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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://github.com/bioperl/bioperl-live/issues
17 CPAN releases are branched from 'master'.
18 ---------------------------------------------------------
20 Philosophy for 1.7.x:
22 In order to reduce the number of dependencies, we are actively encouraging
23 developers wanting to submit new code with additional dependencies to release
24 code in a separate repository and release it on CPAN. We can help assist in this
25 process and can also place this under the 'bioperl' Github organization (and
26 similarly under the bioperl umbrella account in CPAN), though this is not
27 required.
29 We will also be moving additonal code to other repositories and will release
30 them separately on CPAN. Modules considered obsolute (relies on a dead web
31 service or utilizes strict dependencies that are also considered obsolete) will
32 be removed.
34 1.7.3 - "To Be Named"
36 * The following modules have been removed from the BioPerl
37 distribution to be part of a separate distribution. They have
38 been integrated into other module distributions for independent
39 development:
41 Bio::Align::Graphics
42 Bio::AlignIO::nexml
43 Bio::AlignIO::stockholm
44 Bio::Assembly::*
45 Bio::Cluster::*
46 Bio::ClusterI::*
47 Bio::ClusterIO::*
48 Bio::DB::Ace
49 Bio::DB::BioFetch
50 Bio::DB::CUTG
51 Bio::DB::EMBL
52 Bio::DB::EntrezGene
53 Bio::DB::Expression::*
54 Bio::DB::GFF
55 Bio::DB::GFF::Adaptor::*
56 Bio::DB::GFF::Aggregator::*
57 Bio::DB::GFF::Featname
58 Bio::DB::GFF::Feature
59 Bio::DB::GFF::Homol
60 Bio::DB::GFF::RelSegment
61 Bio::DB::GFF::Segment
62 Bio::DB::GFF::Typename
63 Bio::DB::GenBank
64 Bio::DB::GenPept
65 Bio::DB::HIV::*
66 Bio::DB::MeSH
67 Bio::DB::NCBIHelper
68 Bio::DB::Query::GenBank
69 Bio::DB::Query::HIVQuery
70 Bio::DB::RefSeq
71 Bio::DB::SeqFeature::*
72 Bio::DB::SeqVersion::*
73 Bio::DB::SwissProt
74 Bio::DB::TFBS::*
75 Bio::DB::Taxonomy::entrez
76 Bio::DB::Taxonomy::sqlite
77 Bio::DB::Universal
78 Bio::Draw::Pictogram
79 Bio::Factory::MapFactoryI
80 Bio::Index::Hmmer
81 Bio::Index::Stockholm
82 Bio::LiveSeq::*
83 Bio::Map::*
84 Bio::MapIO::*
85 Bio::MolEvol::CodonModel
86 Bio::Nexml::Factory
87 Bio::NexmlIO
88 Bio::Perl
89 Bio::Phenotype::*
90 Bio::PhyloNetwork::*
91 Bio::PopGen::*
92 Bio::Restriction::*
93 Bio::Root::Build
94 Bio::Search::HSP::HMMERHSP
95 Bio::Search::HSP::HmmpfamHSP
96 Bio::Search::Hit::HMMERHit
97 Bio::Search::Hit::HmmpfamHit
98 Bio::Search::Hit::hmmer3Hit
99 Bio::Search::Result::HMMERResult
100 Bio::Search::Result::HmmpfamResult
101 Bio::Search::Result::hmmer3Result
102 Bio::SearchDist
103 Bio::SearchIO::hmmer
104 Bio::SearchIO::hmmer2
105 Bio::SearchIO::hmmer3
106 Bio::SearchIO::hmmer_pull
107 Bio::SeqEvolution::*
108 Bio::SeqFeature::SiRNA::*
109 Bio::SeqIO::abi
110 Bio::SeqIO::agave
111 Bio::SeqIO::alf
112 Bio::SeqIO::chadoxml
113 Bio::SeqIO::chaos
114 Bio::SeqIO::chaosxml
115 Bio::SeqIO::ctf
116 Bio::SeqIO::entrezgene
117 Bio::SeqIO::excel
118 Bio::SeqIO::exp
119 Bio::SeqIO::flybase_chadoxml
120 Bio::SeqIO::nexml
121 Bio::SeqIO::pln
122 Bio::SeqIO::strider
123 Bio::SeqIO::ztr
124 Bio::Structure::*
125 Bio::Taxonomy::*
126 Bio::Tools::AlignFactory
127 Bio::Tools::Analysis::* (except SimpleAnalysisBase)
128 Bio::Tools::Gel
129 Bio::Tools::HMMER::*
130 Bio::Tools::Hmmpfam
131 Bio::Tools::Phylo::Gumby
132 Bio::Tools::Protparam
133 Bio::Tools::Run::RemoteBlast
134 Bio::Tools::SiRNA::*
135 Bio::Tools::dpAlign
136 Bio::Tools::pSW
137 Bio::Tree::AlleleNode
138 Bio::Tree::Draw::Cladogram
139 Bio::TreeIO::nexml
140 Bio::TreeIO::svggraph
141 Bio::Variation::*
143 * The following modules are new in the BioPerl distribution. They
144 have been previously released in the BioPerl-Run distribution.
145 This will enable smaller distributions that provide a
146 Bio::Tool::Run interface, to be only dependent on the BioPerl
147 distribution instead of the whole (very large) BioPerl-Run:
149 Bio::Tools::Run::Analysis
150 Bio::Tools::Run::AnalysisFactory
151 Bio::Tools::Run::Phylo::PhyloBase
152 Bio::Tools::Run::WrapperBase
153 Bio::Tools::Run::WrapperBase::CommandExts
155 * The following programs have been removed:
157 bp_biofetch_genbank_proxy
158 bp_blast2tree
159 bp_bulk_load_gff
160 bp_composite_LD
161 bp_das_server
162 bp_download_query_genbank
163 bp_fast_load_gff
164 bp_flanks
165 bp_genbank2gff
166 bp_generate_histogram
167 bp_heterogeneity_test
168 bp_hivq
169 bp_hmmer_to_table
170 bp_load_gff
171 bp_meta_gff
172 bp_netinstall
173 bp_parse_hmmsearch
174 bp_process_wormbase
175 bp_query_entrez_taxa
176 bp_remote_blast
177 bp_seqfeature_delete
178 bp_seqfeature_gff3
179 bp_seqfeature_load
181 * Because of the move of so many modules and programs into
182 separate distributions, the following modules are no longer
183 prerequisites:
185 Ace
186 Ace::Sequence::Homol
187 Algorithm::Munkres
188 Apache::DBI
189 Archive::Tar
190 Array::Compare
191 Bio::ASN1::EntrezGene
192 Bio::Expression::Contact
193 Bio::Expression::DataSet
194 Bio::Expression::Platform
195 Bio::Expression::Sample
196 Bio::Ext::Align
197 Bio::GMOD::CMap::Utils
198 Bio::Phylo::Factory
199 Bio::Phylo::Forest::Tree
200 Bio::Phylo::IO
201 Bio::Phylo::Matrices
202 Bio::Phylo::Matrices::Datum
203 Bio::Phylo::Matrices::Matrix
204 Bio::SeqFeature::Annotated
205 Bio::SeqIO::staden::read
206 Bio::Tools::Run::Alignment::Clustalw
207 Bio::Tools::Run::Ensembl
208 Bio::Tools::Run::Phylo::Molphy::ProtML
209 Bio::Tools::Run::Phylo::Phylip::Neighbor
210 Bio::Tools::Run::Phylo::Phylip::ProtDist
211 Bio::Tools::Run::Phylo::Phylip::ProtPars
212 Bio::Tools::Run::Samtools
213 CGI
214 CPAN
215 Cache::FileCache
216 Config
217 Convert::Binary::C
218 DBD::Pg
219 DBD::SQLite
220 Data::Stag::XMLWriter
221 Encode
222 English
223 ExtUtils::Install
224 ExtUtils::Manifest
225 File::Glob
226 GD::Simple
227 Getopt::Std
228 Graph::Undirected
229 GraphViz
230 HTML::HeadParser
231 HTML::TableExtract
232 LWP
233 LWP::Simple
234 MIME::Base64
235 Memoize
236 PostScript::TextBlock
237 SVG
238 SVG::Graph
239 SVG::Graph::Data
240 SVG::Graph::Data::Node
241 SVG::Graph::Data::Tree
242 Sort::Naturally
243 Spreadsheet::ParseExcel
244 Term::ReadLine
245 Text::NSP::Measures::2D::Fisher2::twotailed
246 Text::ParseWords
247 Time::Local
248 Tree::DAG_Node
249 URI::Escape
250 WWW::Mechanize
251 XML::Simple
253 * The following is a new prerequisite:
255 Test::RequiresInternet
257 * The deobfuscator has been removed.
