3 Revision history for Bioperl core modules
9 The 1.6 series is derived from subversion HEAD and exists as a separate
10 release branch. This will represent the last of the alternating
11 developer/stable releases. Code in Subversion HEAD will be divided up into
12 several smaller packages, including a developer subdistribution for
13 code considered experimental, unstable, or untested.
15 Full detail of changes included since the 1.5.2 release are online at:
16 http://www.bioperl.org/wiki/Change_log. Bugs remaining to be addressed
17 are online at http://bugzilla.open-bio.org, with specific bugs intended
18 for this release series highlighted in BUGS.
20 The following represent the most important changes:
24 o Feature/Annotation rollback
25 - Problematic changes introduced prior to the 1.5 release have been rolled
26 back. These changes led to subtle bugs involving operator overloading
27 and interface methods.
28 - Behavior is very similar to that for BioPerl 1.4, with tag values being
29 stored generically as simple scalars. Results in a modest speedup.
32 - Split into a separate distribution on CPAN, primarily so development
33 isn't reliant on a complete BioPerl release.
34 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
35 is only available via Subversion (via bioperl-live main trunk)
38 - Common test bed for all BioPerl modules
41 - Common Module::Build-based subclass for all BioPerl modules
44 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
45 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
46 and user agent request posting and retrieval
48 o Test implementation and reorganization
49 - Tests have been reorganized into groups based on classes or use
51 - Automated test coverage is now online:
52 http://www.bioperl.org/wiki/Test_Coverage
53 - After this release, untested modules will be moved into a
54 separate developer distribution until tests can be derived.
55 Also, new modules to be added are expected to have a test suite
56 and adequate test coverage.
58 1.5.2 Developer release
60 Full details of changes since 1.5.1 are available online at:
61 http://www.bioperl.org/wiki/Change_log
62 The following represents a brief overview of the most important changes.
65 - Overhaul. Brand new system fully allows markers to have multiple
66 positions on multiple maps, and to have relative positions. Should be
70 - This module and all the modules in the Taxonomy directory now
71 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
76 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
78 * New methods ancestor(), each_Descendent() and _handle_internal_id().
80 * Allows for different database modules to create Bio::Taxon objects
81 with the same internal id when the same taxon is requested from each.
84 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
86 * No longer includes the fake root node 'root'; there are multiple roots
87 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
90 * get_node() has new option -full
92 * Caches data retrieved from website
95 - Now a Bio::Taxon. Carries out the species name -> specific name munging
96 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
97 backward compatability in species() method.
99 o Bio::Search and Bio::SearchIO
100 - Overhaul. The existing system has been sped up via some minor changes
101 (mostly gain-of-function to the API). Bio::PullParserI is introduced
102 as a potential eventual replacment for the existing system, though as
103 yet only a Hmmpfam parser exists written using it.
106 1.5.1 Developer release
108 o Major problem with how Annotations were written out with
109 Bio::Seq is fixed by reverting to old behavior for
110 Bio::Annotation objects.
115 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
116 expect at l east 9 spaces at the beginning of a line to
117 indicate line wrapping.
119 * Treat multi-line SOURCE sections correctly, this defect broke
120 both common_name() and classification()
122 * parse swissprot fields in genpept file
124 * parse WGS genbank records
127 * Changed regexp for ID line. The capturing parentheses are
128 the same, the difference is an optional repeated-not-semi-
129 colon expression following the captured \S+. This means the
130 regexp works when the division looks like /PRO;/ or when the
131 division looks like /ANG ;/ - the latter is from EMBL
134 * fix ID line parsing: the molecule string can have spaces in
135 it. Like: "genomic DNA"
137 - swiss.pm: bugs #1727, #1734
140 * Added parser for entrezgene ASN1 (text format) files.
141 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
145 - maf.pm coordinate problem fixed
147 o Bio::Taxonomy and Bio::DB::Taxonomy
149 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
150 can be done via Web without downloading all the sequence.
152 o Bio::Tools::Run::RemoteBlast supports more options and complies
153 to changes to the NCBI interface. It is reccomended that you
154 retrieve the data in XML instead of plain-text BLAST report to
155 insure proper parsing and retrieval of all information as NCBI
156 fully expects to change things in the future.
