3 Revision history for Bioperl core modules
8 The 1.6 series is derived from subversion HEAD and exists as a separate
9 release branch. This will represent the last of the alternating
10 developer/stable releases. Code in svn HEAD will be divided up into
11 several smaller packages, including a developer subdistribution for
12 code considered experimental, unstable, or untested.
14 Full detail of changes included since the 1.5.2 release are online at:
15 http://www.bioperl.org/wiki/Change_log. Bugs remaining to be addressed
16 are online at http://bugzilla.open-bio.org, with specific bugs intended
17 for this release series highlighted in BUGS.
19 The following represent the most important changes:
22 - Split into a separate distribution on CPAN, primarily so development
23 isn't reliant on a complete BioPerl release.
24 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
25 is only available via Subversion (via bioperl-live main trunk)
28 - Common test bed for all BioPerl modules
31 - Common Module::Build-based subclass for all BioPerl modules
34 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
35 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
36 and user agent request posting and retrieval
38 o Test implementation and reorganization
39 - Tests have been reorganized into groups based on classes or use
41 - Automated test coverage is now online:
42 http://www.bioperl.org/wiki/Test_Coverage
43 - After this release, untested modules will be moved into a
44 separate developer distribution until tests can be derived.
45 Also, new modules to be added are expected to have a test suite
46 and adequate test coverage.
48 1.5.2 Developer release
49 Full details of changes since 1.5.1 are available online at:
50 http://www.bioperl.org/wiki/Change_log
51 The following represents a brief overview of the most important changes.
54 - Overhaul. Brand new system fully allows markers to have multiple
55 positions on multiple maps, and to have relative positions. Should be
59 - This module and all the modules in the Taxonomy directory now
60 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
65 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
67 * New methods ancestor(), each_Descendent() and _handle_internal_id().
69 * Allows for different database modules to create Bio::Taxon objects
70 with the same internal id when the same taxon is requested from each.
73 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
75 * No longer includes the fake root node 'root'; there are multiple roots
76 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
79 * get_node() has new option -full
81 * Caches data retrieved from website
84 - Now a Bio::Taxon. Carries out the species name -> specific name munging
85 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
86 backward compatability in species() method.
88 o Bio::Search and Bio::SearchIO
89 - Overhaul. The existing system has been sped up via some minor changes
90 (mostly gain-of-function to the API). Bio::PullParserI is introduced
91 as a potential eventual replacment for the existing system, though as
92 yet only a Hmmpfam parser exists written using it.
95 1.5.1 Developer release
97 o Major problem with how Annotations were written out with
98 Bio::Seq is fixed by reverting to old behavior for
99 Bio::Annotation objects.
104 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
105 expect at l east 9 spaces at the beginning of a line to
106 indicate line wrapping.
108 * Treat multi-line SOURCE sections correctly, this defect broke
109 both common_name() and classification()
111 * parse swissprot fields in genpept file
113 * parse WGS genbank records
116 * Changed regexp for ID line. The capturing parentheses are
117 the same, the difference is an optional repeated-not-semi-
118 colon expression following the captured \S+. This means the
119 regexp works when the division looks like /PRO;/ or when the
120 division looks like /ANG ;/ - the latter is from EMBL
123 * fix ID line parsing: the molecule string can have spaces in
124 it. Like: "genomic DNA"
126 - swiss.pm: bugs #1727, #1734
129 * Added parser for entrezgene ASN1 (text format) files.
130 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
134 - maf.pm coordinate problem fixed
136 o Bio::Taxonomy and Bio::DB::Taxonomy
138 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
139 can be done via Web without downloading all the sequence.
141 o Bio::Tools::Run::RemoteBlast supports more options and complies
142 to changes to the NCBI interface. It is reccomended that you
143 retrieve the data in XML instead of plain-text BLAST report to
144 insure proper parsing and retrieval of all information as NCBI
145 fully expects to change things in the future.
147 o Bio::Tree and Bio::TreeIO
149 - Fixes so that re-rooting a tree works properly
151 - Writing out nhx format from a newick/nexus file will properly output
152 bootstrap information. The use must move the internal node labels over
154 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
155 $node->bootstrap($node->id);
158 - Nexus parsing is much more flexible now, does not care about
161 - Cladogram drawing module in Bio::Tree::Draw
163 - Node height and depth now properly calculated
165 - fix tree pruning algorithm so that node with 1 child gets merged
167 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
168 bugs and improvements were added, see Gbrowse mailing list for most of
171 o Bio::DB::GFF partially supports GFF3. See information about
172 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
174 o Better location parsing in Bio::Factory::FTLocationFactory -
175 this is part of the engine for parsing EMBL/GenBank feature table
176 locations. Nested join/order-by/complement are allowed now
178 o Bio::PrimarySeqI->translate now takes named parameters
180 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
181 reconstruction) is now supported. Parsing different models and
182 branch specific parametes are now supported.