259 * The emacs bioperl minor mode is no longer distributed as part of the
260 perl module distributions. See
261 https://github.com/bioperl/emacs-bioperl-mode
264 1.7.2 - "Entebbe"
266 [Bugs]
268 * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
269 * #245 - Code coverage fixes [zmughal,cjfields]
270 * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
271 * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
272 * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
273 * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
274 * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
275 * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
276 * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
277 * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
278 * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
279 * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
281 [Code changes]
283 * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
285 1.7.1 - "Election"
287 [Bugs]
289 * Minor release to incorporate fix for CPAN indexing, which
290 prevented proper updates [cjfields]
291 * Fix problem in managing Target attribute for gff3 [Jukes34]
292 * Minor bug fixes related to NCBI HTTPS support [cjfields]
294 1.7.0 - "Disney"
296 [New site]
298 * We have migrated to Github Pages. This was actually planned, but the
299 recent OBF server compromise forced our hand.
301 Brian Osborne [bosborne] took this under his wing to move docs and has
302 done a tremendous amount of work formatting the site and working out some
303 of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
304 Cantalupo and Franscison Ossandon also helped. Kudos!!
306 * Similarly, the official issue tracker is now Github Issues. This has
307 been updated in the relevant documentation bits (we hope!)
309 [Code changes]
311 * Previously deprecated modules removed
312 * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
313 * Bio::DB::SeqHound has been removed due to the service no longer being
314 available
315 * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
316 reasons due to the server no longer having a valid cert
317 * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
318 * Bio::Coordinate, Bio::SearchIO::blastxml,
319 Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
320 added on CPAN
322 [New features]
324 * Docker instances of tagged releases are available! [hlapp]
325 * NCBI HTTPS support [mjohnson and others]
326 * Bio::SearchIO::infernal
327 - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
328 * Bio::Search::HSP::ModelHSP
329 - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
330 reports [pcantalupo]
331 * Bio::Search::Result::INFERNALResult
332 - Added new module to represent features of Infernal reports [pcantalupo]
333 * Bio::DB::Taxonomy SQLite option [cjfields]
334 * WrapperBase quoted option values [majensen]
335 * Various documentation fixes and updates [bosborne]
337 [Bug Fixes]
339 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
340 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
341 * NeXML parser fixes [fjossandon]
342 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
343 * RT 103272 : SeqFeature database deletion skipped features with a decimal -
344 Joshua Fortriede (Xenbase)
345 * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
346 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
347 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
348 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
349 * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
350 * Issue #84: EMBL format wrapping problem [nyamned]
351 * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
352 * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
353 or compiled C code (when Inline::C is installed) [rocky]
354 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
355 * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
356 * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
357 * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
358 to be consistent with "$hit->bits" behaviour [fjossandon]
359 * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
360 aminoacids made "next_seq" confused and broke the parser [fjossandon]
361 * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
362 Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
363 to "complement(join(A..B,C..D))" [fjossandon]
364 * For the many many many fixes that weren't mentioned - blame the release guy!
366 1.6.924
368 [Significant changes]
370 * Bug/feature issue tracking has moved to GitHub Issues:
371 https://github.com/bioperl/bioperl-live/issues
372 * DB_File has been demoted from "required" to "recommended",
373 which should make easier for Windows users to install BioPerl
374 if they don't need that module.
376 [New features]
378 * Bio::Search::HSP::GenericHSP
379 - Bug #3370, added a "posterior_string" method to retrieve the
380 posterior probability lines (PP) from HMMER3 reports [fjossandon]
381 - Added a "consensus_string" method to retrieve the consensus
382 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
383 * Bio::SearchIO::hmmer2
384 - The number of identical and conserved residues are now calculated
385 directly from the homology line [fjossandon]
386 - Now the Query Length and Hit Length are reported when the alignment
387 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
388 - Implemented the capture of the consensus structure lines [fjossandon]
389 * Bio::SearchIO::hmmer3
390 - The number of identical and conserved residues are now calculated
391 directly from the homology line [fjossandon]
392 - Now the Hit Length is reported when the alignment runs until the end
393 of the sequence/model ('.]' or '[]') [fjossandon]
394 - Implemented the capture of the consensus structure lines [fjossandon]
395 - Implemented the capture of the posterior probability lines [fjossandon]
396 - Completed the development of NHMMER parsing, including alignments [fjossandon]
397 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
398 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
399 "min_score", "min_bits, and "hit_filter" methods from
400 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
401 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
402 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
403 besides Blast, instead of being ignored. Added tests for all moved methods
404 using HMMER outputs and run the full test suite and everything pass [fjossandon]
405 * Bio::SeqIO::MultiFile
406 - Autodetection of file format [fangly]
407 * Bio::Tools::GuessSeqFormat:
408 - Format detection from non-seekable filehandles such as STDIN [fangly]
410 [Bug fixes]
412 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
413 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
414 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
415 * Abstract: Fixed ActivePerl incapability of removing temporary files
416 because of problems closing tied filehandles [fjossandon]
417 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
418 because ActivePerl were producing a ".index.pag" and ".index.dir"
419 files instead of a single ".index" file (like Strawberry Perl).
420 Now those temporary files are correctly considered and deleted. [fjossandon]
421 * Test files: Added missing module requirements (DB_File and Data::Stag)
422 to several tests files that were failing because those modules were
423 not present. Now those test files are correctly skipped instead. [fjossandon]
424 * Blast: Added support to changes in bl2seq from BLAST+ output, which
425 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
426 * Phylip: Return undef in "next_aln" at file end to avoid
427 an infinite loop [yschensandiego]
428 * HMMER3: When a hit description is too long, it is truncated in
429 the Scores table. In those cases, the more complete description from
430 the Annotation line (>>) will be used [fjossandon]
431 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
432 since it is now used by HMMER3 format in alignments [fjossandon]
433 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
434 to return undef if the query/hit length is unknown (like in some
435 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
436 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
437 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
438 added support to multi-query reports, reduced code redundancy,
439 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
440 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
441 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
442 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
443 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
444 * Double-quotes on paths are needed in some places [fjossandon]
445 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
446 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
447 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
448 with the latest changes made in their own repositories [fjossandon]
449 * General synching of files with the master branch [fjossandon]
450 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
451 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
452 * Fixed broken MeSH parser [fjossandon]
453 * Fixed missing detection of format in SeqIO when given a -string [fangly]
455 1.6.923
457 * Major Windows support updates! [fjossandon]
458 * MAKER update to allow for stricter standard codon table [cjfields]
459 * Better support for circular sequences [fjossandon]
460 * Fixes for some complex location types [fjossandon]
461 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
462 * Fix bug #2978 related to BLAST report type [fjossandon]
463 * Deobfuscator fixes [DaveMessina]
465 1.6.922
467 * Address CPAN test failures [cjfields]
468 * Add BIOPROJECT support for Genbank files [hyphaltip]
469 * Better regex support for HMMER3 output [bosborne]
471 1.6.921
473 * Minor update to address CPAN test failures
475 1.6.920
477 * Remove Bio::Biblio and related files [carandraug]
478 - this cause version clashes with an independently-released
479 version of Bio::Biblio
481 1.6.910
483 [New features]
485 * Hash randomization fixes for perl 5.18.x
486 - Note: at least one module (Bio::Map::Physical) still has a failing test;
487 this is documented in bug #3446 and has been TODO'd; we will be pulling
488 Bio::Map and similar modules out of core into separate distributions in the
489 1.7.x release series [cjfields]
491 [New features]
493 * Bio::Seq::SimulatedRead
494 - New module to represent reads taken from other sequences [fangly]
495 * Bio::Root::Root
496 - Support of Clone::Fast as a faster cloning alternative [fangly]
497 * Bio::Root::IO
498 - Moved the format() and variant() methods from Bio::*IO modules to
499 Bio::Root::IO [fangly]
500 - Can now use format() to get the type of IO format in use [fangly]
501 * Bio::Tools::IUPAC
502 - New regexp() method to create regular expressions from IUPAC sequences
503 [fangly]
504 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
505 - Code refresh [fangly]
506 * Bio::DB::Taxonomy
507 - Added support for the Greengenes and Silva taxonomies [fangly]
508 * Bio::Tree::TreeFunctionsI
509 - get_lineage_string() represents a lineage as a string [fangly]
510 - add_trait() returns instead of reporting an error when the column
511 number is exceeded in add_trait() [fangly]
512 - Option to support tree leaves without trait [fangly]
513 - Allow ID of 0 in trait files [fangly]
514 * Bio::DB::Taxonomy::list
515 - Misc optimizations [fangly]
516 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
517 * Bio::DB::Taxonomy::*
518 - get_num_taxa() returns the number of taxa in the database [fangly]
519 * Bio::DB::Fasta and Bio::DB::Qual
520 - support indexing an arbitrary list of files [fangly]
521 - user can supply an arbitrary index file name [fangly]
522 - new option to remove index file at the end [fangly]
523 * Bio::DB::Fasta
524 - now handles IUPAC degenerate residues [fangly]
525 * Bio::PrimarySeq and Bio::PrimarySeqI
526 - speed improvements for large sequences [Ben Woodcroft, fangly]
527 * Bio::PrimaryQual
528 - tightened and optimized quality string validation [fangly]
529 * Bio::SeqIO::fasta
530 - new method and option 'block', to create FASTA output with space
531 intervaled blocks (similar to genbank or EMBL) has been implemented.
