| blob | 03ad9317ca3c594cebe9d8d3cb374187ccc6f2bc |
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::DB::CUTG
54 Bio::DB::EMBL
55 Bio::DB::EntrezGene
56 Bio::DB::Expression
57 Bio::DB::Expression::geo
58 Bio::DB::GFF
59 Bio::DB::GFF::Adaptor::*
60 Bio::DB::GFF::Aggregator::*
61 Bio::DB::GFF::Featname
62 Bio::DB::GFF::Feature
63 Bio::DB::GFF::Homol
64 Bio::DB::GFF::RelSegment
65 Bio::DB::GFF::Segment
66 Bio::DB::GFF::Typename
67 Bio::DB::GenBank
68 Bio::DB::GenPept
69 Bio::DB::NCBIHelper
70 Bio::DB::Query::GenBank
71 Bio::DB::RefSeq
72 Bio::DB::SeqFeature::*
73 Bio::DB::SeqVersion::*
74 Bio::DB::Taxonomy::entrez
75 Bio::DB::Taxonomy::sqlite
76 Bio::Index::Stockholm
77 Bio::LiveSeq::*
78 Bio::Phenotype::*
79 Bio::Root::Build
80 Bio::SearchDist
81 Bio::SeqFeature::SiRNA::*
82 Bio::SeqIO::abi
83 Bio::SeqIO::alf
84 Bio::SeqIO::ctf
85 Bio::SeqIO::exp
86 Bio::SeqIO::pln
87 Bio::SeqIO::ztr
88 Bio::Taxonomy::*
89 Bio::Tools::AlignFactory
90 Bio::Tools::Analysis::DNA::*
91 Bio::Tools::Analysis::Protein::*
92 Bio::Tools::Phylo::Gumby
93 Bio::Tools::Protparam
94 Bio::Tools::SiRNA::*
95 Bio::Tools::dpAlign
96 Bio::Tools::pSW
97 Bio::Variation::*
99 * The following programs have been removed:
101 bp_bulk_load_gff
102 bp_das_server
103 bp_download_query_genbank
104 bp_fast_load_gff
105 bp_flanks
106 bp_genbank2gff
107 bp_generate_histogram
108 bp_load_gff
109 bp_meta_gff
110 bp_netinstall
111 bp_process_wormbase
112 bp_query_entrez_taxa
113 bp_seqfeature_delete
114 bp_seqfeature_gff3
115 bp_seqfeature_load
117 * The following modules are no longer dependencies:
119 Bio::SeqIO::staden::read
120 DBD::Pg
121 DBD::SQLite
122 HTML::HeadParser
123 HTML::TableExtract
124 MIME::Base64
125 Memoize
126 Text::ParseWords
127 URI::Escape
129 [Code changes]
131 * The deobfuscator has been removed.
133 * The script `bp_blast2tree` has been moved to the BioPerl-Run
134 distribution since it's mainly a wrapper to modules in there.
136 * The entire Bio::PopGen namespace, Bio::Tree::AlleleNode
137 module, and scripts bp_composite_LD and bp_heterogeneity_test
138 have been moved into a separate distribution named Bio-PopGen.
140 * All modules related to the NeXML format have been moved into a
141 separate distribution named Bio-NeXMLIO. These are:
143 * Bio::AlignIO::nexml
144 * Bio::Nexml::Factory
145 * Bio::NexmlIO
146 * Bio::SeqIO::nexml
147 * Bio::TreeIO::nexml
149 This also means BioPerl is no longer dependent on Bio-Phylo.
151 * All modules interfacing to ACeDB servers have been moved into a
152 separate distribution named Bio-DB-Ace. These are:
154 * Bio::DB::Ace
155 * Bio::DB::GFF::Adaptor::ace
156 * Bio::DB::GFF::Adaptor::dbi::mysqlace
157 * Bio::DB::GFF::Adaptor::dbi::oracleace
159 This also means BioPerl is no longer dependent on AcePerl.
161 * The module Bio::Draw::Pictogram has been moved to a separate
162 distribution named Bio-Draw-Pictogram. This also means BioPerl
163 is no longer dependent on SVG.
165 * The module Bio::Tree::Draw::Cladogram has been moved to a
166 separate distribution named Bio-Tree-Draw-Cladogram. This also
167 means BioPerl is no longer dependent on PostScript.
169 * The module Bio::TreeIO::svggraph has been moved to a separate
170 distribution named Bio-TreeIO-svggraph. This also means that
171 BioPerl is no longer dependent on SVG-Graph and Tree-DAG_Node.
173 * The module Bio::SeqIO::excel has been moved to a separate
174 distribution named Bio-SeqIO-excel. This also means that
175 BioPerl is no longer dependent on Spreadsheet-ParseExcel.
177 * The entire Bio::PhyloNetwork namespace has been moved to a
178 separate distribution named Bio-PhyloNetwork. This also means
179 that BioPerl is no longer dependent on Algorithm::Munkres,
180 GraphViz, and Array::Compare.
182 * The entire Bio::Asembly namespace has been moved to a separate
183 distribution named Bio-Assembly. This also means that BioPerl
184 is no longer dependent on Bio-SamTools and Sort-Naturally.
186 * The entire Bio::Structure namespace has been moved to a
187 separate distribution named Bio-Structure.
189 * The entire Bio::SeqEvolution namespace has been moved to a
190 separate distribution named Bio-SeqEvolution.
192 * The Bio::Tools::Gel module has been moved into its own
193 distribution named Bio-Tools-Gel.
195 * The entire Bio::Restriction namespace has been moved to a
196 separate distribution named Bio-Restriction.
198 * The module Bio::SeqIO::entrezgene has been moved to the
199 Bio-ASN1-EntrezGene distribution.
201 * The module Bio::MolEvol::CodonModel has moved to a distribution
202 of its own, named after itself.
204 * The module Bio::Perl has moved to a new distribution named
205 Bio-Procedural.
207 * The module Bio::Tools::Run::RemoteBlast has moved to a new
208 distribution named after itself.
210 * The module Bio::Align::Graphics has been moved to a new distribution
211 named after itself. This also means that BioPerl is no longer
212 dependent on GD.
214 * The entire Bio::DB::HIV namespace, the Bio::DB::Query::HIVQuery
215 module, and the the bp_hivq program have been moved to their
216 own distribution named Bio-DB-HIV. This also drops the bioperl
217 dependency on XML-Simple and Term-ReadLine.
219 * The entire Bio::DB::TFBS namespace has been moved to its own
220 distribution named after itself.
222 * All modules to handle HMMER programs output have been moved to their
223 own distribution named Bio-SearchIO-hmmer. This also includes the
224 programs bp_hmmer_to_table and bp_parse_hmmsearch.
226 * Bio::DB::MeSH and related Bio::Phenotype::MeSH modules have moved
227 to their own distribution Bio-DB-MeSH.
229 * The Bio::DB::Universal module has been moved to its own distribution.
231 * The emacs bioperl minor mode is no longer distributed as part of the
232 perl module distributions. See
233 https://github.com/bioperl/emacs-bioperl-mode
235 1.7.2 - "Entebbe"
237 [Bugs]
239 * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
240 * #245 - Code coverage fixes [zmughal,cjfields]
241 * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
242 * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
243 * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
244 * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
245 * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
246 * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
247 * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
248 * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
249 * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
250 * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
252 [Code changes]
254 * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
256 1.7.1 - "Election"
258 [Bugs]
260 * Minor release to incorporate fix for CPAN indexing, which
261 prevented proper updates [cjfields]
262 * Fix problem in managing Target attribute for gff3 [Jukes34]
263 * Minor bug fixes related to NCBI HTTPS support [cjfields]
265 1.7.0 - "Disney"
267 [New site]
269 * We have migrated to Github Pages. This was actually planned, but the
270 recent OBF server compromise forced our hand.
272 Brian Osborne [bosborne] took this under his wing to move docs and has
273 done a tremendous amount of work formatting the site and working out some
274 of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
275 Cantalupo and Franscison Ossandon also helped. Kudos!!
277 * Similarly, the official issue tracker is now Github Issues. This has
278 been updated in the relevant documentation bits (we hope!)
