| blob | 3a13c8c8f0ab3203b083533e75901a58ef94e8ae |
1 Summary of important user-visible changes for BioPerl
2 -----------------------------------------------------
4 {{$NEXT}}
6 * The following modules have been removed from the BioPerl
7 distribution to be part of a separate distribution with
8 independent development:
10 Bio::Symbol::*
12 * The deprecated() method has been deprecated. It is recommended
13 to use Carp::carp to warn.
16 1.7.4 2019-02-05 16:23:53+00:00 Europe/London
18 * Fix Bio::Root::Test, and the testuite, to properly check for
19 internet connection and the NO_NETWORK_TESTING environment
20 variable. Previously, tests that required internet connection
21 were not being skipped, causing tests to fail.
24 1.7.3 2019-01-30 13:30:34+00:00 Europe/London
26 * The following modules have been removed from the BioPerl
27 distribution to be part of a separate distribution. They have
28 been integrated into other module distributions for independent
29 development:
31 Bio::Align::Graphics
32 Bio::AlignIO::nexml
33 Bio::AlignIO::stockholm
34 Bio::Assembly::*
35 Bio::Cluster::*
36 Bio::ClusterI::*
37 Bio::ClusterIO::*
38 Bio::DB::Ace
39 Bio::DB::BioFetch
40 Bio::DB::CUTG
41 Bio::DB::EMBL
42 Bio::DB::EntrezGene
43 Bio::DB::Expression::*
44 Bio::DB::GFF
45 Bio::DB::GFF::Adaptor::*
46 Bio::DB::GFF::Aggregator::*
47 Bio::DB::GFF::Featname
48 Bio::DB::GFF::Feature
49 Bio::DB::GFF::Homol
50 Bio::DB::GFF::RelSegment
51 Bio::DB::GFF::Segment
52 Bio::DB::GFF::Typename
53 Bio::DB::GenBank
54 Bio::DB::GenPept
55 Bio::DB::HIV::*
56 Bio::DB::MeSH
57 Bio::DB::NCBIHelper
58 Bio::DB::Query::GenBank
59 Bio::DB::Query::HIVQuery
60 Bio::DB::RefSeq
61 Bio::DB::SeqFeature::*
62 Bio::DB::SeqVersion::*
63 Bio::DB::SwissProt
64 Bio::DB::TFBS::*
65 Bio::DB::Taxonomy::entrez
66 Bio::DB::Taxonomy::sqlite
67 Bio::DB::Universal
68 Bio::Draw::Pictogram
69 Bio::Factory::MapFactoryI
70 Bio::Index::Hmmer
71 Bio::Index::Stockholm
72 Bio::LiveSeq::*
73 Bio::Map::*
74 Bio::MapIO::*
75 Bio::MolEvol::CodonModel
76 Bio::Nexml::Factory
77 Bio::NexmlIO
78 Bio::Perl
79 Bio::Phenotype::*
80 Bio::PhyloNetwork::*
81 Bio::PopGen::*
82 Bio::Restriction::*
83 Bio::Root::Build
84 Bio::Search::HSP::HMMERHSP
85 Bio::Search::HSP::HmmpfamHSP
86 Bio::Search::Hit::HMMERHit
87 Bio::Search::Hit::HmmpfamHit
88 Bio::Search::Hit::hmmer3Hit
89 Bio::Search::Result::HMMERResult
90 Bio::Search::Result::HmmpfamResult
91 Bio::Search::Result::hmmer3Result
92 Bio::SearchDist
93 Bio::SearchIO::hmmer
94 Bio::SearchIO::hmmer2
95 Bio::SearchIO::hmmer3
96 Bio::SearchIO::hmmer_pull
97 Bio::SeqEvolution::*
98 Bio::SeqFeature::SiRNA::*
99 Bio::SeqIO::abi
100 Bio::SeqIO::agave
101 Bio::SeqIO::alf
102 Bio::SeqIO::chadoxml
103 Bio::SeqIO::chaos
104 Bio::SeqIO::chaosxml
105 Bio::SeqIO::ctf
106 Bio::SeqIO::entrezgene
107 Bio::SeqIO::excel
108 Bio::SeqIO::exp
109 Bio::SeqIO::flybase_chadoxml
110 Bio::SeqIO::lasergene
111 Bio::SeqIO::nexml
112 Bio::SeqIO::pln
113 Bio::SeqIO::strider
114 Bio::SeqIO::ztr
115 Bio::Structure::*
116 Bio::Taxonomy::*
117 Bio::Tools::AlignFactory
118 Bio::Tools::Analysis::* (except SimpleAnalysisBase)
119 Bio::Tools::Gel
120 Bio::Tools::HMMER::*
121 Bio::Tools::Hmmpfam
122 Bio::Tools::Phylo::Gumby
123 Bio::Tools::Protparam
124 Bio::Tools::Run::RemoteBlast
125 Bio::Tools::SiRNA::*
126 Bio::Tools::dpAlign
127 Bio::Tools::pSW
128 Bio::Tree::AlleleNode
129 Bio::Tree::Draw::Cladogram
130 Bio::TreeIO::nexml
131 Bio::TreeIO::svggraph
132 Bio::Variation::*
134 * The following modules are new in the BioPerl distribution. They
135 have been previously released in the BioPerl-Run distribution.
136 This will enable smaller distributions that provide a
137 Bio::Tool::Run interface, to be only dependent on the BioPerl
138 distribution instead of the whole (very large) BioPerl-Run:
140 Bio::Tools::Run::Analysis
141 Bio::Tools::Run::AnalysisFactory
142 Bio::Tools::Run::Phylo::PhyloBase
143 Bio::Tools::Run::WrapperBase
144 Bio::Tools::Run::WrapperBase::CommandExts
146 * The following programs have been removed:
148 bp_biofetch_genbank_proxy
149 bp_blast2tree
150 bp_bulk_load_gff
151 bp_composite_LD
152 bp_das_server
153 bp_download_query_genbank
154 bp_fast_load_gff
155 bp_flanks
156 bp_genbank2gff
157 bp_generate_histogram
158 bp_heterogeneity_test
159 bp_hivq
160 bp_hmmer_to_table
161 bp_load_gff
162 bp_meta_gff
163 bp_netinstall
164 bp_parse_hmmsearch
165 bp_process_wormbase
166 bp_query_entrez_taxa
167 bp_remote_blast
168 bp_seqfeature_delete
169 bp_seqfeature_gff3
170 bp_seqfeature_load
172 * Because of the move of so many modules and programs into
173 separate distributions, the following modules are no longer
174 prerequisites:
176 Ace
177 Ace::Sequence::Homol
178 Algorithm::Munkres
179 Apache::DBI
180 Archive::Tar
181 Array::Compare
182 Bio::ASN1::EntrezGene
183 Bio::Expression::Contact
184 Bio::Expression::DataSet
185 Bio::Expression::Platform
186 Bio::Expression::Sample
187 Bio::Ext::Align
188 Bio::GMOD::CMap::Utils
189 Bio::Phylo::Factory
190 Bio::Phylo::Forest::Tree
191 Bio::Phylo::IO
192 Bio::Phylo::Matrices
193 Bio::Phylo::Matrices::Datum
194 Bio::Phylo::Matrices::Matrix
195 Bio::SeqFeature::Annotated
196 Bio::SeqIO::staden::read
197 Bio::Tools::Run::Alignment::Clustalw
198 Bio::Tools::Run::Ensembl
199 Bio::Tools::Run::Phylo::Molphy::ProtML
200 Bio::Tools::Run::Phylo::Phylip::Neighbor
201 Bio::Tools::Run::Phylo::Phylip::ProtDist
202 Bio::Tools::Run::Phylo::Phylip::ProtPars
203 Bio::Tools::Run::Samtools
204 CGI
205 CPAN
206 Cache::FileCache
207 Config
208 Convert::Binary::C
209 DBD::Pg
210 DBD::SQLite
211 Data::Stag::XMLWriter
212 Encode
213 English
214 ExtUtils::Install
215 ExtUtils::Manifest
216 File::Glob
217 GD::Simple
218 Getopt::Std
219 Graph::Undirected
220 GraphViz
221 HTML::HeadParser
222 HTML::TableExtract
223 LWP
224 LWP::Simple
225 MIME::Base64
226 Memoize
227 PostScript::TextBlock
228 SVG
229 SVG::Graph
230 SVG::Graph::Data
231 SVG::Graph::Data::Node
232 SVG::Graph::Data::Tree
233 Sort::Naturally
234 Spreadsheet::ParseExcel
235 Term::ReadLine
236 Text::NSP::Measures::2D::Fisher2::twotailed
237 Text::ParseWords
238 Time::Local
239 Tree::DAG_Node
240 URI::Escape
241 WWW::Mechanize
242 XML::Simple
244 * The following is a new prerequisite:
246 Test::RequiresInternet
248 * The deobfuscator has been removed.
