$Id: Changes,v 1.23.2.6 2002/07/15 01:42:34 jason Exp $
Revision history for Bioperl core modules
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
Fall 2002.
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
unbalanced trees.
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
sequence.
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