| blob | ece460bc742c16187facc502d0f89893892578a3 |
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::Expression
55 Bio::DB::Expression::geo
56 Bio::DB::GFF
57 Bio::DB::GFF::Adaptor::*
58 Bio::DB::GFF::Aggregator
59 Bio::DB::GFF::Aggregator::*
60 Bio::DB::GFF::Featname
61 Bio::DB::GFF::Feature
62 Bio::DB::GFF::Homol
63 Bio::DB::GFF::RelSegment
64 Bio::DB::GFF::Segment
65 Bio::DB::GFF::Typename
66 Bio::DB::SeqFeature
67 Bio::DB::SeqFeature::*
68 Bio::Index::Stockholm
69 Bio::LiveSeq::*
70 Bio::Phenotype::*
71 Bio::Root::Build
72 Bio::SearchDist
73 Bio::SeqIO::abi
74 Bio::SeqIO::alf
75 Bio::SeqIO::ctf
76 Bio::SeqIO::exp
77 Bio::SeqIO::pln
78 Bio::SeqIO::ztr
79 Bio::Tools::AlignFactory
80 Bio::Tools::Phylo::Gumby
81 Bio::Tools::dpAlign
82 Bio::Tools::pSW
83 Bio::Variation::*
85 * The following programs have been removed:
87 bp_bulk_load_gff
88 bp_das_server
89 bp_fast_load_gff
90 bp_flanks
91 bp_genbank2gff
92 bp_generate_histogram
93 bp_load_gff
94 bp_meta_gff
95 bp_netinstall
96 bp_process_wormbase
97 bp_seqfeature_delete
98 bp_seqfeature_gff3
99 bp_seqfeature_load
101 * The following modules are no longer dependencies:
103 Bio::SeqIO::staden::read
104 DBD::Pg
105 DBD::SQLite
106 MIME::Base64
107 Memoize
108 Text::ParseWords
110 [Code changes]
112 * The deobfuscator has been removed.
114 * The script `bp_blast2tree` has been moved to the BioPerl-Run
115 distribution since it's mainly a wrapper to modules in there.
117 * The entire Bio::PopGen namespace, Bio::Tree::AlleleNode
118 module, and scripts bp_composite_LD and bp_heterogeneity_test
119 have been moved into a separate distribution named Bio-PopGen.
121 * All modules related to the NeXML format have been moved into a
122 separate distribution named Bio-NeXMLIO. These are:
124 * Bio::AlignIO::nexml
125 * Bio::Nexml::Factory
126 * Bio::NexmlIO
127 * Bio::SeqIO::nexml
128 * Bio::TreeIO::nexml
130 This also means BioPerl is no longer dependent on Bio-Phylo.
132 * All modules interfacing to ACeDB servers have been moved into a
133 separate distribution named Bio-DB-Ace. These are:
135 * Bio::DB::Ace
136 * Bio::DB::GFF::Adaptor::ace
137 * Bio::DB::GFF::Adaptor::dbi::mysqlace
138 * Bio::DB::GFF::Adaptor::dbi::oracleace
140 This also means BioPerl is no longer dependent on AcePerl.
142 * The module Bio::Draw::Pictogram has been moved to a separate
143 distribution named Bio-Draw-Pictogram. This also means BioPerl
144 is no longer dependent on SVG.
146 * The module Bio::Tree::Draw::Cladogram has been moved to a
147 separate distribution named Bio-Tree-Draw-Cladogram. This also
148 means BioPerl is no longer dependent on PostScript.
150 * The module Bio::TreeIO::svggraph has been moved to a separate
151 distribution named Bio-TreeIO-svggraph. This also means that
152 BioPerl is no longer dependent on SVG-Graph and Tree-DAG_Node.
154 * The module Bio::SeqIO::excel has been moved to a separate
155 distribution named Bio-SeqIO-excel. This also means that
156 BioPerl is no longer dependent on Spreadsheet-ParseExcel.
158 * The entire Bio::PhyloNetwork namespace has been moved to a
159 separate distribution named Bio-PhyloNetwork. This also means
160 that BioPerl is no longer dependent on Algorithm::Munkres,
161 GraphViz, and Array::Compare.
163 * The entire Bio::Asembly namespace has been moved to a separate
164 distribution named Bio-Assembly. This also means that BioPerl
165 is no longer dependent on Bio-SamTools and Sort-Naturally.
167 * The entire Bio::Structure namespace has been moved to a
168 separate distribution named Bio-Structure.
170 * The entire Bio::SeqEvolution namespace has been moved to a
171 separate distribution named Bio-SeqEvolution.
173 * The Bio::Tools::Gel module has been moved into its own
174 distribution named Bio-Tools-Gel.
176 * The entire Bio::Restriction namespace has been moved to a
177 separate distribution named Bio-Restriction.
179 * The module Bio::SeqIO::entrezgene has been moved to the
180 Bio-ASN1-EntrezGene distribution.
182 * The module Bio::MolEvol::CodonModel has moved to a distribution
183 of its own, named after itself.
185 * The module Bio::Perl has moved to a new distribution named
186 Bio-Procedural.
188 * The module Bio::Tools::Run::RemoteBlast has moved to a new
189 distribution named after itself.
191 * The module Bio::Align::Graphics has been moved to a new distribution
192 named after itself. This also means that BioPerl is no longer
193 dependent on GD.
195 * The entire Bio::DB::HIV namespace, the Bio::DB::Query::HIVQuery
196 module, and the the bp_hivq program have been moved to their
197 own distribution named Bio-DB-HIV. This also drops the bioperl
198 dependency on XML-Simple and Term-ReadLine.
200 * The entire Bio::DB::TFBS namespace has been moved to its own
201 distribution named after itself.
203 * All modules to handle HMMER programs output have been moved to their
204 own distribution named Bio-SearchIO-hmmer. This also includes the
205 programs bp_hmmer_to_table and bp_parse_hmmsearch.
207 * Bio::DB::MeSH and related Bio::Phenotype::MeSH modules have moved
208 to their own distribution Bio-DB-MeSH.
210 * The Bio::DB::Universal module has been moved to its own distribution.
212 * The emacs bioperl minor mode is no longer distributed as part of the
213 perl module distributions. See
214 https://github.com/bioperl/emacs-bioperl-mode
216 1.7.2 - "Entebbe"
218 [Bugs]
220 * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
221 * #245 - Code coverage fixes [zmughal,cjfields]
222 * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
223 * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
224 * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
225 * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
226 * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
227 * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
228 * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
229 * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
230 * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
231 * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
233 [Code changes]
235 * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
237 1.7.1 - "Election"
239 [Bugs]
241 * Minor release to incorporate fix for CPAN indexing, which
242 prevented proper updates [cjfields]
243 * Fix problem in managing Target attribute for gff3 [Jukes34]
244 * Minor bug fixes related to NCBI HTTPS support [cjfields]
246 1.7.0 - "Disney"
248 [New site]
250 * We have migrated to Github Pages. This was actually planned, but the
251 recent OBF server compromise forced our hand.
253 Brian Osborne [bosborne] took this under his wing to move docs and has
254 done a tremendous amount of work formatting the site and working out some
255 of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
256 Cantalupo and Franscison Ossandon also helped. Kudos!!
258 * Similarly, the official issue tracker is now Github Issues. This has
259 been updated in the relevant documentation bits (we hope!)
261 [Code changes]
263 * Previously deprecated modules removed
264 * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
265 * Bio::DB::SeqHound has been removed due to the service no longer being
266 available
267 * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
268 reasons due to the server no longer having a valid cert
269 * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
270 * Bio::Coordinate, Bio::SearchIO::blastxml,
271 Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
272 added on CPAN
274 [New features]
276 * Docker instances of tagged releases are available! [hlapp]
277 * NCBI HTTPS support [mjohnson and others]
278 * Bio::SearchIO::infernal
279 - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
280 * Bio::Search::HSP::ModelHSP
281 - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
282 reports [pcantalupo]
283 * Bio::Search::Result::INFERNALResult
284 - Added new module to represent features of Infernal reports [pcantalupo]
285 * Bio::DB::Taxonomy SQLite option [cjfields]
286 * WrapperBase quoted option values [majensen]
287 * Various documentation fixes and updates [bosborne]
289 [Bug Fixes]
291 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
292 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
293 * NeXML parser fixes [fjossandon]
294 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
295 * RT 103272 : SeqFeature database deletion skipped features with a decimal -
296 Joshua Fortriede (Xenbase)
297 * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
298 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
299 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
300 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
301 * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
302 * Issue #84: EMBL format wrapping problem [nyamned]
303 * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
304 * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
305 or compiled C code (when Inline::C is installed) [rocky]
306 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
307 * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
308 * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
309 * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
310 to be consistent with "$hit->bits" behaviour [fjossandon]
311 * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
312 aminoacids made "next_seq" confused and broke the parser [fjossandon]
313 * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
314 Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
315 to "complement(join(A..B,C..D))" [fjossandon]
316 * For the many many many fixes that weren't mentioned - blame the release guy!
