| blob | d853441e9599511fbc414385c251c2e299335438 |
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::Phylo::Gumby
93 Bio::Tools::dpAlign
94 Bio::Tools::pSW
95 Bio::Variation::*
97 * The following programs have been removed:
99 bp_bulk_load_gff
100 bp_das_server
101 bp_download_query_genbank
102 bp_fast_load_gff
103 bp_flanks
104 bp_genbank2gff
105 bp_generate_histogram
106 bp_load_gff
107 bp_meta_gff
108 bp_netinstall
109 bp_process_wormbase
110 bp_query_entrez_taxa
111 bp_seqfeature_delete
112 bp_seqfeature_gff3
113 bp_seqfeature_load
115 * The following modules are no longer dependencies:
117 Bio::SeqIO::staden::read
118 DBD::Pg
119 DBD::SQLite
120 MIME::Base64
121 Memoize
122 Text::ParseWords
123 URI::Escape
125 [Code changes]
127 * The deobfuscator has been removed.
129 * The script `bp_blast2tree` has been moved to the BioPerl-Run
130 distribution since it's mainly a wrapper to modules in there.
132 * The entire Bio::PopGen namespace, Bio::Tree::AlleleNode
133 module, and scripts bp_composite_LD and bp_heterogeneity_test
134 have been moved into a separate distribution named Bio-PopGen.
136 * All modules related to the NeXML format have been moved into a
137 separate distribution named Bio-NeXMLIO. These are:
139 * Bio::AlignIO::nexml
140 * Bio::Nexml::Factory
141 * Bio::NexmlIO
142 * Bio::SeqIO::nexml
143 * Bio::TreeIO::nexml
145 This also means BioPerl is no longer dependent on Bio-Phylo.
147 * All modules interfacing to ACeDB servers have been moved into a
148 separate distribution named Bio-DB-Ace. These are:
150 * Bio::DB::Ace
151 * Bio::DB::GFF::Adaptor::ace
152 * Bio::DB::GFF::Adaptor::dbi::mysqlace
153 * Bio::DB::GFF::Adaptor::dbi::oracleace
155 This also means BioPerl is no longer dependent on AcePerl.
157 * The module Bio::Draw::Pictogram has been moved to a separate
158 distribution named Bio-Draw-Pictogram. This also means BioPerl
159 is no longer dependent on SVG.
161 * The module Bio::Tree::Draw::Cladogram has been moved to a
162 separate distribution named Bio-Tree-Draw-Cladogram. This also
163 means BioPerl is no longer dependent on PostScript.
165 * The module Bio::TreeIO::svggraph has been moved to a separate
166 distribution named Bio-TreeIO-svggraph. This also means that
167 BioPerl is no longer dependent on SVG-Graph and Tree-DAG_Node.
169 * The module Bio::SeqIO::excel has been moved to a separate
170 distribution named Bio-SeqIO-excel. This also means that
171 BioPerl is no longer dependent on Spreadsheet-ParseExcel.
173 * The entire Bio::PhyloNetwork namespace has been moved to a
174 separate distribution named Bio-PhyloNetwork. This also means
175 that BioPerl is no longer dependent on Algorithm::Munkres,
176 GraphViz, and Array::Compare.
178 * The entire Bio::Asembly namespace has been moved to a separate
179 distribution named Bio-Assembly. This also means that BioPerl
180 is no longer dependent on Bio-SamTools and Sort-Naturally.
182 * The entire Bio::Structure namespace has been moved to a
183 separate distribution named Bio-Structure.
185 * The entire Bio::SeqEvolution namespace has been moved to a
186 separate distribution named Bio-SeqEvolution.
188 * The Bio::Tools::Gel module has been moved into its own
189 distribution named Bio-Tools-Gel.
191 * The entire Bio::Restriction namespace has been moved to a
192 separate distribution named Bio-Restriction.
194 * The module Bio::SeqIO::entrezgene has been moved to the
195 Bio-ASN1-EntrezGene distribution.
197 * The module Bio::MolEvol::CodonModel has moved to a distribution
198 of its own, named after itself.
200 * The module Bio::Perl has moved to a new distribution named
201 Bio-Procedural.
203 * The module Bio::Tools::Run::RemoteBlast has moved to a new
204 distribution named after itself.
206 * The module Bio::Align::Graphics has been moved to a new distribution
207 named after itself. This also means that BioPerl is no longer
208 dependent on GD.
210 * The entire Bio::DB::HIV namespace, the Bio::DB::Query::HIVQuery
211 module, and the the bp_hivq program have been moved to their
212 own distribution named Bio-DB-HIV. This also drops the bioperl
213 dependency on XML-Simple and Term-ReadLine.
215 * The entire Bio::DB::TFBS namespace has been moved to its own
216 distribution named after itself.
218 * All modules to handle HMMER programs output have been moved to their
219 own distribution named Bio-SearchIO-hmmer. This also includes the
220 programs bp_hmmer_to_table and bp_parse_hmmsearch.
222 * Bio::DB::MeSH and related Bio::Phenotype::MeSH modules have moved
223 to their own distribution Bio-DB-MeSH.
225 * The Bio::DB::Universal module has been moved to its own distribution.
227 * The emacs bioperl minor mode is no longer distributed as part of the
228 perl module distributions. See
229 https://github.com/bioperl/emacs-bioperl-mode
231 1.7.2 - "Entebbe"
233 [Bugs]
235 * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
236 * #245 - Code coverage fixes [zmughal,cjfields]
237 * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
238 * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
239 * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
240 * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
241 * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
242 * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
243 * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
244 * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
245 * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
246 * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
248 [Code changes]
250 * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
252 1.7.1 - "Election"
254 [Bugs]
256 * Minor release to incorporate fix for CPAN indexing, which
257 prevented proper updates [cjfields]
258 * Fix problem in managing Target attribute for gff3 [Jukes34]
259 * Minor bug fixes related to NCBI HTTPS support [cjfields]
261 1.7.0 - "Disney"
263 [New site]
265 * We have migrated to Github Pages. This was actually planned, but the
266 recent OBF server compromise forced our hand.
268 Brian Osborne [bosborne] took this under his wing to move docs and has
269 done a tremendous amount of work formatting the site and working out some
270 of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
271 Cantalupo and Franscison Ossandon also helped. Kudos!!
273 * Similarly, the official issue tracker is now Github Issues. This has
274 been updated in the relevant documentation bits (we hope!)
276 [Code changes]
278 * Previously deprecated modules removed
279 * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
280 * Bio::DB::SeqHound has been removed due to the service no longer being
281 available
282 * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
283 reasons due to the server no longer having a valid cert
284 * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
285 * Bio::Coordinate, Bio::SearchIO::blastxml,
286 Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
287 added on CPAN
289 [New features]
291 * Docker instances of tagged releases are available! [hlapp]
292 * NCBI HTTPS support [mjohnson and others]
293 * Bio::SearchIO::infernal
294 - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
295 * Bio::Search::HSP::ModelHSP
296 - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
297 reports [pcantalupo]
298 * Bio::Search::Result::INFERNALResult
299 - Added new module to represent features of Infernal reports [pcantalupo]
300 * Bio::DB::Taxonomy SQLite option [cjfields]
301 * WrapperBase quoted option values [majensen]
302 * Various documentation fixes and updates [bosborne]
304 [Bug Fixes]
306 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
307 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
308 * NeXML parser fixes [fjossandon]
309 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
310 * RT 103272 : SeqFeature database deletion skipped features with a decimal -
311 Joshua Fortriede (Xenbase)
312 * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
313 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
314 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
315 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
316 * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
317 * Issue #84: EMBL format wrapping problem [nyamned]
318 * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
319 * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
320 or compiled C code (when Inline::C is installed) [rocky]
321 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
322 * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
323 * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
324 * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
325 to be consistent with "$hit->bits" behaviour [fjossandon]
326 * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
327 aminoacids made "next_seq" confused and broke the parser [fjossandon]
328 * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
329 Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
330 to "complement(join(A..B,C..D))" [fjossandon]
331 * For the many many many fixes that weren't mentioned - blame the release guy!
333 1.6.924
335 [Significant changes]
337 * Bug/feature issue tracking has moved to GitHub Issues:
338 https://github.com/bioperl/bioperl-live/issues
339 * DB_File has been demoted from "required" to "recommended",
340 which should make easier for Windows users to install BioPerl
341 if they don't need that module.
