| blob | 17109a52e3a9a4e1229efe9aae531b38f71fcb24 |
1 ---------------------------------------------------------
2 Revision history for BioPerl core modules
3 ---------------------------------------------------------
4 The comprehensive history and ongoing development of BioPerl:
6 http://github.com/bioperl/bioperl-live
8 Some of that history is also highlighted on our wiki:
10 http://www.bioperl.org/wiki/Change_log
11 http://www.bioperl.org/wiki/History_of_BioPerl
13 Bugs and requested features list:
15 https://github.com/bioperl/bioperl-live/issues
17 CPAN releases are branched from 'master'.
18 ---------------------------------------------------------
20 Philosophy for 1.7.x:
22 In order to reduce the number of dependencies, we are actively encouraging
23 developers wanting to submit new code with additional dependencies to release
24 code in a separate repository and release it on CPAN. We can help assist in this
25 process and can also place this under the 'bioperl' Github organization (and
26 similarly under the bioperl umbrella account in CPAN), though this is not
27 required.
29 We will also be moving additonal code to other repositories and will release
30 them separately on CPAN. Modules considered obsolute (relies on a dead web
31 service or utilizes strict dependencies that are also considered obsolete) will
32 be removed.
34 1.7.3 - "To Be Named"
36 * The following modules have been moved here from the BioPerl-Run
37 distribution:
39 Bio::Tools::Run::Analysis
40 Bio::Tools::Run::AnalysisFactory
41 Bio::Tools::Run::Phylo::PhyloBase
42 Bio::Tools::Run::WrapperBase
43 Bio::Tools::Run::WrapperBase::CommandExts
45 * The following modules have been removed from the BioPerl
46 distribution to be part of a separate distribution also
47 on CPAN:
49 Bio::AlignIO::stockholm
50 Bio::Cluster::*
51 Bio::ClusterI
52 Bio::ClusterIO
53 Bio::ClusterIO::*
54 Bio::DB::CUTG
55 Bio::DB::EMBL
56 Bio::DB::EntrezGene
57 Bio::DB::Expression
58 Bio::DB::Expression::geo
59 Bio::DB::GFF
60 Bio::DB::GFF::Adaptor::*
61 Bio::DB::GFF::Aggregator
62 Bio::DB::GFF::Aggregator::*
63 Bio::DB::GFF::Featname
64 Bio::DB::GFF::Feature
65 Bio::DB::GFF::Homol
66 Bio::DB::GFF::RelSegment
67 Bio::DB::GFF::Segment
68 Bio::DB::GFF::Typename
69 Bio::DB::GenBank
70 Bio::DB::GenPept
71 Bio::DB::NCBIHelper
72 Bio::DB::Query::GenBank
73 Bio::DB::RefSeq
74 Bio::DB::SeqFeature
75 Bio::DB::SeqFeature::*
76 Bio::DB::Taxonomy::entrez
77 Bio::DB::Taxonomy::sqlite
78 Bio::Index::Stockholm
79 Bio::LiveSeq::*
80 Bio::Phenotype::*
81 Bio::Root::Build
82 Bio::SearchDist
83 Bio::SeqIO::abi
84 Bio::SeqIO::alf
85 Bio::SeqIO::ctf
86 Bio::SeqIO::exp
87 Bio::SeqIO::pln
88 Bio::SeqIO::ztr
89 Bio::Taxonomy
90 Bio::Taxonomy::*
91 Bio::Tools::AlignFactory
92 Bio::Tools::Analysis::DNA::ESEfinder
93 Bio::Tools::Phylo::Gumby
94 Bio::Tools::dpAlign
95 Bio::Tools::pSW
96 Bio::Variation::*
98 * The following programs have been removed:
100 bp_bulk_load_gff
101 bp_das_server
102 bp_download_query_genbank
103 bp_fast_load_gff
104 bp_flanks
105 bp_genbank2gff
106 bp_generate_histogram
107 bp_load_gff
108 bp_meta_gff
109 bp_netinstall
110 bp_process_wormbase
111 bp_query_entrez_taxa
112 bp_seqfeature_delete
113 bp_seqfeature_gff3
114 bp_seqfeature_load
116 * The following modules are no longer dependencies:
118 Bio::SeqIO::staden::read
119 DBD::Pg
120 DBD::SQLite
121 MIME::Base64
122 Memoize
123 Text::ParseWords
124 URI::Escape
126 [Code changes]
128 * The deobfuscator has been removed.
130 * The script `bp_blast2tree` has been moved to the BioPerl-Run
131 distribution since it's mainly a wrapper to modules in there.
133 * The entire Bio::PopGen namespace, Bio::Tree::AlleleNode
134 module, and scripts bp_composite_LD and bp_heterogeneity_test
135 have been moved into a separate distribution named Bio-PopGen.
137 * All modules related to the NeXML format have been moved into a
138 separate distribution named Bio-NeXMLIO. These are:
140 * Bio::AlignIO::nexml
141 * Bio::Nexml::Factory
142 * Bio::NexmlIO
143 * Bio::SeqIO::nexml
144 * Bio::TreeIO::nexml
146 This also means BioPerl is no longer dependent on Bio-Phylo.
148 * All modules interfacing to ACeDB servers have been moved into a
149 separate distribution named Bio-DB-Ace. These are:
151 * Bio::DB::Ace
152 * Bio::DB::GFF::Adaptor::ace
153 * Bio::DB::GFF::Adaptor::dbi::mysqlace
154 * Bio::DB::GFF::Adaptor::dbi::oracleace
156 This also means BioPerl is no longer dependent on AcePerl.
158 * The module Bio::Draw::Pictogram has been moved to a separate
159 distribution named Bio-Draw-Pictogram. This also means BioPerl
160 is no longer dependent on SVG.
162 * The module Bio::Tree::Draw::Cladogram has been moved to a
163 separate distribution named Bio-Tree-Draw-Cladogram. This also
164 means BioPerl is no longer dependent on PostScript.
166 * The module Bio::TreeIO::svggraph has been moved to a separate
167 distribution named Bio-TreeIO-svggraph. This also means that
168 BioPerl is no longer dependent on SVG-Graph and Tree-DAG_Node.
170 * The module Bio::SeqIO::excel has been moved to a separate
171 distribution named Bio-SeqIO-excel. This also means that
172 BioPerl is no longer dependent on Spreadsheet-ParseExcel.
174 * The entire Bio::PhyloNetwork namespace has been moved to a
175 separate distribution named Bio-PhyloNetwork. This also means
176 that BioPerl is no longer dependent on Algorithm::Munkres,
177 GraphViz, and Array::Compare.
179 * The entire Bio::Asembly namespace has been moved to a separate
180 distribution named Bio-Assembly. This also means that BioPerl
181 is no longer dependent on Bio-SamTools and Sort-Naturally.
183 * The entire Bio::Structure namespace has been moved to a
184 separate distribution named Bio-Structure.
186 * The entire Bio::SeqEvolution namespace has been moved to a
187 separate distribution named Bio-SeqEvolution.
189 * The Bio::Tools::Gel module has been moved into its own
190 distribution named Bio-Tools-Gel.
192 * The entire Bio::Restriction namespace has been moved to a
193 separate distribution named Bio-Restriction.
195 * The module Bio::SeqIO::entrezgene has been moved to the
196 Bio-ASN1-EntrezGene distribution.
198 * The module Bio::MolEvol::CodonModel has moved to a distribution
199 of its own, named after itself.
201 * The module Bio::Perl has moved to a new distribution named
202 Bio-Procedural.
204 * The module Bio::Tools::Run::RemoteBlast has moved to a new
205 distribution named after itself.
207 * The module Bio::Align::Graphics has been moved to a new distribution
208 named after itself. This also means that BioPerl is no longer
209 dependent on GD.
211 * The entire Bio::DB::HIV namespace, the Bio::DB::Query::HIVQuery
212 module, and the the bp_hivq program have been moved to their
213 own distribution named Bio-DB-HIV. This also drops the bioperl
214 dependency on XML-Simple and Term-ReadLine.
216 * The entire Bio::DB::TFBS namespace has been moved to its own
217 distribution named after itself.
219 * All modules to handle HMMER programs output have been moved to their
220 own distribution named Bio-SearchIO-hmmer. This also includes the
221 programs bp_hmmer_to_table and bp_parse_hmmsearch.
223 * Bio::DB::MeSH and related Bio::Phenotype::MeSH modules have moved
224 to their own distribution Bio-DB-MeSH.
226 * The Bio::DB::Universal module has been moved to its own distribution.
