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1 ---------------------------------------------------------
2 Revision history for BioPerl core modules
3 ---------------------------------------------------------
4 The comprehensive history and ongoing development of BioPerl:
6 http://github.com/bioperl/bioperl-live
8 Some of that history is also highlighted on our wiki:
10 http://www.bioperl.org/wiki/Change_log
11 http://www.bioperl.org/wiki/History_of_BioPerl
13 Bugs and requested features list:
15 https://redmine.open-bio.org/projects/bioperl
17 CPAN releases are branched from 'master'.
18 ---------------------------------------------------------
20 1.6.1_1 RELEASE_DATE_HERE (first 1.6.2 alpha)
21 [New features]
22 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
23 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
24 [Warren Kretzschmar]
25 * Bio::SeqIO::gbxml
26 - bug 2515 - new contribution [Ryan Golhar, jhannah]
27 * Bio::Assembly::IO
28 - support for reading Maq, Sam and Bowtie files [maj]
29 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
30 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
31 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
32 - bug 2726: reading/writing granularity: whole scaffold or one contig
33 at a time [Joshua Udall, fangly]
34 * Bio::OntologyIO
35 - Added parsing of xrefs to OBO files, which are stored as secondary
36 dbxrefs of the cvterm [Naama Menda]
38 [Bug fixes]
39 * bug 3077 - Bio::SimpleAlign slice() now correctly computes seq coordinates
40 for alignment slices [Ha X. Dang, cjfields]
41 * bug 3116, 3117 - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
42 * bug 3120 - bp_seqfeature_gff3.pl round-trip fixes [genehack, jhannah]
43 * bug 3122 - Catch instances where non-seekable filehandles were being
44 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
45 * bug 3120 - bp_seqfeature_gff3.pl '-y' option [genehack, David Breimann]
46 * bug 3126 - catch description [Toshihiko Akiba]
47 * bug 2983 - fix score/percent ID mixup [Alexie Papanicolaou]
48 * bug 2984 - let LocatableSeq decide on length of phylip aln [Adam Witney,
49 cjfields]
51 [Deprecated]
52 * Bio::Expression modules - these were originally designed to go with the
53 bioperl-microarray suite of tools, however they have never been completed
54 and so have been removed from the distribution. The original code has
55 been moved into the inactive bioperl-microarray suite. [cjfields]
57 [Other]
58 * Repository moved from Subversion (SVN) to
59 http://github.com/bioperl/bioperl-live [cjfields]
60 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
61 Thieme have been moved to their own distribution (Bio-Microarray).
62 [cjfields]
64 1.6.1 Sept. 29, 2009 (point release)
65 * No change from last alpha except VERSION and doc updates [cjfields]
67 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
68 * Fix for silent OBDA bug related to FASTA validation [cjfields]
70 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
71 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
72 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
73 [cjfields]
74 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
76 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
77 * WinXP test fixes [cjfields, maj]
78 * BioPerl.pod added for descriptive information, fixes CPAN indexing
79 [cjfields]
80 * Minor doc fixes [cjfields]
82 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
83 * Fix tests failing due to merging issues [cjfields]
84 * More documentation updates for POD parsing [cjfields]
86 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
87 * Bio::Root::Build
88 - fix YAML meta data generation [cjfields]
90 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
91 * Bio::Align::DNAStatistics
92 - fix divide by zero problem [jason]
93 * Bio::AlignIO::*
94 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
95 * Bio::AlignIO::stockholm
96 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
97 * Bio::Assembly::Tools::ContigSpectrum
98 - function to score contig spectrum [fangly]
99 * Bio::DB::EUtilities
100 - small updates [cjfields]
101 * Bio::DB::Fasta
102 - berkeleydb database now autoindexes wig files and locks correctly
103 [lstein]
104 * Bio::DB::HIV
105 - various small updates for stability; tracking changes to LANL
106 database interface [maj]
107 * Bio::DB::SeqFeature (lots of updates and changes)
108 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
109 - bug 2835 - patch [Dan Bolser]
110 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
111 * Bio::DB::SwissProt
112 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
113 * Bio::Factory::FTLocationFactory
114 - mailing list bug fix [cjfields]
115 * Bio::LocatableSeq
116 - performance work on column_from_residue_number [hartzell]
117 * Bio::Matrix::IO::phylip
118 - bug 2800 - patch to fix phylip parsing [Wei Zou]
119 * Bio::Nexml
120 - Google Summer of Code project from Chase Miller - parsers for Nexml
121 file format [maj, chmille4]
122 * Bio::PopGen
123 - Make Individual, Population, Marker objects AnnotatableI [maj]
124 - simplify LD code [jason]
125 * Bio::RangeI
126 - deal with empty intersection [jason]
127 * Bio::Restriction
128 - significant overhaul of Bio::Restriction system: complete support for
129 external and non-palindromic cutters. [maj]
130 * Bio::Root::Build
131 - CPANPLUS support, no automatic installation [sendu]
132 * Bio::Root::IO
133 - allow IO::String (regression fix) [cjfields]
134 - catch unintentional undef values [cjfields]
135 - throw if non-fh is passed to -fh [maj]
136 * Bio::Root::Root/RootI
137 - small debugging and core fixes [cjfields]
138 * Bio::Root::Test
139 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
140 * Bio::Root::Utilities
141 - bug 2737 - better warnings [cjfields]
142 * Bio::Search
143 - tiling completely refactored, HOWTO added [maj]
144 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
145 will deprecate usage of the older tiling code in the next BioPerl
146 release
147 - small fixes [cjfields]
148 * Bio::SearchIO
149 - Infernal 1.0 output now parsed [cjfields]
150 - new parser for gmap -f9 output [hartzell]
151 - bug 2852 - fix infinite loop in some output [cjfields]
152 - blastxml output now passes all TODO tests [cjfields]
153 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
154 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
155 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
156 * Bio::Seq::LargePrimarySeq
157 - delete tempdirs [cjfields]
158 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
159 * Bio::Seq::Quality