250 * The emacs bioperl minor mode is no longer distributed as part of the
251 perl module distributions. See
252 https://github.com/bioperl/emacs-bioperl-mode
255 1.7.2 - "Entebbe"
257 [Bugs]
259 * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
260 * #245 - Code coverage fixes [zmughal,cjfields]
261 * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
262 * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
263 * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
264 * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
265 * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
266 * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
267 * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
268 * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
269 * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
270 * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
272 [Code changes]
274 * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
276 1.7.1 - "Election"
278 [Bugs]
280 * Minor release to incorporate fix for CPAN indexing, which
281 prevented proper updates [cjfields]
282 * Fix problem in managing Target attribute for gff3 [Jukes34]
283 * Minor bug fixes related to NCBI HTTPS support [cjfields]
285 1.7.0 - "Disney"
287 [New site]
289 * We have migrated to Github Pages. This was actually planned, but the
290 recent OBF server compromise forced our hand.
292 Brian Osborne [bosborne] took this under his wing to move docs and has
293 done a tremendous amount of work formatting the site and working out some
294 of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
295 Cantalupo and Franscison Ossandon also helped. Kudos!!
297 * Similarly, the official issue tracker is now Github Issues. This has
298 been updated in the relevant documentation bits (we hope!)
300 [Code changes]
302 * Previously deprecated modules removed
303 * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
304 * Bio::DB::SeqHound has been removed due to the service no longer being
305 available
306 * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
307 reasons due to the server no longer having a valid cert
308 * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
309 * Bio::Coordinate, Bio::SearchIO::blastxml,
310 Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
311 added on CPAN
313 [New features]
315 * Docker instances of tagged releases are available! [hlapp]
316 * NCBI HTTPS support [mjohnson and others]
317 * Bio::SearchIO::infernal
318 - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
319 * Bio::Search::HSP::ModelHSP
320 - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
321 reports [pcantalupo]
322 * Bio::Search::Result::INFERNALResult
323 - Added new module to represent features of Infernal reports [pcantalupo]
324 * Bio::DB::Taxonomy SQLite option [cjfields]
325 * WrapperBase quoted option values [majensen]
326 * Various documentation fixes and updates [bosborne]
328 [Bug Fixes]
330 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
331 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
332 * NeXML parser fixes [fjossandon]
333 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
334 * RT 103272 : SeqFeature database deletion skipped features with a decimal -
335 Joshua Fortriede (Xenbase)
336 * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
337 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
338 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
339 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
340 * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
341 * Issue #84: EMBL format wrapping problem [nyamned]
342 * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
343 * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
344 or compiled C code (when Inline::C is installed) [rocky]
345 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
346 * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
347 * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
348 * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
349 to be consistent with "$hit->bits" behaviour [fjossandon]
350 * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
351 aminoacids made "next_seq" confused and broke the parser [fjossandon]
352 * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
353 Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
354 to "complement(join(A..B,C..D))" [fjossandon]
355 * For the many many many fixes that weren't mentioned - blame the release guy!
357 1.6.924
359 [Significant changes]
361 * Bug/feature issue tracking has moved to GitHub Issues:
362 https://github.com/bioperl/bioperl-live/issues
363 * DB_File has been demoted from "required" to "recommended",
364 which should make easier for Windows users to install BioPerl
365 if they don't need that module.
367 [New features]
369 * Bio::Search::HSP::GenericHSP
370 - Bug #3370, added a "posterior_string" method to retrieve the
371 posterior probability lines (PP) from HMMER3 reports [fjossandon]
372 - Added a "consensus_string" method to retrieve the consensus
373 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
374 * Bio::SearchIO::hmmer2
375 - The number of identical and conserved residues are now calculated
376 directly from the homology line [fjossandon]
377 - Now the Query Length and Hit Length are reported when the alignment
378 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
379 - Implemented the capture of the consensus structure lines [fjossandon]
380 * Bio::SearchIO::hmmer3
381 - The number of identical and conserved residues are now calculated
382 directly from the homology line [fjossandon]
383 - Now the Hit Length is reported when the alignment runs until the end
384 of the sequence/model ('.]' or '[]') [fjossandon]
385 - Implemented the capture of the consensus structure lines [fjossandon]
386 - Implemented the capture of the posterior probability lines [fjossandon]
387 - Completed the development of NHMMER parsing, including alignments [fjossandon]
388 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
389 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
390 "min_score", "min_bits, and "hit_filter" methods from
391 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
392 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
393 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
394 besides Blast, instead of being ignored. Added tests for all moved methods
395 using HMMER outputs and run the full test suite and everything pass [fjossandon]
396 * Bio::SeqIO::MultiFile
397 - Autodetection of file format [fangly]
398 * Bio::Tools::GuessSeqFormat:
399 - Format detection from non-seekable filehandles such as STDIN [fangly]
401 [Bug fixes]
403 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
404 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
405 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
406 * Abstract: Fixed ActivePerl incapability of removing temporary files
407 because of problems closing tied filehandles [fjossandon]
408 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
409 because ActivePerl were producing a ".index.pag" and ".index.dir"
410 files instead of a single ".index" file (like Strawberry Perl).
411 Now those temporary files are correctly considered and deleted. [fjossandon]
412 * Test files: Added missing module requirements (DB_File and Data::Stag)
413 to several tests files that were failing because those modules were
414 not present. Now those test files are correctly skipped instead. [fjossandon]
415 * Blast: Added support to changes in bl2seq from BLAST+ output, which
416 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
417 * Phylip: Return undef in "next_aln" at file end to avoid
418 an infinite loop [yschensandiego]
419 * HMMER3: When a hit description is too long, it is truncated in
420 the Scores table. In those cases, the more complete description from
421 the Annotation line (>>) will be used [fjossandon]
422 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
423 since it is now used by HMMER3 format in alignments [fjossandon]
424 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
425 to return undef if the query/hit length is unknown (like in some
426 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
427 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
428 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
429 added support to multi-query reports, reduced code redundancy,
430 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
431 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
432 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
433 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
434 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
435 * Double-quotes on paths are needed in some places [fjossandon]
436 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
437 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
438 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
439 with the latest changes made in their own repositories [fjossandon]
440 * General synching of files with the master branch [fjossandon]
441 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
442 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
443 * Fixed broken MeSH parser [fjossandon]
444 * Fixed missing detection of format in SeqIO when given a -string [fangly]
446 1.6.923
448 * Major Windows support updates! [fjossandon]
449 * MAKER update to allow for stricter standard codon table [cjfields]
450 * Better support for circular sequences [fjossandon]
451 * Fixes for some complex location types [fjossandon]
452 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
453 * Fix bug #2978 related to BLAST report type [fjossandon]
454 * Deobfuscator fixes [DaveMessina]
456 1.6.922
458 * Address CPAN test failures [cjfields]
459 * Add BIOPROJECT support for Genbank files [hyphaltip]
460 * Better regex support for HMMER3 output [bosborne]
462 1.6.921
464 * Minor update to address CPAN test failures
466 1.6.920
468 * Remove Bio::Biblio and related files [carandraug]
469 - this cause version clashes with an independently-released
470 version of Bio::Biblio
472 1.6.910
474 [New features]
476 * Hash randomization fixes for perl 5.18.x
477 - Note: at least one module (Bio::Map::Physical) still has a failing test;
478 this is documented in bug #3446 and has been TODO'd; we will be pulling
479 Bio::Map and similar modules out of core into separate distributions in the
480 1.7.x release series [cjfields]
482 [New features]
484 * Bio::Seq::SimulatedRead
485 - New module to represent reads taken from other sequences [fangly]
486 * Bio::Root::Root
487 - Support of Clone::Fast as a faster cloning alternative [fangly]
488 * Bio::Root::IO
489 - Moved the format() and variant() methods from Bio::*IO modules to
490 Bio::Root::IO [fangly]
491 - Can now use format() to get the type of IO format in use [fangly]
492 * Bio::Tools::IUPAC
493 - New regexp() method to create regular expressions from IUPAC sequences
494 [fangly]
495 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
496 - Code refresh [fangly]
497 * Bio::DB::Taxonomy
498 - Added support for the Greengenes and Silva taxonomies [fangly]
499 * Bio::Tree::TreeFunctionsI
500 - get_lineage_string() represents a lineage as a string [fangly]
501 - add_trait() returns instead of reporting an error when the column
502 number is exceeded in add_trait() [fangly]
503 - Option to support tree leaves without trait [fangly]
504 - Allow ID of 0 in trait files [fangly]
505 * Bio::DB::Taxonomy::list
506 - Misc optimizations [fangly]
507 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
508 * Bio::DB::Taxonomy::*
509 - get_num_taxa() returns the number of taxa in the database [fangly]
510 * Bio::DB::Fasta and Bio::DB::Qual
511 - support indexing an arbitrary list of files [fangly]
512 - user can supply an arbitrary index file name [fangly]
513 - new option to remove index file at the end [fangly]
514 * Bio::DB::Fasta
515 - now handles IUPAC degenerate residues [fangly]
516 * Bio::PrimarySeq and Bio::PrimarySeqI
517 - speed improvements for large sequences [Ben Woodcroft, fangly]
518 * Bio::PrimaryQual
519 - tightened and optimized quality string validation [fangly]
520 * Bio::SeqIO::fasta
521 - new method and option 'block', to create FASTA output with space
522 intervaled blocks (similar to genbank or EMBL) has been implemented.
