| blob | f38c65e3ba43cc59ee647a7c15c6ea156b156bff |
1 Summary of important user-visible changes for BioPerl
2 -----------------------------------------------------
4 {{$NEXT}}
5 * Add minimum dependency on base.pm v2.18. Fixes bug in some cases when
6 using SUPER::new() [#307].
8 * Fix test for BSML SAX by using lax parser XML::SAX::PurePerl since
9 the external DTD URL now 404s [#376].
11 * Updated Bio::Tools::CodonTable for the latest version of NCBI
12 genetic code table (version 4.9). Previously, version 4.2 was
13 being used. This update changes codon tables 3, 15, 24, 27-30,
14 32, and 33 [#389, #391].
16 1.7.8 2021-02-02 23:02:18-06:00 America/Chicago
17 * Bio::SeqIO::interpro has been moved to a separate repository to
18 deal with issues with XML::DOM::XPath bitrot [#347]
19 * Pull requests:
20 * Adjust Swiss-Prot FT A..B lines [#348] from @smoe
21 * Update %FTQUAL_NO_QUOTE: List of qualifiers without quote [#339] from
22 @hdevillers
24 1.7.7 2019-12-07 13:41:36-06:00 America/Chicago
26 * The program bp_chaos_plot has been removed.
28 * GD is now no longer a dependency, suggestion or requirement.
30 * #321 - GenBank format fix for un-quoted features, text wrapping
32 * Bio::DB::Query::WebQuery now includes methods for delay(), delay_policy(),
33 and a 'private' _sleep() function that mirror those from
34 Bio::DB::WebDBSeqI, primarily for compliance with potential website
35 restrictions for the number and frequency of queries (e.g. NCBI eUtils).
37 * Fix bug #329, related to Bio::Tree::Statistics::transfer_bootstrap_expectation
38 in last release.
40 1.7.6 2019-08-28 12:37:01+01:00 Europe/London
42 * The program bp_classify_hits_kingdom has been removed and is
43 now part of the examples documentation instead.
45 * GD is now listed as a suggestion instead of a requirement. The
46 bp_chaos_plot program will now work with the GD module.
48 * New method Bio::Tree::Statistics::transfer_bootstrap_expectation
49 to compute Transfer Bootstrap Expectation (TBE) for internal
50 nodes based on the methods outlined in Lemoine et al, Nature,
51 2018.
53 * New method Bio::SeqIO::fasta::next_seq_fast to retrieve next
54 sequence in the stream faster but not perfect.
57 1.7.5 2019-02-11 14:57:45+00:00 Europe/London
59 * The following modules have been removed from the BioPerl
60 distribution to be part of a separate distribution with
61 independent development:
63 Bio::Symbol::*
65 * The Bio::Seq::SeqWithQuality module, which was deprecated since
66 2001, was finally removed.
68 * The deprecated() method has been deprecated. It is recommended
69 to use Carp::carp to warn.
71 * The following methods have been deprecated for a long while and
72 have now been removed:
74 Bio::Align::AlignI->no_residues
75 Bio::Align::AlignI->no_sequences
76 Bio::LocatableSeq->no_gap
77 Bio::LocatableSeq->no_sequences
78 Bio::SeqFeature::Generic->slurp_gff_file
79 Bio::SimpleAlign->no_residues
80 Bio::SimpleAlign->no_sequences
83 1.7.4 2019-02-05 16:23:53+00:00 Europe/London
85 * Fix Bio::Root::Test, and the testuite, to properly check for
86 internet connection and the NO_NETWORK_TESTING environment
87 variable. Previously, tests that required internet connection
88 were not being skipped, causing tests to fail.
91 1.7.3 2019-01-30 13:30:34+00:00 Europe/London
93 * The following modules have been removed from the BioPerl
94 distribution to be part of a separate distribution. They have
95 been integrated into other module distributions for independent
96 development:
98 Bio::Align::Graphics
99 Bio::AlignIO::nexml
100 Bio::AlignIO::stockholm
101 Bio::Assembly::*
102 Bio::Cluster::*
103 Bio::ClusterI::*
104 Bio::ClusterIO::*
105 Bio::DB::Ace
106 Bio::DB::BioFetch
107 Bio::DB::CUTG
108 Bio::DB::EMBL
109 Bio::DB::EntrezGene
110 Bio::DB::Expression::*
111 Bio::DB::GFF
112 Bio::DB::GFF::Adaptor::*
113 Bio::DB::GFF::Aggregator::*
114 Bio::DB::GFF::Featname
115 Bio::DB::GFF::Feature
116 Bio::DB::GFF::Homol
117 Bio::DB::GFF::RelSegment
118 Bio::DB::GFF::Segment
119 Bio::DB::GFF::Typename
120 Bio::DB::GenBank
121 Bio::DB::GenPept
122 Bio::DB::HIV::*
123 Bio::DB::MeSH
124 Bio::DB::NCBIHelper
125 Bio::DB::Query::GenBank
126 Bio::DB::Query::HIVQuery
127 Bio::DB::RefSeq
128 Bio::DB::SeqFeature::*
129 Bio::DB::SeqVersion::*
130 Bio::DB::SwissProt
131 Bio::DB::TFBS::*
132 Bio::DB::Taxonomy::entrez
133 Bio::DB::Taxonomy::sqlite
134 Bio::DB::Universal
135 Bio::Draw::Pictogram
136 Bio::Factory::MapFactoryI
137 Bio::Index::Hmmer
138 Bio::Index::Stockholm
139 Bio::LiveSeq::*
140 Bio::Map::*
141 Bio::MapIO::*
142 Bio::MolEvol::CodonModel
143 Bio::Nexml::Factory
144 Bio::NexmlIO
145 Bio::Perl
146 Bio::Phenotype::*
147 Bio::PhyloNetwork::*
148 Bio::PopGen::*
149 Bio::Restriction::*
150 Bio::Root::Build
151 Bio::Search::HSP::HMMERHSP
152 Bio::Search::HSP::HmmpfamHSP
153 Bio::Search::Hit::HMMERHit
154 Bio::Search::Hit::HmmpfamHit
155 Bio::Search::Hit::hmmer3Hit
156 Bio::Search::Result::HMMERResult
157 Bio::Search::Result::HmmpfamResult
158 Bio::Search::Result::hmmer3Result
159 Bio::SearchDist
160 Bio::SearchIO::hmmer
161 Bio::SearchIO::hmmer2
162 Bio::SearchIO::hmmer3
163 Bio::SearchIO::hmmer_pull
164 Bio::SeqEvolution::*
165 Bio::SeqFeature::SiRNA::*
166 Bio::SeqIO::abi
167 Bio::SeqIO::agave
168 Bio::SeqIO::alf
169 Bio::SeqIO::chadoxml
170 Bio::SeqIO::chaos
171 Bio::SeqIO::chaosxml
172 Bio::SeqIO::ctf
173 Bio::SeqIO::entrezgene
174 Bio::SeqIO::excel
175 Bio::SeqIO::exp
176 Bio::SeqIO::flybase_chadoxml
177 Bio::SeqIO::lasergene
178 Bio::SeqIO::nexml
179 Bio::SeqIO::pln
180 Bio::SeqIO::strider
181 Bio::SeqIO::ztr
182 Bio::Structure::*
183 Bio::Taxonomy::*
184 Bio::Tools::AlignFactory
185 Bio::Tools::Analysis::* (except SimpleAnalysisBase)
186 Bio::Tools::Gel
187 Bio::Tools::HMMER::*
188 Bio::Tools::Hmmpfam
189 Bio::Tools::Phylo::Gumby
190 Bio::Tools::Protparam
191 Bio::Tools::Run::RemoteBlast
192 Bio::Tools::SiRNA::*
193 Bio::Tools::dpAlign
194 Bio::Tools::pSW
195 Bio::Tree::AlleleNode
196 Bio::Tree::Draw::Cladogram
197 Bio::TreeIO::nexml
198 Bio::TreeIO::svggraph
199 Bio::Variation::*
201 * The following modules are new in the BioPerl distribution. They
202 have been previously released in the BioPerl-Run distribution.