318 1.6.924
320 [Significant changes]
322 * Bug/feature issue tracking has moved to GitHub Issues:
323 https://github.com/bioperl/bioperl-live/issues
324 * DB_File has been demoted from "required" to "recommended",
325 which should make easier for Windows users to install BioPerl
326 if they don't need that module.
328 [New features]
330 * Bio::Search::HSP::GenericHSP
331 - Bug #3370, added a "posterior_string" method to retrieve the
332 posterior probability lines (PP) from HMMER3 reports [fjossandon]
333 - Added a "consensus_string" method to retrieve the consensus
334 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
335 * Bio::SearchIO::hmmer2
336 - The number of identical and conserved residues are now calculated
337 directly from the homology line [fjossandon]
338 - Now the Query Length and Hit Length are reported when the alignment
339 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
340 - Implemented the capture of the consensus structure lines [fjossandon]
341 * Bio::SearchIO::hmmer3
342 - The number of identical and conserved residues are now calculated
343 directly from the homology line [fjossandon]
344 - Now the Hit Length is reported when the alignment runs until the end
345 of the sequence/model ('.]' or '[]') [fjossandon]
346 - Implemented the capture of the consensus structure lines [fjossandon]
347 - Implemented the capture of the posterior probability lines [fjossandon]
348 - Completed the development of NHMMER parsing, including alignments [fjossandon]
349 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
350 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
351 "min_score", "min_bits, and "hit_filter" methods from
352 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
353 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
354 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
355 besides Blast, instead of being ignored. Added tests for all moved methods
356 using HMMER outputs and run the full test suite and everything pass [fjossandon]
357 * Bio::SeqIO::MultiFile
358 - Autodetection of file format [fangly]
359 * Bio::Tools::GuessSeqFormat:
360 - Format detection from non-seekable filehandles such as STDIN [fangly]
362 [Bug fixes]
364 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
365 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
366 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
367 * Abstract: Fixed ActivePerl incapability of removing temporary files
368 because of problems closing tied filehandles [fjossandon]
369 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
370 because ActivePerl were producing a ".index.pag" and ".index.dir"
371 files instead of a single ".index" file (like Strawberry Perl).
372 Now those temporary files are correctly considered and deleted. [fjossandon]
373 * Test files: Added missing module requirements (DB_File and Data::Stag)
374 to several tests files that were failing because those modules were
375 not present. Now those test files are correctly skipped instead. [fjossandon]
376 * Blast: Added support to changes in bl2seq from BLAST+ output, which
377 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
378 * Phylip: Return undef in "next_aln" at file end to avoid
379 an infinite loop [yschensandiego]
380 * HMMER3: When a hit description is too long, it is truncated in
381 the Scores table. In those cases, the more complete description from
382 the Annotation line (>>) will be used [fjossandon]
383 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
384 since it is now used by HMMER3 format in alignments [fjossandon]
385 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
386 to return undef if the query/hit length is unknown (like in some
387 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
388 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
389 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
390 added support to multi-query reports, reduced code redundancy,
391 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
392 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
393 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
394 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
395 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
396 * Double-quotes on paths are needed in some places [fjossandon]
397 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
398 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
399 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
400 with the latest changes made in their own repositories [fjossandon]
401 * General synching of files with the master branch [fjossandon]
402 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
403 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
404 * Fixed broken MeSH parser [fjossandon]
405 * Fixed missing detection of format in SeqIO when given a -string [fangly]
407 1.6.923
409 * Major Windows support updates! [fjossandon]
410 * MAKER update to allow for stricter standard codon table [cjfields]
411 * Better support for circular sequences [fjossandon]
412 * Fixes for some complex location types [fjossandon]
413 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
414 * Fix bug #2978 related to BLAST report type [fjossandon]
415 * Deobfuscator fixes [DaveMessina]
417 1.6.922
419 * Address CPAN test failures [cjfields]
420 * Add BIOPROJECT support for Genbank files [hyphaltip]
421 * Better regex support for HMMER3 output [bosborne]
423 1.6.921
425 * Minor update to address CPAN test failures
427 1.6.920
429 * Remove Bio::Biblio and related files [carandraug]
430 - this cause version clashes with an independently-released
431 version of Bio::Biblio
433 1.6.910
435 [New features]
437 * Hash randomization fixes for perl 5.18.x
438 - Note: at least one module (Bio::Map::Physical) still has a failing test;
439 this is documented in bug #3446 and has been TODO'd; we will be pulling
440 Bio::Map and similar modules out of core into separate distributions in the
441 1.7.x release series [cjfields]
443 [New features]
445 * Bio::Seq::SimulatedRead
446 - New module to represent reads taken from other sequences [fangly]
447 * Bio::Root::Root
448 - Support of Clone::Fast as a faster cloning alternative [fangly]
449 * Bio::Root::IO
450 - Moved the format() and variant() methods from Bio::*IO modules to
451 Bio::Root::IO [fangly]
452 - Can now use format() to get the type of IO format in use [fangly]
453 * Bio::Tools::IUPAC
454 - New regexp() method to create regular expressions from IUPAC sequences
455 [fangly]
456 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
457 - Code refresh [fangly]
458 * Bio::DB::Taxonomy
459 - Added support for the Greengenes and Silva taxonomies [fangly]
460 * Bio::Tree::TreeFunctionsI
461 - get_lineage_string() represents a lineage as a string [fangly]
462 - add_trait() returns instead of reporting an error when the column
463 number is exceeded in add_trait() [fangly]
464 - Option to support tree leaves without trait [fangly]
465 - Allow ID of 0 in trait files [fangly]
466 * Bio::DB::Taxonomy::list
467 - Misc optimizations [fangly]
468 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
469 * Bio::DB::Taxonomy::*
470 - get_num_taxa() returns the number of taxa in the database [fangly]
471 * Bio::DB::Fasta and Bio::DB::Qual
472 - support indexing an arbitrary list of files [fangly]
473 - user can supply an arbitrary index file name [fangly]
474 - new option to remove index file at the end [fangly]
475 * Bio::DB::Fasta
476 - now handles IUPAC degenerate residues [fangly]
477 * Bio::PrimarySeq and Bio::PrimarySeqI
478 - speed improvements for large sequences [Ben Woodcroft, fangly]
479 * Bio::PrimaryQual
480 - tightened and optimized quality string validation [fangly]
481 * Bio::SeqIO::fasta
482 - new method and option 'block', to create FASTA output with space
483 intervaled blocks (similar to genbank or EMBL) has been implemented.
484 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
485 in favour of the methods 'width' and 'preferred_id_type` respectively.
486 * Bio::FeatureIO::*
487 - moved from bioperl-live into the separate distribution Bio-FeatureIO
488 * Bio::SeqFeature::Annotated
489 - moved from bioperl-live into the separate distribution Bio-FeatureIO
490 * Bio::Cluster::SequenceFamily
491 - improved performance when using get_members with overlapping multiple
492 criteria
493 * Bio::SearchIO::hmmer3
494 - now supports nhmmer [bosborne]
496 [Bug fixes]
498 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
499 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
500 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
501 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
502 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
503 information was lost in a multi-result blast file [Paul Cantalupo]
504 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
505 total gaps [Paul Cantalupo]
506 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
507 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
508 when end of domain indicator is split across lines [Paul Cantalupo]
509 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
510 cjfields]
511 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
512 instances where blank lines are within sequences [cjfields]
513 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
514 types [fangly]
515 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
516 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
517 cjfields]
518 * Various fixes for Stockholm file indexing and processing [bosborne]
519 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
520 breaks parsing [cjfields]
521 * Fix case where Bio::Seq::Meta* objects with no meta information could not
522 be reverse-complemented [fangly]
523 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
524 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
525 when unsure that values will be numerical [fangly]
526 * Fix undef warnings in Bio::SeqIO::embl [fangly]
527 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
528 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
529 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
530 Sallou]
531 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
532 source_tag and display_name must return a string, not undef [fangly]
533 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
534 add_SeqFeature takes a single argument [fangly]
535 * Use cross-platform filenames and temporary directory in
536 Bio::DB::Taxonomy::flatfile [fangly]
537 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
538 properly identified as existing taxa in the database [fangly]
539 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
540 without also passing a lineage to store [fangly]
541 * Prevent passing a directory to the gi2taxid option (-g) of
542 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
543 [fangly]
544 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
545 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
546 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
547 object before trying to access, and no longer returns repeated sequences.