158 o Bio::Tree and Bio::TreeIO
160 - Fixes so that re-rooting a tree works properly
162 - Writing out nhx format from a newick/nexus file will properly output
163 bootstrap information. The use must move the internal node labels over
165 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
166 $node->bootstrap($node->id);
169 - Nexus parsing is much more flexible now, does not care about
172 - Cladogram drawing module in Bio::Tree::Draw
174 - Node height and depth now properly calculated
176 - fix tree pruning algorithm so that node with 1 child gets merged
178 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
179 bugs and improvements were added, see Gbrowse mailing list for most of
182 o Bio::DB::GFF partially supports GFF3. See information about
183 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
185 o Better location parsing in Bio::Factory::FTLocationFactory -
186 this is part of the engine for parsing EMBL/GenBank feature table
187 locations. Nested join/order-by/complement are allowed now
189 o Bio::PrimarySeqI->translate now takes named parameters
191 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
192 reconstruction) is now supported. Parsing different models and
193 branch specific parametes are now supported.
195 o Bio::Factory::FTLocationFactory - parse hierarchical locations
198 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
199 for getter/setter functions
203 - blast bug #1739; match scientific notation in score
204 and possible e+ values
206 - blast.pm reads more WU-BLAST parameters and parameters, match
207 a full database pathname,
209 - Handle NCBI WEB and newer BLAST formats specifically
210 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
212 - psl off-by-one error fixed
214 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
215 and HSPs can be constructed from them.
217 - HSPs query/hit now have a seqdesc field filled out (this was
218 always available via $hit->description and
219 $result->query_description
221 - hmmer.pm can parse -A0 hmmpfam files
223 - Writer::GbrowseGFF more customizeable.
225 o Bio::Tools::Hmmpfam
226 make e-value default score displayed in gff, rather than raw score
227 allow parse of multiple records
230 1.5 Developer release
232 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
233 provide Jukes-Cantor and Kimura pairwise distance methods,
236 o Bio::AlignIO support for "po" format of POA, and "maf";
237 Bio::AlignIO::largemultifasta is a new alternative to
238 Bio::AlignIO::fasta for temporary file-based manipulation of
239 particularly large multiple sequence alignments.
241 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
242 be treated similarly as an assembled contig.
244 o Bio::CodonUsage provides new rare_codon() and probable_codons()
245 methods for identifying particular codons that encode a given
248 o Bio::Coordinate::Utils provides new from_align() method to build
249 a Bio::Coordinate pair directly from a
250 Bio::Align::AlignI-conforming object.
252 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
253 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
254 web service using standard Pubmed query syntax, and retrieve
257 o Bio::DB::GFF has various sundry bug fixes.
259 o Bio::FeatureIO is a new SeqIO-style subsystem for
260 writing/reading genomic features to/from files. I/O classes
261 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
262 classes only read/write Bio::SeqFeature::Annotated objects.
263 Notably, the GFF v3 class requires features to be typed into the
266 o Bio::Graph namespace contains new modules for manipulation and
267 analysis of protein interaction graphs.
269 o Bio::Graphics has many bug fixes and shiny new glyphs.
271 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
272 indexing for HMMER reports and FASTA qual files, respectively.
274 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
275 new objects that can be placed within a Bio::Map::MapI-compliant
276 genetic/physical map; Bio::Map::Physical provides a new physical
277 map type; Bio::MapIO::fpc provides finger-printed clone mapping
280 o Bio::Matrix::PSM provide new support for postion-specific
281 (scoring) matrices (e.g. profiles, or "possums").
283 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
284 be instantiated without explicitly using Bio::OntologyIO. This
285 is possible through changes to Bio::Ontology::OntologyStore to
286 download ontology files from the web as necessary. Locations of
287 ontology files are hard-coded into
288 Bio::Ontology::DocumentRegistry.
290 o Bio::PopGen includes many new methods and data types for
291 population genetics analyses.
293 o New constructor to Bio::Range, unions(). Given a list of
294 ranges, returns another list of "flattened" ranges --
295 overlapping ranges are merged into a single range with the
296 mininum and maximum coordinates of the entire overlapping group.
298 o Bio::Root::IO now supports -url, in addition to -file and -fh.
299 The new -url argument allows one to specify the network address
300 of a file for input. -url currently only works for GET
301 requests, and thus is read-only.
303 o Bio::SearchIO::hmmer now returns individual Hit objects for each
304 domain alignment (thus containing only one HSP); previously
305 separate alignments would be merged into one hit if the domain
306 involved in the alignments was the same, but this only worked
307 when the repeated domain occured without interruption by any
308 other domain, leading to a confusing mixture of Hit and HSP
311 o Bio::Search::Result::ResultI-compliant report objects now
312 implement the "get_statistics" method to access
313 Bio::Search::StatisticsI objects that encapsulate any
314 statistical parameters associated with the search (e.g. Karlin's
315 lambda for BLAST/FASTA).