280 [Code changes]
282 * Previously deprecated modules removed
283 * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
284 * Bio::DB::SeqHound has been removed due to the service no longer being
285 available
286 * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
287 reasons due to the server no longer having a valid cert
288 * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
289 * Bio::Coordinate, Bio::SearchIO::blastxml,
290 Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
291 added on CPAN
293 [New features]
295 * Docker instances of tagged releases are available! [hlapp]
296 * NCBI HTTPS support [mjohnson and others]
297 * Bio::SearchIO::infernal
298 - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
299 * Bio::Search::HSP::ModelHSP
300 - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
301 reports [pcantalupo]
302 * Bio::Search::Result::INFERNALResult
303 - Added new module to represent features of Infernal reports [pcantalupo]
304 * Bio::DB::Taxonomy SQLite option [cjfields]
305 * WrapperBase quoted option values [majensen]
306 * Various documentation fixes and updates [bosborne]
308 [Bug Fixes]
310 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
311 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
312 * NeXML parser fixes [fjossandon]
313 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
314 * RT 103272 : SeqFeature database deletion skipped features with a decimal -
315 Joshua Fortriede (Xenbase)
316 * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
317 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
318 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
319 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
320 * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
321 * Issue #84: EMBL format wrapping problem [nyamned]
322 * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
323 * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
324 or compiled C code (when Inline::C is installed) [rocky]
325 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
326 * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
327 * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
328 * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
329 to be consistent with "$hit->bits" behaviour [fjossandon]
330 * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
331 aminoacids made "next_seq" confused and broke the parser [fjossandon]
332 * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
333 Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
334 to "complement(join(A..B,C..D))" [fjossandon]
335 * For the many many many fixes that weren't mentioned - blame the release guy!
337 1.6.924
339 [Significant changes]
341 * Bug/feature issue tracking has moved to GitHub Issues:
342 https://github.com/bioperl/bioperl-live/issues
343 * DB_File has been demoted from "required" to "recommended",
344 which should make easier for Windows users to install BioPerl
345 if they don't need that module.
347 [New features]
349 * Bio::Search::HSP::GenericHSP
350 - Bug #3370, added a "posterior_string" method to retrieve the
351 posterior probability lines (PP) from HMMER3 reports [fjossandon]
352 - Added a "consensus_string" method to retrieve the consensus
353 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
354 * Bio::SearchIO::hmmer2
355 - The number of identical and conserved residues are now calculated
356 directly from the homology line [fjossandon]
357 - Now the Query Length and Hit Length are reported when the alignment
358 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
359 - Implemented the capture of the consensus structure lines [fjossandon]
360 * Bio::SearchIO::hmmer3
361 - The number of identical and conserved residues are now calculated
362 directly from the homology line [fjossandon]
363 - Now the Hit Length is reported when the alignment runs until the end
364 of the sequence/model ('.]' or '[]') [fjossandon]
365 - Implemented the capture of the consensus structure lines [fjossandon]
366 - Implemented the capture of the posterior probability lines [fjossandon]
367 - Completed the development of NHMMER parsing, including alignments [fjossandon]
368 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
369 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
370 "min_score", "min_bits, and "hit_filter" methods from
371 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
372 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
373 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
374 besides Blast, instead of being ignored. Added tests for all moved methods
375 using HMMER outputs and run the full test suite and everything pass [fjossandon]
376 * Bio::SeqIO::MultiFile
377 - Autodetection of file format [fangly]
378 * Bio::Tools::GuessSeqFormat:
379 - Format detection from non-seekable filehandles such as STDIN [fangly]
381 [Bug fixes]
383 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
384 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
385 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
386 * Abstract: Fixed ActivePerl incapability of removing temporary files
387 because of problems closing tied filehandles [fjossandon]
388 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
389 because ActivePerl were producing a ".index.pag" and ".index.dir"
390 files instead of a single ".index" file (like Strawberry Perl).
391 Now those temporary files are correctly considered and deleted. [fjossandon]
392 * Test files: Added missing module requirements (DB_File and Data::Stag)
393 to several tests files that were failing because those modules were
394 not present. Now those test files are correctly skipped instead. [fjossandon]
395 * Blast: Added support to changes in bl2seq from BLAST+ output, which
396 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
397 * Phylip: Return undef in "next_aln" at file end to avoid
398 an infinite loop [yschensandiego]
399 * HMMER3: When a hit description is too long, it is truncated in
400 the Scores table. In those cases, the more complete description from
401 the Annotation line (>>) will be used [fjossandon]
402 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
403 since it is now used by HMMER3 format in alignments [fjossandon]
404 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
405 to return undef if the query/hit length is unknown (like in some
406 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
407 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
408 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
409 added support to multi-query reports, reduced code redundancy,
410 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
411 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
412 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
413 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
414 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
415 * Double-quotes on paths are needed in some places [fjossandon]
416 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
417 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
418 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
419 with the latest changes made in their own repositories [fjossandon]
420 * General synching of files with the master branch [fjossandon]
421 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
422 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
423 * Fixed broken MeSH parser [fjossandon]
424 * Fixed missing detection of format in SeqIO when given a -string [fangly]
426 1.6.923
428 * Major Windows support updates! [fjossandon]
429 * MAKER update to allow for stricter standard codon table [cjfields]
430 * Better support for circular sequences [fjossandon]
431 * Fixes for some complex location types [fjossandon]
432 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
433 * Fix bug #2978 related to BLAST report type [fjossandon]
434 * Deobfuscator fixes [DaveMessina]
436 1.6.922
438 * Address CPAN test failures [cjfields]
439 * Add BIOPROJECT support for Genbank files [hyphaltip]
440 * Better regex support for HMMER3 output [bosborne]
442 1.6.921
444 * Minor update to address CPAN test failures
446 1.6.920
448 * Remove Bio::Biblio and related files [carandraug]
449 - this cause version clashes with an independently-released
450 version of Bio::Biblio
452 1.6.910
454 [New features]
456 * Hash randomization fixes for perl 5.18.x
457 - Note: at least one module (Bio::Map::Physical) still has a failing test;
458 this is documented in bug #3446 and has been TODO'd; we will be pulling
459 Bio::Map and similar modules out of core into separate distributions in the
460 1.7.x release series [cjfields]
462 [New features]
464 * Bio::Seq::SimulatedRead
465 - New module to represent reads taken from other sequences [fangly]
466 * Bio::Root::Root
467 - Support of Clone::Fast as a faster cloning alternative [fangly]
468 * Bio::Root::IO
469 - Moved the format() and variant() methods from Bio::*IO modules to
470 Bio::Root::IO [fangly]
471 - Can now use format() to get the type of IO format in use [fangly]
472 * Bio::Tools::IUPAC
473 - New regexp() method to create regular expressions from IUPAC sequences
474 [fangly]
475 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
476 - Code refresh [fangly]
477 * Bio::DB::Taxonomy
478 - Added support for the Greengenes and Silva taxonomies [fangly]
479 * Bio::Tree::TreeFunctionsI
480 - get_lineage_string() represents a lineage as a string [fangly]
481 - add_trait() returns instead of reporting an error when the column
482 number is exceeded in add_trait() [fangly]
483 - Option to support tree leaves without trait [fangly]
484 - Allow ID of 0 in trait files [fangly]
485 * Bio::DB::Taxonomy::list
486 - Misc optimizations [fangly]
487 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
488 * Bio::DB::Taxonomy::*
489 - get_num_taxa() returns the number of taxa in the database [fangly]
490 * Bio::DB::Fasta and Bio::DB::Qual
491 - support indexing an arbitrary list of files [fangly]
492 - user can supply an arbitrary index file name [fangly]
493 - new option to remove index file at the end [fangly]
494 * Bio::DB::Fasta
495 - now handles IUPAC degenerate residues [fangly]
496 * Bio::PrimarySeq and Bio::PrimarySeqI
497 - speed improvements for large sequences [Ben Woodcroft, fangly]
498 * Bio::PrimaryQual
499 - tightened and optimized quality string validation [fangly]
500 * Bio::SeqIO::fasta
501 - new method and option 'block', to create FASTA output with space
502 intervaled blocks (similar to genbank or EMBL) has been implemented.
503 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
504 in favour of the methods 'width' and 'preferred_id_type` respectively.