160 - extract regions based on quality threshold value [Dan Bolser, heikki]
161 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
162 * Bio::SeqFeature::Lite
163 - various Bio::DB::SeqFeature-related fixes [lstein]
164 * Bio::SeqFeature::Tools::TypeMapper
165 - additional terms for GenBank to SO map [scain]
166 * Bio::SeqIO::chadoxml
167 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
168 * Bio::SeqIO::embl
169 - support for CDS records [dave_messina, Sylvia]
170 * Bio::SeqIO::fastq
171 - complete refactoring to handle all FASTQ variants, perform validation,
172 write output. API now conforms with other Bio* parsers and the rest of
173 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
174 [cjfields]
175 * Bio::SeqIO::genbank
176 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
177 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
178 * Bio::SeqIO::largefasta
179 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
180 * Bio::SeqIO::raw
181 - add option for 'single' and 'multiple'
182 * Bio::SeqIO::scf
183 - bug 2881 - fix scf round-tripping [Adam Sj¿gren]
184 * Bio::SeqUtils
185 - bug 2766, 2810 - copy over tags from features, doc fixes [David
186 Jackson]
187 * Bio::SimpleAlign
188 - bug 2793 - patch for add_seq index issue [jhannah, maj]
189 - bug 2801 - throw if args are required [cjfields]
190 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
191 [Tristan Lefebure, maj]
192 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
193 - fix POD and add get_SeqFeatures filter [maj]
194 * Bio::Tools::dpAlign
195 - add support for LocatableSeq [ymc]
196 - to be moved to a separate distribution [cjfields, rbuels]
197 * Bio::Tools::EUtilities
198 - fix for two bugs from mail list [Adam Whitney, cjfields]
199 - add generic ItemContainerI interface for containing same methods
200 [cjfields]
201 * Bio::Tools::HMM
202 - fix up code, add more warnings [cjfields]
203 - to be moved to a separate distribution [cjfields, rbuels]
204 * Bio::Tools::Primer3
205 - bug 2862 - fenceposting issue fixed [maj]
206 * Bio::Tools::Run::RemoteBlast
207 - tests for remote RPS-BLAST [mcook]
208 * Bio::Tools::SeqPattern
209 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
210 * Bio::Tools::tRNAscanSE
211 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
212 * Bio::Tree::*
213 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
214 * Bio::Tree::Statistics
215 - several methods for calculating Fitch-based score, internal trait
216 values, statratio(), sum of leaf distances [heikki]
217 * Bio::Tree::Tree
218 - bug 2869 - add docs indicating edge case where nodes can be
219 prematurely garbage-collected [cjfields]
220 - add as_text() function to create Tree as a string in specified format
221 [maj]
222 * Bio::Tree::TreeFunctionsI
223 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
224 Lefebure, maj]
225 * Bio::TreeIO::newick
226 - fix small semicolon issue [cjfields]
227 * scripts
228 - update to bp_seqfeature_load for SQLite [lstein]
229 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
230 - fastam9_to_table - fix for MPI output [jason]
231 - gccalc - total stats [jason]
232 * General Stuff
233 - POD cleanup re: FEEDBACK section [maj, cjfields]
234 - cleanup or fix dead links [cjfields]
235 - Use of no_* methods (indicating 'number of something') is deprecated
236 in favor of num_* [cjfields]
237 - lots of new tests for the above bugs and refactors [everyone!]
238 - new template for Komodo text editor [cjfields]
240 1.6.0 Winter 2009
241 * Feature/Annotation rollback
242 - Problematic changes introduced prior to the 1.5 release have been
243 rolled back. These changes led to subtle bugs involving operator
244 overloading and interface methods.
245 - Behavior is very similar to that for BioPerl 1.4, with tag values
246 being stored generically as simple scalars. Results in a modest
247 speedup.
248 * Bio::Graphics
249 - Split into a separate distribution on CPAN, primarily so development
250 isn't reliant on a complete BioPerl release.
251 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
252 is only available via Subversion (via bioperl-live main trunk)
253 * Bio::Root::Test
254 - Common test bed for all BioPerl modules
255 * Bio::Root::Build
256 - Common Module::Build-based subclass for all BioPerl modules
257 * Bio::DB::EUtilities
258 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
259 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
260 and user agent request posting and retrieval
261 * Test implementation and reorganization
262 - Tests have been reorganized into groups based on classes or use
263 cases.
264 - Automated test coverage is now online:
265 http://www.bioperl.org/wiki/Test_Coverage
266 - After this release, untested modules will be moved into a
267 separate developer distribution until tests can be derived.
268 Also, new modules to be added are expected to have a test suite
269 and adequate test coverage.
271 1.5.2 Developer release
273 Full details of changes since 1.5.1 are available online at:
274 http://www.bioperl.org/wiki/Change_log
275 The following represents a brief overview of the most important changes.
277 o Bio::Map
278 - Overhaul. Brand new system fully allows markers to have multiple
279 positions on multiple maps, and to have relative positions. Should be
280 backward compatible.
282 o Bio::Taxonomy
283 - This module and all the modules in the Taxonomy directory now
284 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
286 o Bio::DB::Taxonomy
288 - Taxonomy.pm
289 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
291 * New methods ancestor(), each_Descendent() and _handle_internal_id().
293 * Allows for different database modules to create Bio::Taxon objects
294 with the same internal id when the same taxon is requested from each.
296 - flatfile.pm
297 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
299 * No longer includes the fake root node 'root'; there are multiple roots
300 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
302 - entrez.pm
303 * get_node() has new option -full
305 * Caches data retrieved from website
307 o Bio::Species
308 - Now a Bio::Taxon. Carries out the species name -> specific name munging
309 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
310 backward compatability in species() method.
312 o Bio::Search and Bio::SearchIO
313 - Overhaul. The existing system has been sped up via some minor changes
314 (mostly gain-of-function to the API). Bio::PullParserI is introduced
315 as a potential eventual replacment for the existing system, though as
316 yet only a Hmmpfam parser exists written using it.
