Revision history for Bioperl core modules 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