317 o Bio::Seq::LargeLocatableSeq combines the functionality already
318 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
320 o Bio::SeqFeature::Annotated is a replacement for
321 Bio::SeqFeature::Generic. It breaks compliance with the
322 Bio::SeqFeatureI interface because the author was sick of
323 dealing with untyped annotation tags. All
324 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
325 compliant, and accessible through Bio::Annotation::Collection.
327 o Bio::SeqFeature::Primer implements a Tm() method for primer
328 melting point predictions.
330 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
331 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
333 o Bio::Taxonomy::Node now implements the methods necessary for
334 Bio::Species interoperability.
336 o Bio::Tools::CodonTable has new reverse_translate_all() and
337 make_iupac_string() methods.
339 o Bio::Tools::dpAlign now provides sequence profile alignments.
341 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
343 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
346 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
347 for designing small inhibitory RNA.
349 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
350 methods based on a distance matrix.
352 o Bio::Tree::Statistics provides an assess_bootstrap() method to
353 calculate bootstrap support values on a guide tree topology,
354 based on provided bootstrap tree topologies.
356 o Bio::TreeIO now supports the Pagel (PAG) tree format.
362 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
364 o Bio::Graphics will work with gd1 or gd2
367 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
369 - blast.pm Parse multi-line query fields properly
370 - small speed improvements to blasttable.pm and others
372 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
373 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
374 supporting more complex queries
377 1.4. Stable major release
379 Since initial 1.2.0, 3000 separate changes have been made to make this release.
381 o installable scripts
383 o global module version from Bio::Root:Version
386 - major improvements; SVG support
389 - population genetics
390 - support several population genetics types of questions.
391 - Tests for statistical neutrality of mutations
392 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
393 Tests of population structure (Wright's F-statistic: Fst) is in
394 Bio::PopGen::PopStats. Calculating composite linkage
395 disequilibrium (LD) is available in Bio::PopGen::Statistics as
397 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
398 and csv (comma delimited formatted) data.
400 - a directory for implementing population simulations has
401 been added Bio::PopGen::Simulation and 2 simulations - a
402 Coalescent and a simple single-locus multi-allele genetic drift
403 simulation have been provided. This replaces the code in
404 Bio::Tree::RandomTree which has been deprecated until proper
405 methods for generating random phylogenetic trees are
409 - new restrion analysis modules
411 o Bio::Tools::Analysis
412 - web based DNA and Protein analysis framework and several
416 - per residue annotable sequences
419 - Bio::Matrix::PSM - Position Scoring Matrix
420 - Bio::Matrix::IO has been added for generalized parsing of
421 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
422 initial implementations for parsing BLOSUM/PAM and Phylip
423 Distance matricies respectively. A generic matrix
424 implementation for general use was added in
425 Bio::Matrix::Generic.
432 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
433 - small inhibitory RNA
435 o Bio::SeqFeature::Tools
436 - seqFeature mapping tools
437 - Bio::SeqFeature::Tools::Unflattener.pm
438 -- deal with mapping GenBank feature collections into
439 Chado/GFF3 processable feature sets (with SO term mappings)
441 o Bio::Tools::dpAlign
442 - pure perl dynamic programming sequence alignment
445 o new Bio::SearchIO formats
446 - axt and psl: UCSC formats.
447 - blasttable: NCBI -m 8 or -m 9 format from blastall
449 o new Bio::SeqIO formats
450 - chado, tab, kegg, tigr, game
451 - important fixes for old modules
455 o improved Bio::Tools::Genewise
457 o Bio::SeqIO now can recongnize sequence formats automatically from
460 o new parsers in Bio::Tools:
461 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
463 o Bio::DB::Registry bugs fixed
464 - BerkeleyDB-indexed flat files can be used by the OBDA system
465 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
466 used by the OBDA system
469 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
472 o hundreds of new and improved files
476 o Bio::Tree::AlleleNode has been updated to be a container of
477 an Bio::PopGen::Individual object for use in the Coalescent simulations.
482 1.2.3 Stable release update
483 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
485 o Bug #1477 - Sel --> Sec abbreviation fixed
486 o Fix bug #1487 where paring in-between locations when
487 end < start caused the FTLocationFactory logic to fail.
488 o Fix bug #1489 which was not dealing with keywords as an
489 arrayref properly (this is fixed on the main trunk because
490 keywords returns a string and the array is accessible via
492 o Bio::Tree::Tree memory leak (bug #1480) fixed
493 Added a new initialization option -nodelete which
494 won't try and cleanup the containing nodes if this
496 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
497 this was only present on the branch for the 1.2.1 and 1.2.2 series
498 - Also merged main trunk changes to the branch which make
499 newick -> nhx round tripping more effective (storing branch length
500 and bootstrap values in same locate for NodeNHX and Node
501 implementations.) Fixes to TreeIO parsing for labeled internal
502 also required small changes to TreeIO::nhx. Improved
503 tests for this module as well.