505 * Bio::FeatureIO::*
506 - moved from bioperl-live into the separate distribution Bio-FeatureIO
507 * Bio::SeqFeature::Annotated
508 - moved from bioperl-live into the separate distribution Bio-FeatureIO
509 * Bio::Cluster::SequenceFamily
510 - improved performance when using get_members with overlapping multiple
511 criteria
512 * Bio::SearchIO::hmmer3
513 - now supports nhmmer [bosborne]
515 [Bug fixes]
517 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
518 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
519 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
520 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
521 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
522 information was lost in a multi-result blast file [Paul Cantalupo]
523 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
524 total gaps [Paul Cantalupo]
525 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
526 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
527 when end of domain indicator is split across lines [Paul Cantalupo]
528 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
529 cjfields]
530 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
531 instances where blank lines are within sequences [cjfields]
532 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
533 types [fangly]
534 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
535 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
536 cjfields]
537 * Various fixes for Stockholm file indexing and processing [bosborne]
538 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
539 breaks parsing [cjfields]
540 * Fix case where Bio::Seq::Meta* objects with no meta information could not
541 be reverse-complemented [fangly]
542 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
543 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
544 when unsure that values will be numerical [fangly]
545 * Fix undef warnings in Bio::SeqIO::embl [fangly]
546 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
547 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
548 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
549 Sallou]
550 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
551 source_tag and display_name must return a string, not undef [fangly]
552 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
553 add_SeqFeature takes a single argument [fangly]
554 * Use cross-platform filenames and temporary directory in
555 Bio::DB::Taxonomy::flatfile [fangly]
556 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
557 properly identified as existing taxa in the database [fangly]
558 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
559 without also passing a lineage to store [fangly]
560 * Prevent passing a directory to the gi2taxid option (-g) of
561 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
562 [fangly]
563 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
564 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
565 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
566 object before trying to access, and no longer returns repeated sequences.
569 1.6.901 May 18, 2011
571 [Notes]
573 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
574 modules using Ace will also be deprecated [lds, cjfields]
575 * Minor bug fix release
576 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
577 * Address Build.PL issues when DBI is not present [hartzell]
578 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
579 * Remove deprecated code for perl 5.14.0 compat [cjfields]
580 * Due to schema changes and lack of support for older versions, support
581 for NeXML 0.9 is only (very) partially implemented.
582 See: https://redmine.open-bio.org/issues/3207
584 [Bug fixes]
586 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
587 docs [genehack, cjfields]
588 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
589 module version from dist_version (probably not the best way to do this,
590 but it seems to work) [rbuels, cjfields]
593 1.6.900 April 14, 201
595 [Notes]
597 * This will probably be the last release to add significant features to
598 core modules; subsequent releases will be for bug fixes alone.
599 We are planning on a restructuring of core for summer 2011, potentially
600 as part of the Google Summer of Code. This may become BioPerl 2.0.
601 * Version bump represents 'just prior to v 1.7'. We may have point
602 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
603 This code essentially is what is on the github master branch.
605 [New features]
607 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
608 * Bio::Tree refactor
609 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
610 - removal of Scalar::Util::weaken code, which was causing odd headaches
611 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
612 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
613 many others]
614 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
615 [Warren Kretzschmar]
616 * Bio::SeqIO::gbxml
617 - bug 2515 - new contribution [Ryan Golhar, jhannah]
618 * Bio::Assembly::IO
619 - support for reading Maq, Sam and Bowtie files [maj]
620 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
621 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
622 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
623 - bug 2726: reading/writing granularity: whole scaffold or one contig
624 at a time [Joshua Udall, fangly]
625 * Bio::OntologyIO
626 - Added parsing of xrefs to OBO files, which are stored as secondary
627 dbxrefs of the cvterm [Naama Menda]
628 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
629 * PAML code updated to work with PAML 4.4d [DaveMessina]
631 [Bug fixes]
633 * [3198] - sort tabular BLAST hits by score [DaveMessina]
634 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
635 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
636 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
637 [cjfields]
638 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
639 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
640 * [3164] - TreeFunctionsI syntax bug [gjuggler]
641 * [3163] - AssemblyIO speedup [fangly]
642 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
643 hyphaltip]
644 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
645 * [3158] - fix EMBL file mis-parsing [cjfields]
646 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
647 cjfields]
648 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
649 * [3148] - URL change for UniProt [cjfields]
650 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
651 * [3136] - HMMer3 parser fixes [kblin]
652 * [3126] - catch description [Toshihiko Akiba]
653 * [3122] - Catch instances where non-seekable filehandles were being
654 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
655 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
656 [dukeleto, rbuels, cjfields]
657 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
658 jhannah]
659 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
660 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
661 cjfields]
662 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
663 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
664 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
665 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
666 * [3086] - EMBL misparsing long tags [kblin, cjfields]
667 * [3085] - CommandExts and array of files [maj, hyphaltip]
668 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
669 for alignment slices [Ha X. Dang, cjfields]
670 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
671 * [3073] - fix parsing of GenBank files from RDP [cjfields]
672 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
673 * [3064] - All-gap midline BLAST report issues [cjfields]
674 * [3063] - BLASt report RID [Razi Khaja, cjfields]
675 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
676 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
677 * [3039] - correct Newick output root node branch length [gjuggler,
678 DaveMessina]
679 * [3038] - SELEX alignment error [Bernd, cjfields]
680 * [3033] - PrimarySeq ID setting [Bernd, maj]
681 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
682 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
683 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
684 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
685 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
686 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
687 PAML 4.4d [DaveMessina]
688 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
689 DaveMessina]
690 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
691 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
692 * [3017] - using threads with Bio::DB::GenBank [cjfields]
693 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
694 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
695 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
696 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
697 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
698 cjfields]
699 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
700 * [2977] - TreeIO issues [DaveMessina]
701 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
702 * [2944] - Bio::Tools::GFF score [cjfields]
703 * [2942] - correct MapTiling output [maj]
704 * [2939] - PDB residue insertion codes [John May, maj]
705 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
706 * [2928] - GuessSeqFormat raw [maj]
707 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
708 * [2922] - open() directive issue [cjfields]
709 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
710 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
711 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
712 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
713 cjfields]
714 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
715 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
716 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
717 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
718 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
719 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
720 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
721 * [2758] - Bio::AssemblyIO ace problems [fangly]
722 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
723 * [2726] - ace file IO [Josh, fangly]
724 * [2700] - Refactor Build.PL [cjfields]
725 * [2673] - addition of simple Root-based clone() method [cjfields]
726 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
727 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
728 * [2594] - Bio::Species memory leak [cjfields]
729 * [2515] - GenBank XML parser [jhannah]
730 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
731 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
732 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
733 cjfields]
734 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
736 [Deprecated]
738 * Bio::Expression modules - these were originally designed to go with the
739 bioperl-microarray suite of tools, however they have never been completed
740 and so have been removed from the distribution. The original code has
741 been moved into the inactive bioperl-microarray suite. [cjfields]
743 [Other]
745 * Repository moved from Subversion (SVN) to
746 http://github.com/bioperl/bioperl-live [cjfields]
747 * Bug database has moved to Redmine (https://redmine.open-bio.org)