343 [New features]
345 * Bio::Search::HSP::GenericHSP
346 - Bug #3370, added a "posterior_string" method to retrieve the
347 posterior probability lines (PP) from HMMER3 reports [fjossandon]
348 - Added a "consensus_string" method to retrieve the consensus
349 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
350 * Bio::SearchIO::hmmer2
351 - The number of identical and conserved residues are now calculated
352 directly from the homology line [fjossandon]
353 - Now the Query Length and Hit Length are reported when the alignment
354 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
355 - Implemented the capture of the consensus structure lines [fjossandon]
356 * Bio::SearchIO::hmmer3
357 - The number of identical and conserved residues are now calculated
358 directly from the homology line [fjossandon]
359 - Now the Hit Length is reported when the alignment runs until the end
360 of the sequence/model ('.]' or '[]') [fjossandon]
361 - Implemented the capture of the consensus structure lines [fjossandon]
362 - Implemented the capture of the posterior probability lines [fjossandon]
363 - Completed the development of NHMMER parsing, including alignments [fjossandon]
364 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
365 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
366 "min_score", "min_bits, and "hit_filter" methods from
367 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
368 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
369 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
370 besides Blast, instead of being ignored. Added tests for all moved methods
371 using HMMER outputs and run the full test suite and everything pass [fjossandon]
372 * Bio::SeqIO::MultiFile
373 - Autodetection of file format [fangly]
374 * Bio::Tools::GuessSeqFormat:
375 - Format detection from non-seekable filehandles such as STDIN [fangly]
377 [Bug fixes]
379 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
380 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
381 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
382 * Abstract: Fixed ActivePerl incapability of removing temporary files
383 because of problems closing tied filehandles [fjossandon]
384 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
385 because ActivePerl were producing a ".index.pag" and ".index.dir"
386 files instead of a single ".index" file (like Strawberry Perl).
387 Now those temporary files are correctly considered and deleted. [fjossandon]
388 * Test files: Added missing module requirements (DB_File and Data::Stag)
389 to several tests files that were failing because those modules were
390 not present. Now those test files are correctly skipped instead. [fjossandon]
391 * Blast: Added support to changes in bl2seq from BLAST+ output, which
392 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
393 * Phylip: Return undef in "next_aln" at file end to avoid
394 an infinite loop [yschensandiego]
395 * HMMER3: When a hit description is too long, it is truncated in
396 the Scores table. In those cases, the more complete description from
397 the Annotation line (>>) will be used [fjossandon]
398 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
399 since it is now used by HMMER3 format in alignments [fjossandon]
400 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
401 to return undef if the query/hit length is unknown (like in some
402 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
403 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
404 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
405 added support to multi-query reports, reduced code redundancy,
406 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
407 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
408 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
409 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
410 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
411 * Double-quotes on paths are needed in some places [fjossandon]
412 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
413 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
414 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
415 with the latest changes made in their own repositories [fjossandon]
416 * General synching of files with the master branch [fjossandon]
417 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
418 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
419 * Fixed broken MeSH parser [fjossandon]
420 * Fixed missing detection of format in SeqIO when given a -string [fangly]
422 1.6.923
424 * Major Windows support updates! [fjossandon]
425 * MAKER update to allow for stricter standard codon table [cjfields]
426 * Better support for circular sequences [fjossandon]
427 * Fixes for some complex location types [fjossandon]
428 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
429 * Fix bug #2978 related to BLAST report type [fjossandon]
430 * Deobfuscator fixes [DaveMessina]
432 1.6.922
434 * Address CPAN test failures [cjfields]
435 * Add BIOPROJECT support for Genbank files [hyphaltip]
436 * Better regex support for HMMER3 output [bosborne]
438 1.6.921
440 * Minor update to address CPAN test failures
442 1.6.920
444 * Remove Bio::Biblio and related files [carandraug]
445 - this cause version clashes with an independently-released
446 version of Bio::Biblio
448 1.6.910
450 [New features]
452 * Hash randomization fixes for perl 5.18.x
453 - Note: at least one module (Bio::Map::Physical) still has a failing test;
454 this is documented in bug #3446 and has been TODO'd; we will be pulling
455 Bio::Map and similar modules out of core into separate distributions in the
456 1.7.x release series [cjfields]
458 [New features]
460 * Bio::Seq::SimulatedRead
461 - New module to represent reads taken from other sequences [fangly]
462 * Bio::Root::Root
463 - Support of Clone::Fast as a faster cloning alternative [fangly]
464 * Bio::Root::IO
465 - Moved the format() and variant() methods from Bio::*IO modules to
466 Bio::Root::IO [fangly]
467 - Can now use format() to get the type of IO format in use [fangly]
468 * Bio::Tools::IUPAC
469 - New regexp() method to create regular expressions from IUPAC sequences
470 [fangly]
471 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
472 - Code refresh [fangly]
473 * Bio::DB::Taxonomy
474 - Added support for the Greengenes and Silva taxonomies [fangly]
475 * Bio::Tree::TreeFunctionsI
476 - get_lineage_string() represents a lineage as a string [fangly]
477 - add_trait() returns instead of reporting an error when the column
478 number is exceeded in add_trait() [fangly]
479 - Option to support tree leaves without trait [fangly]
480 - Allow ID of 0 in trait files [fangly]
481 * Bio::DB::Taxonomy::list
482 - Misc optimizations [fangly]
483 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
484 * Bio::DB::Taxonomy::*
485 - get_num_taxa() returns the number of taxa in the database [fangly]
486 * Bio::DB::Fasta and Bio::DB::Qual
487 - support indexing an arbitrary list of files [fangly]
488 - user can supply an arbitrary index file name [fangly]
489 - new option to remove index file at the end [fangly]
490 * Bio::DB::Fasta
491 - now handles IUPAC degenerate residues [fangly]
492 * Bio::PrimarySeq and Bio::PrimarySeqI
493 - speed improvements for large sequences [Ben Woodcroft, fangly]
494 * Bio::PrimaryQual
495 - tightened and optimized quality string validation [fangly]
496 * Bio::SeqIO::fasta
497 - new method and option 'block', to create FASTA output with space
498 intervaled blocks (similar to genbank or EMBL) has been implemented.
499 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
500 in favour of the methods 'width' and 'preferred_id_type` respectively.
501 * Bio::FeatureIO::*
502 - moved from bioperl-live into the separate distribution Bio-FeatureIO
503 * Bio::SeqFeature::Annotated
504 - moved from bioperl-live into the separate distribution Bio-FeatureIO
505 * Bio::Cluster::SequenceFamily
506 - improved performance when using get_members with overlapping multiple
507 criteria
508 * Bio::SearchIO::hmmer3
509 - now supports nhmmer [bosborne]
511 [Bug fixes]
513 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
514 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
515 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
516 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
517 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
518 information was lost in a multi-result blast file [Paul Cantalupo]
519 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
520 total gaps [Paul Cantalupo]
521 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
522 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
523 when end of domain indicator is split across lines [Paul Cantalupo]
524 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
525 cjfields]
526 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
527 instances where blank lines are within sequences [cjfields]
528 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
529 types [fangly]
530 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
531 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
532 cjfields]
533 * Various fixes for Stockholm file indexing and processing [bosborne]
534 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
535 breaks parsing [cjfields]
536 * Fix case where Bio::Seq::Meta* objects with no meta information could not
537 be reverse-complemented [fangly]
538 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
539 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
540 when unsure that values will be numerical [fangly]
541 * Fix undef warnings in Bio::SeqIO::embl [fangly]
542 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
543 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
544 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
545 Sallou]
546 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
547 source_tag and display_name must return a string, not undef [fangly]
548 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
549 add_SeqFeature takes a single argument [fangly]
550 * Use cross-platform filenames and temporary directory in
551 Bio::DB::Taxonomy::flatfile [fangly]
552 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
553 properly identified as existing taxa in the database [fangly]
554 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
555 without also passing a lineage to store [fangly]
556 * Prevent passing a directory to the gi2taxid option (-g) of
557 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
558 [fangly]
559 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
560 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
561 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
562 object before trying to access, and no longer returns repeated sequences.
565 1.6.901 May 18, 2011
567 [Notes]
569 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
570 modules using Ace will also be deprecated [lds, cjfields]
571 * Minor bug fix release
572 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
573 * Address Build.PL issues when DBI is not present [hartzell]
574 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
575 * Remove deprecated code for perl 5.14.0 compat [cjfields]
576 * Due to schema changes and lack of support for older versions, support
577 for NeXML 0.9 is only (very) partially implemented.