228 * The emacs bioperl minor mode is no longer distributed as part of the
229 perl module distributions. See
230 https://github.com/bioperl/emacs-bioperl-mode
232 1.7.2 - "Entebbe"
234 [Bugs]
236 * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
237 * #245 - Code coverage fixes [zmughal,cjfields]
238 * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
239 * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
240 * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
241 * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
242 * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
243 * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
244 * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
245 * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
246 * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
247 * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
249 [Code changes]
251 * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
253 1.7.1 - "Election"
255 [Bugs]
257 * Minor release to incorporate fix for CPAN indexing, which
258 prevented proper updates [cjfields]
259 * Fix problem in managing Target attribute for gff3 [Jukes34]
260 * Minor bug fixes related to NCBI HTTPS support [cjfields]
262 1.7.0 - "Disney"
264 [New site]
266 * We have migrated to Github Pages. This was actually planned, but the
267 recent OBF server compromise forced our hand.
269 Brian Osborne [bosborne] took this under his wing to move docs and has
270 done a tremendous amount of work formatting the site and working out some
271 of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
272 Cantalupo and Franscison Ossandon also helped. Kudos!!
274 * Similarly, the official issue tracker is now Github Issues. This has
275 been updated in the relevant documentation bits (we hope!)
277 [Code changes]
279 * Previously deprecated modules removed
280 * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
281 * Bio::DB::SeqHound has been removed due to the service no longer being
282 available
283 * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
284 reasons due to the server no longer having a valid cert
285 * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
286 * Bio::Coordinate, Bio::SearchIO::blastxml,
287 Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
288 added on CPAN
290 [New features]
292 * Docker instances of tagged releases are available! [hlapp]
293 * NCBI HTTPS support [mjohnson and others]
294 * Bio::SearchIO::infernal
295 - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
296 * Bio::Search::HSP::ModelHSP
297 - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
298 reports [pcantalupo]
299 * Bio::Search::Result::INFERNALResult
300 - Added new module to represent features of Infernal reports [pcantalupo]
301 * Bio::DB::Taxonomy SQLite option [cjfields]
302 * WrapperBase quoted option values [majensen]
303 * Various documentation fixes and updates [bosborne]
305 [Bug Fixes]
307 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
308 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
309 * NeXML parser fixes [fjossandon]
310 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
311 * RT 103272 : SeqFeature database deletion skipped features with a decimal -
312 Joshua Fortriede (Xenbase)
313 * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
314 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
315 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
316 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
317 * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
318 * Issue #84: EMBL format wrapping problem [nyamned]
319 * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
320 * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
321 or compiled C code (when Inline::C is installed) [rocky]
322 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
323 * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
324 * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
325 * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
326 to be consistent with "$hit->bits" behaviour [fjossandon]
327 * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
328 aminoacids made "next_seq" confused and broke the parser [fjossandon]
329 * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
330 Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
331 to "complement(join(A..B,C..D))" [fjossandon]
332 * For the many many many fixes that weren't mentioned - blame the release guy!
334 1.6.924
336 [Significant changes]
338 * Bug/feature issue tracking has moved to GitHub Issues:
339 https://github.com/bioperl/bioperl-live/issues
340 * DB_File has been demoted from "required" to "recommended",
341 which should make easier for Windows users to install BioPerl
342 if they don't need that module.
344 [New features]
346 * Bio::Search::HSP::GenericHSP
347 - Bug #3370, added a "posterior_string" method to retrieve the
348 posterior probability lines (PP) from HMMER3 reports [fjossandon]
349 - Added a "consensus_string" method to retrieve the consensus
350 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
351 * Bio::SearchIO::hmmer2
352 - The number of identical and conserved residues are now calculated
353 directly from the homology line [fjossandon]
354 - Now the Query Length and Hit Length are reported when the alignment
355 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
356 - Implemented the capture of the consensus structure lines [fjossandon]
357 * Bio::SearchIO::hmmer3
358 - The number of identical and conserved residues are now calculated
359 directly from the homology line [fjossandon]
360 - Now the Hit Length is reported when the alignment runs until the end
361 of the sequence/model ('.]' or '[]') [fjossandon]
362 - Implemented the capture of the consensus structure lines [fjossandon]
363 - Implemented the capture of the posterior probability lines [fjossandon]
364 - Completed the development of NHMMER parsing, including alignments [fjossandon]
365 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
366 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
367 "min_score", "min_bits, and "hit_filter" methods from
368 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
369 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
370 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
371 besides Blast, instead of being ignored. Added tests for all moved methods
372 using HMMER outputs and run the full test suite and everything pass [fjossandon]
373 * Bio::SeqIO::MultiFile
374 - Autodetection of file format [fangly]
375 * Bio::Tools::GuessSeqFormat:
376 - Format detection from non-seekable filehandles such as STDIN [fangly]
378 [Bug fixes]
380 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
381 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
382 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
383 * Abstract: Fixed ActivePerl incapability of removing temporary files
384 because of problems closing tied filehandles [fjossandon]
385 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
386 because ActivePerl were producing a ".index.pag" and ".index.dir"
387 files instead of a single ".index" file (like Strawberry Perl).
388 Now those temporary files are correctly considered and deleted. [fjossandon]
389 * Test files: Added missing module requirements (DB_File and Data::Stag)
390 to several tests files that were failing because those modules were
391 not present. Now those test files are correctly skipped instead. [fjossandon]
392 * Blast: Added support to changes in bl2seq from BLAST+ output, which
393 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
394 * Phylip: Return undef in "next_aln" at file end to avoid
395 an infinite loop [yschensandiego]
396 * HMMER3: When a hit description is too long, it is truncated in
397 the Scores table. In those cases, the more complete description from
398 the Annotation line (>>) will be used [fjossandon]
399 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
400 since it is now used by HMMER3 format in alignments [fjossandon]
401 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
402 to return undef if the query/hit length is unknown (like in some
403 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
404 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
405 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
406 added support to multi-query reports, reduced code redundancy,
407 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
408 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
409 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
410 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
411 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
412 * Double-quotes on paths are needed in some places [fjossandon]
413 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
414 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
415 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
416 with the latest changes made in their own repositories [fjossandon]
417 * General synching of files with the master branch [fjossandon]
418 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
419 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
420 * Fixed broken MeSH parser [fjossandon]
421 * Fixed missing detection of format in SeqIO when given a -string [fangly]
423 1.6.923
425 * Major Windows support updates! [fjossandon]
426 * MAKER update to allow for stricter standard codon table [cjfields]
427 * Better support for circular sequences [fjossandon]
428 * Fixes for some complex location types [fjossandon]
429 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
430 * Fix bug #2978 related to BLAST report type [fjossandon]
431 * Deobfuscator fixes [DaveMessina]
433 1.6.922
435 * Address CPAN test failures [cjfields]
436 * Add BIOPROJECT support for Genbank files [hyphaltip]
437 * Better regex support for HMMER3 output [bosborne]
439 1.6.921
441 * Minor update to address CPAN test failures
443 1.6.920
445 * Remove Bio::Biblio and related files [carandraug]
446 - this cause version clashes with an independently-released
447 version of Bio::Biblio
449 1.6.910
451 [New features]
453 * Hash randomization fixes for perl 5.18.x
454 - Note: at least one module (Bio::Map::Physical) still has a failing test;
455 this is documented in bug #3446 and has been TODO'd; we will be pulling
456 Bio::Map and similar modules out of core into separate distributions in the
457 1.7.x release series [cjfields]
459 [New features]
461 * Bio::Seq::SimulatedRead
462 - New module to represent reads taken from other sequences [fangly]
463 * Bio::Root::Root
464 - Support of Clone::Fast as a faster cloning alternative [fangly]
465 * Bio::Root::IO
466 - Moved the format() and variant() methods from Bio::*IO modules to
467 Bio::Root::IO [fangly]
468 - Can now use format() to get the type of IO format in use [fangly]
469 * Bio::Tools::IUPAC
470 - New regexp() method to create regular expressions from IUPAC sequences
471 [fangly]
472 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
473 - Code refresh [fangly]
474 * Bio::DB::Taxonomy
475 - Added support for the Greengenes and Silva taxonomies [fangly]
476 * Bio::Tree::TreeFunctionsI
477 - get_lineage_string() represents a lineage as a string [fangly]
478 - add_trait() returns instead of reporting an error when the column
479 number is exceeded in add_trait() [fangly]
480 - Option to support tree leaves without trait [fangly]
481 - Allow ID of 0 in trait files [fangly]
482 * Bio::DB::Taxonomy::list
483 - Misc optimizations [fangly]
484 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
485 * Bio::DB::Taxonomy::*
486 - get_num_taxa() returns the number of taxa in the database [fangly]
487 * Bio::DB::Fasta and Bio::DB::Qual
488 - support indexing an arbitrary list of files [fangly]
489 - user can supply an arbitrary index file name [fangly]
490 - new option to remove index file at the end [fangly]
491 * Bio::DB::Fasta
492 - now handles IUPAC degenerate residues [fangly]
493 * Bio::PrimarySeq and Bio::PrimarySeqI
494 - speed improvements for large sequences [Ben Woodcroft, fangly]
495 * Bio::PrimaryQual
496 - tightened and optimized quality string validation [fangly]
497 * Bio::SeqIO::fasta
498 - new method and option 'block', to create FASTA output with space
499 intervaled blocks (similar to genbank or EMBL) has been implemented.