550 1.6.901 May 18, 2011
552 [Notes]
554 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
555 modules using Ace will also be deprecated [lds, cjfields]
556 * Minor bug fix release
557 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
558 * Address Build.PL issues when DBI is not present [hartzell]
559 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
560 * Remove deprecated code for perl 5.14.0 compat [cjfields]
561 * Due to schema changes and lack of support for older versions, support
562 for NeXML 0.9 is only (very) partially implemented.
563 See: https://redmine.open-bio.org/issues/3207
565 [Bug fixes]
567 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
568 docs [genehack, cjfields]
569 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
570 module version from dist_version (probably not the best way to do this,
571 but it seems to work) [rbuels, cjfields]
574 1.6.900 April 14, 201
576 [Notes]
578 * This will probably be the last release to add significant features to
579 core modules; subsequent releases will be for bug fixes alone.
580 We are planning on a restructuring of core for summer 2011, potentially
581 as part of the Google Summer of Code. This may become BioPerl 2.0.
582 * Version bump represents 'just prior to v 1.7'. We may have point
583 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
584 This code essentially is what is on the github master branch.
586 [New features]
588 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
589 * Bio::Tree refactor
590 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
591 - removal of Scalar::Util::weaken code, which was causing odd headaches
592 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
593 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
594 many others]
595 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
596 [Warren Kretzschmar]
597 * Bio::SeqIO::gbxml
598 - bug 2515 - new contribution [Ryan Golhar, jhannah]
599 * Bio::Assembly::IO
600 - support for reading Maq, Sam and Bowtie files [maj]
601 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
602 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
603 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
604 - bug 2726: reading/writing granularity: whole scaffold or one contig
605 at a time [Joshua Udall, fangly]
606 * Bio::OntologyIO
607 - Added parsing of xrefs to OBO files, which are stored as secondary
608 dbxrefs of the cvterm [Naama Menda]
609 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
610 * PAML code updated to work with PAML 4.4d [DaveMessina]
612 [Bug fixes]
614 * [3198] - sort tabular BLAST hits by score [DaveMessina]
615 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
616 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
617 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
618 [cjfields]
619 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
620 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
621 * [3164] - TreeFunctionsI syntax bug [gjuggler]
622 * [3163] - AssemblyIO speedup [fangly]
623 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
624 hyphaltip]
625 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
626 * [3158] - fix EMBL file mis-parsing [cjfields]
627 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
628 cjfields]
629 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
630 * [3148] - URL change for UniProt [cjfields]
631 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
632 * [3136] - HMMer3 parser fixes [kblin]
633 * [3126] - catch description [Toshihiko Akiba]
634 * [3122] - Catch instances where non-seekable filehandles were being
635 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
636 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
637 [dukeleto, rbuels, cjfields]
638 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
639 jhannah]
640 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
641 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
642 cjfields]
643 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
644 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
645 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
646 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
647 * [3086] - EMBL misparsing long tags [kblin, cjfields]
648 * [3085] - CommandExts and array of files [maj, hyphaltip]
649 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
650 for alignment slices [Ha X. Dang, cjfields]
651 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
652 * [3073] - fix parsing of GenBank files from RDP [cjfields]
653 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
654 * [3064] - All-gap midline BLAST report issues [cjfields]
655 * [3063] - BLASt report RID [Razi Khaja, cjfields]
656 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
657 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
658 * [3039] - correct Newick output root node branch length [gjuggler,
659 DaveMessina]
660 * [3038] - SELEX alignment error [Bernd, cjfields]
661 * [3033] - PrimarySeq ID setting [Bernd, maj]
662 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
663 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
664 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
665 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
666 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
667 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
668 PAML 4.4d [DaveMessina]
669 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
670 DaveMessina]
671 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
672 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
673 * [3017] - using threads with Bio::DB::GenBank [cjfields]
674 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
675 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
676 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
677 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
678 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
679 cjfields]
680 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
681 * [2977] - TreeIO issues [DaveMessina]
682 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
683 * [2944] - Bio::Tools::GFF score [cjfields]
684 * [2942] - correct MapTiling output [maj]
685 * [2939] - PDB residue insertion codes [John May, maj]
686 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
687 * [2928] - GuessSeqFormat raw [maj]
688 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
689 * [2922] - open() directive issue [cjfields]
690 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
691 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
692 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
693 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
694 cjfields]
695 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
696 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
697 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
698 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
699 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
700 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
701 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
702 * [2758] - Bio::AssemblyIO ace problems [fangly]
703 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
704 * [2726] - ace file IO [Josh, fangly]
705 * [2700] - Refactor Build.PL [cjfields]
706 * [2673] - addition of simple Root-based clone() method [cjfields]
707 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
708 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
709 * [2594] - Bio::Species memory leak [cjfields]
710 * [2515] - GenBank XML parser [jhannah]
711 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
712 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
713 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
714 cjfields]
715 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
717 [Deprecated]
719 * Bio::Expression modules - these were originally designed to go with the
720 bioperl-microarray suite of tools, however they have never been completed
721 and so have been removed from the distribution. The original code has
722 been moved into the inactive bioperl-microarray suite. [cjfields]
724 [Other]
726 * Repository moved from Subversion (SVN) to
727 http://github.com/bioperl/bioperl-live [cjfields]
728 * Bug database has moved to Redmine (https://redmine.open-bio.org)
729 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
730 Thieme have been moved to their own distribution (Bio-Microarray).
731 [cjfields]
733 1.6.1 Sept. 29, 2009 (point release)
734 * No change from last alpha except VERSION and doc updates [cjfields]
736 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
737 * Fix for silent OBDA bug related to FASTA validation [cjfields]
739 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
740 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
741 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
742 [cjfields]
743 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
745 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
746 * WinXP test fixes [cjfields, maj]
747 * BioPerl.pod added for descriptive information, fixes CPAN indexing
748 [cjfields]
749 * Minor doc fixes [cjfields]
751 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
752 * Fix tests failing due to merging issues [cjfields]
753 * More documentation updates for POD parsing [cjfields]
755 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
756 * Bio::Root::Build
757 - fix YAML meta data generation [cjfields]
759 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
760 * Bio::Align::DNAStatistics
761 - fix divide by zero problem [jason]
762 * Bio::AlignIO::*
763 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
764 * Bio::AlignIO::stockholm
765 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
766 * Bio::Assembly::Tools::ContigSpectrum
767 - function to score contig spectrum [fangly]
768 * Bio::DB::EUtilities
769 - small updates [cjfields]
770 * Bio::DB::Fasta
771 - berkeleydb database now autoindexes wig files and locks correctly
772 [lstein]
773 * Bio::DB::HIV
774 - various small updates for stability; tracking changes to LANL
775 database interface [maj]
776 * Bio::DB::SeqFeature (lots of updates and changes)
777 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
778 - bug 2835 - patch [Dan Bolser]
779 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
780 * Bio::DB::SwissProt
781 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
782 * Bio::Factory::FTLocationFactory