578 See: https://redmine.open-bio.org/issues/3207
580 [Bug fixes]
582 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
583 docs [genehack, cjfields]
584 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
585 module version from dist_version (probably not the best way to do this,
586 but it seems to work) [rbuels, cjfields]
589 1.6.900 April 14, 201
591 [Notes]
593 * This will probably be the last release to add significant features to
594 core modules; subsequent releases will be for bug fixes alone.
595 We are planning on a restructuring of core for summer 2011, potentially
596 as part of the Google Summer of Code. This may become BioPerl 2.0.
597 * Version bump represents 'just prior to v 1.7'. We may have point
598 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
599 This code essentially is what is on the github master branch.
601 [New features]
603 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
604 * Bio::Tree refactor
605 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
606 - removal of Scalar::Util::weaken code, which was causing odd headaches
607 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
608 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
609 many others]
610 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
611 [Warren Kretzschmar]
612 * Bio::SeqIO::gbxml
613 - bug 2515 - new contribution [Ryan Golhar, jhannah]
614 * Bio::Assembly::IO
615 - support for reading Maq, Sam and Bowtie files [maj]
616 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
617 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
618 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
619 - bug 2726: reading/writing granularity: whole scaffold or one contig
620 at a time [Joshua Udall, fangly]
621 * Bio::OntologyIO
622 - Added parsing of xrefs to OBO files, which are stored as secondary
623 dbxrefs of the cvterm [Naama Menda]
624 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
625 * PAML code updated to work with PAML 4.4d [DaveMessina]
627 [Bug fixes]
629 * [3198] - sort tabular BLAST hits by score [DaveMessina]
630 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
631 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
632 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
633 [cjfields]
634 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
635 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
636 * [3164] - TreeFunctionsI syntax bug [gjuggler]
637 * [3163] - AssemblyIO speedup [fangly]
638 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
639 hyphaltip]
640 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
641 * [3158] - fix EMBL file mis-parsing [cjfields]
642 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
643 cjfields]
644 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
645 * [3148] - URL change for UniProt [cjfields]
646 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
647 * [3136] - HMMer3 parser fixes [kblin]
648 * [3126] - catch description [Toshihiko Akiba]
649 * [3122] - Catch instances where non-seekable filehandles were being
650 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
651 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
652 [dukeleto, rbuels, cjfields]
653 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
654 jhannah]
655 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
656 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
657 cjfields]
658 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
659 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
660 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
661 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
662 * [3086] - EMBL misparsing long tags [kblin, cjfields]
663 * [3085] - CommandExts and array of files [maj, hyphaltip]
664 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
665 for alignment slices [Ha X. Dang, cjfields]
666 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
667 * [3073] - fix parsing of GenBank files from RDP [cjfields]
668 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
669 * [3064] - All-gap midline BLAST report issues [cjfields]
670 * [3063] - BLASt report RID [Razi Khaja, cjfields]
671 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
672 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
673 * [3039] - correct Newick output root node branch length [gjuggler,
674 DaveMessina]
675 * [3038] - SELEX alignment error [Bernd, cjfields]
676 * [3033] - PrimarySeq ID setting [Bernd, maj]
677 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
678 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
679 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
680 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
681 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
682 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
683 PAML 4.4d [DaveMessina]
684 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
685 DaveMessina]
686 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
687 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
688 * [3017] - using threads with Bio::DB::GenBank [cjfields]
689 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
690 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
691 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
692 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
693 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
694 cjfields]
695 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
696 * [2977] - TreeIO issues [DaveMessina]
697 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
698 * [2944] - Bio::Tools::GFF score [cjfields]
699 * [2942] - correct MapTiling output [maj]
700 * [2939] - PDB residue insertion codes [John May, maj]
701 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
702 * [2928] - GuessSeqFormat raw [maj]
703 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
704 * [2922] - open() directive issue [cjfields]
705 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
706 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
707 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
708 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
709 cjfields]
710 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
711 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
712 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
713 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
714 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
715 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
716 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
717 * [2758] - Bio::AssemblyIO ace problems [fangly]
718 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
719 * [2726] - ace file IO [Josh, fangly]
720 * [2700] - Refactor Build.PL [cjfields]
721 * [2673] - addition of simple Root-based clone() method [cjfields]
722 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
723 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
724 * [2594] - Bio::Species memory leak [cjfields]
725 * [2515] - GenBank XML parser [jhannah]
726 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
727 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
728 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
729 cjfields]
730 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
732 [Deprecated]
734 * Bio::Expression modules - these were originally designed to go with the
735 bioperl-microarray suite of tools, however they have never been completed
736 and so have been removed from the distribution. The original code has
737 been moved into the inactive bioperl-microarray suite. [cjfields]
739 [Other]
741 * Repository moved from Subversion (SVN) to
742 http://github.com/bioperl/bioperl-live [cjfields]
743 * Bug database has moved to Redmine (https://redmine.open-bio.org)
744 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
745 Thieme have been moved to their own distribution (Bio-Microarray).
746 [cjfields]
748 1.6.1 Sept. 29, 2009 (point release)
749 * No change from last alpha except VERSION and doc updates [cjfields]
751 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
752 * Fix for silent OBDA bug related to FASTA validation [cjfields]
754 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
755 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
756 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
757 [cjfields]
758 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
760 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
761 * WinXP test fixes [cjfields, maj]
762 * BioPerl.pod added for descriptive information, fixes CPAN indexing
763 [cjfields]
764 * Minor doc fixes [cjfields]
766 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
767 * Fix tests failing due to merging issues [cjfields]
768 * More documentation updates for POD parsing [cjfields]
770 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
771 * Bio::Root::Build
772 - fix YAML meta data generation [cjfields]
774 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
775 * Bio::Align::DNAStatistics
776 - fix divide by zero problem [jason]
777 * Bio::AlignIO::*
778 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
779 * Bio::AlignIO::stockholm
780 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
781 * Bio::Assembly::Tools::ContigSpectrum
782 - function to score contig spectrum [fangly]
783 * Bio::DB::EUtilities
784 - small updates [cjfields]
785 * Bio::DB::Fasta
786 - berkeleydb database now autoindexes wig files and locks correctly
787 [lstein]
788 * Bio::DB::HIV
789 - various small updates for stability; tracking changes to LANL
790 database interface [maj]
791 * Bio::DB::SeqFeature (lots of updates and changes)
792 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
793 - bug 2835 - patch [Dan Bolser]
794 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
795 * Bio::DB::SwissProt
796 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
797 * Bio::Factory::FTLocationFactory
798 - mailing list bug fix [cjfields]
799 * Bio::LocatableSeq
800 - performance work on column_from_residue_number [hartzell]
801 * Bio::Matrix::IO::phylip
802 - bug 2800 - patch to fix phylip parsing [Wei Zou]
803 * Bio::Nexml
804 - Google Summer of Code project from Chase Miller - parsers for Nexml
805 file format [maj, chmille4]
806 * Bio::PopGen
807 - Make Individual, Population, Marker objects AnnotatableI [maj]
808 - simplify LD code [jason]
809 * Bio::RangeI
810 - deal with empty intersection [jason]
811 * Bio::Restriction