319 1.5.1 Developer release
321 o Major problem with how Annotations were written out with
322 Bio::Seq is fixed by reverting to old behavior for
323 Bio::Annotation objects.
325 o Bio::SeqIO
327 - genbank.pm
328 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
329 expect at l east 9 spaces at the beginning of a line to
330 indicate line wrapping.
332 * Treat multi-line SOURCE sections correctly, this defect broke
333 both common_name() and classification()
335 * parse swissprot fields in genpept file
337 * parse WGS genbank records
339 - embl.pm
340 * Changed regexp for ID line. The capturing parentheses are
341 the same, the difference is an optional repeated-not-semi-
342 colon expression following the captured \S+. This means the
343 regexp works when the division looks like /PRO;/ or when the
344 division looks like /ANG ;/ - the latter is from EMBL
345 repbase
347 * fix ID line parsing: the molecule string can have spaces in
348 it. Like: "genomic DNA"
350 - swiss.pm: bugs #1727, #1734
352 - entrezgene.pm
353 * Added parser for entrezgene ASN1 (text format) files.
354 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
356 o Bio::AlignIO
358 - maf.pm coordinate problem fixed
360 o Bio::Taxonomy and Bio::DB::Taxonomy
362 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
363 can be done via Web without downloading all the sequence.
365 o Bio::Tools::Run::RemoteBlast supports more options and complies
366 to changes to the NCBI interface. It is reccomended that you
367 retrieve the data in XML instead of plain-text BLAST report to
368 insure proper parsing and retrieval of all information as NCBI
369 fully expects to change things in the future.
371 o Bio::Tree and Bio::TreeIO
373 - Fixes so that re-rooting a tree works properly
375 - Writing out nhx format from a newick/nexus file will properly output
376 bootstrap information. The use must move the internal node labels over
377 to bootstraps.
378 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
379 $node->bootstrap($node->id);
380 $node->id('');
381 }
382 - Nexus parsing is much more flexible now, does not care about
383 LF.
385 - Cladogram drawing module in Bio::Tree::Draw
387 - Node height and depth now properly calculated
389 - fix tree pruning algorithm so that node with 1 child gets merged
391 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
392 bugs and improvements were added, see Gbrowse mailing list for most of
393 these.
395 o Bio::DB::GFF partially supports GFF3. See information about
396 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
398 o Better location parsing in Bio::Factory::FTLocationFactory -
399 this is part of the engine for parsing EMBL/GenBank feature table
400 locations. Nested join/order-by/complement are allowed now
402 o Bio::PrimarySeqI->translate now takes named parameters
404 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
405 reconstruction) is now supported. Parsing different models and
406 branch specific parametes are now supported.
408 o Bio::Factory::FTLocationFactory - parse hierarchical locations
409 (joins of joins)
411 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
412 for getter/setter functions
414 o Bio::SearchIO
416 - blast bug #1739; match scientific notation in score
417 and possible e+ values
419 - blast.pm reads more WU-BLAST parameters and parameters, match
420 a full database pathname,
422 - Handle NCBI WEB and newer BLAST formats specifically
423 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
425 - psl off-by-one error fixed
427 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
428 and HSPs can be constructed from them.
430 - HSPs query/hit now have a seqdesc field filled out (this was
431 always available via $hit->description and
432 $result->query_description
434 - hmmer.pm can parse -A0 hmmpfam files
436 - Writer::GbrowseGFF more customizeable.
438 o Bio::Tools::Hmmpfam
439 make e-value default score displayed in gff, rather than raw score
440 allow parse of multiple records
443 1.5 Developer release
445 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
446 provide Jukes-Cantor and Kimura pairwise distance methods,
447 respectively.
449 o Bio::AlignIO support for "po" format of POA, and "maf";
450 Bio::AlignIO::largemultifasta is a new alternative to
451 Bio::AlignIO::fasta for temporary file-based manipulation of
452 particularly large multiple sequence alignments.
454 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
455 be treated similarly as an assembled contig.
457 o Bio::CodonUsage provides new rare_codon() and probable_codons()
458 methods for identifying particular codons that encode a given
459 amino acid.
461 o Bio::Coordinate::Utils provides new from_align() method to build
462 a Bio::Coordinate pair directly from a
463 Bio::Align::AlignI-conforming object.
465 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
466 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
467 web service using standard Pubmed query syntax, and retrieve
468 results as XML.
470 o Bio::DB::GFF has various sundry bug fixes.
472 o Bio::FeatureIO is a new SeqIO-style subsystem for
473 writing/reading genomic features to/from files. I/O classes
474 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
475 classes only read/write Bio::SeqFeature::Annotated objects.
476 Notably, the GFF v3 class requires features to be typed into the
477 Sequence Ontology.
479 o Bio::Graph namespace contains new modules for manipulation and
480 analysis of protein interaction graphs.
482 o Bio::Graphics has many bug fixes and shiny new glyphs.
484 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
485 indexing for HMMER reports and FASTA qual files, respectively.
487 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
488 new objects that can be placed within a Bio::Map::MapI-compliant
489 genetic/physical map; Bio::Map::Physical provides a new physical
490 map type; Bio::MapIO::fpc provides finger-printed clone mapping
491 import.
493 o Bio::Matrix::PSM provide new support for postion-specific
494 (scoring) matrices (e.g. profiles, or "possums").
496 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
497 be instantiated without explicitly using Bio::OntologyIO. This
498 is possible through changes to Bio::Ontology::OntologyStore to
499 download ontology files from the web as necessary. Locations of
500 ontology files are hard-coded into
501 Bio::Ontology::DocumentRegistry.
503 o Bio::PopGen includes many new methods and data types for
504 population genetics analyses.
506 o New constructor to Bio::Range, unions(). Given a list of
507 ranges, returns another list of "flattened" ranges --
508 overlapping ranges are merged into a single range with the
509 mininum and maximum coordinates of the entire overlapping group.