532 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
533 in favour of the methods 'width' and 'preferred_id_type` respectively.
534 * Bio::FeatureIO::*
535 - moved from bioperl-live into the separate distribution Bio-FeatureIO
536 * Bio::SeqFeature::Annotated
537 - moved from bioperl-live into the separate distribution Bio-FeatureIO
538 * Bio::Cluster::SequenceFamily
539 - improved performance when using get_members with overlapping multiple
540 criteria
541 * Bio::SearchIO::hmmer3
542 - now supports nhmmer [bosborne]
544 [Bug fixes]
546 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
547 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
548 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
549 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
550 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
551 information was lost in a multi-result blast file [Paul Cantalupo]
552 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
553 total gaps [Paul Cantalupo]
554 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
555 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
556 when end of domain indicator is split across lines [Paul Cantalupo]
557 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
558 cjfields]
559 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
560 instances where blank lines are within sequences [cjfields]
561 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
562 types [fangly]
563 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
564 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
565 cjfields]
566 * Various fixes for Stockholm file indexing and processing [bosborne]
567 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
568 breaks parsing [cjfields]
569 * Fix case where Bio::Seq::Meta* objects with no meta information could not
570 be reverse-complemented [fangly]
571 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
572 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
573 when unsure that values will be numerical [fangly]
574 * Fix undef warnings in Bio::SeqIO::embl [fangly]
575 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
576 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
577 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
578 Sallou]
579 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
580 source_tag and display_name must return a string, not undef [fangly]
581 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
582 add_SeqFeature takes a single argument [fangly]
583 * Use cross-platform filenames and temporary directory in
584 Bio::DB::Taxonomy::flatfile [fangly]
585 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
586 properly identified as existing taxa in the database [fangly]
587 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
588 without also passing a lineage to store [fangly]
589 * Prevent passing a directory to the gi2taxid option (-g) of
590 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
591 [fangly]
592 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
593 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
594 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
595 object before trying to access, and no longer returns repeated sequences.
598 1.6.901 May 18, 2011
600 [Notes]
602 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
603 modules using Ace will also be deprecated [lds, cjfields]
604 * Minor bug fix release
605 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
606 * Address Build.PL issues when DBI is not present [hartzell]
607 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
608 * Remove deprecated code for perl 5.14.0 compat [cjfields]
609 * Due to schema changes and lack of support for older versions, support
610 for NeXML 0.9 is only (very) partially implemented.
611 See: https://redmine.open-bio.org/issues/3207
613 [Bug fixes]
615 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
616 docs [genehack, cjfields]
617 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
618 module version from dist_version (probably not the best way to do this,
619 but it seems to work) [rbuels, cjfields]
622 1.6.900 April 14, 201
624 [Notes]
626 * This will probably be the last release to add significant features to
627 core modules; subsequent releases will be for bug fixes alone.
628 We are planning on a restructuring of core for summer 2011, potentially
629 as part of the Google Summer of Code. This may become BioPerl 2.0.
630 * Version bump represents 'just prior to v 1.7'. We may have point
631 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
632 This code essentially is what is on the github master branch.
634 [New features]
636 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
637 * Bio::Tree refactor
638 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
639 - removal of Scalar::Util::weaken code, which was causing odd headaches
640 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
641 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
642 many others]
643 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
644 [Warren Kretzschmar]
645 * Bio::SeqIO::gbxml
646 - bug 2515 - new contribution [Ryan Golhar, jhannah]
647 * Bio::Assembly::IO
648 - support for reading Maq, Sam and Bowtie files [maj]
649 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
650 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
651 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
652 - bug 2726: reading/writing granularity: whole scaffold or one contig
653 at a time [Joshua Udall, fangly]
654 * Bio::OntologyIO
655 - Added parsing of xrefs to OBO files, which are stored as secondary
656 dbxrefs of the cvterm [Naama Menda]
657 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
658 * PAML code updated to work with PAML 4.4d [DaveMessina]
660 [Bug fixes]
662 * [3198] - sort tabular BLAST hits by score [DaveMessina]
663 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
664 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
665 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
666 [cjfields]
667 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
668 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
669 * [3164] - TreeFunctionsI syntax bug [gjuggler]
670 * [3163] - AssemblyIO speedup [fangly]
671 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
672 hyphaltip]
673 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
674 * [3158] - fix EMBL file mis-parsing [cjfields]
675 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
676 cjfields]
677 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
678 * [3148] - URL change for UniProt [cjfields]
679 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
680 * [3136] - HMMer3 parser fixes [kblin]
681 * [3126] - catch description [Toshihiko Akiba]
682 * [3122] - Catch instances where non-seekable filehandles were being
683 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
684 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
685 [dukeleto, rbuels, cjfields]
686 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
687 jhannah]
688 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
689 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
690 cjfields]
691 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
692 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
693 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
694 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
695 * [3086] - EMBL misparsing long tags [kblin, cjfields]
696 * [3085] - CommandExts and array of files [maj, hyphaltip]
697 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
698 for alignment slices [Ha X. Dang, cjfields]
699 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
700 * [3073] - fix parsing of GenBank files from RDP [cjfields]
701 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
702 * [3064] - All-gap midline BLAST report issues [cjfields]
703 * [3063] - BLASt report RID [Razi Khaja, cjfields]
704 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
705 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
706 * [3039] - correct Newick output root node branch length [gjuggler,
707 DaveMessina]
708 * [3038] - SELEX alignment error [Bernd, cjfields]
709 * [3033] - PrimarySeq ID setting [Bernd, maj]
710 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
711 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
712 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
713 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
714 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
715 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
716 PAML 4.4d [DaveMessina]
717 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
718 DaveMessina]
719 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
720 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
721 * [3017] - using threads with Bio::DB::GenBank [cjfields]
722 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
723 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
724 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
725 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
726 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
727 cjfields]
728 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
729 * [2977] - TreeIO issues [DaveMessina]
730 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
731 * [2944] - Bio::Tools::GFF score [cjfields]
732 * [2942] - correct MapTiling output [maj]
733 * [2939] - PDB residue insertion codes [John May, maj]
734 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
735 * [2928] - GuessSeqFormat raw [maj]
736 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
737 * [2922] - open() directive issue [cjfields]
738 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
739 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
740 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
741 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
742 cjfields]
743 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
744 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
745 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
746 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
747 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
748 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
749 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
750 * [2758] - Bio::AssemblyIO ace problems [fangly]
751 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
752 * [2726] - ace file IO [Josh, fangly]
753 * [2700] - Refactor Build.PL [cjfields]
754 * [2673] - addition of simple Root-based clone() method [cjfields]
755 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
756 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
757 * [2594] - Bio::Species memory leak [cjfields]
758 * [2515] - GenBank XML parser [jhannah]
759 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
760 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
761 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
762 cjfields]
763 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
765 [Deprecated]
767 * Bio::Expression modules - these were originally designed to go with the
768 bioperl-microarray suite of tools, however they have never been completed
769 and so have been removed from the distribution. The original code has
770 been moved into the inactive bioperl-microarray suite. [cjfields]
772 [Other]
774 * Repository moved from Subversion (SVN) to
775 http://github.com/bioperl/bioperl-live [cjfields]
776 * Bug database has moved to Redmine (https://redmine.open-bio.org)