523 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
524 in favour of the methods 'width' and 'preferred_id_type` respectively.
525 * Bio::FeatureIO::*
526 - moved from bioperl-live into the separate distribution Bio-FeatureIO
527 * Bio::SeqFeature::Annotated
528 - moved from bioperl-live into the separate distribution Bio-FeatureIO
529 * Bio::Cluster::SequenceFamily
530 - improved performance when using get_members with overlapping multiple
531 criteria
532 * Bio::SearchIO::hmmer3
533 - now supports nhmmer [bosborne]
535 [Bug fixes]
537 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
538 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
539 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
540 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
541 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
542 information was lost in a multi-result blast file [Paul Cantalupo]
543 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
544 total gaps [Paul Cantalupo]
545 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
546 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
547 when end of domain indicator is split across lines [Paul Cantalupo]
548 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
549 cjfields]
550 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
551 instances where blank lines are within sequences [cjfields]
552 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
553 types [fangly]
554 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
555 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
556 cjfields]
557 * Various fixes for Stockholm file indexing and processing [bosborne]
558 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
559 breaks parsing [cjfields]
560 * Fix case where Bio::Seq::Meta* objects with no meta information could not
561 be reverse-complemented [fangly]
562 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
563 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
564 when unsure that values will be numerical [fangly]
565 * Fix undef warnings in Bio::SeqIO::embl [fangly]
566 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
567 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
568 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
569 Sallou]
570 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
571 source_tag and display_name must return a string, not undef [fangly]
572 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
573 add_SeqFeature takes a single argument [fangly]
574 * Use cross-platform filenames and temporary directory in
575 Bio::DB::Taxonomy::flatfile [fangly]
576 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
577 properly identified as existing taxa in the database [fangly]
578 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
579 without also passing a lineage to store [fangly]
580 * Prevent passing a directory to the gi2taxid option (-g) of
581 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
582 [fangly]
583 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
584 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
585 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
586 object before trying to access, and no longer returns repeated sequences.
589 1.6.901 May 18, 2011
591 [Notes]
593 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
594 modules using Ace will also be deprecated [lds, cjfields]
595 * Minor bug fix release
596 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
597 * Address Build.PL issues when DBI is not present [hartzell]
598 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
599 * Remove deprecated code for perl 5.14.0 compat [cjfields]
600 * Due to schema changes and lack of support for older versions, support
601 for NeXML 0.9 is only (very) partially implemented.
602 See: https://redmine.open-bio.org/issues/3207
604 [Bug fixes]
606 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
607 docs [genehack, cjfields]
608 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
609 module version from dist_version (probably not the best way to do this,
610 but it seems to work) [rbuels, cjfields]
613 1.6.900 April 14, 201
615 [Notes]
617 * This will probably be the last release to add significant features to
618 core modules; subsequent releases will be for bug fixes alone.
619 We are planning on a restructuring of core for summer 2011, potentially
620 as part of the Google Summer of Code. This may become BioPerl 2.0.
621 * Version bump represents 'just prior to v 1.7'. We may have point
622 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
623 This code essentially is what is on the github master branch.
625 [New features]
627 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
628 * Bio::Tree refactor
629 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
630 - removal of Scalar::Util::weaken code, which was causing odd headaches
631 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
632 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
633 many others]
634 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
635 [Warren Kretzschmar]
636 * Bio::SeqIO::gbxml
637 - bug 2515 - new contribution [Ryan Golhar, jhannah]
638 * Bio::Assembly::IO
639 - support for reading Maq, Sam and Bowtie files [maj]
640 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
641 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
642 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
643 - bug 2726: reading/writing granularity: whole scaffold or one contig
644 at a time [Joshua Udall, fangly]
645 * Bio::OntologyIO
646 - Added parsing of xrefs to OBO files, which are stored as secondary
647 dbxrefs of the cvterm [Naama Menda]
648 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
649 * PAML code updated to work with PAML 4.4d [DaveMessina]
651 [Bug fixes]
653 * [3198] - sort tabular BLAST hits by score [DaveMessina]
654 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
655 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
656 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
657 [cjfields]
658 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
659 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
660 * [3164] - TreeFunctionsI syntax bug [gjuggler]
661 * [3163] - AssemblyIO speedup [fangly]
662 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
663 hyphaltip]
664 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
665 * [3158] - fix EMBL file mis-parsing [cjfields]
666 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
667 cjfields]
668 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
669 * [3148] - URL change for UniProt [cjfields]
670 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
671 * [3136] - HMMer3 parser fixes [kblin]
672 * [3126] - catch description [Toshihiko Akiba]
673 * [3122] - Catch instances where non-seekable filehandles were being
674 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
675 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
676 [dukeleto, rbuels, cjfields]
677 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
678 jhannah]
679 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
680 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
681 cjfields]
682 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
683 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
684 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
685 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
686 * [3086] - EMBL misparsing long tags [kblin, cjfields]
687 * [3085] - CommandExts and array of files [maj, hyphaltip]
688 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
689 for alignment slices [Ha X. Dang, cjfields]
690 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
691 * [3073] - fix parsing of GenBank files from RDP [cjfields]
692 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
693 * [3064] - All-gap midline BLAST report issues [cjfields]
694 * [3063] - BLASt report RID [Razi Khaja, cjfields]
695 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
696 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
697 * [3039] - correct Newick output root node branch length [gjuggler,
698 DaveMessina]
699 * [3038] - SELEX alignment error [Bernd, cjfields]
700 * [3033] - PrimarySeq ID setting [Bernd, maj]
701 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
702 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
703 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
704 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
705 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
706 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
707 PAML 4.4d [DaveMessina]
708 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
709 DaveMessina]
710 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
711 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
712 * [3017] - using threads with Bio::DB::GenBank [cjfields]
713 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
714 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
715 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
716 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
717 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
718 cjfields]
719 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
720 * [2977] - TreeIO issues [DaveMessina]
721 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
722 * [2944] - Bio::Tools::GFF score [cjfields]
723 * [2942] - correct MapTiling output [maj]
724 * [2939] - PDB residue insertion codes [John May, maj]
725 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
726 * [2928] - GuessSeqFormat raw [maj]
727 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
728 * [2922] - open() directive issue [cjfields]
729 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
730 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
731 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
732 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
733 cjfields]
734 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
735 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
736 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
737 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
738 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
739 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
740 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
741 * [2758] - Bio::AssemblyIO ace problems [fangly]
742 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
743 * [2726] - ace file IO [Josh, fangly]
744 * [2700] - Refactor Build.PL [cjfields]
745 * [2673] - addition of simple Root-based clone() method [cjfields]
746 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
747 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
748 * [2594] - Bio::Species memory leak [cjfields]
749 * [2515] - GenBank XML parser [jhannah]
750 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
751 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
752 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
753 cjfields]
754 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
756 [Deprecated]
758 * Bio::Expression modules - these were originally designed to go with the
759 bioperl-microarray suite of tools, however they have never been completed
760 and so have been removed from the distribution. The original code has
761 been moved into the inactive bioperl-microarray suite. [cjfields]
763 [Other]
765 * Repository moved from Subversion (SVN) to
766 http://github.com/bioperl/bioperl-live [cjfields]
767 * Bug database has moved to Redmine (https://redmine.open-bio.org)