203 This will enable smaller distributions that provide a
204 Bio::Tool::Run interface, to be only dependent on the BioPerl
205 distribution instead of the whole (very large) BioPerl-Run:
207 Bio::Tools::Run::Analysis
208 Bio::Tools::Run::AnalysisFactory
209 Bio::Tools::Run::Phylo::PhyloBase
210 Bio::Tools::Run::WrapperBase
211 Bio::Tools::Run::WrapperBase::CommandExts
213 * The following programs have been removed:
215 bp_biofetch_genbank_proxy
216 bp_blast2tree
217 bp_bulk_load_gff
218 bp_composite_LD
219 bp_das_server
220 bp_download_query_genbank
221 bp_fast_load_gff
222 bp_flanks
223 bp_genbank2gff
224 bp_generate_histogram
225 bp_heterogeneity_test
226 bp_hivq
227 bp_hmmer_to_table
228 bp_load_gff
229 bp_meta_gff
230 bp_netinstall
231 bp_parse_hmmsearch
232 bp_process_wormbase
233 bp_query_entrez_taxa
234 bp_remote_blast
235 bp_seqfeature_delete
236 bp_seqfeature_gff3
237 bp_seqfeature_load
239 * Because of the move of so many modules and programs into
240 separate distributions, the following modules are no longer
241 prerequisites:
243 Ace
244 Ace::Sequence::Homol
245 Algorithm::Munkres
246 Apache::DBI
247 Archive::Tar
248 Array::Compare
249 Bio::ASN1::EntrezGene
250 Bio::Expression::Contact
251 Bio::Expression::DataSet
252 Bio::Expression::Platform
253 Bio::Expression::Sample
254 Bio::Ext::Align
255 Bio::GMOD::CMap::Utils
256 Bio::Phylo::Factory
257 Bio::Phylo::Forest::Tree
258 Bio::Phylo::IO
259 Bio::Phylo::Matrices
260 Bio::Phylo::Matrices::Datum
261 Bio::Phylo::Matrices::Matrix
262 Bio::SeqFeature::Annotated
263 Bio::SeqIO::staden::read
264 Bio::Tools::Run::Alignment::Clustalw
265 Bio::Tools::Run::Ensembl
266 Bio::Tools::Run::Phylo::Molphy::ProtML
267 Bio::Tools::Run::Phylo::Phylip::Neighbor
268 Bio::Tools::Run::Phylo::Phylip::ProtDist
269 Bio::Tools::Run::Phylo::Phylip::ProtPars
270 Bio::Tools::Run::Samtools
271 CGI
272 CPAN
273 Cache::FileCache
274 Config
275 Convert::Binary::C
276 DBD::Pg
277 DBD::SQLite
278 Data::Stag::XMLWriter
279 Encode
280 English
281 ExtUtils::Install
282 ExtUtils::Manifest
283 File::Glob
284 GD::Simple
285 Getopt::Std
286 Graph::Undirected
287 GraphViz
288 HTML::HeadParser
289 HTML::TableExtract
290 LWP
291 LWP::Simple
292 MIME::Base64
293 Memoize
294 PostScript::TextBlock
295 SVG
296 SVG::Graph
297 SVG::Graph::Data
298 SVG::Graph::Data::Node
299 SVG::Graph::Data::Tree
300 Sort::Naturally
301 Spreadsheet::ParseExcel
302 Term::ReadLine
303 Text::NSP::Measures::2D::Fisher2::twotailed
304 Text::ParseWords
305 Time::Local
306 Tree::DAG_Node
307 URI::Escape
308 WWW::Mechanize
309 XML::Simple
311 * The following is a new prerequisite:
313 Test::RequiresInternet
315 * The deobfuscator has been removed.
317 * The emacs bioperl minor mode is no longer distributed as part of the
318 perl module distributions. See
319 https://github.com/bioperl/emacs-bioperl-mode
322 1.7.2 - "Entebbe"
324 [Bugs]
326 * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
327 * #245 - Code coverage fixes [zmughal,cjfields]
328 * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
329 * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
330 * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
331 * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
332 * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
333 * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
334 * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
335 * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
336 * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
337 * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
339 [Code changes]
341 * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
343 1.7.1 - "Election"
345 [Bugs]
347 * Minor release to incorporate fix for CPAN indexing, which
348 prevented proper updates [cjfields]
349 * Fix problem in managing Target attribute for gff3 [Jukes34]
350 * Minor bug fixes related to NCBI HTTPS support [cjfields]
352 1.7.0 - "Disney"
354 [New site]
356 * We have migrated to Github Pages. This was actually planned, but the
357 recent OBF server compromise forced our hand.
359 Brian Osborne [bosborne] took this under his wing to move docs and has
360 done a tremendous amount of work formatting the site and working out some
361 of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
362 Cantalupo and Franscison Ossandon also helped. Kudos!!
364 * Similarly, the official issue tracker is now Github Issues. This has
365 been updated in the relevant documentation bits (we hope!)
367 [Code changes]
369 * Previously deprecated modules removed
370 * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
371 * Bio::DB::SeqHound has been removed due to the service no longer being
372 available
373 * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
374 reasons due to the server no longer having a valid cert
375 * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
376 * Bio::Coordinate, Bio::SearchIO::blastxml,
377 Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
378 added on CPAN
380 [New features]
382 * Docker instances of tagged releases are available! [hlapp]
383 * NCBI HTTPS support [mjohnson and others]
384 * Bio::SearchIO::infernal
385 - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
386 * Bio::Search::HSP::ModelHSP
387 - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
388 reports [pcantalupo]
389 * Bio::Search::Result::INFERNALResult
390 - Added new module to represent features of Infernal reports [pcantalupo]
391 * Bio::DB::Taxonomy SQLite option [cjfields]
392 * WrapperBase quoted option values [majensen]
393 * Various documentation fixes and updates [bosborne]
395 [Bug Fixes]
397 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
398 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
399 * NeXML parser fixes [fjossandon]
400 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
401 * RT 103272 : SeqFeature database deletion skipped features with a decimal -
402 Joshua Fortriede (Xenbase)
403 * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
404 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
405 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
406 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
407 * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
408 * Issue #84: EMBL format wrapping problem [nyamned]
409 * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
410 * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
411 or compiled C code (when Inline::C is installed) [rocky]
412 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
413 * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
414 * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
415 * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
416 to be consistent with "$hit->bits" behaviour [fjossandon]
417 * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
418 aminoacids made "next_seq" confused and broke the parser [fjossandon]
419 * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
420 Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
421 to "complement(join(A..B,C..D))" [fjossandon]
422 * For the many many many fixes that weren't mentioned - blame the release guy!
424 1.6.924
426 [Significant changes]
428 * Bug/feature issue tracking has moved to GitHub Issues:
429 https://github.com/bioperl/bioperl-live/issues
430 * DB_File has been demoted from "required" to "recommended",
431 which should make easier for Windows users to install BioPerl
432 if they don't need that module.
434 [New features]
436 * Bio::Search::HSP::GenericHSP
437 - Bug #3370, added a "posterior_string" method to retrieve the
438 posterior probability lines (PP) from HMMER3 reports [fjossandon]
439 - Added a "consensus_string" method to retrieve the consensus
440 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
441 * Bio::SearchIO::hmmer2
442 - The number of identical and conserved residues are now calculated
443 directly from the homology line [fjossandon]
444 - Now the Query Length and Hit Length are reported when the alignment
445 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
446 - Implemented the capture of the consensus structure lines [fjossandon]
447 * Bio::SearchIO::hmmer3
448 - The number of identical and conserved residues are now calculated
449 directly from the homology line [fjossandon]
450 - Now the Hit Length is reported when the alignment runs until the end
451 of the sequence/model ('.]' or '[]') [fjossandon]
452 - Implemented the capture of the consensus structure lines [fjossandon]
453 - Implemented the capture of the posterior probability lines [fjossandon]
454 - Completed the development of NHMMER parsing, including alignments [fjossandon]
455 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
456 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
457 "min_score", "min_bits, and "hit_filter" methods from
458 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
459 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
460 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
461 besides Blast, instead of being ignored. Added tests for all moved methods
462 using HMMER outputs and run the full test suite and everything pass [fjossandon]
463 * Bio::SeqIO::MultiFile
464 - Autodetection of file format [fangly]
465 * Bio::Tools::GuessSeqFormat:
466 - Format detection from non-seekable filehandles such as STDIN [fangly]
468 [Bug fixes]
470 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
471 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
472 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
473 * Abstract: Fixed ActivePerl incapability of removing temporary files
474 because of problems closing tied filehandles [fjossandon]
475 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
476 because ActivePerl were producing a ".index.pag" and ".index.dir"
477 files instead of a single ".index" file (like Strawberry Perl).