777 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
778 Thieme have been moved to their own distribution (Bio-Microarray).
779 [cjfields]
781 1.6.1 Sept. 29, 2009 (point release)
782 * No change from last alpha except VERSION and doc updates [cjfields]
784 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
785 * Fix for silent OBDA bug related to FASTA validation [cjfields]
787 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
788 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
789 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
790 [cjfields]
791 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
793 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
794 * WinXP test fixes [cjfields, maj]
795 * BioPerl.pod added for descriptive information, fixes CPAN indexing
796 [cjfields]
797 * Minor doc fixes [cjfields]
799 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
800 * Fix tests failing due to merging issues [cjfields]
801 * More documentation updates for POD parsing [cjfields]
803 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
804 * Bio::Root::Build
805 - fix YAML meta data generation [cjfields]
807 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
808 * Bio::Align::DNAStatistics
809 - fix divide by zero problem [jason]
810 * Bio::AlignIO::*
811 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
812 * Bio::AlignIO::stockholm
813 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
814 * Bio::Assembly::Tools::ContigSpectrum
815 - function to score contig spectrum [fangly]
816 * Bio::DB::EUtilities
817 - small updates [cjfields]
818 * Bio::DB::Fasta
819 - berkeleydb database now autoindexes wig files and locks correctly
820 [lstein]
821 * Bio::DB::HIV
822 - various small updates for stability; tracking changes to LANL
823 database interface [maj]
824 * Bio::DB::SeqFeature (lots of updates and changes)
825 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
826 - bug 2835 - patch [Dan Bolser]
827 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
828 * Bio::DB::SwissProt
829 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
830 * Bio::Factory::FTLocationFactory
831 - mailing list bug fix [cjfields]
832 * Bio::LocatableSeq
833 - performance work on column_from_residue_number [hartzell]
834 * Bio::Matrix::IO::phylip
835 - bug 2800 - patch to fix phylip parsing [Wei Zou]
836 * Bio::Nexml
837 - Google Summer of Code project from Chase Miller - parsers for Nexml
838 file format [maj, chmille4]
839 * Bio::PopGen
840 - Make Individual, Population, Marker objects AnnotatableI [maj]
841 - simplify LD code [jason]
842 * Bio::RangeI
843 - deal with empty intersection [jason]
844 * Bio::Restriction
845 - significant overhaul of Bio::Restriction system: complete support for
846 external and non-palindromic cutters. [maj]
847 * Bio::Root::Build
848 - CPANPLUS support, no automatic installation [sendu]
849 * Bio::Root::IO
850 - allow IO::String (regression fix) [cjfields]
851 - catch unintentional undef values [cjfields]
852 - throw if non-fh is passed to -fh [maj]
853 * Bio::Root::Root/RootI
854 - small debugging and core fixes [cjfields]
855 * Bio::Root::Test
856 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
857 * Bio::Root::Utilities
858 - bug 2737 - better warnings [cjfields]
859 * Bio::Search
860 - tiling completely refactored, HOWTO added [maj]
861 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
862 will deprecate usage of the older tiling code in the next BioPerl
863 release
864 - small fixes [cjfields]
865 * Bio::SearchIO
866 - Infernal 1.0 output now parsed [cjfields]
867 - new parser for gmap -f9 output [hartzell]
868 - bug 2852 - fix infinite loop in some output [cjfields]
869 - blastxml output now passes all TODO tests [cjfields]
870 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
871 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
872 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
873 * Bio::Seq::LargePrimarySeq
874 - delete tempdirs [cjfields]
875 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
876 * Bio::Seq::Quality
877 - extract regions based on quality threshold value [Dan Bolser, heikki]
878 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
879 * Bio::SeqFeature::Lite
880 - various Bio::DB::SeqFeature-related fixes [lstein]
881 * Bio::SeqFeature::Tools::TypeMapper
882 - additional terms for GenBank to SO map [scain]
883 * Bio::SeqIO::chadoxml
884 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
885 * Bio::SeqIO::embl
886 - support for CDS records [dave_messina, Sylvia]
887 * Bio::SeqIO::fastq
888 - complete refactoring to handle all FASTQ variants, perform validation,
889 write output. API now conforms with other Bio* parsers and the rest of
890 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
891 [cjfields]
892 * Bio::SeqIO::genbank
893 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
894 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
895 * Bio::SeqIO::largefasta
896 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
897 * Bio::SeqIO::raw
898 - add option for 'single' and 'multiple'
899 * Bio::SeqIO::scf
900 - bug 2881 - fix scf round-tripping [Adam Søgren]
901 * Bio::SeqUtils
902 - bug 2766, 2810 - copy over tags from features, doc fixes [David
903 Jackson]
904 * Bio::SimpleAlign
905 - bug 2793 - patch for add_seq index issue [jhannah, maj]
906 - bug 2801 - throw if args are required [cjfields]
907 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
908 [Tristan Lefebure, maj]
909 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
910 - fix POD and add get_SeqFeatures filter [maj]
911 * Bio::Tools::dpAlign
912 - add support for LocatableSeq [ymc]
913 - to be moved to a separate distribution [cjfields, rbuels]
914 * Bio::Tools::EUtilities
915 - fix for two bugs from mail list [Adam Whitney, cjfields]
916 - add generic ItemContainerI interface for containing same methods
917 [cjfields]
918 * Bio::Tools::HMM
919 - fix up code, add more warnings [cjfields]
920 - to be moved to a separate distribution [cjfields, rbuels]
921 * Bio::Tools::Primer3
922 - bug 2862 - fenceposting issue fixed [maj]
923 * Bio::Tools::Run::RemoteBlast
924 - tests for remote RPS-BLAST [mcook]
925 * Bio::Tools::SeqPattern
926 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
927 * Bio::Tools::tRNAscanSE
928 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
929 * Bio::Tree::*
930 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
931 * Bio::Tree::Statistics
932 - several methods for calculating Fitch-based score, internal trait
933 values, statratio(), sum of leaf distances [heikki]
934 * Bio::Tree::Tree
935 - bug 2869 - add docs indicating edge case where nodes can be
936 prematurely garbage-collected [cjfields]
937 - add as_text() function to create Tree as a string in specified format
938 [maj]
939 * Bio::Tree::TreeFunctionsI
940 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
941 Lefebure, maj]
942 * Bio::TreeIO::newick
943 - fix small semicolon issue [cjfields]
944 * scripts
945 - update to bp_seqfeature_load for SQLite [lstein]
946 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
947 - fastam9_to_table - fix for MPI output [jason]
948 - gccalc - total stats [jason]
949 * General Stuff
950 - POD cleanup re: FEEDBACK section [maj, cjfields]
951 - cleanup or fix dead links [cjfields]
952 - Use of no_* methods (indicating 'number of something') is deprecated
953 in favor of num_* [cjfields]
954 - lots of new tests for the above bugs and refactors [everyone!]
955 - new template for Komodo text editor [cjfields]
957 1.6.0 Winter 2009
958 * Feature/Annotation rollback
959 - Problematic changes introduced prior to the 1.5 release have been
960 rolled back. These changes led to subtle bugs involving operator
961 overloading and interface methods.
962 - Behavior is very similar to that for BioPerl 1.4, with tag values
963 being stored generically as simple scalars. Results in a modest
964 speedup.
965 * Bio::Graphics
966 - Split into a separate distribution on CPAN, primarily so development
967 isn't reliant on a complete BioPerl release.
968 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
969 is only available via Subversion (via bioperl-live main trunk)
970 * Bio::Root::Test
971 - Common test bed for all BioPerl modules
972 * Bio::Root::Build
973 - Common Module::Build-based subclass for all BioPerl modules
974 * Bio::DB::EUtilities
975 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
976 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
977 and user agent request posting and retrieval
978 * Test implementation and reorganization
979 - Tests have been reorganized into groups based on classes or use
980 cases.
981 - Automated test coverage is now online:
982 http://www.bioperl.org/wiki/Test_Coverage
983 - After this release, untested modules will be moved into a
984 separate developer distribution until tests can be derived.
985 Also, new modules to be added are expected to have a test suite
986 and adequate test coverage.
988 1.5.2 Developer release
990 Full details of changes since 1.5.1 are available online at:
991 http://www.bioperl.org/wiki/Change_log
992 The following represents a brief overview of the most important changes.
994 o Bio::Map
995 - Overhaul. Brand new system fully allows markers to have multiple
996 positions on multiple maps, and to have relative positions. Should be
997 backward compatible.
999 o Bio::Taxonomy
1000 - This module and all the modules in the Taxonomy directory now
1001 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
1003 o Bio::DB::Taxonomy
1005 - Taxonomy.pm
1006 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
1008 * New methods ancestor(), each_Descendent() and _handle_internal_id().
1010 * Allows for different database modules to create Bio::Taxon objects
1011 with the same internal id when the same taxon is requested from each.
1013 - flatfile.pm
1014 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
1016 * No longer includes the fake root node 'root'; there are multiple roots
1017 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
1019 - entrez.pm
1020 * get_node() has new option -full
1022 * Caches data retrieved from website
1024 o Bio::Species
1025 - Now a Bio::Taxon. Carries out the species name -> specific name munging
1026 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
1027 backward compatability in species() method.
1029 o Bio::Search and Bio::SearchIO
1030 - Overhaul. The existing system has been sped up via some minor changes
1031 (mostly gain-of-function to the API). Bio::PullParserI is introduced
1032 as a potential eventual replacment for the existing system, though as
1033 yet only a Hmmpfam parser exists written using it.
1036 1.5.1 Developer release
1038 o Major problem with how Annotations were written out with
1039 Bio::Seq is fixed by reverting to old behavior for
1040 Bio::Annotation objects.
1042 o Bio::SeqIO
1044 - genbank.pm
1045 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
1046 expect at l east 9 spaces at the beginning of a line to
1047 indicate line wrapping.
