| blob | 824728ad1a9417aa87165da0192fa38773e728b7 |
1 Summary of important user-visible changes for BioPerl
2 -----------------------------------------------------
4 {{$NEXT}}
6 1.7.4 2019-02-05 16:23:53+00:00 Europe/London
8 * Fix Bio::Root::Test, and the testuite, to properly check for
9 internet connection and the NO_NETWORK_TESTING environment
10 variable. Previously, tests that required internet connection
11 were not being skipped, causing tests to fail.
14 1.7.3 2019-01-30 13:30:34+00:00 Europe/London
16 * The following modules have been removed from the BioPerl
17 distribution to be part of a separate distribution. They have
18 been integrated into other module distributions for independent
19 development:
21 Bio::Align::Graphics
22 Bio::AlignIO::nexml
23 Bio::AlignIO::stockholm
24 Bio::Assembly::*
25 Bio::Cluster::*
26 Bio::ClusterI::*
27 Bio::ClusterIO::*
28 Bio::DB::Ace
29 Bio::DB::BioFetch
30 Bio::DB::CUTG
31 Bio::DB::EMBL
32 Bio::DB::EntrezGene
33 Bio::DB::Expression::*
34 Bio::DB::GFF
35 Bio::DB::GFF::Adaptor::*
36 Bio::DB::GFF::Aggregator::*
37 Bio::DB::GFF::Featname
38 Bio::DB::GFF::Feature
39 Bio::DB::GFF::Homol
40 Bio::DB::GFF::RelSegment
41 Bio::DB::GFF::Segment
42 Bio::DB::GFF::Typename
43 Bio::DB::GenBank
44 Bio::DB::GenPept
45 Bio::DB::HIV::*
46 Bio::DB::MeSH
47 Bio::DB::NCBIHelper
48 Bio::DB::Query::GenBank
49 Bio::DB::Query::HIVQuery
50 Bio::DB::RefSeq
51 Bio::DB::SeqFeature::*
52 Bio::DB::SeqVersion::*
53 Bio::DB::SwissProt
54 Bio::DB::TFBS::*
55 Bio::DB::Taxonomy::entrez
56 Bio::DB::Taxonomy::sqlite
57 Bio::DB::Universal
58 Bio::Draw::Pictogram
59 Bio::Factory::MapFactoryI
60 Bio::Index::Hmmer
61 Bio::Index::Stockholm
62 Bio::LiveSeq::*
63 Bio::Map::*
64 Bio::MapIO::*
65 Bio::MolEvol::CodonModel
66 Bio::Nexml::Factory
67 Bio::NexmlIO
68 Bio::Perl
69 Bio::Phenotype::*
70 Bio::PhyloNetwork::*
71 Bio::PopGen::*
72 Bio::Restriction::*
73 Bio::Root::Build
74 Bio::Search::HSP::HMMERHSP
75 Bio::Search::HSP::HmmpfamHSP
76 Bio::Search::Hit::HMMERHit
77 Bio::Search::Hit::HmmpfamHit
78 Bio::Search::Hit::hmmer3Hit
79 Bio::Search::Result::HMMERResult
80 Bio::Search::Result::HmmpfamResult
81 Bio::Search::Result::hmmer3Result
82 Bio::SearchDist
83 Bio::SearchIO::hmmer
84 Bio::SearchIO::hmmer2
85 Bio::SearchIO::hmmer3
86 Bio::SearchIO::hmmer_pull
87 Bio::SeqEvolution::*
88 Bio::SeqFeature::SiRNA::*
89 Bio::SeqIO::abi
90 Bio::SeqIO::agave
91 Bio::SeqIO::alf
92 Bio::SeqIO::chadoxml
93 Bio::SeqIO::chaos
94 Bio::SeqIO::chaosxml
95 Bio::SeqIO::ctf
96 Bio::SeqIO::entrezgene
97 Bio::SeqIO::excel
98 Bio::SeqIO::exp
99 Bio::SeqIO::flybase_chadoxml
100 Bio::SeqIO::lasergene
101 Bio::SeqIO::nexml
102 Bio::SeqIO::pln
103 Bio::SeqIO::strider
104 Bio::SeqIO::ztr
105 Bio::Structure::*
106 Bio::Taxonomy::*
107 Bio::Tools::AlignFactory
108 Bio::Tools::Analysis::* (except SimpleAnalysisBase)
109 Bio::Tools::Gel
110 Bio::Tools::HMMER::*
111 Bio::Tools::Hmmpfam
112 Bio::Tools::Phylo::Gumby
113 Bio::Tools::Protparam
114 Bio::Tools::Run::RemoteBlast
115 Bio::Tools::SiRNA::*
116 Bio::Tools::dpAlign
117 Bio::Tools::pSW
118 Bio::Tree::AlleleNode
119 Bio::Tree::Draw::Cladogram
120 Bio::TreeIO::nexml
121 Bio::TreeIO::svggraph
122 Bio::Variation::*
124 * The following modules are new in the BioPerl distribution. They
125 have been previously released in the BioPerl-Run distribution.
126 This will enable smaller distributions that provide a
127 Bio::Tool::Run interface, to be only dependent on the BioPerl
128 distribution instead of the whole (very large) BioPerl-Run:
130 Bio::Tools::Run::Analysis
131 Bio::Tools::Run::AnalysisFactory
132 Bio::Tools::Run::Phylo::PhyloBase
133 Bio::Tools::Run::WrapperBase
134 Bio::Tools::Run::WrapperBase::CommandExts
136 * The following programs have been removed:
138 bp_biofetch_genbank_proxy
139 bp_blast2tree
140 bp_bulk_load_gff
141 bp_composite_LD
142 bp_das_server
143 bp_download_query_genbank
144 bp_fast_load_gff
145 bp_flanks
146 bp_genbank2gff
147 bp_generate_histogram
148 bp_heterogeneity_test
149 bp_hivq
150 bp_hmmer_to_table
151 bp_load_gff
152 bp_meta_gff
153 bp_netinstall
154 bp_parse_hmmsearch
155 bp_process_wormbase
156 bp_query_entrez_taxa
157 bp_remote_blast
158 bp_seqfeature_delete
159 bp_seqfeature_gff3
160 bp_seqfeature_load
162 * Because of the move of so many modules and programs into
163 separate distributions, the following modules are no longer
164 prerequisites:
166 Ace
167 Ace::Sequence::Homol
168 Algorithm::Munkres
169 Apache::DBI
170 Archive::Tar
171 Array::Compare
172 Bio::ASN1::EntrezGene
173 Bio::Expression::Contact
174 Bio::Expression::DataSet
175 Bio::Expression::Platform
176 Bio::Expression::Sample
177 Bio::Ext::Align
178 Bio::GMOD::CMap::Utils
179 Bio::Phylo::Factory
180 Bio::Phylo::Forest::Tree
181 Bio::Phylo::IO
182 Bio::Phylo::Matrices
183 Bio::Phylo::Matrices::Datum
184 Bio::Phylo::Matrices::Matrix
185 Bio::SeqFeature::Annotated
186 Bio::SeqIO::staden::read
187 Bio::Tools::Run::Alignment::Clustalw
188 Bio::Tools::Run::Ensembl
189 Bio::Tools::Run::Phylo::Molphy::ProtML
190 Bio::Tools::Run::Phylo::Phylip::Neighbor
191 Bio::Tools::Run::Phylo::Phylip::ProtDist
192 Bio::Tools::Run::Phylo::Phylip::ProtPars
193 Bio::Tools::Run::Samtools
194 CGI
195 CPAN
196 Cache::FileCache
197 Config
198 Convert::Binary::C
199 DBD::Pg
200 DBD::SQLite
201 Data::Stag::XMLWriter
202 Encode
203 English
204 ExtUtils::Install
205 ExtUtils::Manifest
206 File::Glob
207 GD::Simple
208 Getopt::Std
209 Graph::Undirected
210 GraphViz
211 HTML::HeadParser
212 HTML::TableExtract
213 LWP
214 LWP::Simple
215 MIME::Base64
216 Memoize
217 PostScript::TextBlock
218 SVG
219 SVG::Graph
220 SVG::Graph::Data
221 SVG::Graph::Data::Node
222 SVG::Graph::Data::Tree
223 Sort::Naturally
224 Spreadsheet::ParseExcel
225 Term::ReadLine
226 Text::NSP::Measures::2D::Fisher2::twotailed
227 Text::ParseWords
228 Time::Local
229 Tree::DAG_Node
230 URI::Escape
231 WWW::Mechanize
232 XML::Simple
234 * The following is a new prerequisite:
236 Test::RequiresInternet
238 * The deobfuscator has been removed.