184 o Bio::Factory::FTLocationFactory - parse hierarchical locations
187 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
188 for getter/setter functions
192 - blast bug #1739; match scientific notation in score
193 and possible e+ values
195 - blast.pm reads more WU-BLAST parameters and parameters, match
196 a full database pathname,
198 - Handle NCBI WEB and newer BLAST formats specifically
199 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
201 - psl off-by-one error fixed
203 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
204 and HSPs can be constructed from them.
206 - HSPs query/hit now have a seqdesc field filled out (this was
207 always available via $hit->description and
208 $result->query_description
210 - hmmer.pm can parse -A0 hmmpfam files
212 - Writer::GbrowseGFF more customizeable.
214 o Bio::Tools::Hmmpfam
215 make e-value default score displayed in gff, rather than raw score
216 allow parse of multiple records
219 1.5 Developer release
221 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
222 provide Jukes-Cantor and Kimura pairwise distance methods,
225 o Bio::AlignIO support for "po" format of POA, and "maf";
226 Bio::AlignIO::largemultifasta is a new alternative to
227 Bio::AlignIO::fasta for temporary file-based manipulation of
228 particularly large multiple sequence alignments.
230 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
231 be treated similarly as an assembled contig.
233 o Bio::CodonUsage provides new rare_codon() and probable_codons()
234 methods for identifying particular codons that encode a given
237 o Bio::Coordinate::Utils provides new from_align() method to build
238 a Bio::Coordinate pair directly from a
239 Bio::Align::AlignI-conforming object.
241 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
242 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
243 web service using standard Pubmed query syntax, and retrieve
246 o Bio::DB::GFF has various sundry bug fixes.
248 o Bio::FeatureIO is a new SeqIO-style subsystem for
249 writing/reading genomic features to/from files. I/O classes
250 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
251 classes only read/write Bio::SeqFeature::Annotated objects.
252 Notably, the GFF v3 class requires features to be typed into the
255 o Bio::Graph namespace contains new modules for manipulation and
256 analysis of protein interaction graphs.
258 o Bio::Graphics has many bug fixes and shiny new glyphs.
260 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
261 indexing for HMMER reports and FASTA qual files, respectively.
263 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
264 new objects that can be placed within a Bio::Map::MapI-compliant
265 genetic/physical map; Bio::Map::Physical provides a new physical
266 map type; Bio::MapIO::fpc provides finger-printed clone mapping
269 o Bio::Matrix::PSM provide new support for postion-specific
270 (scoring) matrices (e.g. profiles, or "possums").
272 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
273 be instantiated without explicitly using Bio::OntologyIO. This
274 is possible through changes to Bio::Ontology::OntologyStore to
275 download ontology files from the web as necessary. Locations of
276 ontology files are hard-coded into
277 Bio::Ontology::DocumentRegistry.
279 o Bio::PopGen includes many new methods and data types for
280 population genetics analyses.
282 o New constructor to Bio::Range, unions(). Given a list of
283 ranges, returns another list of "flattened" ranges --
284 overlapping ranges are merged into a single range with the
285 mininum and maximum coordinates of the entire overlapping group.
287 o Bio::Root::IO now supports -url, in addition to -file and -fh.
288 The new -url argument allows one to specify the network address
289 of a file for input. -url currently only works for GET
290 requests, and thus is read-only.
292 o Bio::SearchIO::hmmer now returns individual Hit objects for each
293 domain alignment (thus containing only one HSP); previously
294 separate alignments would be merged into one hit if the domain
295 involved in the alignments was the same, but this only worked
296 when the repeated domain occured without interruption by any
297 other domain, leading to a confusing mixture of Hit and HSP
300 o Bio::Search::Result::ResultI-compliant report objects now
301 implement the "get_statistics" method to access
302 Bio::Search::StatisticsI objects that encapsulate any
303 statistical parameters associated with the search (e.g. Karlin's
304 lambda for BLAST/FASTA).
306 o Bio::Seq::LargeLocatableSeq combines the functionality already
307 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
309 o Bio::SeqFeature::Annotated is a replacement for
310 Bio::SeqFeature::Generic. It breaks compliance with the
311 Bio::SeqFeatureI interface because the author was sick of
312 dealing with untyped annotation tags. All
313 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
314 compliant, and accessible through Bio::Annotation::Collection.
