$Id: Changes,v 1.30.2.3 2003/03/19 16:58:11 heikki Exp $ Revision history for Bioperl core modules 1.2.1 Stable release update o Inclusion of WrapperBase, a needed component for StandAloneBlast o Addition from main trunk of Ontology objects, principly to allow BioSQL releases against 1.2.1 o Fixes and cleanup of Bio::Coordinate modules o A fix to Bio::Index::EMBL allowing retrieval of entries using the primary accession number o Other bug fixes, including bpindex GenBank fix 1.2 Stable major release o More functionality added to Bio::Perl, the newbie module o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2 Support for New Hampshire Extended (NHX) format parsing. o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome, Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight Hmmpfam parser. o New ontology parsing Bio::Ontology o Bug fixes in Bio::SearchIO for HMMer parsing, support for multi-report (mlib) fasta reports, support for waba and exonerate. o Bio::ClusterIO for parsing Unigene clusters o Bio::Assembly added for representing phrap and ace assembly clusters. o Rudimentary support for writing Chado XML (see GMOD project: www.gmod.org for more information) o Bio::Coordinate for mapping between different coordinate systems such as protein -> cDNA -> Exon -> DNA and back. Useful for mapping features into different coordinate systems. o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries with the get_Stream_by_query method and supports the latest NCBI eutils interface. o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast object for extracting subsets of features : currently only supports extraction by location. 1.1.1 Developer release o Deprecated modules are now listed in the DEPRECATED file o New HowTo documents located in doc/howto describing a domain of Bioperl. o Note that bugs are now stored at bugzilla.bioperl.org and all old bugs are searchable through the bugzilla interface. o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign have been addressed. o Support for Genewise parsing in Bio::Tools::Genewise o Start of Ontology framework with Bio::Ontology o Speedup to the Bio::Root::Root object method _rearrange. A global _load_module method was implemented to simplify the dynamic loading of modules ala Bio::SeqIO::genbank. This method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO, etc). o Several performance improvements to sequence parsing in Bio::SeqIO. Attempt to speedup by reducing object creation overhead. o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved method for sequence retrieval with their E-utils CGI scripts. More work to support Entrez queries to their fullest is planned before 1.2 release. o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot) 1.1 Developer release o Bio::Tools::Run has been broken off into a new pkg bioperl-run, this separation removes some of the complexity in our test suite and separates the core modules in bioperl from those that need external programs to run. o With latest ExtUtils::MakeMaker module installed SGI/IRIX should not run into trouble running the makefile o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly read,create,and write locations for grouped/split locations (like mRNA features on genomic sequence). o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml) and PAML (codeml,aaml, etc) parsing. o Bio::Tree:: objects expanded to handle testing monophyly, paraphyly, least common ancestor, etc. o Bio::Coordinate for mapping locations from different coordinate spaces o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer added for parsing hmmpfam and hmmsearch output. o Bio::SearchIO::Writer::TextResultWriter for outputting a pseudo-blast textfile format 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::Tools::Blast is officially deprecated. Please see Bio::SearchIO for BLAST and FastA parsing. o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts Bio::LocationI objects as well as start/end. 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. See http://obda.open-bio.org for more information. 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 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