505 - Fixed bugs in BLAST parsing which couldn't parse NCBI
506 gapped blast properly (was losing hit significance values due to
507 the extra unexpeted column).
508 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
509 integer overflow (# of letters in nt seq dbs is > MAX_INT)
510 although doesn't try to correct it - will get the negative
511 number for you. Added a test for this as well.
512 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
513 has no top-level family classification scores but does have scores and
514 alignments for individual domains.
515 - Parsing FASTA reports where ungapped percent ID is < 10 and the
516 regular expression to match the line was missing the possibility of
517 an extra space. This is rare, which is why we probably did not
519 - BLAST parsing picks up more of the statistics/parameter fields
520 at the bottom of reports. Still not fully complete.
521 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
522 were fixed to include many improvements and added flexiblity
523 in outputting the files. Bug #1495 was also fixed in the process.
525 - Update for GFF3 compatibility.
526 - Added scripts for importing from UCSC and GenBank.
527 - Added a 1.2003 version number.
530 - Added a 1.2003 version number.
531 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
532 properly writing keywords out.
533 o Bio::SeqIO::genbank
534 - Fixed bug/enhancement #1513 where dates of
535 the form D-MMM-YYYY were not parsed. Even though this is
536 invalid format we can handle it - and also cleanup the date
537 string so it is properly formatted.
538 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
539 and written with Genbank format. Similarly bug #1515 is fixed to
540 parse in the ORIGIN text.
541 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
542 to specify the ID type, one of (accession accession.version
543 display primary). See Bio::SeqIO::preferred_id_type method
544 documentation for more information.
545 o Unigene parsing updated to handle file format changes by NCBI
547 1.2.2 Stable release update
549 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
550 - auto-discover ontology name
551 - bug in parsing relationships when certain characters are in the term
552 - fixed hard-coded prefix for term identifiers
553 - various smaller issues
555 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
556 of Bio::Ontology::TermI
558 o brought the OBDA Registry code up to latest specs
562 - accession number retrieval fixed
564 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
566 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
567 #1459 which now properly report alignment start/end info
568 for translated BLAST/FASTA searches.
570 o Bio::TreeIO::newick can parse labeled internal nodes
572 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
573 for BLASTX if if you provide -report_type => 'BLASTX' when
574 initializing a BPbl2seq object. Bioperl 1.3 will have better
575 support for bl2seq in the SearchIO system.
577 o Bio::Root::IO support a -noclose boolean flag which will not
578 close a filehandle upon object cleanup - useful when sharing
579 a filehandle among objects. Additionally code added s.t.
580 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
582 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
584 o Bio::SeqIO::genbank
585 - bug #1456 fixed which generated extra sequence lines
586 - write moltype correctly for genpept
588 1.2.1 Stable release update
590 o Inclusion of WrapperBase, a needed component for StandAloneBlast
592 o Addition from main trunk of Ontology objects, principly to allow
593 BioSQL releases against 1.2.1
595 o Fixes and cleanup of Bio::Coordinate modules
597 o A fix to Bio::Index::EMBL allowing retrieval of entries using
598 the primary accession number
600 o Other bug fixes, including bpindex GenBank fix
602 o Bio::SeqIO::genbank bug #1389 fixed
604 1.2 Stable major release
606 o More functionality added to Bio::Perl, the newbie module
608 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
609 Support for New Hampshire Extended (NHX) format parsing.
611 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
612 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
615 o New ontology parsing Bio::Ontology
617 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
618 multi-report (mlib) fasta reports, support for waba and exonerate.
620 o Bio::ClusterIO for parsing Unigene clusters
622 o Bio::Assembly added for representing phrap and ace assembly clusters.
624 o Rudimentary support for writing Chado XML (see
625 GMOD project: www.gmod.org for more information)
627 o Bio::Coordinate for mapping between different coordinate systems such
628 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
629 features into different coordinate systems.
631 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
632 with the get_Stream_by_query method and supports the latest
633 NCBI eutils interface.
635 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
636 object for extracting subsets of features : currently only
637 supports extraction by location.
639 1.1.1 Developer release
641 o Deprecated modules are now listed in the DEPRECATED file
643 o New HowTo documents located in doc/howto describing
646 o Note that bugs are now stored at bugzilla.bioperl.org
647 and all old bugs are searchable through the bugzilla interface.