478 Now those temporary files are correctly considered and deleted. [fjossandon]
479 * Test files: Added missing module requirements (DB_File and Data::Stag)
480 to several tests files that were failing because those modules were
481 not present. Now those test files are correctly skipped instead. [fjossandon]
482 * Blast: Added support to changes in bl2seq from BLAST+ output, which
483 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
484 * Phylip: Return undef in "next_aln" at file end to avoid
485 an infinite loop [yschensandiego]
486 * HMMER3: When a hit description is too long, it is truncated in
487 the Scores table. In those cases, the more complete description from
488 the Annotation line (>>) will be used [fjossandon]
489 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
490 since it is now used by HMMER3 format in alignments [fjossandon]
491 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
492 to return undef if the query/hit length is unknown (like in some
493 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
494 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
495 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
496 added support to multi-query reports, reduced code redundancy,
497 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
498 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
499 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
500 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
501 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
502 * Double-quotes on paths are needed in some places [fjossandon]
503 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
504 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
505 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
506 with the latest changes made in their own repositories [fjossandon]
507 * General synching of files with the master branch [fjossandon]
508 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
509 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
510 * Fixed broken MeSH parser [fjossandon]
511 * Fixed missing detection of format in SeqIO when given a -string [fangly]
513 1.6.923
515 * Major Windows support updates! [fjossandon]
516 * MAKER update to allow for stricter standard codon table [cjfields]
517 * Better support for circular sequences [fjossandon]
518 * Fixes for some complex location types [fjossandon]
519 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
520 * Fix bug #2978 related to BLAST report type [fjossandon]
521 * Deobfuscator fixes [DaveMessina]
523 1.6.922
525 * Address CPAN test failures [cjfields]
526 * Add BIOPROJECT support for Genbank files [hyphaltip]
527 * Better regex support for HMMER3 output [bosborne]
529 1.6.921
531 * Minor update to address CPAN test failures
533 1.6.920
535 * Remove Bio::Biblio and related files [carandraug]
536 - this cause version clashes with an independently-released
537 version of Bio::Biblio
539 1.6.910
541 [New features]
543 * Hash randomization fixes for perl 5.18.x
544 - Note: at least one module (Bio::Map::Physical) still has a failing test;
545 this is documented in bug #3446 and has been TODO'd; we will be pulling
546 Bio::Map and similar modules out of core into separate distributions in the
547 1.7.x release series [cjfields]
549 [New features]
551 * Bio::Seq::SimulatedRead
552 - New module to represent reads taken from other sequences [fangly]
553 * Bio::Root::Root
554 - Support of Clone::Fast as a faster cloning alternative [fangly]
555 * Bio::Root::IO
556 - Moved the format() and variant() methods from Bio::*IO modules to
557 Bio::Root::IO [fangly]
558 - Can now use format() to get the type of IO format in use [fangly]
559 * Bio::Tools::IUPAC
560 - New regexp() method to create regular expressions from IUPAC sequences
561 [fangly]
562 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
563 - Code refresh [fangly]
564 * Bio::DB::Taxonomy
565 - Added support for the Greengenes and Silva taxonomies [fangly]
566 * Bio::Tree::TreeFunctionsI
567 - get_lineage_string() represents a lineage as a string [fangly]
568 - add_trait() returns instead of reporting an error when the column
569 number is exceeded in add_trait() [fangly]
570 - Option to support tree leaves without trait [fangly]
571 - Allow ID of 0 in trait files [fangly]
572 * Bio::DB::Taxonomy::list
573 - Misc optimizations [fangly]
574 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
575 * Bio::DB::Taxonomy::*
576 - get_num_taxa() returns the number of taxa in the database [fangly]
577 * Bio::DB::Fasta and Bio::DB::Qual
578 - support indexing an arbitrary list of files [fangly]
579 - user can supply an arbitrary index file name [fangly]
580 - new option to remove index file at the end [fangly]
581 * Bio::DB::Fasta
582 - now handles IUPAC degenerate residues [fangly]
583 * Bio::PrimarySeq and Bio::PrimarySeqI
584 - speed improvements for large sequences [Ben Woodcroft, fangly]
585 * Bio::PrimaryQual
586 - tightened and optimized quality string validation [fangly]
587 * Bio::SeqIO::fasta
588 - new method and option 'block', to create FASTA output with space
589 intervaled blocks (similar to genbank or EMBL) has been implemented.
590 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
591 in favour of the methods 'width' and 'preferred_id_type` respectively.
592 * Bio::FeatureIO::*
593 - moved from bioperl-live into the separate distribution Bio-FeatureIO
594 * Bio::SeqFeature::Annotated
595 - moved from bioperl-live into the separate distribution Bio-FeatureIO
596 * Bio::Cluster::SequenceFamily
597 - improved performance when using get_members with overlapping multiple
598 criteria
599 * Bio::SearchIO::hmmer3
600 - now supports nhmmer [bosborne]
602 [Bug fixes]
604 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
605 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
606 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
607 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
608 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
609 information was lost in a multi-result blast file [Paul Cantalupo]
610 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
611 total gaps [Paul Cantalupo]
612 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
613 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
614 when end of domain indicator is split across lines [Paul Cantalupo]
615 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
616 cjfields]
617 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
618 instances where blank lines are within sequences [cjfields]
619 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
620 types [fangly]
621 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
622 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
623 cjfields]
624 * Various fixes for Stockholm file indexing and processing [bosborne]
625 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
626 breaks parsing [cjfields]
627 * Fix case where Bio::Seq::Meta* objects with no meta information could not
628 be reverse-complemented [fangly]
629 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
630 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
631 when unsure that values will be numerical [fangly]
632 * Fix undef warnings in Bio::SeqIO::embl [fangly]
633 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
634 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
635 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
636 Sallou]
637 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
638 source_tag and display_name must return a string, not undef [fangly]
639 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
640 add_SeqFeature takes a single argument [fangly]
641 * Use cross-platform filenames and temporary directory in
642 Bio::DB::Taxonomy::flatfile [fangly]
643 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
644 properly identified as existing taxa in the database [fangly]
645 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
646 without also passing a lineage to store [fangly]
647 * Prevent passing a directory to the gi2taxid option (-g) of
648 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
649 [fangly]
650 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
651 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
652 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
653 object before trying to access, and no longer returns repeated sequences.
656 1.6.901 May 18, 2011
658 [Notes]
660 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
661 modules using Ace will also be deprecated [lds, cjfields]
662 * Minor bug fix release
663 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
664 * Address Build.PL issues when DBI is not present [hartzell]
665 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
666 * Remove deprecated code for perl 5.14.0 compat [cjfields]
667 * Due to schema changes and lack of support for older versions, support
668 for NeXML 0.9 is only (very) partially implemented.
669 See: https://redmine.open-bio.org/issues/3207
671 [Bug fixes]
673 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
674 docs [genehack, cjfields]
675 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
676 module version from dist_version (probably not the best way to do this,
677 but it seems to work) [rbuels, cjfields]
680 1.6.900 April 14, 201
682 [Notes]
684 * This will probably be the last release to add significant features to
685 core modules; subsequent releases will be for bug fixes alone.
686 We are planning on a restructuring of core for summer 2011, potentially
687 as part of the Google Summer of Code. This may become BioPerl 2.0.
688 * Version bump represents 'just prior to v 1.7'. We may have point
689 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
690 This code essentially is what is on the github master branch.
692 [New features]
694 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
695 * Bio::Tree refactor
696 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
697 - removal of Scalar::Util::weaken code, which was causing odd headaches
698 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
699 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
700 many others]
701 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
702 [Warren Kretzschmar]
703 * Bio::SeqIO::gbxml
704 - bug 2515 - new contribution [Ryan Golhar, jhannah]
705 * Bio::Assembly::IO
706 - support for reading Maq, Sam and Bowtie files [maj]
707 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
708 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
709 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
710 - bug 2726: reading/writing granularity: whole scaffold or one contig
711 at a time [Joshua Udall, fangly]
712 * Bio::OntologyIO
713 - Added parsing of xrefs to OBO files, which are stored as secondary
714 dbxrefs of the cvterm [Naama Menda]
715 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
716 * PAML code updated to work with PAML 4.4d [DaveMessina]
718 [Bug fixes]
720 * [3198] - sort tabular BLAST hits by score [DaveMessina]
721 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
722 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
723 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
724 [cjfields]
725 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
726 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
727 * [3164] - TreeFunctionsI syntax bug [gjuggler]
728 * [3163] - AssemblyIO speedup [fangly]
729 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
730 hyphaltip]
731 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
732 * [3158] - fix EMBL file mis-parsing [cjfields]
733 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
734 cjfields]
735 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
736 * [3148] - URL change for UniProt [cjfields]
737 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
738 * [3136] - HMMer3 parser fixes [kblin]
739 * [3126] - catch description [Toshihiko Akiba]
740 * [3122] - Catch instances where non-seekable filehandles were being
741 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
742 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
743 [dukeleto, rbuels, cjfields]
744 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
745 jhannah]
746 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
747 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
748 cjfields]
749 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
750 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
751 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
752 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
753 * [3086] - EMBL misparsing long tags [kblin, cjfields]
754 * [3085] - CommandExts and array of files [maj, hyphaltip]
755 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
756 for alignment slices [Ha X. Dang, cjfields]
757 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
758 * [3073] - fix parsing of GenBank files from RDP [cjfields]
759 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
760 * [3064] - All-gap midline BLAST report issues [cjfields]
761 * [3063] - BLASt report RID [Razi Khaja, cjfields]
762 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
763 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
764 * [3039] - correct Newick output root node branch length [gjuggler,
765 DaveMessina]
766 * [3038] - SELEX alignment error [Bernd, cjfields]
767 * [3033] - PrimarySeq ID setting [Bernd, maj]
768 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
769 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
770 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
771 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
772 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
773 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
774 PAML 4.4d [DaveMessina]
775 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
776 DaveMessina]
777 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
778 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
779 * [3017] - using threads with Bio::DB::GenBank [cjfields]
780 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
781 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
782 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
783 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
784 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
785 cjfields]
786 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
787 * [2977] - TreeIO issues [DaveMessina]
788 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
789 * [2944] - Bio::Tools::GFF score [cjfields]
790 * [2942] - correct MapTiling output [maj]
791 * [2939] - PDB residue insertion codes [John May, maj]
792 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
793 * [2928] - GuessSeqFormat raw [maj]
794 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
795 * [2922] - open() directive issue [cjfields]
796 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
797 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
798 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
799 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
800 cjfields]
801 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
802 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
803 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
804 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
805 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
806 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
807 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
808 * [2758] - Bio::AssemblyIO ace problems [fangly]
809 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
810 * [2726] - ace file IO [Josh, fangly]
811 * [2700] - Refactor Build.PL [cjfields]
812 * [2673] - addition of simple Root-based clone() method [cjfields]
813 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
814 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
815 * [2594] - Bio::Species memory leak [cjfields]
816 * [2515] - GenBank XML parser [jhannah]
817 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
818 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
819 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
820 cjfields]
821 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
823 [Deprecated]
825 * Bio::Expression modules - these were originally designed to go with the
826 bioperl-microarray suite of tools, however they have never been completed
827 and so have been removed from the distribution. The original code has
828 been moved into the inactive bioperl-microarray suite. [cjfields]
830 [Other]
832 * Repository moved from Subversion (SVN) to
833 http://github.com/bioperl/bioperl-live [cjfields]
834 * Bug database has moved to Redmine (https://redmine.open-bio.org)
