$Id: Changes,v 1.23.2.4 2002/06/04 22:53:32 jason Exp $
Revision history for Bioperl core modules
1.0.1 Bug fix release
o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
and mixed (3.3 - 3.4) versions of FASTA.
o Small API change to add methods for completeness across
implementations of Bio::Search objects. These new methods
in the interface are implemented by the GenericXX object as well
as the BlastXX objects.
* Bio::Search::Result::ResultI
- hits() method returns list of all Hits (next_hit is an
iterator method)
* Bio::Search::Hit::HitI
- hsps() method returns list of all HSPs (next_hsp is an
iterator method)
o The Bio::SearchIO::Writer classes have been fixed to handle results
created from either psiblast (Search::BlastXX objects) or
blast|fasta|blastxml objects (Search::GenericXX objects). More work
has to be done here to make it work properly and will nee major
API changes.
o Bugs in Bio::Tools::HMMER fixed, including
* #1178 - Root::IO destructor wasn't being called
* #1034 - filter_on_cutoff now behaves properly
o Bio::SeqFeature::Computation initialization args fixed and
tests added.
o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
o Updated FAQ with more example based answers to typical questions
o Bug #1202 was fixed which would improperly join together qual values
parsed by Bio::SeqIO::qual when a trailing space was not present before
the newline.
1.0.0 Major Stable Release
This represents a major release of bioperl with significant
improvements over the 0.7.x series of releases.
o Bio::Biblio contains modules for Bibliographic data.
Bio::DB::Biblio contains the query modules. Additionally one can
parse medlinexml from the ebi bibliographic query service (BQS)
system and Pubmed xml from NCBI. See Martin Senger's
documentation in Bio::Biblio for more information.
o Bio::DB::Registry is a sequence database registry part of Open
Bioinformatics Database Access. Additionally Bio::DB::Flat was
introduced to support the cross-project OBDA standard for
indexed flatfiles. See http://obda.open-bio.org for more
information. This project is under active development so the
modules in this release represent preliminary implementations.
o File-based and In-Memory Sequence caching is provided by
Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
local database.
o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
been added by Lincoln Stein.
o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
o Bio::Map and Bio::MapIO for biological map navigation and a
framework afor parsing them in.
o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
Future work will integrate Pasteur Institute's Pise and EBI's openBSA
analysis queues for remote analysis.
o Bio::AnnotationCollectionI and Bio::Annotation::Collection
introduced as new objects for handling Sequence Annotation
information (dblinks, references, etc) and is more robust that
previous annotation handling object.
o Bio::SearchIO was introduced to support an extensible framework
for sequence database search results. Currently blast, NCBI XML
blast format (-m 7), and FastA parsing are implemented. The
Bio::Search objects were added to represent the Result, Hit, and
HSP objects retrieved from a search. To support this new
direction Bio::Tools::Blast is officially deprecated.
o Bio::SearchIO::Writer system allows output of Bio::Search
objects in a tabular or HTML form.
o Bio::DB::GFF is Lincoln Stein's database implementation of GFF
files which can be used for DAS backends and is part of the
Generic Model Organism Database project (http://gmod.sourceforge.net).
o Bio::Tree and Bio::TreeIO namespaces and modules were added to
support representation and parsing of phylogenetic trees.
o Bio::Structure as added in 0.9.1 and includes a pdb parser and
objects to represent protein structure.
o More Multiple Sequence formats have been added for parsing or writing.
o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
Bio::LocationI objects as well as start/end.
o Bio::SimpleAlign now supports two methods for calculating
average and overall percentage identity.
o 30% speedup was achieved in SeqIO genbank and embl parsers,
future releases will focus on an event based parsing system
where we hope to achieve improved parsing speeds.
o A FAQ has been started and is included in the release to provide
a starting point for frequent questions and issues.
0.9.3 Developer's release
o Event based parsing system improved (SearchIO). With parsers for
XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
Additionally a lazy parsing system for text and html blast reports was
added and is called psiblast (name subject to change in future releases).
o Bio::Search objects improved and standardized with associated Interfaces
written. The concept of a search "Hit" was standardized to be called
"hit" consistently and the use of "subject" was deprecated in all active
modules.
o Bio::Structure added (since 0.9.1) for Protein structure objects
and PDB parser to retrieve and write these structures from data files.
o Several important Bio::DB::GFF bug fixes for handling features that
are mapped to multiple reference points. Updated mysql adaptor
so as to be able to store large (>100 megabase) chunks of DNA into
Bio::DB::GFF databases.