649 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
652 o Support for Genewise parsing in Bio::Tools::Genewise
654 o Start of Ontology framework with Bio::Ontology
656 o Speedup to the Bio::Root::Root object method _rearrange.
657 A global _load_module method was implemented to simplify the
658 dynamic loading of modules ala Bio::SeqIO::genbank. This
659 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
662 o Several performance improvements to sequence parsing in Bio::SeqIO.
663 Attempt to speedup by reducing object creation overhead.
665 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
666 method for sequence retrieval with their E-utils CGI scripts.
667 More work to support Entrez queries to their fullest is planned
670 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
672 1.1 Developer release
674 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
675 this separation removes some of the complexity in our test suite
676 and separates the core modules in bioperl from those that need
677 external programs to run.
679 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
680 not run into trouble running the makefile
682 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
683 read,create,and write locations for grouped/split locations
684 (like mRNA features on genomic sequence).
686 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
687 and PAML (codeml,aaml, etc) parsing.
689 o Bio::Tree:: objects expanded to handle testing monophyly,
690 paraphyly, least common ancestor, etc.
692 o Bio::Coordinate for mapping locations from different coordinate spaces
694 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
695 added for parsing hmmpfam and hmmsearch output.
697 o Bio::SearchIO::Writer::TextResultWriter for outputting
698 a pseudo-blast textfile format
701 1.0.2 Bug fix release
703 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
704 in this release will not work after December 2002 when NCBI
705 shuts off the old Entrez cgi scripts. We have already fixed
706 on our main development branch and the functionality will be
707 available in the next stable bioperl release (1.2) slated for
710 o Numerous parsing bugs in Bio::SearchIO::fasta found through
711 testset by Robin Emig. These were fixed as was the get_aln
712 method in Bio::Search::HSP::GenericHSP to handle the extra
713 context sequence that is provided with a FastA alignment.
715 o Migrating differences between Bio::Search::XX::BlastXX to
716 Bio::Search::XX::GenericXX objects. This included mechanism
717 to retrieve whole list of HSPs from Hits and whole list of Hits from
718 Results in addition to the current next_XX iterator methods that
719 are available. Added seq_inds() method to GenericHSP which identifies
720 indexes in the query or hit sequences where conserved,identical,gaps,
721 or mismatch residues are located (adapted from Steve Chervitz's
722 implementation in BlastHSP).
724 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
725 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
727 o Bio::Graphics glyph set improved and extended for GBrowse release
729 o Bio::Tree::Tree get_nodes implementation improvement thanks
730 to Howard Ross notice performance problem when writing out
733 o Bio::Location::Fuzzy::new named parameter -loc_type became
734 -location_type, Bio::Location::Simple::new named parameter
735 -seqid becamse -seq_id.
737 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
738 was mis-detecting that gaps should be placed at the beginning of
739 the alignment when the best alignment starts internally in the
742 1.0.1 Bug fix release
744 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
746 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
747 and mixed (3.3 - 3.4) versions of FASTA.
749 o Small API change to add methods for completeness across
750 implementations of Bio::Search objects. These new methods
751 in the interface are implemented by the GenericXX object as well
752 as the BlastXX objects.
753 * Bio::Search::Result::ResultI
754 - hits() method returns list of all Hits (next_hit is an
757 * Bio::Search::Hit::HitI
758 - hsps() method returns list of all HSPs (next_hsp is an
761 o The Bio::SearchIO::Writer classes have been fixed to handle results
762 created from either psiblast (Search::BlastXX objects) or
763 blast|fasta|blastxml objects (Search::GenericXX objects). More work
764 has to be done here to make it work properly and will nee major
767 o Bugs in Bio::Tools::HMMER fixed, including
768 * #1178 - Root::IO destructor wasn't being called
769 * #1034 - filter_on_cutoff now behaves properly
771 o Bio::SeqFeature::Computation initialization args fixed and
774 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
776 o Updated FAQ with more example based answers to typical questions
778 o Bug #1202 was fixed which would improperly join together qual values
779 parsed by Bio::SeqIO::qual when a trailing space was not present before
782 1.0.0 Major Stable Release
784 This represents a major release of bioperl with significant
785 improvements over the 0.7.x series of releases.
787 o Bio::Tools::Blast is officially deprecated. Please see
788 Bio::SearchIO for BLAST and FastA parsing.
790 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
791 Bio::LocationI objects as well as start/end.
793 o Bio::Biblio contains modules for Bibliographic data.
794 Bio::DB::Biblio contains the query modules. Additionally one can
795 parse medlinexml from the ebi bibliographic query service (BQS)
796 system and Pubmed xml from NCBI. See Martin Senger's
797 documentation in Bio::Biblio for more information.