748 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
749 Thieme have been moved to their own distribution (Bio-Microarray).
750 [cjfields]
752 1.6.1 Sept. 29, 2009 (point release)
753 * No change from last alpha except VERSION and doc updates [cjfields]
755 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
756 * Fix for silent OBDA bug related to FASTA validation [cjfields]
758 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
759 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
760 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
761 [cjfields]
762 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
764 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
765 * WinXP test fixes [cjfields, maj]
766 * BioPerl.pod added for descriptive information, fixes CPAN indexing
767 [cjfields]
768 * Minor doc fixes [cjfields]
770 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
771 * Fix tests failing due to merging issues [cjfields]
772 * More documentation updates for POD parsing [cjfields]
774 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
775 * Bio::Root::Build
776 - fix YAML meta data generation [cjfields]
778 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
779 * Bio::Align::DNAStatistics
780 - fix divide by zero problem [jason]
781 * Bio::AlignIO::*
782 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
783 * Bio::AlignIO::stockholm
784 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
785 * Bio::Assembly::Tools::ContigSpectrum
786 - function to score contig spectrum [fangly]
787 * Bio::DB::EUtilities
788 - small updates [cjfields]
789 * Bio::DB::Fasta
790 - berkeleydb database now autoindexes wig files and locks correctly
791 [lstein]
792 * Bio::DB::HIV
793 - various small updates for stability; tracking changes to LANL
794 database interface [maj]
795 * Bio::DB::SeqFeature (lots of updates and changes)
796 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
797 - bug 2835 - patch [Dan Bolser]
798 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
799 * Bio::DB::SwissProt
800 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
801 * Bio::Factory::FTLocationFactory
802 - mailing list bug fix [cjfields]
803 * Bio::LocatableSeq
804 - performance work on column_from_residue_number [hartzell]
805 * Bio::Matrix::IO::phylip
806 - bug 2800 - patch to fix phylip parsing [Wei Zou]
807 * Bio::Nexml
808 - Google Summer of Code project from Chase Miller - parsers for Nexml
809 file format [maj, chmille4]
810 * Bio::PopGen
811 - Make Individual, Population, Marker objects AnnotatableI [maj]
812 - simplify LD code [jason]
813 * Bio::RangeI
814 - deal with empty intersection [jason]
815 * Bio::Restriction
816 - significant overhaul of Bio::Restriction system: complete support for
817 external and non-palindromic cutters. [maj]
818 * Bio::Root::Build
819 - CPANPLUS support, no automatic installation [sendu]
820 * Bio::Root::IO
821 - allow IO::String (regression fix) [cjfields]
822 - catch unintentional undef values [cjfields]
823 - throw if non-fh is passed to -fh [maj]
824 * Bio::Root::Root/RootI
825 - small debugging and core fixes [cjfields]
826 * Bio::Root::Test
827 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
828 * Bio::Root::Utilities
829 - bug 2737 - better warnings [cjfields]
830 * Bio::Search
831 - tiling completely refactored, HOWTO added [maj]
832 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
833 will deprecate usage of the older tiling code in the next BioPerl
834 release
835 - small fixes [cjfields]
836 * Bio::SearchIO
837 - Infernal 1.0 output now parsed [cjfields]
838 - new parser for gmap -f9 output [hartzell]
839 - bug 2852 - fix infinite loop in some output [cjfields]
840 - blastxml output now passes all TODO tests [cjfields]
841 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
842 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
843 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
844 * Bio::Seq::LargePrimarySeq
845 - delete tempdirs [cjfields]
846 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
847 * Bio::Seq::Quality
848 - extract regions based on quality threshold value [Dan Bolser, heikki]
849 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
850 * Bio::SeqFeature::Lite
851 - various Bio::DB::SeqFeature-related fixes [lstein]
852 * Bio::SeqFeature::Tools::TypeMapper
853 - additional terms for GenBank to SO map [scain]
854 * Bio::SeqIO::chadoxml
855 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
856 * Bio::SeqIO::embl
857 - support for CDS records [dave_messina, Sylvia]
858 * Bio::SeqIO::fastq
859 - complete refactoring to handle all FASTQ variants, perform validation,
860 write output. API now conforms with other Bio* parsers and the rest of
861 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
862 [cjfields]
863 * Bio::SeqIO::genbank
864 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
865 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
866 * Bio::SeqIO::largefasta
867 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
868 * Bio::SeqIO::raw
869 - add option for 'single' and 'multiple'
870 * Bio::SeqIO::scf
871 - bug 2881 - fix scf round-tripping [Adam Søgren]
872 * Bio::SeqUtils
873 - bug 2766, 2810 - copy over tags from features, doc fixes [David
874 Jackson]
875 * Bio::SimpleAlign
876 - bug 2793 - patch for add_seq index issue [jhannah, maj]
877 - bug 2801 - throw if args are required [cjfields]
878 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
879 [Tristan Lefebure, maj]
880 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
881 - fix POD and add get_SeqFeatures filter [maj]
882 * Bio::Tools::dpAlign
883 - add support for LocatableSeq [ymc]
884 - to be moved to a separate distribution [cjfields, rbuels]
885 * Bio::Tools::EUtilities
886 - fix for two bugs from mail list [Adam Whitney, cjfields]
887 - add generic ItemContainerI interface for containing same methods
888 [cjfields]
889 * Bio::Tools::HMM
890 - fix up code, add more warnings [cjfields]
891 - to be moved to a separate distribution [cjfields, rbuels]
892 * Bio::Tools::Primer3
893 - bug 2862 - fenceposting issue fixed [maj]
894 * Bio::Tools::Run::RemoteBlast
895 - tests for remote RPS-BLAST [mcook]
896 * Bio::Tools::SeqPattern
897 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
898 * Bio::Tools::tRNAscanSE
899 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
900 * Bio::Tree::*
901 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
902 * Bio::Tree::Statistics
903 - several methods for calculating Fitch-based score, internal trait
904 values, statratio(), sum of leaf distances [heikki]
905 * Bio::Tree::Tree
906 - bug 2869 - add docs indicating edge case where nodes can be
907 prematurely garbage-collected [cjfields]
908 - add as_text() function to create Tree as a string in specified format
909 [maj]
910 * Bio::Tree::TreeFunctionsI
911 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
912 Lefebure, maj]
913 * Bio::TreeIO::newick
914 - fix small semicolon issue [cjfields]
915 * scripts
916 - update to bp_seqfeature_load for SQLite [lstein]
917 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
918 - fastam9_to_table - fix for MPI output [jason]
919 - gccalc - total stats [jason]
920 * General Stuff
921 - POD cleanup re: FEEDBACK section [maj, cjfields]
922 - cleanup or fix dead links [cjfields]
923 - Use of no_* methods (indicating 'number of something') is deprecated
924 in favor of num_* [cjfields]
925 - lots of new tests for the above bugs and refactors [everyone!]
926 - new template for Komodo text editor [cjfields]
928 1.6.0 Winter 2009
929 * Feature/Annotation rollback
930 - Problematic changes introduced prior to the 1.5 release have been
931 rolled back. These changes led to subtle bugs involving operator
932 overloading and interface methods.
933 - Behavior is very similar to that for BioPerl 1.4, with tag values
934 being stored generically as simple scalars. Results in a modest
935 speedup.
936 * Bio::Graphics
937 - Split into a separate distribution on CPAN, primarily so development
938 isn't reliant on a complete BioPerl release.
939 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
940 is only available via Subversion (via bioperl-live main trunk)
941 * Bio::Root::Test
942 - Common test bed for all BioPerl modules
943 * Bio::Root::Build
944 - Common Module::Build-based subclass for all BioPerl modules
945 * Bio::DB::EUtilities
946 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
947 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
948 and user agent request posting and retrieval
949 * Test implementation and reorganization
950 - Tests have been reorganized into groups based on classes or use
951 cases.
952 - Automated test coverage is now online:
953 http://www.bioperl.org/wiki/Test_Coverage
954 - After this release, untested modules will be moved into a
955 separate developer distribution until tests can be derived.
956 Also, new modules to be added are expected to have a test suite
957 and adequate test coverage.
959 1.5.2 Developer release
961 Full details of changes since 1.5.1 are available online at:
962 http://www.bioperl.org/wiki/Change_log
963 The following represents a brief overview of the most important changes.
965 o Bio::Map
966 - Overhaul. Brand new system fully allows markers to have multiple
967 positions on multiple maps, and to have relative positions. Should be
968 backward compatible.
970 o Bio::Taxonomy
971 - This module and all the modules in the Taxonomy directory now
972 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
974 o Bio::DB::Taxonomy
976 - Taxonomy.pm
977 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
979 * New methods ancestor(), each_Descendent() and _handle_internal_id().
981 * Allows for different database modules to create Bio::Taxon objects
982 with the same internal id when the same taxon is requested from each.
984 - flatfile.pm
985 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
987 * No longer includes the fake root node 'root'; there are multiple roots
988 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
990 - entrez.pm
991 * get_node() has new option -full
993 * Caches data retrieved from website
995 o Bio::Species
996 - Now a Bio::Taxon. Carries out the species name -> specific name munging
997 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
998 backward compatability in species() method.
1000 o Bio::Search and Bio::SearchIO
1001 - Overhaul. The existing system has been sped up via some minor changes
1002 (mostly gain-of-function to the API). Bio::PullParserI is introduced
1003 as a potential eventual replacment for the existing system, though as
1004 yet only a Hmmpfam parser exists written using it.
1007 1.5.1 Developer release
1009 o Major problem with how Annotations were written out with
1010 Bio::Seq is fixed by reverting to old behavior for
1011 Bio::Annotation objects.
1013 o Bio::SeqIO
1015 - genbank.pm
1016 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
1017 expect at l east 9 spaces at the beginning of a line to
1018 indicate line wrapping.
1020 * Treat multi-line SOURCE sections correctly, this defect broke
1021 both common_name() and classification()
1023 * parse swissprot fields in genpept file
1025 * parse WGS genbank records
1027 - embl.pm
1028 * Changed regexp for ID line. The capturing parentheses are
1029 the same, the difference is an optional repeated-not-semi-
1030 colon expression following the captured \S+. This means the
1031 regexp works when the division looks like /PRO;/ or when the
1032 division looks like /ANG ;/ - the latter is from EMBL
1033 repbase
1035 * fix ID line parsing: the molecule string can have spaces in
1036 it. Like: "genomic DNA"
1038 - swiss.pm: bugs #1727, #1734
1040 - entrezgene.pm
1041 * Added parser for entrezgene ASN1 (text format) files.
1042 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
1044 o Bio::AlignIO
1046 - maf.pm coordinate problem fixed
1048 o Bio::Taxonomy and Bio::DB::Taxonomy
1050 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
1051 can be done via Web without downloading all the sequence.
1053 o Bio::Tools::Run::RemoteBlast supports more options and complies
1054 to changes to the NCBI interface. It is reccomended that you
1055 retrieve the data in XML instead of plain-text BLAST report to
1056 insure proper parsing and retrieval of all information as NCBI
1057 fully expects to change things in the future.