500 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
501 in favour of the methods 'width' and 'preferred_id_type` respectively.
502 * Bio::FeatureIO::*
503 - moved from bioperl-live into the separate distribution Bio-FeatureIO
504 * Bio::SeqFeature::Annotated
505 - moved from bioperl-live into the separate distribution Bio-FeatureIO
506 * Bio::Cluster::SequenceFamily
507 - improved performance when using get_members with overlapping multiple
508 criteria
509 * Bio::SearchIO::hmmer3
510 - now supports nhmmer [bosborne]
512 [Bug fixes]
514 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
515 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
516 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
517 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
518 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
519 information was lost in a multi-result blast file [Paul Cantalupo]
520 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
521 total gaps [Paul Cantalupo]
522 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
523 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
524 when end of domain indicator is split across lines [Paul Cantalupo]
525 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
526 cjfields]
527 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
528 instances where blank lines are within sequences [cjfields]
529 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
530 types [fangly]
531 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
532 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
533 cjfields]
534 * Various fixes for Stockholm file indexing and processing [bosborne]
535 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
536 breaks parsing [cjfields]
537 * Fix case where Bio::Seq::Meta* objects with no meta information could not
538 be reverse-complemented [fangly]
539 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
540 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
541 when unsure that values will be numerical [fangly]
542 * Fix undef warnings in Bio::SeqIO::embl [fangly]
543 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
544 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
545 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
546 Sallou]
547 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
548 source_tag and display_name must return a string, not undef [fangly]
549 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
550 add_SeqFeature takes a single argument [fangly]
551 * Use cross-platform filenames and temporary directory in
552 Bio::DB::Taxonomy::flatfile [fangly]
553 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
554 properly identified as existing taxa in the database [fangly]
555 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
556 without also passing a lineage to store [fangly]
557 * Prevent passing a directory to the gi2taxid option (-g) of
558 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
559 [fangly]
560 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
561 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
562 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
563 object before trying to access, and no longer returns repeated sequences.
566 1.6.901 May 18, 2011
568 [Notes]
570 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
571 modules using Ace will also be deprecated [lds, cjfields]
572 * Minor bug fix release
573 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
574 * Address Build.PL issues when DBI is not present [hartzell]
575 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
576 * Remove deprecated code for perl 5.14.0 compat [cjfields]
577 * Due to schema changes and lack of support for older versions, support
578 for NeXML 0.9 is only (very) partially implemented.
579 See: https://redmine.open-bio.org/issues/3207
581 [Bug fixes]
583 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
584 docs [genehack, cjfields]
585 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
586 module version from dist_version (probably not the best way to do this,
587 but it seems to work) [rbuels, cjfields]
590 1.6.900 April 14, 201
592 [Notes]
594 * This will probably be the last release to add significant features to
595 core modules; subsequent releases will be for bug fixes alone.
596 We are planning on a restructuring of core for summer 2011, potentially
597 as part of the Google Summer of Code. This may become BioPerl 2.0.
598 * Version bump represents 'just prior to v 1.7'. We may have point
599 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
600 This code essentially is what is on the github master branch.
602 [New features]
604 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
605 * Bio::Tree refactor
606 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
607 - removal of Scalar::Util::weaken code, which was causing odd headaches
608 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
609 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
610 many others]
611 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
612 [Warren Kretzschmar]
613 * Bio::SeqIO::gbxml
614 - bug 2515 - new contribution [Ryan Golhar, jhannah]
615 * Bio::Assembly::IO
616 - support for reading Maq, Sam and Bowtie files [maj]
617 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
618 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
619 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
620 - bug 2726: reading/writing granularity: whole scaffold or one contig
621 at a time [Joshua Udall, fangly]
622 * Bio::OntologyIO
623 - Added parsing of xrefs to OBO files, which are stored as secondary
624 dbxrefs of the cvterm [Naama Menda]
625 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
626 * PAML code updated to work with PAML 4.4d [DaveMessina]
628 [Bug fixes]
630 * [3198] - sort tabular BLAST hits by score [DaveMessina]
631 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
632 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
633 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
634 [cjfields]
635 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
636 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
637 * [3164] - TreeFunctionsI syntax bug [gjuggler]
638 * [3163] - AssemblyIO speedup [fangly]
639 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
640 hyphaltip]
641 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
642 * [3158] - fix EMBL file mis-parsing [cjfields]
643 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
644 cjfields]
645 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
646 * [3148] - URL change for UniProt [cjfields]
647 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
648 * [3136] - HMMer3 parser fixes [kblin]
649 * [3126] - catch description [Toshihiko Akiba]
650 * [3122] - Catch instances where non-seekable filehandles were being
651 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
652 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
653 [dukeleto, rbuels, cjfields]
654 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
655 jhannah]
656 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
657 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
658 cjfields]
659 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
660 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
661 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
662 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
663 * [3086] - EMBL misparsing long tags [kblin, cjfields]
664 * [3085] - CommandExts and array of files [maj, hyphaltip]
665 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
666 for alignment slices [Ha X. Dang, cjfields]
667 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
668 * [3073] - fix parsing of GenBank files from RDP [cjfields]
669 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
670 * [3064] - All-gap midline BLAST report issues [cjfields]
671 * [3063] - BLASt report RID [Razi Khaja, cjfields]
672 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
673 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
674 * [3039] - correct Newick output root node branch length [gjuggler,
675 DaveMessina]
676 * [3038] - SELEX alignment error [Bernd, cjfields]
677 * [3033] - PrimarySeq ID setting [Bernd, maj]
678 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
679 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
680 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
681 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
682 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
683 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
684 PAML 4.4d [DaveMessina]
685 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
686 DaveMessina]
687 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
688 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
689 * [3017] - using threads with Bio::DB::GenBank [cjfields]
690 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
691 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
692 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
693 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
694 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
695 cjfields]
696 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
697 * [2977] - TreeIO issues [DaveMessina]
698 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
699 * [2944] - Bio::Tools::GFF score [cjfields]
700 * [2942] - correct MapTiling output [maj]
701 * [2939] - PDB residue insertion codes [John May, maj]
702 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
703 * [2928] - GuessSeqFormat raw [maj]
704 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
705 * [2922] - open() directive issue [cjfields]
706 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
707 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
708 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
709 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
710 cjfields]
711 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
712 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
713 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
714 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
715 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
716 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
717 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
718 * [2758] - Bio::AssemblyIO ace problems [fangly]
719 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
720 * [2726] - ace file IO [Josh, fangly]
721 * [2700] - Refactor Build.PL [cjfields]
722 * [2673] - addition of simple Root-based clone() method [cjfields]
723 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
724 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
725 * [2594] - Bio::Species memory leak [cjfields]
726 * [2515] - GenBank XML parser [jhannah]
727 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
728 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
729 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
730 cjfields]
731 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
733 [Deprecated]
735 * Bio::Expression modules - these were originally designed to go with the
736 bioperl-microarray suite of tools, however they have never been completed
737 and so have been removed from the distribution. The original code has
738 been moved into the inactive bioperl-microarray suite. [cjfields]
740 [Other]
742 * Repository moved from Subversion (SVN) to
743 http://github.com/bioperl/bioperl-live [cjfields]
744 * Bug database has moved to Redmine (https://redmine.open-bio.org)