316 o Bio::SeqFeature::Primer implements a Tm() method for primer
317 melting point predictions.
319 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
320 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
322 o Bio::Taxonomy::Node now implements the methods necessary for
323 Bio::Species interoperability.
325 o Bio::Tools::CodonTable has new reverse_translate_all() and
326 make_iupac_string() methods.
328 o Bio::Tools::dpAlign now provides sequence profile alignments.
330 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
332 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
335 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
336 for designing small inhibitory RNA.
338 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
339 methods based on a distance matrix.
341 o Bio::Tree::Statistics provides an assess_bootstrap() method to
342 calculate bootstrap support values on a guide tree topology,
343 based on provided bootstrap tree topologies.
345 o Bio::TreeIO now supports the Pagel (PAG) tree format.
351 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
353 o Bio::Graphics will work with gd1 or gd2
356 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
358 - blast.pm Parse multi-line query fields properly
359 - small speed improvements to blasttable.pm and others
361 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
362 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
363 supporting more complex queries
366 1.4. Stable major release
368 Since initial 1.2.0, 3000 separate changes have been made to make this release.
370 o installable scripts
372 o global module version from Bio::Root:Version
375 - major improvements; SVG support
378 - population genetics
379 - support several population genetics types of questions.
380 - Tests for statistical neutrality of mutations
381 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
382 Tests of population structure (Wright's F-statistic: Fst) is in
383 Bio::PopGen::PopStats. Calculating composite linkage
384 disequilibrium (LD) is available in Bio::PopGen::Statistics as
386 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
387 and csv (comma delimited formatted) data.
389 - a directory for implementing population simulations has
390 been added Bio::PopGen::Simulation and 2 simulations - a
391 Coalescent and a simple single-locus multi-allele genetic drift
392 simulation have been provided. This replaces the code in
393 Bio::Tree::RandomTree which has been deprecated until proper
394 methods for generating random phylogenetic trees are
398 - new restrion analysis modules
400 o Bio::Tools::Analysis
401 - web based DNA and Protein analysis framework and several
405 - per residue annotable sequences
408 - Bio::Matrix::PSM - Position Scoring Matrix
409 - Bio::Matrix::IO has been added for generalized parsing of
410 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
411 initial implementations for parsing BLOSUM/PAM and Phylip
412 Distance matricies respectively. A generic matrix
413 implementation for general use was added in
414 Bio::Matrix::Generic.
421 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
422 - small inhibitory RNA
424 o Bio::SeqFeature::Tools
425 - seqFeature mapping tools
426 - Bio::SeqFeature::Tools::Unflattener.pm
427 -- deal with mapping GenBank feature collections into
428 Chado/GFF3 processable feature sets (with SO term mappings)
430 o Bio::Tools::dpAlign
431 - pure perl dynamic programming sequence alignment
434 o new Bio::SearchIO formats
435 - axt and psl: UCSC formats.
436 - blasttable: NCBI -m 8 or -m 9 format from blastall
438 o new Bio::SeqIO formats
439 - chado, tab, kegg, tigr, game
440 - important fixes for old modules
444 o improved Bio::Tools::Genewise
446 o Bio::SeqIO now can recongnize sequence formats automatically from
449 o new parsers in Bio::Tools:
450 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
452 o Bio::DB::Registry bugs fixed
453 - BerkeleyDB-indexed flat files can be used by the OBDA system
454 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
455 used by the OBDA system
458 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
461 o hundreds of new and improved files
465 o Bio::Tree::AlleleNode has been updated to be a container of
466 an Bio::PopGen::Individual object for use in the Coalescent simulations.
471 1.2.3 Stable release update
472 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
474 o Bug #1477 - Sel --> Sec abbreviation fixed
475 o Fix bug #1487 where paring in-between locations when
476 end < start caused the FTLocationFactory logic to fail.
477 o Fix bug #1489 which was not dealing with keywords as an
478 arrayref properly (this is fixed on the main trunk because
479 keywords returns a string and the array is accessible via
481 o Bio::Tree::Tree memory leak (bug #1480) fixed
482 Added a new initialization option -nodelete which
483 won't try and cleanup the containing nodes if this
485 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
486 this was only present on the branch for the 1.2.1 and 1.2.2 series
487 - Also merged main trunk changes to the branch which make
488 newick -> nhx round tripping more effective (storing branch length
489 and bootstrap values in same locate for NodeNHX and Node
490 implementations.) Fixes to TreeIO parsing for labeled internal
491 also required small changes to TreeIO::nhx. Improved
492 tests for this module as well.