511 o Bio::Root::IO now supports -url, in addition to -file and -fh.
512 The new -url argument allows one to specify the network address
513 of a file for input. -url currently only works for GET
514 requests, and thus is read-only.
516 o Bio::SearchIO::hmmer now returns individual Hit objects for each
517 domain alignment (thus containing only one HSP); previously
518 separate alignments would be merged into one hit if the domain
519 involved in the alignments was the same, but this only worked
520 when the repeated domain occured without interruption by any
521 other domain, leading to a confusing mixture of Hit and HSP
522 objects.
524 o Bio::Search::Result::ResultI-compliant report objects now
525 implement the "get_statistics" method to access
526 Bio::Search::StatisticsI objects that encapsulate any
527 statistical parameters associated with the search (e.g. Karlin's
528 lambda for BLAST/FASTA).
530 o Bio::Seq::LargeLocatableSeq combines the functionality already
531 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
533 o Bio::SeqFeature::Annotated is a replacement for
534 Bio::SeqFeature::Generic. It breaks compliance with the
535 Bio::SeqFeatureI interface because the author was sick of
536 dealing with untyped annotation tags. All
537 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
538 compliant, and accessible through Bio::Annotation::Collection.
540 o Bio::SeqFeature::Primer implements a Tm() method for primer
541 melting point predictions.
543 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
544 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
546 o Bio::Taxonomy::Node now implements the methods necessary for
547 Bio::Species interoperability.
549 o Bio::Tools::CodonTable has new reverse_translate_all() and
550 make_iupac_string() methods.
552 o Bio::Tools::dpAlign now provides sequence profile alignments.
554 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
556 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
557 parsers.
559 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
560 for designing small inhibitory RNA.
562 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
563 methods based on a distance matrix.
565 o Bio::Tree::Statistics provides an assess_bootstrap() method to
566 calculate bootstrap support values on a guide tree topology,
567 based on provided bootstrap tree topologies.
569 o Bio::TreeIO now supports the Pagel (PAG) tree format.
571 1.4 branch
573 1.4.1
575 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
577 o Bio::Graphics will work with gd1 or gd2
579 o Bio::SearchIO
580 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
581 (RF lines alone)
582 - blast.pm Parse multi-line query fields properly
583 - small speed improvements to blasttable.pm and others
585 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
586 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
587 supporting more complex queries
590 1.4. Stable major release
592 Since initial 1.2.0, 3000 separate changes have been made to make this release.
594 o installable scripts
596 o global module version from Bio::Root:Version
598 o Bio::Graphics
599 - major improvements; SVG support
601 o Bio::Popgen
602 - population genetics
603 - support several population genetics types of questions.
604 - Tests for statistical neutrality of mutations
605 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
606 Tests of population structure (Wright's F-statistic: Fst) is in
607 Bio::PopGen::PopStats. Calculating composite linkage
608 disequilibrium (LD) is available in Bio::PopGen::Statistics as
609 well.
610 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
611 and csv (comma delimited formatted) data.
613 - a directory for implementing population simulations has
614 been added Bio::PopGen::Simulation and 2 simulations - a
615 Coalescent and a simple single-locus multi-allele genetic drift
616 simulation have been provided. This replaces the code in
617 Bio::Tree::RandomTree which has been deprecated until proper
618 methods for generating random phylogenetic trees are
619 implemented.
621 o Bio::Restriction
622 - new restrion analysis modules
624 o Bio::Tools::Analysis
625 - web based DNA and Protein analysis framework and several
626 implementations
628 o Bio::Seq::Meta
629 - per residue annotable sequences
631 o Bio::Matrix
632 - Bio::Matrix::PSM - Position Scoring Matrix
633 - Bio::Matrix::IO has been added for generalized parsing of
634 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
635 initial implementations for parsing BLOSUM/PAM and Phylip
636 Distance matricies respectively. A generic matrix
637 implementation for general use was added in
638 Bio::Matrix::Generic.
640 o Bio::Ontology
641 - major changes
643 o Bio:Tree
645 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
646 - small inhibitory RNA
648 o Bio::SeqFeature::Tools
649 - seqFeature mapping tools
650 - Bio::SeqFeature::Tools::Unflattener.pm
651 -- deal with mapping GenBank feature collections into
652 Chado/GFF3 processable feature sets (with SO term mappings)
654 o Bio::Tools::dpAlign
655 - pure perl dynamic programming sequence alignment
656 - needs Bioperl-ext
658 o new Bio::SearchIO formats
659 - axt and psl: UCSC formats.
660 - blasttable: NCBI -m 8 or -m 9 format from blastall
662 o new Bio::SeqIO formats
663 - chado, tab, kegg, tigr, game
664 - important fixes for old modules
666 o Bio::AlignIO: maf
668 o improved Bio::Tools::Genewise
670 o Bio::SeqIO now can recongnize sequence formats automatically from
671 stream
673 o new parsers in Bio::Tools:
674 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
676 o Bio::DB::Registry bugs fixed
677 - BerkeleyDB-indexed flat files can be used by the OBDA system
678 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
679 used by the OBDA system
681 o several new HOWTOs
682 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
683 Databases
685 o hundreds of new and improved files
688 o
689 o Bio::Tree::AlleleNode has been updated to be a container of
690 an Bio::PopGen::Individual object for use in the Coalescent simulations.
693 1.2 Branch
695 1.2.3 Stable release update
696 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
697 handling.
698 o Bug #1477 - Sel --> Sec abbreviation fixed
699 o Fix bug #1487 where paring in-between locations when
700 end < start caused the FTLocationFactory logic to fail.
701 o Fix bug #1489 which was not dealing with keywords as an
702 arrayref properly (this is fixed on the main trunk because
703 keywords returns a string and the array is accessible via
704 get_keywords).
705 o Bio::Tree::Tree memory leak (bug #1480) fixed
706 Added a new initialization option -nodelete which
707 won't try and cleanup the containing nodes if this
708 is true.