745 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
746 Thieme have been moved to their own distribution (Bio-Microarray).
747 [cjfields]
749 1.6.1 Sept. 29, 2009 (point release)
750 * No change from last alpha except VERSION and doc updates [cjfields]
752 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
753 * Fix for silent OBDA bug related to FASTA validation [cjfields]
755 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
756 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
757 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
758 [cjfields]
759 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
761 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
762 * WinXP test fixes [cjfields, maj]
763 * BioPerl.pod added for descriptive information, fixes CPAN indexing
764 [cjfields]
765 * Minor doc fixes [cjfields]
767 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
768 * Fix tests failing due to merging issues [cjfields]
769 * More documentation updates for POD parsing [cjfields]
771 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
772 * Bio::Root::Build
773 - fix YAML meta data generation [cjfields]
775 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
776 * Bio::Align::DNAStatistics
777 - fix divide by zero problem [jason]
778 * Bio::AlignIO::*
779 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
780 * Bio::AlignIO::stockholm
781 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
782 * Bio::Assembly::Tools::ContigSpectrum
783 - function to score contig spectrum [fangly]
784 * Bio::DB::EUtilities
785 - small updates [cjfields]
786 * Bio::DB::Fasta
787 - berkeleydb database now autoindexes wig files and locks correctly
788 [lstein]
789 * Bio::DB::HIV
790 - various small updates for stability; tracking changes to LANL
791 database interface [maj]
792 * Bio::DB::SeqFeature (lots of updates and changes)
793 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
794 - bug 2835 - patch [Dan Bolser]
795 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
796 * Bio::DB::SwissProt
797 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
798 * Bio::Factory::FTLocationFactory
799 - mailing list bug fix [cjfields]
800 * Bio::LocatableSeq
801 - performance work on column_from_residue_number [hartzell]
802 * Bio::Matrix::IO::phylip
803 - bug 2800 - patch to fix phylip parsing [Wei Zou]
804 * Bio::Nexml
805 - Google Summer of Code project from Chase Miller - parsers for Nexml
806 file format [maj, chmille4]
807 * Bio::PopGen
808 - Make Individual, Population, Marker objects AnnotatableI [maj]
809 - simplify LD code [jason]
810 * Bio::RangeI
811 - deal with empty intersection [jason]
812 * Bio::Restriction
813 - significant overhaul of Bio::Restriction system: complete support for
814 external and non-palindromic cutters. [maj]
815 * Bio::Root::Build
816 - CPANPLUS support, no automatic installation [sendu]
817 * Bio::Root::IO
818 - allow IO::String (regression fix) [cjfields]
819 - catch unintentional undef values [cjfields]
820 - throw if non-fh is passed to -fh [maj]
821 * Bio::Root::Root/RootI
822 - small debugging and core fixes [cjfields]
823 * Bio::Root::Test
824 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
825 * Bio::Root::Utilities
826 - bug 2737 - better warnings [cjfields]
827 * Bio::Search
828 - tiling completely refactored, HOWTO added [maj]
829 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
830 will deprecate usage of the older tiling code in the next BioPerl
831 release
832 - small fixes [cjfields]
833 * Bio::SearchIO
834 - Infernal 1.0 output now parsed [cjfields]
835 - new parser for gmap -f9 output [hartzell]
836 - bug 2852 - fix infinite loop in some output [cjfields]
837 - blastxml output now passes all TODO tests [cjfields]
838 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
839 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
840 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
841 * Bio::Seq::LargePrimarySeq
842 - delete tempdirs [cjfields]
843 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
844 * Bio::Seq::Quality
845 - extract regions based on quality threshold value [Dan Bolser, heikki]
846 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
847 * Bio::SeqFeature::Lite
848 - various Bio::DB::SeqFeature-related fixes [lstein]
849 * Bio::SeqFeature::Tools::TypeMapper
850 - additional terms for GenBank to SO map [scain]
851 * Bio::SeqIO::chadoxml
852 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
853 * Bio::SeqIO::embl
854 - support for CDS records [dave_messina, Sylvia]
855 * Bio::SeqIO::fastq
856 - complete refactoring to handle all FASTQ variants, perform validation,
857 write output. API now conforms with other Bio* parsers and the rest of
858 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
859 [cjfields]
860 * Bio::SeqIO::genbank
861 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
862 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
863 * Bio::SeqIO::largefasta
864 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
865 * Bio::SeqIO::raw
866 - add option for 'single' and 'multiple'
867 * Bio::SeqIO::scf
868 - bug 2881 - fix scf round-tripping [Adam Søgren]
869 * Bio::SeqUtils
870 - bug 2766, 2810 - copy over tags from features, doc fixes [David
871 Jackson]
872 * Bio::SimpleAlign
873 - bug 2793 - patch for add_seq index issue [jhannah, maj]
874 - bug 2801 - throw if args are required [cjfields]
875 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
876 [Tristan Lefebure, maj]
877 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
878 - fix POD and add get_SeqFeatures filter [maj]
879 * Bio::Tools::dpAlign
880 - add support for LocatableSeq [ymc]
881 - to be moved to a separate distribution [cjfields, rbuels]
882 * Bio::Tools::EUtilities
883 - fix for two bugs from mail list [Adam Whitney, cjfields]
884 - add generic ItemContainerI interface for containing same methods
885 [cjfields]
886 * Bio::Tools::HMM
887 - fix up code, add more warnings [cjfields]
888 - to be moved to a separate distribution [cjfields, rbuels]
889 * Bio::Tools::Primer3
890 - bug 2862 - fenceposting issue fixed [maj]
891 * Bio::Tools::Run::RemoteBlast
892 - tests for remote RPS-BLAST [mcook]
893 * Bio::Tools::SeqPattern
894 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
895 * Bio::Tools::tRNAscanSE
896 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
897 * Bio::Tree::*
898 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
899 * Bio::Tree::Statistics
900 - several methods for calculating Fitch-based score, internal trait
901 values, statratio(), sum of leaf distances [heikki]
902 * Bio::Tree::Tree
903 - bug 2869 - add docs indicating edge case where nodes can be
904 prematurely garbage-collected [cjfields]
905 - add as_text() function to create Tree as a string in specified format
906 [maj]
907 * Bio::Tree::TreeFunctionsI
908 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
909 Lefebure, maj]
910 * Bio::TreeIO::newick
911 - fix small semicolon issue [cjfields]
912 * scripts
913 - update to bp_seqfeature_load for SQLite [lstein]
914 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
915 - fastam9_to_table - fix for MPI output [jason]
916 - gccalc - total stats [jason]
917 * General Stuff
918 - POD cleanup re: FEEDBACK section [maj, cjfields]
919 - cleanup or fix dead links [cjfields]
920 - Use of no_* methods (indicating 'number of something') is deprecated
921 in favor of num_* [cjfields]
922 - lots of new tests for the above bugs and refactors [everyone!]
923 - new template for Komodo text editor [cjfields]
925 1.6.0 Winter 2009
926 * Feature/Annotation rollback
927 - Problematic changes introduced prior to the 1.5 release have been
928 rolled back. These changes led to subtle bugs involving operator
929 overloading and interface methods.
930 - Behavior is very similar to that for BioPerl 1.4, with tag values
931 being stored generically as simple scalars. Results in a modest
932 speedup.
933 * Bio::Graphics
934 - Split into a separate distribution on CPAN, primarily so development
935 isn't reliant on a complete BioPerl release.
936 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
937 is only available via Subversion (via bioperl-live main trunk)
938 * Bio::Root::Test
939 - Common test bed for all BioPerl modules
940 * Bio::Root::Build
941 - Common Module::Build-based subclass for all BioPerl modules
942 * Bio::DB::EUtilities
943 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
944 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
945 and user agent request posting and retrieval
946 * Test implementation and reorganization
947 - Tests have been reorganized into groups based on classes or use
948 cases.
949 - Automated test coverage is now online:
950 http://www.bioperl.org/wiki/Test_Coverage
951 - After this release, untested modules will be moved into a
952 separate developer distribution until tests can be derived.
953 Also, new modules to be added are expected to have a test suite
954 and adequate test coverage.
956 1.5.2 Developer release
958 Full details of changes since 1.5.1 are available online at:
959 http://www.bioperl.org/wiki/Change_log
960 The following represents a brief overview of the most important changes.
962 o Bio::Map
963 - Overhaul. Brand new system fully allows markers to have multiple
964 positions on multiple maps, and to have relative positions. Should be
965 backward compatible.
967 o Bio::Taxonomy
968 - This module and all the modules in the Taxonomy directory now
969 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
971 o Bio::DB::Taxonomy
973 - Taxonomy.pm
974 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
976 * New methods ancestor(), each_Descendent() and _handle_internal_id().
978 * Allows for different database modules to create Bio::Taxon objects
979 with the same internal id when the same taxon is requested from each.
981 - flatfile.pm
982 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
984 * No longer includes the fake root node 'root'; there are multiple roots
985 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
987 - entrez.pm
988 * get_node() has new option -full
990 * Caches data retrieved from website
992 o Bio::Species
993 - Now a Bio::Taxon. Carries out the species name -> specific name munging
994 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
995 backward compatability in species() method.
997 o Bio::Search and Bio::SearchIO
998 - Overhaul. The existing system has been sped up via some minor changes
999 (mostly gain-of-function to the API). Bio::PullParserI is introduced
1000 as a potential eventual replacment for the existing system, though as
1001 yet only a Hmmpfam parser exists written using it.
1004 1.5.1 Developer release
1006 o Major problem with how Annotations were written out with
1007 Bio::Seq is fixed by reverting to old behavior for
1008 Bio::Annotation objects.
1010 o Bio::SeqIO
1012 - genbank.pm
1013 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
1014 expect at l east 9 spaces at the beginning of a line to
1015 indicate line wrapping.
1017 * Treat multi-line SOURCE sections correctly, this defect broke
1018 both common_name() and classification()
1020 * parse swissprot fields in genpept file
1022 * parse WGS genbank records
1024 - embl.pm
1025 * Changed regexp for ID line. The capturing parentheses are
1026 the same, the difference is an optional repeated-not-semi-
1027 colon expression following the captured \S+. This means the
1028 regexp works when the division looks like /PRO;/ or when the
1029 division looks like /ANG ;/ - the latter is from EMBL
1030 repbase
1032 * fix ID line parsing: the molecule string can have spaces in
1033 it. Like: "genomic DNA"
1035 - swiss.pm: bugs #1727, #1734
1037 - entrezgene.pm
1038 * Added parser for entrezgene ASN1 (text format) files.