812 - significant overhaul of Bio::Restriction system: complete support for
813 external and non-palindromic cutters. [maj]
814 * Bio::Root::Build
815 - CPANPLUS support, no automatic installation [sendu]
816 * Bio::Root::IO
817 - allow IO::String (regression fix) [cjfields]
818 - catch unintentional undef values [cjfields]
819 - throw if non-fh is passed to -fh [maj]
820 * Bio::Root::Root/RootI
821 - small debugging and core fixes [cjfields]
822 * Bio::Root::Test
823 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
824 * Bio::Root::Utilities
825 - bug 2737 - better warnings [cjfields]
826 * Bio::Search
827 - tiling completely refactored, HOWTO added [maj]
828 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
829 will deprecate usage of the older tiling code in the next BioPerl
830 release
831 - small fixes [cjfields]
832 * Bio::SearchIO
833 - Infernal 1.0 output now parsed [cjfields]
834 - new parser for gmap -f9 output [hartzell]
835 - bug 2852 - fix infinite loop in some output [cjfields]
836 - blastxml output now passes all TODO tests [cjfields]
837 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
838 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
839 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
840 * Bio::Seq::LargePrimarySeq
841 - delete tempdirs [cjfields]
842 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
843 * Bio::Seq::Quality
844 - extract regions based on quality threshold value [Dan Bolser, heikki]
845 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
846 * Bio::SeqFeature::Lite
847 - various Bio::DB::SeqFeature-related fixes [lstein]
848 * Bio::SeqFeature::Tools::TypeMapper
849 - additional terms for GenBank to SO map [scain]
850 * Bio::SeqIO::chadoxml
851 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
852 * Bio::SeqIO::embl
853 - support for CDS records [dave_messina, Sylvia]
854 * Bio::SeqIO::fastq
855 - complete refactoring to handle all FASTQ variants, perform validation,
856 write output. API now conforms with other Bio* parsers and the rest of
857 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
858 [cjfields]
859 * Bio::SeqIO::genbank
860 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
861 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
862 * Bio::SeqIO::largefasta
863 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
864 * Bio::SeqIO::raw
865 - add option for 'single' and 'multiple'
866 * Bio::SeqIO::scf
867 - bug 2881 - fix scf round-tripping [Adam Søgren]
868 * Bio::SeqUtils
869 - bug 2766, 2810 - copy over tags from features, doc fixes [David
870 Jackson]
871 * Bio::SimpleAlign
872 - bug 2793 - patch for add_seq index issue [jhannah, maj]
873 - bug 2801 - throw if args are required [cjfields]
874 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
875 [Tristan Lefebure, maj]
876 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
877 - fix POD and add get_SeqFeatures filter [maj]
878 * Bio::Tools::dpAlign
879 - add support for LocatableSeq [ymc]
880 - to be moved to a separate distribution [cjfields, rbuels]
881 * Bio::Tools::EUtilities
882 - fix for two bugs from mail list [Adam Whitney, cjfields]
883 - add generic ItemContainerI interface for containing same methods
884 [cjfields]
885 * Bio::Tools::HMM
886 - fix up code, add more warnings [cjfields]
887 - to be moved to a separate distribution [cjfields, rbuels]
888 * Bio::Tools::Primer3
889 - bug 2862 - fenceposting issue fixed [maj]
890 * Bio::Tools::Run::RemoteBlast
891 - tests for remote RPS-BLAST [mcook]
892 * Bio::Tools::SeqPattern
893 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
894 * Bio::Tools::tRNAscanSE
895 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
896 * Bio::Tree::*
897 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
898 * Bio::Tree::Statistics
899 - several methods for calculating Fitch-based score, internal trait
900 values, statratio(), sum of leaf distances [heikki]
901 * Bio::Tree::Tree
902 - bug 2869 - add docs indicating edge case where nodes can be
903 prematurely garbage-collected [cjfields]
904 - add as_text() function to create Tree as a string in specified format
905 [maj]
906 * Bio::Tree::TreeFunctionsI
907 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
908 Lefebure, maj]
909 * Bio::TreeIO::newick
910 - fix small semicolon issue [cjfields]
911 * scripts
912 - update to bp_seqfeature_load for SQLite [lstein]
913 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
914 - fastam9_to_table - fix for MPI output [jason]
915 - gccalc - total stats [jason]
916 * General Stuff
917 - POD cleanup re: FEEDBACK section [maj, cjfields]
918 - cleanup or fix dead links [cjfields]
919 - Use of no_* methods (indicating 'number of something') is deprecated
920 in favor of num_* [cjfields]
921 - lots of new tests for the above bugs and refactors [everyone!]
922 - new template for Komodo text editor [cjfields]
924 1.6.0 Winter 2009
925 * Feature/Annotation rollback
926 - Problematic changes introduced prior to the 1.5 release have been
927 rolled back. These changes led to subtle bugs involving operator
928 overloading and interface methods.
929 - Behavior is very similar to that for BioPerl 1.4, with tag values
930 being stored generically as simple scalars. Results in a modest
931 speedup.
932 * Bio::Graphics
933 - Split into a separate distribution on CPAN, primarily so development
934 isn't reliant on a complete BioPerl release.
935 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
936 is only available via Subversion (via bioperl-live main trunk)
937 * Bio::Root::Test
938 - Common test bed for all BioPerl modules
939 * Bio::Root::Build
940 - Common Module::Build-based subclass for all BioPerl modules
941 * Bio::DB::EUtilities
942 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
943 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
944 and user agent request posting and retrieval
945 * Test implementation and reorganization
946 - Tests have been reorganized into groups based on classes or use
947 cases.
948 - Automated test coverage is now online:
949 http://www.bioperl.org/wiki/Test_Coverage
950 - After this release, untested modules will be moved into a
951 separate developer distribution until tests can be derived.
952 Also, new modules to be added are expected to have a test suite
953 and adequate test coverage.
955 1.5.2 Developer release
957 Full details of changes since 1.5.1 are available online at:
958 http://www.bioperl.org/wiki/Change_log
959 The following represents a brief overview of the most important changes.
961 o Bio::Map
962 - Overhaul. Brand new system fully allows markers to have multiple
963 positions on multiple maps, and to have relative positions. Should be
964 backward compatible.
966 o Bio::Taxonomy
967 - This module and all the modules in the Taxonomy directory now
968 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
970 o Bio::DB::Taxonomy
972 - Taxonomy.pm
973 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
975 * New methods ancestor(), each_Descendent() and _handle_internal_id().
977 * Allows for different database modules to create Bio::Taxon objects
978 with the same internal id when the same taxon is requested from each.
980 - flatfile.pm
981 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
983 * No longer includes the fake root node 'root'; there are multiple roots
984 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
986 - entrez.pm
987 * get_node() has new option -full
989 * Caches data retrieved from website
991 o Bio::Species
992 - Now a Bio::Taxon. Carries out the species name -> specific name munging
993 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
994 backward compatability in species() method.
996 o Bio::Search and Bio::SearchIO
997 - Overhaul. The existing system has been sped up via some minor changes
998 (mostly gain-of-function to the API). Bio::PullParserI is introduced
999 as a potential eventual replacment for the existing system, though as
1000 yet only a Hmmpfam parser exists written using it.
1003 1.5.1 Developer release
1005 o Major problem with how Annotations were written out with
1006 Bio::Seq is fixed by reverting to old behavior for
1007 Bio::Annotation objects.
1009 o Bio::SeqIO
1011 - genbank.pm
1012 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
1013 expect at l east 9 spaces at the beginning of a line to
1014 indicate line wrapping.
1016 * Treat multi-line SOURCE sections correctly, this defect broke
1017 both common_name() and classification()
1019 * parse swissprot fields in genpept file
1021 * parse WGS genbank records
1023 - embl.pm
1024 * Changed regexp for ID line. The capturing parentheses are
1025 the same, the difference is an optional repeated-not-semi-
1026 colon expression following the captured \S+. This means the
1027 regexp works when the division looks like /PRO;/ or when the
1028 division looks like /ANG ;/ - the latter is from EMBL
1029 repbase
1031 * fix ID line parsing: the molecule string can have spaces in
1032 it. Like: "genomic DNA"
1034 - swiss.pm: bugs #1727, #1734
1036 - entrezgene.pm
1037 * Added parser for entrezgene ASN1 (text format) files.
1038 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
1040 o Bio::AlignIO
1042 - maf.pm coordinate problem fixed
1044 o Bio::Taxonomy and Bio::DB::Taxonomy
1046 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
1047 can be done via Web without downloading all the sequence.
1049 o Bio::Tools::Run::RemoteBlast supports more options and complies
1050 to changes to the NCBI interface. It is reccomended that you
1051 retrieve the data in XML instead of plain-text BLAST report to
1052 insure proper parsing and retrieval of all information as NCBI
1053 fully expects to change things in the future.
1055 o Bio::Tree and Bio::TreeIO
1057 - Fixes so that re-rooting a tree works properly
1059 - Writing out nhx format from a newick/nexus file will properly output
1060 bootstrap information. The use must move the internal node labels over
1061 to bootstraps.
1062 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
1063 $node->bootstrap($node->id);
1064 $node->id('');
1065 }
1066 - Nexus parsing is much more flexible now, does not care about
1067 LF.
1069 - Cladogram drawing module in Bio::Tree::Draw
1071 - Node height and depth now properly calculated
1073 - fix tree pruning algorithm so that node with 1 child gets merged
1075 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
1076 bugs and improvements were added, see Gbrowse mailing list for most of
1077 these.