0.9.2 Developer's release
o Bio::Search and Bio::SearchIO system introduced for event based
parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
in text and XML and FASTA reports in standard output format.
o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
generator is included in Bio::TreeIO::RandomTrees and a
statistics module for evaluating.
o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
server for DAS servers.
o Bio::Tools::BPlite is provides more robust parsing of BLAST
files. The entire BPlite system migrated to using Bio::Root::IO
for the data stream.
o Bio::Tools::Alignment for Consed and sequence Trimming
functionality.
o Bio::Structure for Protein structure information and parsing
o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
cgi-bin entry point which should be more reliable.
o Bio::Map and Bio::MapIO for biological map navigation and a
framework afor parsing them in. Only preliminary work here.
o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
Future work will integrate Pise and allow submission of analysis on
remote servers.
o Bio::AnnotationCollectionI and Bio::Annotation::Collection
introduced as new objects for handling Sequence Annotation
information (dblinks, references, etc) and is more robust that
previous system.
o Bio::Tools::FASTAParser introduced.
o Scripts from the bioperl script submission project and new
scripts from bioperl authors are included in "scripts" directory.
o Factory objects and interfaces are being introduced and are more
strictly enforced.
o Bio::Root::Root introduced as the base object while
Bio::Root::RootI is now simply an interface.
o Bio::DB::RefSeq provides database access to copy of the NCBI
RefSeq database using the EBI dbfetch script.
0.9.0 Developer's release
o perl version at least 5.005 is now required instead of perl 5.004
o Bio::Tools::Run::RemoteBlast is available for running remote
blast jobs at NCBI.
o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
Also added are related modules UTR3, UTR5, Exon, Intron,
Promotor, PolyA and Transcript.
o Speedup of translate method in PrimarySeq
o Bio::SimpleAlign has new methods: location_from_column(), slice(),
select(), dot(), get_seq_by_pos(), column_from_residue_number()
o Various fixes to Variation toolkit
o Bio::DB::EMBL provides database access to EMBL sequence data.
Bio::DB::Universal provides a central way to point to indexes
and dbs in a single interface.
o Bio::DB::GFF - a database suitable for running DAS servers locally.
o Bio::Factory::EMBOSS is still in design phase as is
Bio::Factory::ApplicationFactoryI
o Dia models for bioperl design are provided in the models/ directory
0.7.2 Bug fix release
o documentation fixes in many modules - SYNOPSIS code verified
to be runnable in many (but not all modules)
o corrected MANIFEST file from 0.7.1 release
o Bug fix in Bio::SeqIO::FTHelper to properly handle
split locations
o Bio::SeqIO::genbank
* Correct parsing and writing of genbank format with protein data
* moltype and molecule separation
o Bio::SeqIO::largefasta fix to avoid inifinite loops
o Bio::SimpleAlign fixed to correctly handle consensus
sequence calculation
o Bio::Tools::HMMER supports hmmer 2.2g
o Bio::Tools::BPlite to support report type specific parsing. Most
major changes are not on the 0.7 branch.
o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
with File::Spec
o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
in several types of mutations:
1.) AA level: deletion, complex
2.) AA level: complex, inframe
3.) RNA level: silent
o BPbl2seq parsing of empty reports will not die, but will return
a valid, empty, Bio::SeqFeature::SimilarityFeature for
$report->query() and $report->subject() methods. So an easy
way to test if report was empty is to see if
$report->query->seqname is undefined.
0.7.1 Bug fix release
o Better parsing of genbank/EMBL files especially fixing bugs
related to Feature table parsing and locations on remote
sequences. Additionally, species name parsing was better.
o Bio::SeqIO::genbank can parse now NCBI produced genbank database
which include a number of header lines.
o More strict genbank and EMBL format writing (corrected number of
spaces where appropriate).
o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
for related BPlite BUGS that are unresolved in this release.
o Bio::DB::GenBank, Bio::DB::GenPept have less problems
downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
use expasy mirrors or EBI dbfetch cgi-script.
o A moderate number of documentation improvements were made as
well to provide a better code synopsis in each module.
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