1059 o Bio::Tree and Bio::TreeIO
1061 - Fixes so that re-rooting a tree works properly
1063 - Writing out nhx format from a newick/nexus file will properly output
1064 bootstrap information. The use must move the internal node labels over
1065 to bootstraps.
1066 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
1067 $node->bootstrap($node->id);
1068 $node->id('');
1069 }
1070 - Nexus parsing is much more flexible now, does not care about
1071 LF.
1073 - Cladogram drawing module in Bio::Tree::Draw
1075 - Node height and depth now properly calculated
1077 - fix tree pruning algorithm so that node with 1 child gets merged
1079 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
1080 bugs and improvements were added, see Gbrowse mailing list for most of
1081 these.
1083 o Bio::DB::GFF partially supports GFF3. See information about
1084 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
1086 o Better location parsing in Bio::Factory::FTLocationFactory -
1087 this is part of the engine for parsing EMBL/GenBank feature table
1088 locations. Nested join/order-by/complement are allowed now
1090 o Bio::PrimarySeqI->translate now takes named parameters
1092 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
1093 reconstruction) is now supported. Parsing different models and
1094 branch specific parametes are now supported.
1096 o Bio::Factory::FTLocationFactory - parse hierarchical locations
1097 (joins of joins)
1099 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
1100 for getter/setter functions
1102 o Bio::SearchIO
1104 - blast bug #1739; match scientific notation in score
1105 and possible e+ values
1107 - blast.pm reads more WU-BLAST parameters and parameters, match
1108 a full database pathname,
1110 - Handle NCBI WEB and newer BLAST formats specifically
1111 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
1113 - psl off-by-one error fixed
1115 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
1116 and HSPs can be constructed from them.
1118 - HSPs query/hit now have a seqdesc field filled out (this was
1119 always available via $hit->description and
1120 $result->query_description
1122 - hmmer.pm can parse -A0 hmmpfam files
1124 - Writer::GbrowseGFF more customizeable.
1126 o Bio::Tools::Hmmpfam
1127 make e-value default score displayed in gff, rather than raw score
1128 allow parse of multiple records
1131 1.5 Developer release
1133 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
1134 provide Jukes-Cantor and Kimura pairwise distance methods,
1135 respectively.
1137 o Bio::AlignIO support for "po" format of POA, and "maf";
1138 Bio::AlignIO::largemultifasta is a new alternative to
1139 Bio::AlignIO::fasta for temporary file-based manipulation of
1140 particularly large multiple sequence alignments.
1142 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
1143 be treated similarly as an assembled contig.
1145 o Bio::CodonUsage provides new rare_codon() and probable_codons()
1146 methods for identifying particular codons that encode a given
1147 amino acid.
1149 o Bio::Coordinate::Utils provides new from_align() method to build
1150 a Bio::Coordinate pair directly from a
1151 Bio::Align::AlignI-conforming object.
1153 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
1154 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
1155 web service using standard Pubmed query syntax, and retrieve
1156 results as XML.
1158 o Bio::DB::GFF has various sundry bug fixes.
1160 o Bio::FeatureIO is a new SeqIO-style subsystem for
1161 writing/reading genomic features to/from files. I/O classes
1162 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
1163 classes only read/write Bio::SeqFeature::Annotated objects.
1164 Notably, the GFF v3 class requires features to be typed into the
1165 Sequence Ontology.
1167 o Bio::Graph namespace contains new modules for manipulation and
1168 analysis of protein interaction graphs.
1170 o Bio::Graphics has many bug fixes and shiny new glyphs.
1172 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
1173 indexing for HMMER reports and FASTA qual files, respectively.
1175 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
1176 new objects that can be placed within a Bio::Map::MapI-compliant
1177 genetic/physical map; Bio::Map::Physical provides a new physical
1178 map type; Bio::MapIO::fpc provides finger-printed clone mapping
1179 import.
1181 o Bio::Matrix::PSM provide new support for postion-specific
1182 (scoring) matrices (e.g. profiles, or "possums").
1184 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
1185 be instantiated without explicitly using Bio::OntologyIO. This
1186 is possible through changes to Bio::Ontology::OntologyStore to
1187 download ontology files from the web as necessary. Locations of
1188 ontology files are hard-coded into
1189 Bio::Ontology::DocumentRegistry.
1191 o Bio::PopGen includes many new methods and data types for
1192 population genetics analyses.
1194 o New constructor to Bio::Range, unions(). Given a list of
1195 ranges, returns another list of "flattened" ranges --
1196 overlapping ranges are merged into a single range with the
1197 mininum and maximum coordinates of the entire overlapping group.
1199 o Bio::Root::IO now supports -url, in addition to -file and -fh.
1200 The new -url argument allows one to specify the network address
1201 of a file for input. -url currently only works for GET
1202 requests, and thus is read-only.
1204 o Bio::SearchIO::hmmer now returns individual Hit objects for each
1205 domain alignment (thus containing only one HSP); previously
1206 separate alignments would be merged into one hit if the domain
1207 involved in the alignments was the same, but this only worked
1208 when the repeated domain occured without interruption by any
1209 other domain, leading to a confusing mixture of Hit and HSP
1210 objects.
1212 o Bio::Search::Result::ResultI-compliant report objects now
1213 implement the "get_statistics" method to access
1214 Bio::Search::StatisticsI objects that encapsulate any
1215 statistical parameters associated with the search (e.g. Karlin's
1216 lambda for BLAST/FASTA).
1218 o Bio::Seq::LargeLocatableSeq combines the functionality already
1219 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
1221 o Bio::SeqFeature::Annotated is a replacement for
1222 Bio::SeqFeature::Generic. It breaks compliance with the
1223 Bio::SeqFeatureI interface because the author was sick of
1224 dealing with untyped annotation tags. All
1225 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
1226 compliant, and accessible through Bio::Annotation::Collection.
1228 o Bio::SeqFeature::Primer implements a Tm() method for primer
1229 melting point predictions.
1231 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
1232 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
1234 o Bio::Taxonomy::Node now implements the methods necessary for
1235 Bio::Species interoperability.
1237 o Bio::Tools::CodonTable has new reverse_translate_all() and
1238 make_iupac_string() methods.
1240 o Bio::Tools::dpAlign now provides sequence profile alignments.
1242 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
1244 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
1245 parsers.
1247 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
1248 for designing small inhibitory RNA.
1250 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
1251 methods based on a distance matrix.
1253 o Bio::Tree::Statistics provides an assess_bootstrap() method to
1254 calculate bootstrap support values on a guide tree topology,
1255 based on provided bootstrap tree topologies.
1257 o Bio::TreeIO now supports the Pagel (PAG) tree format.
1259 1.4 branch
1261 1.4.1
1263 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
1265 o Bio::Graphics will work with gd1 or gd2
1267 o Bio::SearchIO
1268 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
1269 (RF lines alone)
1270 - blast.pm Parse multi-line query fields properly
1271 - small speed improvements to blasttable.pm and others
1273 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
1274 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
1275 supporting more complex queries
1278 1.4. Stable major release
1280 Since initial 1.2.0, 3000 separate changes have been made to make this release.
1282 o installable scripts
1284 o global module version from Bio::Root:Version
1286 o Bio::Graphics
1287 - major improvements; SVG support
1289 o Bio::Popgen
1290 - population genetics
1291 - support several population genetics types of questions.
1292 - Tests for statistical neutrality of mutations
1293 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
1294 Tests of population structure (Wright's F-statistic: Fst) is in
1295 Bio::PopGen::PopStats. Calculating composite linkage
1296 disequilibrium (LD) is available in Bio::PopGen::Statistics as
1297 well.
1298 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1299 and csv (comma delimited formatted) data.
1301 - a directory for implementing population simulations has
1302 been added Bio::PopGen::Simulation and 2 simulations - a
1303 Coalescent and a simple single-locus multi-allele genetic drift
1304 simulation have been provided. This replaces the code in
1305 Bio::Tree::RandomTree which has been deprecated until proper
1306 methods for generating random phylogenetic trees are
1307 implemented.