768 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
769 Thieme have been moved to their own distribution (Bio-Microarray).
770 [cjfields]
772 1.6.1 Sept. 29, 2009 (point release)
773 * No change from last alpha except VERSION and doc updates [cjfields]
775 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
776 * Fix for silent OBDA bug related to FASTA validation [cjfields]
778 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
779 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
780 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
781 [cjfields]
782 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
784 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
785 * WinXP test fixes [cjfields, maj]
786 * BioPerl.pod added for descriptive information, fixes CPAN indexing
787 [cjfields]
788 * Minor doc fixes [cjfields]
790 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
791 * Fix tests failing due to merging issues [cjfields]
792 * More documentation updates for POD parsing [cjfields]
794 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
795 * Bio::Root::Build
796 - fix YAML meta data generation [cjfields]
798 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
799 * Bio::Align::DNAStatistics
800 - fix divide by zero problem [jason]
801 * Bio::AlignIO::*
802 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
803 * Bio::AlignIO::stockholm
804 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
805 * Bio::Assembly::Tools::ContigSpectrum
806 - function to score contig spectrum [fangly]
807 * Bio::DB::EUtilities
808 - small updates [cjfields]
809 * Bio::DB::Fasta
810 - berkeleydb database now autoindexes wig files and locks correctly
811 [lstein]
812 * Bio::DB::HIV
813 - various small updates for stability; tracking changes to LANL
814 database interface [maj]
815 * Bio::DB::SeqFeature (lots of updates and changes)
816 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
817 - bug 2835 - patch [Dan Bolser]
818 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
819 * Bio::DB::SwissProt
820 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
821 * Bio::Factory::FTLocationFactory
822 - mailing list bug fix [cjfields]
823 * Bio::LocatableSeq
824 - performance work on column_from_residue_number [hartzell]
825 * Bio::Matrix::IO::phylip
826 - bug 2800 - patch to fix phylip parsing [Wei Zou]
827 * Bio::Nexml
828 - Google Summer of Code project from Chase Miller - parsers for Nexml
829 file format [maj, chmille4]
830 * Bio::PopGen
831 - Make Individual, Population, Marker objects AnnotatableI [maj]
832 - simplify LD code [jason]
833 * Bio::RangeI
834 - deal with empty intersection [jason]
835 * Bio::Restriction
836 - significant overhaul of Bio::Restriction system: complete support for
837 external and non-palindromic cutters. [maj]
838 * Bio::Root::Build
839 - CPANPLUS support, no automatic installation [sendu]
840 * Bio::Root::IO
841 - allow IO::String (regression fix) [cjfields]
842 - catch unintentional undef values [cjfields]
843 - throw if non-fh is passed to -fh [maj]
844 * Bio::Root::Root/RootI
845 - small debugging and core fixes [cjfields]
846 * Bio::Root::Test
847 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
848 * Bio::Root::Utilities
849 - bug 2737 - better warnings [cjfields]
850 * Bio::Search
851 - tiling completely refactored, HOWTO added [maj]
852 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
853 will deprecate usage of the older tiling code in the next BioPerl
854 release
855 - small fixes [cjfields]
856 * Bio::SearchIO
857 - Infernal 1.0 output now parsed [cjfields]
858 - new parser for gmap -f9 output [hartzell]
859 - bug 2852 - fix infinite loop in some output [cjfields]
860 - blastxml output now passes all TODO tests [cjfields]
861 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
862 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
863 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
864 * Bio::Seq::LargePrimarySeq
865 - delete tempdirs [cjfields]
866 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
867 * Bio::Seq::Quality
868 - extract regions based on quality threshold value [Dan Bolser, heikki]
869 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
870 * Bio::SeqFeature::Lite
871 - various Bio::DB::SeqFeature-related fixes [lstein]
872 * Bio::SeqFeature::Tools::TypeMapper
873 - additional terms for GenBank to SO map [scain]
874 * Bio::SeqIO::chadoxml
875 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
876 * Bio::SeqIO::embl
877 - support for CDS records [dave_messina, Sylvia]
878 * Bio::SeqIO::fastq
879 - complete refactoring to handle all FASTQ variants, perform validation,
880 write output. API now conforms with other Bio* parsers and the rest of
881 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
882 [cjfields]
883 * Bio::SeqIO::genbank
884 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
885 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
886 * Bio::SeqIO::largefasta
887 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
888 * Bio::SeqIO::raw
889 - add option for 'single' and 'multiple'
890 * Bio::SeqIO::scf
891 - bug 2881 - fix scf round-tripping [Adam Søgren]
892 * Bio::SeqUtils
893 - bug 2766, 2810 - copy over tags from features, doc fixes [David
894 Jackson]
895 * Bio::SimpleAlign
896 - bug 2793 - patch for add_seq index issue [jhannah, maj]
897 - bug 2801 - throw if args are required [cjfields]
898 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
899 [Tristan Lefebure, maj]
900 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
901 - fix POD and add get_SeqFeatures filter [maj]
902 * Bio::Tools::dpAlign
903 - add support for LocatableSeq [ymc]
904 - to be moved to a separate distribution [cjfields, rbuels]
905 * Bio::Tools::EUtilities
906 - fix for two bugs from mail list [Adam Whitney, cjfields]
907 - add generic ItemContainerI interface for containing same methods
908 [cjfields]
909 * Bio::Tools::HMM
910 - fix up code, add more warnings [cjfields]
911 - to be moved to a separate distribution [cjfields, rbuels]
912 * Bio::Tools::Primer3
913 - bug 2862 - fenceposting issue fixed [maj]
914 * Bio::Tools::Run::RemoteBlast
915 - tests for remote RPS-BLAST [mcook]
916 * Bio::Tools::SeqPattern
917 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
918 * Bio::Tools::tRNAscanSE
919 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
920 * Bio::Tree::*
921 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
922 * Bio::Tree::Statistics
923 - several methods for calculating Fitch-based score, internal trait
924 values, statratio(), sum of leaf distances [heikki]
925 * Bio::Tree::Tree
926 - bug 2869 - add docs indicating edge case where nodes can be
927 prematurely garbage-collected [cjfields]
928 - add as_text() function to create Tree as a string in specified format
929 [maj]
930 * Bio::Tree::TreeFunctionsI
931 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
932 Lefebure, maj]
933 * Bio::TreeIO::newick
934 - fix small semicolon issue [cjfields]
935 * scripts
936 - update to bp_seqfeature_load for SQLite [lstein]
937 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
938 - fastam9_to_table - fix for MPI output [jason]
939 - gccalc - total stats [jason]
940 * General Stuff
941 - POD cleanup re: FEEDBACK section [maj, cjfields]
942 - cleanup or fix dead links [cjfields]
943 - Use of no_* methods (indicating 'number of something') is deprecated
944 in favor of num_* [cjfields]
945 - lots of new tests for the above bugs and refactors [everyone!]
946 - new template for Komodo text editor [cjfields]
948 1.6.0 Winter 2009
949 * Feature/Annotation rollback
950 - Problematic changes introduced prior to the 1.5 release have been
951 rolled back. These changes led to subtle bugs involving operator
952 overloading and interface methods.
953 - Behavior is very similar to that for BioPerl 1.4, with tag values
954 being stored generically as simple scalars. Results in a modest
955 speedup.
956 * Bio::Graphics
957 - Split into a separate distribution on CPAN, primarily so development
958 isn't reliant on a complete BioPerl release.
959 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
960 is only available via Subversion (via bioperl-live main trunk)
961 * Bio::Root::Test
962 - Common test bed for all BioPerl modules
963 * Bio::Root::Build
964 - Common Module::Build-based subclass for all BioPerl modules
965 * Bio::DB::EUtilities
966 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
967 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
968 and user agent request posting and retrieval
969 * Test implementation and reorganization
970 - Tests have been reorganized into groups based on classes or use
971 cases.
972 - Automated test coverage is now online:
973 http://www.bioperl.org/wiki/Test_Coverage
974 - After this release, untested modules will be moved into a
975 separate developer distribution until tests can be derived.
976 Also, new modules to be added are expected to have a test suite
977 and adequate test coverage.
979 1.5.2 Developer release
981 Full details of changes since 1.5.1 are available online at:
982 http://www.bioperl.org/wiki/Change_log
983 The following represents a brief overview of the most important changes.
985 o Bio::Map
986 - Overhaul. Brand new system fully allows markers to have multiple
987 positions on multiple maps, and to have relative positions. Should be
988 backward compatible.
990 o Bio::Taxonomy
991 - This module and all the modules in the Taxonomy directory now
992 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
994 o Bio::DB::Taxonomy
996 - Taxonomy.pm
997 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
999 * New methods ancestor(), each_Descendent() and _handle_internal_id().
1001 * Allows for different database modules to create Bio::Taxon objects
1002 with the same internal id when the same taxon is requested from each.
1004 - flatfile.pm
1005 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
1007 * No longer includes the fake root node 'root'; there are multiple roots
1008 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
1010 - entrez.pm
1011 * get_node() has new option -full
1013 * Caches data retrieved from website
1015 o Bio::Species
1016 - Now a Bio::Taxon. Carries out the species name -> specific name munging
1017 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
1018 backward compatability in species() method.
1020 o Bio::Search and Bio::SearchIO
1021 - Overhaul. The existing system has been sped up via some minor changes
1022 (mostly gain-of-function to the API). Bio::PullParserI is introduced
1023 as a potential eventual replacment for the existing system, though as
1024 yet only a Hmmpfam parser exists written using it.
1027 1.5.1 Developer release
1029 o Major problem with how Annotations were written out with
1030 Bio::Seq is fixed by reverting to old behavior for
1031 Bio::Annotation objects.
1033 o Bio::SeqIO
1035 - genbank.pm
1036 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
1037 expect at l east 9 spaces at the beginning of a line to
1038 indicate line wrapping.
