| blob | a4bdd5dae36534b0e2cc4a36790da1cde3423a6f |
1 Summary of important user-visible changes for BioPerl
2 -----------------------------------------------------
4 {{$NEXT}}
6 * The deprecated() method has been deprecated. It is recommended
7 to use Carp::carp to warn.
10 1.7.4 2019-02-05 16:23:53+00:00 Europe/London
12 * Fix Bio::Root::Test, and the testuite, to properly check for
13 internet connection and the NO_NETWORK_TESTING environment
14 variable. Previously, tests that required internet connection
15 were not being skipped, causing tests to fail.
18 1.7.3 2019-01-30 13:30:34+00:00 Europe/London
20 * The following modules have been removed from the BioPerl
21 distribution to be part of a separate distribution. They have
22 been integrated into other module distributions for independent
23 development:
25 Bio::Align::Graphics
26 Bio::AlignIO::nexml
27 Bio::AlignIO::stockholm
28 Bio::Assembly::*
29 Bio::Cluster::*
30 Bio::ClusterI::*
31 Bio::ClusterIO::*
32 Bio::DB::Ace
33 Bio::DB::BioFetch
34 Bio::DB::CUTG
35 Bio::DB::EMBL
36 Bio::DB::EntrezGene
37 Bio::DB::Expression::*
38 Bio::DB::GFF
39 Bio::DB::GFF::Adaptor::*
40 Bio::DB::GFF::Aggregator::*
41 Bio::DB::GFF::Featname
42 Bio::DB::GFF::Feature
43 Bio::DB::GFF::Homol
44 Bio::DB::GFF::RelSegment
45 Bio::DB::GFF::Segment
46 Bio::DB::GFF::Typename
47 Bio::DB::GenBank
48 Bio::DB::GenPept
49 Bio::DB::HIV::*
50 Bio::DB::MeSH
51 Bio::DB::NCBIHelper
52 Bio::DB::Query::GenBank
53 Bio::DB::Query::HIVQuery
54 Bio::DB::RefSeq
55 Bio::DB::SeqFeature::*
56 Bio::DB::SeqVersion::*
57 Bio::DB::SwissProt
58 Bio::DB::TFBS::*
59 Bio::DB::Taxonomy::entrez
60 Bio::DB::Taxonomy::sqlite
61 Bio::DB::Universal
62 Bio::Draw::Pictogram
63 Bio::Factory::MapFactoryI
64 Bio::Index::Hmmer
65 Bio::Index::Stockholm
66 Bio::LiveSeq::*
67 Bio::Map::*
68 Bio::MapIO::*
69 Bio::MolEvol::CodonModel
70 Bio::Nexml::Factory
71 Bio::NexmlIO
72 Bio::Perl
73 Bio::Phenotype::*
74 Bio::PhyloNetwork::*
75 Bio::PopGen::*
76 Bio::Restriction::*
77 Bio::Root::Build
78 Bio::Search::HSP::HMMERHSP
79 Bio::Search::HSP::HmmpfamHSP
80 Bio::Search::Hit::HMMERHit
81 Bio::Search::Hit::HmmpfamHit
82 Bio::Search::Hit::hmmer3Hit
83 Bio::Search::Result::HMMERResult
84 Bio::Search::Result::HmmpfamResult
85 Bio::Search::Result::hmmer3Result
86 Bio::SearchDist
87 Bio::SearchIO::hmmer
88 Bio::SearchIO::hmmer2
89 Bio::SearchIO::hmmer3
90 Bio::SearchIO::hmmer_pull
91 Bio::SeqEvolution::*
92 Bio::SeqFeature::SiRNA::*
93 Bio::SeqIO::abi
94 Bio::SeqIO::agave
95 Bio::SeqIO::alf
96 Bio::SeqIO::chadoxml
97 Bio::SeqIO::chaos
98 Bio::SeqIO::chaosxml
99 Bio::SeqIO::ctf
100 Bio::SeqIO::entrezgene
101 Bio::SeqIO::excel
102 Bio::SeqIO::exp
103 Bio::SeqIO::flybase_chadoxml
104 Bio::SeqIO::lasergene
105 Bio::SeqIO::nexml
106 Bio::SeqIO::pln
107 Bio::SeqIO::strider
108 Bio::SeqIO::ztr
109 Bio::Structure::*
110 Bio::Taxonomy::*
111 Bio::Tools::AlignFactory
112 Bio::Tools::Analysis::* (except SimpleAnalysisBase)
113 Bio::Tools::Gel
114 Bio::Tools::HMMER::*
115 Bio::Tools::Hmmpfam
116 Bio::Tools::Phylo::Gumby
117 Bio::Tools::Protparam
118 Bio::Tools::Run::RemoteBlast
119 Bio::Tools::SiRNA::*
120 Bio::Tools::dpAlign
121 Bio::Tools::pSW
122 Bio::Tree::AlleleNode
123 Bio::Tree::Draw::Cladogram
124 Bio::TreeIO::nexml
125 Bio::TreeIO::svggraph
126 Bio::Variation::*
128 * The following modules are new in the BioPerl distribution. They
129 have been previously released in the BioPerl-Run distribution.
130 This will enable smaller distributions that provide a
131 Bio::Tool::Run interface, to be only dependent on the BioPerl
132 distribution instead of the whole (very large) BioPerl-Run:
134 Bio::Tools::Run::Analysis
135 Bio::Tools::Run::AnalysisFactory
136 Bio::Tools::Run::Phylo::PhyloBase
137 Bio::Tools::Run::WrapperBase
138 Bio::Tools::Run::WrapperBase::CommandExts
140 * The following programs have been removed:
142 bp_biofetch_genbank_proxy
143 bp_blast2tree
144 bp_bulk_load_gff
145 bp_composite_LD
146 bp_das_server
147 bp_download_query_genbank
148 bp_fast_load_gff
149 bp_flanks
150 bp_genbank2gff
151 bp_generate_histogram
152 bp_heterogeneity_test
153 bp_hivq
154 bp_hmmer_to_table
155 bp_load_gff
156 bp_meta_gff
157 bp_netinstall
158 bp_parse_hmmsearch
159 bp_process_wormbase
160 bp_query_entrez_taxa
161 bp_remote_blast
162 bp_seqfeature_delete
163 bp_seqfeature_gff3
164 bp_seqfeature_load
166 * Because of the move of so many modules and programs into
167 separate distributions, the following modules are no longer
168 prerequisites:
170 Ace
171 Ace::Sequence::Homol
172 Algorithm::Munkres
173 Apache::DBI
174 Archive::Tar
175 Array::Compare
176 Bio::ASN1::EntrezGene
177 Bio::Expression::Contact
178 Bio::Expression::DataSet
179 Bio::Expression::Platform
180 Bio::Expression::Sample
181 Bio::Ext::Align
182 Bio::GMOD::CMap::Utils
183 Bio::Phylo::Factory
184 Bio::Phylo::Forest::Tree
185 Bio::Phylo::IO
186 Bio::Phylo::Matrices
187 Bio::Phylo::Matrices::Datum
188 Bio::Phylo::Matrices::Matrix
189 Bio::SeqFeature::Annotated
190 Bio::SeqIO::staden::read
191 Bio::Tools::Run::Alignment::Clustalw
192 Bio::Tools::Run::Ensembl
193 Bio::Tools::Run::Phylo::Molphy::ProtML
194 Bio::Tools::Run::Phylo::Phylip::Neighbor
195 Bio::Tools::Run::Phylo::Phylip::ProtDist
196 Bio::Tools::Run::Phylo::Phylip::ProtPars
197 Bio::Tools::Run::Samtools
198 CGI
199 CPAN
200 Cache::FileCache
201 Config
202 Convert::Binary::C
203 DBD::Pg
204 DBD::SQLite
205 Data::Stag::XMLWriter
206 Encode
207 English
208 ExtUtils::Install
209 ExtUtils::Manifest
210 File::Glob
211 GD::Simple
212 Getopt::Std
213 Graph::Undirected
214 GraphViz
215 HTML::HeadParser
216 HTML::TableExtract
217 LWP
218 LWP::Simple
219 MIME::Base64
220 Memoize
221 PostScript::TextBlock
222 SVG
223 SVG::Graph
224 SVG::Graph::Data
225 SVG::Graph::Data::Node
226 SVG::Graph::Data::Tree
227 Sort::Naturally
228 Spreadsheet::ParseExcel
229 Term::ReadLine
230 Text::NSP::Measures::2D::Fisher2::twotailed
231 Text::ParseWords
232 Time::Local
233 Tree::DAG_Node
234 URI::Escape
235 WWW::Mechanize
236 XML::Simple
238 * The following is a new prerequisite:
240 Test::RequiresInternet
242 * The deobfuscator has been removed.