835 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
836 Thieme have been moved to their own distribution (Bio-Microarray).
837 [cjfields]
839 1.6.1 Sept. 29, 2009 (point release)
840 * No change from last alpha except VERSION and doc updates [cjfields]
842 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
843 * Fix for silent OBDA bug related to FASTA validation [cjfields]
845 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
846 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
847 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
848 [cjfields]
849 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
851 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
852 * WinXP test fixes [cjfields, maj]
853 * BioPerl.pod added for descriptive information, fixes CPAN indexing
854 [cjfields]
855 * Minor doc fixes [cjfields]
857 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
858 * Fix tests failing due to merging issues [cjfields]
859 * More documentation updates for POD parsing [cjfields]
861 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
862 * Bio::Root::Build
863 - fix YAML meta data generation [cjfields]
865 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
866 * Bio::Align::DNAStatistics
867 - fix divide by zero problem [jason]
868 * Bio::AlignIO::*
869 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
870 * Bio::AlignIO::stockholm
871 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
872 * Bio::Assembly::Tools::ContigSpectrum
873 - function to score contig spectrum [fangly]
874 * Bio::DB::EUtilities
875 - small updates [cjfields]
876 * Bio::DB::Fasta
877 - berkeleydb database now autoindexes wig files and locks correctly
878 [lstein]
879 * Bio::DB::HIV
880 - various small updates for stability; tracking changes to LANL
881 database interface [maj]
882 * Bio::DB::SeqFeature (lots of updates and changes)
883 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
884 - bug 2835 - patch [Dan Bolser]
885 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
886 * Bio::DB::SwissProt
887 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
888 * Bio::Factory::FTLocationFactory
889 - mailing list bug fix [cjfields]
890 * Bio::LocatableSeq
891 - performance work on column_from_residue_number [hartzell]
892 * Bio::Matrix::IO::phylip
893 - bug 2800 - patch to fix phylip parsing [Wei Zou]
894 * Bio::Nexml
895 - Google Summer of Code project from Chase Miller - parsers for Nexml
896 file format [maj, chmille4]
897 * Bio::PopGen
898 - Make Individual, Population, Marker objects AnnotatableI [maj]
899 - simplify LD code [jason]
900 * Bio::RangeI
901 - deal with empty intersection [jason]
902 * Bio::Restriction
903 - significant overhaul of Bio::Restriction system: complete support for
904 external and non-palindromic cutters. [maj]
905 * Bio::Root::Build
906 - CPANPLUS support, no automatic installation [sendu]
907 * Bio::Root::IO
908 - allow IO::String (regression fix) [cjfields]
909 - catch unintentional undef values [cjfields]
910 - throw if non-fh is passed to -fh [maj]
911 * Bio::Root::Root/RootI
912 - small debugging and core fixes [cjfields]
913 * Bio::Root::Test
914 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
915 * Bio::Root::Utilities
916 - bug 2737 - better warnings [cjfields]
917 * Bio::Search
918 - tiling completely refactored, HOWTO added [maj]
919 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
920 will deprecate usage of the older tiling code in the next BioPerl
921 release
922 - small fixes [cjfields]
923 * Bio::SearchIO
924 - Infernal 1.0 output now parsed [cjfields]
925 - new parser for gmap -f9 output [hartzell]
926 - bug 2852 - fix infinite loop in some output [cjfields]
927 - blastxml output now passes all TODO tests [cjfields]
928 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
929 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
930 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
931 * Bio::Seq::LargePrimarySeq
932 - delete tempdirs [cjfields]
933 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
934 * Bio::Seq::Quality
935 - extract regions based on quality threshold value [Dan Bolser, heikki]
936 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
937 * Bio::SeqFeature::Lite
938 - various Bio::DB::SeqFeature-related fixes [lstein]
939 * Bio::SeqFeature::Tools::TypeMapper
940 - additional terms for GenBank to SO map [scain]
941 * Bio::SeqIO::chadoxml
942 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
943 * Bio::SeqIO::embl
944 - support for CDS records [dave_messina, Sylvia]
945 * Bio::SeqIO::fastq
946 - complete refactoring to handle all FASTQ variants, perform validation,
947 write output. API now conforms with other Bio* parsers and the rest of
948 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
949 [cjfields]
950 * Bio::SeqIO::genbank
951 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
952 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
953 * Bio::SeqIO::largefasta
954 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
955 * Bio::SeqIO::raw
956 - add option for 'single' and 'multiple'
957 * Bio::SeqIO::scf
958 - bug 2881 - fix scf round-tripping [Adam Søgren]
959 * Bio::SeqUtils
960 - bug 2766, 2810 - copy over tags from features, doc fixes [David
961 Jackson]
962 * Bio::SimpleAlign
963 - bug 2793 - patch for add_seq index issue [jhannah, maj]
964 - bug 2801 - throw if args are required [cjfields]
965 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
966 [Tristan Lefebure, maj]
967 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
968 - fix POD and add get_SeqFeatures filter [maj]
969 * Bio::Tools::dpAlign
970 - add support for LocatableSeq [ymc]
971 - to be moved to a separate distribution [cjfields, rbuels]
972 * Bio::Tools::EUtilities
973 - fix for two bugs from mail list [Adam Whitney, cjfields]
974 - add generic ItemContainerI interface for containing same methods
975 [cjfields]
976 * Bio::Tools::HMM
977 - fix up code, add more warnings [cjfields]
978 - to be moved to a separate distribution [cjfields, rbuels]
979 * Bio::Tools::Primer3
980 - bug 2862 - fenceposting issue fixed [maj]
981 * Bio::Tools::Run::RemoteBlast
982 - tests for remote RPS-BLAST [mcook]
983 * Bio::Tools::SeqPattern
984 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
985 * Bio::Tools::tRNAscanSE
986 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
987 * Bio::Tree::*
988 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
989 * Bio::Tree::Statistics
990 - several methods for calculating Fitch-based score, internal trait
991 values, statratio(), sum of leaf distances [heikki]
992 * Bio::Tree::Tree
993 - bug 2869 - add docs indicating edge case where nodes can be
994 prematurely garbage-collected [cjfields]
995 - add as_text() function to create Tree as a string in specified format
996 [maj]
997 * Bio::Tree::TreeFunctionsI
998 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
999 Lefebure, maj]
1000 * Bio::TreeIO::newick
1001 - fix small semicolon issue [cjfields]
1002 * scripts
1003 - update to bp_seqfeature_load for SQLite [lstein]
1004 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
1005 - fastam9_to_table - fix for MPI output [jason]
1006 - gccalc - total stats [jason]
1007 * General Stuff
1008 - POD cleanup re: FEEDBACK section [maj, cjfields]
1009 - cleanup or fix dead links [cjfields]
1010 - Use of no_* methods (indicating 'number of something') is deprecated
1011 in favor of num_* [cjfields]
1012 - lots of new tests for the above bugs and refactors [everyone!]
1013 - new template for Komodo text editor [cjfields]
1015 1.6.0 Winter 2009
1016 * Feature/Annotation rollback
1017 - Problematic changes introduced prior to the 1.5 release have been
1018 rolled back. These changes led to subtle bugs involving operator
1019 overloading and interface methods.
1020 - Behavior is very similar to that for BioPerl 1.4, with tag values
1021 being stored generically as simple scalars. Results in a modest
1022 speedup.
1023 * Bio::Graphics
1024 - Split into a separate distribution on CPAN, primarily so development
1025 isn't reliant on a complete BioPerl release.
1026 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
1027 is only available via Subversion (via bioperl-live main trunk)
1028 * Bio::Root::Test
1029 - Common test bed for all BioPerl modules
1030 * Bio::Root::Build
1031 - Common Module::Build-based subclass for all BioPerl modules
1032 * Bio::DB::EUtilities
1033 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
1034 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
1035 and user agent request posting and retrieval
1036 * Test implementation and reorganization
1037 - Tests have been reorganized into groups based on classes or use
1038 cases.
1039 - Automated test coverage is now online:
1040 http://www.bioperl.org/wiki/Test_Coverage
1041 - After this release, untested modules will be moved into a
1042 separate developer distribution until tests can be derived.
1043 Also, new modules to be added are expected to have a test suite
1044 and adequate test coverage.
1046 1.5.2 Developer release
1048 Full details of changes since 1.5.1 are available online at:
1049 http://www.bioperl.org/wiki/Change_log
1050 The following represents a brief overview of the most important changes.
1052 o Bio::Map
1053 - Overhaul. Brand new system fully allows markers to have multiple
1054 positions on multiple maps, and to have relative positions. Should be
1055 backward compatible.
1057 o Bio::Taxonomy
1058 - This module and all the modules in the Taxonomy directory now
1059 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
1061 o Bio::DB::Taxonomy
1063 - Taxonomy.pm
1064 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
1066 * New methods ancestor(), each_Descendent() and _handle_internal_id().