1040 * Treat multi-line SOURCE sections correctly, this defect broke
1041 both common_name() and classification()
1043 * parse swissprot fields in genpept file
1045 * parse WGS genbank records
1047 - embl.pm
1048 * Changed regexp for ID line. The capturing parentheses are
1049 the same, the difference is an optional repeated-not-semi-
1050 colon expression following the captured \S+. This means the
1051 regexp works when the division looks like /PRO;/ or when the
1052 division looks like /ANG ;/ - the latter is from EMBL
1053 repbase
1055 * fix ID line parsing: the molecule string can have spaces in
1056 it. Like: "genomic DNA"
1058 - swiss.pm: bugs #1727, #1734
1060 - entrezgene.pm
1061 * Added parser for entrezgene ASN1 (text format) files.
1062 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
1064 o Bio::AlignIO
1066 - maf.pm coordinate problem fixed
1068 o Bio::Taxonomy and Bio::DB::Taxonomy
1070 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
1071 can be done via Web without downloading all the sequence.
1073 o Bio::Tools::Run::RemoteBlast supports more options and complies
1074 to changes to the NCBI interface. It is reccomended that you
1075 retrieve the data in XML instead of plain-text BLAST report to
1076 insure proper parsing and retrieval of all information as NCBI
1077 fully expects to change things in the future.
1079 o Bio::Tree and Bio::TreeIO
1081 - Fixes so that re-rooting a tree works properly
1083 - Writing out nhx format from a newick/nexus file will properly output
1084 bootstrap information. The use must move the internal node labels over
1085 to bootstraps.
1086 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
1087 $node->bootstrap($node->id);
1088 $node->id('');
1089 }
1090 - Nexus parsing is much more flexible now, does not care about
1091 LF.
1093 - Cladogram drawing module in Bio::Tree::Draw
1095 - Node height and depth now properly calculated
1097 - fix tree pruning algorithm so that node with 1 child gets merged
1099 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
1100 bugs and improvements were added, see Gbrowse mailing list for most of
1101 these.
1103 o Bio::DB::GFF partially supports GFF3. See information about
1104 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
1106 o Better location parsing in Bio::Factory::FTLocationFactory -
1107 this is part of the engine for parsing EMBL/GenBank feature table
1108 locations. Nested join/order-by/complement are allowed now
1110 o Bio::PrimarySeqI->translate now takes named parameters
1112 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
1113 reconstruction) is now supported. Parsing different models and
1114 branch specific parametes are now supported.
1116 o Bio::Factory::FTLocationFactory - parse hierarchical locations
1117 (joins of joins)
1119 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
1120 for getter/setter functions
1122 o Bio::SearchIO
1124 - blast bug #1739; match scientific notation in score
1125 and possible e+ values
1127 - blast.pm reads more WU-BLAST parameters and parameters, match
1128 a full database pathname,
1130 - Handle NCBI WEB and newer BLAST formats specifically
1131 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
1133 - psl off-by-one error fixed
1135 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
1136 and HSPs can be constructed from them.
1138 - HSPs query/hit now have a seqdesc field filled out (this was
1139 always available via $hit->description and
1140 $result->query_description
1142 - hmmer.pm can parse -A0 hmmpfam files
1144 - Writer::GbrowseGFF more customizeable.
1146 o Bio::Tools::Hmmpfam
1147 make e-value default score displayed in gff, rather than raw score
1148 allow parse of multiple records
1151 1.5 Developer release
1153 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
1154 provide Jukes-Cantor and Kimura pairwise distance methods,
1155 respectively.
1157 o Bio::AlignIO support for "po" format of POA, and "maf";
1158 Bio::AlignIO::largemultifasta is a new alternative to
1159 Bio::AlignIO::fasta for temporary file-based manipulation of
1160 particularly large multiple sequence alignments.
1162 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
1163 be treated similarly as an assembled contig.
1165 o Bio::CodonUsage provides new rare_codon() and probable_codons()
1166 methods for identifying particular codons that encode a given
1167 amino acid.
1169 o Bio::Coordinate::Utils provides new from_align() method to build
1170 a Bio::Coordinate pair directly from a
1171 Bio::Align::AlignI-conforming object.
1173 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
1174 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
1175 web service using standard Pubmed query syntax, and retrieve
1176 results as XML.
1178 o Bio::DB::GFF has various sundry bug fixes.
1180 o Bio::FeatureIO is a new SeqIO-style subsystem for
1181 writing/reading genomic features to/from files. I/O classes
1182 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
1183 classes only read/write Bio::SeqFeature::Annotated objects.
1184 Notably, the GFF v3 class requires features to be typed into the
1185 Sequence Ontology.
1187 o Bio::Graph namespace contains new modules for manipulation and
1188 analysis of protein interaction graphs.
1190 o Bio::Graphics has many bug fixes and shiny new glyphs.
1192 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
1193 indexing for HMMER reports and FASTA qual files, respectively.
1195 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
1196 new objects that can be placed within a Bio::Map::MapI-compliant
1197 genetic/physical map; Bio::Map::Physical provides a new physical
1198 map type; Bio::MapIO::fpc provides finger-printed clone mapping
1199 import.
1201 o Bio::Matrix::PSM provide new support for postion-specific
1202 (scoring) matrices (e.g. profiles, or "possums").
1204 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
1205 be instantiated without explicitly using Bio::OntologyIO. This
1206 is possible through changes to Bio::Ontology::OntologyStore to
1207 download ontology files from the web as necessary. Locations of
1208 ontology files are hard-coded into
1209 Bio::Ontology::DocumentRegistry.
1211 o Bio::PopGen includes many new methods and data types for
1212 population genetics analyses.
1214 o New constructor to Bio::Range, unions(). Given a list of
1215 ranges, returns another list of "flattened" ranges --
1216 overlapping ranges are merged into a single range with the
1217 mininum and maximum coordinates of the entire overlapping group.
1219 o Bio::Root::IO now supports -url, in addition to -file and -fh.
1220 The new -url argument allows one to specify the network address
1221 of a file for input. -url currently only works for GET
1222 requests, and thus is read-only.
1224 o Bio::SearchIO::hmmer now returns individual Hit objects for each
1225 domain alignment (thus containing only one HSP); previously
1226 separate alignments would be merged into one hit if the domain
1227 involved in the alignments was the same, but this only worked
1228 when the repeated domain occured without interruption by any
1229 other domain, leading to a confusing mixture of Hit and HSP
1230 objects.
1232 o Bio::Search::Result::ResultI-compliant report objects now
1233 implement the "get_statistics" method to access
1234 Bio::Search::StatisticsI objects that encapsulate any
1235 statistical parameters associated with the search (e.g. Karlin's
1236 lambda for BLAST/FASTA).
1238 o Bio::Seq::LargeLocatableSeq combines the functionality already
1239 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
1241 o Bio::SeqFeature::Annotated is a replacement for
1242 Bio::SeqFeature::Generic. It breaks compliance with the
1243 Bio::SeqFeatureI interface because the author was sick of
1244 dealing with untyped annotation tags. All
1245 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
1246 compliant, and accessible through Bio::Annotation::Collection.
1248 o Bio::SeqFeature::Primer implements a Tm() method for primer
1249 melting point predictions.
1251 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
1252 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
1254 o Bio::Taxonomy::Node now implements the methods necessary for
1255 Bio::Species interoperability.
1257 o Bio::Tools::CodonTable has new reverse_translate_all() and
1258 make_iupac_string() methods.
1260 o Bio::Tools::dpAlign now provides sequence profile alignments.
1262 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
1264 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
1265 parsers.
1267 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
1268 for designing small inhibitory RNA.
1270 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
1271 methods based on a distance matrix.
1273 o Bio::Tree::Statistics provides an assess_bootstrap() method to
1274 calculate bootstrap support values on a guide tree topology,
1275 based on provided bootstrap tree topologies.
1277 o Bio::TreeIO now supports the Pagel (PAG) tree format.
1279 1.4 branch
1281 1.4.1
1283 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
1285 o Bio::Graphics will work with gd1 or gd2
1287 o Bio::SearchIO
1288 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
1289 (RF lines alone)
1290 - blast.pm Parse multi-line query fields properly
1291 - small speed improvements to blasttable.pm and others
1293 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
1294 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
1295 supporting more complex queries
1298 1.4. Stable major release
1300 Since initial 1.2.0, 3000 separate changes have been made to make this release.
1302 o installable scripts
1304 o global module version from Bio::Root:Version
1306 o Bio::Graphics
1307 - major improvements; SVG support
1309 o Bio::Popgen
1310 - population genetics
1311 - support several population genetics types of questions.
1312 - Tests for statistical neutrality of mutations
1313 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
1314 Tests of population structure (Wright's F-statistic: Fst) is in
1315 Bio::PopGen::PopStats. Calculating composite linkage
1316 disequilibrium (LD) is available in Bio::PopGen::Statistics as
1317 well.
1318 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1319 and csv (comma delimited formatted) data.