1079 o Bio::DB::GFF partially supports GFF3. See information about
1080 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
1082 o Better location parsing in Bio::Factory::FTLocationFactory -
1083 this is part of the engine for parsing EMBL/GenBank feature table
1084 locations. Nested join/order-by/complement are allowed now
1086 o Bio::PrimarySeqI->translate now takes named parameters
1088 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
1089 reconstruction) is now supported. Parsing different models and
1090 branch specific parametes are now supported.
1092 o Bio::Factory::FTLocationFactory - parse hierarchical locations
1093 (joins of joins)
1095 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
1096 for getter/setter functions
1098 o Bio::SearchIO
1100 - blast bug #1739; match scientific notation in score
1101 and possible e+ values
1103 - blast.pm reads more WU-BLAST parameters and parameters, match
1104 a full database pathname,
1106 - Handle NCBI WEB and newer BLAST formats specifically
1107 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
1109 - psl off-by-one error fixed
1111 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
1112 and HSPs can be constructed from them.
1114 - HSPs query/hit now have a seqdesc field filled out (this was
1115 always available via $hit->description and
1116 $result->query_description
1118 - hmmer.pm can parse -A0 hmmpfam files
1120 - Writer::GbrowseGFF more customizeable.
1122 o Bio::Tools::Hmmpfam
1123 make e-value default score displayed in gff, rather than raw score
1124 allow parse of multiple records
1127 1.5 Developer release
1129 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
1130 provide Jukes-Cantor and Kimura pairwise distance methods,
1131 respectively.
1133 o Bio::AlignIO support for "po" format of POA, and "maf";
1134 Bio::AlignIO::largemultifasta is a new alternative to
1135 Bio::AlignIO::fasta for temporary file-based manipulation of
1136 particularly large multiple sequence alignments.
1138 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
1139 be treated similarly as an assembled contig.
1141 o Bio::CodonUsage provides new rare_codon() and probable_codons()
1142 methods for identifying particular codons that encode a given
1143 amino acid.
1145 o Bio::Coordinate::Utils provides new from_align() method to build
1146 a Bio::Coordinate pair directly from a
1147 Bio::Align::AlignI-conforming object.
1149 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
1150 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
1151 web service using standard Pubmed query syntax, and retrieve
1152 results as XML.
1154 o Bio::DB::GFF has various sundry bug fixes.
1156 o Bio::FeatureIO is a new SeqIO-style subsystem for
1157 writing/reading genomic features to/from files. I/O classes
1158 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
1159 classes only read/write Bio::SeqFeature::Annotated objects.
1160 Notably, the GFF v3 class requires features to be typed into the
1161 Sequence Ontology.
1163 o Bio::Graph namespace contains new modules for manipulation and
1164 analysis of protein interaction graphs.
1166 o Bio::Graphics has many bug fixes and shiny new glyphs.
1168 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
1169 indexing for HMMER reports and FASTA qual files, respectively.
1171 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
1172 new objects that can be placed within a Bio::Map::MapI-compliant
1173 genetic/physical map; Bio::Map::Physical provides a new physical
1174 map type; Bio::MapIO::fpc provides finger-printed clone mapping
1175 import.
1177 o Bio::Matrix::PSM provide new support for postion-specific
1178 (scoring) matrices (e.g. profiles, or "possums").
1180 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
1181 be instantiated without explicitly using Bio::OntologyIO. This
1182 is possible through changes to Bio::Ontology::OntologyStore to
1183 download ontology files from the web as necessary. Locations of
1184 ontology files are hard-coded into
1185 Bio::Ontology::DocumentRegistry.
1187 o Bio::PopGen includes many new methods and data types for
1188 population genetics analyses.
1190 o New constructor to Bio::Range, unions(). Given a list of
1191 ranges, returns another list of "flattened" ranges --
1192 overlapping ranges are merged into a single range with the
1193 mininum and maximum coordinates of the entire overlapping group.
1195 o Bio::Root::IO now supports -url, in addition to -file and -fh.
1196 The new -url argument allows one to specify the network address
1197 of a file for input. -url currently only works for GET
1198 requests, and thus is read-only.
1200 o Bio::SearchIO::hmmer now returns individual Hit objects for each
1201 domain alignment (thus containing only one HSP); previously
1202 separate alignments would be merged into one hit if the domain
1203 involved in the alignments was the same, but this only worked
1204 when the repeated domain occured without interruption by any
1205 other domain, leading to a confusing mixture of Hit and HSP
1206 objects.
1208 o Bio::Search::Result::ResultI-compliant report objects now
1209 implement the "get_statistics" method to access
1210 Bio::Search::StatisticsI objects that encapsulate any
1211 statistical parameters associated with the search (e.g. Karlin's
1212 lambda for BLAST/FASTA).
1214 o Bio::Seq::LargeLocatableSeq combines the functionality already
1215 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
1217 o Bio::SeqFeature::Annotated is a replacement for
1218 Bio::SeqFeature::Generic. It breaks compliance with the
1219 Bio::SeqFeatureI interface because the author was sick of
1220 dealing with untyped annotation tags. All
1221 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
1222 compliant, and accessible through Bio::Annotation::Collection.
1224 o Bio::SeqFeature::Primer implements a Tm() method for primer
1225 melting point predictions.
1227 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
1228 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
1230 o Bio::Taxonomy::Node now implements the methods necessary for
1231 Bio::Species interoperability.
1233 o Bio::Tools::CodonTable has new reverse_translate_all() and
1234 make_iupac_string() methods.
1236 o Bio::Tools::dpAlign now provides sequence profile alignments.
1238 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
1240 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
1241 parsers.
1243 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
1244 for designing small inhibitory RNA.
1246 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
1247 methods based on a distance matrix.
1249 o Bio::Tree::Statistics provides an assess_bootstrap() method to
1250 calculate bootstrap support values on a guide tree topology,
1251 based on provided bootstrap tree topologies.
1253 o Bio::TreeIO now supports the Pagel (PAG) tree format.
1255 1.4 branch
1257 1.4.1
1259 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
1261 o Bio::Graphics will work with gd1 or gd2
1263 o Bio::SearchIO
1264 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
1265 (RF lines alone)
1266 - blast.pm Parse multi-line query fields properly
1267 - small speed improvements to blasttable.pm and others
1269 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
1270 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
1271 supporting more complex queries
1274 1.4. Stable major release
1276 Since initial 1.2.0, 3000 separate changes have been made to make this release.
1278 o installable scripts
1280 o global module version from Bio::Root:Version
1282 o Bio::Graphics
1283 - major improvements; SVG support
1285 o Bio::Popgen
1286 - population genetics
1287 - support several population genetics types of questions.
1288 - Tests for statistical neutrality of mutations
1289 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
1290 Tests of population structure (Wright's F-statistic: Fst) is in
1291 Bio::PopGen::PopStats. Calculating composite linkage
1292 disequilibrium (LD) is available in Bio::PopGen::Statistics as
1293 well.
1294 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1295 and csv (comma delimited formatted) data.
1297 - a directory for implementing population simulations has
1298 been added Bio::PopGen::Simulation and 2 simulations - a
1299 Coalescent and a simple single-locus multi-allele genetic drift
1300 simulation have been provided. This replaces the code in
1301 Bio::Tree::RandomTree which has been deprecated until proper
1302 methods for generating random phylogenetic trees are
1303 implemented.
1305 o Bio::Restriction
1306 - new restrion analysis modules
1308 o Bio::Tools::Analysis
1309 - web based DNA and Protein analysis framework and several
1310 implementations
1312 o Bio::Seq::Meta
1313 - per residue annotable sequences
1315 o Bio::Matrix
1316 - Bio::Matrix::PSM - Position Scoring Matrix
1317 - Bio::Matrix::IO has been added for generalized parsing of
1318 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1319 initial implementations for parsing BLOSUM/PAM and Phylip
1320 Distance matricies respectively. A generic matrix
1321 implementation for general use was added in
1322 Bio::Matrix::Generic.
1324 o Bio::Ontology
1325 - major changes
1327 o Bio:Tree
1329 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1330 - small inhibitory RNA
1332 o Bio::SeqFeature::Tools
1333 - seqFeature mapping tools
1334 - Bio::SeqFeature::Tools::Unflattener.pm
1335 -- deal with mapping GenBank feature collections into
1336 Chado/GFF3 processable feature sets (with SO term mappings)
1338 o Bio::Tools::dpAlign
1339 - pure perl dynamic programming sequence alignment
1340 - needs Bioperl-ext
1342 o new Bio::SearchIO formats
1343 - axt and psl: UCSC formats.