494 - Fixed bugs in BLAST parsing which couldn't parse NCBI
495 gapped blast properly (was losing hit significance values due to
496 the extra unexpeted column).
497 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
498 integer overflow (# of letters in nt seq dbs is > MAX_INT)
499 although doesn't try to correct it - will get the negative
500 number for you. Added a test for this as well.
501 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
502 has no top-level family classification scores but does have scores and
503 alignments for individual domains.
504 - Parsing FASTA reports where ungapped percent ID is < 10 and the
505 regular expression to match the line was missing the possibility of
506 an extra space. This is rare, which is why we probably did not
508 - BLAST parsing picks up more of the statistics/parameter fields
509 at the bottom of reports. Still not fully complete.
510 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
511 were fixed to include many improvements and added flexiblity
512 in outputting the files. Bug #1495 was also fixed in the process.
514 - Update for GFF3 compatibility.
515 - Added scripts for importing from UCSC and GenBank.
516 - Added a 1.2003 version number.
519 - Added a 1.2003 version number.
520 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
521 properly writing keywords out.
522 o Bio::SeqIO::genbank
523 - Fixed bug/enhancement #1513 where dates of
524 the form D-MMM-YYYY were not parsed. Even though this is
525 invalid format we can handle it - and also cleanup the date
526 string so it is properly formatted.
527 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
528 and written with Genbank format. Similarly bug #1515 is fixed to
529 parse in the ORIGIN text.
530 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
531 to specify the ID type, one of (accession accession.version
532 display primary). See Bio::SeqIO::preferred_id_type method
533 documentation for more information.
534 o Unigene parsing updated to handle file format changes by NCBI
536 1.2.2 Stable release update
538 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
539 - auto-discover ontology name
540 - bug in parsing relationships when certain characters are in the term
541 - fixed hard-coded prefix for term identifiers
542 - various smaller issues
544 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
545 of Bio::Ontology::TermI
547 o brought the OBDA Registry code up to latest specs
551 - accession number retrieval fixed
553 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
555 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
556 #1459 which now properly report alignment start/end info
557 for translated BLAST/FASTA searches.
559 o Bio::TreeIO::newick can parse labeled internal nodes
561 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
562 for BLASTX if if you provide -report_type => 'BLASTX' when
563 initializing a BPbl2seq object. Bioperl 1.3 will have better
564 support for bl2seq in the SearchIO system.
566 o Bio::Root::IO support a -noclose boolean flag which will not
567 close a filehandle upon object cleanup - useful when sharing
568 a filehandle among objects. Additionally code added s.t.
569 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
571 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
573 o Bio::SeqIO::genbank
574 - bug #1456 fixed which generated extra sequence lines
575 - write moltype correctly for genpept
577 1.2.1 Stable release update
579 o Inclusion of WrapperBase, a needed component for StandAloneBlast
581 o Addition from main trunk of Ontology objects, principly to allow
582 BioSQL releases against 1.2.1
584 o Fixes and cleanup of Bio::Coordinate modules
586 o A fix to Bio::Index::EMBL allowing retrieval of entries using
587 the primary accession number
589 o Other bug fixes, including bpindex GenBank fix
591 o Bio::SeqIO::genbank bug #1389 fixed
593 1.2 Stable major release
595 o More functionality added to Bio::Perl, the newbie module
597 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
598 Support for New Hampshire Extended (NHX) format parsing.
600 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
601 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
604 o New ontology parsing Bio::Ontology
606 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
607 multi-report (mlib) fasta reports, support for waba and exonerate.
609 o Bio::ClusterIO for parsing Unigene clusters
611 o Bio::Assembly added for representing phrap and ace assembly clusters.
613 o Rudimentary support for writing Chado XML (see
614 GMOD project: www.gmod.org for more information)
616 o Bio::Coordinate for mapping between different coordinate systems such
617 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
618 features into different coordinate systems.
620 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
621 with the get_Stream_by_query method and supports the latest
622 NCBI eutils interface.
624 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
625 object for extracting subsets of features : currently only
626 supports extraction by location.
628 1.1.1 Developer release
630 o Deprecated modules are now listed in the DEPRECATED file
632 o New HowTo documents located in doc/howto describing
635 o Note that bugs are now stored at bugzilla.bioperl.org
636 and all old bugs are searchable through the bugzilla interface.
638 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
641 o Support for Genewise parsing in Bio::Tools::Genewise
643 o Start of Ontology framework with Bio::Ontology
645 o Speedup to the Bio::Root::Root object method _rearrange.