1321 - a directory for implementing population simulations has
1322 been added Bio::PopGen::Simulation and 2 simulations - a
1323 Coalescent and a simple single-locus multi-allele genetic drift
1324 simulation have been provided. This replaces the code in
1325 Bio::Tree::RandomTree which has been deprecated until proper
1326 methods for generating random phylogenetic trees are
1327 implemented.
1329 o Bio::Restriction
1330 - new restrion analysis modules
1332 o Bio::Tools::Analysis
1333 - web based DNA and Protein analysis framework and several
1334 implementations
1336 o Bio::Seq::Meta
1337 - per residue annotable sequences
1339 o Bio::Matrix
1340 - Bio::Matrix::PSM - Position Scoring Matrix
1341 - Bio::Matrix::IO has been added for generalized parsing of
1342 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1343 initial implementations for parsing BLOSUM/PAM and Phylip
1344 Distance matricies respectively. A generic matrix
1345 implementation for general use was added in
1346 Bio::Matrix::Generic.
1348 o Bio::Ontology
1349 - major changes
1351 o Bio:Tree
1353 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1354 - small inhibitory RNA
1356 o Bio::SeqFeature::Tools
1357 - seqFeature mapping tools
1358 - Bio::SeqFeature::Tools::Unflattener.pm
1359 -- deal with mapping GenBank feature collections into
1360 Chado/GFF3 processable feature sets (with SO term mappings)
1362 o Bio::Tools::dpAlign
1363 - pure perl dynamic programming sequence alignment
1364 - needs Bioperl-ext
1366 o new Bio::SearchIO formats
1367 - axt and psl: UCSC formats.
1368 - blasttable: NCBI -m 8 or -m 9 format from blastall
1370 o new Bio::SeqIO formats
1371 - chado, tab, kegg, tigr, game
1372 - important fixes for old modules
1374 o Bio::AlignIO: maf
1376 o improved Bio::Tools::Genewise
1378 o Bio::SeqIO now can recongnize sequence formats automatically from
1379 stream
1381 o new parsers in Bio::Tools:
1382 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1384 o Bio::DB::Registry bugs fixed
1385 - BerkeleyDB-indexed flat files can be used by the OBDA system
1386 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1387 used by the OBDA system
1389 o several new HOWTOs
1390 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1391 Databases
1393 o hundreds of new and improved files
1396 o
1397 o Bio::Tree::AlleleNode has been updated to be a container of
1398 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1401 1.2 Branch
1403 1.2.3 Stable release update
1404 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1405 handling.
1406 o Bug #1477 - Sel --> Sec abbreviation fixed
1407 o Fix bug #1487 where paring in-between locations when
1408 end < start caused the FTLocationFactory logic to fail.
1409 o Fix bug #1489 which was not dealing with keywords as an
1410 arrayref properly (this is fixed on the main trunk because
1411 keywords returns a string and the array is accessible via
1412 get_keywords).
1413 o Bio::Tree::Tree memory leak (bug #1480) fixed
1414 Added a new initialization option -nodelete which
1415 won't try and cleanup the containing nodes if this
1416 is true.
1417 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1418 this was only present on the branch for the 1.2.1 and 1.2.2 series
1419 - Also merged main trunk changes to the branch which make
1420 newick -> nhx round tripping more effective (storing branch length
1421 and bootstrap values in same locate for NodeNHX and Node
1422 implementations.) Fixes to TreeIO parsing for labeled internal
1423 also required small changes to TreeIO::nhx. Improved
1424 tests for this module as well.
1425 o Bio::SearchIO
1426 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1427 gapped blast properly (was losing hit significance values due to
1428 the extra unexpeted column).
1429 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1430 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1431 although doesn't try to correct it - will get the negative
1432 number for you. Added a test for this as well.
1433 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1434 has no top-level family classification scores but does have scores and
1435 alignments for individual domains.
1436 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1437 regular expression to match the line was missing the possibility of
1438 an extra space. This is rare, which is why we probably did not
1439 catch it before.
1440 - BLAST parsing picks up more of the statistics/parameter fields
1441 at the bottom of reports. Still not fully complete.
1442 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1443 were fixed to include many improvements and added flexiblity
1444 in outputting the files. Bug #1495 was also fixed in the process.
1445 o Bio::DB::GFF
1446 - Update for GFF3 compatibility.
1447 - Added scripts for importing from UCSC and GenBank.
1448 - Added a 1.2003 version number.
1449 o Bio::Graphics
1450 - Updated tutorial.
1451 - Added a 1.2003 version number.
1452 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1453 properly writing keywords out.
1454 o Bio::SeqIO::genbank
1455 - Fixed bug/enhancement #1513 where dates of
1456 the form D-MMM-YYYY were not parsed. Even though this is
1457 invalid format we can handle it - and also cleanup the date
1458 string so it is properly formatted.
1459 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1460 and written with Genbank format. Similarly bug #1515 is fixed to
1461 parse in the ORIGIN text.
1462 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1463 to specify the ID type, one of (accession accession.version
1464 display primary). See Bio::SeqIO::preferred_id_type method
1465 documentation for more information.
1466 o Unigene parsing updated to handle file format changes by NCBI
1468 1.2.2 Stable release update
1470 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1471 - auto-discover ontology name
1472 - bug in parsing relationships when certain characters are in the term
1473 - fixed hard-coded prefix for term identifiers
1474 - various smaller issues
1476 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1477 of Bio::Ontology::TermI
1479 o brought the OBDA Registry code up to latest specs
1481 o Bio::DB::GenBank
1482 - eutils URL change
1483 - accession number retrieval fixed
1485 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1487 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1488 #1459 which now properly report alignment start/end info
1489 for translated BLAST/FASTA searches.
1491 o Bio::TreeIO::newick can parse labeled internal nodes
1493 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1494 for BLASTX if if you provide -report_type => 'BLASTX' when
1495 initializing a BPbl2seq object. Bioperl 1.3 will have better
1496 support for bl2seq in the SearchIO system.
1498 o Bio::Root::IO support a -noclose boolean flag which will not
1499 close a filehandle upon object cleanup - useful when sharing
1500 a filehandle among objects. Additionally code added s.t.
1501 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1503 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1505 o Bio::SeqIO::genbank
1506 - bug #1456 fixed which generated extra sequence lines
1507 - write moltype correctly for genpept
1509 1.2.1 Stable release update
1511 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1513 o Addition from main trunk of Ontology objects, principly to allow
1514 BioSQL releases against 1.2.1
1516 o Fixes and cleanup of Bio::Coordinate modules
1518 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1519 the primary accession number
1521 o Other bug fixes, including bpindex GenBank fix
1523 o Bio::SeqIO::genbank bug #1389 fixed
1525 1.2 Stable major release
1527 o More functionality added to Bio::Perl, the newbie module
1529 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1530 Support for New Hampshire Extended (NHX) format parsing.
1532 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1533 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1534 Hmmpfam parser.
1536 o New ontology parsing Bio::Ontology
1538 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1539 multi-report (mlib) fasta reports, support for waba and exonerate.
1541 o Bio::ClusterIO for parsing Unigene clusters
1543 o Bio::Assembly added for representing phrap and ace assembly clusters.
1545 o Rudimentary support for writing Chado XML (see
1546 GMOD project: www.gmod.org for more information)
1548 o Bio::Coordinate for mapping between different coordinate systems such
1549 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1550 features into different coordinate systems.
1552 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1553 with the get_Stream_by_query method and supports the latest
1554 NCBI eutils interface.
1556 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1557 object for extracting subsets of features : currently only
1558 supports extraction by location.
1560 1.1.1 Developer release
1562 o Deprecated modules are now listed in the DEPRECATED file
1564 o New HowTo documents located in doc/howto describing
1565 a domain of Bioperl.
1567 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1568 and all old bugs are searchable through the bugzilla interface.
1570 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1571 have been addressed.
1573 o Support for Genewise parsing in Bio::Tools::Genewise
1575 o Start of Ontology framework with Bio::Ontology
1577 o Speedup to the Bio::Root::Root object method _rearrange.
1578 A global _load_module method was implemented to simplify the
1579 dynamic loading of modules ala Bio::SeqIO::genbank. This
1580 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1581 etc).
1583 o Several performance improvements to sequence parsing in Bio::SeqIO.
1584 Attempt to speedup by reducing object creation overhead.
1586 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1587 method for sequence retrieval with their E-utils CGI scripts.
1588 More work to support Entrez queries to their fullest is planned
1589 before 1.2 release.
1591 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1593 1.1 Developer release
1595 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1596 this separation removes some of the complexity in our test suite
1597 and separates the core modules in bioperl from those that need
1598 external programs to run.
1600 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1601 not run into trouble running the makefile
1603 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1604 read,create,and write locations for grouped/split locations
1605 (like mRNA features on genomic sequence).
1607 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1608 and PAML (codeml,aaml, etc) parsing.
1610 o Bio::Tree:: objects expanded to handle testing monophyly,
1611 paraphyly, least common ancestor, etc.