1039 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
1041 o Bio::AlignIO
1043 - maf.pm coordinate problem fixed
1045 o Bio::Taxonomy and Bio::DB::Taxonomy
1047 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
1048 can be done via Web without downloading all the sequence.
1050 o Bio::Tools::Run::RemoteBlast supports more options and complies
1051 to changes to the NCBI interface. It is reccomended that you
1052 retrieve the data in XML instead of plain-text BLAST report to
1053 insure proper parsing and retrieval of all information as NCBI
1054 fully expects to change things in the future.
1056 o Bio::Tree and Bio::TreeIO
1058 - Fixes so that re-rooting a tree works properly
1060 - Writing out nhx format from a newick/nexus file will properly output
1061 bootstrap information. The use must move the internal node labels over
1062 to bootstraps.
1063 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
1064 $node->bootstrap($node->id);
1065 $node->id('');
1066 }
1067 - Nexus parsing is much more flexible now, does not care about
1068 LF.
1070 - Cladogram drawing module in Bio::Tree::Draw
1072 - Node height and depth now properly calculated
1074 - fix tree pruning algorithm so that node with 1 child gets merged
1076 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
1077 bugs and improvements were added, see Gbrowse mailing list for most of
1078 these.
1080 o Bio::DB::GFF partially supports GFF3. See information about
1081 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
1083 o Better location parsing in Bio::Factory::FTLocationFactory -
1084 this is part of the engine for parsing EMBL/GenBank feature table
1085 locations. Nested join/order-by/complement are allowed now
1087 o Bio::PrimarySeqI->translate now takes named parameters
1089 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
1090 reconstruction) is now supported. Parsing different models and
1091 branch specific parametes are now supported.
1093 o Bio::Factory::FTLocationFactory - parse hierarchical locations
1094 (joins of joins)
1096 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
1097 for getter/setter functions
1099 o Bio::SearchIO
1101 - blast bug #1739; match scientific notation in score
1102 and possible e+ values
1104 - blast.pm reads more WU-BLAST parameters and parameters, match
1105 a full database pathname,
1107 - Handle NCBI WEB and newer BLAST formats specifically
1108 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
1110 - psl off-by-one error fixed
1112 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
1113 and HSPs can be constructed from them.
1115 - HSPs query/hit now have a seqdesc field filled out (this was
1116 always available via $hit->description and
1117 $result->query_description
1119 - hmmer.pm can parse -A0 hmmpfam files
1121 - Writer::GbrowseGFF more customizeable.
1123 o Bio::Tools::Hmmpfam
1124 make e-value default score displayed in gff, rather than raw score
1125 allow parse of multiple records
1128 1.5 Developer release
1130 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
1131 provide Jukes-Cantor and Kimura pairwise distance methods,
1132 respectively.
1134 o Bio::AlignIO support for "po" format of POA, and "maf";
1135 Bio::AlignIO::largemultifasta is a new alternative to
1136 Bio::AlignIO::fasta for temporary file-based manipulation of
1137 particularly large multiple sequence alignments.
1139 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
1140 be treated similarly as an assembled contig.
1142 o Bio::CodonUsage provides new rare_codon() and probable_codons()
1143 methods for identifying particular codons that encode a given
1144 amino acid.
1146 o Bio::Coordinate::Utils provides new from_align() method to build
1147 a Bio::Coordinate pair directly from a
1148 Bio::Align::AlignI-conforming object.
1150 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
1151 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
1152 web service using standard Pubmed query syntax, and retrieve
1153 results as XML.
1155 o Bio::DB::GFF has various sundry bug fixes.
1157 o Bio::FeatureIO is a new SeqIO-style subsystem for
1158 writing/reading genomic features to/from files. I/O classes
1159 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
1160 classes only read/write Bio::SeqFeature::Annotated objects.
1161 Notably, the GFF v3 class requires features to be typed into the
1162 Sequence Ontology.
1164 o Bio::Graph namespace contains new modules for manipulation and
1165 analysis of protein interaction graphs.
1167 o Bio::Graphics has many bug fixes and shiny new glyphs.
1169 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
1170 indexing for HMMER reports and FASTA qual files, respectively.
1172 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
1173 new objects that can be placed within a Bio::Map::MapI-compliant
1174 genetic/physical map; Bio::Map::Physical provides a new physical
1175 map type; Bio::MapIO::fpc provides finger-printed clone mapping
1176 import.
1178 o Bio::Matrix::PSM provide new support for postion-specific
1179 (scoring) matrices (e.g. profiles, or "possums").
1181 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
1182 be instantiated without explicitly using Bio::OntologyIO. This
1183 is possible through changes to Bio::Ontology::OntologyStore to
1184 download ontology files from the web as necessary. Locations of
1185 ontology files are hard-coded into
1186 Bio::Ontology::DocumentRegistry.
1188 o Bio::PopGen includes many new methods and data types for
1189 population genetics analyses.
1191 o New constructor to Bio::Range, unions(). Given a list of
1192 ranges, returns another list of "flattened" ranges --
1193 overlapping ranges are merged into a single range with the
1194 mininum and maximum coordinates of the entire overlapping group.
1196 o Bio::Root::IO now supports -url, in addition to -file and -fh.
1197 The new -url argument allows one to specify the network address
1198 of a file for input. -url currently only works for GET
1199 requests, and thus is read-only.
1201 o Bio::SearchIO::hmmer now returns individual Hit objects for each
1202 domain alignment (thus containing only one HSP); previously
1203 separate alignments would be merged into one hit if the domain
1204 involved in the alignments was the same, but this only worked
1205 when the repeated domain occured without interruption by any
1206 other domain, leading to a confusing mixture of Hit and HSP
1207 objects.
1209 o Bio::Search::Result::ResultI-compliant report objects now
1210 implement the "get_statistics" method to access
1211 Bio::Search::StatisticsI objects that encapsulate any
1212 statistical parameters associated with the search (e.g. Karlin's
1213 lambda for BLAST/FASTA).
1215 o Bio::Seq::LargeLocatableSeq combines the functionality already
1216 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
1218 o Bio::SeqFeature::Annotated is a replacement for
1219 Bio::SeqFeature::Generic. It breaks compliance with the
1220 Bio::SeqFeatureI interface because the author was sick of
1221 dealing with untyped annotation tags. All
1222 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
1223 compliant, and accessible through Bio::Annotation::Collection.
1225 o Bio::SeqFeature::Primer implements a Tm() method for primer
1226 melting point predictions.
1228 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
1229 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
1231 o Bio::Taxonomy::Node now implements the methods necessary for
1232 Bio::Species interoperability.
1234 o Bio::Tools::CodonTable has new reverse_translate_all() and
1235 make_iupac_string() methods.
1237 o Bio::Tools::dpAlign now provides sequence profile alignments.
1239 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
1241 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
1242 parsers.
1244 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
1245 for designing small inhibitory RNA.
1247 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
1248 methods based on a distance matrix.
1250 o Bio::Tree::Statistics provides an assess_bootstrap() method to
1251 calculate bootstrap support values on a guide tree topology,
1252 based on provided bootstrap tree topologies.
1254 o Bio::TreeIO now supports the Pagel (PAG) tree format.
1256 1.4 branch
1258 1.4.1
1260 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
1262 o Bio::Graphics will work with gd1 or gd2
1264 o Bio::SearchIO
1265 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
1266 (RF lines alone)
1267 - blast.pm Parse multi-line query fields properly
1268 - small speed improvements to blasttable.pm and others
1270 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
1271 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
1272 supporting more complex queries
1275 1.4. Stable major release
1277 Since initial 1.2.0, 3000 separate changes have been made to make this release.
1279 o installable scripts
1281 o global module version from Bio::Root:Version
1283 o Bio::Graphics
1284 - major improvements; SVG support
1286 o Bio::Popgen
1287 - population genetics
1288 - support several population genetics types of questions.
1289 - Tests for statistical neutrality of mutations
1290 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
1291 Tests of population structure (Wright's F-statistic: Fst) is in
1292 Bio::PopGen::PopStats. Calculating composite linkage
1293 disequilibrium (LD) is available in Bio::PopGen::Statistics as
1294 well.
1295 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1296 and csv (comma delimited formatted) data.
1298 - a directory for implementing population simulations has
1299 been added Bio::PopGen::Simulation and 2 simulations - a
1300 Coalescent and a simple single-locus multi-allele genetic drift
1301 simulation have been provided. This replaces the code in
1302 Bio::Tree::RandomTree which has been deprecated until proper
1303 methods for generating random phylogenetic trees are
1304 implemented.