1309 o Bio::Restriction
1310 - new restrion analysis modules
1312 o Bio::Tools::Analysis
1313 - web based DNA and Protein analysis framework and several
1314 implementations
1316 o Bio::Seq::Meta
1317 - per residue annotable sequences
1319 o Bio::Matrix
1320 - Bio::Matrix::PSM - Position Scoring Matrix
1321 - Bio::Matrix::IO has been added for generalized parsing of
1322 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1323 initial implementations for parsing BLOSUM/PAM and Phylip
1324 Distance matricies respectively. A generic matrix
1325 implementation for general use was added in
1326 Bio::Matrix::Generic.
1328 o Bio::Ontology
1329 - major changes
1331 o Bio:Tree
1333 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1334 - small inhibitory RNA
1336 o Bio::SeqFeature::Tools
1337 - seqFeature mapping tools
1338 - Bio::SeqFeature::Tools::Unflattener.pm
1339 -- deal with mapping GenBank feature collections into
1340 Chado/GFF3 processable feature sets (with SO term mappings)
1342 o Bio::Tools::dpAlign
1343 - pure perl dynamic programming sequence alignment
1344 - needs Bioperl-ext
1346 o new Bio::SearchIO formats
1347 - axt and psl: UCSC formats.
1348 - blasttable: NCBI -m 8 or -m 9 format from blastall
1350 o new Bio::SeqIO formats
1351 - chado, tab, kegg, tigr, game
1352 - important fixes for old modules
1354 o Bio::AlignIO: maf
1356 o improved Bio::Tools::Genewise
1358 o Bio::SeqIO now can recongnize sequence formats automatically from
1359 stream
1361 o new parsers in Bio::Tools:
1362 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1364 o Bio::DB::Registry bugs fixed
1365 - BerkeleyDB-indexed flat files can be used by the OBDA system
1366 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1367 used by the OBDA system
1369 o several new HOWTOs
1370 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1371 Databases
1373 o hundreds of new and improved files
1376 o
1377 o Bio::Tree::AlleleNode has been updated to be a container of
1378 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1381 1.2 Branch
1383 1.2.3 Stable release update
1384 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1385 handling.
1386 o Bug #1477 - Sel --> Sec abbreviation fixed
1387 o Fix bug #1487 where paring in-between locations when
1388 end < start caused the FTLocationFactory logic to fail.
1389 o Fix bug #1489 which was not dealing with keywords as an
1390 arrayref properly (this is fixed on the main trunk because
1391 keywords returns a string and the array is accessible via
1392 get_keywords).
1393 o Bio::Tree::Tree memory leak (bug #1480) fixed
1394 Added a new initialization option -nodelete which
1395 won't try and cleanup the containing nodes if this
1396 is true.
1397 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1398 this was only present on the branch for the 1.2.1 and 1.2.2 series
1399 - Also merged main trunk changes to the branch which make
1400 newick -> nhx round tripping more effective (storing branch length
1401 and bootstrap values in same locate for NodeNHX and Node
1402 implementations.) Fixes to TreeIO parsing for labeled internal
1403 also required small changes to TreeIO::nhx. Improved
1404 tests for this module as well.
1405 o Bio::SearchIO
1406 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1407 gapped blast properly (was losing hit significance values due to
1408 the extra unexpeted column).
1409 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1410 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1411 although doesn't try to correct it - will get the negative
1412 number for you. Added a test for this as well.
1413 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1414 has no top-level family classification scores but does have scores and
1415 alignments for individual domains.
1416 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1417 regular expression to match the line was missing the possibility of
1418 an extra space. This is rare, which is why we probably did not
1419 catch it before.
1420 - BLAST parsing picks up more of the statistics/parameter fields
1421 at the bottom of reports. Still not fully complete.
1422 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1423 were fixed to include many improvements and added flexiblity
1424 in outputting the files. Bug #1495 was also fixed in the process.
1425 o Bio::DB::GFF
1426 - Update for GFF3 compatibility.
1427 - Added scripts for importing from UCSC and GenBank.
1428 - Added a 1.2003 version number.
1429 o Bio::Graphics
1430 - Updated tutorial.
1431 - Added a 1.2003 version number.
1432 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1433 properly writing keywords out.
1434 o Bio::SeqIO::genbank
1435 - Fixed bug/enhancement #1513 where dates of
1436 the form D-MMM-YYYY were not parsed. Even though this is
1437 invalid format we can handle it - and also cleanup the date
1438 string so it is properly formatted.
1439 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1440 and written with Genbank format. Similarly bug #1515 is fixed to
1441 parse in the ORIGIN text.
1442 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1443 to specify the ID type, one of (accession accession.version
1444 display primary). See Bio::SeqIO::preferred_id_type method
1445 documentation for more information.
1446 o Unigene parsing updated to handle file format changes by NCBI
1448 1.2.2 Stable release update
1450 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1451 - auto-discover ontology name
1452 - bug in parsing relationships when certain characters are in the term
1453 - fixed hard-coded prefix for term identifiers
1454 - various smaller issues
1456 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1457 of Bio::Ontology::TermI
1459 o brought the OBDA Registry code up to latest specs
1461 o Bio::DB::GenBank
1462 - eutils URL change
1463 - accession number retrieval fixed
1465 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1467 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1468 #1459 which now properly report alignment start/end info
1469 for translated BLAST/FASTA searches.
1471 o Bio::TreeIO::newick can parse labeled internal nodes
1473 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1474 for BLASTX if if you provide -report_type => 'BLASTX' when
1475 initializing a BPbl2seq object. Bioperl 1.3 will have better
1476 support for bl2seq in the SearchIO system.
1478 o Bio::Root::IO support a -noclose boolean flag which will not
1479 close a filehandle upon object cleanup - useful when sharing
1480 a filehandle among objects. Additionally code added s.t.
1481 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1483 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1485 o Bio::SeqIO::genbank
1486 - bug #1456 fixed which generated extra sequence lines
1487 - write moltype correctly for genpept
1489 1.2.1 Stable release update
1491 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1493 o Addition from main trunk of Ontology objects, principly to allow
1494 BioSQL releases against 1.2.1
1496 o Fixes and cleanup of Bio::Coordinate modules
1498 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1499 the primary accession number
1501 o Other bug fixes, including bpindex GenBank fix
1503 o Bio::SeqIO::genbank bug #1389 fixed
1505 1.2 Stable major release
1507 o More functionality added to Bio::Perl, the newbie module
1509 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1510 Support for New Hampshire Extended (NHX) format parsing.
1512 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1513 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1514 Hmmpfam parser.
1516 o New ontology parsing Bio::Ontology
1518 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1519 multi-report (mlib) fasta reports, support for waba and exonerate.
1521 o Bio::ClusterIO for parsing Unigene clusters
1523 o Bio::Assembly added for representing phrap and ace assembly clusters.
1525 o Rudimentary support for writing Chado XML (see
1526 GMOD project: www.gmod.org for more information)
1528 o Bio::Coordinate for mapping between different coordinate systems such
1529 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1530 features into different coordinate systems.
1532 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1533 with the get_Stream_by_query method and supports the latest
1534 NCBI eutils interface.
1536 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1537 object for extracting subsets of features : currently only
1538 supports extraction by location.
1540 1.1.1 Developer release
1542 o Deprecated modules are now listed in the DEPRECATED file
1544 o New HowTo documents located in doc/howto describing
1545 a domain of Bioperl.
1547 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1548 and all old bugs are searchable through the bugzilla interface.
1550 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1551 have been addressed.
1553 o Support for Genewise parsing in Bio::Tools::Genewise
1555 o Start of Ontology framework with Bio::Ontology
1557 o Speedup to the Bio::Root::Root object method _rearrange.
1558 A global _load_module method was implemented to simplify the
1559 dynamic loading of modules ala Bio::SeqIO::genbank. This
1560 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1561 etc).
1563 o Several performance improvements to sequence parsing in Bio::SeqIO.
1564 Attempt to speedup by reducing object creation overhead.
1566 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1567 method for sequence retrieval with their E-utils CGI scripts.
1568 More work to support Entrez queries to their fullest is planned
1569 before 1.2 release.
1571 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1573 1.1 Developer release
1575 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1576 this separation removes some of the complexity in our test suite
1577 and separates the core modules in bioperl from those that need
1578 external programs to run.
1580 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1581 not run into trouble running the makefile
1583 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1584 read,create,and write locations for grouped/split locations
1585 (like mRNA features on genomic sequence).
1587 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1588 and PAML (codeml,aaml, etc) parsing.
1590 o Bio::Tree:: objects expanded to handle testing monophyly,
1591 paraphyly, least common ancestor, etc.
1593 o Bio::Coordinate for mapping locations from different coordinate spaces
1595 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1596 added for parsing hmmpfam and hmmsearch output.
1598 o Bio::SearchIO::Writer::TextResultWriter for outputting
1599 a pseudo-blast textfile format
1602 1.0.2 Bug fix release
1604 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1605 in this release will not work after December 2002 when NCBI
1606 shuts off the old Entrez cgi scripts. We have already fixed
1607 on our main development branch and the functionality will be
1608 available in the next stable bioperl release (1.2) slated for
1609 Fall 2002.
1611 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1612 testset by Robin Emig. These were fixed as was the get_aln
1613 method in Bio::Search::HSP::GenericHSP to handle the extra
1614 context sequence that is provided with a FastA alignment.