1613 o Bio::Coordinate for mapping locations from different coordinate spaces
1615 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1616 added for parsing hmmpfam and hmmsearch output.
1618 o Bio::SearchIO::Writer::TextResultWriter for outputting
1619 a pseudo-blast textfile format
1622 1.0.2 Bug fix release
1624 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1625 in this release will not work after December 2002 when NCBI
1626 shuts off the old Entrez cgi scripts. We have already fixed
1627 on our main development branch and the functionality will be
1628 available in the next stable bioperl release (1.2) slated for
1629 Fall 2002.
1631 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1632 testset by Robin Emig. These were fixed as was the get_aln
1633 method in Bio::Search::HSP::GenericHSP to handle the extra
1634 context sequence that is provided with a FastA alignment.
1636 o Migrating differences between Bio::Search::XX::BlastXX to
1637 Bio::Search::XX::GenericXX objects. This included mechanism
1638 to retrieve whole list of HSPs from Hits and whole list of Hits from
1639 Results in addition to the current next_XX iterator methods that
1640 are available. Added seq_inds() method to GenericHSP which identifies
1641 indexes in the query or hit sequences where conserved,identical,gaps,
1642 or mismatch residues are located (adapted from Steve Chervitz's
1643 implementation in BlastHSP).
1645 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1646 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1648 o Bio::Graphics glyph set improved and extended for GBrowse release
1650 o Bio::Tree::Tree get_nodes implementation improvement thanks
1651 to Howard Ross notice performance problem when writing out
1652 unbalanced trees.
1654 o Bio::Location::Fuzzy::new named parameter -loc_type became
1655 -location_type, Bio::Location::Simple::new named parameter
1656 -seqid becamse -seq_id.
1658 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1659 was mis-detecting that gaps should be placed at the beginning of
1660 the alignment when the best alignment starts internally in the
1661 sequence.
1663 1.0.1 Bug fix release
1665 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1667 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1668 and mixed (3.3 - 3.4) versions of FASTA.
1670 o Small API change to add methods for completeness across
1671 implementations of Bio::Search objects. These new methods
1672 in the interface are implemented by the GenericXX object as well
1673 as the BlastXX objects.
1674 * Bio::Search::Result::ResultI
1675 - hits() method returns list of all Hits (next_hit is an
1676 iterator method)
1678 * Bio::Search::Hit::HitI
1679 - hsps() method returns list of all HSPs (next_hsp is an
1680 iterator method)
1682 o The Bio::SearchIO::Writer classes have been fixed to handle results
1683 created from either psiblast (Search::BlastXX objects) or
1684 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1685 has to be done here to make it work properly and will nee major
1686 API changes.
1688 o Bugs in Bio::Tools::HMMER fixed, including
1689 * #1178 - Root::IO destructor wasn't being called
1690 * #1034 - filter_on_cutoff now behaves properly
1692 o Bio::SeqFeature::Computation initialization args fixed and
1693 tests added.
1695 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1697 o Updated FAQ with more example based answers to typical questions
1699 o Bug #1202 was fixed which would improperly join together qual values
1700 parsed by Bio::SeqIO::qual when a trailing space was not present before
1701 the newline.
1703 1.0.0 Major Stable Release
1705 This represents a major release of bioperl with significant
1706 improvements over the 0.7.x series of releases.
1708 o Bio::Tools::Blast is officially deprecated. Please see
1709 Bio::SearchIO for BLAST and FastA parsing.
1711 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1712 Bio::LocationI objects as well as start/end.
1714 o Bio::Biblio contains modules for Bibliographic data.
1715 Bio::DB::Biblio contains the query modules. Additionally one can
1716 parse medlinexml from the ebi bibliographic query service (BQS)
1717 system and Pubmed xml from NCBI. See Martin Senger's
1718 documentation in Bio::Biblio for more information.
1720 o Bio::DB::Registry is a sequence database registry part of
1721 Open Bioinformatics Database Access. See
1722 http://obda.open-bio.org for more information.
1724 o File-based and In-Memory Sequence caching is provided by
1725 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1726 local database.
1728 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1729 been added by Lincoln Stein.
1731 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1733 o A FAQ has been started and is included in the release to provide
1734 a starting point for frequent questions and issues.
1736 0.9.3 Developer's release
1738 o Event based parsing system improved (SearchIO). With parsers for
1739 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1740 Additionally a lazy parsing system for text and html blast reports was
1741 added and is called psiblast (name subject to change in future releases).
1743 o Bio::Search objects improved and standardized with associated Interfaces
1744 written. The concept of a search "Hit" was standardized to be called
1745 "hit" consistently and the use of "subject" was deprecated in all active
1746 modules.
1748 o Bio::Structure added (since 0.9.1) for Protein structure objects
1749 and PDB parser to retrieve and write these structures from data files.
1751 o Several important Bio::DB::GFF bug fixes for handling features that
1752 are mapped to multiple reference points. Updated mysql adaptor
1753 so as to be able to store large (>100 megabase) chunks of DNA into
1754 Bio::DB::GFF databases.
1756 0.9.2 Developer's release
1758 o Bio::Search and Bio::SearchIO system introduced for event based
1759 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1760 in text and XML and FASTA reports in standard output format.
1762 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1763 generator is included in Bio::TreeIO::RandomTrees and a
1764 statistics module for evaluating.
1766 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1767 server for DAS servers.
1769 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1770 files. The entire BPlite system migrated to using Bio::Root::IO
1771 for the data stream.
1773 o Bio::Tools::Alignment for Consed and sequence Trimming
1774 functionality.
1776 o Bio::Structure for Protein structure information and parsing
1778 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1779 cgi-bin entry point which should be more reliable.
1781 o Bio::Map and Bio::MapIO for biological map navigation and a
1782 framework afor parsing them in. Only preliminary work here.
1784 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1785 Future work will integrate Pise and allow submission of analysis on
1786 remote servers.
1788 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1789 introduced as new objects for handling Sequence Annotation
1790 information (dblinks, references, etc) and is more robust that
1791 previous system.
1793 o Bio::Tools::FASTAParser introduced.
1795 o Scripts from the bioperl script submission project and new
1796 scripts from bioperl authors are included in "scripts" directory.
1798 o Factory objects and interfaces are being introduced and are more
1799 strictly enforced.
1801 o Bio::Root::Root introduced as the base object while
1802 Bio::Root::RootI is now simply an interface.
1804 o Bio::DB::RefSeq provides database access to copy of the NCBI
1805 RefSeq database using the EBI dbfetch script.
1807 0.9.0 Developer's release
1809 o perl version at least 5.005 is now required instead of perl 5.004
1811 o Bio::Tools::Run::RemoteBlast is available for running remote
1812 blast jobs at NCBI.
1814 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1816 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1817 Also added are related modules UTR3, UTR5, Exon, Intron,
1818 Promotor, PolyA and Transcript.
1820 o Speedup of translate method in PrimarySeq
1822 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1823 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1825 o Various fixes to Variation toolkit
1827 o Bio::DB::EMBL provides database access to EMBL sequence data.
1828 Bio::DB::Universal provides a central way to point to indexes
1829 and dbs in a single interface.
1831 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1833 o Bio::Factory::EMBOSS is still in design phase as is
1834 Bio::Factory::ApplicationFactoryI
1836 o Dia models for bioperl design are provided in the models/ directory
1838 0.7.2 Bug fix release
1840 o documentation fixes in many modules - SYNOPSIS code verified
1841 to be runnable in many (but not all modules)
1843 o corrected MANIFEST file from 0.7.1 release
1845 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1846 split locations
1848 o Bio::SeqIO::genbank
1849 * Correct parsing and writing of genbank format with protein data
1850 * moltype and molecule separation
1852 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1854 o Bio::SimpleAlign fixed to correctly handle consensus
1855 sequence calculation
1857 o Bio::Tools::HMMER supports hmmer 2.2g
1859 o Bio::Tools::BPlite to support report type specific parsing. Most
1860 major changes are not on the 0.7 branch.
1862 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1863 with File::Spec
1865 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1866 in several types of mutations:
1867 1.) AA level: deletion, complex
1868 2.) AA level: complex, inframe
1869 3.) RNA level: silent
1871 o BPbl2seq parsing of empty reports will not die, but will return
1872 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1873 $report->query() and $report->subject() methods. So an easy
1874 way to test if report was empty is to see if
1875 $report->query->seqname is undefined.
1877 0.7.1 Bug fix release
1879 o Better parsing of genbank/EMBL files especially fixing bugs
1880 related to Feature table parsing and locations on remote
1881 sequences. Additionally, species name parsing was better.
1883 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1884 which include a number of header lines.
1886 o More strict genbank and EMBL format writing (corrected number of
1887 spaces where appropriate).
1889 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1890 for related BPlite BUGS that are unresolved in this release.
1892 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1893 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1894 use expasy mirrors or EBI dbfetch cgi-script.
1896 o A moderate number of documentation improvements were made as
1897 well to provide a better code synopsis in each module.