1306 o Bio::Restriction
1307 - new restrion analysis modules
1309 o Bio::Tools::Analysis
1310 - web based DNA and Protein analysis framework and several
1311 implementations
1313 o Bio::Seq::Meta
1314 - per residue annotable sequences
1316 o Bio::Matrix
1317 - Bio::Matrix::PSM - Position Scoring Matrix
1318 - Bio::Matrix::IO has been added for generalized parsing of
1319 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1320 initial implementations for parsing BLOSUM/PAM and Phylip
1321 Distance matricies respectively. A generic matrix
1322 implementation for general use was added in
1323 Bio::Matrix::Generic.
1325 o Bio::Ontology
1326 - major changes
1328 o Bio:Tree
1330 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1331 - small inhibitory RNA
1333 o Bio::SeqFeature::Tools
1334 - seqFeature mapping tools
1335 - Bio::SeqFeature::Tools::Unflattener.pm
1336 -- deal with mapping GenBank feature collections into
1337 Chado/GFF3 processable feature sets (with SO term mappings)
1339 o Bio::Tools::dpAlign
1340 - pure perl dynamic programming sequence alignment
1341 - needs Bioperl-ext
1343 o new Bio::SearchIO formats
1344 - axt and psl: UCSC formats.
1345 - blasttable: NCBI -m 8 or -m 9 format from blastall
1347 o new Bio::SeqIO formats
1348 - chado, tab, kegg, tigr, game
1349 - important fixes for old modules
1351 o Bio::AlignIO: maf
1353 o improved Bio::Tools::Genewise
1355 o Bio::SeqIO now can recongnize sequence formats automatically from
1356 stream
1358 o new parsers in Bio::Tools:
1359 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1361 o Bio::DB::Registry bugs fixed
1362 - BerkeleyDB-indexed flat files can be used by the OBDA system
1363 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1364 used by the OBDA system
1366 o several new HOWTOs
1367 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1368 Databases
1370 o hundreds of new and improved files
1373 o
1374 o Bio::Tree::AlleleNode has been updated to be a container of
1375 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1378 1.2 Branch
1380 1.2.3 Stable release update
1381 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1382 handling.
1383 o Bug #1477 - Sel --> Sec abbreviation fixed
1384 o Fix bug #1487 where paring in-between locations when
1385 end < start caused the FTLocationFactory logic to fail.
1386 o Fix bug #1489 which was not dealing with keywords as an
1387 arrayref properly (this is fixed on the main trunk because
1388 keywords returns a string and the array is accessible via
1389 get_keywords).
1390 o Bio::Tree::Tree memory leak (bug #1480) fixed
1391 Added a new initialization option -nodelete which
1392 won't try and cleanup the containing nodes if this
1393 is true.
1394 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1395 this was only present on the branch for the 1.2.1 and 1.2.2 series
1396 - Also merged main trunk changes to the branch which make
1397 newick -> nhx round tripping more effective (storing branch length
1398 and bootstrap values in same locate for NodeNHX and Node
1399 implementations.) Fixes to TreeIO parsing for labeled internal
1400 also required small changes to TreeIO::nhx. Improved
1401 tests for this module as well.
1402 o Bio::SearchIO
1403 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1404 gapped blast properly (was losing hit significance values due to
1405 the extra unexpeted column).
1406 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1407 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1408 although doesn't try to correct it - will get the negative
1409 number for you. Added a test for this as well.
1410 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1411 has no top-level family classification scores but does have scores and
1412 alignments for individual domains.
1413 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1414 regular expression to match the line was missing the possibility of
1415 an extra space. This is rare, which is why we probably did not
1416 catch it before.
1417 - BLAST parsing picks up more of the statistics/parameter fields
1418 at the bottom of reports. Still not fully complete.
1419 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1420 were fixed to include many improvements and added flexiblity
1421 in outputting the files. Bug #1495 was also fixed in the process.
1422 o Bio::DB::GFF
1423 - Update for GFF3 compatibility.
1424 - Added scripts for importing from UCSC and GenBank.
1425 - Added a 1.2003 version number.
1426 o Bio::Graphics
1427 - Updated tutorial.
1428 - Added a 1.2003 version number.
1429 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1430 properly writing keywords out.
1431 o Bio::SeqIO::genbank
1432 - Fixed bug/enhancement #1513 where dates of
1433 the form D-MMM-YYYY were not parsed. Even though this is
1434 invalid format we can handle it - and also cleanup the date
1435 string so it is properly formatted.
1436 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1437 and written with Genbank format. Similarly bug #1515 is fixed to
1438 parse in the ORIGIN text.
1439 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1440 to specify the ID type, one of (accession accession.version
1441 display primary). See Bio::SeqIO::preferred_id_type method
1442 documentation for more information.
1443 o Unigene parsing updated to handle file format changes by NCBI
1445 1.2.2 Stable release update
1447 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1448 - auto-discover ontology name
1449 - bug in parsing relationships when certain characters are in the term
1450 - fixed hard-coded prefix for term identifiers
1451 - various smaller issues
1453 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1454 of Bio::Ontology::TermI
1456 o brought the OBDA Registry code up to latest specs
1458 o Bio::DB::GenBank
1459 - eutils URL change
1460 - accession number retrieval fixed
1462 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1464 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1465 #1459 which now properly report alignment start/end info
1466 for translated BLAST/FASTA searches.
1468 o Bio::TreeIO::newick can parse labeled internal nodes
1470 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1471 for BLASTX if if you provide -report_type => 'BLASTX' when
1472 initializing a BPbl2seq object. Bioperl 1.3 will have better
1473 support for bl2seq in the SearchIO system.
1475 o Bio::Root::IO support a -noclose boolean flag which will not
1476 close a filehandle upon object cleanup - useful when sharing
1477 a filehandle among objects. Additionally code added s.t.
1478 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1480 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1482 o Bio::SeqIO::genbank
1483 - bug #1456 fixed which generated extra sequence lines
1484 - write moltype correctly for genpept
1486 1.2.1 Stable release update
1488 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1490 o Addition from main trunk of Ontology objects, principly to allow
1491 BioSQL releases against 1.2.1
1493 o Fixes and cleanup of Bio::Coordinate modules
1495 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1496 the primary accession number
1498 o Other bug fixes, including bpindex GenBank fix
1500 o Bio::SeqIO::genbank bug #1389 fixed
1502 1.2 Stable major release
1504 o More functionality added to Bio::Perl, the newbie module
1506 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1507 Support for New Hampshire Extended (NHX) format parsing.
1509 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1510 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1511 Hmmpfam parser.
1513 o New ontology parsing Bio::Ontology
1515 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1516 multi-report (mlib) fasta reports, support for waba and exonerate.
1518 o Bio::ClusterIO for parsing Unigene clusters
1520 o Bio::Assembly added for representing phrap and ace assembly clusters.
1522 o Rudimentary support for writing Chado XML (see
1523 GMOD project: www.gmod.org for more information)
1525 o Bio::Coordinate for mapping between different coordinate systems such
1526 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1527 features into different coordinate systems.
1529 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1530 with the get_Stream_by_query method and supports the latest
1531 NCBI eutils interface.
1533 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1534 object for extracting subsets of features : currently only
1535 supports extraction by location.
1537 1.1.1 Developer release
1539 o Deprecated modules are now listed in the DEPRECATED file
1541 o New HowTo documents located in doc/howto describing
1542 a domain of Bioperl.
1544 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1545 and all old bugs are searchable through the bugzilla interface.
1547 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1548 have been addressed.
1550 o Support for Genewise parsing in Bio::Tools::Genewise
1552 o Start of Ontology framework with Bio::Ontology
1554 o Speedup to the Bio::Root::Root object method _rearrange.
1555 A global _load_module method was implemented to simplify the
1556 dynamic loading of modules ala Bio::SeqIO::genbank. This
1557 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1558 etc).
1560 o Several performance improvements to sequence parsing in Bio::SeqIO.
1561 Attempt to speedup by reducing object creation overhead.
1563 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1564 method for sequence retrieval with their E-utils CGI scripts.
1565 More work to support Entrez queries to their fullest is planned
1566 before 1.2 release.
1568 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1570 1.1 Developer release
1572 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1573 this separation removes some of the complexity in our test suite
1574 and separates the core modules in bioperl from those that need
1575 external programs to run.
1577 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1578 not run into trouble running the makefile
1580 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1581 read,create,and write locations for grouped/split locations
1582 (like mRNA features on genomic sequence).
1584 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1585 and PAML (codeml,aaml, etc) parsing.
1587 o Bio::Tree:: objects expanded to handle testing monophyly,
1588 paraphyly, least common ancestor, etc.
1590 o Bio::Coordinate for mapping locations from different coordinate spaces
1592 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1593 added for parsing hmmpfam and hmmsearch output.