646 A global _load_module method was implemented to simplify the
647 dynamic loading of modules ala Bio::SeqIO::genbank. This
648 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
651 o Several performance improvements to sequence parsing in Bio::SeqIO.
652 Attempt to speedup by reducing object creation overhead.
654 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
655 method for sequence retrieval with their E-utils CGI scripts.
656 More work to support Entrez queries to their fullest is planned
659 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
661 1.1 Developer release
663 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
664 this separation removes some of the complexity in our test suite
665 and separates the core modules in bioperl from those that need
666 external programs to run.
668 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
669 not run into trouble running the makefile
671 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
672 read,create,and write locations for grouped/split locations
673 (like mRNA features on genomic sequence).
675 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
676 and PAML (codeml,aaml, etc) parsing.
678 o Bio::Tree:: objects expanded to handle testing monophyly,
679 paraphyly, least common ancestor, etc.
681 o Bio::Coordinate for mapping locations from different coordinate spaces
683 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
684 added for parsing hmmpfam and hmmsearch output.
686 o Bio::SearchIO::Writer::TextResultWriter for outputting
687 a pseudo-blast textfile format
690 1.0.2 Bug fix release
692 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
693 in this release will not work after December 2002 when NCBI
694 shuts off the old Entrez cgi scripts. We have already fixed
695 on our main development branch and the functionality will be
696 available in the next stable bioperl release (1.2) slated for
699 o Numerous parsing bugs in Bio::SearchIO::fasta found through
700 testset by Robin Emig. These were fixed as was the get_aln
701 method in Bio::Search::HSP::GenericHSP to handle the extra
702 context sequence that is provided with a FastA alignment.
704 o Migrating differences between Bio::Search::XX::BlastXX to
705 Bio::Search::XX::GenericXX objects. This included mechanism
706 to retrieve whole list of HSPs from Hits and whole list of Hits from
707 Results in addition to the current next_XX iterator methods that
708 are available. Added seq_inds() method to GenericHSP which identifies
709 indexes in the query or hit sequences where conserved,identical,gaps,
710 or mismatch residues are located (adapted from Steve Chervitz's
711 implementation in BlastHSP).
713 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
714 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
716 o Bio::Graphics glyph set improved and extended for GBrowse release
718 o Bio::Tree::Tree get_nodes implementation improvement thanks
719 to Howard Ross notice performance problem when writing out
722 o Bio::Location::Fuzzy::new named parameter -loc_type became
723 -location_type, Bio::Location::Simple::new named parameter
724 -seqid becamse -seq_id.
726 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
727 was mis-detecting that gaps should be placed at the beginning of
728 the alignment when the best alignment starts internally in the
731 1.0.1 Bug fix release
733 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
735 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
736 and mixed (3.3 - 3.4) versions of FASTA.
738 o Small API change to add methods for completeness across
739 implementations of Bio::Search objects. These new methods
740 in the interface are implemented by the GenericXX object as well
741 as the BlastXX objects.
742 * Bio::Search::Result::ResultI
743 - hits() method returns list of all Hits (next_hit is an
746 * Bio::Search::Hit::HitI
747 - hsps() method returns list of all HSPs (next_hsp is an
750 o The Bio::SearchIO::Writer classes have been fixed to handle results
751 created from either psiblast (Search::BlastXX objects) or
752 blast|fasta|blastxml objects (Search::GenericXX objects). More work
753 has to be done here to make it work properly and will nee major
756 o Bugs in Bio::Tools::HMMER fixed, including
757 * #1178 - Root::IO destructor wasn't being called
758 * #1034 - filter_on_cutoff now behaves properly
760 o Bio::SeqFeature::Computation initialization args fixed and
763 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
765 o Updated FAQ with more example based answers to typical questions
767 o Bug #1202 was fixed which would improperly join together qual values
768 parsed by Bio::SeqIO::qual when a trailing space was not present before
771 1.0.0 Major Stable Release
773 This represents a major release of bioperl with significant
774 improvements over the 0.7.x series of releases.
776 o Bio::Tools::Blast is officially deprecated. Please see
777 Bio::SearchIO for BLAST and FastA parsing.
779 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
780 Bio::LocationI objects as well as start/end.
782 o Bio::Biblio contains modules for Bibliographic data.
783 Bio::DB::Biblio contains the query modules. Additionally one can
784 parse medlinexml from the ebi bibliographic query service (BQS)
785 system and Pubmed xml from NCBI. See Martin Senger's
786 documentation in Bio::Biblio for more information.