709 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
710 this was only present on the branch for the 1.2.1 and 1.2.2 series
711 - Also merged main trunk changes to the branch which make
712 newick -> nhx round tripping more effective (storing branch length
713 and bootstrap values in same locate for NodeNHX and Node
714 implementations.) Fixes to TreeIO parsing for labeled internal
715 also required small changes to TreeIO::nhx. Improved
716 tests for this module as well.
717 o Bio::SearchIO
718 - Fixed bugs in BLAST parsing which couldn't parse NCBI
719 gapped blast properly (was losing hit significance values due to
720 the extra unexpeted column).
721 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
722 integer overflow (# of letters in nt seq dbs is > MAX_INT)
723 although doesn't try to correct it - will get the negative
724 number for you. Added a test for this as well.
725 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
726 has no top-level family classification scores but does have scores and
727 alignments for individual domains.
728 - Parsing FASTA reports where ungapped percent ID is < 10 and the
729 regular expression to match the line was missing the possibility of
730 an extra space. This is rare, which is why we probably did not
731 catch it before.
732 - BLAST parsing picks up more of the statistics/parameter fields
733 at the bottom of reports. Still not fully complete.
734 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
735 were fixed to include many improvements and added flexiblity
736 in outputting the files. Bug #1495 was also fixed in the process.
737 o Bio::DB::GFF
738 - Update for GFF3 compatibility.
739 - Added scripts for importing from UCSC and GenBank.
740 - Added a 1.2003 version number.
741 o Bio::Graphics
742 - Updated tutorial.
743 - Added a 1.2003 version number.
744 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
745 properly writing keywords out.
746 o Bio::SeqIO::genbank
747 - Fixed bug/enhancement #1513 where dates of
748 the form D-MMM-YYYY were not parsed. Even though this is
749 invalid format we can handle it - and also cleanup the date
750 string so it is properly formatted.
751 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
752 and written with Genbank format. Similarly bug #1515 is fixed to
753 parse in the ORIGIN text.
754 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
755 to specify the ID type, one of (accession accession.version
756 display primary). See Bio::SeqIO::preferred_id_type method
757 documentation for more information.
758 o Unigene parsing updated to handle file format changes by NCBI
760 1.2.2 Stable release update
762 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
763 - auto-discover ontology name
764 - bug in parsing relationships when certain characters are in the term
765 - fixed hard-coded prefix for term identifiers
766 - various smaller issues
768 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
769 of Bio::Ontology::TermI
771 o brought the OBDA Registry code up to latest specs
773 o Bio::DB::GenBank
774 - eutils URL change
775 - accession number retrieval fixed
777 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
779 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
780 #1459 which now properly report alignment start/end info
781 for translated BLAST/FASTA searches.
783 o Bio::TreeIO::newick can parse labeled internal nodes
785 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
786 for BLASTX if if you provide -report_type => 'BLASTX' when
787 initializing a BPbl2seq object. Bioperl 1.3 will have better
788 support for bl2seq in the SearchIO system.
790 o Bio::Root::IO support a -noclose boolean flag which will not
791 close a filehandle upon object cleanup - useful when sharing
792 a filehandle among objects. Additionally code added s.t.
793 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
795 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
797 o Bio::SeqIO::genbank
798 - bug #1456 fixed which generated extra sequence lines
799 - write moltype correctly for genpept
801 1.2.1 Stable release update
803 o Inclusion of WrapperBase, a needed component for StandAloneBlast
805 o Addition from main trunk of Ontology objects, principly to allow
806 BioSQL releases against 1.2.1
808 o Fixes and cleanup of Bio::Coordinate modules
810 o A fix to Bio::Index::EMBL allowing retrieval of entries using
811 the primary accession number
813 o Other bug fixes, including bpindex GenBank fix
815 o Bio::SeqIO::genbank bug #1389 fixed
817 1.2 Stable major release
819 o More functionality added to Bio::Perl, the newbie module
821 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
822 Support for New Hampshire Extended (NHX) format parsing.
824 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
825 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
826 Hmmpfam parser.
828 o New ontology parsing Bio::Ontology
830 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
831 multi-report (mlib) fasta reports, support for waba and exonerate.
833 o Bio::ClusterIO for parsing Unigene clusters
835 o Bio::Assembly added for representing phrap and ace assembly clusters.
837 o Rudimentary support for writing Chado XML (see
838 GMOD project: www.gmod.org for more information)
840 o Bio::Coordinate for mapping between different coordinate systems such
841 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
842 features into different coordinate systems.
844 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
845 with the get_Stream_by_query method and supports the latest
846 NCBI eutils interface.
848 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
849 object for extracting subsets of features : currently only
850 supports extraction by location.
852 1.1.1 Developer release
854 o Deprecated modules are now listed in the DEPRECATED file
856 o New HowTo documents located in doc/howto describing
857 a domain of Bioperl.
859 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
860 and all old bugs are searchable through the bugzilla interface.
862 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
863 have been addressed.
865 o Support for Genewise parsing in Bio::Tools::Genewise
867 o Start of Ontology framework with Bio::Ontology
869 o Speedup to the Bio::Root::Root object method _rearrange.
870 A global _load_module method was implemented to simplify the
871 dynamic loading of modules ala Bio::SeqIO::genbank. This
872 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
873 etc).
875 o Several performance improvements to sequence parsing in Bio::SeqIO.
876 Attempt to speedup by reducing object creation overhead.
878 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
879 method for sequence retrieval with their E-utils CGI scripts.
880 More work to support Entrez queries to their fullest is planned
881 before 1.2 release.
883 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
885 1.1 Developer release
887 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
888 this separation removes some of the complexity in our test suite
889 and separates the core modules in bioperl from those that need
890 external programs to run.
892 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
893 not run into trouble running the makefile
895 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
896 read,create,and write locations for grouped/split locations
897 (like mRNA features on genomic sequence).
899 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
900 and PAML (codeml,aaml, etc) parsing.
