| blob | 2dd737737ad52962e790fdcc3cdae4b5c0302675 |
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::Expression
56 Bio::DB::Expression::geo
57 Bio::DB::GFF
58 Bio::DB::GFF::Adaptor::*
59 Bio::DB::GFF::Aggregator
60 Bio::DB::GFF::Aggregator::*
61 Bio::DB::GFF::Featname
62 Bio::DB::GFF::Feature
63 Bio::DB::GFF::Homol
64 Bio::DB::GFF::RelSegment
65 Bio::DB::GFF::Segment
66 Bio::DB::GFF::Typename
67 Bio::DB::SeqFeature
68 Bio::DB::SeqFeature::*
69 Bio::DB::Taxonomy::sqlite
70 Bio::Index::Stockholm
71 Bio::LiveSeq::*
72 Bio::Phenotype::*
73 Bio::Root::Build
74 Bio::SearchDist
75 Bio::SeqIO::abi
76 Bio::SeqIO::alf
77 Bio::SeqIO::ctf
78 Bio::SeqIO::exp
79 Bio::SeqIO::pln
80 Bio::SeqIO::ztr
81 Bio::Tools::AlignFactory
82 Bio::Tools::Phylo::Gumby
83 Bio::Tools::dpAlign
84 Bio::Tools::pSW
85 Bio::Variation::*
87 * The following programs have been removed:
89 bp_bulk_load_gff
90 bp_das_server
91 bp_fast_load_gff
92 bp_flanks
93 bp_genbank2gff
94 bp_generate_histogram
95 bp_load_gff
96 bp_meta_gff
97 bp_netinstall
98 bp_process_wormbase
99 bp_seqfeature_delete
100 bp_seqfeature_gff3
101 bp_seqfeature_load
103 * The following modules are no longer dependencies:
105 Bio::SeqIO::staden::read
106 DBD::Pg
107 DBD::SQLite
108 MIME::Base64
109 Memoize
110 Text::ParseWords
112 [Code changes]
114 * The deobfuscator has been removed.
116 * The script `bp_blast2tree` has been moved to the BioPerl-Run
117 distribution since it's mainly a wrapper to modules in there.
119 * The entire Bio::PopGen namespace, Bio::Tree::AlleleNode
120 module, and scripts bp_composite_LD and bp_heterogeneity_test
121 have been moved into a separate distribution named Bio-PopGen.
123 * All modules related to the NeXML format have been moved into a
124 separate distribution named Bio-NeXMLIO. These are:
126 * Bio::AlignIO::nexml
127 * Bio::Nexml::Factory
128 * Bio::NexmlIO
129 * Bio::SeqIO::nexml
130 * Bio::TreeIO::nexml
132 This also means BioPerl is no longer dependent on Bio-Phylo.
134 * All modules interfacing to ACeDB servers have been moved into a
135 separate distribution named Bio-DB-Ace. These are:
137 * Bio::DB::Ace
138 * Bio::DB::GFF::Adaptor::ace
139 * Bio::DB::GFF::Adaptor::dbi::mysqlace
140 * Bio::DB::GFF::Adaptor::dbi::oracleace
142 This also means BioPerl is no longer dependent on AcePerl.
144 * The module Bio::Draw::Pictogram has been moved to a separate
145 distribution named Bio-Draw-Pictogram. This also means BioPerl
146 is no longer dependent on SVG.
148 * The module Bio::Tree::Draw::Cladogram has been moved to a
149 separate distribution named Bio-Tree-Draw-Cladogram. This also
150 means BioPerl is no longer dependent on PostScript.
152 * The module Bio::TreeIO::svggraph has been moved to a separate
153 distribution named Bio-TreeIO-svggraph. This also means that
154 BioPerl is no longer dependent on SVG-Graph and Tree-DAG_Node.
156 * The module Bio::SeqIO::excel has been moved to a separate
157 distribution named Bio-SeqIO-excel. This also means that
158 BioPerl is no longer dependent on Spreadsheet-ParseExcel.
160 * The entire Bio::PhyloNetwork namespace has been moved to a
161 separate distribution named Bio-PhyloNetwork. This also means
162 that BioPerl is no longer dependent on Algorithm::Munkres,
163 GraphViz, and Array::Compare.
165 * The entire Bio::Asembly namespace has been moved to a separate
166 distribution named Bio-Assembly. This also means that BioPerl
167 is no longer dependent on Bio-SamTools and Sort-Naturally.