1068 * Allows for different database modules to create Bio::Taxon objects
1069 with the same internal id when the same taxon is requested from each.
1071 - flatfile.pm
1072 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
1074 * No longer includes the fake root node 'root'; there are multiple roots
1075 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
1077 - entrez.pm
1078 * get_node() has new option -full
1080 * Caches data retrieved from website
1082 o Bio::Species
1083 - Now a Bio::Taxon. Carries out the species name -> specific name munging
1084 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
1085 backward compatability in species() method.
1087 o Bio::Search and Bio::SearchIO
1088 - Overhaul. The existing system has been sped up via some minor changes
1089 (mostly gain-of-function to the API). Bio::PullParserI is introduced
1090 as a potential eventual replacment for the existing system, though as
1091 yet only a Hmmpfam parser exists written using it.
1094 1.5.1 Developer release
1096 o Major problem with how Annotations were written out with
1097 Bio::Seq is fixed by reverting to old behavior for
1098 Bio::Annotation objects.
1100 o Bio::SeqIO
1102 - genbank.pm
1103 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
1104 expect at l east 9 spaces at the beginning of a line to
1105 indicate line wrapping.
1107 * Treat multi-line SOURCE sections correctly, this defect broke
1108 both common_name() and classification()
1110 * parse swissprot fields in genpept file
1112 * parse WGS genbank records
1114 - embl.pm
1115 * Changed regexp for ID line. The capturing parentheses are
1116 the same, the difference is an optional repeated-not-semi-
1117 colon expression following the captured \S+. This means the
1118 regexp works when the division looks like /PRO;/ or when the
1119 division looks like /ANG ;/ - the latter is from EMBL
1120 repbase
1122 * fix ID line parsing: the molecule string can have spaces in
1123 it. Like: "genomic DNA"
1125 - swiss.pm: bugs #1727, #1734
1127 - entrezgene.pm
1128 * Added parser for entrezgene ASN1 (text format) files.
1129 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
1131 o Bio::AlignIO
1133 - maf.pm coordinate problem fixed
1135 o Bio::Taxonomy and Bio::DB::Taxonomy
1137 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
1138 can be done via Web without downloading all the sequence.
1140 o Bio::Tools::Run::RemoteBlast supports more options and complies
1141 to changes to the NCBI interface. It is reccomended that you
1142 retrieve the data in XML instead of plain-text BLAST report to
1143 insure proper parsing and retrieval of all information as NCBI
1144 fully expects to change things in the future.
1146 o Bio::Tree and Bio::TreeIO
1148 - Fixes so that re-rooting a tree works properly
1150 - Writing out nhx format from a newick/nexus file will properly output
1151 bootstrap information. The use must move the internal node labels over
1152 to bootstraps.
1153 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
1154 $node->bootstrap($node->id);
1155 $node->id('');
1156 }
1157 - Nexus parsing is much more flexible now, does not care about
1158 LF.
1160 - Cladogram drawing module in Bio::Tree::Draw
1162 - Node height and depth now properly calculated
1164 - fix tree pruning algorithm so that node with 1 child gets merged
1166 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
1167 bugs and improvements were added, see Gbrowse mailing list for most of
1168 these.
1170 o Bio::DB::GFF partially supports GFF3. See information about
1171 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
1173 o Better location parsing in Bio::Factory::FTLocationFactory -
1174 this is part of the engine for parsing EMBL/GenBank feature table
1175 locations. Nested join/order-by/complement are allowed now
1177 o Bio::PrimarySeqI->translate now takes named parameters
1179 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
1180 reconstruction) is now supported. Parsing different models and
1181 branch specific parametes are now supported.
1183 o Bio::Factory::FTLocationFactory - parse hierarchical locations
1184 (joins of joins)
1186 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
1187 for getter/setter functions
1189 o Bio::SearchIO
1191 - blast bug #1739; match scientific notation in score
1192 and possible e+ values
1194 - blast.pm reads more WU-BLAST parameters and parameters, match
1195 a full database pathname,
1197 - Handle NCBI WEB and newer BLAST formats specifically
1198 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
1200 - psl off-by-one error fixed
1202 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
1203 and HSPs can be constructed from them.
1205 - HSPs query/hit now have a seqdesc field filled out (this was
1206 always available via $hit->description and
1207 $result->query_description
1209 - hmmer.pm can parse -A0 hmmpfam files
1211 - Writer::GbrowseGFF more customizeable.
1213 o Bio::Tools::Hmmpfam
1214 make e-value default score displayed in gff, rather than raw score
1215 allow parse of multiple records
1218 1.5 Developer release
1220 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
1221 provide Jukes-Cantor and Kimura pairwise distance methods,
1222 respectively.
1224 o Bio::AlignIO support for "po" format of POA, and "maf";
1225 Bio::AlignIO::largemultifasta is a new alternative to
1226 Bio::AlignIO::fasta for temporary file-based manipulation of
1227 particularly large multiple sequence alignments.
1229 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
1230 be treated similarly as an assembled contig.
1232 o Bio::CodonUsage provides new rare_codon() and probable_codons()
1233 methods for identifying particular codons that encode a given
1234 amino acid.
1236 o Bio::Coordinate::Utils provides new from_align() method to build
1237 a Bio::Coordinate pair directly from a
1238 Bio::Align::AlignI-conforming object.
1240 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
1241 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
1242 web service using standard Pubmed query syntax, and retrieve
1243 results as XML.
1245 o Bio::DB::GFF has various sundry bug fixes.
1247 o Bio::FeatureIO is a new SeqIO-style subsystem for
1248 writing/reading genomic features to/from files. I/O classes
1249 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
1250 classes only read/write Bio::SeqFeature::Annotated objects.
1251 Notably, the GFF v3 class requires features to be typed into the
1252 Sequence Ontology.
1254 o Bio::Graph namespace contains new modules for manipulation and
1255 analysis of protein interaction graphs.
1257 o Bio::Graphics has many bug fixes and shiny new glyphs.
1259 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
1260 indexing for HMMER reports and FASTA qual files, respectively.
1262 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
1263 new objects that can be placed within a Bio::Map::MapI-compliant
1264 genetic/physical map; Bio::Map::Physical provides a new physical
1265 map type; Bio::MapIO::fpc provides finger-printed clone mapping
1266 import.
1268 o Bio::Matrix::PSM provide new support for postion-specific
1269 (scoring) matrices (e.g. profiles, or "possums").
1271 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
1272 be instantiated without explicitly using Bio::OntologyIO. This
1273 is possible through changes to Bio::Ontology::OntologyStore to
1274 download ontology files from the web as necessary. Locations of
1275 ontology files are hard-coded into
1276 Bio::Ontology::DocumentRegistry.
1278 o Bio::PopGen includes many new methods and data types for
1279 population genetics analyses.
1281 o New constructor to Bio::Range, unions(). Given a list of
1282 ranges, returns another list of "flattened" ranges --
1283 overlapping ranges are merged into a single range with the
1284 mininum and maximum coordinates of the entire overlapping group.
1286 o Bio::Root::IO now supports -url, in addition to -file and -fh.
1287 The new -url argument allows one to specify the network address
1288 of a file for input. -url currently only works for GET
1289 requests, and thus is read-only.
1291 o Bio::SearchIO::hmmer now returns individual Hit objects for each
1292 domain alignment (thus containing only one HSP); previously
1293 separate alignments would be merged into one hit if the domain
1294 involved in the alignments was the same, but this only worked
1295 when the repeated domain occured without interruption by any
1296 other domain, leading to a confusing mixture of Hit and HSP
1297 objects.
1299 o Bio::Search::Result::ResultI-compliant report objects now
1300 implement the "get_statistics" method to access
1301 Bio::Search::StatisticsI objects that encapsulate any
1302 statistical parameters associated with the search (e.g. Karlin's
1303 lambda for BLAST/FASTA).
1305 o Bio::Seq::LargeLocatableSeq combines the functionality already
1306 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
1308 o Bio::SeqFeature::Annotated is a replacement for
1309 Bio::SeqFeature::Generic. It breaks compliance with the
1310 Bio::SeqFeatureI interface because the author was sick of
1311 dealing with untyped annotation tags. All
1312 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
1313 compliant, and accessible through Bio::Annotation::Collection.
1315 o Bio::SeqFeature::Primer implements a Tm() method for primer
1316 melting point predictions.
1318 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
1319 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
1321 o Bio::Taxonomy::Node now implements the methods necessary for
1322 Bio::Species interoperability.
1324 o Bio::Tools::CodonTable has new reverse_translate_all() and
1325 make_iupac_string() methods.
1327 o Bio::Tools::dpAlign now provides sequence profile alignments.
1329 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
1331 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
1332 parsers.
1334 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
1335 for designing small inhibitory RNA.
1337 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
1338 methods based on a distance matrix.
1340 o Bio::Tree::Statistics provides an assess_bootstrap() method to
1341 calculate bootstrap support values on a guide tree topology,
1342 based on provided bootstrap tree topologies.
1344 o Bio::TreeIO now supports the Pagel (PAG) tree format.