799 o Bio::DB::Registry is a sequence database registry part of
800 Open Bioinformatics Database Access. See
801 http://obda.open-bio.org for more information.
803 o File-based and In-Memory Sequence caching is provided by
804 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
807 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
808 been added by Lincoln Stein.
810 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
812 o A FAQ has been started and is included in the release to provide
813 a starting point for frequent questions and issues.
815 0.9.3 Developer's release
817 o Event based parsing system improved (SearchIO). With parsers for
818 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
819 Additionally a lazy parsing system for text and html blast reports was
820 added and is called psiblast (name subject to change in future releases).
822 o Bio::Search objects improved and standardized with associated Interfaces
823 written. The concept of a search "Hit" was standardized to be called
824 "hit" consistently and the use of "subject" was deprecated in all active
827 o Bio::Structure added (since 0.9.1) for Protein structure objects
828 and PDB parser to retrieve and write these structures from data files.
830 o Several important Bio::DB::GFF bug fixes for handling features that
831 are mapped to multiple reference points. Updated mysql adaptor
832 so as to be able to store large (>100 megabase) chunks of DNA into
833 Bio::DB::GFF databases.
835 0.9.2 Developer's release
837 o Bio::Search and Bio::SearchIO system introduced for event based
838 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
839 in text and XML and FASTA reports in standard output format.
841 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
842 generator is included in Bio::TreeIO::RandomTrees and a
843 statistics module for evaluating.
845 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
846 server for DAS servers.
848 o Bio::Tools::BPlite is provides more robust parsing of BLAST
849 files. The entire BPlite system migrated to using Bio::Root::IO
852 o Bio::Tools::Alignment for Consed and sequence Trimming
855 o Bio::Structure for Protein structure information and parsing
857 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
858 cgi-bin entry point which should be more reliable.
860 o Bio::Map and Bio::MapIO for biological map navigation and a
861 framework afor parsing them in. Only preliminary work here.
863 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
864 Future work will integrate Pise and allow submission of analysis on
867 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
868 introduced as new objects for handling Sequence Annotation
869 information (dblinks, references, etc) and is more robust that
872 o Bio::Tools::FASTAParser introduced.
874 o Scripts from the bioperl script submission project and new
875 scripts from bioperl authors are included in "scripts" directory.
877 o Factory objects and interfaces are being introduced and are more
880 o Bio::Root::Root introduced as the base object while
881 Bio::Root::RootI is now simply an interface.
883 o Bio::DB::RefSeq provides database access to copy of the NCBI
884 RefSeq database using the EBI dbfetch script.
886 0.9.0 Developer's release
888 o perl version at least 5.005 is now required instead of perl 5.004
890 o Bio::Tools::Run::RemoteBlast is available for running remote
893 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
895 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
896 Also added are related modules UTR3, UTR5, Exon, Intron,
897 Promotor, PolyA and Transcript.
899 o Speedup of translate method in PrimarySeq
901 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
902 select(), dot(), get_seq_by_pos(), column_from_residue_number()
904 o Various fixes to Variation toolkit
906 o Bio::DB::EMBL provides database access to EMBL sequence data.
907 Bio::DB::Universal provides a central way to point to indexes
908 and dbs in a single interface.
910 o Bio::DB::GFF - a database suitable for running DAS servers locally.
912 o Bio::Factory::EMBOSS is still in design phase as is
913 Bio::Factory::ApplicationFactoryI
915 o Dia models for bioperl design are provided in the models/ directory
917 0.7.2 Bug fix release
919 o documentation fixes in many modules - SYNOPSIS code verified
920 to be runnable in many (but not all modules)
922 o corrected MANIFEST file from 0.7.1 release
924 o Bug fix in Bio::SeqIO::FTHelper to properly handle
927 o Bio::SeqIO::genbank
928 * Correct parsing and writing of genbank format with protein data
929 * moltype and molecule separation
931 o Bio::SeqIO::largefasta fix to avoid inifinite loops
933 o Bio::SimpleAlign fixed to correctly handle consensus
936 o Bio::Tools::HMMER supports hmmer 2.2g
938 o Bio::Tools::BPlite to support report type specific parsing. Most
939 major changes are not on the 0.7 branch.
941 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
944 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
945 in several types of mutations:
946 1.) AA level: deletion, complex
947 2.) AA level: complex, inframe
948 3.) RNA level: silent
950 o BPbl2seq parsing of empty reports will not die, but will return
951 a valid, empty, Bio::SeqFeature::SimilarityFeature for
952 $report->query() and $report->subject() methods. So an easy
953 way to test if report was empty is to see if
954 $report->query->seqname is undefined.