244 * The emacs bioperl minor mode is no longer distributed as part of the
245 perl module distributions. See
246 https://github.com/bioperl/emacs-bioperl-mode
249 1.7.2 - "Entebbe"
251 [Bugs]
253 * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
254 * #245 - Code coverage fixes [zmughal,cjfields]
255 * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
256 * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
257 * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
258 * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
259 * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
260 * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
261 * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
262 * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
263 * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
264 * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
266 [Code changes]
268 * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
270 1.7.1 - "Election"
272 [Bugs]
274 * Minor release to incorporate fix for CPAN indexing, which
275 prevented proper updates [cjfields]
276 * Fix problem in managing Target attribute for gff3 [Jukes34]
277 * Minor bug fixes related to NCBI HTTPS support [cjfields]
279 1.7.0 - "Disney"
281 [New site]
283 * We have migrated to Github Pages. This was actually planned, but the
284 recent OBF server compromise forced our hand.
286 Brian Osborne [bosborne] took this under his wing to move docs and has
287 done a tremendous amount of work formatting the site and working out some
288 of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
289 Cantalupo and Franscison Ossandon also helped. Kudos!!
291 * Similarly, the official issue tracker is now Github Issues. This has
292 been updated in the relevant documentation bits (we hope!)
294 [Code changes]
296 * Previously deprecated modules removed
297 * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
298 * Bio::DB::SeqHound has been removed due to the service no longer being
299 available
300 * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
301 reasons due to the server no longer having a valid cert
302 * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
303 * Bio::Coordinate, Bio::SearchIO::blastxml,
304 Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
305 added on CPAN
307 [New features]
309 * Docker instances of tagged releases are available! [hlapp]
310 * NCBI HTTPS support [mjohnson and others]
311 * Bio::SearchIO::infernal
312 - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
313 * Bio::Search::HSP::ModelHSP
314 - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
315 reports [pcantalupo]
316 * Bio::Search::Result::INFERNALResult
317 - Added new module to represent features of Infernal reports [pcantalupo]
318 * Bio::DB::Taxonomy SQLite option [cjfields]
319 * WrapperBase quoted option values [majensen]
320 * Various documentation fixes and updates [bosborne]
322 [Bug Fixes]
324 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
325 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
326 * NeXML parser fixes [fjossandon]
327 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
328 * RT 103272 : SeqFeature database deletion skipped features with a decimal -
329 Joshua Fortriede (Xenbase)
330 * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
331 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
332 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
333 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
334 * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
335 * Issue #84: EMBL format wrapping problem [nyamned]
336 * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
337 * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
338 or compiled C code (when Inline::C is installed) [rocky]
339 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
340 * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
341 * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
342 * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
343 to be consistent with "$hit->bits" behaviour [fjossandon]
344 * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
345 aminoacids made "next_seq" confused and broke the parser [fjossandon]
346 * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
347 Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
348 to "complement(join(A..B,C..D))" [fjossandon]
349 * For the many many many fixes that weren't mentioned - blame the release guy!
351 1.6.924
353 [Significant changes]
355 * Bug/feature issue tracking has moved to GitHub Issues:
356 https://github.com/bioperl/bioperl-live/issues
357 * DB_File has been demoted from "required" to "recommended",
358 which should make easier for Windows users to install BioPerl
359 if they don't need that module.
361 [New features]
363 * Bio::Search::HSP::GenericHSP
364 - Bug #3370, added a "posterior_string" method to retrieve the
365 posterior probability lines (PP) from HMMER3 reports [fjossandon]
366 - Added a "consensus_string" method to retrieve the consensus
367 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
368 * Bio::SearchIO::hmmer2
369 - The number of identical and conserved residues are now calculated
370 directly from the homology line [fjossandon]
371 - Now the Query Length and Hit Length are reported when the alignment
372 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
373 - Implemented the capture of the consensus structure lines [fjossandon]
374 * Bio::SearchIO::hmmer3
375 - The number of identical and conserved residues are now calculated
376 directly from the homology line [fjossandon]
377 - Now the Hit Length is reported when the alignment runs until the end
378 of the sequence/model ('.]' or '[]') [fjossandon]
379 - Implemented the capture of the consensus structure lines [fjossandon]
380 - Implemented the capture of the posterior probability lines [fjossandon]
381 - Completed the development of NHMMER parsing, including alignments [fjossandon]
382 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
383 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
384 "min_score", "min_bits, and "hit_filter" methods from
385 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
386 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
387 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
388 besides Blast, instead of being ignored. Added tests for all moved methods
389 using HMMER outputs and run the full test suite and everything pass [fjossandon]
390 * Bio::SeqIO::MultiFile
391 - Autodetection of file format [fangly]
392 * Bio::Tools::GuessSeqFormat:
393 - Format detection from non-seekable filehandles such as STDIN [fangly]
395 [Bug fixes]
397 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
398 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
399 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
400 * Abstract: Fixed ActivePerl incapability of removing temporary files
401 because of problems closing tied filehandles [fjossandon]
402 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
403 because ActivePerl were producing a ".index.pag" and ".index.dir"
404 files instead of a single ".index" file (like Strawberry Perl).
405 Now those temporary files are correctly considered and deleted. [fjossandon]
406 * Test files: Added missing module requirements (DB_File and Data::Stag)
407 to several tests files that were failing because those modules were
408 not present. Now those test files are correctly skipped instead. [fjossandon]
409 * Blast: Added support to changes in bl2seq from BLAST+ output, which
410 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
411 * Phylip: Return undef in "next_aln" at file end to avoid
412 an infinite loop [yschensandiego]
413 * HMMER3: When a hit description is too long, it is truncated in
414 the Scores table. In those cases, the more complete description from
415 the Annotation line (>>) will be used [fjossandon]
416 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
417 since it is now used by HMMER3 format in alignments [fjossandon]
418 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
419 to return undef if the query/hit length is unknown (like in some
420 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
421 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
422 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
423 added support to multi-query reports, reduced code redundancy,
424 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
425 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
426 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
427 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
428 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
429 * Double-quotes on paths are needed in some places [fjossandon]
430 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
431 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
432 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
433 with the latest changes made in their own repositories [fjossandon]
434 * General synching of files with the master branch [fjossandon]
435 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
436 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
437 * Fixed broken MeSH parser [fjossandon]
438 * Fixed missing detection of format in SeqIO when given a -string [fangly]
440 1.6.923
442 * Major Windows support updates! [fjossandon]
443 * MAKER update to allow for stricter standard codon table [cjfields]
444 * Better support for circular sequences [fjossandon]
445 * Fixes for some complex location types [fjossandon]
446 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
447 * Fix bug #2978 related to BLAST report type [fjossandon]
448 * Deobfuscator fixes [DaveMessina]
450 1.6.922
452 * Address CPAN test failures [cjfields]
453 * Add BIOPROJECT support for Genbank files [hyphaltip]
454 * Better regex support for HMMER3 output [bosborne]
456 1.6.921
458 * Minor update to address CPAN test failures
460 1.6.920
462 * Remove Bio::Biblio and related files [carandraug]
463 - this cause version clashes with an independently-released
464 version of Bio::Biblio
466 1.6.910
468 [New features]
470 * Hash randomization fixes for perl 5.18.x
471 - Note: at least one module (Bio::Map::Physical) still has a failing test;
472 this is documented in bug #3446 and has been TODO'd; we will be pulling
473 Bio::Map and similar modules out of core into separate distributions in the
474 1.7.x release series [cjfields]
476 [New features]
478 * Bio::Seq::SimulatedRead
479 - New module to represent reads taken from other sequences [fangly]
480 * Bio::Root::Root
481 - Support of Clone::Fast as a faster cloning alternative [fangly]
482 * Bio::Root::IO
483 - Moved the format() and variant() methods from Bio::*IO modules to
484 Bio::Root::IO [fangly]
485 - Can now use format() to get the type of IO format in use [fangly]
486 * Bio::Tools::IUPAC
487 - New regexp() method to create regular expressions from IUPAC sequences
488 [fangly]
489 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
490 - Code refresh [fangly]
491 * Bio::DB::Taxonomy
492 - Added support for the Greengenes and Silva taxonomies [fangly]
493 * Bio::Tree::TreeFunctionsI
494 - get_lineage_string() represents a lineage as a string [fangly]
495 - add_trait() returns instead of reporting an error when the column
496 number is exceeded in add_trait() [fangly]
497 - Option to support tree leaves without trait [fangly]
498 - Allow ID of 0 in trait files [fangly]
499 * Bio::DB::Taxonomy::list
500 - Misc optimizations [fangly]
501 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
502 * Bio::DB::Taxonomy::*
503 - get_num_taxa() returns the number of taxa in the database [fangly]
504 * Bio::DB::Fasta and Bio::DB::Qual
505 - support indexing an arbitrary list of files [fangly]
506 - user can supply an arbitrary index file name [fangly]
507 - new option to remove index file at the end [fangly]
508 * Bio::DB::Fasta
509 - now handles IUPAC degenerate residues [fangly]
510 * Bio::PrimarySeq and Bio::PrimarySeqI
511 - speed improvements for large sequences [Ben Woodcroft, fangly]
512 * Bio::PrimaryQual
513 - tightened and optimized quality string validation [fangly]
514 * Bio::SeqIO::fasta
515 - new method and option 'block', to create FASTA output with space
516 intervaled blocks (similar to genbank or EMBL) has been implemented.