1344 - blasttable: NCBI -m 8 or -m 9 format from blastall
1346 o new Bio::SeqIO formats
1347 - chado, tab, kegg, tigr, game
1348 - important fixes for old modules
1350 o Bio::AlignIO: maf
1352 o improved Bio::Tools::Genewise
1354 o Bio::SeqIO now can recongnize sequence formats automatically from
1355 stream
1357 o new parsers in Bio::Tools:
1358 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1360 o Bio::DB::Registry bugs fixed
1361 - BerkeleyDB-indexed flat files can be used by the OBDA system
1362 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1363 used by the OBDA system
1365 o several new HOWTOs
1366 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1367 Databases
1369 o hundreds of new and improved files
1372 o
1373 o Bio::Tree::AlleleNode has been updated to be a container of
1374 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1377 1.2 Branch
1379 1.2.3 Stable release update
1380 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1381 handling.
1382 o Bug #1477 - Sel --> Sec abbreviation fixed
1383 o Fix bug #1487 where paring in-between locations when
1384 end < start caused the FTLocationFactory logic to fail.
1385 o Fix bug #1489 which was not dealing with keywords as an
1386 arrayref properly (this is fixed on the main trunk because
1387 keywords returns a string and the array is accessible via
1388 get_keywords).
1389 o Bio::Tree::Tree memory leak (bug #1480) fixed
1390 Added a new initialization option -nodelete which
1391 won't try and cleanup the containing nodes if this
1392 is true.
1393 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1394 this was only present on the branch for the 1.2.1 and 1.2.2 series
1395 - Also merged main trunk changes to the branch which make
1396 newick -> nhx round tripping more effective (storing branch length
1397 and bootstrap values in same locate for NodeNHX and Node
1398 implementations.) Fixes to TreeIO parsing for labeled internal
1399 also required small changes to TreeIO::nhx. Improved
1400 tests for this module as well.
1401 o Bio::SearchIO
1402 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1403 gapped blast properly (was losing hit significance values due to
1404 the extra unexpeted column).
1405 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1406 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1407 although doesn't try to correct it - will get the negative
1408 number for you. Added a test for this as well.
1409 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1410 has no top-level family classification scores but does have scores and
1411 alignments for individual domains.
1412 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1413 regular expression to match the line was missing the possibility of
1414 an extra space. This is rare, which is why we probably did not
1415 catch it before.
1416 - BLAST parsing picks up more of the statistics/parameter fields
1417 at the bottom of reports. Still not fully complete.
1418 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1419 were fixed to include many improvements and added flexiblity
1420 in outputting the files. Bug #1495 was also fixed in the process.
1421 o Bio::DB::GFF
1422 - Update for GFF3 compatibility.
1423 - Added scripts for importing from UCSC and GenBank.
1424 - Added a 1.2003 version number.
1425 o Bio::Graphics
1426 - Updated tutorial.
1427 - Added a 1.2003 version number.
1428 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1429 properly writing keywords out.
1430 o Bio::SeqIO::genbank
1431 - Fixed bug/enhancement #1513 where dates of
1432 the form D-MMM-YYYY were not parsed. Even though this is
1433 invalid format we can handle it - and also cleanup the date
1434 string so it is properly formatted.
1435 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1436 and written with Genbank format. Similarly bug #1515 is fixed to
1437 parse in the ORIGIN text.
1438 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1439 to specify the ID type, one of (accession accession.version
1440 display primary). See Bio::SeqIO::preferred_id_type method
1441 documentation for more information.
1442 o Unigene parsing updated to handle file format changes by NCBI
1444 1.2.2 Stable release update
1446 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1447 - auto-discover ontology name
1448 - bug in parsing relationships when certain characters are in the term
1449 - fixed hard-coded prefix for term identifiers
1450 - various smaller issues
1452 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1453 of Bio::Ontology::TermI
1455 o brought the OBDA Registry code up to latest specs
1457 o Bio::DB::GenBank
1458 - eutils URL change
1459 - accession number retrieval fixed
1461 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1463 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1464 #1459 which now properly report alignment start/end info
1465 for translated BLAST/FASTA searches.
1467 o Bio::TreeIO::newick can parse labeled internal nodes
1469 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1470 for BLASTX if if you provide -report_type => 'BLASTX' when
1471 initializing a BPbl2seq object. Bioperl 1.3 will have better
1472 support for bl2seq in the SearchIO system.
1474 o Bio::Root::IO support a -noclose boolean flag which will not
1475 close a filehandle upon object cleanup - useful when sharing
1476 a filehandle among objects. Additionally code added s.t.
1477 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1479 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1481 o Bio::SeqIO::genbank
1482 - bug #1456 fixed which generated extra sequence lines
1483 - write moltype correctly for genpept
1485 1.2.1 Stable release update
1487 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1489 o Addition from main trunk of Ontology objects, principly to allow
1490 BioSQL releases against 1.2.1
1492 o Fixes and cleanup of Bio::Coordinate modules
1494 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1495 the primary accession number
1497 o Other bug fixes, including bpindex GenBank fix
1499 o Bio::SeqIO::genbank bug #1389 fixed
1501 1.2 Stable major release
1503 o More functionality added to Bio::Perl, the newbie module
1505 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1506 Support for New Hampshire Extended (NHX) format parsing.
1508 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1509 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1510 Hmmpfam parser.
1512 o New ontology parsing Bio::Ontology
1514 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1515 multi-report (mlib) fasta reports, support for waba and exonerate.
1517 o Bio::ClusterIO for parsing Unigene clusters
1519 o Bio::Assembly added for representing phrap and ace assembly clusters.
1521 o Rudimentary support for writing Chado XML (see
1522 GMOD project: www.gmod.org for more information)
1524 o Bio::Coordinate for mapping between different coordinate systems such
1525 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1526 features into different coordinate systems.
1528 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1529 with the get_Stream_by_query method and supports the latest
1530 NCBI eutils interface.
1532 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1533 object for extracting subsets of features : currently only
1534 supports extraction by location.
1536 1.1.1 Developer release
1538 o Deprecated modules are now listed in the DEPRECATED file
1540 o New HowTo documents located in doc/howto describing
1541 a domain of Bioperl.
1543 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1544 and all old bugs are searchable through the bugzilla interface.
1546 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1547 have been addressed.
1549 o Support for Genewise parsing in Bio::Tools::Genewise
1551 o Start of Ontology framework with Bio::Ontology
1553 o Speedup to the Bio::Root::Root object method _rearrange.
1554 A global _load_module method was implemented to simplify the
1555 dynamic loading of modules ala Bio::SeqIO::genbank. This
1556 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1557 etc).
1559 o Several performance improvements to sequence parsing in Bio::SeqIO.
1560 Attempt to speedup by reducing object creation overhead.
1562 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1563 method for sequence retrieval with their E-utils CGI scripts.
1564 More work to support Entrez queries to their fullest is planned
1565 before 1.2 release.
1567 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1569 1.1 Developer release
1571 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1572 this separation removes some of the complexity in our test suite
1573 and separates the core modules in bioperl from those that need
1574 external programs to run.
1576 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1577 not run into trouble running the makefile
1579 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1580 read,create,and write locations for grouped/split locations
1581 (like mRNA features on genomic sequence).
1583 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1584 and PAML (codeml,aaml, etc) parsing.
1586 o Bio::Tree:: objects expanded to handle testing monophyly,
1587 paraphyly, least common ancestor, etc.
1589 o Bio::Coordinate for mapping locations from different coordinate spaces
1591 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1592 added for parsing hmmpfam and hmmsearch output.
1594 o Bio::SearchIO::Writer::TextResultWriter for outputting
1595 a pseudo-blast textfile format
1598 1.0.2 Bug fix release
1600 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1601 in this release will not work after December 2002 when NCBI
1602 shuts off the old Entrez cgi scripts. We have already fixed
1603 on our main development branch and the functionality will be
1604 available in the next stable bioperl release (1.2) slated for
1605 Fall 2002.
1607 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1608 testset by Robin Emig. These were fixed as was the get_aln
1609 method in Bio::Search::HSP::GenericHSP to handle the extra
1610 context sequence that is provided with a FastA alignment.
1612 o Migrating differences between Bio::Search::XX::BlastXX to
1613 Bio::Search::XX::GenericXX objects. This included mechanism
1614 to retrieve whole list of HSPs from Hits and whole list of Hits from
1615 Results in addition to the current next_XX iterator methods that
1616 are available. Added seq_inds() method to GenericHSP which identifies
1617 indexes in the query or hit sequences where conserved,identical,gaps,
1618 or mismatch residues are located (adapted from Steve Chervitz's
1619 implementation in BlastHSP).