902 o Bio::Tree:: objects expanded to handle testing monophyly,
903 paraphyly, least common ancestor, etc.
905 o Bio::Coordinate for mapping locations from different coordinate spaces
907 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
908 added for parsing hmmpfam and hmmsearch output.
910 o Bio::SearchIO::Writer::TextResultWriter for outputting
911 a pseudo-blast textfile format
914 1.0.2 Bug fix release
916 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
917 in this release will not work after December 2002 when NCBI
918 shuts off the old Entrez cgi scripts. We have already fixed
919 on our main development branch and the functionality will be
920 available in the next stable bioperl release (1.2) slated for
921 Fall 2002.
923 o Numerous parsing bugs in Bio::SearchIO::fasta found through
924 testset by Robin Emig. These were fixed as was the get_aln
925 method in Bio::Search::HSP::GenericHSP to handle the extra
926 context sequence that is provided with a FastA alignment.
928 o Migrating differences between Bio::Search::XX::BlastXX to
929 Bio::Search::XX::GenericXX objects. This included mechanism
930 to retrieve whole list of HSPs from Hits and whole list of Hits from
931 Results in addition to the current next_XX iterator methods that
932 are available. Added seq_inds() method to GenericHSP which identifies
933 indexes in the query or hit sequences where conserved,identical,gaps,
934 or mismatch residues are located (adapted from Steve Chervitz's
935 implementation in BlastHSP).
937 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
938 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
940 o Bio::Graphics glyph set improved and extended for GBrowse release
942 o Bio::Tree::Tree get_nodes implementation improvement thanks
943 to Howard Ross notice performance problem when writing out
944 unbalanced trees.
946 o Bio::Location::Fuzzy::new named parameter -loc_type became
947 -location_type, Bio::Location::Simple::new named parameter
948 -seqid becamse -seq_id.
950 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
951 was mis-detecting that gaps should be placed at the beginning of
952 the alignment when the best alignment starts internally in the
953 sequence.
955 1.0.1 Bug fix release
957 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
959 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
960 and mixed (3.3 - 3.4) versions of FASTA.
962 o Small API change to add methods for completeness across
963 implementations of Bio::Search objects. These new methods
964 in the interface are implemented by the GenericXX object as well
965 as the BlastXX objects.
966 * Bio::Search::Result::ResultI
967 - hits() method returns list of all Hits (next_hit is an
968 iterator method)
970 * Bio::Search::Hit::HitI
971 - hsps() method returns list of all HSPs (next_hsp is an
972 iterator method)
974 o The Bio::SearchIO::Writer classes have been fixed to handle results
975 created from either psiblast (Search::BlastXX objects) or
976 blast|fasta|blastxml objects (Search::GenericXX objects). More work
977 has to be done here to make it work properly and will nee major
978 API changes.
980 o Bugs in Bio::Tools::HMMER fixed, including
981 * #1178 - Root::IO destructor wasn't being called
982 * #1034 - filter_on_cutoff now behaves properly
984 o Bio::SeqFeature::Computation initialization args fixed and
985 tests added.
987 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
989 o Updated FAQ with more example based answers to typical questions
991 o Bug #1202 was fixed which would improperly join together qual values
992 parsed by Bio::SeqIO::qual when a trailing space was not present before
993 the newline.
995 1.0.0 Major Stable Release
997 This represents a major release of bioperl with significant
998 improvements over the 0.7.x series of releases.
1000 o Bio::Tools::Blast is officially deprecated. Please see
1001 Bio::SearchIO for BLAST and FastA parsing.
1003 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1004 Bio::LocationI objects as well as start/end.
1006 o Bio::Biblio contains modules for Bibliographic data.
1007 Bio::DB::Biblio contains the query modules. Additionally one can
1008 parse medlinexml from the ebi bibliographic query service (BQS)
1009 system and Pubmed xml from NCBI. See Martin Senger's
1010 documentation in Bio::Biblio for more information.
1012 o Bio::DB::Registry is a sequence database registry part of
1013 Open Bioinformatics Database Access. See
1014 http://obda.open-bio.org for more information.
1016 o File-based and In-Memory Sequence caching is provided by
1017 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1018 local database.
1020 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1021 been added by Lincoln Stein.
1023 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1025 o A FAQ has been started and is included in the release to provide
1026 a starting point for frequent questions and issues.
1028 0.9.3 Developer's release
1030 o Event based parsing system improved (SearchIO). With parsers for
1031 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1032 Additionally a lazy parsing system for text and html blast reports was
1033 added and is called psiblast (name subject to change in future releases).
1035 o Bio::Search objects improved and standardized with associated Interfaces
1036 written. The concept of a search "Hit" was standardized to be called
1037 "hit" consistently and the use of "subject" was deprecated in all active
1038 modules.
1040 o Bio::Structure added (since 0.9.1) for Protein structure objects
1041 and PDB parser to retrieve and write these structures from data files.
1043 o Several important Bio::DB::GFF bug fixes for handling features that
1044 are mapped to multiple reference points. Updated mysql adaptor
1045 so as to be able to store large (>100 megabase) chunks of DNA into
1046 Bio::DB::GFF databases.
1048 0.9.2 Developer's release
1050 o Bio::Search and Bio::SearchIO system introduced for event based
1051 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1052 in text and XML and FASTA reports in standard output format.
1054 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1055 generator is included in Bio::TreeIO::RandomTrees and a
1056 statistics module for evaluating.
1058 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1059 server for DAS servers.
1061 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1062 files. The entire BPlite system migrated to using Bio::Root::IO
1063 for the data stream.
1065 o Bio::Tools::Alignment for Consed and sequence Trimming
1066 functionality.
1068 o Bio::Structure for Protein structure information and parsing
1070 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1071 cgi-bin entry point which should be more reliable.
1073 o Bio::Map and Bio::MapIO for biological map navigation and a
1074 framework afor parsing them in. Only preliminary work here.
1076 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1077 Future work will integrate Pise and allow submission of analysis on
1078 remote servers.