517 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
518 in favour of the methods 'width' and 'preferred_id_type` respectively.
519 * Bio::FeatureIO::*
520 - moved from bioperl-live into the separate distribution Bio-FeatureIO
521 * Bio::SeqFeature::Annotated
522 - moved from bioperl-live into the separate distribution Bio-FeatureIO
523 * Bio::Cluster::SequenceFamily
524 - improved performance when using get_members with overlapping multiple
525 criteria
526 * Bio::SearchIO::hmmer3
527 - now supports nhmmer [bosborne]
529 [Bug fixes]
531 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
532 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
533 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
534 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
535 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
536 information was lost in a multi-result blast file [Paul Cantalupo]
537 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
538 total gaps [Paul Cantalupo]
539 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
540 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
541 when end of domain indicator is split across lines [Paul Cantalupo]
542 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
543 cjfields]
544 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
545 instances where blank lines are within sequences [cjfields]
546 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
547 types [fangly]
548 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
549 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
550 cjfields]
551 * Various fixes for Stockholm file indexing and processing [bosborne]
552 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
553 breaks parsing [cjfields]
554 * Fix case where Bio::Seq::Meta* objects with no meta information could not
555 be reverse-complemented [fangly]
556 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
557 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
558 when unsure that values will be numerical [fangly]
559 * Fix undef warnings in Bio::SeqIO::embl [fangly]
560 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
561 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
562 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
563 Sallou]
564 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
565 source_tag and display_name must return a string, not undef [fangly]
566 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
567 add_SeqFeature takes a single argument [fangly]
568 * Use cross-platform filenames and temporary directory in
569 Bio::DB::Taxonomy::flatfile [fangly]
570 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
571 properly identified as existing taxa in the database [fangly]
572 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
573 without also passing a lineage to store [fangly]
574 * Prevent passing a directory to the gi2taxid option (-g) of
575 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
576 [fangly]
577 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
578 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
579 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
580 object before trying to access, and no longer returns repeated sequences.
583 1.6.901 May 18, 2011
585 [Notes]
587 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
588 modules using Ace will also be deprecated [lds, cjfields]
589 * Minor bug fix release
590 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
591 * Address Build.PL issues when DBI is not present [hartzell]
592 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
593 * Remove deprecated code for perl 5.14.0 compat [cjfields]
594 * Due to schema changes and lack of support for older versions, support
595 for NeXML 0.9 is only (very) partially implemented.
596 See: https://redmine.open-bio.org/issues/3207
598 [Bug fixes]
600 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
601 docs [genehack, cjfields]
602 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
603 module version from dist_version (probably not the best way to do this,
604 but it seems to work) [rbuels, cjfields]
607 1.6.900 April 14, 201
609 [Notes]
611 * This will probably be the last release to add significant features to
612 core modules; subsequent releases will be for bug fixes alone.
613 We are planning on a restructuring of core for summer 2011, potentially
614 as part of the Google Summer of Code. This may become BioPerl 2.0.
615 * Version bump represents 'just prior to v 1.7'. We may have point
616 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
617 This code essentially is what is on the github master branch.
619 [New features]
621 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
622 * Bio::Tree refactor
623 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
624 - removal of Scalar::Util::weaken code, which was causing odd headaches
625 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
626 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
627 many others]
628 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
629 [Warren Kretzschmar]
630 * Bio::SeqIO::gbxml
631 - bug 2515 - new contribution [Ryan Golhar, jhannah]
632 * Bio::Assembly::IO
633 - support for reading Maq, Sam and Bowtie files [maj]
634 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
635 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
636 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
637 - bug 2726: reading/writing granularity: whole scaffold or one contig
638 at a time [Joshua Udall, fangly]
639 * Bio::OntologyIO
640 - Added parsing of xrefs to OBO files, which are stored as secondary
641 dbxrefs of the cvterm [Naama Menda]
642 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
643 * PAML code updated to work with PAML 4.4d [DaveMessina]
645 [Bug fixes]
647 * [3198] - sort tabular BLAST hits by score [DaveMessina]
648 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
649 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
650 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
651 [cjfields]
652 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
653 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
654 * [3164] - TreeFunctionsI syntax bug [gjuggler]
655 * [3163] - AssemblyIO speedup [fangly]
656 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
657 hyphaltip]
658 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
659 * [3158] - fix EMBL file mis-parsing [cjfields]
660 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
661 cjfields]
662 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
663 * [3148] - URL change for UniProt [cjfields]
664 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
665 * [3136] - HMMer3 parser fixes [kblin]
666 * [3126] - catch description [Toshihiko Akiba]
667 * [3122] - Catch instances where non-seekable filehandles were being
668 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
669 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
670 [dukeleto, rbuels, cjfields]
671 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
672 jhannah]
673 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
674 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
675 cjfields]
676 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
677 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
678 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
679 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
680 * [3086] - EMBL misparsing long tags [kblin, cjfields]
681 * [3085] - CommandExts and array of files [maj, hyphaltip]
682 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
683 for alignment slices [Ha X. Dang, cjfields]
684 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
685 * [3073] - fix parsing of GenBank files from RDP [cjfields]
686 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
687 * [3064] - All-gap midline BLAST report issues [cjfields]
688 * [3063] - BLASt report RID [Razi Khaja, cjfields]
689 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
690 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
691 * [3039] - correct Newick output root node branch length [gjuggler,
692 DaveMessina]
693 * [3038] - SELEX alignment error [Bernd, cjfields]
694 * [3033] - PrimarySeq ID setting [Bernd, maj]
695 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
696 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
697 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
698 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
699 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
700 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
701 PAML 4.4d [DaveMessina]
702 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
703 DaveMessina]
704 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
705 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
706 * [3017] - using threads with Bio::DB::GenBank [cjfields]
707 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
708 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
709 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
710 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
711 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
712 cjfields]
713 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
714 * [2977] - TreeIO issues [DaveMessina]
715 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
716 * [2944] - Bio::Tools::GFF score [cjfields]
717 * [2942] - correct MapTiling output [maj]
718 * [2939] - PDB residue insertion codes [John May, maj]
719 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
720 * [2928] - GuessSeqFormat raw [maj]
721 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
722 * [2922] - open() directive issue [cjfields]
723 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
724 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
725 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
726 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
727 cjfields]
728 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
729 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
730 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
731 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
732 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
733 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
734 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
735 * [2758] - Bio::AssemblyIO ace problems [fangly]
736 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
737 * [2726] - ace file IO [Josh, fangly]
738 * [2700] - Refactor Build.PL [cjfields]
739 * [2673] - addition of simple Root-based clone() method [cjfields]
740 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
741 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
742 * [2594] - Bio::Species memory leak [cjfields]
743 * [2515] - GenBank XML parser [jhannah]
744 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
745 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
746 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
747 cjfields]
748 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
750 [Deprecated]
752 * Bio::Expression modules - these were originally designed to go with the
753 bioperl-microarray suite of tools, however they have never been completed
754 and so have been removed from the distribution. The original code has
755 been moved into the inactive bioperl-microarray suite. [cjfields]
757 [Other]
759 * Repository moved from Subversion (SVN) to
760 http://github.com/bioperl/bioperl-live [cjfields]
761 * Bug database has moved to Redmine (https://redmine.open-bio.org)