1900 0.7 Large number of changes, including refactoring of the
1901 Object system, new parsers, new functionality and
1902 all round better system. Highlights are:
1905 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1906 Bio::Root::IO for I/O and file/handle capabilities.
1908 o Imported BPlite modules from Ian Korf for BLAST
1909 parsing. This is considered the supported BLAST parser;
1910 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1912 o Improved Sequence Feature model. Added complete location
1913 modelling (with fuzzy and compound locations). See
1914 Bio::LocationI and the modules under Bio/Location. Added
1915 support in Genbank/EMBL format parsing to completely parse
1916 feature tables for complex locations.
1918 o Moved special support for databanks etc to specialized modules under
1919 Bio/Seq/. One of these supports very large sequences through
1920 a temporary file as a backend.
1922 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1923 CDS retrieval and exon shuffling.
1925 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1927 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1928 DB/GDB (the latter has platform-specific limitations).
1930 o New analysis parser framework for HT sequence annotation (see
1931 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1933 o New Alignment IO framework
1935 o New Index modules (Swissprot)
1937 o New modules for running Blast within perl
1938 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1939 Multiple Sequence Alignment tools ClustalW and TCoffee
1940 (Bio::Tools::Run::Alignment).
1942 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1943 documentation across the package.
1945 o Much improved cross platform support. Many known incompatibilities
1946 have been fixed; however, NT and Mac do not work across the entire
1947 setup (see PLATFORMS).
1949 o Many bug fixes, code restructuring, etc. Overall stability and
1950 maintainability benefit a lot.
1952 o A total of 957 automatic tests
1955 0.6.2
1957 There are very few functionality changes but a large
1958 number of software improvements/bug fixes across the package.
1960 o The EMBL/GenBank parsing are improved.
1962 o The Swissprot reading is improved. Swissprot writing
1963 is disabled as it doesn't work at all. This needs to
1964 wait for 0.7 release
1966 o BLAST reports with no hits are correctly parsed.
1968 o Several other bugs of the BLAST parser (regular expressions, ...)
1969 fixed.
1971 o Old syntax calls have been replaced with more modern syntax
1973 o Modules that did not work at all, in particular the Sim4
1974 set have been removed
1976 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1977 have improved compliance with interface specs and documentation
1979 o Mailing list documentation updated throughout the distribution
1981 o Most minor bug fixes have happened.
1983 o The scripts in /examples now work and have the modern syntax
1984 rather than the deprecated syntax
1987 0.6.1 Sun April 2 2000
1989 o Sequences can have Sequence Features attached to them
1990 - The sequence features can be read from or written to
1991 EMBL and GenBank style flat files
1993 o Objects for Annotation, including References (but not
1994 full medline abstracts), Database links and Comments are
1995 provided
1997 o A Species object to represent nodes on a taxonomy tree
1998 is provided
2000 o The ability to parse HMMER and Sim4 output has been added
2002 o The Blast parsing has been improved, with better PSI-BLAST
2003 support and better overall behaviour.
2005 o Flat file indexed databases provide both random access
2006 and sequential access to their component sequences.
2008 o A CodonTable object has been written with all known
2009 CodonTables accessible.
2011 o A number of new lightweight analysis tools have been
2012 added, such as molecular weight determination.
2014 The 0.6 release also has improved software engineering
2016 o The sequence objects have been rewritten, providing more
2017 maintainable and easier to implement objects. These
2018 objects are backwardly compatible with the 0.05.1 objects
2020 o Many objects are defined in terms of interfaces and then
2021 a Perl implementation has been provided. The interfaces
2022 are found in the 'I' files (module names ending in 'I').
2024 This means that it is possible to wrap C/CORBA/SQL access
2025 as true "bioperl" objects, compatible with the rest of
2026 bioperl.
2028 o The SeqIO system has been overhauled to provide better
2029 processing and perl-like automatic interpretation of <>
2030 over arguments.
2032 o Many more tests have been added (a total of 172 automatic
2033 tests are now run before release).
2037 0.05.1 Tue Jun 29 05:30:44 1999
2038 - Central distribution now requires Perl 5.004. This was
2039 done to get around 5.003-based problems in Bio/Index/*
2040 and SimpleAlign.
2041 - Various bug fixes in the Bio::Tools::Blast modules
2042 including better exception handling and PSI-Blast
2043 support. See Bio/Tools/Blast/CHANGES for more.
2044 - Fixed the Parse mechanism in Seq.pm to use readseq.
2045 Follow the instructions in README for how to install
2046 it (basically, you have to edit Parse.pm).
2047 - Improved documentation of Seq.pm, indicating where
2048 objects are returned and where strings are returned.
2049 - Fixed uninitialized warnings in Bio::Root::Object.pm
2050 and Bio::Tools::SeqPattern.pm.
2051 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
2053 0.05 Sun Apr 25 01:14:11 1999
2054 - Bio::Tools::Blast modules have less memory problems
2055 and faster parsing. Webblast uses LWP and supports
2056 more functionality. See Bio/Tools/Blast/CHANGES for more.
2057 - The Bio::SeqIO system has been started, moving the
2058 sequence reformatting code out of the sequence object
2059 - The Bio::Index:: system has been started, providing
2060 generic index capabilities and specifically works for
2061 Fasta formatted databases and EMBL .dat formatted
2062 databases
2063 - The Bio::DB:: system started, providing access to
2064 databases, both via flat file + index (see above) and
2065 via http to NCBI
2066 - The scripts/ directory, where industrial strength scripts
2067 are put has been started.
2068 - Many changes - a better distribution all round.
2070 0.04.4 Wed Feb 17 02:20:13 1999
2071 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
2072 (see Bio::Tools::Blast::CHANGES).
2073 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
2074 - Beefed up the t/Fasta.t test script.
2075 - Small fix in Bio::Seq::type() (now always returns a string).
2076 - Changed Bio::Root::Utilities::get_newline_char() to
2077 get_newline() since it could return more than one char.
2078 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
2079 - Changed default timeout to 20 seconds (was 3).
2080 - Moved lengthy modification notes to the bottom of some files.
2081 - Fixed SimpleAlign write_fasta bug.
2082 - Beefed up SimpleAlign.t test
2084 0.04.3 Thu Feb 4 07:48:53 1999
2085 - Bio::Root::Object.pm and Global.pm now detect when
2086 script is run as a CGI and suppress output that is only
2087 appropriate when running interactively.
2088 - Bio::Root::Err::_set_context() adds name of script ($0).
2089 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
2090 regarding the use of the static objects via the qw(:obj) tag.
2091 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
2092 CORE::reverse, avoiding Perl warnings.
2093 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
2094 example scripts (see Bio::Tools::Blast::CHANGES).
2095 - examples/seq/seqtools.pl no longer always warns about using
2096 -prot or -nucl command-line arguments; only when using the
2097 -debug argument.
2098 - Methods added to Bio::Root::Utilities: create_filehandle(),
2099 get_newline_char(), and taste_file() to generalize filehandle
2100 creation and autodetect newline characters in files/streams
2101 (see bug report #19).
2102 - Bio::Root::IOManager::read() now handles timeouts and uses
2103 Utilities::create_filehandle().
2104 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
2105 of hardwiring in "\n".
2106 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
2108 0.04.2 Wed Dec 30 02:27:36 1998
2109 - Bug fixes in Bio::Tools::Blast modules, version 0.073
2110 (see Bio::Tools::Blast::CHANGES).
2111 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
2112 to CORE::reverse (prevents ambiguous warnings with 5.005).
2113 - Appending '.tmp.bioperl' to temporary files created by
2114 Bio::Root::Utilities::compress() or uncompress() to
2115 make it easy to identify & cleanup these files as needed.
2116 - Developers: Created CVS branch release-0-04-bug from
2117 release-0-04-1. Before making bug fixes to the 0.04.1 release,
2118 be sure to cvs checkout this branch into a clean area.
2120 0.04.1 Wed Dec 16 05:39:15 1998
2121 - Bug fixes in Bio::Tools::Blast modules, version 0.072
2122 (see Bio::Tools::Blast::CHANGES).
2123 - Compile/SW/Makefile.PL now removes *.o and *.a files
2124 with make clean.
2126 0.04 Tue Dec 8 07:49:19 1998
2127 - Lots of new modules added including:
2128 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
2129 and Bio/Compile directory containing XS-linked C code for
2130 creating Smith-Waterman sequence alignments from within Perl.
2131 * Steve Chervitz's Blast distribution has been incorporated.
2132 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
2133 - Bio/examples directory for demo scripts for all included modules.
2134 - Bio/t directory containing test suit for all included modules.
2135 - For changes specific to the Blast-related modules prior to
2136 incorporation in this central distribution, see the CHANGES
2137 file in the Bio/Tools/Blast directory.
2139 0.01 Tue Sep 8 14:23:22 1998
2140 - original version from central CVS tree; created by h2xs 1.18