240 * The emacs bioperl minor mode is no longer distributed as part of the
241 perl module distributions. See
242 https://github.com/bioperl/emacs-bioperl-mode
245 1.7.2 - "Entebbe"
247 [Bugs]
249 * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
250 * #245 - Code coverage fixes [zmughal,cjfields]
251 * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
252 * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
253 * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
254 * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
255 * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
256 * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
257 * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
258 * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
259 * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
260 * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
262 [Code changes]
264 * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
266 1.7.1 - "Election"
268 [Bugs]
270 * Minor release to incorporate fix for CPAN indexing, which
271 prevented proper updates [cjfields]
272 * Fix problem in managing Target attribute for gff3 [Jukes34]
273 * Minor bug fixes related to NCBI HTTPS support [cjfields]
275 1.7.0 - "Disney"
277 [New site]
279 * We have migrated to Github Pages. This was actually planned, but the
280 recent OBF server compromise forced our hand.
282 Brian Osborne [bosborne] took this under his wing to move docs and has
283 done a tremendous amount of work formatting the site and working out some
284 of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
285 Cantalupo and Franscison Ossandon also helped. Kudos!!
287 * Similarly, the official issue tracker is now Github Issues. This has
288 been updated in the relevant documentation bits (we hope!)
290 [Code changes]
292 * Previously deprecated modules removed
293 * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
294 * Bio::DB::SeqHound has been removed due to the service no longer being
295 available
296 * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
297 reasons due to the server no longer having a valid cert
298 * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
299 * Bio::Coordinate, Bio::SearchIO::blastxml,
300 Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
301 added on CPAN
303 [New features]
305 * Docker instances of tagged releases are available! [hlapp]
306 * NCBI HTTPS support [mjohnson and others]
307 * Bio::SearchIO::infernal
308 - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
309 * Bio::Search::HSP::ModelHSP
310 - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
311 reports [pcantalupo]
312 * Bio::Search::Result::INFERNALResult
313 - Added new module to represent features of Infernal reports [pcantalupo]
314 * Bio::DB::Taxonomy SQLite option [cjfields]
315 * WrapperBase quoted option values [majensen]
316 * Various documentation fixes and updates [bosborne]
318 [Bug Fixes]
320 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
321 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
322 * NeXML parser fixes [fjossandon]
323 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
324 * RT 103272 : SeqFeature database deletion skipped features with a decimal -
325 Joshua Fortriede (Xenbase)
326 * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
327 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
328 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
329 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
330 * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
331 * Issue #84: EMBL format wrapping problem [nyamned]
332 * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
333 * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
334 or compiled C code (when Inline::C is installed) [rocky]
335 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
336 * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
337 * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
338 * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
339 to be consistent with "$hit->bits" behaviour [fjossandon]
340 * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
341 aminoacids made "next_seq" confused and broke the parser [fjossandon]
342 * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
343 Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
344 to "complement(join(A..B,C..D))" [fjossandon]
345 * For the many many many fixes that weren't mentioned - blame the release guy!
347 1.6.924
349 [Significant changes]
351 * Bug/feature issue tracking has moved to GitHub Issues:
352 https://github.com/bioperl/bioperl-live/issues
353 * DB_File has been demoted from "required" to "recommended",
354 which should make easier for Windows users to install BioPerl
355 if they don't need that module.
357 [New features]
359 * Bio::Search::HSP::GenericHSP
360 - Bug #3370, added a "posterior_string" method to retrieve the
361 posterior probability lines (PP) from HMMER3 reports [fjossandon]
362 - Added a "consensus_string" method to retrieve the consensus
363 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
364 * Bio::SearchIO::hmmer2
365 - The number of identical and conserved residues are now calculated
366 directly from the homology line [fjossandon]
367 - Now the Query Length and Hit Length are reported when the alignment
368 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
369 - Implemented the capture of the consensus structure lines [fjossandon]
370 * Bio::SearchIO::hmmer3
371 - The number of identical and conserved residues are now calculated
372 directly from the homology line [fjossandon]
373 - Now the Hit Length is reported when the alignment runs until the end
374 of the sequence/model ('.]' or '[]') [fjossandon]
375 - Implemented the capture of the consensus structure lines [fjossandon]
376 - Implemented the capture of the posterior probability lines [fjossandon]
377 - Completed the development of NHMMER parsing, including alignments [fjossandon]
378 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
379 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
380 "min_score", "min_bits, and "hit_filter" methods from
381 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
382 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
383 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
384 besides Blast, instead of being ignored. Added tests for all moved methods
385 using HMMER outputs and run the full test suite and everything pass [fjossandon]
386 * Bio::SeqIO::MultiFile
387 - Autodetection of file format [fangly]
388 * Bio::Tools::GuessSeqFormat:
389 - Format detection from non-seekable filehandles such as STDIN [fangly]
391 [Bug fixes]
393 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
394 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
395 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
396 * Abstract: Fixed ActivePerl incapability of removing temporary files
397 because of problems closing tied filehandles [fjossandon]
398 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
399 because ActivePerl were producing a ".index.pag" and ".index.dir"
400 files instead of a single ".index" file (like Strawberry Perl).
401 Now those temporary files are correctly considered and deleted. [fjossandon]
402 * Test files: Added missing module requirements (DB_File and Data::Stag)
403 to several tests files that were failing because those modules were
404 not present. Now those test files are correctly skipped instead. [fjossandon]
405 * Blast: Added support to changes in bl2seq from BLAST+ output, which
406 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
407 * Phylip: Return undef in "next_aln" at file end to avoid
408 an infinite loop [yschensandiego]
409 * HMMER3: When a hit description is too long, it is truncated in
410 the Scores table. In those cases, the more complete description from
411 the Annotation line (>>) will be used [fjossandon]
412 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
413 since it is now used by HMMER3 format in alignments [fjossandon]
414 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
415 to return undef if the query/hit length is unknown (like in some
416 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
417 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
418 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
419 added support to multi-query reports, reduced code redundancy,
420 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
421 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
422 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
423 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
424 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
425 * Double-quotes on paths are needed in some places [fjossandon]
426 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
427 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
428 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
429 with the latest changes made in their own repositories [fjossandon]
430 * General synching of files with the master branch [fjossandon]
431 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
432 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
433 * Fixed broken MeSH parser [fjossandon]
434 * Fixed missing detection of format in SeqIO when given a -string [fangly]
436 1.6.923
438 * Major Windows support updates! [fjossandon]
439 * MAKER update to allow for stricter standard codon table [cjfields]
440 * Better support for circular sequences [fjossandon]
441 * Fixes for some complex location types [fjossandon]
442 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
443 * Fix bug #2978 related to BLAST report type [fjossandon]
444 * Deobfuscator fixes [DaveMessina]
446 1.6.922
448 * Address CPAN test failures [cjfields]
449 * Add BIOPROJECT support for Genbank files [hyphaltip]
450 * Better regex support for HMMER3 output [bosborne]
452 1.6.921
454 * Minor update to address CPAN test failures
456 1.6.920
458 * Remove Bio::Biblio and related files [carandraug]
459 - this cause version clashes with an independently-released
460 version of Bio::Biblio
462 1.6.910
464 [New features]
466 * Hash randomization fixes for perl 5.18.x
467 - Note: at least one module (Bio::Map::Physical) still has a failing test;
468 this is documented in bug #3446 and has been TODO'd; we will be pulling
469 Bio::Map and similar modules out of core into separate distributions in the
470 1.7.x release series [cjfields]
472 [New features]
474 * Bio::Seq::SimulatedRead
475 - New module to represent reads taken from other sequences [fangly]
476 * Bio::Root::Root
477 - Support of Clone::Fast as a faster cloning alternative [fangly]
478 * Bio::Root::IO
479 - Moved the format() and variant() methods from Bio::*IO modules to
480 Bio::Root::IO [fangly]
481 - Can now use format() to get the type of IO format in use [fangly]
482 * Bio::Tools::IUPAC
483 - New regexp() method to create regular expressions from IUPAC sequences
484 [fangly]
485 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
486 - Code refresh [fangly]
487 * Bio::DB::Taxonomy
488 - Added support for the Greengenes and Silva taxonomies [fangly]
489 * Bio::Tree::TreeFunctionsI
490 - get_lineage_string() represents a lineage as a string [fangly]
491 - add_trait() returns instead of reporting an error when the column
492 number is exceeded in add_trait() [fangly]
493 - Option to support tree leaves without trait [fangly]
494 - Allow ID of 0 in trait files [fangly]
495 * Bio::DB::Taxonomy::list
496 - Misc optimizations [fangly]
497 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
498 * Bio::DB::Taxonomy::*
499 - get_num_taxa() returns the number of taxa in the database [fangly]
500 * Bio::DB::Fasta and Bio::DB::Qual
501 - support indexing an arbitrary list of files [fangly]
502 - user can supply an arbitrary index file name [fangly]
503 - new option to remove index file at the end [fangly]
504 * Bio::DB::Fasta
505 - now handles IUPAC degenerate residues [fangly]
506 * Bio::PrimarySeq and Bio::PrimarySeqI
507 - speed improvements for large sequences [Ben Woodcroft, fangly]
508 * Bio::PrimaryQual
509 - tightened and optimized quality string validation [fangly]
510 * Bio::SeqIO::fasta
511 - new method and option 'block', to create FASTA output with space
512 intervaled blocks (similar to genbank or EMBL) has been implemented.