762 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
763 Thieme have been moved to their own distribution (Bio-Microarray).
764 [cjfields]
766 1.6.1 Sept. 29, 2009 (point release)
767 * No change from last alpha except VERSION and doc updates [cjfields]
769 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
770 * Fix for silent OBDA bug related to FASTA validation [cjfields]
772 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
773 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
774 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
775 [cjfields]
776 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
778 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
779 * WinXP test fixes [cjfields, maj]
780 * BioPerl.pod added for descriptive information, fixes CPAN indexing
781 [cjfields]
782 * Minor doc fixes [cjfields]
784 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
785 * Fix tests failing due to merging issues [cjfields]
786 * More documentation updates for POD parsing [cjfields]
788 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
789 * Bio::Root::Build
790 - fix YAML meta data generation [cjfields]
792 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
793 * Bio::Align::DNAStatistics
794 - fix divide by zero problem [jason]
795 * Bio::AlignIO::*
796 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
797 * Bio::AlignIO::stockholm
798 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
799 * Bio::Assembly::Tools::ContigSpectrum
800 - function to score contig spectrum [fangly]
801 * Bio::DB::EUtilities
802 - small updates [cjfields]
803 * Bio::DB::Fasta
804 - berkeleydb database now autoindexes wig files and locks correctly
805 [lstein]
806 * Bio::DB::HIV
807 - various small updates for stability; tracking changes to LANL
808 database interface [maj]
809 * Bio::DB::SeqFeature (lots of updates and changes)
810 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
811 - bug 2835 - patch [Dan Bolser]
812 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
813 * Bio::DB::SwissProt
814 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
815 * Bio::Factory::FTLocationFactory
816 - mailing list bug fix [cjfields]
817 * Bio::LocatableSeq
818 - performance work on column_from_residue_number [hartzell]
819 * Bio::Matrix::IO::phylip
820 - bug 2800 - patch to fix phylip parsing [Wei Zou]
821 * Bio::Nexml
822 - Google Summer of Code project from Chase Miller - parsers for Nexml
823 file format [maj, chmille4]
824 * Bio::PopGen
825 - Make Individual, Population, Marker objects AnnotatableI [maj]
826 - simplify LD code [jason]
827 * Bio::RangeI
828 - deal with empty intersection [jason]
829 * Bio::Restriction
830 - significant overhaul of Bio::Restriction system: complete support for
831 external and non-palindromic cutters. [maj]
832 * Bio::Root::Build
833 - CPANPLUS support, no automatic installation [sendu]
834 * Bio::Root::IO
835 - allow IO::String (regression fix) [cjfields]
836 - catch unintentional undef values [cjfields]
837 - throw if non-fh is passed to -fh [maj]
838 * Bio::Root::Root/RootI
839 - small debugging and core fixes [cjfields]
840 * Bio::Root::Test
841 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
842 * Bio::Root::Utilities
843 - bug 2737 - better warnings [cjfields]
844 * Bio::Search
845 - tiling completely refactored, HOWTO added [maj]
846 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
847 will deprecate usage of the older tiling code in the next BioPerl
848 release
849 - small fixes [cjfields]
850 * Bio::SearchIO
851 - Infernal 1.0 output now parsed [cjfields]
852 - new parser for gmap -f9 output [hartzell]
853 - bug 2852 - fix infinite loop in some output [cjfields]
854 - blastxml output now passes all TODO tests [cjfields]
855 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
856 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
857 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
858 * Bio::Seq::LargePrimarySeq
859 - delete tempdirs [cjfields]
860 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
861 * Bio::Seq::Quality
862 - extract regions based on quality threshold value [Dan Bolser, heikki]
863 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
864 * Bio::SeqFeature::Lite
865 - various Bio::DB::SeqFeature-related fixes [lstein]
866 * Bio::SeqFeature::Tools::TypeMapper
867 - additional terms for GenBank to SO map [scain]
868 * Bio::SeqIO::chadoxml
869 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
870 * Bio::SeqIO::embl
871 - support for CDS records [dave_messina, Sylvia]
872 * Bio::SeqIO::fastq
873 - complete refactoring to handle all FASTQ variants, perform validation,
874 write output. API now conforms with other Bio* parsers and the rest of
875 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
876 [cjfields]
877 * Bio::SeqIO::genbank
878 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
879 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
880 * Bio::SeqIO::largefasta
881 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
882 * Bio::SeqIO::raw
883 - add option for 'single' and 'multiple'
884 * Bio::SeqIO::scf
885 - bug 2881 - fix scf round-tripping [Adam Søgren]
886 * Bio::SeqUtils
887 - bug 2766, 2810 - copy over tags from features, doc fixes [David
888 Jackson]
889 * Bio::SimpleAlign
890 - bug 2793 - patch for add_seq index issue [jhannah, maj]
891 - bug 2801 - throw if args are required [cjfields]
892 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
893 [Tristan Lefebure, maj]
894 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
895 - fix POD and add get_SeqFeatures filter [maj]
896 * Bio::Tools::dpAlign
897 - add support for LocatableSeq [ymc]
898 - to be moved to a separate distribution [cjfields, rbuels]
899 * Bio::Tools::EUtilities
900 - fix for two bugs from mail list [Adam Whitney, cjfields]
901 - add generic ItemContainerI interface for containing same methods
902 [cjfields]
903 * Bio::Tools::HMM
904 - fix up code, add more warnings [cjfields]
905 - to be moved to a separate distribution [cjfields, rbuels]
906 * Bio::Tools::Primer3
907 - bug 2862 - fenceposting issue fixed [maj]
908 * Bio::Tools::Run::RemoteBlast
909 - tests for remote RPS-BLAST [mcook]
910 * Bio::Tools::SeqPattern
911 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
912 * Bio::Tools::tRNAscanSE
913 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
914 * Bio::Tree::*
915 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
916 * Bio::Tree::Statistics
917 - several methods for calculating Fitch-based score, internal trait
918 values, statratio(), sum of leaf distances [heikki]
919 * Bio::Tree::Tree
920 - bug 2869 - add docs indicating edge case where nodes can be
921 prematurely garbage-collected [cjfields]
922 - add as_text() function to create Tree as a string in specified format
923 [maj]
924 * Bio::Tree::TreeFunctionsI
925 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
926 Lefebure, maj]
927 * Bio::TreeIO::newick
928 - fix small semicolon issue [cjfields]
929 * scripts
930 - update to bp_seqfeature_load for SQLite [lstein]
931 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
932 - fastam9_to_table - fix for MPI output [jason]
933 - gccalc - total stats [jason]
934 * General Stuff
935 - POD cleanup re: FEEDBACK section [maj, cjfields]
936 - cleanup or fix dead links [cjfields]
937 - Use of no_* methods (indicating 'number of something') is deprecated
938 in favor of num_* [cjfields]
939 - lots of new tests for the above bugs and refactors [everyone!]
940 - new template for Komodo text editor [cjfields]
942 1.6.0 Winter 2009
943 * Feature/Annotation rollback
944 - Problematic changes introduced prior to the 1.5 release have been
945 rolled back. These changes led to subtle bugs involving operator
946 overloading and interface methods.
947 - Behavior is very similar to that for BioPerl 1.4, with tag values
948 being stored generically as simple scalars. Results in a modest
949 speedup.
950 * Bio::Graphics
951 - Split into a separate distribution on CPAN, primarily so development
952 isn't reliant on a complete BioPerl release.
953 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
954 is only available via Subversion (via bioperl-live main trunk)
955 * Bio::Root::Test
956 - Common test bed for all BioPerl modules
957 * Bio::Root::Build
958 - Common Module::Build-based subclass for all BioPerl modules
959 * Bio::DB::EUtilities
960 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
961 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
962 and user agent request posting and retrieval
963 * Test implementation and reorganization
964 - Tests have been reorganized into groups based on classes or use
965 cases.
966 - Automated test coverage is now online:
967 http://www.bioperl.org/wiki/Test_Coverage
968 - After this release, untested modules will be moved into a
969 separate developer distribution until tests can be derived.
970 Also, new modules to be added are expected to have a test suite
971 and adequate test coverage.
973 1.5.2 Developer release
975 Full details of changes since 1.5.1 are available online at:
976 http://www.bioperl.org/wiki/Change_log
977 The following represents a brief overview of the most important changes.
979 o Bio::Map
980 - Overhaul. Brand new system fully allows markers to have multiple
981 positions on multiple maps, and to have relative positions. Should be
982 backward compatible.
984 o Bio::Taxonomy
985 - This module and all the modules in the Taxonomy directory now
986 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
988 o Bio::DB::Taxonomy
990 - Taxonomy.pm
991 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
993 * New methods ancestor(), each_Descendent() and _handle_internal_id().
995 * Allows for different database modules to create Bio::Taxon objects
996 with the same internal id when the same taxon is requested from each.
998 - flatfile.pm
999 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
1001 * No longer includes the fake root node 'root'; there are multiple roots
1002 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
1004 - entrez.pm
1005 * get_node() has new option -full
1007 * Caches data retrieved from website
1009 o Bio::Species
1010 - Now a Bio::Taxon. Carries out the species name -> specific name munging
1011 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
1012 backward compatability in species() method.
1014 o Bio::Search and Bio::SearchIO
1015 - Overhaul. The existing system has been sped up via some minor changes
1016 (mostly gain-of-function to the API). Bio::PullParserI is introduced
1017 as a potential eventual replacment for the existing system, though as
1018 yet only a Hmmpfam parser exists written using it.
1021 1.5.1 Developer release
1023 o Major problem with how Annotations were written out with
1024 Bio::Seq is fixed by reverting to old behavior for
1025 Bio::Annotation objects.
1027 o Bio::SeqIO
1029 - genbank.pm
1030 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
1031 expect at l east 9 spaces at the beginning of a line to
1032 indicate line wrapping.