1346 1.4 branch
1348 1.4.1
1350 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
1352 o Bio::Graphics will work with gd1 or gd2
1354 o Bio::SearchIO
1355 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
1356 (RF lines alone)
1357 - blast.pm Parse multi-line query fields properly
1358 - small speed improvements to blasttable.pm and others
1360 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
1361 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
1362 supporting more complex queries
1365 1.4. Stable major release
1367 Since initial 1.2.0, 3000 separate changes have been made to make this release.
1369 o installable scripts
1371 o global module version from Bio::Root:Version
1373 o Bio::Graphics
1374 - major improvements; SVG support
1376 o Bio::Popgen
1377 - population genetics
1378 - support several population genetics types of questions.
1379 - Tests for statistical neutrality of mutations
1380 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
1381 Tests of population structure (Wright's F-statistic: Fst) is in
1382 Bio::PopGen::PopStats. Calculating composite linkage
1383 disequilibrium (LD) is available in Bio::PopGen::Statistics as
1384 well.
1385 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1386 and csv (comma delimited formatted) data.
1388 - a directory for implementing population simulations has
1389 been added Bio::PopGen::Simulation and 2 simulations - a
1390 Coalescent and a simple single-locus multi-allele genetic drift
1391 simulation have been provided. This replaces the code in
1392 Bio::Tree::RandomTree which has been deprecated until proper
1393 methods for generating random phylogenetic trees are
1394 implemented.
1396 o Bio::Restriction
1397 - new restrion analysis modules
1399 o Bio::Tools::Analysis
1400 - web based DNA and Protein analysis framework and several
1401 implementations
1403 o Bio::Seq::Meta
1404 - per residue annotable sequences
1406 o Bio::Matrix
1407 - Bio::Matrix::PSM - Position Scoring Matrix
1408 - Bio::Matrix::IO has been added for generalized parsing of
1409 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1410 initial implementations for parsing BLOSUM/PAM and Phylip
1411 Distance matricies respectively. A generic matrix
1412 implementation for general use was added in
1413 Bio::Matrix::Generic.
1415 o Bio::Ontology
1416 - major changes
1418 o Bio:Tree
1420 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1421 - small inhibitory RNA
1423 o Bio::SeqFeature::Tools
1424 - seqFeature mapping tools
1425 - Bio::SeqFeature::Tools::Unflattener.pm
1426 -- deal with mapping GenBank feature collections into
1427 Chado/GFF3 processable feature sets (with SO term mappings)
1429 o Bio::Tools::dpAlign
1430 - pure perl dynamic programming sequence alignment
1431 - needs Bioperl-ext
1433 o new Bio::SearchIO formats
1434 - axt and psl: UCSC formats.
1435 - blasttable: NCBI -m 8 or -m 9 format from blastall
1437 o new Bio::SeqIO formats
1438 - chado, tab, kegg, tigr, game
1439 - important fixes for old modules
1441 o Bio::AlignIO: maf
1443 o improved Bio::Tools::Genewise
1445 o Bio::SeqIO now can recongnize sequence formats automatically from
1446 stream
1448 o new parsers in Bio::Tools:
1449 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1451 o Bio::DB::Registry bugs fixed
1452 - BerkeleyDB-indexed flat files can be used by the OBDA system
1453 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1454 used by the OBDA system
1456 o several new HOWTOs
1457 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1458 Databases
1460 o hundreds of new and improved files
1463 o
1464 o Bio::Tree::AlleleNode has been updated to be a container of
1465 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1468 1.2 Branch
1470 1.2.3 Stable release update
1471 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1472 handling.
1473 o Bug #1477 - Sel --> Sec abbreviation fixed
1474 o Fix bug #1487 where paring in-between locations when
1475 end < start caused the FTLocationFactory logic to fail.
1476 o Fix bug #1489 which was not dealing with keywords as an
1477 arrayref properly (this is fixed on the main trunk because
1478 keywords returns a string and the array is accessible via
1479 get_keywords).
1480 o Bio::Tree::Tree memory leak (bug #1480) fixed
1481 Added a new initialization option -nodelete which
1482 won't try and cleanup the containing nodes if this
1483 is true.
1484 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1485 this was only present on the branch for the 1.2.1 and 1.2.2 series
1486 - Also merged main trunk changes to the branch which make
1487 newick -> nhx round tripping more effective (storing branch length
1488 and bootstrap values in same locate for NodeNHX and Node
1489 implementations.) Fixes to TreeIO parsing for labeled internal
1490 also required small changes to TreeIO::nhx. Improved
1491 tests for this module as well.
1492 o Bio::SearchIO
1493 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1494 gapped blast properly (was losing hit significance values due to
1495 the extra unexpeted column).
1496 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1497 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1498 although doesn't try to correct it - will get the negative
1499 number for you. Added a test for this as well.
1500 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1501 has no top-level family classification scores but does have scores and
1502 alignments for individual domains.
1503 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1504 regular expression to match the line was missing the possibility of
1505 an extra space. This is rare, which is why we probably did not
1506 catch it before.
1507 - BLAST parsing picks up more of the statistics/parameter fields
1508 at the bottom of reports. Still not fully complete.
1509 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1510 were fixed to include many improvements and added flexiblity
1511 in outputting the files. Bug #1495 was also fixed in the process.
1512 o Bio::DB::GFF
1513 - Update for GFF3 compatibility.
1514 - Added scripts for importing from UCSC and GenBank.
1515 - Added a 1.2003 version number.
1516 o Bio::Graphics
1517 - Updated tutorial.
1518 - Added a 1.2003 version number.
1519 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1520 properly writing keywords out.
1521 o Bio::SeqIO::genbank
1522 - Fixed bug/enhancement #1513 where dates of
1523 the form D-MMM-YYYY were not parsed. Even though this is
1524 invalid format we can handle it - and also cleanup the date
1525 string so it is properly formatted.
1526 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1527 and written with Genbank format. Similarly bug #1515 is fixed to
1528 parse in the ORIGIN text.
1529 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1530 to specify the ID type, one of (accession accession.version
1531 display primary). See Bio::SeqIO::preferred_id_type method
1532 documentation for more information.
1533 o Unigene parsing updated to handle file format changes by NCBI
1535 1.2.2 Stable release update
1537 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1538 - auto-discover ontology name
1539 - bug in parsing relationships when certain characters are in the term
1540 - fixed hard-coded prefix for term identifiers
1541 - various smaller issues
1543 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1544 of Bio::Ontology::TermI
1546 o brought the OBDA Registry code up to latest specs
1548 o Bio::DB::GenBank
1549 - eutils URL change
1550 - accession number retrieval fixed
1552 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1554 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1555 #1459 which now properly report alignment start/end info
1556 for translated BLAST/FASTA searches.
1558 o Bio::TreeIO::newick can parse labeled internal nodes
1560 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1561 for BLASTX if if you provide -report_type => 'BLASTX' when
1562 initializing a BPbl2seq object. Bioperl 1.3 will have better
1563 support for bl2seq in the SearchIO system.
1565 o Bio::Root::IO support a -noclose boolean flag which will not
1566 close a filehandle upon object cleanup - useful when sharing
1567 a filehandle among objects. Additionally code added s.t.
1568 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1570 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1572 o Bio::SeqIO::genbank
1573 - bug #1456 fixed which generated extra sequence lines
1574 - write moltype correctly for genpept
1576 1.2.1 Stable release update
1578 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1580 o Addition from main trunk of Ontology objects, principly to allow
1581 BioSQL releases against 1.2.1
1583 o Fixes and cleanup of Bio::Coordinate modules
1585 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1586 the primary accession number
1588 o Other bug fixes, including bpindex GenBank fix
1590 o Bio::SeqIO::genbank bug #1389 fixed
1592 1.2 Stable major release
1594 o More functionality added to Bio::Perl, the newbie module
1596 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1597 Support for New Hampshire Extended (NHX) format parsing.
1599 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1600 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1601 Hmmpfam parser.
1603 o New ontology parsing Bio::Ontology
1605 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1606 multi-report (mlib) fasta reports, support for waba and exonerate.
1608 o Bio::ClusterIO for parsing Unigene clusters
1610 o Bio::Assembly added for representing phrap and ace assembly clusters.
1612 o Rudimentary support for writing Chado XML (see
1613 GMOD project: www.gmod.org for more information)
1615 o Bio::Coordinate for mapping between different coordinate systems such
1616 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1617 features into different coordinate systems.
1619 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1620 with the get_Stream_by_query method and supports the latest
1621 NCBI eutils interface.
1623 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1624 object for extracting subsets of features : currently only
1625 supports extraction by location.
1627 1.1.1 Developer release
1629 o Deprecated modules are now listed in the DEPRECATED file
1631 o New HowTo documents located in doc/howto describing
1632 a domain of Bioperl.
1634 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1635 and all old bugs are searchable through the bugzilla interface.
1637 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1638 have been addressed.
1640 o Support for Genewise parsing in Bio::Tools::Genewise
1642 o Start of Ontology framework with Bio::Ontology
1644 o Speedup to the Bio::Root::Root object method _rearrange.
1645 A global _load_module method was implemented to simplify the
1646 dynamic loading of modules ala Bio::SeqIO::genbank. This
1647 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1648 etc).
1650 o Several performance improvements to sequence parsing in Bio::SeqIO.
1651 Attempt to speedup by reducing object creation overhead.
1653 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1654 method for sequence retrieval with their E-utils CGI scripts.