169 * The entire Bio::Structure namespace has been moved to a
170 separate distribution named Bio-Structure.
172 * The entire Bio::SeqEvolution namespace has been moved to a
173 separate distribution named Bio-SeqEvolution.
175 * The Bio::Tools::Gel module has been moved into its own
176 distribution named Bio-Tools-Gel.
178 * The entire Bio::Restriction namespace has been moved to a
179 separate distribution named Bio-Restriction.
181 * The module Bio::SeqIO::entrezgene has been moved to the
182 Bio-ASN1-EntrezGene distribution.
184 * The module Bio::MolEvol::CodonModel has moved to a distribution
185 of its own, named after itself.
187 * The module Bio::Perl has moved to a new distribution named
188 Bio-Procedural.
190 * The module Bio::Tools::Run::RemoteBlast has moved to a new
191 distribution named after itself.
193 * The module Bio::Align::Graphics has been moved to a new distribution
194 named after itself. This also means that BioPerl is no longer
195 dependent on GD.
197 * The entire Bio::DB::HIV namespace, the Bio::DB::Query::HIVQuery
198 module, and the the bp_hivq program have been moved to their
199 own distribution named Bio-DB-HIV. This also drops the bioperl
200 dependency on XML-Simple and Term-ReadLine.
202 * The entire Bio::DB::TFBS namespace has been moved to its own
203 distribution named after itself.
205 * All modules to handle HMMER programs output have been moved to their
206 own distribution named Bio-SearchIO-hmmer. This also includes the
207 programs bp_hmmer_to_table and bp_parse_hmmsearch.
209 * Bio::DB::MeSH and related Bio::Phenotype::MeSH modules have moved
210 to their own distribution Bio-DB-MeSH.
212 * The Bio::DB::Universal module has been moved to its own distribution.
214 * The emacs bioperl minor mode is no longer distributed as part of the
215 perl module distributions. See
216 https://github.com/bioperl/emacs-bioperl-mode
218 1.7.2 - "Entebbe"
220 [Bugs]
222 * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
223 * #245 - Code coverage fixes [zmughal,cjfields]
224 * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
225 * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
226 * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
227 * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
228 * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
229 * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
230 * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
231 * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
232 * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
233 * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
235 [Code changes]
237 * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
239 1.7.1 - "Election"
241 [Bugs]
243 * Minor release to incorporate fix for CPAN indexing, which
244 prevented proper updates [cjfields]
245 * Fix problem in managing Target attribute for gff3 [Jukes34]
246 * Minor bug fixes related to NCBI HTTPS support [cjfields]
248 1.7.0 - "Disney"
250 [New site]
252 * We have migrated to Github Pages. This was actually planned, but the
253 recent OBF server compromise forced our hand.
255 Brian Osborne [bosborne] took this under his wing to move docs and has
256 done a tremendous amount of work formatting the site and working out some
257 of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
258 Cantalupo and Franscison Ossandon also helped. Kudos!!
260 * Similarly, the official issue tracker is now Github Issues. This has
261 been updated in the relevant documentation bits (we hope!)
263 [Code changes]
265 * Previously deprecated modules removed
266 * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
267 * Bio::DB::SeqHound has been removed due to the service no longer being
268 available
269 * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
270 reasons due to the server no longer having a valid cert
271 * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
272 * Bio::Coordinate, Bio::SearchIO::blastxml,
273 Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
274 added on CPAN
276 [New features]
278 * Docker instances of tagged releases are available! [hlapp]
279 * NCBI HTTPS support [mjohnson and others]
280 * Bio::SearchIO::infernal
281 - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
282 * Bio::Search::HSP::ModelHSP
283 - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
284 reports [pcantalupo]
285 * Bio::Search::Result::INFERNALResult
286 - Added new module to represent features of Infernal reports [pcantalupo]
287 * Bio::DB::Taxonomy SQLite option [cjfields]
288 * WrapperBase quoted option values [majensen]
289 * Various documentation fixes and updates [bosborne]
291 [Bug Fixes]
293 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
294 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
295 * NeXML parser fixes [fjossandon]
296 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
297 * RT 103272 : SeqFeature database deletion skipped features with a decimal -
298 Joshua Fortriede (Xenbase)
299 * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
300 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
301 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
302 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
303 * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
304 * Issue #84: EMBL format wrapping problem [nyamned]
305 * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
306 * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
307 or compiled C code (when Inline::C is installed) [rocky]
308 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
309 * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
310 * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
311 * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
312 to be consistent with "$hit->bits" behaviour [fjossandon]
313 * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
314 aminoacids made "next_seq" confused and broke the parser [fjossandon]
315 * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
316 Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
317 to "complement(join(A..B,C..D))" [fjossandon]
318 * For the many many many fixes that weren't mentioned - blame the release guy!