788 o Bio::DB::Registry is a sequence database registry part of
789 Open Bioinformatics Database Access. See
790 http://obda.open-bio.org for more information.
792 o File-based and In-Memory Sequence caching is provided by
793 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
796 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
797 been added by Lincoln Stein.
799 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
801 o A FAQ has been started and is included in the release to provide
802 a starting point for frequent questions and issues.
804 0.9.3 Developer's release
806 o Event based parsing system improved (SearchIO). With parsers for
807 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
808 Additionally a lazy parsing system for text and html blast reports was
809 added and is called psiblast (name subject to change in future releases).
811 o Bio::Search objects improved and standardized with associated Interfaces
812 written. The concept of a search "Hit" was standardized to be called
813 "hit" consistently and the use of "subject" was deprecated in all active
816 o Bio::Structure added (since 0.9.1) for Protein structure objects
817 and PDB parser to retrieve and write these structures from data files.
819 o Several important Bio::DB::GFF bug fixes for handling features that
820 are mapped to multiple reference points. Updated mysql adaptor
821 so as to be able to store large (>100 megabase) chunks of DNA into
822 Bio::DB::GFF databases.
824 0.9.2 Developer's release
826 o Bio::Search and Bio::SearchIO system introduced for event based
827 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
828 in text and XML and FASTA reports in standard output format.
830 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
831 generator is included in Bio::TreeIO::RandomTrees and a
832 statistics module for evaluating.
834 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
835 server for DAS servers.
837 o Bio::Tools::BPlite is provides more robust parsing of BLAST
838 files. The entire BPlite system migrated to using Bio::Root::IO
841 o Bio::Tools::Alignment for Consed and sequence Trimming
844 o Bio::Structure for Protein structure information and parsing
846 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
847 cgi-bin entry point which should be more reliable.
849 o Bio::Map and Bio::MapIO for biological map navigation and a
850 framework afor parsing them in. Only preliminary work here.
852 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
853 Future work will integrate Pise and allow submission of analysis on
856 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
857 introduced as new objects for handling Sequence Annotation
858 information (dblinks, references, etc) and is more robust that
861 o Bio::Tools::FASTAParser introduced.
863 o Scripts from the bioperl script submission project and new
864 scripts from bioperl authors are included in "scripts" directory.
866 o Factory objects and interfaces are being introduced and are more
869 o Bio::Root::Root introduced as the base object while
870 Bio::Root::RootI is now simply an interface.
872 o Bio::DB::RefSeq provides database access to copy of the NCBI
873 RefSeq database using the EBI dbfetch script.
875 0.9.0 Developer's release
877 o perl version at least 5.005 is now required instead of perl 5.004
879 o Bio::Tools::Run::RemoteBlast is available for running remote
882 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
884 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
885 Also added are related modules UTR3, UTR5, Exon, Intron,
886 Promotor, PolyA and Transcript.
888 o Speedup of translate method in PrimarySeq
890 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
891 select(), dot(), get_seq_by_pos(), column_from_residue_number()
893 o Various fixes to Variation toolkit
895 o Bio::DB::EMBL provides database access to EMBL sequence data.
896 Bio::DB::Universal provides a central way to point to indexes
897 and dbs in a single interface.
899 o Bio::DB::GFF - a database suitable for running DAS servers locally.
901 o Bio::Factory::EMBOSS is still in design phase as is
902 Bio::Factory::ApplicationFactoryI
904 o Dia models for bioperl design are provided in the models/ directory
906 0.7.2 Bug fix release
908 o documentation fixes in many modules - SYNOPSIS code verified
909 to be runnable in many (but not all modules)
911 o corrected MANIFEST file from 0.7.1 release
913 o Bug fix in Bio::SeqIO::FTHelper to properly handle
916 o Bio::SeqIO::genbank
917 * Correct parsing and writing of genbank format with protein data
918 * moltype and molecule separation
920 o Bio::SeqIO::largefasta fix to avoid inifinite loops
922 o Bio::SimpleAlign fixed to correctly handle consensus
925 o Bio::Tools::HMMER supports hmmer 2.2g
927 o Bio::Tools::BPlite to support report type specific parsing. Most
928 major changes are not on the 0.7 branch.
930 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
933 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
934 in several types of mutations:
935 1.) AA level: deletion, complex
936 2.) AA level: complex, inframe
937 3.) RNA level: silent
939 o BPbl2seq parsing of empty reports will not die, but will return
940 a valid, empty, Bio::SeqFeature::SimilarityFeature for
941 $report->query() and $report->subject() methods. So an easy
942 way to test if report was empty is to see if
943 $report->query->seqname is undefined.