1049 * Treat multi-line SOURCE sections correctly, this defect broke
1050 both common_name() and classification()
1052 * parse swissprot fields in genpept file
1054 * parse WGS genbank records
1056 - embl.pm
1057 * Changed regexp for ID line. The capturing parentheses are
1058 the same, the difference is an optional repeated-not-semi-
1059 colon expression following the captured \S+. This means the
1060 regexp works when the division looks like /PRO;/ or when the
1061 division looks like /ANG ;/ - the latter is from EMBL
1062 repbase
1064 * fix ID line parsing: the molecule string can have spaces in
1065 it. Like: "genomic DNA"
1067 - swiss.pm: bugs #1727, #1734
1069 - entrezgene.pm
1070 * Added parser for entrezgene ASN1 (text format) files.
1071 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
1073 o Bio::AlignIO
1075 - maf.pm coordinate problem fixed
1077 o Bio::Taxonomy and Bio::DB::Taxonomy
1079 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
1080 can be done via Web without downloading all the sequence.
1082 o Bio::Tools::Run::RemoteBlast supports more options and complies
1083 to changes to the NCBI interface. It is reccomended that you
1084 retrieve the data in XML instead of plain-text BLAST report to
1085 insure proper parsing and retrieval of all information as NCBI
1086 fully expects to change things in the future.
1088 o Bio::Tree and Bio::TreeIO
1090 - Fixes so that re-rooting a tree works properly
1092 - Writing out nhx format from a newick/nexus file will properly output
1093 bootstrap information. The use must move the internal node labels over
1094 to bootstraps.
1095 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
1096 $node->bootstrap($node->id);
1097 $node->id('');
1098 }
1099 - Nexus parsing is much more flexible now, does not care about
1100 LF.
1102 - Cladogram drawing module in Bio::Tree::Draw
1104 - Node height and depth now properly calculated
1106 - fix tree pruning algorithm so that node with 1 child gets merged
1108 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
1109 bugs and improvements were added, see Gbrowse mailing list for most of
1110 these.
1112 o Bio::DB::GFF partially supports GFF3. See information about
1113 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
1115 o Better location parsing in Bio::Factory::FTLocationFactory -
1116 this is part of the engine for parsing EMBL/GenBank feature table
1117 locations. Nested join/order-by/complement are allowed now
1119 o Bio::PrimarySeqI->translate now takes named parameters
1121 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
1122 reconstruction) is now supported. Parsing different models and
1123 branch specific parametes are now supported.
1125 o Bio::Factory::FTLocationFactory - parse hierarchical locations
1126 (joins of joins)
1128 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
1129 for getter/setter functions
1131 o Bio::SearchIO
1133 - blast bug #1739; match scientific notation in score
1134 and possible e+ values
1136 - blast.pm reads more WU-BLAST parameters and parameters, match
1137 a full database pathname,
1139 - Handle NCBI WEB and newer BLAST formats specifically
1140 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
1142 - psl off-by-one error fixed
1144 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
1145 and HSPs can be constructed from them.
1147 - HSPs query/hit now have a seqdesc field filled out (this was
1148 always available via $hit->description and
1149 $result->query_description
1151 - hmmer.pm can parse -A0 hmmpfam files
1153 - Writer::GbrowseGFF more customizeable.
1155 o Bio::Tools::Hmmpfam
1156 make e-value default score displayed in gff, rather than raw score
1157 allow parse of multiple records
1160 1.5 Developer release
1162 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
1163 provide Jukes-Cantor and Kimura pairwise distance methods,
1164 respectively.
1166 o Bio::AlignIO support for "po" format of POA, and "maf";
1167 Bio::AlignIO::largemultifasta is a new alternative to
1168 Bio::AlignIO::fasta for temporary file-based manipulation of
1169 particularly large multiple sequence alignments.
1171 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
1172 be treated similarly as an assembled contig.
1174 o Bio::CodonUsage provides new rare_codon() and probable_codons()
1175 methods for identifying particular codons that encode a given
1176 amino acid.
1178 o Bio::Coordinate::Utils provides new from_align() method to build
1179 a Bio::Coordinate pair directly from a
1180 Bio::Align::AlignI-conforming object.
1182 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
1183 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
1184 web service using standard Pubmed query syntax, and retrieve
1185 results as XML.
1187 o Bio::DB::GFF has various sundry bug fixes.
1189 o Bio::FeatureIO is a new SeqIO-style subsystem for
1190 writing/reading genomic features to/from files. I/O classes
1191 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
1192 classes only read/write Bio::SeqFeature::Annotated objects.
1193 Notably, the GFF v3 class requires features to be typed into the
1194 Sequence Ontology.
1196 o Bio::Graph namespace contains new modules for manipulation and
1197 analysis of protein interaction graphs.
1199 o Bio::Graphics has many bug fixes and shiny new glyphs.
1201 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
1202 indexing for HMMER reports and FASTA qual files, respectively.
1204 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
1205 new objects that can be placed within a Bio::Map::MapI-compliant
1206 genetic/physical map; Bio::Map::Physical provides a new physical
1207 map type; Bio::MapIO::fpc provides finger-printed clone mapping
1208 import.
1210 o Bio::Matrix::PSM provide new support for postion-specific
1211 (scoring) matrices (e.g. profiles, or "possums").
1213 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
1214 be instantiated without explicitly using Bio::OntologyIO. This
1215 is possible through changes to Bio::Ontology::OntologyStore to
1216 download ontology files from the web as necessary. Locations of
1217 ontology files are hard-coded into
1218 Bio::Ontology::DocumentRegistry.
1220 o Bio::PopGen includes many new methods and data types for
1221 population genetics analyses.
1223 o New constructor to Bio::Range, unions(). Given a list of
1224 ranges, returns another list of "flattened" ranges --
1225 overlapping ranges are merged into a single range with the
1226 mininum and maximum coordinates of the entire overlapping group.
1228 o Bio::Root::IO now supports -url, in addition to -file and -fh.
1229 The new -url argument allows one to specify the network address
1230 of a file for input. -url currently only works for GET
1231 requests, and thus is read-only.
1233 o Bio::SearchIO::hmmer now returns individual Hit objects for each
1234 domain alignment (thus containing only one HSP); previously
1235 separate alignments would be merged into one hit if the domain
1236 involved in the alignments was the same, but this only worked
1237 when the repeated domain occured without interruption by any
1238 other domain, leading to a confusing mixture of Hit and HSP
1239 objects.
1241 o Bio::Search::Result::ResultI-compliant report objects now
1242 implement the "get_statistics" method to access
1243 Bio::Search::StatisticsI objects that encapsulate any
1244 statistical parameters associated with the search (e.g. Karlin's
1245 lambda for BLAST/FASTA).
1247 o Bio::Seq::LargeLocatableSeq combines the functionality already
1248 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
1250 o Bio::SeqFeature::Annotated is a replacement for
1251 Bio::SeqFeature::Generic. It breaks compliance with the
1252 Bio::SeqFeatureI interface because the author was sick of
1253 dealing with untyped annotation tags. All
1254 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
1255 compliant, and accessible through Bio::Annotation::Collection.
1257 o Bio::SeqFeature::Primer implements a Tm() method for primer
1258 melting point predictions.
1260 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
1261 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
1263 o Bio::Taxonomy::Node now implements the methods necessary for
1264 Bio::Species interoperability.
1266 o Bio::Tools::CodonTable has new reverse_translate_all() and
1267 make_iupac_string() methods.
1269 o Bio::Tools::dpAlign now provides sequence profile alignments.
1271 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
1273 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
1274 parsers.
1276 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
1277 for designing small inhibitory RNA.
1279 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
1280 methods based on a distance matrix.
1282 o Bio::Tree::Statistics provides an assess_bootstrap() method to
1283 calculate bootstrap support values on a guide tree topology,
1284 based on provided bootstrap tree topologies.
1286 o Bio::TreeIO now supports the Pagel (PAG) tree format.
1288 1.4 branch
1290 1.4.1
1292 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
1294 o Bio::Graphics will work with gd1 or gd2
1296 o Bio::SearchIO
1297 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
1298 (RF lines alone)
1299 - blast.pm Parse multi-line query fields properly
1300 - small speed improvements to blasttable.pm and others
1302 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
1303 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
1304 supporting more complex queries
1307 1.4. Stable major release
1309 Since initial 1.2.0, 3000 separate changes have been made to make this release.
1311 o installable scripts
1313 o global module version from Bio::Root:Version
1315 o Bio::Graphics
1316 - major improvements; SVG support
1318 o Bio::Popgen
1319 - population genetics
1320 - support several population genetics types of questions.
1321 - Tests for statistical neutrality of mutations
1322 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
1323 Tests of population structure (Wright's F-statistic: Fst) is in
1324 Bio::PopGen::PopStats. Calculating composite linkage
1325 disequilibrium (LD) is available in Bio::PopGen::Statistics as
1326 well.
1327 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1328 and csv (comma delimited formatted) data.
1330 - a directory for implementing population simulations has
1331 been added Bio::PopGen::Simulation and 2 simulations - a
1332 Coalescent and a simple single-locus multi-allele genetic drift
1333 simulation have been provided. This replaces the code in
1334 Bio::Tree::RandomTree which has been deprecated until proper
1335 methods for generating random phylogenetic trees are
1336 implemented.