783 - mailing list bug fix [cjfields]
784 * Bio::LocatableSeq
785 - performance work on column_from_residue_number [hartzell]
786 * Bio::Matrix::IO::phylip
787 - bug 2800 - patch to fix phylip parsing [Wei Zou]
788 * Bio::Nexml
789 - Google Summer of Code project from Chase Miller - parsers for Nexml
790 file format [maj, chmille4]
791 * Bio::PopGen
792 - Make Individual, Population, Marker objects AnnotatableI [maj]
793 - simplify LD code [jason]
794 * Bio::RangeI
795 - deal with empty intersection [jason]
796 * Bio::Restriction
797 - significant overhaul of Bio::Restriction system: complete support for
798 external and non-palindromic cutters. [maj]
799 * Bio::Root::Build
800 - CPANPLUS support, no automatic installation [sendu]
801 * Bio::Root::IO
802 - allow IO::String (regression fix) [cjfields]
803 - catch unintentional undef values [cjfields]
804 - throw if non-fh is passed to -fh [maj]
805 * Bio::Root::Root/RootI
806 - small debugging and core fixes [cjfields]
807 * Bio::Root::Test
808 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
809 * Bio::Root::Utilities
810 - bug 2737 - better warnings [cjfields]
811 * Bio::Search
812 - tiling completely refactored, HOWTO added [maj]
813 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
814 will deprecate usage of the older tiling code in the next BioPerl
815 release
816 - small fixes [cjfields]
817 * Bio::SearchIO
818 - Infernal 1.0 output now parsed [cjfields]
819 - new parser for gmap -f9 output [hartzell]
820 - bug 2852 - fix infinite loop in some output [cjfields]
821 - blastxml output now passes all TODO tests [cjfields]
822 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
823 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
824 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
825 * Bio::Seq::LargePrimarySeq
826 - delete tempdirs [cjfields]
827 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
828 * Bio::Seq::Quality
829 - extract regions based on quality threshold value [Dan Bolser, heikki]
830 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
831 * Bio::SeqFeature::Lite
832 - various Bio::DB::SeqFeature-related fixes [lstein]
833 * Bio::SeqFeature::Tools::TypeMapper
834 - additional terms for GenBank to SO map [scain]
835 * Bio::SeqIO::chadoxml
836 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
837 * Bio::SeqIO::embl
838 - support for CDS records [dave_messina, Sylvia]
839 * Bio::SeqIO::fastq
840 - complete refactoring to handle all FASTQ variants, perform validation,
841 write output. API now conforms with other Bio* parsers and the rest of
842 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
843 [cjfields]
844 * Bio::SeqIO::genbank
845 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
846 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
847 * Bio::SeqIO::largefasta
848 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
849 * Bio::SeqIO::raw
850 - add option for 'single' and 'multiple'
851 * Bio::SeqIO::scf
852 - bug 2881 - fix scf round-tripping [Adam Søgren]
853 * Bio::SeqUtils
854 - bug 2766, 2810 - copy over tags from features, doc fixes [David
855 Jackson]
856 * Bio::SimpleAlign
857 - bug 2793 - patch for add_seq index issue [jhannah, maj]
858 - bug 2801 - throw if args are required [cjfields]
859 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
860 [Tristan Lefebure, maj]
861 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
862 - fix POD and add get_SeqFeatures filter [maj]
863 * Bio::Tools::dpAlign
864 - add support for LocatableSeq [ymc]
865 - to be moved to a separate distribution [cjfields, rbuels]
866 * Bio::Tools::EUtilities
867 - fix for two bugs from mail list [Adam Whitney, cjfields]
868 - add generic ItemContainerI interface for containing same methods
869 [cjfields]
870 * Bio::Tools::HMM
871 - fix up code, add more warnings [cjfields]
872 - to be moved to a separate distribution [cjfields, rbuels]
873 * Bio::Tools::Primer3
874 - bug 2862 - fenceposting issue fixed [maj]
875 * Bio::Tools::Run::RemoteBlast
876 - tests for remote RPS-BLAST [mcook]
877 * Bio::Tools::SeqPattern
878 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
879 * Bio::Tools::tRNAscanSE
880 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
881 * Bio::Tree::*
882 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
883 * Bio::Tree::Statistics
884 - several methods for calculating Fitch-based score, internal trait
885 values, statratio(), sum of leaf distances [heikki]
886 * Bio::Tree::Tree
887 - bug 2869 - add docs indicating edge case where nodes can be
888 prematurely garbage-collected [cjfields]
889 - add as_text() function to create Tree as a string in specified format
890 [maj]
891 * Bio::Tree::TreeFunctionsI
892 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
893 Lefebure, maj]
894 * Bio::TreeIO::newick
895 - fix small semicolon issue [cjfields]
896 * scripts
897 - update to bp_seqfeature_load for SQLite [lstein]
898 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
899 - fastam9_to_table - fix for MPI output [jason]
900 - gccalc - total stats [jason]
901 * General Stuff
902 - POD cleanup re: FEEDBACK section [maj, cjfields]
903 - cleanup or fix dead links [cjfields]
904 - Use of no_* methods (indicating 'number of something') is deprecated
905 in favor of num_* [cjfields]
906 - lots of new tests for the above bugs and refactors [everyone!]
907 - new template for Komodo text editor [cjfields]
909 1.6.0 Winter 2009
910 * Feature/Annotation rollback
911 - Problematic changes introduced prior to the 1.5 release have been
912 rolled back. These changes led to subtle bugs involving operator
913 overloading and interface methods.
914 - Behavior is very similar to that for BioPerl 1.4, with tag values
915 being stored generically as simple scalars. Results in a modest
916 speedup.
917 * Bio::Graphics
918 - Split into a separate distribution on CPAN, primarily so development
919 isn't reliant on a complete BioPerl release.
920 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
921 is only available via Subversion (via bioperl-live main trunk)
922 * Bio::Root::Test
923 - Common test bed for all BioPerl modules
924 * Bio::Root::Build
925 - Common Module::Build-based subclass for all BioPerl modules
926 * Bio::DB::EUtilities
927 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
928 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
929 and user agent request posting and retrieval
930 * Test implementation and reorganization
931 - Tests have been reorganized into groups based on classes or use
932 cases.
933 - Automated test coverage is now online:
934 http://www.bioperl.org/wiki/Test_Coverage
935 - After this release, untested modules will be moved into a
936 separate developer distribution until tests can be derived.
937 Also, new modules to be added are expected to have a test suite
938 and adequate test coverage.
940 1.5.2 Developer release
942 Full details of changes since 1.5.1 are available online at:
943 http://www.bioperl.org/wiki/Change_log
944 The following represents a brief overview of the most important changes.
946 o Bio::Map
947 - Overhaul. Brand new system fully allows markers to have multiple
948 positions on multiple maps, and to have relative positions. Should be
949 backward compatible.
951 o Bio::Taxonomy
952 - This module and all the modules in the Taxonomy directory now
953 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
955 o Bio::DB::Taxonomy
957 - Taxonomy.pm
958 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
960 * New methods ancestor(), each_Descendent() and _handle_internal_id().
962 * Allows for different database modules to create Bio::Taxon objects
963 with the same internal id when the same taxon is requested from each.
965 - flatfile.pm
966 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
968 * No longer includes the fake root node 'root'; there are multiple roots
969 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
971 - entrez.pm
972 * get_node() has new option -full
974 * Caches data retrieved from website
976 o Bio::Species
977 - Now a Bio::Taxon. Carries out the species name -> specific name munging
978 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
979 backward compatability in species() method.
981 o Bio::Search and Bio::SearchIO
982 - Overhaul. The existing system has been sped up via some minor changes
983 (mostly gain-of-function to the API). Bio::PullParserI is introduced
984 as a potential eventual replacment for the existing system, though as
985 yet only a Hmmpfam parser exists written using it.
988 1.5.1 Developer release
990 o Major problem with how Annotations were written out with
991 Bio::Seq is fixed by reverting to old behavior for
992 Bio::Annotation objects.
994 o Bio::SeqIO
996 - genbank.pm
997 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
998 expect at l east 9 spaces at the beginning of a line to
999 indicate line wrapping.
1001 * Treat multi-line SOURCE sections correctly, this defect broke
1002 both common_name() and classification()
1004 * parse swissprot fields in genpept file
1006 * parse WGS genbank records
1008 - embl.pm
1009 * Changed regexp for ID line. The capturing parentheses are
1010 the same, the difference is an optional repeated-not-semi-
1011 colon expression following the captured \S+. This means the
1012 regexp works when the division looks like /PRO;/ or when the
1013 division looks like /ANG ;/ - the latter is from EMBL
1014 repbase
1016 * fix ID line parsing: the molecule string can have spaces in
1017 it. Like: "genomic DNA"
1019 - swiss.pm: bugs #1727, #1734
1021 - entrezgene.pm
1022 * Added parser for entrezgene ASN1 (text format) files.
1023 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
1025 o Bio::AlignIO
1027 - maf.pm coordinate problem fixed
1029 o Bio::Taxonomy and Bio::DB::Taxonomy
1031 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
1032 can be done via Web without downloading all the sequence.
1034 o Bio::Tools::Run::RemoteBlast supports more options and complies
1035 to changes to the NCBI interface. It is reccomended that you
1036 retrieve the data in XML instead of plain-text BLAST report to
1037 insure proper parsing and retrieval of all information as NCBI
1038 fully expects to change things in the future.
1040 o Bio::Tree and Bio::TreeIO
1042 - Fixes so that re-rooting a tree works properly
1044 - Writing out nhx format from a newick/nexus file will properly output
1045 bootstrap information. The use must move the internal node labels over
1046 to bootstraps.