513 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
514 in favour of the methods 'width' and 'preferred_id_type` respectively.
515 * Bio::FeatureIO::*
516 - moved from bioperl-live into the separate distribution Bio-FeatureIO
517 * Bio::SeqFeature::Annotated
518 - moved from bioperl-live into the separate distribution Bio-FeatureIO
519 * Bio::Cluster::SequenceFamily
520 - improved performance when using get_members with overlapping multiple
521 criteria
522 * Bio::SearchIO::hmmer3
523 - now supports nhmmer [bosborne]
525 [Bug fixes]
527 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
528 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
529 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
530 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
531 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
532 information was lost in a multi-result blast file [Paul Cantalupo]
533 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
534 total gaps [Paul Cantalupo]
535 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
536 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
537 when end of domain indicator is split across lines [Paul Cantalupo]
538 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
539 cjfields]
540 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
541 instances where blank lines are within sequences [cjfields]
542 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
543 types [fangly]
544 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
545 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
546 cjfields]
547 * Various fixes for Stockholm file indexing and processing [bosborne]
548 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
549 breaks parsing [cjfields]
550 * Fix case where Bio::Seq::Meta* objects with no meta information could not
551 be reverse-complemented [fangly]
552 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
553 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
554 when unsure that values will be numerical [fangly]
555 * Fix undef warnings in Bio::SeqIO::embl [fangly]
556 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
557 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
558 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
559 Sallou]
560 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
561 source_tag and display_name must return a string, not undef [fangly]
562 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
563 add_SeqFeature takes a single argument [fangly]
564 * Use cross-platform filenames and temporary directory in
565 Bio::DB::Taxonomy::flatfile [fangly]
566 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
567 properly identified as existing taxa in the database [fangly]
568 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
569 without also passing a lineage to store [fangly]
570 * Prevent passing a directory to the gi2taxid option (-g) of
571 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
572 [fangly]
573 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
574 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
575 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
576 object before trying to access, and no longer returns repeated sequences.
579 1.6.901 May 18, 2011
581 [Notes]
583 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
584 modules using Ace will also be deprecated [lds, cjfields]
585 * Minor bug fix release
586 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
587 * Address Build.PL issues when DBI is not present [hartzell]
588 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
589 * Remove deprecated code for perl 5.14.0 compat [cjfields]
590 * Due to schema changes and lack of support for older versions, support
591 for NeXML 0.9 is only (very) partially implemented.
592 See: https://redmine.open-bio.org/issues/3207
594 [Bug fixes]
596 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
597 docs [genehack, cjfields]
598 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
599 module version from dist_version (probably not the best way to do this,
600 but it seems to work) [rbuels, cjfields]
603 1.6.900 April 14, 201
605 [Notes]
607 * This will probably be the last release to add significant features to
608 core modules; subsequent releases will be for bug fixes alone.
609 We are planning on a restructuring of core for summer 2011, potentially
610 as part of the Google Summer of Code. This may become BioPerl 2.0.
611 * Version bump represents 'just prior to v 1.7'. We may have point
612 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
613 This code essentially is what is on the github master branch.
615 [New features]
617 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
618 * Bio::Tree refactor
619 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
620 - removal of Scalar::Util::weaken code, which was causing odd headaches
621 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
622 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
623 many others]
624 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
625 [Warren Kretzschmar]
626 * Bio::SeqIO::gbxml
627 - bug 2515 - new contribution [Ryan Golhar, jhannah]
628 * Bio::Assembly::IO
629 - support for reading Maq, Sam and Bowtie files [maj]
630 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
631 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
632 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
633 - bug 2726: reading/writing granularity: whole scaffold or one contig
634 at a time [Joshua Udall, fangly]
635 * Bio::OntologyIO
636 - Added parsing of xrefs to OBO files, which are stored as secondary
637 dbxrefs of the cvterm [Naama Menda]
638 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
639 * PAML code updated to work with PAML 4.4d [DaveMessina]
641 [Bug fixes]
643 * [3198] - sort tabular BLAST hits by score [DaveMessina]
644 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
645 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
646 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
647 [cjfields]
648 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
649 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
650 * [3164] - TreeFunctionsI syntax bug [gjuggler]
651 * [3163] - AssemblyIO speedup [fangly]
652 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
653 hyphaltip]
654 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
655 * [3158] - fix EMBL file mis-parsing [cjfields]
656 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
657 cjfields]
658 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
659 * [3148] - URL change for UniProt [cjfields]
660 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
661 * [3136] - HMMer3 parser fixes [kblin]
662 * [3126] - catch description [Toshihiko Akiba]
663 * [3122] - Catch instances where non-seekable filehandles were being
664 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
665 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
666 [dukeleto, rbuels, cjfields]
667 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
668 jhannah]
669 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
670 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
671 cjfields]
672 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
673 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
674 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
675 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
676 * [3086] - EMBL misparsing long tags [kblin, cjfields]
677 * [3085] - CommandExts and array of files [maj, hyphaltip]
678 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
679 for alignment slices [Ha X. Dang, cjfields]
680 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
681 * [3073] - fix parsing of GenBank files from RDP [cjfields]
682 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
683 * [3064] - All-gap midline BLAST report issues [cjfields]
684 * [3063] - BLASt report RID [Razi Khaja, cjfields]
685 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
686 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
687 * [3039] - correct Newick output root node branch length [gjuggler,
688 DaveMessina]
689 * [3038] - SELEX alignment error [Bernd, cjfields]
690 * [3033] - PrimarySeq ID setting [Bernd, maj]
691 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
692 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
693 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
694 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
695 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
696 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
697 PAML 4.4d [DaveMessina]
698 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
699 DaveMessina]
700 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
701 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
702 * [3017] - using threads with Bio::DB::GenBank [cjfields]
703 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
704 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
705 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
706 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
707 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
708 cjfields]
709 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
710 * [2977] - TreeIO issues [DaveMessina]
711 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
712 * [2944] - Bio::Tools::GFF score [cjfields]
713 * [2942] - correct MapTiling output [maj]
714 * [2939] - PDB residue insertion codes [John May, maj]
715 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
716 * [2928] - GuessSeqFormat raw [maj]
717 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
718 * [2922] - open() directive issue [cjfields]
719 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
720 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
721 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
722 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
723 cjfields]
724 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
725 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
726 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
727 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
728 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
729 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
730 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
731 * [2758] - Bio::AssemblyIO ace problems [fangly]
732 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
733 * [2726] - ace file IO [Josh, fangly]
734 * [2700] - Refactor Build.PL [cjfields]
735 * [2673] - addition of simple Root-based clone() method [cjfields]
736 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
737 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
738 * [2594] - Bio::Species memory leak [cjfields]
739 * [2515] - GenBank XML parser [jhannah]
740 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
741 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
742 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
743 cjfields]
744 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
746 [Deprecated]
748 * Bio::Expression modules - these were originally designed to go with the
749 bioperl-microarray suite of tools, however they have never been completed
750 and so have been removed from the distribution. The original code has
751 been moved into the inactive bioperl-microarray suite. [cjfields]
753 [Other]
755 * Repository moved from Subversion (SVN) to
756 http://github.com/bioperl/bioperl-live [cjfields]
757 * Bug database has moved to Redmine (https://redmine.open-bio.org)