945 0.7.1 Bug fix release
947 o Better parsing of genbank/EMBL files especially fixing bugs
948 related to Feature table parsing and locations on remote
949 sequences. Additionally, species name parsing was better.
951 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
952 which include a number of header lines.
954 o More strict genbank and EMBL format writing (corrected number of
955 spaces where appropriate).
957 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
958 for related BPlite BUGS that are unresolved in this release.
960 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
961 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
962 use expasy mirrors or EBI dbfetch cgi-script.
964 o A moderate number of documentation improvements were made as
965 well to provide a better code synopsis in each module.
968 0.7 Large number of changes, including refactoring of the
969 Object system, new parsers, new functionality and
970 all round better system. Highlights are:
973 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
974 Bio::Root::IO for I/O and file/handle capabilities.
976 o Imported BPlite modules from Ian Korf for BLAST
977 parsing. This is considered the supported BLAST parser;
978 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
980 o Improved Sequence Feature model. Added complete location
981 modelling (with fuzzy and compound locations). See
982 Bio::LocationI and the modules under Bio/Location. Added
983 support in Genbank/EMBL format parsing to completely parse
984 feature tables for complex locations.
986 o Moved special support for databanks etc to specialized modules under
987 Bio/Seq/. One of these supports very large sequences through
988 a temporary file as a backend.
990 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
991 CDS retrieval and exon shuffling.
993 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
995 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
996 DB/GDB (the latter has platform-specific limitations).
998 o New analysis parser framework for HT sequence annotation (see
999 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1001 o New Alignment IO framework
1003 o New Index modules (Swissprot)
1005 o New modules for running Blast within perl
1006 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1007 Multiple Sequence Alignment tools ClustalW and TCoffee
1008 (Bio::Tools::Run::Alignment).
1010 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1011 documentation across the package.
1013 o Much improved cross platform support. Many known incompatibilities
1014 have been fixed; however, NT and Mac do not work across the entire
1015 setup (see PLATFORMS).
1017 o Many bug fixes, code restructuring, etc. Overall stability and
1018 maintainability benefit a lot.
1020 o A total of 957 automatic tests
1025 There are very few functionality changes but a large
1026 number of software improvements/bug fixes across the package.
1028 o The EMBL/GenBank parsing are improved.
1030 o The Swissprot reading is improved. Swissprot writing
1031 is disabled as it doesn't work at all. This needs to
1032 wait for 0.7 release
1034 o BLAST reports with no hits are correctly parsed.
1036 o Several other bugs of the BLAST parser (regular expressions, ...)
1039 o Old syntax calls have been replaced with more modern syntax
1041 o Modules that did not work at all, in particular the Sim4
1042 set have been removed
1044 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1045 have improved compliance with interface specs and documentation
1047 o Mailing list documentation updated throughout the distribution
1049 o Most minor bug fixes have happened.
1051 o The scripts in /examples now work and have the modern syntax
1052 rather than the deprecated syntax
1055 0.6.1 Sun April 2 2000
1057 o Sequences can have Sequence Features attached to them
1058 - The sequence features can be read from or written to
1059 EMBL and GenBank style flat files
1061 o Objects for Annotation, including References (but not
1062 full medline abstracts), Database links and Comments are
1065 o A Species object to represent nodes on a taxonomy tree
1068 o The ability to parse HMMER and Sim4 output has been added
1070 o The Blast parsing has been improved, with better PSI-BLAST
1071 support and better overall behaviour.
1073 o Flat file indexed databases provide both random access
1074 and sequential access to their component sequences.
1076 o A CodonTable object has been written with all known
1077 CodonTables accessible.
1079 o A number of new lightweight analysis tools have been
1080 added, such as molecular weight determination.
1082 The 0.6 release also has improved software engineering
1084 o The sequence objects have been rewritten, providing more
1085 maintainable and easier to implement objects. These
1086 objects are backwardly compatible with the 0.05.1 objects
1088 o Many objects are defined in terms of interfaces and then
1089 a Perl implementation has been provided. The interfaces
1090 are found in the 'I' files (module names ending in 'I').
1092 This means that it is possible to wrap C/CORBA/SQL access
1093 as true "bioperl" objects, compatible with the rest of
1096 o The SeqIO system has been overhauled to provide better
1097 processing and perl-like automatic interpretation of <>
1100 o Many more tests have been added (a total of 172 automatic
1101 tests are now run before release).
