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ef5a1dd759
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.
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| audio | ||
| benchmarks | ||
| biology | ||
| cad | ||
| chat | ||
| comms | ||
| converters | ||
| cross | ||
| databases | ||
| devel | ||
| distfiles | ||
| editors | ||
| emulators | ||
| finance | ||
| fonts | ||
| games | ||
| graphics | ||
| ham | ||
| japanese | ||
| lang | ||
| licenses | ||
| math | ||
| mbone | ||
| meta-pkgs | ||
| misc | ||
| mk | ||
| net | ||
| news | ||
| packages | ||
| parallel | ||
| pkgtools | ||
| security | ||
| shells | ||
| sysutils | ||
| templates | ||
| textproc | ||
| time | ||
| wm | ||
| www | ||
| x11 | ||
| Makefile | ||
| Packages.txt | ||
| pkglocate | ||
| README | ||
$NetBSD: README,v 1.11 2000/07/23 18:02:33 fredb Exp $ Welcome to the NetBSD Packages Collection ========================================= In brief, the NetBSD Packages Collection is a set of software utilities and libraries which have been ported to NetBSD. The packages collection software can retrieve the software from its home site, assuming you are connected in some way to the Internet, verify its integrity, apply any patches, configure the software for NetBSD, and build it. Any prerequisite software will also be built and installed for you. Installation and de-installation of software is managed by the packaging utilities. The packages collection is made into a tar_file every week: ftp://ftp.netbsd.org/pub/NetBSD/NetBSD-current/tar_files/pkgsrc.tar.gz and you can sup the pkgsrc tree using the `pkgsrc' name for the collection. The pkgsrc tree is laid out in various categories, and, within that, the various packages themselves. You need to have root privileges to install packages. We are looking at ways to remove this restriction. + To install a package on your system, you need to change into the directory of the package, and type "make install". + If you've made a mistake, and decided that you don't want that package on your system, then type "pkg_delete <pkg-name>", or "make deinstall" while in the directory for the package. + To find out all the packages that you have installed on your system, type "pkg_info". + To remove the work directory, type "make clean", and "make clean-depends" will clean up any working directories for other packages that are built in the process of making your package. + Optionally, you can periodically run "make clean" from the top level pkgsrc directory. This will delete extracted and built files, but will not affect the retreived source sets in pkgsrc/distfiles. + You can set variables to customise the behaviour (where packages are installed, various options for individual packages etc), by setting variables in /etc/mk.conf. The pkgsrc/mk/mk.conf.example file provides some examples for customisation. The best way to find out what packages are in the collection is to move to the top-level pkgsrc directory (this will usually be /usr/pkgsrc), and type "make readme". This will create a file called README.html in the top-level pkgsrc directory, and also in all category and package directories. You can then see what packages are available, along with a short (one-line) comment about the function of the package, and a pointer to a fuller description, by using a browser like lynx (see pkgsrc/www/lynx) or Mozilla (pkgsrc/www/mozilla), or Communicator. This is also available online as ftp://ftp.netbsd.org/pub/NetBSD/packages/pkgsrc/README.html. Another way to find out what packages are in the collection is to move to the top-level pkgsrc directory and type "make index". This will create pkgsrc/INDEX which can be viewed via "make print-index | more". You can also search for particular packages or keywords via "make search key=<somekeyword>". It is also possible to use the packaging software to install pre-compiled binary packages by typing "pkg_add <URL-of-binary-pkg>". To see what binary packages are available, see: ftp://ftp.netbsd.org/pub/NetBSD/packages/<release>/<arch>/All/ where <release> is the NetBSD release, and <arch> is the hardware architecture. One limitation of using binary packages provided from ftp.netbsd.org is that all mk.conf options were set to the defaults at compile time. LOCALBASE, in particular, defaults to /usr/pkg, so non-X binaries will be installed in /usr/pkg/bin, man pages will be installed in /usr/pkg/man... When a packaged tool has major compile time choices, such as support for multiple graphic toolkit libraries, the different options may be available as separate packages. For more information on the packages collection see the file Packages.txt where you found this README, or in your top-level pkgsrc directory.