1034 * Treat multi-line SOURCE sections correctly, this defect broke
1035 both common_name() and classification()
1037 * parse swissprot fields in genpept file
1039 * parse WGS genbank records
1041 - embl.pm
1042 * Changed regexp for ID line. The capturing parentheses are
1043 the same, the difference is an optional repeated-not-semi-
1044 colon expression following the captured \S+. This means the
1045 regexp works when the division looks like /PRO;/ or when the
1046 division looks like /ANG ;/ - the latter is from EMBL
1047 repbase
1049 * fix ID line parsing: the molecule string can have spaces in
1050 it. Like: "genomic DNA"
1052 - swiss.pm: bugs #1727, #1734
1054 - entrezgene.pm
1055 * Added parser for entrezgene ASN1 (text format) files.
1056 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
1058 o Bio::AlignIO
1060 - maf.pm coordinate problem fixed
1062 o Bio::Taxonomy and Bio::DB::Taxonomy
1064 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
1065 can be done via Web without downloading all the sequence.
1067 o Bio::Tools::Run::RemoteBlast supports more options and complies
1068 to changes to the NCBI interface. It is reccomended that you
1069 retrieve the data in XML instead of plain-text BLAST report to
1070 insure proper parsing and retrieval of all information as NCBI
1071 fully expects to change things in the future.
1073 o Bio::Tree and Bio::TreeIO
1075 - Fixes so that re-rooting a tree works properly
1077 - Writing out nhx format from a newick/nexus file will properly output
1078 bootstrap information. The use must move the internal node labels over
1079 to bootstraps.
1080 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
1081 $node->bootstrap($node->id);
1082 $node->id('');
1083 }
1084 - Nexus parsing is much more flexible now, does not care about
1085 LF.
1087 - Cladogram drawing module in Bio::Tree::Draw
1089 - Node height and depth now properly calculated
1091 - fix tree pruning algorithm so that node with 1 child gets merged
1093 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
1094 bugs and improvements were added, see Gbrowse mailing list for most of
1095 these.
1097 o Bio::DB::GFF partially supports GFF3. See information about
1098 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
1100 o Better location parsing in Bio::Factory::FTLocationFactory -
1101 this is part of the engine for parsing EMBL/GenBank feature table
1102 locations. Nested join/order-by/complement are allowed now
1104 o Bio::PrimarySeqI->translate now takes named parameters
1106 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
1107 reconstruction) is now supported. Parsing different models and
1108 branch specific parametes are now supported.
1110 o Bio::Factory::FTLocationFactory - parse hierarchical locations
1111 (joins of joins)
1113 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
1114 for getter/setter functions
1116 o Bio::SearchIO
1118 - blast bug #1739; match scientific notation in score
1119 and possible e+ values
1121 - blast.pm reads more WU-BLAST parameters and parameters, match
1122 a full database pathname,
1124 - Handle NCBI WEB and newer BLAST formats specifically
1125 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
1127 - psl off-by-one error fixed
1129 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
1130 and HSPs can be constructed from them.
1132 - HSPs query/hit now have a seqdesc field filled out (this was
1133 always available via $hit->description and
1134 $result->query_description
1136 - hmmer.pm can parse -A0 hmmpfam files
1138 - Writer::GbrowseGFF more customizeable.
1140 o Bio::Tools::Hmmpfam
1141 make e-value default score displayed in gff, rather than raw score
1142 allow parse of multiple records
1145 1.5 Developer release
1147 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
1148 provide Jukes-Cantor and Kimura pairwise distance methods,
1149 respectively.
1151 o Bio::AlignIO support for "po" format of POA, and "maf";
1152 Bio::AlignIO::largemultifasta is a new alternative to
1153 Bio::AlignIO::fasta for temporary file-based manipulation of
1154 particularly large multiple sequence alignments.
1156 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
1157 be treated similarly as an assembled contig.
1159 o Bio::CodonUsage provides new rare_codon() and probable_codons()
1160 methods for identifying particular codons that encode a given
1161 amino acid.
1163 o Bio::Coordinate::Utils provides new from_align() method to build
1164 a Bio::Coordinate pair directly from a
1165 Bio::Align::AlignI-conforming object.
1167 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
1168 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
1169 web service using standard Pubmed query syntax, and retrieve
1170 results as XML.
1172 o Bio::DB::GFF has various sundry bug fixes.
1174 o Bio::FeatureIO is a new SeqIO-style subsystem for
1175 writing/reading genomic features to/from files. I/O classes
1176 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
1177 classes only read/write Bio::SeqFeature::Annotated objects.
1178 Notably, the GFF v3 class requires features to be typed into the
1179 Sequence Ontology.
1181 o Bio::Graph namespace contains new modules for manipulation and
1182 analysis of protein interaction graphs.
1184 o Bio::Graphics has many bug fixes and shiny new glyphs.
1186 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
1187 indexing for HMMER reports and FASTA qual files, respectively.
1189 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
1190 new objects that can be placed within a Bio::Map::MapI-compliant
1191 genetic/physical map; Bio::Map::Physical provides a new physical
1192 map type; Bio::MapIO::fpc provides finger-printed clone mapping
1193 import.
1195 o Bio::Matrix::PSM provide new support for postion-specific
1196 (scoring) matrices (e.g. profiles, or "possums").
1198 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
1199 be instantiated without explicitly using Bio::OntologyIO. This
1200 is possible through changes to Bio::Ontology::OntologyStore to
1201 download ontology files from the web as necessary. Locations of
1202 ontology files are hard-coded into
1203 Bio::Ontology::DocumentRegistry.
1205 o Bio::PopGen includes many new methods and data types for
1206 population genetics analyses.
1208 o New constructor to Bio::Range, unions(). Given a list of
1209 ranges, returns another list of "flattened" ranges --
1210 overlapping ranges are merged into a single range with the
1211 mininum and maximum coordinates of the entire overlapping group.
1213 o Bio::Root::IO now supports -url, in addition to -file and -fh.
1214 The new -url argument allows one to specify the network address
1215 of a file for input. -url currently only works for GET
1216 requests, and thus is read-only.
1218 o Bio::SearchIO::hmmer now returns individual Hit objects for each
1219 domain alignment (thus containing only one HSP); previously
1220 separate alignments would be merged into one hit if the domain
1221 involved in the alignments was the same, but this only worked
1222 when the repeated domain occured without interruption by any
1223 other domain, leading to a confusing mixture of Hit and HSP
1224 objects.
1226 o Bio::Search::Result::ResultI-compliant report objects now
1227 implement the "get_statistics" method to access
1228 Bio::Search::StatisticsI objects that encapsulate any
1229 statistical parameters associated with the search (e.g. Karlin's
1230 lambda for BLAST/FASTA).
1232 o Bio::Seq::LargeLocatableSeq combines the functionality already
1233 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
1235 o Bio::SeqFeature::Annotated is a replacement for
1236 Bio::SeqFeature::Generic. It breaks compliance with the
1237 Bio::SeqFeatureI interface because the author was sick of
1238 dealing with untyped annotation tags. All
1239 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
1240 compliant, and accessible through Bio::Annotation::Collection.
1242 o Bio::SeqFeature::Primer implements a Tm() method for primer
1243 melting point predictions.
1245 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
1246 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
1248 o Bio::Taxonomy::Node now implements the methods necessary for
1249 Bio::Species interoperability.
1251 o Bio::Tools::CodonTable has new reverse_translate_all() and
1252 make_iupac_string() methods.
1254 o Bio::Tools::dpAlign now provides sequence profile alignments.
1256 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
1258 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
1259 parsers.
1261 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
1262 for designing small inhibitory RNA.
1264 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
1265 methods based on a distance matrix.
1267 o Bio::Tree::Statistics provides an assess_bootstrap() method to
1268 calculate bootstrap support values on a guide tree topology,
1269 based on provided bootstrap tree topologies.
1271 o Bio::TreeIO now supports the Pagel (PAG) tree format.
1273 1.4 branch
1275 1.4.1
1277 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
1279 o Bio::Graphics will work with gd1 or gd2
1281 o Bio::SearchIO
1282 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
1283 (RF lines alone)
1284 - blast.pm Parse multi-line query fields properly
1285 - small speed improvements to blasttable.pm and others
1287 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
1288 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
1289 supporting more complex queries
1292 1.4. Stable major release
1294 Since initial 1.2.0, 3000 separate changes have been made to make this release.
1296 o installable scripts
1298 o global module version from Bio::Root:Version
1300 o Bio::Graphics
1301 - major improvements; SVG support
1303 o Bio::Popgen
1304 - population genetics
1305 - support several population genetics types of questions.
1306 - Tests for statistical neutrality of mutations
1307 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
1308 Tests of population structure (Wright's F-statistic: Fst) is in
1309 Bio::PopGen::PopStats. Calculating composite linkage
1310 disequilibrium (LD) is available in Bio::PopGen::Statistics as
1311 well.
1312 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1313 and csv (comma delimited formatted) data.
1315 - a directory for implementing population simulations has
1316 been added Bio::PopGen::Simulation and 2 simulations - a
1317 Coalescent and a simple single-locus multi-allele genetic drift
1318 simulation have been provided. This replaces the code in
1319 Bio::Tree::RandomTree which has been deprecated until proper
1320 methods for generating random phylogenetic trees are
1321 implemented.