1105 0.05.1 Tue Jun 29 05:30:44 1999
1106 - Central distribution now requires Perl 5.004. This was
1107 done to get around 5.003-based problems in Bio/Index/*
1109 - Various bug fixes in the Bio::Tools::Blast modules
1110 including better exception handling and PSI-Blast
1111 support. See Bio/Tools/Blast/CHANGES for more.
1112 - Fixed the Parse mechanism in Seq.pm to use readseq.
1113 Follow the instructions in README for how to install
1114 it (basically, you have to edit Parse.pm).
1115 - Improved documentation of Seq.pm, indicating where
1116 objects are returned and where strings are returned.
1117 - Fixed uninitialized warnings in Bio::Root::Object.pm
1118 and Bio::Tools::SeqPattern.pm.
1119 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1121 0.05 Sun Apr 25 01:14:11 1999
1122 - Bio::Tools::Blast modules have less memory problems
1123 and faster parsing. Webblast uses LWP and supports
1124 more functionality. See Bio/Tools/Blast/CHANGES for more.
1125 - The Bio::SeqIO system has been started, moving the
1126 sequence reformatting code out of the sequence object
1127 - The Bio::Index:: system has been started, providing
1128 generic index capabilities and specifically works for
1129 Fasta formatted databases and EMBL .dat formatted
1131 - The Bio::DB:: system started, providing access to
1132 databases, both via flat file + index (see above) and
1134 - The scripts/ directory, where industrial strength scripts
1135 are put has been started.
1136 - Many changes - a better distribution all round.
1138 0.04.4 Wed Feb 17 02:20:13 1999
1139 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1140 (see Bio::Tools::Blast::CHANGES).
1141 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1142 - Beefed up the t/Fasta.t test script.
1143 - Small fix in Bio::Seq::type() (now always returns a string).
1144 - Changed Bio::Root::Utilities::get_newline_char() to
1145 get_newline() since it could return more than one char.
1146 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1147 - Changed default timeout to 20 seconds (was 3).
1148 - Moved lengthy modification notes to the bottom of some files.
1149 - Fixed SimpleAlign write_fasta bug.
1150 - Beefed up SimpleAlign.t test
1152 0.04.3 Thu Feb 4 07:48:53 1999
1153 - Bio::Root::Object.pm and Global.pm now detect when
1154 script is run as a CGI and suppress output that is only
1155 appropriate when running interactively.
1156 - Bio::Root::Err::_set_context() adds name of script ($0).
1157 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1158 regarding the use of the static objects via the qw(:obj) tag.
1159 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1160 CORE::reverse, avoiding Perl warnings.
1161 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1162 example scripts (see Bio::Tools::Blast::CHANGES).
1163 - examples/seq/seqtools.pl no longer always warns about using
1164 -prot or -nucl command-line arguments; only when using the
1166 - Methods added to Bio::Root::Utilities: create_filehandle(),
1167 get_newline_char(), and taste_file() to generalize filehandle
1168 creation and autodetect newline characters in files/streams
1169 (see bug report #19).
1170 - Bio::Root::IOManager::read() now handles timeouts and uses
1171 Utilities::create_filehandle().
1172 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1173 of hardwiring in "\n".
1174 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1176 0.04.2 Wed Dec 30 02:27:36 1998
1177 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1178 (see Bio::Tools::Blast::CHANGES).
1179 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1180 to CORE::reverse (prevents ambiguous warnings with 5.005).
1181 - Appending '.tmp.bioperl' to temporary files created by
1182 Bio::Root::Utilities::compress() or uncompress() to
1183 make it easy to identify & cleanup these files as needed.
1184 - Developers: Created CVS branch release-0-04-bug from
1185 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1186 be sure to cvs checkout this branch into a clean area.
1188 0.04.1 Wed Dec 16 05:39:15 1998
1189 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1190 (see Bio::Tools::Blast::CHANGES).
1191 - Compile/SW/Makefile.PL now removes *.o and *.a files
1194 0.04 Tue Dec 8 07:49:19 1998
1195 - Lots of new modules added including:
1196 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1197 and Bio/Compile directory containing XS-linked C code for
1198 creating Smith-Waterman sequence alignments from within Perl.
1199 * Steve Chervitz's Blast distribution has been incorporated.
1200 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1201 - Bio/examples directory for demo scripts for all included modules.
1202 - Bio/t directory containing test suit for all included modules.
1203 - For changes specific to the Blast-related modules prior to
1204 incorporation in this central distribution, see the CHANGES
1205 file in the Bio/Tools/Blast directory.
1207 0.01 Tue Sep 8 14:23:22 1998
1208 - original version from central CVS tree; created by h2xs 1.18