3 Thu Feb 4 07:48:53 1999
- Bio::Root::Object.pm and Global.pm now detect when
script is run as a CGI and suppress output that is only
appropriate when running interactively.
- Bio::Root::Err::_set_context() adds name of script ($0).
- Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
regarding the use of the static objects via the qw(:obj) tag.
- Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
CORE::reverse, avoiding Perl warnings.
- Bug fixes in Bio::Tools::Blast modules (version 0.074) and
example scripts (see Bio::Tools::Blast::CHANGES).
- examples/seq/seqtools.pl no longer always warns about using
-prot or -nucl command-line arguments; only when using the
-debug argument.
- Methods added to Bio::Root::Utilities: create_filehandle(),
get_newline_char(), and taste_file() to generalize filehandle
creation and autodetect newline characters in files/streams
(see bug report #19).
- Bio::Root::IOManager::read() now handles timeouts and uses
Utilities::create_filehandle().
- Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
of hardwiring in "\n".
- Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
0.04.2 Wed Dec 30 02:27:36 1998
- Bug fixes in Bio::Tools::Blast modules, version 0.073
(see Bio::Tools::Blast::CHANGES).
- Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
to CORE::reverse (prevents ambiguous warnings with 5.005).
- Appending '.tmp.bioperl' to temporary files created by
Bio::Root::Utilities::compress() or uncompress() to
make it easy to identify & cleanup these files as needed.
- Developers: Created CVS branch release-0-04-bug from
release-0-04-1. Before making bug fixes to the 0.04.1 release,
be sure to cvs checkout this branch into a clean area.
0.04.1 Wed Dec 16 05:39:15 1998
- Bug fixes in Bio::Tools::Blast modules, version 0.072
(see Bio::Tools::Blast::CHANGES).
- Compile/SW/Makefile.PL now removes *.o and *.a files
with make clean.
0.04 Tue Dec 8 07:49:19 1998
- Lots of new modules added including:
* Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
and Bio/Compile directory containing XS-linked C code for
creating Smith-Waterman sequence alignments from within Perl.
* Steve Chervitz's Blast distribution has been incorporated.
* Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
- Bio/examples directory for demo scripts for all included modules.
- Bio/t directory containing test suit for all included modules.
- For changes specific to the Blast-related modules prior to
incorporation in this central distribution, see the CHANGES
file in the Bio/Tools/Blast directory.
0.01 Tue Sep 8 14:23:22 1998
- original version from central CVS tree; created by h2xs 1.18