1655 More work to support Entrez queries to their fullest is planned
1656 before 1.2 release.
1658 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1660 1.1 Developer release
1662 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1663 this separation removes some of the complexity in our test suite
1664 and separates the core modules in bioperl from those that need
1665 external programs to run.
1667 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1668 not run into trouble running the makefile
1670 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1671 read,create,and write locations for grouped/split locations
1672 (like mRNA features on genomic sequence).
1674 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1675 and PAML (codeml,aaml, etc) parsing.
1677 o Bio::Tree:: objects expanded to handle testing monophyly,
1678 paraphyly, least common ancestor, etc.
1680 o Bio::Coordinate for mapping locations from different coordinate spaces
1682 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1683 added for parsing hmmpfam and hmmsearch output.
1685 o Bio::SearchIO::Writer::TextResultWriter for outputting
1686 a pseudo-blast textfile format
1689 1.0.2 Bug fix release
1691 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1692 in this release will not work after December 2002 when NCBI
1693 shuts off the old Entrez cgi scripts. We have already fixed
1694 on our main development branch and the functionality will be
1695 available in the next stable bioperl release (1.2) slated for
1696 Fall 2002.
1698 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1699 testset by Robin Emig. These were fixed as was the get_aln
1700 method in Bio::Search::HSP::GenericHSP to handle the extra
1701 context sequence that is provided with a FastA alignment.
1703 o Migrating differences between Bio::Search::XX::BlastXX to
1704 Bio::Search::XX::GenericXX objects. This included mechanism
1705 to retrieve whole list of HSPs from Hits and whole list of Hits from
1706 Results in addition to the current next_XX iterator methods that
1707 are available. Added seq_inds() method to GenericHSP which identifies
1708 indexes in the query or hit sequences where conserved,identical,gaps,
1709 or mismatch residues are located (adapted from Steve Chervitz's
1710 implementation in BlastHSP).
1712 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1713 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1715 o Bio::Graphics glyph set improved and extended for GBrowse release
1717 o Bio::Tree::Tree get_nodes implementation improvement thanks
1718 to Howard Ross notice performance problem when writing out
1719 unbalanced trees.
1721 o Bio::Location::Fuzzy::new named parameter -loc_type became
1722 -location_type, Bio::Location::Simple::new named parameter
1723 -seqid becamse -seq_id.
1725 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1726 was mis-detecting that gaps should be placed at the beginning of
1727 the alignment when the best alignment starts internally in the
1728 sequence.
1730 1.0.1 Bug fix release
1732 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1734 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1735 and mixed (3.3 - 3.4) versions of FASTA.
1737 o Small API change to add methods for completeness across
1738 implementations of Bio::Search objects. These new methods
1739 in the interface are implemented by the GenericXX object as well
1740 as the BlastXX objects.
1741 * Bio::Search::Result::ResultI
1742 - hits() method returns list of all Hits (next_hit is an
1743 iterator method)
1745 * Bio::Search::Hit::HitI
1746 - hsps() method returns list of all HSPs (next_hsp is an
1747 iterator method)
1749 o The Bio::SearchIO::Writer classes have been fixed to handle results
1750 created from either psiblast (Search::BlastXX objects) or
1751 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1752 has to be done here to make it work properly and will nee major
1753 API changes.
1755 o Bugs in Bio::Tools::HMMER fixed, including
1756 * #1178 - Root::IO destructor wasn't being called
1757 * #1034 - filter_on_cutoff now behaves properly
1759 o Bio::SeqFeature::Computation initialization args fixed and
1760 tests added.
1762 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1764 o Updated FAQ with more example based answers to typical questions
1766 o Bug #1202 was fixed which would improperly join together qual values
1767 parsed by Bio::SeqIO::qual when a trailing space was not present before
1768 the newline.
1770 1.0.0 Major Stable Release
1772 This represents a major release of bioperl with significant
1773 improvements over the 0.7.x series of releases.
1775 o Bio::Tools::Blast is officially deprecated. Please see
1776 Bio::SearchIO for BLAST and FastA parsing.
1778 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1779 Bio::LocationI objects as well as start/end.
1781 o Bio::Biblio contains modules for Bibliographic data.
1782 Bio::DB::Biblio contains the query modules. Additionally one can
1783 parse medlinexml from the ebi bibliographic query service (BQS)
1784 system and Pubmed xml from NCBI. See Martin Senger's
1785 documentation in Bio::Biblio for more information.
1787 o Bio::DB::Registry is a sequence database registry part of
1788 Open Bioinformatics Database Access. See
1789 http://obda.open-bio.org for more information.
1791 o File-based and In-Memory Sequence caching is provided by
1792 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1793 local database.
1795 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1796 been added by Lincoln Stein.
1798 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1800 o A FAQ has been started and is included in the release to provide
1801 a starting point for frequent questions and issues.
1803 0.9.3 Developer's release
1805 o Event based parsing system improved (SearchIO). With parsers for
1806 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1807 Additionally a lazy parsing system for text and html blast reports was
1808 added and is called psiblast (name subject to change in future releases).
1810 o Bio::Search objects improved and standardized with associated Interfaces
1811 written. The concept of a search "Hit" was standardized to be called
1812 "hit" consistently and the use of "subject" was deprecated in all active
1813 modules.
1815 o Bio::Structure added (since 0.9.1) for Protein structure objects
1816 and PDB parser to retrieve and write these structures from data files.
1818 o Several important Bio::DB::GFF bug fixes for handling features that
1819 are mapped to multiple reference points. Updated mysql adaptor
1820 so as to be able to store large (>100 megabase) chunks of DNA into
1821 Bio::DB::GFF databases.
1823 0.9.2 Developer's release
1825 o Bio::Search and Bio::SearchIO system introduced for event based
1826 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1827 in text and XML and FASTA reports in standard output format.
1829 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1830 generator is included in Bio::TreeIO::RandomTrees and a
1831 statistics module for evaluating.
1833 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1834 server for DAS servers.
1836 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1837 files. The entire BPlite system migrated to using Bio::Root::IO
1838 for the data stream.
1840 o Bio::Tools::Alignment for Consed and sequence Trimming
1841 functionality.
1843 o Bio::Structure for Protein structure information and parsing
1845 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1846 cgi-bin entry point which should be more reliable.
1848 o Bio::Map and Bio::MapIO for biological map navigation and a
1849 framework afor parsing them in. Only preliminary work here.
1851 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1852 Future work will integrate Pise and allow submission of analysis on
1853 remote servers.
1855 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1856 introduced as new objects for handling Sequence Annotation
1857 information (dblinks, references, etc) and is more robust that
1858 previous system.
1860 o Bio::Tools::FASTAParser introduced.
1862 o Scripts from the bioperl script submission project and new
1863 scripts from bioperl authors are included in "scripts" directory.
1865 o Factory objects and interfaces are being introduced and are more
1866 strictly enforced.
1868 o Bio::Root::Root introduced as the base object while
1869 Bio::Root::RootI is now simply an interface.
1871 o Bio::DB::RefSeq provides database access to copy of the NCBI
1872 RefSeq database using the EBI dbfetch script.
1874 0.9.0 Developer's release
1876 o perl version at least 5.005 is now required instead of perl 5.004
1878 o Bio::Tools::Run::RemoteBlast is available for running remote
1879 blast jobs at NCBI.
1881 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1883 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1884 Also added are related modules UTR3, UTR5, Exon, Intron,
1885 Promotor, PolyA and Transcript.
1887 o Speedup of translate method in PrimarySeq
1889 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1890 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1892 o Various fixes to Variation toolkit
1894 o Bio::DB::EMBL provides database access to EMBL sequence data.
1895 Bio::DB::Universal provides a central way to point to indexes
1896 and dbs in a single interface.
1898 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1900 o Bio::Factory::EMBOSS is still in design phase as is
1901 Bio::Factory::ApplicationFactoryI
1903 o Dia models for bioperl design are provided in the models/ directory
1905 0.7.2 Bug fix release
1907 o documentation fixes in many modules - SYNOPSIS code verified
1908 to be runnable in many (but not all modules)
1910 o corrected MANIFEST file from 0.7.1 release
1912 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1913 split locations
1915 o Bio::SeqIO::genbank
1916 * Correct parsing and writing of genbank format with protein data
1917 * moltype and molecule separation
1919 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1921 o Bio::SimpleAlign fixed to correctly handle consensus
1922 sequence calculation
1924 o Bio::Tools::HMMER supports hmmer 2.2g
1926 o Bio::Tools::BPlite to support report type specific parsing. Most
1927 major changes are not on the 0.7 branch.
1929 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1930 with File::Spec
1932 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1933 in several types of mutations:
1934 1.) AA level: deletion, complex
1935 2.) AA level: complex, inframe
1936 3.) RNA level: silent
1938 o BPbl2seq parsing of empty reports will not die, but will return
1939 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1940 $report->query() and $report->subject() methods. So an easy
1941 way to test if report was empty is to see if
1942 $report->query->seqname is undefined.
1944 0.7.1 Bug fix release
1946 o Better parsing of genbank/EMBL files especially fixing bugs
1947 related to Feature table parsing and locations on remote
1948 sequences. Additionally, species name parsing was better.
1950 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1951 which include a number of header lines.
1953 o More strict genbank and EMBL format writing (corrected number of
1954 spaces where appropriate).