956 0.7.1 Bug fix release
958 o Better parsing of genbank/EMBL files especially fixing bugs
959 related to Feature table parsing and locations on remote
960 sequences. Additionally, species name parsing was better.
962 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
963 which include a number of header lines.
965 o More strict genbank and EMBL format writing (corrected number of
966 spaces where appropriate).
968 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
969 for related BPlite BUGS that are unresolved in this release.
971 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
972 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
973 use expasy mirrors or EBI dbfetch cgi-script.
975 o A moderate number of documentation improvements were made as
976 well to provide a better code synopsis in each module.
979 0.7 Large number of changes, including refactoring of the
980 Object system, new parsers, new functionality and
981 all round better system. Highlights are:
984 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
985 Bio::Root::IO for I/O and file/handle capabilities.
987 o Imported BPlite modules from Ian Korf for BLAST
988 parsing. This is considered the supported BLAST parser;
989 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
991 o Improved Sequence Feature model. Added complete location
992 modelling (with fuzzy and compound locations). See
993 Bio::LocationI and the modules under Bio/Location. Added
994 support in Genbank/EMBL format parsing to completely parse
995 feature tables for complex locations.
997 o Moved special support for databanks etc to specialized modules under
998 Bio/Seq/. One of these supports very large sequences through
999 a temporary file as a backend.
1001 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1002 CDS retrieval and exon shuffling.
1004 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1006 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1007 DB/GDB (the latter has platform-specific limitations).
1009 o New analysis parser framework for HT sequence annotation (see
1010 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1012 o New Alignment IO framework
1014 o New Index modules (Swissprot)
1016 o New modules for running Blast within perl
1017 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1018 Multiple Sequence Alignment tools ClustalW and TCoffee
1019 (Bio::Tools::Run::Alignment).
1021 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1022 documentation across the package.
1024 o Much improved cross platform support. Many known incompatibilities
1025 have been fixed; however, NT and Mac do not work across the entire
1026 setup (see PLATFORMS).
1028 o Many bug fixes, code restructuring, etc. Overall stability and
1029 maintainability benefit a lot.
1031 o A total of 957 automatic tests
1036 There are very few functionality changes but a large
1037 number of software improvements/bug fixes across the package.
1039 o The EMBL/GenBank parsing are improved.
1041 o The Swissprot reading is improved. Swissprot writing
1042 is disabled as it doesn't work at all. This needs to
1043 wait for 0.7 release
1045 o BLAST reports with no hits are correctly parsed.
1047 o Several other bugs of the BLAST parser (regular expressions, ...)
1050 o Old syntax calls have been replaced with more modern syntax
1052 o Modules that did not work at all, in particular the Sim4
1053 set have been removed
1055 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1056 have improved compliance with interface specs and documentation
1058 o Mailing list documentation updated throughout the distribution
1060 o Most minor bug fixes have happened.
1062 o The scripts in /examples now work and have the modern syntax
1063 rather than the deprecated syntax
1066 0.6.1 Sun April 2 2000
1068 o Sequences can have Sequence Features attached to them
1069 - The sequence features can be read from or written to
1070 EMBL and GenBank style flat files
1072 o Objects for Annotation, including References (but not
1073 full medline abstracts), Database links and Comments are
1076 o A Species object to represent nodes on a taxonomy tree
1079 o The ability to parse HMMER and Sim4 output has been added
1081 o The Blast parsing has been improved, with better PSI-BLAST
1082 support and better overall behaviour.
1084 o Flat file indexed databases provide both random access
1085 and sequential access to their component sequences.
1087 o A CodonTable object has been written with all known
1088 CodonTables accessible.
1090 o A number of new lightweight analysis tools have been
1091 added, such as molecular weight determination.
1093 The 0.6 release also has improved software engineering
1095 o The sequence objects have been rewritten, providing more
1096 maintainable and easier to implement objects. These
1097 objects are backwardly compatible with the 0.05.1 objects
1099 o Many objects are defined in terms of interfaces and then
1100 a Perl implementation has been provided. The interfaces
1101 are found in the 'I' files (module names ending in 'I').
1103 This means that it is possible to wrap C/CORBA/SQL access
1104 as true "bioperl" objects, compatible with the rest of
1107 o The SeqIO system has been overhauled to provide better
1108 processing and perl-like automatic interpretation of <>
1111 o Many more tests have been added (a total of 172 automatic
1112 tests are now run before release).