1616 o Migrating differences between Bio::Search::XX::BlastXX to
1617 Bio::Search::XX::GenericXX objects. This included mechanism
1618 to retrieve whole list of HSPs from Hits and whole list of Hits from
1619 Results in addition to the current next_XX iterator methods that
1620 are available. Added seq_inds() method to GenericHSP which identifies
1621 indexes in the query or hit sequences where conserved,identical,gaps,
1622 or mismatch residues are located (adapted from Steve Chervitz's
1623 implementation in BlastHSP).
1625 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1626 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1628 o Bio::Graphics glyph set improved and extended for GBrowse release
1630 o Bio::Tree::Tree get_nodes implementation improvement thanks
1631 to Howard Ross notice performance problem when writing out
1632 unbalanced trees.
1634 o Bio::Location::Fuzzy::new named parameter -loc_type became
1635 -location_type, Bio::Location::Simple::new named parameter
1636 -seqid becamse -seq_id.
1638 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1639 was mis-detecting that gaps should be placed at the beginning of
1640 the alignment when the best alignment starts internally in the
1641 sequence.
1643 1.0.1 Bug fix release
1645 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1647 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1648 and mixed (3.3 - 3.4) versions of FASTA.
1650 o Small API change to add methods for completeness across
1651 implementations of Bio::Search objects. These new methods
1652 in the interface are implemented by the GenericXX object as well
1653 as the BlastXX objects.
1654 * Bio::Search::Result::ResultI
1655 - hits() method returns list of all Hits (next_hit is an
1656 iterator method)
1658 * Bio::Search::Hit::HitI
1659 - hsps() method returns list of all HSPs (next_hsp is an
1660 iterator method)
1662 o The Bio::SearchIO::Writer classes have been fixed to handle results
1663 created from either psiblast (Search::BlastXX objects) or
1664 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1665 has to be done here to make it work properly and will nee major
1666 API changes.
1668 o Bugs in Bio::Tools::HMMER fixed, including
1669 * #1178 - Root::IO destructor wasn't being called
1670 * #1034 - filter_on_cutoff now behaves properly
1672 o Bio::SeqFeature::Computation initialization args fixed and
1673 tests added.
1675 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1677 o Updated FAQ with more example based answers to typical questions
1679 o Bug #1202 was fixed which would improperly join together qual values
1680 parsed by Bio::SeqIO::qual when a trailing space was not present before
1681 the newline.
1683 1.0.0 Major Stable Release
1685 This represents a major release of bioperl with significant
1686 improvements over the 0.7.x series of releases.
1688 o Bio::Tools::Blast is officially deprecated. Please see
1689 Bio::SearchIO for BLAST and FastA parsing.
1691 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1692 Bio::LocationI objects as well as start/end.
1694 o Bio::Biblio contains modules for Bibliographic data.
1695 Bio::DB::Biblio contains the query modules. Additionally one can
1696 parse medlinexml from the ebi bibliographic query service (BQS)
1697 system and Pubmed xml from NCBI. See Martin Senger's
1698 documentation in Bio::Biblio for more information.
1700 o Bio::DB::Registry is a sequence database registry part of
1701 Open Bioinformatics Database Access. See
1702 http://obda.open-bio.org for more information.
1704 o File-based and In-Memory Sequence caching is provided by
1705 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1706 local database.
1708 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1709 been added by Lincoln Stein.
1711 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1713 o A FAQ has been started and is included in the release to provide
1714 a starting point for frequent questions and issues.
1716 0.9.3 Developer's release
1718 o Event based parsing system improved (SearchIO). With parsers for
1719 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1720 Additionally a lazy parsing system for text and html blast reports was
1721 added and is called psiblast (name subject to change in future releases).
1723 o Bio::Search objects improved and standardized with associated Interfaces
1724 written. The concept of a search "Hit" was standardized to be called
1725 "hit" consistently and the use of "subject" was deprecated in all active
1726 modules.
1728 o Bio::Structure added (since 0.9.1) for Protein structure objects
1729 and PDB parser to retrieve and write these structures from data files.
1731 o Several important Bio::DB::GFF bug fixes for handling features that
1732 are mapped to multiple reference points. Updated mysql adaptor
1733 so as to be able to store large (>100 megabase) chunks of DNA into
1734 Bio::DB::GFF databases.
1736 0.9.2 Developer's release
1738 o Bio::Search and Bio::SearchIO system introduced for event based
1739 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1740 in text and XML and FASTA reports in standard output format.
1742 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1743 generator is included in Bio::TreeIO::RandomTrees and a
1744 statistics module for evaluating.
1746 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1747 server for DAS servers.
1749 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1750 files. The entire BPlite system migrated to using Bio::Root::IO
1751 for the data stream.
1753 o Bio::Tools::Alignment for Consed and sequence Trimming
1754 functionality.
1756 o Bio::Structure for Protein structure information and parsing
1758 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1759 cgi-bin entry point which should be more reliable.
1761 o Bio::Map and Bio::MapIO for biological map navigation and a
1762 framework afor parsing them in. Only preliminary work here.
1764 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1765 Future work will integrate Pise and allow submission of analysis on
1766 remote servers.
1768 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1769 introduced as new objects for handling Sequence Annotation
1770 information (dblinks, references, etc) and is more robust that
1771 previous system.
1773 o Bio::Tools::FASTAParser introduced.
1775 o Scripts from the bioperl script submission project and new
1776 scripts from bioperl authors are included in "scripts" directory.
1778 o Factory objects and interfaces are being introduced and are more
1779 strictly enforced.
1781 o Bio::Root::Root introduced as the base object while
1782 Bio::Root::RootI is now simply an interface.
1784 o Bio::DB::RefSeq provides database access to copy of the NCBI
1785 RefSeq database using the EBI dbfetch script.
1787 0.9.0 Developer's release
1789 o perl version at least 5.005 is now required instead of perl 5.004
1791 o Bio::Tools::Run::RemoteBlast is available for running remote
1792 blast jobs at NCBI.
1794 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1796 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1797 Also added are related modules UTR3, UTR5, Exon, Intron,
1798 Promotor, PolyA and Transcript.
1800 o Speedup of translate method in PrimarySeq
1802 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1803 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1805 o Various fixes to Variation toolkit
1807 o Bio::DB::EMBL provides database access to EMBL sequence data.
1808 Bio::DB::Universal provides a central way to point to indexes
1809 and dbs in a single interface.
1811 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1813 o Bio::Factory::EMBOSS is still in design phase as is
1814 Bio::Factory::ApplicationFactoryI
1816 o Dia models for bioperl design are provided in the models/ directory
1818 0.7.2 Bug fix release
1820 o documentation fixes in many modules - SYNOPSIS code verified
1821 to be runnable in many (but not all modules)
1823 o corrected MANIFEST file from 0.7.1 release
1825 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1826 split locations
1828 o Bio::SeqIO::genbank
1829 * Correct parsing and writing of genbank format with protein data
1830 * moltype and molecule separation
1832 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1834 o Bio::SimpleAlign fixed to correctly handle consensus
1835 sequence calculation
1837 o Bio::Tools::HMMER supports hmmer 2.2g
1839 o Bio::Tools::BPlite to support report type specific parsing. Most
1840 major changes are not on the 0.7 branch.
1842 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1843 with File::Spec
1845 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1846 in several types of mutations:
1847 1.) AA level: deletion, complex
1848 2.) AA level: complex, inframe
1849 3.) RNA level: silent
1851 o BPbl2seq parsing of empty reports will not die, but will return
1852 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1853 $report->query() and $report->subject() methods. So an easy
1854 way to test if report was empty is to see if
1855 $report->query->seqname is undefined.
1857 0.7.1 Bug fix release
1859 o Better parsing of genbank/EMBL files especially fixing bugs
1860 related to Feature table parsing and locations on remote
1861 sequences. Additionally, species name parsing was better.
1863 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1864 which include a number of header lines.
1866 o More strict genbank and EMBL format writing (corrected number of
1867 spaces where appropriate).
1869 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1870 for related BPlite BUGS that are unresolved in this release.
1872 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1873 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1874 use expasy mirrors or EBI dbfetch cgi-script.
1876 o A moderate number of documentation improvements were made as
1877 well to provide a better code synopsis in each module.
1880 0.7 Large number of changes, including refactoring of the
1881 Object system, new parsers, new functionality and
1882 all round better system. Highlights are:
1885 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1886 Bio::Root::IO for I/O and file/handle capabilities.