758 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
759 Thieme have been moved to their own distribution (Bio-Microarray).
760 [cjfields]
762 1.6.1 Sept. 29, 2009 (point release)
763 * No change from last alpha except VERSION and doc updates [cjfields]
765 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
766 * Fix for silent OBDA bug related to FASTA validation [cjfields]
768 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
769 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
770 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
771 [cjfields]
772 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
774 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
775 * WinXP test fixes [cjfields, maj]
776 * BioPerl.pod added for descriptive information, fixes CPAN indexing
777 [cjfields]
778 * Minor doc fixes [cjfields]
780 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
781 * Fix tests failing due to merging issues [cjfields]
782 * More documentation updates for POD parsing [cjfields]
784 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
785 * Bio::Root::Build
786 - fix YAML meta data generation [cjfields]
788 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
789 * Bio::Align::DNAStatistics
790 - fix divide by zero problem [jason]
791 * Bio::AlignIO::*
792 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
793 * Bio::AlignIO::stockholm
794 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
795 * Bio::Assembly::Tools::ContigSpectrum
796 - function to score contig spectrum [fangly]
797 * Bio::DB::EUtilities
798 - small updates [cjfields]
799 * Bio::DB::Fasta
800 - berkeleydb database now autoindexes wig files and locks correctly
801 [lstein]
802 * Bio::DB::HIV
803 - various small updates for stability; tracking changes to LANL
804 database interface [maj]
805 * Bio::DB::SeqFeature (lots of updates and changes)
806 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
807 - bug 2835 - patch [Dan Bolser]
808 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
809 * Bio::DB::SwissProt
810 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
811 * Bio::Factory::FTLocationFactory
812 - mailing list bug fix [cjfields]
813 * Bio::LocatableSeq
814 - performance work on column_from_residue_number [hartzell]
815 * Bio::Matrix::IO::phylip
816 - bug 2800 - patch to fix phylip parsing [Wei Zou]
817 * Bio::Nexml
818 - Google Summer of Code project from Chase Miller - parsers for Nexml
819 file format [maj, chmille4]
820 * Bio::PopGen
821 - Make Individual, Population, Marker objects AnnotatableI [maj]
822 - simplify LD code [jason]
823 * Bio::RangeI
824 - deal with empty intersection [jason]
825 * Bio::Restriction
826 - significant overhaul of Bio::Restriction system: complete support for
827 external and non-palindromic cutters. [maj]
828 * Bio::Root::Build
829 - CPANPLUS support, no automatic installation [sendu]
830 * Bio::Root::IO
831 - allow IO::String (regression fix) [cjfields]
832 - catch unintentional undef values [cjfields]
833 - throw if non-fh is passed to -fh [maj]
834 * Bio::Root::Root/RootI
835 - small debugging and core fixes [cjfields]
836 * Bio::Root::Test
837 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
838 * Bio::Root::Utilities
839 - bug 2737 - better warnings [cjfields]
840 * Bio::Search
841 - tiling completely refactored, HOWTO added [maj]
842 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
843 will deprecate usage of the older tiling code in the next BioPerl
844 release
845 - small fixes [cjfields]
846 * Bio::SearchIO
847 - Infernal 1.0 output now parsed [cjfields]
848 - new parser for gmap -f9 output [hartzell]
849 - bug 2852 - fix infinite loop in some output [cjfields]
850 - blastxml output now passes all TODO tests [cjfields]
851 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
852 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
853 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
854 * Bio::Seq::LargePrimarySeq
855 - delete tempdirs [cjfields]
856 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
857 * Bio::Seq::Quality
858 - extract regions based on quality threshold value [Dan Bolser, heikki]
859 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
860 * Bio::SeqFeature::Lite
861 - various Bio::DB::SeqFeature-related fixes [lstein]
862 * Bio::SeqFeature::Tools::TypeMapper
863 - additional terms for GenBank to SO map [scain]
864 * Bio::SeqIO::chadoxml
865 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
866 * Bio::SeqIO::embl
867 - support for CDS records [dave_messina, Sylvia]
868 * Bio::SeqIO::fastq
869 - complete refactoring to handle all FASTQ variants, perform validation,
870 write output. API now conforms with other Bio* parsers and the rest of
871 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
872 [cjfields]
873 * Bio::SeqIO::genbank
874 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
875 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
876 * Bio::SeqIO::largefasta
877 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
878 * Bio::SeqIO::raw
879 - add option for 'single' and 'multiple'
880 * Bio::SeqIO::scf
881 - bug 2881 - fix scf round-tripping [Adam Søgren]
882 * Bio::SeqUtils
883 - bug 2766, 2810 - copy over tags from features, doc fixes [David
884 Jackson]
885 * Bio::SimpleAlign
886 - bug 2793 - patch for add_seq index issue [jhannah, maj]
887 - bug 2801 - throw if args are required [cjfields]
888 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
889 [Tristan Lefebure, maj]
890 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
891 - fix POD and add get_SeqFeatures filter [maj]
892 * Bio::Tools::dpAlign
893 - add support for LocatableSeq [ymc]
894 - to be moved to a separate distribution [cjfields, rbuels]
895 * Bio::Tools::EUtilities
896 - fix for two bugs from mail list [Adam Whitney, cjfields]
897 - add generic ItemContainerI interface for containing same methods
898 [cjfields]
899 * Bio::Tools::HMM
900 - fix up code, add more warnings [cjfields]
901 - to be moved to a separate distribution [cjfields, rbuels]
902 * Bio::Tools::Primer3
903 - bug 2862 - fenceposting issue fixed [maj]
904 * Bio::Tools::Run::RemoteBlast
905 - tests for remote RPS-BLAST [mcook]
906 * Bio::Tools::SeqPattern
907 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
908 * Bio::Tools::tRNAscanSE
909 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
910 * Bio::Tree::*
911 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
912 * Bio::Tree::Statistics
913 - several methods for calculating Fitch-based score, internal trait
914 values, statratio(), sum of leaf distances [heikki]
915 * Bio::Tree::Tree
916 - bug 2869 - add docs indicating edge case where nodes can be
917 prematurely garbage-collected [cjfields]
918 - add as_text() function to create Tree as a string in specified format
919 [maj]
920 * Bio::Tree::TreeFunctionsI
921 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
922 Lefebure, maj]
923 * Bio::TreeIO::newick
924 - fix small semicolon issue [cjfields]
925 * scripts
926 - update to bp_seqfeature_load for SQLite [lstein]
927 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
928 - fastam9_to_table - fix for MPI output [jason]
929 - gccalc - total stats [jason]
930 * General Stuff
931 - POD cleanup re: FEEDBACK section [maj, cjfields]
932 - cleanup or fix dead links [cjfields]
933 - Use of no_* methods (indicating 'number of something') is deprecated
934 in favor of num_* [cjfields]
935 - lots of new tests for the above bugs and refactors [everyone!]
936 - new template for Komodo text editor [cjfields]
938 1.6.0 Winter 2009
939 * Feature/Annotation rollback
940 - Problematic changes introduced prior to the 1.5 release have been
941 rolled back. These changes led to subtle bugs involving operator
942 overloading and interface methods.
943 - Behavior is very similar to that for BioPerl 1.4, with tag values
944 being stored generically as simple scalars. Results in a modest
945 speedup.
946 * Bio::Graphics
947 - Split into a separate distribution on CPAN, primarily so development
948 isn't reliant on a complete BioPerl release.
949 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
950 is only available via Subversion (via bioperl-live main trunk)
951 * Bio::Root::Test
952 - Common test bed for all BioPerl modules
953 * Bio::Root::Build
954 - Common Module::Build-based subclass for all BioPerl modules
955 * Bio::DB::EUtilities
956 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
957 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
958 and user agent request posting and retrieval
959 * Test implementation and reorganization
960 - Tests have been reorganized into groups based on classes or use
961 cases.
962 - Automated test coverage is now online:
963 http://www.bioperl.org/wiki/Test_Coverage
964 - After this release, untested modules will be moved into a
965 separate developer distribution until tests can be derived.
966 Also, new modules to be added are expected to have a test suite
967 and adequate test coverage.
969 1.5.2 Developer release
971 Full details of changes since 1.5.1 are available online at:
972 http://www.bioperl.org/wiki/Change_log
973 The following represents a brief overview of the most important changes.
975 o Bio::Map
976 - Overhaul. Brand new system fully allows markers to have multiple
977 positions on multiple maps, and to have relative positions. Should be
978 backward compatible.
980 o Bio::Taxonomy
981 - This module and all the modules in the Taxonomy directory now
982 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
984 o Bio::DB::Taxonomy
986 - Taxonomy.pm
987 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
989 * New methods ancestor(), each_Descendent() and _handle_internal_id().
991 * Allows for different database modules to create Bio::Taxon objects
992 with the same internal id when the same taxon is requested from each.
994 - flatfile.pm
995 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
997 * No longer includes the fake root node 'root'; there are multiple roots
998 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
1000 - entrez.pm
1001 * get_node() has new option -full
1003 * Caches data retrieved from website
1005 o Bio::Species
1006 - Now a Bio::Taxon. Carries out the species name -> specific name munging
1007 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
1008 backward compatability in species() method.
1010 o Bio::Search and Bio::SearchIO
1011 - Overhaul. The existing system has been sped up via some minor changes
1012 (mostly gain-of-function to the API). Bio::PullParserI is introduced
1013 as a potential eventual replacment for the existing system, though as
1014 yet only a Hmmpfam parser exists written using it.
1017 1.5.1 Developer release
1019 o Major problem with how Annotations were written out with
1020 Bio::Seq is fixed by reverting to old behavior for
1021 Bio::Annotation objects.
1023 o Bio::SeqIO
1025 - genbank.pm
1026 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
1027 expect at l east 9 spaces at the beginning of a line to
1028 indicate line wrapping.