1047 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
1048 $node->bootstrap($node->id);
1049 $node->id('');
1050 }
1051 - Nexus parsing is much more flexible now, does not care about
1052 LF.
1054 - Cladogram drawing module in Bio::Tree::Draw
1056 - Node height and depth now properly calculated
1058 - fix tree pruning algorithm so that node with 1 child gets merged
1060 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
1061 bugs and improvements were added, see Gbrowse mailing list for most of
1062 these.
1064 o Bio::DB::GFF partially supports GFF3. See information about
1065 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
1067 o Better location parsing in Bio::Factory::FTLocationFactory -
1068 this is part of the engine for parsing EMBL/GenBank feature table
1069 locations. Nested join/order-by/complement are allowed now
1071 o Bio::PrimarySeqI->translate now takes named parameters
1073 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
1074 reconstruction) is now supported. Parsing different models and
1075 branch specific parametes are now supported.
1077 o Bio::Factory::FTLocationFactory - parse hierarchical locations
1078 (joins of joins)
1080 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
1081 for getter/setter functions
1083 o Bio::SearchIO
1085 - blast bug #1739; match scientific notation in score
1086 and possible e+ values
1088 - blast.pm reads more WU-BLAST parameters and parameters, match
1089 a full database pathname,
1091 - Handle NCBI WEB and newer BLAST formats specifically
1092 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
1094 - psl off-by-one error fixed
1096 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
1097 and HSPs can be constructed from them.
1099 - HSPs query/hit now have a seqdesc field filled out (this was
1100 always available via $hit->description and
1101 $result->query_description
1103 - hmmer.pm can parse -A0 hmmpfam files
1105 - Writer::GbrowseGFF more customizeable.
1107 o Bio::Tools::Hmmpfam
1108 make e-value default score displayed in gff, rather than raw score
1109 allow parse of multiple records
1112 1.5 Developer release
1114 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
1115 provide Jukes-Cantor and Kimura pairwise distance methods,
1116 respectively.
1118 o Bio::AlignIO support for "po" format of POA, and "maf";
1119 Bio::AlignIO::largemultifasta is a new alternative to
1120 Bio::AlignIO::fasta for temporary file-based manipulation of
1121 particularly large multiple sequence alignments.
1123 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
1124 be treated similarly as an assembled contig.
1126 o Bio::CodonUsage provides new rare_codon() and probable_codons()
1127 methods for identifying particular codons that encode a given
1128 amino acid.
1130 o Bio::Coordinate::Utils provides new from_align() method to build
1131 a Bio::Coordinate pair directly from a
1132 Bio::Align::AlignI-conforming object.
1134 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
1135 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
1136 web service using standard Pubmed query syntax, and retrieve
1137 results as XML.
1139 o Bio::DB::GFF has various sundry bug fixes.
1141 o Bio::FeatureIO is a new SeqIO-style subsystem for
1142 writing/reading genomic features to/from files. I/O classes
1143 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
1144 classes only read/write Bio::SeqFeature::Annotated objects.
1145 Notably, the GFF v3 class requires features to be typed into the
1146 Sequence Ontology.
1148 o Bio::Graph namespace contains new modules for manipulation and
1149 analysis of protein interaction graphs.
1151 o Bio::Graphics has many bug fixes and shiny new glyphs.
1153 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
1154 indexing for HMMER reports and FASTA qual files, respectively.
1156 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
1157 new objects that can be placed within a Bio::Map::MapI-compliant
1158 genetic/physical map; Bio::Map::Physical provides a new physical
1159 map type; Bio::MapIO::fpc provides finger-printed clone mapping
1160 import.
1162 o Bio::Matrix::PSM provide new support for postion-specific
1163 (scoring) matrices (e.g. profiles, or "possums").
1165 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
1166 be instantiated without explicitly using Bio::OntologyIO. This
1167 is possible through changes to Bio::Ontology::OntologyStore to
1168 download ontology files from the web as necessary. Locations of
1169 ontology files are hard-coded into
1170 Bio::Ontology::DocumentRegistry.
1172 o Bio::PopGen includes many new methods and data types for
1173 population genetics analyses.
1175 o New constructor to Bio::Range, unions(). Given a list of
1176 ranges, returns another list of "flattened" ranges --
1177 overlapping ranges are merged into a single range with the
1178 mininum and maximum coordinates of the entire overlapping group.
1180 o Bio::Root::IO now supports -url, in addition to -file and -fh.
1181 The new -url argument allows one to specify the network address
1182 of a file for input. -url currently only works for GET
1183 requests, and thus is read-only.
1185 o Bio::SearchIO::hmmer now returns individual Hit objects for each
1186 domain alignment (thus containing only one HSP); previously
1187 separate alignments would be merged into one hit if the domain
1188 involved in the alignments was the same, but this only worked
1189 when the repeated domain occured without interruption by any
1190 other domain, leading to a confusing mixture of Hit and HSP
1191 objects.
1193 o Bio::Search::Result::ResultI-compliant report objects now
1194 implement the "get_statistics" method to access
1195 Bio::Search::StatisticsI objects that encapsulate any
1196 statistical parameters associated with the search (e.g. Karlin's
1197 lambda for BLAST/FASTA).
1199 o Bio::Seq::LargeLocatableSeq combines the functionality already
1200 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
1202 o Bio::SeqFeature::Annotated is a replacement for
1203 Bio::SeqFeature::Generic. It breaks compliance with the
1204 Bio::SeqFeatureI interface because the author was sick of
1205 dealing with untyped annotation tags. All
1206 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
1207 compliant, and accessible through Bio::Annotation::Collection.
1209 o Bio::SeqFeature::Primer implements a Tm() method for primer
1210 melting point predictions.
1212 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
1213 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
1215 o Bio::Taxonomy::Node now implements the methods necessary for
1216 Bio::Species interoperability.
1218 o Bio::Tools::CodonTable has new reverse_translate_all() and
1219 make_iupac_string() methods.
1221 o Bio::Tools::dpAlign now provides sequence profile alignments.
1223 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
1225 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
1226 parsers.
1228 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
1229 for designing small inhibitory RNA.
1231 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
1232 methods based on a distance matrix.
1234 o Bio::Tree::Statistics provides an assess_bootstrap() method to
1235 calculate bootstrap support values on a guide tree topology,
1236 based on provided bootstrap tree topologies.
1238 o Bio::TreeIO now supports the Pagel (PAG) tree format.
1240 1.4 branch
1242 1.4.1
1244 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
1246 o Bio::Graphics will work with gd1 or gd2
1248 o Bio::SearchIO
1249 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
1250 (RF lines alone)
1251 - blast.pm Parse multi-line query fields properly
1252 - small speed improvements to blasttable.pm and others
1254 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
1255 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
1256 supporting more complex queries
1259 1.4. Stable major release
1261 Since initial 1.2.0, 3000 separate changes have been made to make this release.
1263 o installable scripts
1265 o global module version from Bio::Root:Version
1267 o Bio::Graphics
1268 - major improvements; SVG support
1270 o Bio::Popgen
1271 - population genetics
1272 - support several population genetics types of questions.
1273 - Tests for statistical neutrality of mutations
1274 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
1275 Tests of population structure (Wright's F-statistic: Fst) is in
1276 Bio::PopGen::PopStats. Calculating composite linkage
1277 disequilibrium (LD) is available in Bio::PopGen::Statistics as
1278 well.
1279 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1280 and csv (comma delimited formatted) data.
1282 - a directory for implementing population simulations has
1283 been added Bio::PopGen::Simulation and 2 simulations - a
1284 Coalescent and a simple single-locus multi-allele genetic drift
1285 simulation have been provided. This replaces the code in
1286 Bio::Tree::RandomTree which has been deprecated until proper
1287 methods for generating random phylogenetic trees are
1288 implemented.
1290 o Bio::Restriction
1291 - new restrion analysis modules
1293 o Bio::Tools::Analysis
1294 - web based DNA and Protein analysis framework and several
1295 implementations
1297 o Bio::Seq::Meta
1298 - per residue annotable sequences
1300 o Bio::Matrix
1301 - Bio::Matrix::PSM - Position Scoring Matrix
1302 - Bio::Matrix::IO has been added for generalized parsing of
1303 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1304 initial implementations for parsing BLOSUM/PAM and Phylip
1305 Distance matricies respectively. A generic matrix
1306 implementation for general use was added in
1307 Bio::Matrix::Generic.
1309 o Bio::Ontology
1310 - major changes
1312 o Bio:Tree
1314 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1315 - small inhibitory RNA
1317 o Bio::SeqFeature::Tools
1318 - seqFeature mapping tools
1319 - Bio::SeqFeature::Tools::Unflattener.pm
1320 -- deal with mapping GenBank feature collections into
1321 Chado/GFF3 processable feature sets (with SO term mappings)
1323 o Bio::Tools::dpAlign
1324 - pure perl dynamic programming sequence alignment
1325 - needs Bioperl-ext
1327 o new Bio::SearchIO formats
1328 - axt and psl: UCSC formats.