1080 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1081 introduced as new objects for handling Sequence Annotation
1082 information (dblinks, references, etc) and is more robust that
1083 previous system.
1085 o Bio::Tools::FASTAParser introduced.
1087 o Scripts from the bioperl script submission project and new
1088 scripts from bioperl authors are included in "scripts" directory.
1090 o Factory objects and interfaces are being introduced and are more
1091 strictly enforced.
1093 o Bio::Root::Root introduced as the base object while
1094 Bio::Root::RootI is now simply an interface.
1096 o Bio::DB::RefSeq provides database access to copy of the NCBI
1097 RefSeq database using the EBI dbfetch script.
1099 0.9.0 Developer's release
1101 o perl version at least 5.005 is now required instead of perl 5.004
1103 o Bio::Tools::Run::RemoteBlast is available for running remote
1104 blast jobs at NCBI.
1106 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1108 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1109 Also added are related modules UTR3, UTR5, Exon, Intron,
1110 Promotor, PolyA and Transcript.
1112 o Speedup of translate method in PrimarySeq
1114 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1115 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1117 o Various fixes to Variation toolkit
1119 o Bio::DB::EMBL provides database access to EMBL sequence data.
1120 Bio::DB::Universal provides a central way to point to indexes
1121 and dbs in a single interface.
1123 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1125 o Bio::Factory::EMBOSS is still in design phase as is
1126 Bio::Factory::ApplicationFactoryI
1128 o Dia models for bioperl design are provided in the models/ directory
1130 0.7.2 Bug fix release
1132 o documentation fixes in many modules - SYNOPSIS code verified
1133 to be runnable in many (but not all modules)
1135 o corrected MANIFEST file from 0.7.1 release
1137 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1138 split locations
1140 o Bio::SeqIO::genbank
1141 * Correct parsing and writing of genbank format with protein data
1142 * moltype and molecule separation
1144 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1146 o Bio::SimpleAlign fixed to correctly handle consensus
1147 sequence calculation
1149 o Bio::Tools::HMMER supports hmmer 2.2g
1151 o Bio::Tools::BPlite to support report type specific parsing. Most
1152 major changes are not on the 0.7 branch.
1154 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1155 with File::Spec
1157 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1158 in several types of mutations:
1159 1.) AA level: deletion, complex
1160 2.) AA level: complex, inframe
1161 3.) RNA level: silent
1163 o BPbl2seq parsing of empty reports will not die, but will return
1164 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1165 $report->query() and $report->subject() methods. So an easy
1166 way to test if report was empty is to see if
1167 $report->query->seqname is undefined.
1169 0.7.1 Bug fix release
1171 o Better parsing of genbank/EMBL files especially fixing bugs
1172 related to Feature table parsing and locations on remote
1173 sequences. Additionally, species name parsing was better.
1175 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1176 which include a number of header lines.
1178 o More strict genbank and EMBL format writing (corrected number of
1179 spaces where appropriate).
1181 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1182 for related BPlite BUGS that are unresolved in this release.
1184 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1185 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1186 use expasy mirrors or EBI dbfetch cgi-script.
1188 o A moderate number of documentation improvements were made as
1189 well to provide a better code synopsis in each module.
1192 0.7 Large number of changes, including refactoring of the
1193 Object system, new parsers, new functionality and
1194 all round better system. Highlights are:
1197 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1198 Bio::Root::IO for I/O and file/handle capabilities.
1200 o Imported BPlite modules from Ian Korf for BLAST
1201 parsing. This is considered the supported BLAST parser;
1202 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1204 o Improved Sequence Feature model. Added complete location
1205 modelling (with fuzzy and compound locations). See
1206 Bio::LocationI and the modules under Bio/Location. Added
1207 support in Genbank/EMBL format parsing to completely parse
1208 feature tables for complex locations.
1210 o Moved special support for databanks etc to specialized modules under
1211 Bio/Seq/. One of these supports very large sequences through
1212 a temporary file as a backend.
1214 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1215 CDS retrieval and exon shuffling.
1217 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1219 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1220 DB/GDB (the latter has platform-specific limitations).
1222 o New analysis parser framework for HT sequence annotation (see
1223 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1225 o New Alignment IO framework
1227 o New Index modules (Swissprot)
1229 o New modules for running Blast within perl
1230 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1231 Multiple Sequence Alignment tools ClustalW and TCoffee
1232 (Bio::Tools::Run::Alignment).
1234 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1235 documentation across the package.
1237 o Much improved cross platform support. Many known incompatibilities
1238 have been fixed; however, NT and Mac do not work across the entire
1239 setup (see PLATFORMS).
1241 o Many bug fixes, code restructuring, etc. Overall stability and
1242 maintainability benefit a lot.
1244 o A total of 957 automatic tests
1247 0.6.2
1249 There are very few functionality changes but a large
1250 number of software improvements/bug fixes across the package.
1252 o The EMBL/GenBank parsing are improved.
1254 o The Swissprot reading is improved. Swissprot writing
1255 is disabled as it doesn't work at all. This needs to
1256 wait for 0.7 release
1258 o BLAST reports with no hits are correctly parsed.
1260 o Several other bugs of the BLAST parser (regular expressions, ...)
1261 fixed.
1263 o Old syntax calls have been replaced with more modern syntax
1265 o Modules that did not work at all, in particular the Sim4
1266 set have been removed
1268 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1269 have improved compliance with interface specs and documentation
1271 o Mailing list documentation updated throughout the distribution
1273 o Most minor bug fixes have happened.
1275 o The scripts in /examples now work and have the modern syntax
1276 rather than the deprecated syntax
1279 0.6.1 Sun April 2 2000
1281 o Sequences can have Sequence Features attached to them
1282 - The sequence features can be read from or written to
1283 EMBL and GenBank style flat files
1285 o Objects for Annotation, including References (but not
1286 full medline abstracts), Database links and Comments are
1287 provided
1289 o A Species object to represent nodes on a taxonomy tree
1290 is provided
1292 o The ability to parse HMMER and Sim4 output has been added
1294 o The Blast parsing has been improved, with better PSI-BLAST
1295 support and better overall behaviour.