1030 * Treat multi-line SOURCE sections correctly, this defect broke
1031 both common_name() and classification()
1033 * parse swissprot fields in genpept file
1035 * parse WGS genbank records
1037 - embl.pm
1038 * Changed regexp for ID line. The capturing parentheses are
1039 the same, the difference is an optional repeated-not-semi-
1040 colon expression following the captured \S+. This means the
1041 regexp works when the division looks like /PRO;/ or when the
1042 division looks like /ANG ;/ - the latter is from EMBL
1043 repbase
1045 * fix ID line parsing: the molecule string can have spaces in
1046 it. Like: "genomic DNA"
1048 - swiss.pm: bugs #1727, #1734
1050 - entrezgene.pm
1051 * Added parser for entrezgene ASN1 (text format) files.
1052 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
1054 o Bio::AlignIO
1056 - maf.pm coordinate problem fixed
1058 o Bio::Taxonomy and Bio::DB::Taxonomy
1060 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
1061 can be done via Web without downloading all the sequence.
1063 o Bio::Tools::Run::RemoteBlast supports more options and complies
1064 to changes to the NCBI interface. It is reccomended that you
1065 retrieve the data in XML instead of plain-text BLAST report to
1066 insure proper parsing and retrieval of all information as NCBI
1067 fully expects to change things in the future.
1069 o Bio::Tree and Bio::TreeIO
1071 - Fixes so that re-rooting a tree works properly
1073 - Writing out nhx format from a newick/nexus file will properly output
1074 bootstrap information. The use must move the internal node labels over
1075 to bootstraps.
1076 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
1077 $node->bootstrap($node->id);
1078 $node->id('');
1079 }
1080 - Nexus parsing is much more flexible now, does not care about
1081 LF.
1083 - Cladogram drawing module in Bio::Tree::Draw
1085 - Node height and depth now properly calculated
1087 - fix tree pruning algorithm so that node with 1 child gets merged
1089 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
1090 bugs and improvements were added, see Gbrowse mailing list for most of
1091 these.
1093 o Bio::DB::GFF partially supports GFF3. See information about
1094 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
1096 o Better location parsing in Bio::Factory::FTLocationFactory -
1097 this is part of the engine for parsing EMBL/GenBank feature table
1098 locations. Nested join/order-by/complement are allowed now
1100 o Bio::PrimarySeqI->translate now takes named parameters
1102 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
1103 reconstruction) is now supported. Parsing different models and
1104 branch specific parametes are now supported.
1106 o Bio::Factory::FTLocationFactory - parse hierarchical locations
1107 (joins of joins)
1109 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
1110 for getter/setter functions
1112 o Bio::SearchIO
1114 - blast bug #1739; match scientific notation in score
1115 and possible e+ values
1117 - blast.pm reads more WU-BLAST parameters and parameters, match
1118 a full database pathname,
1120 - Handle NCBI WEB and newer BLAST formats specifically
1121 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
1123 - psl off-by-one error fixed
1125 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
1126 and HSPs can be constructed from them.
1128 - HSPs query/hit now have a seqdesc field filled out (this was
1129 always available via $hit->description and
1130 $result->query_description
1132 - hmmer.pm can parse -A0 hmmpfam files
1134 - Writer::GbrowseGFF more customizeable.
1136 o Bio::Tools::Hmmpfam
1137 make e-value default score displayed in gff, rather than raw score
1138 allow parse of multiple records
1141 1.5 Developer release
1143 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
1144 provide Jukes-Cantor and Kimura pairwise distance methods,
1145 respectively.
1147 o Bio::AlignIO support for "po" format of POA, and "maf";
1148 Bio::AlignIO::largemultifasta is a new alternative to
1149 Bio::AlignIO::fasta for temporary file-based manipulation of
1150 particularly large multiple sequence alignments.
1152 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
1153 be treated similarly as an assembled contig.
1155 o Bio::CodonUsage provides new rare_codon() and probable_codons()
1156 methods for identifying particular codons that encode a given
1157 amino acid.
1159 o Bio::Coordinate::Utils provides new from_align() method to build
1160 a Bio::Coordinate pair directly from a
1161 Bio::Align::AlignI-conforming object.
1163 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
1164 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
1165 web service using standard Pubmed query syntax, and retrieve
1166 results as XML.
1168 o Bio::DB::GFF has various sundry bug fixes.
1170 o Bio::FeatureIO is a new SeqIO-style subsystem for
1171 writing/reading genomic features to/from files. I/O classes
1172 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
1173 classes only read/write Bio::SeqFeature::Annotated objects.
1174 Notably, the GFF v3 class requires features to be typed into the
1175 Sequence Ontology.
1177 o Bio::Graph namespace contains new modules for manipulation and
1178 analysis of protein interaction graphs.
1180 o Bio::Graphics has many bug fixes and shiny new glyphs.
1182 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
1183 indexing for HMMER reports and FASTA qual files, respectively.
1185 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
1186 new objects that can be placed within a Bio::Map::MapI-compliant
1187 genetic/physical map; Bio::Map::Physical provides a new physical
1188 map type; Bio::MapIO::fpc provides finger-printed clone mapping
1189 import.
1191 o Bio::Matrix::PSM provide new support for postion-specific
1192 (scoring) matrices (e.g. profiles, or "possums").
1194 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
1195 be instantiated without explicitly using Bio::OntologyIO. This
1196 is possible through changes to Bio::Ontology::OntologyStore to
1197 download ontology files from the web as necessary. Locations of
1198 ontology files are hard-coded into
1199 Bio::Ontology::DocumentRegistry.
1201 o Bio::PopGen includes many new methods and data types for
1202 population genetics analyses.
1204 o New constructor to Bio::Range, unions(). Given a list of
1205 ranges, returns another list of "flattened" ranges --
1206 overlapping ranges are merged into a single range with the
1207 mininum and maximum coordinates of the entire overlapping group.
1209 o Bio::Root::IO now supports -url, in addition to -file and -fh.
1210 The new -url argument allows one to specify the network address
1211 of a file for input. -url currently only works for GET
1212 requests, and thus is read-only.
1214 o Bio::SearchIO::hmmer now returns individual Hit objects for each
1215 domain alignment (thus containing only one HSP); previously
1216 separate alignments would be merged into one hit if the domain
1217 involved in the alignments was the same, but this only worked
1218 when the repeated domain occured without interruption by any
1219 other domain, leading to a confusing mixture of Hit and HSP
1220 objects.
1222 o Bio::Search::Result::ResultI-compliant report objects now
1223 implement the "get_statistics" method to access
1224 Bio::Search::StatisticsI objects that encapsulate any
1225 statistical parameters associated with the search (e.g. Karlin's
1226 lambda for BLAST/FASTA).
1228 o Bio::Seq::LargeLocatableSeq combines the functionality already
1229 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
1231 o Bio::SeqFeature::Annotated is a replacement for
1232 Bio::SeqFeature::Generic. It breaks compliance with the
1233 Bio::SeqFeatureI interface because the author was sick of
1234 dealing with untyped annotation tags. All
1235 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
1236 compliant, and accessible through Bio::Annotation::Collection.
1238 o Bio::SeqFeature::Primer implements a Tm() method for primer
1239 melting point predictions.
1241 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
1242 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
1244 o Bio::Taxonomy::Node now implements the methods necessary for
1245 Bio::Species interoperability.
1247 o Bio::Tools::CodonTable has new reverse_translate_all() and
1248 make_iupac_string() methods.
1250 o Bio::Tools::dpAlign now provides sequence profile alignments.
1252 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
1254 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
1255 parsers.
1257 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
1258 for designing small inhibitory RNA.
1260 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
1261 methods based on a distance matrix.
1263 o Bio::Tree::Statistics provides an assess_bootstrap() method to
1264 calculate bootstrap support values on a guide tree topology,
1265 based on provided bootstrap tree topologies.
1267 o Bio::TreeIO now supports the Pagel (PAG) tree format.
1269 1.4 branch
1271 1.4.1
1273 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
1275 o Bio::Graphics will work with gd1 or gd2
1277 o Bio::SearchIO
1278 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
1279 (RF lines alone)
1280 - blast.pm Parse multi-line query fields properly
1281 - small speed improvements to blasttable.pm and others
1283 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
1284 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
1285 supporting more complex queries
1288 1.4. Stable major release
1290 Since initial 1.2.0, 3000 separate changes have been made to make this release.
1292 o installable scripts
1294 o global module version from Bio::Root:Version
1296 o Bio::Graphics
1297 - major improvements; SVG support
1299 o Bio::Popgen
1300 - population genetics
1301 - support several population genetics types of questions.
1302 - Tests for statistical neutrality of mutations
1303 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
1304 Tests of population structure (Wright's F-statistic: Fst) is in
1305 Bio::PopGen::PopStats. Calculating composite linkage
1306 disequilibrium (LD) is available in Bio::PopGen::Statistics as
1307 well.
1308 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1309 and csv (comma delimited formatted) data.
1311 - a directory for implementing population simulations has
1312 been added Bio::PopGen::Simulation and 2 simulations - a
1313 Coalescent and a simple single-locus multi-allele genetic drift
1314 simulation have been provided. This replaces the code in
1315 Bio::Tree::RandomTree which has been deprecated until proper
1316 methods for generating random phylogenetic trees are
1317 implemented.