1956 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1957 for related BPlite BUGS that are unresolved in this release.
1959 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1960 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1961 use expasy mirrors or EBI dbfetch cgi-script.
1963 o A moderate number of documentation improvements were made as
1964 well to provide a better code synopsis in each module.
1967 0.7 Large number of changes, including refactoring of the
1968 Object system, new parsers, new functionality and
1969 all round better system. Highlights are:
1972 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1973 Bio::Root::IO for I/O and file/handle capabilities.
1975 o Imported BPlite modules from Ian Korf for BLAST
1976 parsing. This is considered the supported BLAST parser;
1977 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1979 o Improved Sequence Feature model. Added complete location
1980 modelling (with fuzzy and compound locations). See
1981 Bio::LocationI and the modules under Bio/Location. Added
1982 support in Genbank/EMBL format parsing to completely parse
1983 feature tables for complex locations.
1985 o Moved special support for databanks etc to specialized modules under
1986 Bio/Seq/. One of these supports very large sequences through
1987 a temporary file as a backend.
1989 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1990 CDS retrieval and exon shuffling.
1992 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1994 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1995 DB/GDB (the latter has platform-specific limitations).
1997 o New analysis parser framework for HT sequence annotation (see
1998 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
2000 o New Alignment IO framework
2002 o New Index modules (Swissprot)
2004 o New modules for running Blast within perl
2005 (Bio::Tools::Run::StandAloneBlast). Added modules for running
2006 Multiple Sequence Alignment tools ClustalW and TCoffee
2007 (Bio::Tools::Run::Alignment).
2009 o New Cookbook-style tutorial (see bptutorial.pl). Improved
2010 documentation across the package.
2012 o Much improved cross platform support. Many known incompatibilities
2013 have been fixed; however, NT and Mac do not work across the entire
2014 setup (see PLATFORMS).
2016 o Many bug fixes, code restructuring, etc. Overall stability and
2017 maintainability benefit a lot.
2019 o A total of 957 automatic tests
2022 0.6.2
2024 There are very few functionality changes but a large
2025 number of software improvements/bug fixes across the package.
2027 o The EMBL/GenBank parsing are improved.
2029 o The Swissprot reading is improved. Swissprot writing
2030 is disabled as it doesn't work at all. This needs to
2031 wait for 0.7 release
2033 o BLAST reports with no hits are correctly parsed.
2035 o Several other bugs of the BLAST parser (regular expressions, ...)
2036 fixed.
2038 o Old syntax calls have been replaced with more modern syntax
2040 o Modules that did not work at all, in particular the Sim4
2041 set have been removed
2043 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
2044 have improved compliance with interface specs and documentation
2046 o Mailing list documentation updated throughout the distribution
2048 o Most minor bug fixes have happened.
2050 o The scripts in /examples now work and have the modern syntax
2051 rather than the deprecated syntax
2054 0.6.1 Sun April 2 2000
2056 o Sequences can have Sequence Features attached to them
2057 - The sequence features can be read from or written to
2058 EMBL and GenBank style flat files
2060 o Objects for Annotation, including References (but not
2061 full medline abstracts), Database links and Comments are
2062 provided
2064 o A Species object to represent nodes on a taxonomy tree
2065 is provided
2067 o The ability to parse HMMER and Sim4 output has been added
2069 o The Blast parsing has been improved, with better PSI-BLAST
2070 support and better overall behaviour.
2072 o Flat file indexed databases provide both random access
2073 and sequential access to their component sequences.
2075 o A CodonTable object has been written with all known
2076 CodonTables accessible.
2078 o A number of new lightweight analysis tools have been
2079 added, such as molecular weight determination.
2081 The 0.6 release also has improved software engineering
2083 o The sequence objects have been rewritten, providing more
2084 maintainable and easier to implement objects. These
2085 objects are backwardly compatible with the 0.05.1 objects
2087 o Many objects are defined in terms of interfaces and then
2088 a Perl implementation has been provided. The interfaces
2089 are found in the 'I' files (module names ending in 'I').
2091 This means that it is possible to wrap C/CORBA/SQL access
2092 as true "bioperl" objects, compatible with the rest of
2093 bioperl.
2095 o The SeqIO system has been overhauled to provide better
2096 processing and perl-like automatic interpretation of <>
2097 over arguments.
2099 o Many more tests have been added (a total of 172 automatic
2100 tests are now run before release).
2104 0.05.1 Tue Jun 29 05:30:44 1999
2105 - Central distribution now requires Perl 5.004. This was
2106 done to get around 5.003-based problems in Bio/Index/*
2107 and SimpleAlign.
2108 - Various bug fixes in the Bio::Tools::Blast modules
2109 including better exception handling and PSI-Blast
2110 support. See Bio/Tools/Blast/CHANGES for more.
2111 - Fixed the Parse mechanism in Seq.pm to use readseq.
2112 Follow the instructions in README for how to install
2113 it (basically, you have to edit Parse.pm).
2114 - Improved documentation of Seq.pm, indicating where
2115 objects are returned and where strings are returned.
2116 - Fixed uninitialized warnings in Bio::Root::Object.pm
2117 and Bio::Tools::SeqPattern.pm.
2118 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
2120 0.05 Sun Apr 25 01:14:11 1999
2121 - Bio::Tools::Blast modules have less memory problems
2122 and faster parsing. Webblast uses LWP and supports
2123 more functionality. See Bio/Tools/Blast/CHANGES for more.
2124 - The Bio::SeqIO system has been started, moving the
2125 sequence reformatting code out of the sequence object
2126 - The Bio::Index:: system has been started, providing
2127 generic index capabilities and specifically works for
2128 Fasta formatted databases and EMBL .dat formatted
2129 databases
2130 - The Bio::DB:: system started, providing access to
2131 databases, both via flat file + index (see above) and
2132 via http to NCBI
2133 - The scripts/ directory, where industrial strength scripts
2134 are put has been started.
2135 - Many changes - a better distribution all round.
2137 0.04.4 Wed Feb 17 02:20:13 1999
2138 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
2139 (see Bio::Tools::Blast::CHANGES).
2140 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
2141 - Beefed up the t/Fasta.t test script.
2142 - Small fix in Bio::Seq::type() (now always returns a string).
2143 - Changed Bio::Root::Utilities::get_newline_char() to
2144 get_newline() since it could return more than one char.
2145 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
2146 - Changed default timeout to 20 seconds (was 3).
2147 - Moved lengthy modification notes to the bottom of some files.
2148 - Fixed SimpleAlign write_fasta bug.
2149 - Beefed up SimpleAlign.t test
2151 0.04.3 Thu Feb 4 07:48:53 1999
2152 - Bio::Root::Object.pm and Global.pm now detect when
2153 script is run as a CGI and suppress output that is only
2154 appropriate when running interactively.
2155 - Bio::Root::Err::_set_context() adds name of script ($0).
2156 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
2157 regarding the use of the static objects via the qw(:obj) tag.
2158 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
2159 CORE::reverse, avoiding Perl warnings.
2160 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
2161 example scripts (see Bio::Tools::Blast::CHANGES).
2162 - examples/seq/seqtools.pl no longer always warns about using
2163 -prot or -nucl command-line arguments; only when using the
2164 -debug argument.
2165 - Methods added to Bio::Root::Utilities: create_filehandle(),
2166 get_newline_char(), and taste_file() to generalize filehandle
2167 creation and autodetect newline characters in files/streams
2168 (see bug report #19).
2169 - Bio::Root::IOManager::read() now handles timeouts and uses
2170 Utilities::create_filehandle().
2171 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
2172 of hardwiring in "\n".
2173 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
2175 0.04.2 Wed Dec 30 02:27:36 1998
2176 - Bug fixes in Bio::Tools::Blast modules, version 0.073
2177 (see Bio::Tools::Blast::CHANGES).
2178 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
2179 to CORE::reverse (prevents ambiguous warnings with 5.005).
2180 - Appending '.tmp.bioperl' to temporary files created by
2181 Bio::Root::Utilities::compress() or uncompress() to
2182 make it easy to identify & cleanup these files as needed.
2183 - Developers: Created CVS branch release-0-04-bug from
2184 release-0-04-1. Before making bug fixes to the 0.04.1 release,
2185 be sure to cvs checkout this branch into a clean area.
2187 0.04.1 Wed Dec 16 05:39:15 1998
2188 - Bug fixes in Bio::Tools::Blast modules, version 0.072
2189 (see Bio::Tools::Blast::CHANGES).
2190 - Compile/SW/Makefile.PL now removes *.o and *.a files
2191 with make clean.
2193 0.04 Tue Dec 8 07:49:19 1998
2194 - Lots of new modules added including:
2195 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
2196 and Bio/Compile directory containing XS-linked C code for
2197 creating Smith-Waterman sequence alignments from within Perl.
2198 * Steve Chervitz's Blast distribution has been incorporated.
2199 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
2200 - Bio/examples directory for demo scripts for all included modules.
2201 - Bio/t directory containing test suit for all included modules.
2202 - For changes specific to the Blast-related modules prior to
2203 incorporation in this central distribution, see the CHANGES
2204 file in the Bio/Tools/Blast directory.
2206 0.01 Tue Sep 8 14:23:22 1998
2207 - original version from central CVS tree; created by h2xs 1.18