1338 o Bio::Restriction
1339 - new restrion analysis modules
1341 o Bio::Tools::Analysis
1342 - web based DNA and Protein analysis framework and several
1343 implementations
1345 o Bio::Seq::Meta
1346 - per residue annotable sequences
1348 o Bio::Matrix
1349 - Bio::Matrix::PSM - Position Scoring Matrix
1350 - Bio::Matrix::IO has been added for generalized parsing of
1351 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1352 initial implementations for parsing BLOSUM/PAM and Phylip
1353 Distance matricies respectively. A generic matrix
1354 implementation for general use was added in
1355 Bio::Matrix::Generic.
1357 o Bio::Ontology
1358 - major changes
1360 o Bio:Tree
1362 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1363 - small inhibitory RNA
1365 o Bio::SeqFeature::Tools
1366 - seqFeature mapping tools
1367 - Bio::SeqFeature::Tools::Unflattener.pm
1368 -- deal with mapping GenBank feature collections into
1369 Chado/GFF3 processable feature sets (with SO term mappings)
1371 o Bio::Tools::dpAlign
1372 - pure perl dynamic programming sequence alignment
1373 - needs Bioperl-ext
1375 o new Bio::SearchIO formats
1376 - axt and psl: UCSC formats.
1377 - blasttable: NCBI -m 8 or -m 9 format from blastall
1379 o new Bio::SeqIO formats
1380 - chado, tab, kegg, tigr, game
1381 - important fixes for old modules
1383 o Bio::AlignIO: maf
1385 o improved Bio::Tools::Genewise
1387 o Bio::SeqIO now can recongnize sequence formats automatically from
1388 stream
1390 o new parsers in Bio::Tools:
1391 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1393 o Bio::DB::Registry bugs fixed
1394 - BerkeleyDB-indexed flat files can be used by the OBDA system
1395 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1396 used by the OBDA system
1398 o several new HOWTOs
1399 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1400 Databases
1402 o hundreds of new and improved files
1405 o
1406 o Bio::Tree::AlleleNode has been updated to be a container of
1407 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1410 1.2 Branch
1412 1.2.3 Stable release update
1413 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1414 handling.
1415 o Bug #1477 - Sel --> Sec abbreviation fixed
1416 o Fix bug #1487 where paring in-between locations when
1417 end < start caused the FTLocationFactory logic to fail.
1418 o Fix bug #1489 which was not dealing with keywords as an
1419 arrayref properly (this is fixed on the main trunk because
1420 keywords returns a string and the array is accessible via
1421 get_keywords).
1422 o Bio::Tree::Tree memory leak (bug #1480) fixed
1423 Added a new initialization option -nodelete which
1424 won't try and cleanup the containing nodes if this
1425 is true.
1426 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1427 this was only present on the branch for the 1.2.1 and 1.2.2 series
1428 - Also merged main trunk changes to the branch which make
1429 newick -> nhx round tripping more effective (storing branch length
1430 and bootstrap values in same locate for NodeNHX and Node
1431 implementations.) Fixes to TreeIO parsing for labeled internal
1432 also required small changes to TreeIO::nhx. Improved
1433 tests for this module as well.
1434 o Bio::SearchIO
1435 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1436 gapped blast properly (was losing hit significance values due to
1437 the extra unexpeted column).
1438 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1439 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1440 although doesn't try to correct it - will get the negative
1441 number for you. Added a test for this as well.
1442 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1443 has no top-level family classification scores but does have scores and
1444 alignments for individual domains.
1445 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1446 regular expression to match the line was missing the possibility of
1447 an extra space. This is rare, which is why we probably did not
1448 catch it before.
1449 - BLAST parsing picks up more of the statistics/parameter fields
1450 at the bottom of reports. Still not fully complete.
1451 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1452 were fixed to include many improvements and added flexiblity
1453 in outputting the files. Bug #1495 was also fixed in the process.
1454 o Bio::DB::GFF
1455 - Update for GFF3 compatibility.
1456 - Added scripts for importing from UCSC and GenBank.
1457 - Added a 1.2003 version number.
1458 o Bio::Graphics
1459 - Updated tutorial.
1460 - Added a 1.2003 version number.
1461 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1462 properly writing keywords out.
1463 o Bio::SeqIO::genbank
1464 - Fixed bug/enhancement #1513 where dates of
1465 the form D-MMM-YYYY were not parsed. Even though this is
1466 invalid format we can handle it - and also cleanup the date
1467 string so it is properly formatted.
1468 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1469 and written with Genbank format. Similarly bug #1515 is fixed to
1470 parse in the ORIGIN text.
1471 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1472 to specify the ID type, one of (accession accession.version
1473 display primary). See Bio::SeqIO::preferred_id_type method
1474 documentation for more information.
1475 o Unigene parsing updated to handle file format changes by NCBI
1477 1.2.2 Stable release update
1479 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1480 - auto-discover ontology name
1481 - bug in parsing relationships when certain characters are in the term
1482 - fixed hard-coded prefix for term identifiers
1483 - various smaller issues
1485 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1486 of Bio::Ontology::TermI
1488 o brought the OBDA Registry code up to latest specs
1490 o Bio::DB::GenBank
1491 - eutils URL change
1492 - accession number retrieval fixed
1494 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1496 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1497 #1459 which now properly report alignment start/end info
1498 for translated BLAST/FASTA searches.
1500 o Bio::TreeIO::newick can parse labeled internal nodes
1502 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1503 for BLASTX if if you provide -report_type => 'BLASTX' when
1504 initializing a BPbl2seq object. Bioperl 1.3 will have better
1505 support for bl2seq in the SearchIO system.
1507 o Bio::Root::IO support a -noclose boolean flag which will not
1508 close a filehandle upon object cleanup - useful when sharing
1509 a filehandle among objects. Additionally code added s.t.
1510 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1512 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1514 o Bio::SeqIO::genbank
1515 - bug #1456 fixed which generated extra sequence lines
1516 - write moltype correctly for genpept
1518 1.2.1 Stable release update
1520 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1522 o Addition from main trunk of Ontology objects, principly to allow
1523 BioSQL releases against 1.2.1
1525 o Fixes and cleanup of Bio::Coordinate modules
1527 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1528 the primary accession number
1530 o Other bug fixes, including bpindex GenBank fix
1532 o Bio::SeqIO::genbank bug #1389 fixed
1534 1.2 Stable major release
1536 o More functionality added to Bio::Perl, the newbie module
1538 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1539 Support for New Hampshire Extended (NHX) format parsing.
1541 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1542 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1543 Hmmpfam parser.
1545 o New ontology parsing Bio::Ontology
1547 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1548 multi-report (mlib) fasta reports, support for waba and exonerate.
1550 o Bio::ClusterIO for parsing Unigene clusters
1552 o Bio::Assembly added for representing phrap and ace assembly clusters.
1554 o Rudimentary support for writing Chado XML (see
1555 GMOD project: www.gmod.org for more information)
1557 o Bio::Coordinate for mapping between different coordinate systems such
1558 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1559 features into different coordinate systems.
1561 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1562 with the get_Stream_by_query method and supports the latest
1563 NCBI eutils interface.
1565 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1566 object for extracting subsets of features : currently only
1567 supports extraction by location.
1569 1.1.1 Developer release
1571 o Deprecated modules are now listed in the DEPRECATED file
1573 o New HowTo documents located in doc/howto describing
1574 a domain of Bioperl.
1576 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1577 and all old bugs are searchable through the bugzilla interface.
1579 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1580 have been addressed.
1582 o Support for Genewise parsing in Bio::Tools::Genewise
1584 o Start of Ontology framework with Bio::Ontology
1586 o Speedup to the Bio::Root::Root object method _rearrange.
1587 A global _load_module method was implemented to simplify the
1588 dynamic loading of modules ala Bio::SeqIO::genbank. This
1589 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1590 etc).
1592 o Several performance improvements to sequence parsing in Bio::SeqIO.
1593 Attempt to speedup by reducing object creation overhead.
1595 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1596 method for sequence retrieval with their E-utils CGI scripts.
1597 More work to support Entrez queries to their fullest is planned
1598 before 1.2 release.
1600 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1602 1.1 Developer release
1604 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1605 this separation removes some of the complexity in our test suite
1606 and separates the core modules in bioperl from those that need
1607 external programs to run.
1609 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1610 not run into trouble running the makefile
1612 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1613 read,create,and write locations for grouped/split locations
1614 (like mRNA features on genomic sequence).
1616 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1617 and PAML (codeml,aaml, etc) parsing.
1619 o Bio::Tree:: objects expanded to handle testing monophyly,
1620 paraphyly, least common ancestor, etc.
1622 o Bio::Coordinate for mapping locations from different coordinate spaces
1624 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1625 added for parsing hmmpfam and hmmsearch output.