1319 o Bio::Restriction
1320 - new restrion analysis modules
1322 o Bio::Tools::Analysis
1323 - web based DNA and Protein analysis framework and several
1324 implementations
1326 o Bio::Seq::Meta
1327 - per residue annotable sequences
1329 o Bio::Matrix
1330 - Bio::Matrix::PSM - Position Scoring Matrix
1331 - Bio::Matrix::IO has been added for generalized parsing of
1332 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1333 initial implementations for parsing BLOSUM/PAM and Phylip
1334 Distance matricies respectively. A generic matrix
1335 implementation for general use was added in
1336 Bio::Matrix::Generic.
1338 o Bio::Ontology
1339 - major changes
1341 o Bio:Tree
1343 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1344 - small inhibitory RNA
1346 o Bio::SeqFeature::Tools
1347 - seqFeature mapping tools
1348 - Bio::SeqFeature::Tools::Unflattener.pm
1349 -- deal with mapping GenBank feature collections into
1350 Chado/GFF3 processable feature sets (with SO term mappings)
1352 o Bio::Tools::dpAlign
1353 - pure perl dynamic programming sequence alignment
1354 - needs Bioperl-ext
1356 o new Bio::SearchIO formats
1357 - axt and psl: UCSC formats.
1358 - blasttable: NCBI -m 8 or -m 9 format from blastall
1360 o new Bio::SeqIO formats
1361 - chado, tab, kegg, tigr, game
1362 - important fixes for old modules
1364 o Bio::AlignIO: maf
1366 o improved Bio::Tools::Genewise
1368 o Bio::SeqIO now can recongnize sequence formats automatically from
1369 stream
1371 o new parsers in Bio::Tools:
1372 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1374 o Bio::DB::Registry bugs fixed
1375 - BerkeleyDB-indexed flat files can be used by the OBDA system
1376 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1377 used by the OBDA system
1379 o several new HOWTOs
1380 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1381 Databases
1383 o hundreds of new and improved files
1386 o
1387 o Bio::Tree::AlleleNode has been updated to be a container of
1388 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1391 1.2 Branch
1393 1.2.3 Stable release update
1394 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1395 handling.
1396 o Bug #1477 - Sel --> Sec abbreviation fixed
1397 o Fix bug #1487 where paring in-between locations when
1398 end < start caused the FTLocationFactory logic to fail.
1399 o Fix bug #1489 which was not dealing with keywords as an
1400 arrayref properly (this is fixed on the main trunk because
1401 keywords returns a string and the array is accessible via
1402 get_keywords).
1403 o Bio::Tree::Tree memory leak (bug #1480) fixed
1404 Added a new initialization option -nodelete which
1405 won't try and cleanup the containing nodes if this
1406 is true.
1407 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1408 this was only present on the branch for the 1.2.1 and 1.2.2 series
1409 - Also merged main trunk changes to the branch which make
1410 newick -> nhx round tripping more effective (storing branch length
1411 and bootstrap values in same locate for NodeNHX and Node
1412 implementations.) Fixes to TreeIO parsing for labeled internal
1413 also required small changes to TreeIO::nhx. Improved
1414 tests for this module as well.
1415 o Bio::SearchIO
1416 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1417 gapped blast properly (was losing hit significance values due to
1418 the extra unexpeted column).
1419 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1420 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1421 although doesn't try to correct it - will get the negative
1422 number for you. Added a test for this as well.
1423 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1424 has no top-level family classification scores but does have scores and
1425 alignments for individual domains.
1426 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1427 regular expression to match the line was missing the possibility of
1428 an extra space. This is rare, which is why we probably did not
1429 catch it before.
1430 - BLAST parsing picks up more of the statistics/parameter fields
1431 at the bottom of reports. Still not fully complete.
1432 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1433 were fixed to include many improvements and added flexiblity
1434 in outputting the files. Bug #1495 was also fixed in the process.
1435 o Bio::DB::GFF
1436 - Update for GFF3 compatibility.
1437 - Added scripts for importing from UCSC and GenBank.
1438 - Added a 1.2003 version number.
1439 o Bio::Graphics
1440 - Updated tutorial.
1441 - Added a 1.2003 version number.
1442 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1443 properly writing keywords out.
1444 o Bio::SeqIO::genbank
1445 - Fixed bug/enhancement #1513 where dates of
1446 the form D-MMM-YYYY were not parsed. Even though this is
1447 invalid format we can handle it - and also cleanup the date
1448 string so it is properly formatted.
1449 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1450 and written with Genbank format. Similarly bug #1515 is fixed to
1451 parse in the ORIGIN text.
1452 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1453 to specify the ID type, one of (accession accession.version
1454 display primary). See Bio::SeqIO::preferred_id_type method
1455 documentation for more information.
1456 o Unigene parsing updated to handle file format changes by NCBI
1458 1.2.2 Stable release update
1460 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1461 - auto-discover ontology name
1462 - bug in parsing relationships when certain characters are in the term
1463 - fixed hard-coded prefix for term identifiers
1464 - various smaller issues
1466 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1467 of Bio::Ontology::TermI
1469 o brought the OBDA Registry code up to latest specs
1471 o Bio::DB::GenBank
1472 - eutils URL change
1473 - accession number retrieval fixed
1475 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1477 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1478 #1459 which now properly report alignment start/end info
1479 for translated BLAST/FASTA searches.
1481 o Bio::TreeIO::newick can parse labeled internal nodes
1483 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1484 for BLASTX if if you provide -report_type => 'BLASTX' when
1485 initializing a BPbl2seq object. Bioperl 1.3 will have better
1486 support for bl2seq in the SearchIO system.
1488 o Bio::Root::IO support a -noclose boolean flag which will not
1489 close a filehandle upon object cleanup - useful when sharing
1490 a filehandle among objects. Additionally code added s.t.
1491 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1493 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1495 o Bio::SeqIO::genbank
1496 - bug #1456 fixed which generated extra sequence lines
1497 - write moltype correctly for genpept
1499 1.2.1 Stable release update
1501 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1503 o Addition from main trunk of Ontology objects, principly to allow
1504 BioSQL releases against 1.2.1
1506 o Fixes and cleanup of Bio::Coordinate modules
1508 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1509 the primary accession number
1511 o Other bug fixes, including bpindex GenBank fix
1513 o Bio::SeqIO::genbank bug #1389 fixed
1515 1.2 Stable major release
1517 o More functionality added to Bio::Perl, the newbie module
1519 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1520 Support for New Hampshire Extended (NHX) format parsing.
1522 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1523 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1524 Hmmpfam parser.
1526 o New ontology parsing Bio::Ontology
1528 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1529 multi-report (mlib) fasta reports, support for waba and exonerate.
1531 o Bio::ClusterIO for parsing Unigene clusters
1533 o Bio::Assembly added for representing phrap and ace assembly clusters.
1535 o Rudimentary support for writing Chado XML (see
1536 GMOD project: www.gmod.org for more information)
1538 o Bio::Coordinate for mapping between different coordinate systems such
1539 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1540 features into different coordinate systems.
1542 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1543 with the get_Stream_by_query method and supports the latest
1544 NCBI eutils interface.
1546 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1547 object for extracting subsets of features : currently only
1548 supports extraction by location.
1550 1.1.1 Developer release
1552 o Deprecated modules are now listed in the DEPRECATED file
1554 o New HowTo documents located in doc/howto describing
1555 a domain of Bioperl.
1557 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1558 and all old bugs are searchable through the bugzilla interface.
1560 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1561 have been addressed.
1563 o Support for Genewise parsing in Bio::Tools::Genewise
1565 o Start of Ontology framework with Bio::Ontology
1567 o Speedup to the Bio::Root::Root object method _rearrange.
1568 A global _load_module method was implemented to simplify the
1569 dynamic loading of modules ala Bio::SeqIO::genbank. This
1570 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1571 etc).
1573 o Several performance improvements to sequence parsing in Bio::SeqIO.
1574 Attempt to speedup by reducing object creation overhead.
1576 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1577 method for sequence retrieval with their E-utils CGI scripts.
1578 More work to support Entrez queries to their fullest is planned
1579 before 1.2 release.
1581 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1583 1.1 Developer release
1585 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1586 this separation removes some of the complexity in our test suite
1587 and separates the core modules in bioperl from those that need
1588 external programs to run.
1590 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1591 not run into trouble running the makefile
1593 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1594 read,create,and write locations for grouped/split locations
1595 (like mRNA features on genomic sequence).
1597 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1598 and PAML (codeml,aaml, etc) parsing.
1600 o Bio::Tree:: objects expanded to handle testing monophyly,
1601 paraphyly, least common ancestor, etc.
1603 o Bio::Coordinate for mapping locations from different coordinate spaces
1605 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1606 added for parsing hmmpfam and hmmsearch output.