1621 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1622 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1624 o Bio::Graphics glyph set improved and extended for GBrowse release
1626 o Bio::Tree::Tree get_nodes implementation improvement thanks
1627 to Howard Ross notice performance problem when writing out
1628 unbalanced trees.
1630 o Bio::Location::Fuzzy::new named parameter -loc_type became
1631 -location_type, Bio::Location::Simple::new named parameter
1632 -seqid becamse -seq_id.
1634 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1635 was mis-detecting that gaps should be placed at the beginning of
1636 the alignment when the best alignment starts internally in the
1637 sequence.
1639 1.0.1 Bug fix release
1641 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1643 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1644 and mixed (3.3 - 3.4) versions of FASTA.
1646 o Small API change to add methods for completeness across
1647 implementations of Bio::Search objects. These new methods
1648 in the interface are implemented by the GenericXX object as well
1649 as the BlastXX objects.
1650 * Bio::Search::Result::ResultI
1651 - hits() method returns list of all Hits (next_hit is an
1652 iterator method)
1654 * Bio::Search::Hit::HitI
1655 - hsps() method returns list of all HSPs (next_hsp is an
1656 iterator method)
1658 o The Bio::SearchIO::Writer classes have been fixed to handle results
1659 created from either psiblast (Search::BlastXX objects) or
1660 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1661 has to be done here to make it work properly and will nee major
1662 API changes.
1664 o Bugs in Bio::Tools::HMMER fixed, including
1665 * #1178 - Root::IO destructor wasn't being called
1666 * #1034 - filter_on_cutoff now behaves properly
1668 o Bio::SeqFeature::Computation initialization args fixed and
1669 tests added.
1671 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1673 o Updated FAQ with more example based answers to typical questions
1675 o Bug #1202 was fixed which would improperly join together qual values
1676 parsed by Bio::SeqIO::qual when a trailing space was not present before
1677 the newline.
1679 1.0.0 Major Stable Release
1681 This represents a major release of bioperl with significant
1682 improvements over the 0.7.x series of releases.
1684 o Bio::Tools::Blast is officially deprecated. Please see
1685 Bio::SearchIO for BLAST and FastA parsing.
1687 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1688 Bio::LocationI objects as well as start/end.
1690 o Bio::Biblio contains modules for Bibliographic data.
1691 Bio::DB::Biblio contains the query modules. Additionally one can
1692 parse medlinexml from the ebi bibliographic query service (BQS)
1693 system and Pubmed xml from NCBI. See Martin Senger's
1694 documentation in Bio::Biblio for more information.
1696 o Bio::DB::Registry is a sequence database registry part of
1697 Open Bioinformatics Database Access. See
1698 http://obda.open-bio.org for more information.
1700 o File-based and In-Memory Sequence caching is provided by
1701 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1702 local database.
1704 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1705 been added by Lincoln Stein.
1707 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1709 o A FAQ has been started and is included in the release to provide
1710 a starting point for frequent questions and issues.
1712 0.9.3 Developer's release
1714 o Event based parsing system improved (SearchIO). With parsers for
1715 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1716 Additionally a lazy parsing system for text and html blast reports was
1717 added and is called psiblast (name subject to change in future releases).
1719 o Bio::Search objects improved and standardized with associated Interfaces
1720 written. The concept of a search "Hit" was standardized to be called
1721 "hit" consistently and the use of "subject" was deprecated in all active
1722 modules.
1724 o Bio::Structure added (since 0.9.1) for Protein structure objects
1725 and PDB parser to retrieve and write these structures from data files.
1727 o Several important Bio::DB::GFF bug fixes for handling features that
1728 are mapped to multiple reference points. Updated mysql adaptor
1729 so as to be able to store large (>100 megabase) chunks of DNA into
1730 Bio::DB::GFF databases.
1732 0.9.2 Developer's release
1734 o Bio::Search and Bio::SearchIO system introduced for event based
1735 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1736 in text and XML and FASTA reports in standard output format.
1738 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1739 generator is included in Bio::TreeIO::RandomTrees and a
1740 statistics module for evaluating.
1742 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1743 server for DAS servers.
1745 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1746 files. The entire BPlite system migrated to using Bio::Root::IO
1747 for the data stream.
1749 o Bio::Tools::Alignment for Consed and sequence Trimming
1750 functionality.
1752 o Bio::Structure for Protein structure information and parsing
1754 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1755 cgi-bin entry point which should be more reliable.
1757 o Bio::Map and Bio::MapIO for biological map navigation and a
1758 framework afor parsing them in. Only preliminary work here.
1760 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1761 Future work will integrate Pise and allow submission of analysis on
1762 remote servers.
1764 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1765 introduced as new objects for handling Sequence Annotation
1766 information (dblinks, references, etc) and is more robust that
1767 previous system.
1769 o Bio::Tools::FASTAParser introduced.
1771 o Scripts from the bioperl script submission project and new
1772 scripts from bioperl authors are included in "scripts" directory.
1774 o Factory objects and interfaces are being introduced and are more
1775 strictly enforced.
1777 o Bio::Root::Root introduced as the base object while
1778 Bio::Root::RootI is now simply an interface.
1780 o Bio::DB::RefSeq provides database access to copy of the NCBI
1781 RefSeq database using the EBI dbfetch script.
1783 0.9.0 Developer's release
1785 o perl version at least 5.005 is now required instead of perl 5.004
1787 o Bio::Tools::Run::RemoteBlast is available for running remote
1788 blast jobs at NCBI.
1790 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1792 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1793 Also added are related modules UTR3, UTR5, Exon, Intron,
1794 Promotor, PolyA and Transcript.
1796 o Speedup of translate method in PrimarySeq
1798 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1799 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1801 o Various fixes to Variation toolkit
1803 o Bio::DB::EMBL provides database access to EMBL sequence data.
1804 Bio::DB::Universal provides a central way to point to indexes
1805 and dbs in a single interface.
1807 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1809 o Bio::Factory::EMBOSS is still in design phase as is
1810 Bio::Factory::ApplicationFactoryI
1812 o Dia models for bioperl design are provided in the models/ directory
1814 0.7.2 Bug fix release
1816 o documentation fixes in many modules - SYNOPSIS code verified
1817 to be runnable in many (but not all modules)
1819 o corrected MANIFEST file from 0.7.1 release
1821 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1822 split locations
1824 o Bio::SeqIO::genbank
1825 * Correct parsing and writing of genbank format with protein data
1826 * moltype and molecule separation
1828 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1830 o Bio::SimpleAlign fixed to correctly handle consensus
1831 sequence calculation
1833 o Bio::Tools::HMMER supports hmmer 2.2g
1835 o Bio::Tools::BPlite to support report type specific parsing. Most
1836 major changes are not on the 0.7 branch.
1838 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1839 with File::Spec
1841 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1842 in several types of mutations:
1843 1.) AA level: deletion, complex
1844 2.) AA level: complex, inframe
1845 3.) RNA level: silent
1847 o BPbl2seq parsing of empty reports will not die, but will return
1848 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1849 $report->query() and $report->subject() methods. So an easy
1850 way to test if report was empty is to see if
1851 $report->query->seqname is undefined.
1853 0.7.1 Bug fix release
1855 o Better parsing of genbank/EMBL files especially fixing bugs
1856 related to Feature table parsing and locations on remote
1857 sequences. Additionally, species name parsing was better.
1859 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1860 which include a number of header lines.
1862 o More strict genbank and EMBL format writing (corrected number of
1863 spaces where appropriate).
1865 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1866 for related BPlite BUGS that are unresolved in this release.
1868 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1869 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1870 use expasy mirrors or EBI dbfetch cgi-script.
1872 o A moderate number of documentation improvements were made as
1873 well to provide a better code synopsis in each module.
1876 0.7 Large number of changes, including refactoring of the
1877 Object system, new parsers, new functionality and
1878 all round better system. Highlights are:
1881 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1882 Bio::Root::IO for I/O and file/handle capabilities.
1884 o Imported BPlite modules from Ian Korf for BLAST
1885 parsing. This is considered the supported BLAST parser;
1886 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1888 o Improved Sequence Feature model. Added complete location
1889 modelling (with fuzzy and compound locations). See
1890 Bio::LocationI and the modules under Bio/Location. Added
1891 support in Genbank/EMBL format parsing to completely parse
1892 feature tables for complex locations.