1297 o Flat file indexed databases provide both random access
1298 and sequential access to their component sequences.
1300 o A CodonTable object has been written with all known
1301 CodonTables accessible.
1303 o A number of new lightweight analysis tools have been
1304 added, such as molecular weight determination.
1306 The 0.6 release also has improved software engineering
1308 o The sequence objects have been rewritten, providing more
1309 maintainable and easier to implement objects. These
1310 objects are backwardly compatible with the 0.05.1 objects
1312 o Many objects are defined in terms of interfaces and then
1313 a Perl implementation has been provided. The interfaces
1314 are found in the 'I' files (module names ending in 'I').
1316 This means that it is possible to wrap C/CORBA/SQL access
1317 as true "bioperl" objects, compatible with the rest of
1318 bioperl.
1320 o The SeqIO system has been overhauled to provide better
1321 processing and perl-like automatic interpretation of <>
1322 over arguments.
1324 o Many more tests have been added (a total of 172 automatic
1325 tests are now run before release).
1329 0.05.1 Tue Jun 29 05:30:44 1999
1330 - Central distribution now requires Perl 5.004. This was
1331 done to get around 5.003-based problems in Bio/Index/*
1332 and SimpleAlign.
1333 - Various bug fixes in the Bio::Tools::Blast modules
1334 including better exception handling and PSI-Blast
1335 support. See Bio/Tools/Blast/CHANGES for more.
1336 - Fixed the Parse mechanism in Seq.pm to use readseq.
1337 Follow the instructions in README for how to install
1338 it (basically, you have to edit Parse.pm).
1339 - Improved documentation of Seq.pm, indicating where
1340 objects are returned and where strings are returned.
1341 - Fixed uninitialized warnings in Bio::Root::Object.pm
1342 and Bio::Tools::SeqPattern.pm.
1343 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1345 0.05 Sun Apr 25 01:14:11 1999
1346 - Bio::Tools::Blast modules have less memory problems
1347 and faster parsing. Webblast uses LWP and supports
1348 more functionality. See Bio/Tools/Blast/CHANGES for more.
1349 - The Bio::SeqIO system has been started, moving the
1350 sequence reformatting code out of the sequence object
1351 - The Bio::Index:: system has been started, providing
1352 generic index capabilities and specifically works for
1353 Fasta formatted databases and EMBL .dat formatted
1354 databases
1355 - The Bio::DB:: system started, providing access to
1356 databases, both via flat file + index (see above) and
1357 via http to NCBI
1358 - The scripts/ directory, where industrial strength scripts
1359 are put has been started.
1360 - Many changes - a better distribution all round.
1362 0.04.4 Wed Feb 17 02:20:13 1999
1363 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1364 (see Bio::Tools::Blast::CHANGES).
1365 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1366 - Beefed up the t/Fasta.t test script.
1367 - Small fix in Bio::Seq::type() (now always returns a string).
1368 - Changed Bio::Root::Utilities::get_newline_char() to
1369 get_newline() since it could return more than one char.
1370 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1371 - Changed default timeout to 20 seconds (was 3).
1372 - Moved lengthy modification notes to the bottom of some files.
1373 - Fixed SimpleAlign write_fasta bug.
1374 - Beefed up SimpleAlign.t test
1376 0.04.3 Thu Feb 4 07:48:53 1999
1377 - Bio::Root::Object.pm and Global.pm now detect when
1378 script is run as a CGI and suppress output that is only
1379 appropriate when running interactively.
1380 - Bio::Root::Err::_set_context() adds name of script ($0).
1381 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1382 regarding the use of the static objects via the qw(:obj) tag.
1383 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1384 CORE::reverse, avoiding Perl warnings.
1385 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1386 example scripts (see Bio::Tools::Blast::CHANGES).
1387 - examples/seq/seqtools.pl no longer always warns about using
1388 -prot or -nucl command-line arguments; only when using the
1389 -debug argument.
1390 - Methods added to Bio::Root::Utilities: create_filehandle(),
1391 get_newline_char(), and taste_file() to generalize filehandle
1392 creation and autodetect newline characters in files/streams
1393 (see bug report #19).
1394 - Bio::Root::IOManager::read() now handles timeouts and uses
1395 Utilities::create_filehandle().
1396 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1397 of hardwiring in "\n".
1398 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1400 0.04.2 Wed Dec 30 02:27:36 1998
1401 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1402 (see Bio::Tools::Blast::CHANGES).
1403 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1404 to CORE::reverse (prevents ambiguous warnings with 5.005).
1405 - Appending '.tmp.bioperl' to temporary files created by
1406 Bio::Root::Utilities::compress() or uncompress() to
1407 make it easy to identify & cleanup these files as needed.
1408 - Developers: Created CVS branch release-0-04-bug from
1409 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1410 be sure to cvs checkout this branch into a clean area.
1412 0.04.1 Wed Dec 16 05:39:15 1998
1413 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1414 (see Bio::Tools::Blast::CHANGES).
1415 - Compile/SW/Makefile.PL now removes *.o and *.a files
1416 with make clean.
1418 0.04 Tue Dec 8 07:49:19 1998
1419 - Lots of new modules added including:
1420 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1421 and Bio/Compile directory containing XS-linked C code for
1422 creating Smith-Waterman sequence alignments from within Perl.
1423 * Steve Chervitz's Blast distribution has been incorporated.
1424 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1425 - Bio/examples directory for demo scripts for all included modules.
1426 - Bio/t directory containing test suit for all included modules.
1427 - For changes specific to the Blast-related modules prior to
1428 incorporation in this central distribution, see the CHANGES
1429 file in the Bio/Tools/Blast directory.
1431 0.01 Tue Sep 8 14:23:22 1998
1432 - original version from central CVS tree; created by h2xs 1.18