1595 o Bio::SearchIO::Writer::TextResultWriter for outputting
1596 a pseudo-blast textfile format
1599 1.0.2 Bug fix release
1601 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1602 in this release will not work after December 2002 when NCBI
1603 shuts off the old Entrez cgi scripts. We have already fixed
1604 on our main development branch and the functionality will be
1605 available in the next stable bioperl release (1.2) slated for
1606 Fall 2002.
1608 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1609 testset by Robin Emig. These were fixed as was the get_aln
1610 method in Bio::Search::HSP::GenericHSP to handle the extra
1611 context sequence that is provided with a FastA alignment.
1613 o Migrating differences between Bio::Search::XX::BlastXX to
1614 Bio::Search::XX::GenericXX objects. This included mechanism
1615 to retrieve whole list of HSPs from Hits and whole list of Hits from
1616 Results in addition to the current next_XX iterator methods that
1617 are available. Added seq_inds() method to GenericHSP which identifies
1618 indexes in the query or hit sequences where conserved,identical,gaps,
1619 or mismatch residues are located (adapted from Steve Chervitz's
1620 implementation in BlastHSP).
1622 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1623 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1625 o Bio::Graphics glyph set improved and extended for GBrowse release
1627 o Bio::Tree::Tree get_nodes implementation improvement thanks
1628 to Howard Ross notice performance problem when writing out
1629 unbalanced trees.
1631 o Bio::Location::Fuzzy::new named parameter -loc_type became
1632 -location_type, Bio::Location::Simple::new named parameter
1633 -seqid becamse -seq_id.
1635 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1636 was mis-detecting that gaps should be placed at the beginning of
1637 the alignment when the best alignment starts internally in the
1638 sequence.
1640 1.0.1 Bug fix release
1642 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1644 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1645 and mixed (3.3 - 3.4) versions of FASTA.
1647 o Small API change to add methods for completeness across
1648 implementations of Bio::Search objects. These new methods
1649 in the interface are implemented by the GenericXX object as well
1650 as the BlastXX objects.
1651 * Bio::Search::Result::ResultI
1652 - hits() method returns list of all Hits (next_hit is an
1653 iterator method)
1655 * Bio::Search::Hit::HitI
1656 - hsps() method returns list of all HSPs (next_hsp is an
1657 iterator method)
1659 o The Bio::SearchIO::Writer classes have been fixed to handle results
1660 created from either psiblast (Search::BlastXX objects) or
1661 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1662 has to be done here to make it work properly and will nee major
1663 API changes.
1665 o Bugs in Bio::Tools::HMMER fixed, including
1666 * #1178 - Root::IO destructor wasn't being called
1667 * #1034 - filter_on_cutoff now behaves properly
1669 o Bio::SeqFeature::Computation initialization args fixed and
1670 tests added.
1672 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1674 o Updated FAQ with more example based answers to typical questions
1676 o Bug #1202 was fixed which would improperly join together qual values
1677 parsed by Bio::SeqIO::qual when a trailing space was not present before
1678 the newline.
1680 1.0.0 Major Stable Release
1682 This represents a major release of bioperl with significant
1683 improvements over the 0.7.x series of releases.
1685 o Bio::Tools::Blast is officially deprecated. Please see
1686 Bio::SearchIO for BLAST and FastA parsing.
1688 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1689 Bio::LocationI objects as well as start/end.
1691 o Bio::Biblio contains modules for Bibliographic data.
1692 Bio::DB::Biblio contains the query modules. Additionally one can
1693 parse medlinexml from the ebi bibliographic query service (BQS)
1694 system and Pubmed xml from NCBI. See Martin Senger's
1695 documentation in Bio::Biblio for more information.
1697 o Bio::DB::Registry is a sequence database registry part of
1698 Open Bioinformatics Database Access. See
1699 http://obda.open-bio.org for more information.
1701 o File-based and In-Memory Sequence caching is provided by
1702 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1703 local database.
1705 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1706 been added by Lincoln Stein.
1708 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1710 o A FAQ has been started and is included in the release to provide
1711 a starting point for frequent questions and issues.
1713 0.9.3 Developer's release
1715 o Event based parsing system improved (SearchIO). With parsers for
1716 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1717 Additionally a lazy parsing system for text and html blast reports was
1718 added and is called psiblast (name subject to change in future releases).
1720 o Bio::Search objects improved and standardized with associated Interfaces
1721 written. The concept of a search "Hit" was standardized to be called
1722 "hit" consistently and the use of "subject" was deprecated in all active
1723 modules.
1725 o Bio::Structure added (since 0.9.1) for Protein structure objects
1726 and PDB parser to retrieve and write these structures from data files.
1728 o Several important Bio::DB::GFF bug fixes for handling features that
1729 are mapped to multiple reference points. Updated mysql adaptor
1730 so as to be able to store large (>100 megabase) chunks of DNA into
1731 Bio::DB::GFF databases.
1733 0.9.2 Developer's release
1735 o Bio::Search and Bio::SearchIO system introduced for event based
1736 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1737 in text and XML and FASTA reports in standard output format.
1739 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1740 generator is included in Bio::TreeIO::RandomTrees and a
1741 statistics module for evaluating.
1743 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1744 server for DAS servers.
1746 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1747 files. The entire BPlite system migrated to using Bio::Root::IO
1748 for the data stream.
1750 o Bio::Tools::Alignment for Consed and sequence Trimming
1751 functionality.
1753 o Bio::Structure for Protein structure information and parsing
1755 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1756 cgi-bin entry point which should be more reliable.
1758 o Bio::Map and Bio::MapIO for biological map navigation and a
1759 framework afor parsing them in. Only preliminary work here.
1761 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1762 Future work will integrate Pise and allow submission of analysis on
1763 remote servers.
1765 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1766 introduced as new objects for handling Sequence Annotation
1767 information (dblinks, references, etc) and is more robust that
1768 previous system.
1770 o Bio::Tools::FASTAParser introduced.
1772 o Scripts from the bioperl script submission project and new
1773 scripts from bioperl authors are included in "scripts" directory.
1775 o Factory objects and interfaces are being introduced and are more
1776 strictly enforced.
1778 o Bio::Root::Root introduced as the base object while
1779 Bio::Root::RootI is now simply an interface.
1781 o Bio::DB::RefSeq provides database access to copy of the NCBI
1782 RefSeq database using the EBI dbfetch script.
1784 0.9.0 Developer's release
1786 o perl version at least 5.005 is now required instead of perl 5.004
1788 o Bio::Tools::Run::RemoteBlast is available for running remote
1789 blast jobs at NCBI.
1791 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1793 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1794 Also added are related modules UTR3, UTR5, Exon, Intron,
1795 Promotor, PolyA and Transcript.
1797 o Speedup of translate method in PrimarySeq
1799 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1800 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1802 o Various fixes to Variation toolkit
1804 o Bio::DB::EMBL provides database access to EMBL sequence data.
1805 Bio::DB::Universal provides a central way to point to indexes
1806 and dbs in a single interface.
1808 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1810 o Bio::Factory::EMBOSS is still in design phase as is
1811 Bio::Factory::ApplicationFactoryI
1813 o Dia models for bioperl design are provided in the models/ directory
1815 0.7.2 Bug fix release
1817 o documentation fixes in many modules - SYNOPSIS code verified
1818 to be runnable in many (but not all modules)
1820 o corrected MANIFEST file from 0.7.1 release
1822 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1823 split locations
1825 o Bio::SeqIO::genbank
1826 * Correct parsing and writing of genbank format with protein data
1827 * moltype and molecule separation
1829 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1831 o Bio::SimpleAlign fixed to correctly handle consensus
1832 sequence calculation
1834 o Bio::Tools::HMMER supports hmmer 2.2g
1836 o Bio::Tools::BPlite to support report type specific parsing. Most
1837 major changes are not on the 0.7 branch.
1839 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1840 with File::Spec
1842 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1843 in several types of mutations:
1844 1.) AA level: deletion, complex
1845 2.) AA level: complex, inframe
1846 3.) RNA level: silent
1848 o BPbl2seq parsing of empty reports will not die, but will return
1849 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1850 $report->query() and $report->subject() methods. So an easy
1851 way to test if report was empty is to see if
1852 $report->query->seqname is undefined.
1854 0.7.1 Bug fix release
1856 o Better parsing of genbank/EMBL files especially fixing bugs
1857 related to Feature table parsing and locations on remote
1858 sequences. Additionally, species name parsing was better.
1860 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1861 which include a number of header lines.
1863 o More strict genbank and EMBL format writing (corrected number of
1864 spaces where appropriate).
1866 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1867 for related BPlite BUGS that are unresolved in this release.
1869 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1870 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1871 use expasy mirrors or EBI dbfetch cgi-script.
1873 o A moderate number of documentation improvements were made as
1874 well to provide a better code synopsis in each module.