320 1.6.924
322 [Significant changes]
324 * Bug/feature issue tracking has moved to GitHub Issues:
325 https://github.com/bioperl/bioperl-live/issues
326 * DB_File has been demoted from "required" to "recommended",
327 which should make easier for Windows users to install BioPerl
328 if they don't need that module.
330 [New features]
332 * Bio::Search::HSP::GenericHSP
333 - Bug #3370, added a "posterior_string" method to retrieve the
334 posterior probability lines (PP) from HMMER3 reports [fjossandon]
335 - Added a "consensus_string" method to retrieve the consensus
336 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
337 * Bio::SearchIO::hmmer2
338 - The number of identical and conserved residues are now calculated
339 directly from the homology line [fjossandon]
340 - Now the Query Length and Hit Length are reported when the alignment
341 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
342 - Implemented the capture of the consensus structure lines [fjossandon]
343 * Bio::SearchIO::hmmer3
344 - The number of identical and conserved residues are now calculated
345 directly from the homology line [fjossandon]
346 - Now the Hit Length is reported when the alignment runs until the end
347 of the sequence/model ('.]' or '[]') [fjossandon]
348 - Implemented the capture of the consensus structure lines [fjossandon]
349 - Implemented the capture of the posterior probability lines [fjossandon]
350 - Completed the development of NHMMER parsing, including alignments [fjossandon]
351 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
352 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
353 "min_score", "min_bits, and "hit_filter" methods from
354 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
355 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
356 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
357 besides Blast, instead of being ignored. Added tests for all moved methods
358 using HMMER outputs and run the full test suite and everything pass [fjossandon]
359 * Bio::SeqIO::MultiFile
360 - Autodetection of file format [fangly]
361 * Bio::Tools::GuessSeqFormat:
362 - Format detection from non-seekable filehandles such as STDIN [fangly]
364 [Bug fixes]
366 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
367 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
368 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
369 * Abstract: Fixed ActivePerl incapability of removing temporary files
370 because of problems closing tied filehandles [fjossandon]
371 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
372 because ActivePerl were producing a ".index.pag" and ".index.dir"
373 files instead of a single ".index" file (like Strawberry Perl).
374 Now those temporary files are correctly considered and deleted. [fjossandon]
375 * Test files: Added missing module requirements (DB_File and Data::Stag)
376 to several tests files that were failing because those modules were
377 not present. Now those test files are correctly skipped instead. [fjossandon]
378 * Blast: Added support to changes in bl2seq from BLAST+ output, which
379 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
380 * Phylip: Return undef in "next_aln" at file end to avoid
381 an infinite loop [yschensandiego]
382 * HMMER3: When a hit description is too long, it is truncated in
383 the Scores table. In those cases, the more complete description from
384 the Annotation line (>>) will be used [fjossandon]
385 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
386 since it is now used by HMMER3 format in alignments [fjossandon]
387 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
388 to return undef if the query/hit length is unknown (like in some
389 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
390 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
391 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
392 added support to multi-query reports, reduced code redundancy,
393 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
394 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
395 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
396 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
397 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
398 * Double-quotes on paths are needed in some places [fjossandon]
399 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
400 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
401 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
402 with the latest changes made in their own repositories [fjossandon]
403 * General synching of files with the master branch [fjossandon]
404 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
405 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
406 * Fixed broken MeSH parser [fjossandon]
407 * Fixed missing detection of format in SeqIO when given a -string [fangly]
409 1.6.923
411 * Major Windows support updates! [fjossandon]
412 * MAKER update to allow for stricter standard codon table [cjfields]
413 * Better support for circular sequences [fjossandon]
414 * Fixes for some complex location types [fjossandon]
415 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
416 * Fix bug #2978 related to BLAST report type [fjossandon]
417 * Deobfuscator fixes [DaveMessina]
419 1.6.922
421 * Address CPAN test failures [cjfields]
422 * Add BIOPROJECT support for Genbank files [hyphaltip]