1608 o Bio::SearchIO::Writer::TextResultWriter for outputting
1609 a pseudo-blast textfile format
1612 1.0.2 Bug fix release
1614 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1615 in this release will not work after December 2002 when NCBI
1616 shuts off the old Entrez cgi scripts. We have already fixed
1617 on our main development branch and the functionality will be
1618 available in the next stable bioperl release (1.2) slated for
1619 Fall 2002.
1621 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1622 testset by Robin Emig. These were fixed as was the get_aln
1623 method in Bio::Search::HSP::GenericHSP to handle the extra
1624 context sequence that is provided with a FastA alignment.
1626 o Migrating differences between Bio::Search::XX::BlastXX to
1627 Bio::Search::XX::GenericXX objects. This included mechanism
1628 to retrieve whole list of HSPs from Hits and whole list of Hits from
1629 Results in addition to the current next_XX iterator methods that
1630 are available. Added seq_inds() method to GenericHSP which identifies
1631 indexes in the query or hit sequences where conserved,identical,gaps,
1632 or mismatch residues are located (adapted from Steve Chervitz's
1633 implementation in BlastHSP).
1635 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1636 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1638 o Bio::Graphics glyph set improved and extended for GBrowse release
1640 o Bio::Tree::Tree get_nodes implementation improvement thanks
1641 to Howard Ross notice performance problem when writing out
1642 unbalanced trees.
1644 o Bio::Location::Fuzzy::new named parameter -loc_type became
1645 -location_type, Bio::Location::Simple::new named parameter
1646 -seqid becamse -seq_id.
1648 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1649 was mis-detecting that gaps should be placed at the beginning of
1650 the alignment when the best alignment starts internally in the
1651 sequence.
1653 1.0.1 Bug fix release
1655 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1657 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1658 and mixed (3.3 - 3.4) versions of FASTA.
1660 o Small API change to add methods for completeness across
1661 implementations of Bio::Search objects. These new methods
1662 in the interface are implemented by the GenericXX object as well
1663 as the BlastXX objects.
1664 * Bio::Search::Result::ResultI
1665 - hits() method returns list of all Hits (next_hit is an
1666 iterator method)
1668 * Bio::Search::Hit::HitI
1669 - hsps() method returns list of all HSPs (next_hsp is an
1670 iterator method)
1672 o The Bio::SearchIO::Writer classes have been fixed to handle results
1673 created from either psiblast (Search::BlastXX objects) or
1674 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1675 has to be done here to make it work properly and will nee major
1676 API changes.
1678 o Bugs in Bio::Tools::HMMER fixed, including
1679 * #1178 - Root::IO destructor wasn't being called
1680 * #1034 - filter_on_cutoff now behaves properly
1682 o Bio::SeqFeature::Computation initialization args fixed and
1683 tests added.
1685 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1687 o Updated FAQ with more example based answers to typical questions
1689 o Bug #1202 was fixed which would improperly join together qual values
1690 parsed by Bio::SeqIO::qual when a trailing space was not present before
1691 the newline.
1693 1.0.0 Major Stable Release
1695 This represents a major release of bioperl with significant
1696 improvements over the 0.7.x series of releases.
1698 o Bio::Tools::Blast is officially deprecated. Please see
1699 Bio::SearchIO for BLAST and FastA parsing.
1701 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1702 Bio::LocationI objects as well as start/end.
1704 o Bio::Biblio contains modules for Bibliographic data.
1705 Bio::DB::Biblio contains the query modules. Additionally one can
1706 parse medlinexml from the ebi bibliographic query service (BQS)
1707 system and Pubmed xml from NCBI. See Martin Senger's
1708 documentation in Bio::Biblio for more information.
1710 o Bio::DB::Registry is a sequence database registry part of
1711 Open Bioinformatics Database Access. See
1712 http://obda.open-bio.org for more information.
1714 o File-based and In-Memory Sequence caching is provided by
1715 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1716 local database.
1718 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1719 been added by Lincoln Stein.
1721 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1723 o A FAQ has been started and is included in the release to provide
1724 a starting point for frequent questions and issues.
1726 0.9.3 Developer's release
1728 o Event based parsing system improved (SearchIO). With parsers for
1729 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1730 Additionally a lazy parsing system for text and html blast reports was
1731 added and is called psiblast (name subject to change in future releases).
1733 o Bio::Search objects improved and standardized with associated Interfaces
1734 written. The concept of a search "Hit" was standardized to be called
1735 "hit" consistently and the use of "subject" was deprecated in all active
1736 modules.
1738 o Bio::Structure added (since 0.9.1) for Protein structure objects
1739 and PDB parser to retrieve and write these structures from data files.
1741 o Several important Bio::DB::GFF bug fixes for handling features that
1742 are mapped to multiple reference points. Updated mysql adaptor
1743 so as to be able to store large (>100 megabase) chunks of DNA into
1744 Bio::DB::GFF databases.
1746 0.9.2 Developer's release
1748 o Bio::Search and Bio::SearchIO system introduced for event based
1749 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1750 in text and XML and FASTA reports in standard output format.
1752 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1753 generator is included in Bio::TreeIO::RandomTrees and a
1754 statistics module for evaluating.
1756 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1757 server for DAS servers.
1759 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1760 files. The entire BPlite system migrated to using Bio::Root::IO
1761 for the data stream.
1763 o Bio::Tools::Alignment for Consed and sequence Trimming
1764 functionality.
1766 o Bio::Structure for Protein structure information and parsing
1768 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1769 cgi-bin entry point which should be more reliable.
1771 o Bio::Map and Bio::MapIO for biological map navigation and a
1772 framework afor parsing them in. Only preliminary work here.
1774 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1775 Future work will integrate Pise and allow submission of analysis on
1776 remote servers.
1778 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1779 introduced as new objects for handling Sequence Annotation
1780 information (dblinks, references, etc) and is more robust that
1781 previous system.
1783 o Bio::Tools::FASTAParser introduced.
1785 o Scripts from the bioperl script submission project and new
1786 scripts from bioperl authors are included in "scripts" directory.
1788 o Factory objects and interfaces are being introduced and are more
1789 strictly enforced.
1791 o Bio::Root::Root introduced as the base object while
1792 Bio::Root::RootI is now simply an interface.
1794 o Bio::DB::RefSeq provides database access to copy of the NCBI
1795 RefSeq database using the EBI dbfetch script.
1797 0.9.0 Developer's release
1799 o perl version at least 5.005 is now required instead of perl 5.004
1801 o Bio::Tools::Run::RemoteBlast is available for running remote
1802 blast jobs at NCBI.
1804 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1806 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1807 Also added are related modules UTR3, UTR5, Exon, Intron,
1808 Promotor, PolyA and Transcript.
1810 o Speedup of translate method in PrimarySeq
1812 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1813 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1815 o Various fixes to Variation toolkit
1817 o Bio::DB::EMBL provides database access to EMBL sequence data.
1818 Bio::DB::Universal provides a central way to point to indexes
1819 and dbs in a single interface.
1821 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1823 o Bio::Factory::EMBOSS is still in design phase as is
1824 Bio::Factory::ApplicationFactoryI
1826 o Dia models for bioperl design are provided in the models/ directory
1828 0.7.2 Bug fix release
1830 o documentation fixes in many modules - SYNOPSIS code verified
1831 to be runnable in many (but not all modules)
1833 o corrected MANIFEST file from 0.7.1 release
1835 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1836 split locations
1838 o Bio::SeqIO::genbank
1839 * Correct parsing and writing of genbank format with protein data
1840 * moltype and molecule separation
1842 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1844 o Bio::SimpleAlign fixed to correctly handle consensus
1845 sequence calculation
1847 o Bio::Tools::HMMER supports hmmer 2.2g
1849 o Bio::Tools::BPlite to support report type specific parsing. Most
1850 major changes are not on the 0.7 branch.
1852 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1853 with File::Spec
1855 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1856 in several types of mutations:
1857 1.) AA level: deletion, complex
1858 2.) AA level: complex, inframe
1859 3.) RNA level: silent
1861 o BPbl2seq parsing of empty reports will not die, but will return
1862 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1863 $report->query() and $report->subject() methods. So an easy
1864 way to test if report was empty is to see if
1865 $report->query->seqname is undefined.
1867 0.7.1 Bug fix release
1869 o Better parsing of genbank/EMBL files especially fixing bugs
1870 related to Feature table parsing and locations on remote
1871 sequences. Additionally, species name parsing was better.
1873 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1874 which include a number of header lines.
1876 o More strict genbank and EMBL format writing (corrected number of
1877 spaces where appropriate).
1879 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1880 for related BPlite BUGS that are unresolved in this release.
1882 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1883 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1884 use expasy mirrors or EBI dbfetch cgi-script.
1886 o A moderate number of documentation improvements were made as
1887 well to provide a better code synopsis in each module.