1323 o Bio::Restriction
1324 - new restrion analysis modules
1326 o Bio::Tools::Analysis
1327 - web based DNA and Protein analysis framework and several
1328 implementations
1330 o Bio::Seq::Meta
1331 - per residue annotable sequences
1333 o Bio::Matrix
1334 - Bio::Matrix::PSM - Position Scoring Matrix
1335 - Bio::Matrix::IO has been added for generalized parsing of
1336 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1337 initial implementations for parsing BLOSUM/PAM and Phylip
1338 Distance matricies respectively. A generic matrix
1339 implementation for general use was added in
1340 Bio::Matrix::Generic.
1342 o Bio::Ontology
1343 - major changes
1345 o Bio:Tree
1347 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1348 - small inhibitory RNA
1350 o Bio::SeqFeature::Tools
1351 - seqFeature mapping tools
1352 - Bio::SeqFeature::Tools::Unflattener.pm
1353 -- deal with mapping GenBank feature collections into
1354 Chado/GFF3 processable feature sets (with SO term mappings)
1356 o Bio::Tools::dpAlign
1357 - pure perl dynamic programming sequence alignment
1358 - needs Bioperl-ext
1360 o new Bio::SearchIO formats
1361 - axt and psl: UCSC formats.
1362 - blasttable: NCBI -m 8 or -m 9 format from blastall
1364 o new Bio::SeqIO formats
1365 - chado, tab, kegg, tigr, game
1366 - important fixes for old modules
1368 o Bio::AlignIO: maf
1370 o improved Bio::Tools::Genewise
1372 o Bio::SeqIO now can recongnize sequence formats automatically from
1373 stream
1375 o new parsers in Bio::Tools:
1376 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1378 o Bio::DB::Registry bugs fixed
1379 - BerkeleyDB-indexed flat files can be used by the OBDA system
1380 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1381 used by the OBDA system
1383 o several new HOWTOs
1384 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1385 Databases
1387 o hundreds of new and improved files
1390 o
1391 o Bio::Tree::AlleleNode has been updated to be a container of
1392 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1395 1.2 Branch
1397 1.2.3 Stable release update
1398 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1399 handling.
1400 o Bug #1477 - Sel --> Sec abbreviation fixed
1401 o Fix bug #1487 where paring in-between locations when
1402 end < start caused the FTLocationFactory logic to fail.
1403 o Fix bug #1489 which was not dealing with keywords as an
1404 arrayref properly (this is fixed on the main trunk because
1405 keywords returns a string and the array is accessible via
1406 get_keywords).
1407 o Bio::Tree::Tree memory leak (bug #1480) fixed
1408 Added a new initialization option -nodelete which
1409 won't try and cleanup the containing nodes if this
1410 is true.
1411 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1412 this was only present on the branch for the 1.2.1 and 1.2.2 series
1413 - Also merged main trunk changes to the branch which make
1414 newick -> nhx round tripping more effective (storing branch length
1415 and bootstrap values in same locate for NodeNHX and Node
1416 implementations.) Fixes to TreeIO parsing for labeled internal
1417 also required small changes to TreeIO::nhx. Improved
1418 tests for this module as well.
1419 o Bio::SearchIO
1420 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1421 gapped blast properly (was losing hit significance values due to
1422 the extra unexpeted column).
1423 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1424 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1425 although doesn't try to correct it - will get the negative
1426 number for you. Added a test for this as well.
1427 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1428 has no top-level family classification scores but does have scores and
1429 alignments for individual domains.
1430 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1431 regular expression to match the line was missing the possibility of
1432 an extra space. This is rare, which is why we probably did not
1433 catch it before.
1434 - BLAST parsing picks up more of the statistics/parameter fields
1435 at the bottom of reports. Still not fully complete.
1436 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1437 were fixed to include many improvements and added flexiblity
1438 in outputting the files. Bug #1495 was also fixed in the process.
1439 o Bio::DB::GFF
1440 - Update for GFF3 compatibility.
1441 - Added scripts for importing from UCSC and GenBank.
1442 - Added a 1.2003 version number.
1443 o Bio::Graphics
1444 - Updated tutorial.
1445 - Added a 1.2003 version number.
1446 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1447 properly writing keywords out.
1448 o Bio::SeqIO::genbank
1449 - Fixed bug/enhancement #1513 where dates of
1450 the form D-MMM-YYYY were not parsed. Even though this is
1451 invalid format we can handle it - and also cleanup the date
1452 string so it is properly formatted.
1453 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1454 and written with Genbank format. Similarly bug #1515 is fixed to
1455 parse in the ORIGIN text.
1456 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1457 to specify the ID type, one of (accession accession.version
1458 display primary). See Bio::SeqIO::preferred_id_type method
1459 documentation for more information.
1460 o Unigene parsing updated to handle file format changes by NCBI
1462 1.2.2 Stable release update
1464 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1465 - auto-discover ontology name
1466 - bug in parsing relationships when certain characters are in the term
1467 - fixed hard-coded prefix for term identifiers
1468 - various smaller issues
1470 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1471 of Bio::Ontology::TermI
1473 o brought the OBDA Registry code up to latest specs
1475 o Bio::DB::GenBank
1476 - eutils URL change
1477 - accession number retrieval fixed
1479 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1481 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1482 #1459 which now properly report alignment start/end info
1483 for translated BLAST/FASTA searches.
1485 o Bio::TreeIO::newick can parse labeled internal nodes
1487 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1488 for BLASTX if if you provide -report_type => 'BLASTX' when
1489 initializing a BPbl2seq object. Bioperl 1.3 will have better
1490 support for bl2seq in the SearchIO system.
1492 o Bio::Root::IO support a -noclose boolean flag which will not
1493 close a filehandle upon object cleanup - useful when sharing
1494 a filehandle among objects. Additionally code added s.t.
1495 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1497 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1499 o Bio::SeqIO::genbank
1500 - bug #1456 fixed which generated extra sequence lines
1501 - write moltype correctly for genpept
1503 1.2.1 Stable release update
1505 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1507 o Addition from main trunk of Ontology objects, principly to allow
1508 BioSQL releases against 1.2.1
1510 o Fixes and cleanup of Bio::Coordinate modules
1512 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1513 the primary accession number
1515 o Other bug fixes, including bpindex GenBank fix
1517 o Bio::SeqIO::genbank bug #1389 fixed
1519 1.2 Stable major release
1521 o More functionality added to Bio::Perl, the newbie module
1523 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1524 Support for New Hampshire Extended (NHX) format parsing.
1526 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1527 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1528 Hmmpfam parser.
1530 o New ontology parsing Bio::Ontology
1532 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1533 multi-report (mlib) fasta reports, support for waba and exonerate.
1535 o Bio::ClusterIO for parsing Unigene clusters
1537 o Bio::Assembly added for representing phrap and ace assembly clusters.
1539 o Rudimentary support for writing Chado XML (see
1540 GMOD project: www.gmod.org for more information)
1542 o Bio::Coordinate for mapping between different coordinate systems such
1543 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1544 features into different coordinate systems.
1546 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1547 with the get_Stream_by_query method and supports the latest
1548 NCBI eutils interface.
1550 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1551 object for extracting subsets of features : currently only
1552 supports extraction by location.
1554 1.1.1 Developer release
1556 o Deprecated modules are now listed in the DEPRECATED file
1558 o New HowTo documents located in doc/howto describing
1559 a domain of Bioperl.
1561 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1562 and all old bugs are searchable through the bugzilla interface.
1564 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1565 have been addressed.
1567 o Support for Genewise parsing in Bio::Tools::Genewise
1569 o Start of Ontology framework with Bio::Ontology
1571 o Speedup to the Bio::Root::Root object method _rearrange.
1572 A global _load_module method was implemented to simplify the
1573 dynamic loading of modules ala Bio::SeqIO::genbank. This
1574 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1575 etc).
1577 o Several performance improvements to sequence parsing in Bio::SeqIO.
1578 Attempt to speedup by reducing object creation overhead.
1580 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1581 method for sequence retrieval with their E-utils CGI scripts.
1582 More work to support Entrez queries to their fullest is planned
1583 before 1.2 release.
1585 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1587 1.1 Developer release
1589 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1590 this separation removes some of the complexity in our test suite
1591 and separates the core modules in bioperl from those that need
1592 external programs to run.
1594 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1595 not run into trouble running the makefile
1597 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1598 read,create,and write locations for grouped/split locations
1599 (like mRNA features on genomic sequence).
1601 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1602 and PAML (codeml,aaml, etc) parsing.
1604 o Bio::Tree:: objects expanded to handle testing monophyly,
1605 paraphyly, least common ancestor, etc.
1607 o Bio::Coordinate for mapping locations from different coordinate spaces
1609 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1610 added for parsing hmmpfam and hmmsearch output.