1329 - blasttable: NCBI -m 8 or -m 9 format from blastall
1331 o new Bio::SeqIO formats
1332 - chado, tab, kegg, tigr, game
1333 - important fixes for old modules
1335 o Bio::AlignIO: maf
1337 o improved Bio::Tools::Genewise
1339 o Bio::SeqIO now can recongnize sequence formats automatically from
1340 stream
1342 o new parsers in Bio::Tools:
1343 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1345 o Bio::DB::Registry bugs fixed
1346 - BerkeleyDB-indexed flat files can be used by the OBDA system
1347 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1348 used by the OBDA system
1350 o several new HOWTOs
1351 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1352 Databases
1354 o hundreds of new and improved files
1357 o
1358 o Bio::Tree::AlleleNode has been updated to be a container of
1359 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1362 1.2 Branch
1364 1.2.3 Stable release update
1365 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1366 handling.
1367 o Bug #1477 - Sel --> Sec abbreviation fixed
1368 o Fix bug #1487 where paring in-between locations when
1369 end < start caused the FTLocationFactory logic to fail.
1370 o Fix bug #1489 which was not dealing with keywords as an
1371 arrayref properly (this is fixed on the main trunk because
1372 keywords returns a string and the array is accessible via
1373 get_keywords).
1374 o Bio::Tree::Tree memory leak (bug #1480) fixed
1375 Added a new initialization option -nodelete which
1376 won't try and cleanup the containing nodes if this
1377 is true.
1378 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1379 this was only present on the branch for the 1.2.1 and 1.2.2 series
1380 - Also merged main trunk changes to the branch which make
1381 newick -> nhx round tripping more effective (storing branch length
1382 and bootstrap values in same locate for NodeNHX and Node
1383 implementations.) Fixes to TreeIO parsing for labeled internal
1384 also required small changes to TreeIO::nhx. Improved
1385 tests for this module as well.
1386 o Bio::SearchIO
1387 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1388 gapped blast properly (was losing hit significance values due to
1389 the extra unexpeted column).
1390 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1391 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1392 although doesn't try to correct it - will get the negative
1393 number for you. Added a test for this as well.
1394 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1395 has no top-level family classification scores but does have scores and
1396 alignments for individual domains.
1397 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1398 regular expression to match the line was missing the possibility of
1399 an extra space. This is rare, which is why we probably did not
1400 catch it before.
1401 - BLAST parsing picks up more of the statistics/parameter fields
1402 at the bottom of reports. Still not fully complete.
1403 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1404 were fixed to include many improvements and added flexiblity
1405 in outputting the files. Bug #1495 was also fixed in the process.
1406 o Bio::DB::GFF
1407 - Update for GFF3 compatibility.
1408 - Added scripts for importing from UCSC and GenBank.
1409 - Added a 1.2003 version number.
1410 o Bio::Graphics
1411 - Updated tutorial.
1412 - Added a 1.2003 version number.
1413 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1414 properly writing keywords out.
1415 o Bio::SeqIO::genbank
1416 - Fixed bug/enhancement #1513 where dates of
1417 the form D-MMM-YYYY were not parsed. Even though this is
1418 invalid format we can handle it - and also cleanup the date
1419 string so it is properly formatted.
1420 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1421 and written with Genbank format. Similarly bug #1515 is fixed to
1422 parse in the ORIGIN text.
1423 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1424 to specify the ID type, one of (accession accession.version
1425 display primary). See Bio::SeqIO::preferred_id_type method
1426 documentation for more information.
1427 o Unigene parsing updated to handle file format changes by NCBI
1429 1.2.2 Stable release update
1431 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1432 - auto-discover ontology name
1433 - bug in parsing relationships when certain characters are in the term
1434 - fixed hard-coded prefix for term identifiers
1435 - various smaller issues
1437 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1438 of Bio::Ontology::TermI
1440 o brought the OBDA Registry code up to latest specs
1442 o Bio::DB::GenBank
1443 - eutils URL change
1444 - accession number retrieval fixed
1446 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1448 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1449 #1459 which now properly report alignment start/end info
1450 for translated BLAST/FASTA searches.
1452 o Bio::TreeIO::newick can parse labeled internal nodes
1454 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1455 for BLASTX if if you provide -report_type => 'BLASTX' when
1456 initializing a BPbl2seq object. Bioperl 1.3 will have better
1457 support for bl2seq in the SearchIO system.
1459 o Bio::Root::IO support a -noclose boolean flag which will not
1460 close a filehandle upon object cleanup - useful when sharing
1461 a filehandle among objects. Additionally code added s.t.
1462 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1464 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1466 o Bio::SeqIO::genbank
1467 - bug #1456 fixed which generated extra sequence lines
1468 - write moltype correctly for genpept
1470 1.2.1 Stable release update
1472 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1474 o Addition from main trunk of Ontology objects, principly to allow
1475 BioSQL releases against 1.2.1
1477 o Fixes and cleanup of Bio::Coordinate modules
1479 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1480 the primary accession number
1482 o Other bug fixes, including bpindex GenBank fix
1484 o Bio::SeqIO::genbank bug #1389 fixed
1486 1.2 Stable major release
1488 o More functionality added to Bio::Perl, the newbie module
1490 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1491 Support for New Hampshire Extended (NHX) format parsing.
1493 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1494 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1495 Hmmpfam parser.
1497 o New ontology parsing Bio::Ontology
1499 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1500 multi-report (mlib) fasta reports, support for waba and exonerate.
1502 o Bio::ClusterIO for parsing Unigene clusters
1504 o Bio::Assembly added for representing phrap and ace assembly clusters.
1506 o Rudimentary support for writing Chado XML (see
1507 GMOD project: www.gmod.org for more information)
1509 o Bio::Coordinate for mapping between different coordinate systems such
1510 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1511 features into different coordinate systems.
1513 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1514 with the get_Stream_by_query method and supports the latest
1515 NCBI eutils interface.
1517 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1518 object for extracting subsets of features : currently only
1519 supports extraction by location.
1521 1.1.1 Developer release
1523 o Deprecated modules are now listed in the DEPRECATED file
1525 o New HowTo documents located in doc/howto describing
1526 a domain of Bioperl.
1528 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1529 and all old bugs are searchable through the bugzilla interface.
1531 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1532 have been addressed.
1534 o Support for Genewise parsing in Bio::Tools::Genewise
1536 o Start of Ontology framework with Bio::Ontology
1538 o Speedup to the Bio::Root::Root object method _rearrange.
1539 A global _load_module method was implemented to simplify the
1540 dynamic loading of modules ala Bio::SeqIO::genbank. This
1541 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1542 etc).
1544 o Several performance improvements to sequence parsing in Bio::SeqIO.
1545 Attempt to speedup by reducing object creation overhead.
1547 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1548 method for sequence retrieval with their E-utils CGI scripts.
1549 More work to support Entrez queries to their fullest is planned
1550 before 1.2 release.
1552 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1554 1.1 Developer release
1556 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1557 this separation removes some of the complexity in our test suite
1558 and separates the core modules in bioperl from those that need
1559 external programs to run.
1561 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1562 not run into trouble running the makefile
1564 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1565 read,create,and write locations for grouped/split locations
1566 (like mRNA features on genomic sequence).
1568 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1569 and PAML (codeml,aaml, etc) parsing.
1571 o Bio::Tree:: objects expanded to handle testing monophyly,
1572 paraphyly, least common ancestor, etc.
1574 o Bio::Coordinate for mapping locations from different coordinate spaces
1576 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1577 added for parsing hmmpfam and hmmsearch output.
1579 o Bio::SearchIO::Writer::TextResultWriter for outputting
1580 a pseudo-blast textfile format
1583 1.0.2 Bug fix release
1585 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1586 in this release will not work after December 2002 when NCBI
1587 shuts off the old Entrez cgi scripts. We have already fixed
1588 on our main development branch and the functionality will be
1589 available in the next stable bioperl release (1.2) slated for
1590 Fall 2002.
1592 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1593 testset by Robin Emig. These were fixed as was the get_aln
1594 method in Bio::Search::HSP::GenericHSP to handle the extra
1595 context sequence that is provided with a FastA alignment.