1627 o Bio::SearchIO::Writer::TextResultWriter for outputting
1628 a pseudo-blast textfile format
1631 1.0.2 Bug fix release
1633 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1634 in this release will not work after December 2002 when NCBI
1635 shuts off the old Entrez cgi scripts. We have already fixed
1636 on our main development branch and the functionality will be
1637 available in the next stable bioperl release (1.2) slated for
1638 Fall 2002.
1640 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1641 testset by Robin Emig. These were fixed as was the get_aln
1642 method in Bio::Search::HSP::GenericHSP to handle the extra
1643 context sequence that is provided with a FastA alignment.
1645 o Migrating differences between Bio::Search::XX::BlastXX to
1646 Bio::Search::XX::GenericXX objects. This included mechanism
1647 to retrieve whole list of HSPs from Hits and whole list of Hits from
1648 Results in addition to the current next_XX iterator methods that
1649 are available. Added seq_inds() method to GenericHSP which identifies
1650 indexes in the query or hit sequences where conserved,identical,gaps,
1651 or mismatch residues are located (adapted from Steve Chervitz's
1652 implementation in BlastHSP).
1654 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1655 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1657 o Bio::Graphics glyph set improved and extended for GBrowse release
1659 o Bio::Tree::Tree get_nodes implementation improvement thanks
1660 to Howard Ross notice performance problem when writing out
1661 unbalanced trees.
1663 o Bio::Location::Fuzzy::new named parameter -loc_type became
1664 -location_type, Bio::Location::Simple::new named parameter
1665 -seqid becamse -seq_id.
1667 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1668 was mis-detecting that gaps should be placed at the beginning of
1669 the alignment when the best alignment starts internally in the
1670 sequence.
1672 1.0.1 Bug fix release
1674 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1676 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1677 and mixed (3.3 - 3.4) versions of FASTA.
1679 o Small API change to add methods for completeness across
1680 implementations of Bio::Search objects. These new methods
1681 in the interface are implemented by the GenericXX object as well
1682 as the BlastXX objects.
1683 * Bio::Search::Result::ResultI
1684 - hits() method returns list of all Hits (next_hit is an
1685 iterator method)
1687 * Bio::Search::Hit::HitI
1688 - hsps() method returns list of all HSPs (next_hsp is an
1689 iterator method)
1691 o The Bio::SearchIO::Writer classes have been fixed to handle results
1692 created from either psiblast (Search::BlastXX objects) or
1693 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1694 has to be done here to make it work properly and will nee major
1695 API changes.
1697 o Bugs in Bio::Tools::HMMER fixed, including
1698 * #1178 - Root::IO destructor wasn't being called
1699 * #1034 - filter_on_cutoff now behaves properly
1701 o Bio::SeqFeature::Computation initialization args fixed and
1702 tests added.
1704 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1706 o Updated FAQ with more example based answers to typical questions
1708 o Bug #1202 was fixed which would improperly join together qual values
1709 parsed by Bio::SeqIO::qual when a trailing space was not present before
1710 the newline.
1712 1.0.0 Major Stable Release
1714 This represents a major release of bioperl with significant
1715 improvements over the 0.7.x series of releases.
1717 o Bio::Tools::Blast is officially deprecated. Please see
1718 Bio::SearchIO for BLAST and FastA parsing.
1720 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1721 Bio::LocationI objects as well as start/end.
1723 o Bio::Biblio contains modules for Bibliographic data.
1724 Bio::DB::Biblio contains the query modules. Additionally one can
1725 parse medlinexml from the ebi bibliographic query service (BQS)
1726 system and Pubmed xml from NCBI. See Martin Senger's
1727 documentation in Bio::Biblio for more information.
1729 o Bio::DB::Registry is a sequence database registry part of
1730 Open Bioinformatics Database Access. See
1731 http://obda.open-bio.org for more information.
1733 o File-based and In-Memory Sequence caching is provided by
1734 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1735 local database.
1737 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1738 been added by Lincoln Stein.
1740 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1742 o A FAQ has been started and is included in the release to provide
1743 a starting point for frequent questions and issues.
1745 0.9.3 Developer's release
1747 o Event based parsing system improved (SearchIO). With parsers for
1748 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1749 Additionally a lazy parsing system for text and html blast reports was
1750 added and is called psiblast (name subject to change in future releases).
1752 o Bio::Search objects improved and standardized with associated Interfaces
1753 written. The concept of a search "Hit" was standardized to be called
1754 "hit" consistently and the use of "subject" was deprecated in all active
1755 modules.
1757 o Bio::Structure added (since 0.9.1) for Protein structure objects
1758 and PDB parser to retrieve and write these structures from data files.
1760 o Several important Bio::DB::GFF bug fixes for handling features that
1761 are mapped to multiple reference points. Updated mysql adaptor
1762 so as to be able to store large (>100 megabase) chunks of DNA into
1763 Bio::DB::GFF databases.
1765 0.9.2 Developer's release
1767 o Bio::Search and Bio::SearchIO system introduced for event based
1768 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1769 in text and XML and FASTA reports in standard output format.
1771 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1772 generator is included in Bio::TreeIO::RandomTrees and a
1773 statistics module for evaluating.
1775 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1776 server for DAS servers.
1778 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1779 files. The entire BPlite system migrated to using Bio::Root::IO
1780 for the data stream.
1782 o Bio::Tools::Alignment for Consed and sequence Trimming
1783 functionality.
1785 o Bio::Structure for Protein structure information and parsing
1787 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1788 cgi-bin entry point which should be more reliable.
1790 o Bio::Map and Bio::MapIO for biological map navigation and a
1791 framework afor parsing them in. Only preliminary work here.
1793 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1794 Future work will integrate Pise and allow submission of analysis on
1795 remote servers.
1797 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1798 introduced as new objects for handling Sequence Annotation
1799 information (dblinks, references, etc) and is more robust that
1800 previous system.
1802 o Bio::Tools::FASTAParser introduced.
1804 o Scripts from the bioperl script submission project and new
1805 scripts from bioperl authors are included in "scripts" directory.
1807 o Factory objects and interfaces are being introduced and are more
1808 strictly enforced.
1810 o Bio::Root::Root introduced as the base object while
1811 Bio::Root::RootI is now simply an interface.
1813 o Bio::DB::RefSeq provides database access to copy of the NCBI
1814 RefSeq database using the EBI dbfetch script.
1816 0.9.0 Developer's release
1818 o perl version at least 5.005 is now required instead of perl 5.004
1820 o Bio::Tools::Run::RemoteBlast is available for running remote
1821 blast jobs at NCBI.
1823 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1825 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1826 Also added are related modules UTR3, UTR5, Exon, Intron,
1827 Promotor, PolyA and Transcript.
1829 o Speedup of translate method in PrimarySeq
1831 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1832 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1834 o Various fixes to Variation toolkit
1836 o Bio::DB::EMBL provides database access to EMBL sequence data.
1837 Bio::DB::Universal provides a central way to point to indexes
1838 and dbs in a single interface.
1840 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1842 o Bio::Factory::EMBOSS is still in design phase as is
1843 Bio::Factory::ApplicationFactoryI
1845 o Dia models for bioperl design are provided in the models/ directory
1847 0.7.2 Bug fix release
1849 o documentation fixes in many modules - SYNOPSIS code verified
1850 to be runnable in many (but not all modules)
1852 o corrected MANIFEST file from 0.7.1 release
1854 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1855 split locations
1857 o Bio::SeqIO::genbank
1858 * Correct parsing and writing of genbank format with protein data
1859 * moltype and molecule separation
1861 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1863 o Bio::SimpleAlign fixed to correctly handle consensus
1864 sequence calculation
1866 o Bio::Tools::HMMER supports hmmer 2.2g
1868 o Bio::Tools::BPlite to support report type specific parsing. Most
1869 major changes are not on the 0.7 branch.
1871 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1872 with File::Spec
1874 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1875 in several types of mutations:
1876 1.) AA level: deletion, complex
1877 2.) AA level: complex, inframe
1878 3.) RNA level: silent
1880 o BPbl2seq parsing of empty reports will not die, but will return
1881 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1882 $report->query() and $report->subject() methods. So an easy
1883 way to test if report was empty is to see if
1884 $report->query->seqname is undefined.
1886 0.7.1 Bug fix release
1888 o Better parsing of genbank/EMBL files especially fixing bugs
1889 related to Feature table parsing and locations on remote
1890 sequences. Additionally, species name parsing was better.
1892 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1893 which include a number of header lines.
1895 o More strict genbank and EMBL format writing (corrected number of
1896 spaces where appropriate).
1898 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1899 for related BPlite BUGS that are unresolved in this release.
1901 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1902 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1903 use expasy mirrors or EBI dbfetch cgi-script.
1905 o A moderate number of documentation improvements were made as
1906 well to provide a better code synopsis in each module.