1890 0.7 Large number of changes, including refactoring of the
1891 Object system, new parsers, new functionality and
1892 all round better system. Highlights are:
1895 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1896 Bio::Root::IO for I/O and file/handle capabilities.
1898 o Imported BPlite modules from Ian Korf for BLAST
1899 parsing. This is considered the supported BLAST parser;
1900 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1902 o Improved Sequence Feature model. Added complete location
1903 modelling (with fuzzy and compound locations). See
1904 Bio::LocationI and the modules under Bio/Location. Added
1905 support in Genbank/EMBL format parsing to completely parse
1906 feature tables for complex locations.
1908 o Moved special support for databanks etc to specialized modules under
1909 Bio/Seq/. One of these supports very large sequences through
1910 a temporary file as a backend.
1912 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1913 CDS retrieval and exon shuffling.
1915 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1917 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1918 DB/GDB (the latter has platform-specific limitations).
1920 o New analysis parser framework for HT sequence annotation (see
1921 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1923 o New Alignment IO framework
1925 o New Index modules (Swissprot)
1927 o New modules for running Blast within perl
1928 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1929 Multiple Sequence Alignment tools ClustalW and TCoffee
1930 (Bio::Tools::Run::Alignment).
1932 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1933 documentation across the package.
1935 o Much improved cross platform support. Many known incompatibilities
1936 have been fixed; however, NT and Mac do not work across the entire
1937 setup (see PLATFORMS).
1939 o Many bug fixes, code restructuring, etc. Overall stability and
1940 maintainability benefit a lot.
1942 o A total of 957 automatic tests
1945 0.6.2
1947 There are very few functionality changes but a large
1948 number of software improvements/bug fixes across the package.
1950 o The EMBL/GenBank parsing are improved.
1952 o The Swissprot reading is improved. Swissprot writing
1953 is disabled as it doesn't work at all. This needs to
1954 wait for 0.7 release
1956 o BLAST reports with no hits are correctly parsed.
1958 o Several other bugs of the BLAST parser (regular expressions, ...)
1959 fixed.
1961 o Old syntax calls have been replaced with more modern syntax
1963 o Modules that did not work at all, in particular the Sim4
1964 set have been removed
1966 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1967 have improved compliance with interface specs and documentation
1969 o Mailing list documentation updated throughout the distribution
1971 o Most minor bug fixes have happened.
1973 o The scripts in /examples now work and have the modern syntax
1974 rather than the deprecated syntax
1977 0.6.1 Sun April 2 2000
1979 o Sequences can have Sequence Features attached to them
1980 - The sequence features can be read from or written to
1981 EMBL and GenBank style flat files
1983 o Objects for Annotation, including References (but not
1984 full medline abstracts), Database links and Comments are
1985 provided
1987 o A Species object to represent nodes on a taxonomy tree
1988 is provided
1990 o The ability to parse HMMER and Sim4 output has been added
1992 o The Blast parsing has been improved, with better PSI-BLAST
1993 support and better overall behaviour.
1995 o Flat file indexed databases provide both random access
1996 and sequential access to their component sequences.
1998 o A CodonTable object has been written with all known
1999 CodonTables accessible.
2001 o A number of new lightweight analysis tools have been
2002 added, such as molecular weight determination.
2004 The 0.6 release also has improved software engineering
2006 o The sequence objects have been rewritten, providing more
2007 maintainable and easier to implement objects. These
2008 objects are backwardly compatible with the 0.05.1 objects
2010 o Many objects are defined in terms of interfaces and then
2011 a Perl implementation has been provided. The interfaces
2012 are found in the 'I' files (module names ending in 'I').
2014 This means that it is possible to wrap C/CORBA/SQL access
2015 as true "bioperl" objects, compatible with the rest of
2016 bioperl.
2018 o The SeqIO system has been overhauled to provide better
2019 processing and perl-like automatic interpretation of <>
2020 over arguments.
2022 o Many more tests have been added (a total of 172 automatic
2023 tests are now run before release).
2027 0.05.1 Tue Jun 29 05:30:44 1999
2028 - Central distribution now requires Perl 5.004. This was
2029 done to get around 5.003-based problems in Bio/Index/*
2030 and SimpleAlign.
2031 - Various bug fixes in the Bio::Tools::Blast modules
2032 including better exception handling and PSI-Blast
2033 support. See Bio/Tools/Blast/CHANGES for more.
2034 - Fixed the Parse mechanism in Seq.pm to use readseq.
2035 Follow the instructions in README for how to install
2036 it (basically, you have to edit Parse.pm).
2037 - Improved documentation of Seq.pm, indicating where
2038 objects are returned and where strings are returned.
2039 - Fixed uninitialized warnings in Bio::Root::Object.pm
2040 and Bio::Tools::SeqPattern.pm.
2041 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
2043 0.05 Sun Apr 25 01:14:11 1999
2044 - Bio::Tools::Blast modules have less memory problems
2045 and faster parsing. Webblast uses LWP and supports
2046 more functionality. See Bio/Tools/Blast/CHANGES for more.
2047 - The Bio::SeqIO system has been started, moving the
2048 sequence reformatting code out of the sequence object
2049 - The Bio::Index:: system has been started, providing
2050 generic index capabilities and specifically works for
2051 Fasta formatted databases and EMBL .dat formatted
2052 databases
2053 - The Bio::DB:: system started, providing access to
2054 databases, both via flat file + index (see above) and
2055 via http to NCBI
2056 - The scripts/ directory, where industrial strength scripts
2057 are put has been started.
2058 - Many changes - a better distribution all round.
2060 0.04.4 Wed Feb 17 02:20:13 1999
2061 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
2062 (see Bio::Tools::Blast::CHANGES).
2063 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
2064 - Beefed up the t/Fasta.t test script.
2065 - Small fix in Bio::Seq::type() (now always returns a string).
2066 - Changed Bio::Root::Utilities::get_newline_char() to
2067 get_newline() since it could return more than one char.
2068 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
2069 - Changed default timeout to 20 seconds (was 3).
2070 - Moved lengthy modification notes to the bottom of some files.
2071 - Fixed SimpleAlign write_fasta bug.
2072 - Beefed up SimpleAlign.t test
2074 0.04.3 Thu Feb 4 07:48:53 1999
2075 - Bio::Root::Object.pm and Global.pm now detect when
2076 script is run as a CGI and suppress output that is only
2077 appropriate when running interactively.
2078 - Bio::Root::Err::_set_context() adds name of script ($0).
2079 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
2080 regarding the use of the static objects via the qw(:obj) tag.
2081 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
2082 CORE::reverse, avoiding Perl warnings.
2083 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
2084 example scripts (see Bio::Tools::Blast::CHANGES).
2085 - examples/seq/seqtools.pl no longer always warns about using
2086 -prot or -nucl command-line arguments; only when using the
2087 -debug argument.
2088 - Methods added to Bio::Root::Utilities: create_filehandle(),
2089 get_newline_char(), and taste_file() to generalize filehandle
2090 creation and autodetect newline characters in files/streams
2091 (see bug report #19).
2092 - Bio::Root::IOManager::read() now handles timeouts and uses
2093 Utilities::create_filehandle().
2094 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
2095 of hardwiring in "\n".
2096 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
2098 0.04.2 Wed Dec 30 02:27:36 1998
2099 - Bug fixes in Bio::Tools::Blast modules, version 0.073
2100 (see Bio::Tools::Blast::CHANGES).
2101 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
2102 to CORE::reverse (prevents ambiguous warnings with 5.005).
2103 - Appending '.tmp.bioperl' to temporary files created by
2104 Bio::Root::Utilities::compress() or uncompress() to
2105 make it easy to identify & cleanup these files as needed.
2106 - Developers: Created CVS branch release-0-04-bug from
2107 release-0-04-1. Before making bug fixes to the 0.04.1 release,
2108 be sure to cvs checkout this branch into a clean area.
2110 0.04.1 Wed Dec 16 05:39:15 1998
2111 - Bug fixes in Bio::Tools::Blast modules, version 0.072
2112 (see Bio::Tools::Blast::CHANGES).
2113 - Compile/SW/Makefile.PL now removes *.o and *.a files
2114 with make clean.
2116 0.04 Tue Dec 8 07:49:19 1998
2117 - Lots of new modules added including:
2118 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
2119 and Bio/Compile directory containing XS-linked C code for
2120 creating Smith-Waterman sequence alignments from within Perl.
2121 * Steve Chervitz's Blast distribution has been incorporated.
2122 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
2123 - Bio/examples directory for demo scripts for all included modules.
2124 - Bio/t directory containing test suit for all included modules.
2125 - For changes specific to the Blast-related modules prior to
2126 incorporation in this central distribution, see the CHANGES
2127 file in the Bio/Tools/Blast directory.
2129 0.01 Tue Sep 8 14:23:22 1998
2130 - original version from central CVS tree; created by h2xs 1.18