1597 o Migrating differences between Bio::Search::XX::BlastXX to
1598 Bio::Search::XX::GenericXX objects. This included mechanism
1599 to retrieve whole list of HSPs from Hits and whole list of Hits from
1600 Results in addition to the current next_XX iterator methods that
1601 are available. Added seq_inds() method to GenericHSP which identifies
1602 indexes in the query or hit sequences where conserved,identical,gaps,
1603 or mismatch residues are located (adapted from Steve Chervitz's
1604 implementation in BlastHSP).
1606 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1607 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1609 o Bio::Graphics glyph set improved and extended for GBrowse release
1611 o Bio::Tree::Tree get_nodes implementation improvement thanks
1612 to Howard Ross notice performance problem when writing out
1613 unbalanced trees.
1615 o Bio::Location::Fuzzy::new named parameter -loc_type became
1616 -location_type, Bio::Location::Simple::new named parameter
1617 -seqid becamse -seq_id.
1619 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1620 was mis-detecting that gaps should be placed at the beginning of
1621 the alignment when the best alignment starts internally in the
1622 sequence.
1624 1.0.1 Bug fix release
1626 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1628 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1629 and mixed (3.3 - 3.4) versions of FASTA.
1631 o Small API change to add methods for completeness across
1632 implementations of Bio::Search objects. These new methods
1633 in the interface are implemented by the GenericXX object as well
1634 as the BlastXX objects.
1635 * Bio::Search::Result::ResultI
1636 - hits() method returns list of all Hits (next_hit is an
1637 iterator method)
1639 * Bio::Search::Hit::HitI
1640 - hsps() method returns list of all HSPs (next_hsp is an
1641 iterator method)
1643 o The Bio::SearchIO::Writer classes have been fixed to handle results
1644 created from either psiblast (Search::BlastXX objects) or
1645 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1646 has to be done here to make it work properly and will nee major
1647 API changes.
1649 o Bugs in Bio::Tools::HMMER fixed, including
1650 * #1178 - Root::IO destructor wasn't being called
1651 * #1034 - filter_on_cutoff now behaves properly
1653 o Bio::SeqFeature::Computation initialization args fixed and
1654 tests added.
1656 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1658 o Updated FAQ with more example based answers to typical questions
1660 o Bug #1202 was fixed which would improperly join together qual values
1661 parsed by Bio::SeqIO::qual when a trailing space was not present before
1662 the newline.
1664 1.0.0 Major Stable Release
1666 This represents a major release of bioperl with significant
1667 improvements over the 0.7.x series of releases.
1669 o Bio::Tools::Blast is officially deprecated. Please see
1670 Bio::SearchIO for BLAST and FastA parsing.
1672 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1673 Bio::LocationI objects as well as start/end.
1675 o Bio::Biblio contains modules for Bibliographic data.
1676 Bio::DB::Biblio contains the query modules. Additionally one can
1677 parse medlinexml from the ebi bibliographic query service (BQS)
1678 system and Pubmed xml from NCBI. See Martin Senger's
1679 documentation in Bio::Biblio for more information.
1681 o Bio::DB::Registry is a sequence database registry part of
1682 Open Bioinformatics Database Access. See
1683 http://obda.open-bio.org for more information.
1685 o File-based and In-Memory Sequence caching is provided by
1686 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1687 local database.
1689 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1690 been added by Lincoln Stein.
1692 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1694 o A FAQ has been started and is included in the release to provide
1695 a starting point for frequent questions and issues.
1697 0.9.3 Developer's release
1699 o Event based parsing system improved (SearchIO). With parsers for
1700 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1701 Additionally a lazy parsing system for text and html blast reports was
1702 added and is called psiblast (name subject to change in future releases).
1704 o Bio::Search objects improved and standardized with associated Interfaces
1705 written. The concept of a search "Hit" was standardized to be called
1706 "hit" consistently and the use of "subject" was deprecated in all active
1707 modules.
1709 o Bio::Structure added (since 0.9.1) for Protein structure objects
1710 and PDB parser to retrieve and write these structures from data files.
1712 o Several important Bio::DB::GFF bug fixes for handling features that
1713 are mapped to multiple reference points. Updated mysql adaptor
1714 so as to be able to store large (>100 megabase) chunks of DNA into
1715 Bio::DB::GFF databases.
1717 0.9.2 Developer's release
1719 o Bio::Search and Bio::SearchIO system introduced for event based
1720 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1721 in text and XML and FASTA reports in standard output format.
1723 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1724 generator is included in Bio::TreeIO::RandomTrees and a
1725 statistics module for evaluating.
1727 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1728 server for DAS servers.
1730 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1731 files. The entire BPlite system migrated to using Bio::Root::IO
1732 for the data stream.
1734 o Bio::Tools::Alignment for Consed and sequence Trimming
1735 functionality.
1737 o Bio::Structure for Protein structure information and parsing
1739 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1740 cgi-bin entry point which should be more reliable.
1742 o Bio::Map and Bio::MapIO for biological map navigation and a
1743 framework afor parsing them in. Only preliminary work here.
1745 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1746 Future work will integrate Pise and allow submission of analysis on
1747 remote servers.
1749 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1750 introduced as new objects for handling Sequence Annotation
1751 information (dblinks, references, etc) and is more robust that
1752 previous system.
1754 o Bio::Tools::FASTAParser introduced.
1756 o Scripts from the bioperl script submission project and new
1757 scripts from bioperl authors are included in "scripts" directory.
1759 o Factory objects and interfaces are being introduced and are more
1760 strictly enforced.
1762 o Bio::Root::Root introduced as the base object while
1763 Bio::Root::RootI is now simply an interface.
1765 o Bio::DB::RefSeq provides database access to copy of the NCBI
1766 RefSeq database using the EBI dbfetch script.
1768 0.9.0 Developer's release
1770 o perl version at least 5.005 is now required instead of perl 5.004
1772 o Bio::Tools::Run::RemoteBlast is available for running remote
1773 blast jobs at NCBI.
1775 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1777 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1778 Also added are related modules UTR3, UTR5, Exon, Intron,
1779 Promotor, PolyA and Transcript.
1781 o Speedup of translate method in PrimarySeq
1783 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1784 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1786 o Various fixes to Variation toolkit
1788 o Bio::DB::EMBL provides database access to EMBL sequence data.
1789 Bio::DB::Universal provides a central way to point to indexes
1790 and dbs in a single interface.
1792 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1794 o Bio::Factory::EMBOSS is still in design phase as is
1795 Bio::Factory::ApplicationFactoryI
1797 o Dia models for bioperl design are provided in the models/ directory
1799 0.7.2 Bug fix release
1801 o documentation fixes in many modules - SYNOPSIS code verified
1802 to be runnable in many (but not all modules)
1804 o corrected MANIFEST file from 0.7.1 release
1806 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1807 split locations
1809 o Bio::SeqIO::genbank
1810 * Correct parsing and writing of genbank format with protein data
1811 * moltype and molecule separation
1813 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1815 o Bio::SimpleAlign fixed to correctly handle consensus
1816 sequence calculation
1818 o Bio::Tools::HMMER supports hmmer 2.2g
1820 o Bio::Tools::BPlite to support report type specific parsing. Most
1821 major changes are not on the 0.7 branch.
1823 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1824 with File::Spec
1826 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1827 in several types of mutations:
1828 1.) AA level: deletion, complex
1829 2.) AA level: complex, inframe
1830 3.) RNA level: silent
1832 o BPbl2seq parsing of empty reports will not die, but will return
1833 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1834 $report->query() and $report->subject() methods. So an easy
1835 way to test if report was empty is to see if
1836 $report->query->seqname is undefined.
1838 0.7.1 Bug fix release
1840 o Better parsing of genbank/EMBL files especially fixing bugs
1841 related to Feature table parsing and locations on remote
1842 sequences. Additionally, species name parsing was better.
1844 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1845 which include a number of header lines.
1847 o More strict genbank and EMBL format writing (corrected number of
1848 spaces where appropriate).
1850 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1851 for related BPlite BUGS that are unresolved in this release.
1853 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1854 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1855 use expasy mirrors or EBI dbfetch cgi-script.
1857 o A moderate number of documentation improvements were made as
1858 well to provide a better code synopsis in each module.
1861 0.7 Large number of changes, including refactoring of the
1862 Object system, new parsers, new functionality and
1863 all round better system. Highlights are:
1866 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1867 Bio::Root::IO for I/O and file/handle capabilities.