1612 o Bio::SearchIO::Writer::TextResultWriter for outputting
1613 a pseudo-blast textfile format
1616 1.0.2 Bug fix release
1618 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1619 in this release will not work after December 2002 when NCBI
1620 shuts off the old Entrez cgi scripts. We have already fixed
1621 on our main development branch and the functionality will be
1622 available in the next stable bioperl release (1.2) slated for
1623 Fall 2002.
1625 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1626 testset by Robin Emig. These were fixed as was the get_aln
1627 method in Bio::Search::HSP::GenericHSP to handle the extra
1628 context sequence that is provided with a FastA alignment.
1630 o Migrating differences between Bio::Search::XX::BlastXX to
1631 Bio::Search::XX::GenericXX objects. This included mechanism
1632 to retrieve whole list of HSPs from Hits and whole list of Hits from
1633 Results in addition to the current next_XX iterator methods that
1634 are available. Added seq_inds() method to GenericHSP which identifies
1635 indexes in the query or hit sequences where conserved,identical,gaps,
1636 or mismatch residues are located (adapted from Steve Chervitz's
1637 implementation in BlastHSP).
1639 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1640 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1642 o Bio::Graphics glyph set improved and extended for GBrowse release
1644 o Bio::Tree::Tree get_nodes implementation improvement thanks
1645 to Howard Ross notice performance problem when writing out
1646 unbalanced trees.
1648 o Bio::Location::Fuzzy::new named parameter -loc_type became
1649 -location_type, Bio::Location::Simple::new named parameter
1650 -seqid becamse -seq_id.
1652 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1653 was mis-detecting that gaps should be placed at the beginning of
1654 the alignment when the best alignment starts internally in the
1655 sequence.
1657 1.0.1 Bug fix release
1659 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1661 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1662 and mixed (3.3 - 3.4) versions of FASTA.
1664 o Small API change to add methods for completeness across
1665 implementations of Bio::Search objects. These new methods
1666 in the interface are implemented by the GenericXX object as well
1667 as the BlastXX objects.
1668 * Bio::Search::Result::ResultI
1669 - hits() method returns list of all Hits (next_hit is an
1670 iterator method)
1672 * Bio::Search::Hit::HitI
1673 - hsps() method returns list of all HSPs (next_hsp is an
1674 iterator method)
1676 o The Bio::SearchIO::Writer classes have been fixed to handle results
1677 created from either psiblast (Search::BlastXX objects) or
1678 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1679 has to be done here to make it work properly and will nee major
1680 API changes.
1682 o Bugs in Bio::Tools::HMMER fixed, including
1683 * #1178 - Root::IO destructor wasn't being called
1684 * #1034 - filter_on_cutoff now behaves properly
1686 o Bio::SeqFeature::Computation initialization args fixed and
1687 tests added.
1689 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1691 o Updated FAQ with more example based answers to typical questions
1693 o Bug #1202 was fixed which would improperly join together qual values
1694 parsed by Bio::SeqIO::qual when a trailing space was not present before
1695 the newline.
1697 1.0.0 Major Stable Release
1699 This represents a major release of bioperl with significant
1700 improvements over the 0.7.x series of releases.
1702 o Bio::Tools::Blast is officially deprecated. Please see
1703 Bio::SearchIO for BLAST and FastA parsing.
1705 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1706 Bio::LocationI objects as well as start/end.
1708 o Bio::Biblio contains modules for Bibliographic data.
1709 Bio::DB::Biblio contains the query modules. Additionally one can
1710 parse medlinexml from the ebi bibliographic query service (BQS)
1711 system and Pubmed xml from NCBI. See Martin Senger's
1712 documentation in Bio::Biblio for more information.
1714 o Bio::DB::Registry is a sequence database registry part of
1715 Open Bioinformatics Database Access. See
1716 http://obda.open-bio.org for more information.
1718 o File-based and In-Memory Sequence caching is provided by
1719 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1720 local database.
1722 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1723 been added by Lincoln Stein.
1725 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1727 o A FAQ has been started and is included in the release to provide
1728 a starting point for frequent questions and issues.
1730 0.9.3 Developer's release
1732 o Event based parsing system improved (SearchIO). With parsers for
1733 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1734 Additionally a lazy parsing system for text and html blast reports was
1735 added and is called psiblast (name subject to change in future releases).
1737 o Bio::Search objects improved and standardized with associated Interfaces
1738 written. The concept of a search "Hit" was standardized to be called
1739 "hit" consistently and the use of "subject" was deprecated in all active
1740 modules.
1742 o Bio::Structure added (since 0.9.1) for Protein structure objects
1743 and PDB parser to retrieve and write these structures from data files.
1745 o Several important Bio::DB::GFF bug fixes for handling features that
1746 are mapped to multiple reference points. Updated mysql adaptor
1747 so as to be able to store large (>100 megabase) chunks of DNA into
1748 Bio::DB::GFF databases.
1750 0.9.2 Developer's release
1752 o Bio::Search and Bio::SearchIO system introduced for event based
1753 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1754 in text and XML and FASTA reports in standard output format.
1756 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1757 generator is included in Bio::TreeIO::RandomTrees and a
1758 statistics module for evaluating.
1760 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1761 server for DAS servers.
1763 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1764 files. The entire BPlite system migrated to using Bio::Root::IO
1765 for the data stream.
1767 o Bio::Tools::Alignment for Consed and sequence Trimming
1768 functionality.
1770 o Bio::Structure for Protein structure information and parsing
1772 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1773 cgi-bin entry point which should be more reliable.
1775 o Bio::Map and Bio::MapIO for biological map navigation and a
1776 framework afor parsing them in. Only preliminary work here.
1778 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1779 Future work will integrate Pise and allow submission of analysis on
1780 remote servers.
1782 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1783 introduced as new objects for handling Sequence Annotation
1784 information (dblinks, references, etc) and is more robust that
1785 previous system.
1787 o Bio::Tools::FASTAParser introduced.
1789 o Scripts from the bioperl script submission project and new
1790 scripts from bioperl authors are included in "scripts" directory.
1792 o Factory objects and interfaces are being introduced and are more
1793 strictly enforced.
1795 o Bio::Root::Root introduced as the base object while
1796 Bio::Root::RootI is now simply an interface.
1798 o Bio::DB::RefSeq provides database access to copy of the NCBI
1799 RefSeq database using the EBI dbfetch script.
1801 0.9.0 Developer's release
1803 o perl version at least 5.005 is now required instead of perl 5.004
1805 o Bio::Tools::Run::RemoteBlast is available for running remote
1806 blast jobs at NCBI.
1808 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1810 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1811 Also added are related modules UTR3, UTR5, Exon, Intron,
1812 Promotor, PolyA and Transcript.
1814 o Speedup of translate method in PrimarySeq
1816 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1817 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1819 o Various fixes to Variation toolkit
1821 o Bio::DB::EMBL provides database access to EMBL sequence data.
1822 Bio::DB::Universal provides a central way to point to indexes
1823 and dbs in a single interface.
1825 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1827 o Bio::Factory::EMBOSS is still in design phase as is
1828 Bio::Factory::ApplicationFactoryI
1830 o Dia models for bioperl design are provided in the models/ directory
1832 0.7.2 Bug fix release
1834 o documentation fixes in many modules - SYNOPSIS code verified
1835 to be runnable in many (but not all modules)
1837 o corrected MANIFEST file from 0.7.1 release
1839 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1840 split locations
1842 o Bio::SeqIO::genbank
1843 * Correct parsing and writing of genbank format with protein data
1844 * moltype and molecule separation
1846 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1848 o Bio::SimpleAlign fixed to correctly handle consensus
1849 sequence calculation
1851 o Bio::Tools::HMMER supports hmmer 2.2g
1853 o Bio::Tools::BPlite to support report type specific parsing. Most
1854 major changes are not on the 0.7 branch.
1856 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1857 with File::Spec
1859 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1860 in several types of mutations:
1861 1.) AA level: deletion, complex
1862 2.) AA level: complex, inframe
1863 3.) RNA level: silent
1865 o BPbl2seq parsing of empty reports will not die, but will return
1866 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1867 $report->query() and $report->subject() methods. So an easy
1868 way to test if report was empty is to see if
1869 $report->query->seqname is undefined.
1871 0.7.1 Bug fix release
1873 o Better parsing of genbank/EMBL files especially fixing bugs
1874 related to Feature table parsing and locations on remote
1875 sequences. Additionally, species name parsing was better.
1877 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1878 which include a number of header lines.
1880 o More strict genbank and EMBL format writing (corrected number of
1881 spaces where appropriate).
1883 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1884 for related BPlite BUGS that are unresolved in this release.
1886 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1887 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1888 use expasy mirrors or EBI dbfetch cgi-script.
1890 o A moderate number of documentation improvements were made as
1891 well to provide a better code synopsis in each module.