1877 0.7 Large number of changes, including refactoring of the
1878 Object system, new parsers, new functionality and
1879 all round better system. Highlights are:
1882 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1883 Bio::Root::IO for I/O and file/handle capabilities.
1885 o Imported BPlite modules from Ian Korf for BLAST
1886 parsing. This is considered the supported BLAST parser;
1887 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1889 o Improved Sequence Feature model. Added complete location
1890 modelling (with fuzzy and compound locations). See
1891 Bio::LocationI and the modules under Bio/Location. Added
1892 support in Genbank/EMBL format parsing to completely parse
1893 feature tables for complex locations.
1895 o Moved special support for databanks etc to specialized modules under
1896 Bio/Seq/. One of these supports very large sequences through
1897 a temporary file as a backend.
1899 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1900 CDS retrieval and exon shuffling.
1902 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1904 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1905 DB/GDB (the latter has platform-specific limitations).
1907 o New analysis parser framework for HT sequence annotation (see
1908 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1910 o New Alignment IO framework
1912 o New Index modules (Swissprot)
1914 o New modules for running Blast within perl
1915 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1916 Multiple Sequence Alignment tools ClustalW and TCoffee
1917 (Bio::Tools::Run::Alignment).
1919 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1920 documentation across the package.
1922 o Much improved cross platform support. Many known incompatibilities
1923 have been fixed; however, NT and Mac do not work across the entire
1924 setup (see PLATFORMS).
1926 o Many bug fixes, code restructuring, etc. Overall stability and
1927 maintainability benefit a lot.
1929 o A total of 957 automatic tests
1932 0.6.2
1934 There are very few functionality changes but a large
1935 number of software improvements/bug fixes across the package.
1937 o The EMBL/GenBank parsing are improved.
1939 o The Swissprot reading is improved. Swissprot writing
1940 is disabled as it doesn't work at all. This needs to
1941 wait for 0.7 release
1943 o BLAST reports with no hits are correctly parsed.
1945 o Several other bugs of the BLAST parser (regular expressions, ...)
1946 fixed.
1948 o Old syntax calls have been replaced with more modern syntax
1950 o Modules that did not work at all, in particular the Sim4
1951 set have been removed
1953 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1954 have improved compliance with interface specs and documentation
1956 o Mailing list documentation updated throughout the distribution
1958 o Most minor bug fixes have happened.
1960 o The scripts in /examples now work and have the modern syntax
1961 rather than the deprecated syntax
1964 0.6.1 Sun April 2 2000
1966 o Sequences can have Sequence Features attached to them
1967 - The sequence features can be read from or written to
1968 EMBL and GenBank style flat files
1970 o Objects for Annotation, including References (but not
1971 full medline abstracts), Database links and Comments are
1972 provided
1974 o A Species object to represent nodes on a taxonomy tree
1975 is provided
1977 o The ability to parse HMMER and Sim4 output has been added
1979 o The Blast parsing has been improved, with better PSI-BLAST
1980 support and better overall behaviour.
1982 o Flat file indexed databases provide both random access
1983 and sequential access to their component sequences.
1985 o A CodonTable object has been written with all known
1986 CodonTables accessible.
1988 o A number of new lightweight analysis tools have been
1989 added, such as molecular weight determination.
1991 The 0.6 release also has improved software engineering
1993 o The sequence objects have been rewritten, providing more
1994 maintainable and easier to implement objects. These
1995 objects are backwardly compatible with the 0.05.1 objects
1997 o Many objects are defined in terms of interfaces and then
1998 a Perl implementation has been provided. The interfaces
1999 are found in the 'I' files (module names ending in 'I').
2001 This means that it is possible to wrap C/CORBA/SQL access
2002 as true "bioperl" objects, compatible with the rest of
2003 bioperl.
2005 o The SeqIO system has been overhauled to provide better
2006 processing and perl-like automatic interpretation of <>
2007 over arguments.
2009 o Many more tests have been added (a total of 172 automatic
2010 tests are now run before release).
2014 0.05.1 Tue Jun 29 05:30:44 1999
2015 - Central distribution now requires Perl 5.004. This was
2016 done to get around 5.003-based problems in Bio/Index/*
2017 and SimpleAlign.
2018 - Various bug fixes in the Bio::Tools::Blast modules
2019 including better exception handling and PSI-Blast
2020 support. See Bio/Tools/Blast/CHANGES for more.
2021 - Fixed the Parse mechanism in Seq.pm to use readseq.
2022 Follow the instructions in README for how to install
2023 it (basically, you have to edit Parse.pm).
2024 - Improved documentation of Seq.pm, indicating where
2025 objects are returned and where strings are returned.
2026 - Fixed uninitialized warnings in Bio::Root::Object.pm
2027 and Bio::Tools::SeqPattern.pm.
2028 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
2030 0.05 Sun Apr 25 01:14:11 1999
2031 - Bio::Tools::Blast modules have less memory problems
2032 and faster parsing. Webblast uses LWP and supports
2033 more functionality. See Bio/Tools/Blast/CHANGES for more.
2034 - The Bio::SeqIO system has been started, moving the
2035 sequence reformatting code out of the sequence object
2036 - The Bio::Index:: system has been started, providing
2037 generic index capabilities and specifically works for
2038 Fasta formatted databases and EMBL .dat formatted
2039 databases
2040 - The Bio::DB:: system started, providing access to
2041 databases, both via flat file + index (see above) and
2042 via http to NCBI
2043 - The scripts/ directory, where industrial strength scripts
2044 are put has been started.
2045 - Many changes - a better distribution all round.
2047 0.04.4 Wed Feb 17 02:20:13 1999
2048 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
2049 (see Bio::Tools::Blast::CHANGES).
2050 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
2051 - Beefed up the t/Fasta.t test script.
2052 - Small fix in Bio::Seq::type() (now always returns a string).
2053 - Changed Bio::Root::Utilities::get_newline_char() to
2054 get_newline() since it could return more than one char.
2055 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
2056 - Changed default timeout to 20 seconds (was 3).
2057 - Moved lengthy modification notes to the bottom of some files.
2058 - Fixed SimpleAlign write_fasta bug.
2059 - Beefed up SimpleAlign.t test
2061 0.04.3 Thu Feb 4 07:48:53 1999
2062 - Bio::Root::Object.pm and Global.pm now detect when
2063 script is run as a CGI and suppress output that is only
2064 appropriate when running interactively.
2065 - Bio::Root::Err::_set_context() adds name of script ($0).
2066 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
2067 regarding the use of the static objects via the qw(:obj) tag.
2068 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
2069 CORE::reverse, avoiding Perl warnings.
2070 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
2071 example scripts (see Bio::Tools::Blast::CHANGES).
2072 - examples/seq/seqtools.pl no longer always warns about using
2073 -prot or -nucl command-line arguments; only when using the
2074 -debug argument.
2075 - Methods added to Bio::Root::Utilities: create_filehandle(),
2076 get_newline_char(), and taste_file() to generalize filehandle
2077 creation and autodetect newline characters in files/streams
2078 (see bug report #19).
2079 - Bio::Root::IOManager::read() now handles timeouts and uses
2080 Utilities::create_filehandle().
2081 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
2082 of hardwiring in "\n".
2083 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
2085 0.04.2 Wed Dec 30 02:27:36 1998
2086 - Bug fixes in Bio::Tools::Blast modules, version 0.073
2087 (see Bio::Tools::Blast::CHANGES).
2088 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
2089 to CORE::reverse (prevents ambiguous warnings with 5.005).
2090 - Appending '.tmp.bioperl' to temporary files created by
2091 Bio::Root::Utilities::compress() or uncompress() to
2092 make it easy to identify & cleanup these files as needed.
2093 - Developers: Created CVS branch release-0-04-bug from
2094 release-0-04-1. Before making bug fixes to the 0.04.1 release,
2095 be sure to cvs checkout this branch into a clean area.
2097 0.04.1 Wed Dec 16 05:39:15 1998
2098 - Bug fixes in Bio::Tools::Blast modules, version 0.072
2099 (see Bio::Tools::Blast::CHANGES).
2100 - Compile/SW/Makefile.PL now removes *.o and *.a files
2101 with make clean.
2103 0.04 Tue Dec 8 07:49:19 1998
2104 - Lots of new modules added including:
2105 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
2106 and Bio/Compile directory containing XS-linked C code for
2107 creating Smith-Waterman sequence alignments from within Perl.
2108 * Steve Chervitz's Blast distribution has been incorporated.
2109 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
2110 - Bio/examples directory for demo scripts for all included modules.
2111 - Bio/t directory containing test suit for all included modules.
2112 - For changes specific to the Blast-related modules prior to
2113 incorporation in this central distribution, see the CHANGES
2114 file in the Bio/Tools/Blast directory.
2116 0.01 Tue Sep 8 14:23:22 1998
2117 - original version from central CVS tree; created by h2xs 1.18