1894 o Moved special support for databanks etc to specialized modules under
1895 Bio/Seq/. One of these supports very large sequences through
1896 a temporary file as a backend.
1898 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1899 CDS retrieval and exon shuffling.
1901 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1903 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1904 DB/GDB (the latter has platform-specific limitations).
1906 o New analysis parser framework for HT sequence annotation (see
1907 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1909 o New Alignment IO framework
1911 o New Index modules (Swissprot)
1913 o New modules for running Blast within perl
1914 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1915 Multiple Sequence Alignment tools ClustalW and TCoffee
1916 (Bio::Tools::Run::Alignment).
1918 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1919 documentation across the package.
1921 o Much improved cross platform support. Many known incompatibilities
1922 have been fixed; however, NT and Mac do not work across the entire
1923 setup (see PLATFORMS).
1925 o Many bug fixes, code restructuring, etc. Overall stability and
1926 maintainability benefit a lot.
1928 o A total of 957 automatic tests
1931 0.6.2
1933 There are very few functionality changes but a large
1934 number of software improvements/bug fixes across the package.
1936 o The EMBL/GenBank parsing are improved.
1938 o The Swissprot reading is improved. Swissprot writing
1939 is disabled as it doesn't work at all. This needs to
1940 wait for 0.7 release
1942 o BLAST reports with no hits are correctly parsed.
1944 o Several other bugs of the BLAST parser (regular expressions, ...)
1945 fixed.
1947 o Old syntax calls have been replaced with more modern syntax
1949 o Modules that did not work at all, in particular the Sim4
1950 set have been removed
1952 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1953 have improved compliance with interface specs and documentation
1955 o Mailing list documentation updated throughout the distribution
1957 o Most minor bug fixes have happened.
1959 o The scripts in /examples now work and have the modern syntax
1960 rather than the deprecated syntax
1963 0.6.1 Sun April 2 2000
1965 o Sequences can have Sequence Features attached to them
1966 - The sequence features can be read from or written to
1967 EMBL and GenBank style flat files
1969 o Objects for Annotation, including References (but not
1970 full medline abstracts), Database links and Comments are
1971 provided
1973 o A Species object to represent nodes on a taxonomy tree
1974 is provided
1976 o The ability to parse HMMER and Sim4 output has been added
1978 o The Blast parsing has been improved, with better PSI-BLAST
1979 support and better overall behaviour.
1981 o Flat file indexed databases provide both random access
1982 and sequential access to their component sequences.
1984 o A CodonTable object has been written with all known
1985 CodonTables accessible.
1987 o A number of new lightweight analysis tools have been
1988 added, such as molecular weight determination.
1990 The 0.6 release also has improved software engineering
1992 o The sequence objects have been rewritten, providing more
1993 maintainable and easier to implement objects. These
1994 objects are backwardly compatible with the 0.05.1 objects
1996 o Many objects are defined in terms of interfaces and then
1997 a Perl implementation has been provided. The interfaces
1998 are found in the 'I' files (module names ending in 'I').
2000 This means that it is possible to wrap C/CORBA/SQL access
2001 as true "bioperl" objects, compatible with the rest of
2002 bioperl.
2004 o The SeqIO system has been overhauled to provide better
2005 processing and perl-like automatic interpretation of <>
2006 over arguments.
2008 o Many more tests have been added (a total of 172 automatic
2009 tests are now run before release).
2013 0.05.1 Tue Jun 29 05:30:44 1999
2014 - Central distribution now requires Perl 5.004. This was
2015 done to get around 5.003-based problems in Bio/Index/*
2016 and SimpleAlign.
2017 - Various bug fixes in the Bio::Tools::Blast modules
2018 including better exception handling and PSI-Blast
2019 support. See Bio/Tools/Blast/CHANGES for more.
2020 - Fixed the Parse mechanism in Seq.pm to use readseq.
2021 Follow the instructions in README for how to install
2022 it (basically, you have to edit Parse.pm).
2023 - Improved documentation of Seq.pm, indicating where
2024 objects are returned and where strings are returned.
2025 - Fixed uninitialized warnings in Bio::Root::Object.pm
2026 and Bio::Tools::SeqPattern.pm.
2027 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
2029 0.05 Sun Apr 25 01:14:11 1999
2030 - Bio::Tools::Blast modules have less memory problems
2031 and faster parsing. Webblast uses LWP and supports
2032 more functionality. See Bio/Tools/Blast/CHANGES for more.
2033 - The Bio::SeqIO system has been started, moving the
2034 sequence reformatting code out of the sequence object
2035 - The Bio::Index:: system has been started, providing
2036 generic index capabilities and specifically works for
2037 Fasta formatted databases and EMBL .dat formatted
2038 databases
2039 - The Bio::DB:: system started, providing access to
2040 databases, both via flat file + index (see above) and
2041 via http to NCBI
2042 - The scripts/ directory, where industrial strength scripts
2043 are put has been started.
2044 - Many changes - a better distribution all round.
2046 0.04.4 Wed Feb 17 02:20:13 1999
2047 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
2048 (see Bio::Tools::Blast::CHANGES).
2049 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
2050 - Beefed up the t/Fasta.t test script.
2051 - Small fix in Bio::Seq::type() (now always returns a string).
2052 - Changed Bio::Root::Utilities::get_newline_char() to
2053 get_newline() since it could return more than one char.
2054 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
2055 - Changed default timeout to 20 seconds (was 3).
2056 - Moved lengthy modification notes to the bottom of some files.
2057 - Fixed SimpleAlign write_fasta bug.
2058 - Beefed up SimpleAlign.t test
2060 0.04.3 Thu Feb 4 07:48:53 1999
2061 - Bio::Root::Object.pm and Global.pm now detect when
2062 script is run as a CGI and suppress output that is only
2063 appropriate when running interactively.
2064 - Bio::Root::Err::_set_context() adds name of script ($0).
2065 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
2066 regarding the use of the static objects via the qw(:obj) tag.
2067 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
2068 CORE::reverse, avoiding Perl warnings.
2069 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
2070 example scripts (see Bio::Tools::Blast::CHANGES).
2071 - examples/seq/seqtools.pl no longer always warns about using
2072 -prot or -nucl command-line arguments; only when using the
2073 -debug argument.
2074 - Methods added to Bio::Root::Utilities: create_filehandle(),
2075 get_newline_char(), and taste_file() to generalize filehandle
2076 creation and autodetect newline characters in files/streams
2077 (see bug report #19).
2078 - Bio::Root::IOManager::read() now handles timeouts and uses
2079 Utilities::create_filehandle().
2080 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
2081 of hardwiring in "\n".
2082 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
2084 0.04.2 Wed Dec 30 02:27:36 1998
2085 - Bug fixes in Bio::Tools::Blast modules, version 0.073
2086 (see Bio::Tools::Blast::CHANGES).
2087 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
2088 to CORE::reverse (prevents ambiguous warnings with 5.005).
2089 - Appending '.tmp.bioperl' to temporary files created by
2090 Bio::Root::Utilities::compress() or uncompress() to
2091 make it easy to identify & cleanup these files as needed.
2092 - Developers: Created CVS branch release-0-04-bug from
2093 release-0-04-1. Before making bug fixes to the 0.04.1 release,
2094 be sure to cvs checkout this branch into a clean area.
2096 0.04.1 Wed Dec 16 05:39:15 1998
2097 - Bug fixes in Bio::Tools::Blast modules, version 0.072
2098 (see Bio::Tools::Blast::CHANGES).
2099 - Compile/SW/Makefile.PL now removes *.o and *.a files
2100 with make clean.
2102 0.04 Tue Dec 8 07:49:19 1998
2103 - Lots of new modules added including:
2104 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
2105 and Bio/Compile directory containing XS-linked C code for
2106 creating Smith-Waterman sequence alignments from within Perl.
2107 * Steve Chervitz's Blast distribution has been incorporated.
2108 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
2109 - Bio/examples directory for demo scripts for all included modules.
2110 - Bio/t directory containing test suit for all included modules.
2111 - For changes specific to the Blast-related modules prior to
2112 incorporation in this central distribution, see the CHANGES
2113 file in the Bio/Tools/Blast directory.
2115 0.01 Tue Sep 8 14:23:22 1998
2116 - original version from central CVS tree; created by h2xs 1.18