1116 0.05.1 Tue Jun 29 05:30:44 1999
1117 - Central distribution now requires Perl 5.004. This was
1118 done to get around 5.003-based problems in Bio/Index/*
1120 - Various bug fixes in the Bio::Tools::Blast modules
1121 including better exception handling and PSI-Blast
1122 support. See Bio/Tools/Blast/CHANGES for more.
1123 - Fixed the Parse mechanism in Seq.pm to use readseq.
1124 Follow the instructions in README for how to install
1125 it (basically, you have to edit Parse.pm).
1126 - Improved documentation of Seq.pm, indicating where
1127 objects are returned and where strings are returned.
1128 - Fixed uninitialized warnings in Bio::Root::Object.pm
1129 and Bio::Tools::SeqPattern.pm.
1130 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1132 0.05 Sun Apr 25 01:14:11 1999
1133 - Bio::Tools::Blast modules have less memory problems
1134 and faster parsing. Webblast uses LWP and supports
1135 more functionality. See Bio/Tools/Blast/CHANGES for more.
1136 - The Bio::SeqIO system has been started, moving the
1137 sequence reformatting code out of the sequence object
1138 - The Bio::Index:: system has been started, providing
1139 generic index capabilities and specifically works for
1140 Fasta formatted databases and EMBL .dat formatted
1142 - The Bio::DB:: system started, providing access to
1143 databases, both via flat file + index (see above) and
1145 - The scripts/ directory, where industrial strength scripts
1146 are put has been started.
1147 - Many changes - a better distribution all round.
1149 0.04.4 Wed Feb 17 02:20:13 1999
1150 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1151 (see Bio::Tools::Blast::CHANGES).
1152 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1153 - Beefed up the t/Fasta.t test script.
1154 - Small fix in Bio::Seq::type() (now always returns a string).
1155 - Changed Bio::Root::Utilities::get_newline_char() to
1156 get_newline() since it could return more than one char.
1157 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1158 - Changed default timeout to 20 seconds (was 3).
1159 - Moved lengthy modification notes to the bottom of some files.
1160 - Fixed SimpleAlign write_fasta bug.
1161 - Beefed up SimpleAlign.t test
1163 0.04.3 Thu Feb 4 07:48:53 1999
1164 - Bio::Root::Object.pm and Global.pm now detect when
1165 script is run as a CGI and suppress output that is only
1166 appropriate when running interactively.
1167 - Bio::Root::Err::_set_context() adds name of script ($0).
1168 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1169 regarding the use of the static objects via the qw(:obj) tag.
1170 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1171 CORE::reverse, avoiding Perl warnings.
1172 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1173 example scripts (see Bio::Tools::Blast::CHANGES).
1174 - examples/seq/seqtools.pl no longer always warns about using
1175 -prot or -nucl command-line arguments; only when using the
1177 - Methods added to Bio::Root::Utilities: create_filehandle(),
1178 get_newline_char(), and taste_file() to generalize filehandle
1179 creation and autodetect newline characters in files/streams
1180 (see bug report #19).
1181 - Bio::Root::IOManager::read() now handles timeouts and uses
1182 Utilities::create_filehandle().
1183 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1184 of hardwiring in "\n".
1185 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1187 0.04.2 Wed Dec 30 02:27:36 1998
1188 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1189 (see Bio::Tools::Blast::CHANGES).
1190 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1191 to CORE::reverse (prevents ambiguous warnings with 5.005).
1192 - Appending '.tmp.bioperl' to temporary files created by
1193 Bio::Root::Utilities::compress() or uncompress() to
1194 make it easy to identify & cleanup these files as needed.
1195 - Developers: Created CVS branch release-0-04-bug from
1196 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1197 be sure to cvs checkout this branch into a clean area.
1199 0.04.1 Wed Dec 16 05:39:15 1998
1200 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1201 (see Bio::Tools::Blast::CHANGES).
1202 - Compile/SW/Makefile.PL now removes *.o and *.a files
1205 0.04 Tue Dec 8 07:49:19 1998
1206 - Lots of new modules added including:
1207 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1208 and Bio/Compile directory containing XS-linked C code for
1209 creating Smith-Waterman sequence alignments from within Perl.
1210 * Steve Chervitz's Blast distribution has been incorporated.
1211 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1212 - Bio/examples directory for demo scripts for all included modules.
1213 - Bio/t directory containing test suit for all included modules.
1214 - For changes specific to the Blast-related modules prior to
1215 incorporation in this central distribution, see the CHANGES
1216 file in the Bio/Tools/Blast directory.
1218 0.01 Tue Sep 8 14:23:22 1998
1219 - original version from central CVS tree; created by h2xs 1.18