1869 o Imported BPlite modules from Ian Korf for BLAST
1870 parsing. This is considered the supported BLAST parser;
1871 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1873 o Improved Sequence Feature model. Added complete location
1874 modelling (with fuzzy and compound locations). See
1875 Bio::LocationI and the modules under Bio/Location. Added
1876 support in Genbank/EMBL format parsing to completely parse
1877 feature tables for complex locations.
1879 o Moved special support for databanks etc to specialized modules under
1880 Bio/Seq/. One of these supports very large sequences through
1881 a temporary file as a backend.
1883 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1884 CDS retrieval and exon shuffling.
1886 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1888 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1889 DB/GDB (the latter has platform-specific limitations).
1891 o New analysis parser framework for HT sequence annotation (see
1892 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1894 o New Alignment IO framework
1896 o New Index modules (Swissprot)
1898 o New modules for running Blast within perl
1899 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1900 Multiple Sequence Alignment tools ClustalW and TCoffee
1901 (Bio::Tools::Run::Alignment).
1903 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1904 documentation across the package.
1906 o Much improved cross platform support. Many known incompatibilities
1907 have been fixed; however, NT and Mac do not work across the entire
1908 setup (see PLATFORMS).
1910 o Many bug fixes, code restructuring, etc. Overall stability and
1911 maintainability benefit a lot.
1913 o A total of 957 automatic tests
1916 0.6.2
1918 There are very few functionality changes but a large
1919 number of software improvements/bug fixes across the package.
1921 o The EMBL/GenBank parsing are improved.
1923 o The Swissprot reading is improved. Swissprot writing
1924 is disabled as it doesn't work at all. This needs to
1925 wait for 0.7 release
1927 o BLAST reports with no hits are correctly parsed.
1929 o Several other bugs of the BLAST parser (regular expressions, ...)
1930 fixed.
1932 o Old syntax calls have been replaced with more modern syntax
1934 o Modules that did not work at all, in particular the Sim4
1935 set have been removed
1937 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1938 have improved compliance with interface specs and documentation
1940 o Mailing list documentation updated throughout the distribution
1942 o Most minor bug fixes have happened.
1944 o The scripts in /examples now work and have the modern syntax
1945 rather than the deprecated syntax
1948 0.6.1 Sun April 2 2000
1950 o Sequences can have Sequence Features attached to them
1951 - The sequence features can be read from or written to
1952 EMBL and GenBank style flat files
1954 o Objects for Annotation, including References (but not
1955 full medline abstracts), Database links and Comments are
1956 provided
1958 o A Species object to represent nodes on a taxonomy tree
1959 is provided
1961 o The ability to parse HMMER and Sim4 output has been added
1963 o The Blast parsing has been improved, with better PSI-BLAST
1964 support and better overall behaviour.
1966 o Flat file indexed databases provide both random access
1967 and sequential access to their component sequences.
1969 o A CodonTable object has been written with all known
1970 CodonTables accessible.
1972 o A number of new lightweight analysis tools have been
1973 added, such as molecular weight determination.
1975 The 0.6 release also has improved software engineering
1977 o The sequence objects have been rewritten, providing more
1978 maintainable and easier to implement objects. These
1979 objects are backwardly compatible with the 0.05.1 objects
1981 o Many objects are defined in terms of interfaces and then
1982 a Perl implementation has been provided. The interfaces
1983 are found in the 'I' files (module names ending in 'I').
1985 This means that it is possible to wrap C/CORBA/SQL access
1986 as true "bioperl" objects, compatible with the rest of
1987 bioperl.
1989 o The SeqIO system has been overhauled to provide better
1990 processing and perl-like automatic interpretation of <>
1991 over arguments.
1993 o Many more tests have been added (a total of 172 automatic
1994 tests are now run before release).
1998 0.05.1 Tue Jun 29 05:30:44 1999
1999 - Central distribution now requires Perl 5.004. This was
2000 done to get around 5.003-based problems in Bio/Index/*
2001 and SimpleAlign.
2002 - Various bug fixes in the Bio::Tools::Blast modules
2003 including better exception handling and PSI-Blast
2004 support. See Bio/Tools/Blast/CHANGES for more.
2005 - Fixed the Parse mechanism in Seq.pm to use readseq.
2006 Follow the instructions in README for how to install
2007 it (basically, you have to edit Parse.pm).
2008 - Improved documentation of Seq.pm, indicating where
2009 objects are returned and where strings are returned.
2010 - Fixed uninitialized warnings in Bio::Root::Object.pm
2011 and Bio::Tools::SeqPattern.pm.
2012 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
2014 0.05 Sun Apr 25 01:14:11 1999
2015 - Bio::Tools::Blast modules have less memory problems
2016 and faster parsing. Webblast uses LWP and supports
2017 more functionality. See Bio/Tools/Blast/CHANGES for more.
2018 - The Bio::SeqIO system has been started, moving the
2019 sequence reformatting code out of the sequence object
2020 - The Bio::Index:: system has been started, providing
2021 generic index capabilities and specifically works for
2022 Fasta formatted databases and EMBL .dat formatted
2023 databases
2024 - The Bio::DB:: system started, providing access to
2025 databases, both via flat file + index (see above) and
2026 via http to NCBI
2027 - The scripts/ directory, where industrial strength scripts
2028 are put has been started.
2029 - Many changes - a better distribution all round.
2031 0.04.4 Wed Feb 17 02:20:13 1999
2032 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
2033 (see Bio::Tools::Blast::CHANGES).
2034 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
2035 - Beefed up the t/Fasta.t test script.
2036 - Small fix in Bio::Seq::type() (now always returns a string).
2037 - Changed Bio::Root::Utilities::get_newline_char() to
2038 get_newline() since it could return more than one char.
2039 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
2040 - Changed default timeout to 20 seconds (was 3).
2041 - Moved lengthy modification notes to the bottom of some files.
2042 - Fixed SimpleAlign write_fasta bug.
2043 - Beefed up SimpleAlign.t test
2045 0.04.3 Thu Feb 4 07:48:53 1999
2046 - Bio::Root::Object.pm and Global.pm now detect when
2047 script is run as a CGI and suppress output that is only
2048 appropriate when running interactively.
2049 - Bio::Root::Err::_set_context() adds name of script ($0).
2050 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
2051 regarding the use of the static objects via the qw(:obj) tag.
2052 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
2053 CORE::reverse, avoiding Perl warnings.
2054 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
2055 example scripts (see Bio::Tools::Blast::CHANGES).
2056 - examples/seq/seqtools.pl no longer always warns about using
2057 -prot or -nucl command-line arguments; only when using the
2058 -debug argument.
2059 - Methods added to Bio::Root::Utilities: create_filehandle(),
2060 get_newline_char(), and taste_file() to generalize filehandle
2061 creation and autodetect newline characters in files/streams
2062 (see bug report #19).
2063 - Bio::Root::IOManager::read() now handles timeouts and uses
2064 Utilities::create_filehandle().
2065 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
2066 of hardwiring in "\n".
2067 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
2069 0.04.2 Wed Dec 30 02:27:36 1998
2070 - Bug fixes in Bio::Tools::Blast modules, version 0.073
2071 (see Bio::Tools::Blast::CHANGES).
2072 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
2073 to CORE::reverse (prevents ambiguous warnings with 5.005).
2074 - Appending '.tmp.bioperl' to temporary files created by
2075 Bio::Root::Utilities::compress() or uncompress() to
2076 make it easy to identify & cleanup these files as needed.
2077 - Developers: Created CVS branch release-0-04-bug from
2078 release-0-04-1. Before making bug fixes to the 0.04.1 release,
2079 be sure to cvs checkout this branch into a clean area.
2081 0.04.1 Wed Dec 16 05:39:15 1998
2082 - Bug fixes in Bio::Tools::Blast modules, version 0.072
2083 (see Bio::Tools::Blast::CHANGES).
2084 - Compile/SW/Makefile.PL now removes *.o and *.a files
2085 with make clean.
2087 0.04 Tue Dec 8 07:49:19 1998
2088 - Lots of new modules added including:
2089 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
2090 and Bio/Compile directory containing XS-linked C code for
2091 creating Smith-Waterman sequence alignments from within Perl.
2092 * Steve Chervitz's Blast distribution has been incorporated.
2093 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
2094 - Bio/examples directory for demo scripts for all included modules.
2095 - Bio/t directory containing test suit for all included modules.
2096 - For changes specific to the Blast-related modules prior to
2097 incorporation in this central distribution, see the CHANGES
2098 file in the Bio/Tools/Blast directory.
2100 0.01 Tue Sep 8 14:23:22 1998
2101 - original version from central CVS tree; created by h2xs 1.18