1894 0.7 Large number of changes, including refactoring of the
1895 Object system, new parsers, new functionality and
1896 all round better system. Highlights are:
1899 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1900 Bio::Root::IO for I/O and file/handle capabilities.
1902 o Imported BPlite modules from Ian Korf for BLAST
1903 parsing. This is considered the supported BLAST parser;
1904 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1906 o Improved Sequence Feature model. Added complete location
1907 modelling (with fuzzy and compound locations). See
1908 Bio::LocationI and the modules under Bio/Location. Added
1909 support in Genbank/EMBL format parsing to completely parse
1910 feature tables for complex locations.
1912 o Moved special support for databanks etc to specialized modules under
1913 Bio/Seq/. One of these supports very large sequences through
1914 a temporary file as a backend.
1916 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1917 CDS retrieval and exon shuffling.
1919 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1921 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1922 DB/GDB (the latter has platform-specific limitations).
1924 o New analysis parser framework for HT sequence annotation (see
1925 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1927 o New Alignment IO framework
1929 o New Index modules (Swissprot)
1931 o New modules for running Blast within perl
1932 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1933 Multiple Sequence Alignment tools ClustalW and TCoffee
1934 (Bio::Tools::Run::Alignment).
1936 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1937 documentation across the package.
1939 o Much improved cross platform support. Many known incompatibilities
1940 have been fixed; however, NT and Mac do not work across the entire
1941 setup (see PLATFORMS).
1943 o Many bug fixes, code restructuring, etc. Overall stability and
1944 maintainability benefit a lot.
1946 o A total of 957 automatic tests
1949 0.6.2
1951 There are very few functionality changes but a large
1952 number of software improvements/bug fixes across the package.
1954 o The EMBL/GenBank parsing are improved.
1956 o The Swissprot reading is improved. Swissprot writing
1957 is disabled as it doesn't work at all. This needs to
1958 wait for 0.7 release
1960 o BLAST reports with no hits are correctly parsed.
1962 o Several other bugs of the BLAST parser (regular expressions, ...)
1963 fixed.
1965 o Old syntax calls have been replaced with more modern syntax
1967 o Modules that did not work at all, in particular the Sim4
1968 set have been removed
1970 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1971 have improved compliance with interface specs and documentation
1973 o Mailing list documentation updated throughout the distribution
1975 o Most minor bug fixes have happened.
1977 o The scripts in /examples now work and have the modern syntax
1978 rather than the deprecated syntax
1981 0.6.1 Sun April 2 2000
1983 o Sequences can have Sequence Features attached to them
1984 - The sequence features can be read from or written to
1985 EMBL and GenBank style flat files
1987 o Objects for Annotation, including References (but not
1988 full medline abstracts), Database links and Comments are
1989 provided
1991 o A Species object to represent nodes on a taxonomy tree
1992 is provided
1994 o The ability to parse HMMER and Sim4 output has been added
1996 o The Blast parsing has been improved, with better PSI-BLAST
1997 support and better overall behaviour.
1999 o Flat file indexed databases provide both random access
2000 and sequential access to their component sequences.
2002 o A CodonTable object has been written with all known
2003 CodonTables accessible.
2005 o A number of new lightweight analysis tools have been
2006 added, such as molecular weight determination.
2008 The 0.6 release also has improved software engineering
2010 o The sequence objects have been rewritten, providing more
2011 maintainable and easier to implement objects. These
2012 objects are backwardly compatible with the 0.05.1 objects
2014 o Many objects are defined in terms of interfaces and then
2015 a Perl implementation has been provided. The interfaces
2016 are found in the 'I' files (module names ending in 'I').
2018 This means that it is possible to wrap C/CORBA/SQL access
2019 as true "bioperl" objects, compatible with the rest of
2020 bioperl.
2022 o The SeqIO system has been overhauled to provide better
2023 processing and perl-like automatic interpretation of <>
2024 over arguments.
2026 o Many more tests have been added (a total of 172 automatic
2027 tests are now run before release).
2031 0.05.1 Tue Jun 29 05:30:44 1999
2032 - Central distribution now requires Perl 5.004. This was
2033 done to get around 5.003-based problems in Bio/Index/*
2034 and SimpleAlign.
2035 - Various bug fixes in the Bio::Tools::Blast modules
2036 including better exception handling and PSI-Blast
2037 support. See Bio/Tools/Blast/CHANGES for more.
2038 - Fixed the Parse mechanism in Seq.pm to use readseq.
2039 Follow the instructions in README for how to install
2040 it (basically, you have to edit Parse.pm).
2041 - Improved documentation of Seq.pm, indicating where
2042 objects are returned and where strings are returned.
2043 - Fixed uninitialized warnings in Bio::Root::Object.pm
2044 and Bio::Tools::SeqPattern.pm.
2045 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
2047 0.05 Sun Apr 25 01:14:11 1999
2048 - Bio::Tools::Blast modules have less memory problems
2049 and faster parsing. Webblast uses LWP and supports
2050 more functionality. See Bio/Tools/Blast/CHANGES for more.
2051 - The Bio::SeqIO system has been started, moving the
2052 sequence reformatting code out of the sequence object
2053 - The Bio::Index:: system has been started, providing
2054 generic index capabilities and specifically works for
2055 Fasta formatted databases and EMBL .dat formatted
2056 databases
2057 - The Bio::DB:: system started, providing access to
2058 databases, both via flat file + index (see above) and
2059 via http to NCBI
2060 - The scripts/ directory, where industrial strength scripts
2061 are put has been started.
2062 - Many changes - a better distribution all round.
2064 0.04.4 Wed Feb 17 02:20:13 1999
2065 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
2066 (see Bio::Tools::Blast::CHANGES).
2067 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
2068 - Beefed up the t/Fasta.t test script.
2069 - Small fix in Bio::Seq::type() (now always returns a string).
2070 - Changed Bio::Root::Utilities::get_newline_char() to
2071 get_newline() since it could return more than one char.
2072 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
2073 - Changed default timeout to 20 seconds (was 3).
2074 - Moved lengthy modification notes to the bottom of some files.
2075 - Fixed SimpleAlign write_fasta bug.
2076 - Beefed up SimpleAlign.t test
2078 0.04.3 Thu Feb 4 07:48:53 1999
2079 - Bio::Root::Object.pm and Global.pm now detect when
2080 script is run as a CGI and suppress output that is only
2081 appropriate when running interactively.
2082 - Bio::Root::Err::_set_context() adds name of script ($0).
2083 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
2084 regarding the use of the static objects via the qw(:obj) tag.
2085 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
2086 CORE::reverse, avoiding Perl warnings.
2087 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
2088 example scripts (see Bio::Tools::Blast::CHANGES).
2089 - examples/seq/seqtools.pl no longer always warns about using
2090 -prot or -nucl command-line arguments; only when using the
2091 -debug argument.
2092 - Methods added to Bio::Root::Utilities: create_filehandle(),
2093 get_newline_char(), and taste_file() to generalize filehandle
2094 creation and autodetect newline characters in files/streams
2095 (see bug report #19).
2096 - Bio::Root::IOManager::read() now handles timeouts and uses
2097 Utilities::create_filehandle().
2098 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
2099 of hardwiring in "\n".
2100 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
2102 0.04.2 Wed Dec 30 02:27:36 1998
2103 - Bug fixes in Bio::Tools::Blast modules, version 0.073
2104 (see Bio::Tools::Blast::CHANGES).
2105 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
2106 to CORE::reverse (prevents ambiguous warnings with 5.005).
2107 - Appending '.tmp.bioperl' to temporary files created by
2108 Bio::Root::Utilities::compress() or uncompress() to
2109 make it easy to identify & cleanup these files as needed.
2110 - Developers: Created CVS branch release-0-04-bug from
2111 release-0-04-1. Before making bug fixes to the 0.04.1 release,
2112 be sure to cvs checkout this branch into a clean area.
2114 0.04.1 Wed Dec 16 05:39:15 1998
2115 - Bug fixes in Bio::Tools::Blast modules, version 0.072
2116 (see Bio::Tools::Blast::CHANGES).
2117 - Compile/SW/Makefile.PL now removes *.o and *.a files
2118 with make clean.
2120 0.04 Tue Dec 8 07:49:19 1998
2121 - Lots of new modules added including:
2122 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
2123 and Bio/Compile directory containing XS-linked C code for
2124 creating Smith-Waterman sequence alignments from within Perl.
2125 * Steve Chervitz's Blast distribution has been incorporated.
2126 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
2127 - Bio/examples directory for demo scripts for all included modules.
2128 - Bio/t directory containing test suit for all included modules.
2129 - For changes specific to the Blast-related modules prior to
2130 incorporation in this central distribution, see the CHANGES
2131 file in the Bio/Tools/Blast directory.
2133 0.01 Tue Sep 8 14:23:22 1998
2134 - original version from central CVS tree; created by h2xs 1.18