1909 0.7 Large number of changes, including refactoring of the
1910 Object system, new parsers, new functionality and
1911 all round better system. Highlights are:
1914 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1915 Bio::Root::IO for I/O and file/handle capabilities.
1917 o Imported BPlite modules from Ian Korf for BLAST
1918 parsing. This is considered the supported BLAST parser;
1919 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1921 o Improved Sequence Feature model. Added complete location
1922 modelling (with fuzzy and compound locations). See
1923 Bio::LocationI and the modules under Bio/Location. Added
1924 support in Genbank/EMBL format parsing to completely parse
1925 feature tables for complex locations.
1927 o Moved special support for databanks etc to specialized modules under
1928 Bio/Seq/. One of these supports very large sequences through
1929 a temporary file as a backend.
1931 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1932 CDS retrieval and exon shuffling.
1934 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1936 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1937 DB/GDB (the latter has platform-specific limitations).
1939 o New analysis parser framework for HT sequence annotation (see
1940 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1942 o New Alignment IO framework
1944 o New Index modules (Swissprot)
1946 o New modules for running Blast within perl
1947 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1948 Multiple Sequence Alignment tools ClustalW and TCoffee
1949 (Bio::Tools::Run::Alignment).
1951 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1952 documentation across the package.
1954 o Much improved cross platform support. Many known incompatibilities
1955 have been fixed; however, NT and Mac do not work across the entire
1956 setup (see PLATFORMS).
1958 o Many bug fixes, code restructuring, etc. Overall stability and
1959 maintainability benefit a lot.
1961 o A total of 957 automatic tests
1964 0.6.2
1966 There are very few functionality changes but a large
1967 number of software improvements/bug fixes across the package.
1969 o The EMBL/GenBank parsing are improved.
1971 o The Swissprot reading is improved. Swissprot writing
1972 is disabled as it doesn't work at all. This needs to
1973 wait for 0.7 release
1975 o BLAST reports with no hits are correctly parsed.
1977 o Several other bugs of the BLAST parser (regular expressions, ...)
1978 fixed.
1980 o Old syntax calls have been replaced with more modern syntax
1982 o Modules that did not work at all, in particular the Sim4
1983 set have been removed
1985 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1986 have improved compliance with interface specs and documentation
1988 o Mailing list documentation updated throughout the distribution
1990 o Most minor bug fixes have happened.
1992 o The scripts in /examples now work and have the modern syntax
1993 rather than the deprecated syntax
1996 0.6.1 Sun April 2 2000
1998 o Sequences can have Sequence Features attached to them
1999 - The sequence features can be read from or written to
2000 EMBL and GenBank style flat files
2002 o Objects for Annotation, including References (but not
2003 full medline abstracts), Database links and Comments are
2004 provided
2006 o A Species object to represent nodes on a taxonomy tree
2007 is provided
2009 o The ability to parse HMMER and Sim4 output has been added
2011 o The Blast parsing has been improved, with better PSI-BLAST
2012 support and better overall behaviour.
2014 o Flat file indexed databases provide both random access
2015 and sequential access to their component sequences.
2017 o A CodonTable object has been written with all known
2018 CodonTables accessible.
2020 o A number of new lightweight analysis tools have been
2021 added, such as molecular weight determination.
2023 The 0.6 release also has improved software engineering
2025 o The sequence objects have been rewritten, providing more
2026 maintainable and easier to implement objects. These
2027 objects are backwardly compatible with the 0.05.1 objects
2029 o Many objects are defined in terms of interfaces and then
2030 a Perl implementation has been provided. The interfaces
2031 are found in the 'I' files (module names ending in 'I').
2033 This means that it is possible to wrap C/CORBA/SQL access
2034 as true "bioperl" objects, compatible with the rest of
2035 bioperl.
2037 o The SeqIO system has been overhauled to provide better
2038 processing and perl-like automatic interpretation of <>
2039 over arguments.
2041 o Many more tests have been added (a total of 172 automatic
2042 tests are now run before release).
2046 0.05.1 Tue Jun 29 05:30:44 1999
2047 - Central distribution now requires Perl 5.004. This was
2048 done to get around 5.003-based problems in Bio/Index/*
2049 and SimpleAlign.
2050 - Various bug fixes in the Bio::Tools::Blast modules
2051 including better exception handling and PSI-Blast
2052 support. See Bio/Tools/Blast/CHANGES for more.
2053 - Fixed the Parse mechanism in Seq.pm to use readseq.
2054 Follow the instructions in README for how to install
2055 it (basically, you have to edit Parse.pm).
2056 - Improved documentation of Seq.pm, indicating where
2057 objects are returned and where strings are returned.
2058 - Fixed uninitialized warnings in Bio::Root::Object.pm
2059 and Bio::Tools::SeqPattern.pm.
2060 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
2062 0.05 Sun Apr 25 01:14:11 1999
2063 - Bio::Tools::Blast modules have less memory problems
2064 and faster parsing. Webblast uses LWP and supports
2065 more functionality. See Bio/Tools/Blast/CHANGES for more.
2066 - The Bio::SeqIO system has been started, moving the
2067 sequence reformatting code out of the sequence object
2068 - The Bio::Index:: system has been started, providing
2069 generic index capabilities and specifically works for
2070 Fasta formatted databases and EMBL .dat formatted
2071 databases
2072 - The Bio::DB:: system started, providing access to
2073 databases, both via flat file + index (see above) and
2074 via http to NCBI
2075 - The scripts/ directory, where industrial strength scripts
2076 are put has been started.
2077 - Many changes - a better distribution all round.
2079 0.04.4 Wed Feb 17 02:20:13 1999
2080 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
2081 (see Bio::Tools::Blast::CHANGES).
2082 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
2083 - Beefed up the t/Fasta.t test script.
2084 - Small fix in Bio::Seq::type() (now always returns a string).
2085 - Changed Bio::Root::Utilities::get_newline_char() to
2086 get_newline() since it could return more than one char.
2087 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
2088 - Changed default timeout to 20 seconds (was 3).
2089 - Moved lengthy modification notes to the bottom of some files.
2090 - Fixed SimpleAlign write_fasta bug.
2091 - Beefed up SimpleAlign.t test
2093 0.04.3 Thu Feb 4 07:48:53 1999
2094 - Bio::Root::Object.pm and Global.pm now detect when
2095 script is run as a CGI and suppress output that is only
2096 appropriate when running interactively.
2097 - Bio::Root::Err::_set_context() adds name of script ($0).
2098 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
2099 regarding the use of the static objects via the qw(:obj) tag.
2100 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
2101 CORE::reverse, avoiding Perl warnings.
2102 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
2103 example scripts (see Bio::Tools::Blast::CHANGES).
2104 - examples/seq/seqtools.pl no longer always warns about using
2105 -prot or -nucl command-line arguments; only when using the
2106 -debug argument.
2107 - Methods added to Bio::Root::Utilities: create_filehandle(),
2108 get_newline_char(), and taste_file() to generalize filehandle
2109 creation and autodetect newline characters in files/streams
2110 (see bug report #19).
2111 - Bio::Root::IOManager::read() now handles timeouts and uses
2112 Utilities::create_filehandle().
2113 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
2114 of hardwiring in "\n".
2115 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
2117 0.04.2 Wed Dec 30 02:27:36 1998
2118 - Bug fixes in Bio::Tools::Blast modules, version 0.073
2119 (see Bio::Tools::Blast::CHANGES).
2120 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
2121 to CORE::reverse (prevents ambiguous warnings with 5.005).
2122 - Appending '.tmp.bioperl' to temporary files created by
2123 Bio::Root::Utilities::compress() or uncompress() to
2124 make it easy to identify & cleanup these files as needed.
2125 - Developers: Created CVS branch release-0-04-bug from
2126 release-0-04-1. Before making bug fixes to the 0.04.1 release,
2127 be sure to cvs checkout this branch into a clean area.
2129 0.04.1 Wed Dec 16 05:39:15 1998
2130 - Bug fixes in Bio::Tools::Blast modules, version 0.072
2131 (see Bio::Tools::Blast::CHANGES).
2132 - Compile/SW/Makefile.PL now removes *.o and *.a files
2133 with make clean.
2135 0.04 Tue Dec 8 07:49:19 1998
2136 - Lots of new modules added including:
2137 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
2138 and Bio/Compile directory containing XS-linked C code for
2139 creating Smith-Waterman sequence alignments from within Perl.
2140 * Steve Chervitz's Blast distribution has been incorporated.
2141 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
2142 - Bio/examples directory for demo scripts for all included modules.
2143 - Bio/t directory containing test suit for all included modules.
2144 - For changes specific to the Blast-related modules prior to
2145 incorporation in this central distribution, see the CHANGES
2146 file in the Bio/Tools/Blast directory.
2148 0.01 Tue Sep 8 14:23:22 1998
2149 - original version from central CVS tree; created by h2xs 1.18