1888 o Imported BPlite modules from Ian Korf for BLAST
1889 parsing. This is considered the supported BLAST parser;
1890 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1892 o Improved Sequence Feature model. Added complete location
1893 modelling (with fuzzy and compound locations). See
1894 Bio::LocationI and the modules under Bio/Location. Added
1895 support in Genbank/EMBL format parsing to completely parse
1896 feature tables for complex locations.
1898 o Moved special support for databanks etc to specialized modules under
1899 Bio/Seq/. One of these supports very large sequences through
1900 a temporary file as a backend.
1902 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1903 CDS retrieval and exon shuffling.
1905 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1907 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1908 DB/GDB (the latter has platform-specific limitations).
1910 o New analysis parser framework for HT sequence annotation (see
1911 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1913 o New Alignment IO framework
1915 o New Index modules (Swissprot)
1917 o New modules for running Blast within perl
1918 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1919 Multiple Sequence Alignment tools ClustalW and TCoffee
1920 (Bio::Tools::Run::Alignment).
1922 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1923 documentation across the package.
1925 o Much improved cross platform support. Many known incompatibilities
1926 have been fixed; however, NT and Mac do not work across the entire
1927 setup (see PLATFORMS).
1929 o Many bug fixes, code restructuring, etc. Overall stability and
1930 maintainability benefit a lot.
1932 o A total of 957 automatic tests
1935 0.6.2
1937 There are very few functionality changes but a large
1938 number of software improvements/bug fixes across the package.
1940 o The EMBL/GenBank parsing are improved.
1942 o The Swissprot reading is improved. Swissprot writing
1943 is disabled as it doesn't work at all. This needs to
1944 wait for 0.7 release
1946 o BLAST reports with no hits are correctly parsed.
1948 o Several other bugs of the BLAST parser (regular expressions, ...)
1949 fixed.
1951 o Old syntax calls have been replaced with more modern syntax
1953 o Modules that did not work at all, in particular the Sim4
1954 set have been removed
1956 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1957 have improved compliance with interface specs and documentation
1959 o Mailing list documentation updated throughout the distribution
1961 o Most minor bug fixes have happened.
1963 o The scripts in /examples now work and have the modern syntax
1964 rather than the deprecated syntax
1967 0.6.1 Sun April 2 2000
1969 o Sequences can have Sequence Features attached to them
1970 - The sequence features can be read from or written to
1971 EMBL and GenBank style flat files
1973 o Objects for Annotation, including References (but not
1974 full medline abstracts), Database links and Comments are
1975 provided
1977 o A Species object to represent nodes on a taxonomy tree
1978 is provided
1980 o The ability to parse HMMER and Sim4 output has been added
1982 o The Blast parsing has been improved, with better PSI-BLAST
1983 support and better overall behaviour.
1985 o Flat file indexed databases provide both random access
1986 and sequential access to their component sequences.
1988 o A CodonTable object has been written with all known
1989 CodonTables accessible.
1991 o A number of new lightweight analysis tools have been
1992 added, such as molecular weight determination.
1994 The 0.6 release also has improved software engineering
1996 o The sequence objects have been rewritten, providing more
1997 maintainable and easier to implement objects. These
1998 objects are backwardly compatible with the 0.05.1 objects
2000 o Many objects are defined in terms of interfaces and then
2001 a Perl implementation has been provided. The interfaces
2002 are found in the 'I' files (module names ending in 'I').
2004 This means that it is possible to wrap C/CORBA/SQL access
2005 as true "bioperl" objects, compatible with the rest of
2006 bioperl.
2008 o The SeqIO system has been overhauled to provide better
2009 processing and perl-like automatic interpretation of <>
2010 over arguments.
2012 o Many more tests have been added (a total of 172 automatic
2013 tests are now run before release).
2017 0.05.1 Tue Jun 29 05:30:44 1999
2018 - Central distribution now requires Perl 5.004. This was
2019 done to get around 5.003-based problems in Bio/Index/*
2020 and SimpleAlign.
2021 - Various bug fixes in the Bio::Tools::Blast modules
2022 including better exception handling and PSI-Blast
2023 support. See Bio/Tools/Blast/CHANGES for more.
2024 - Fixed the Parse mechanism in Seq.pm to use readseq.
2025 Follow the instructions in README for how to install
2026 it (basically, you have to edit Parse.pm).
2027 - Improved documentation of Seq.pm, indicating where
2028 objects are returned and where strings are returned.
2029 - Fixed uninitialized warnings in Bio::Root::Object.pm
2030 and Bio::Tools::SeqPattern.pm.
2031 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
2033 0.05 Sun Apr 25 01:14:11 1999
2034 - Bio::Tools::Blast modules have less memory problems
2035 and faster parsing. Webblast uses LWP and supports
2036 more functionality. See Bio/Tools/Blast/CHANGES for more.
2037 - The Bio::SeqIO system has been started, moving the
2038 sequence reformatting code out of the sequence object
2039 - The Bio::Index:: system has been started, providing
2040 generic index capabilities and specifically works for
2041 Fasta formatted databases and EMBL .dat formatted
2042 databases
2043 - The Bio::DB:: system started, providing access to
2044 databases, both via flat file + index (see above) and
2045 via http to NCBI
2046 - The scripts/ directory, where industrial strength scripts
2047 are put has been started.
2048 - Many changes - a better distribution all round.
2050 0.04.4 Wed Feb 17 02:20:13 1999
2051 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
2052 (see Bio::Tools::Blast::CHANGES).
2053 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
2054 - Beefed up the t/Fasta.t test script.
2055 - Small fix in Bio::Seq::type() (now always returns a string).
2056 - Changed Bio::Root::Utilities::get_newline_char() to
2057 get_newline() since it could return more than one char.
2058 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
2059 - Changed default timeout to 20 seconds (was 3).
2060 - Moved lengthy modification notes to the bottom of some files.
2061 - Fixed SimpleAlign write_fasta bug.
2062 - Beefed up SimpleAlign.t test
2064 0.04.3 Thu Feb 4 07:48:53 1999
2065 - Bio::Root::Object.pm and Global.pm now detect when
2066 script is run as a CGI and suppress output that is only
2067 appropriate when running interactively.
2068 - Bio::Root::Err::_set_context() adds name of script ($0).
2069 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
2070 regarding the use of the static objects via the qw(:obj) tag.
2071 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
2072 CORE::reverse, avoiding Perl warnings.
2073 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
2074 example scripts (see Bio::Tools::Blast::CHANGES).
2075 - examples/seq/seqtools.pl no longer always warns about using
2076 -prot or -nucl command-line arguments; only when using the
2077 -debug argument.
2078 - Methods added to Bio::Root::Utilities: create_filehandle(),
2079 get_newline_char(), and taste_file() to generalize filehandle
2080 creation and autodetect newline characters in files/streams
2081 (see bug report #19).
2082 - Bio::Root::IOManager::read() now handles timeouts and uses
2083 Utilities::create_filehandle().
2084 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
2085 of hardwiring in "\n".
2086 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
2088 0.04.2 Wed Dec 30 02:27:36 1998
2089 - Bug fixes in Bio::Tools::Blast modules, version 0.073
2090 (see Bio::Tools::Blast::CHANGES).
2091 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
2092 to CORE::reverse (prevents ambiguous warnings with 5.005).
2093 - Appending '.tmp.bioperl' to temporary files created by
2094 Bio::Root::Utilities::compress() or uncompress() to
2095 make it easy to identify & cleanup these files as needed.
2096 - Developers: Created CVS branch release-0-04-bug from
2097 release-0-04-1. Before making bug fixes to the 0.04.1 release,
2098 be sure to cvs checkout this branch into a clean area.
2100 0.04.1 Wed Dec 16 05:39:15 1998
2101 - Bug fixes in Bio::Tools::Blast modules, version 0.072
2102 (see Bio::Tools::Blast::CHANGES).
2103 - Compile/SW/Makefile.PL now removes *.o and *.a files
2104 with make clean.
2106 0.04 Tue Dec 8 07:49:19 1998
2107 - Lots of new modules added including:
2108 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
2109 and Bio/Compile directory containing XS-linked C code for
2110 creating Smith-Waterman sequence alignments from within Perl.
2111 * Steve Chervitz's Blast distribution has been incorporated.
2112 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
2113 - Bio/examples directory for demo scripts for all included modules.
2114 - Bio/t directory containing test suit for all included modules.
2115 - For changes specific to the Blast-related modules prior to
2116 incorporation in this central distribution, see the CHANGES
2117 file in the Bio/Tools/Blast directory.
2119 0.01 Tue Sep 8 14:23:22 1998
2120 - original version from central CVS tree; created by h2xs 1.18