423 * Better regex support for HMMER3 output [bosborne]
425 1.6.921
427 * Minor update to address CPAN test failures
429 1.6.920
431 * Remove Bio::Biblio and related files [carandraug]
432 - this cause version clashes with an independently-released
433 version of Bio::Biblio
435 1.6.910
437 [New features]
439 * Hash randomization fixes for perl 5.18.x
440 - Note: at least one module (Bio::Map::Physical) still has a failing test;
441 this is documented in bug #3446 and has been TODO'd; we will be pulling
442 Bio::Map and similar modules out of core into separate distributions in the
443 1.7.x release series [cjfields]
445 [New features]
447 * Bio::Seq::SimulatedRead
448 - New module to represent reads taken from other sequences [fangly]
449 * Bio::Root::Root
450 - Support of Clone::Fast as a faster cloning alternative [fangly]
451 * Bio::Root::IO
452 - Moved the format() and variant() methods from Bio::*IO modules to
453 Bio::Root::IO [fangly]
454 - Can now use format() to get the type of IO format in use [fangly]
455 * Bio::Tools::IUPAC
456 - New regexp() method to create regular expressions from IUPAC sequences
457 [fangly]
458 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
459 - Code refresh [fangly]
460 * Bio::DB::Taxonomy
461 - Added support for the Greengenes and Silva taxonomies [fangly]
462 * Bio::Tree::TreeFunctionsI
463 - get_lineage_string() represents a lineage as a string [fangly]
464 - add_trait() returns instead of reporting an error when the column
465 number is exceeded in add_trait() [fangly]
466 - Option to support tree leaves without trait [fangly]
467 - Allow ID of 0 in trait files [fangly]
468 * Bio::DB::Taxonomy::list
469 - Misc optimizations [fangly]
470 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
471 * Bio::DB::Taxonomy::*
472 - get_num_taxa() returns the number of taxa in the database [fangly]
473 * Bio::DB::Fasta and Bio::DB::Qual
474 - support indexing an arbitrary list of files [fangly]
475 - user can supply an arbitrary index file name [fangly]
476 - new option to remove index file at the end [fangly]
477 * Bio::DB::Fasta
478 - now handles IUPAC degenerate residues [fangly]
479 * Bio::PrimarySeq and Bio::PrimarySeqI
480 - speed improvements for large sequences [Ben Woodcroft, fangly]
481 * Bio::PrimaryQual
482 - tightened and optimized quality string validation [fangly]
483 * Bio::SeqIO::fasta
484 - new method and option 'block', to create FASTA output with space
485 intervaled blocks (similar to genbank or EMBL) has been implemented.
486 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
487 in favour of the methods 'width' and 'preferred_id_type` respectively.
488 * Bio::FeatureIO::*
489 - moved from bioperl-live into the separate distribution Bio-FeatureIO
490 * Bio::SeqFeature::Annotated
491 - moved from bioperl-live into the separate distribution Bio-FeatureIO
492 * Bio::Cluster::SequenceFamily
493 - improved performance when using get_members with overlapping multiple
494 criteria
495 * Bio::SearchIO::hmmer3
496 - now supports nhmmer [bosborne]
498 [Bug fixes]
500 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
501 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
502 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
503 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
504 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
505 information was lost in a multi-result blast file [Paul Cantalupo]
506 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
507 total gaps [Paul Cantalupo]
508 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
509 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
510 when end of domain indicator is split across lines [Paul Cantalupo]
511 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
512 cjfields]
513 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
514 instances where blank lines are within sequences [cjfields]
515 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
516 types [fangly]
517 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
518 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
519 cjfields]
520 * Various fixes for Stockholm file indexing and processing [bosborne]
521 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
522 breaks parsing [cjfields]
523 * Fix case where Bio::Seq::Meta* objects with no meta information could not
524 be reverse-complemented [fangly]
525 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
526 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
527 when unsure that values will be numerical [fangly]
528 * Fix undef warnings in Bio::SeqIO::embl [fangly]
529 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
530 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
531 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
532 Sallou]
533 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
534 source_tag and display_name must return a string, not undef [fangly]
535 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
536 add_SeqFeature takes a single argument [fangly]
537 * Use cross-platform filenames and temporary directory in
538 Bio::DB::Taxonomy::flatfile [fangly]
539 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
540 properly identified as existing taxa in the database [fangly]
541 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
542 without also passing a lineage to store [fangly]
543 * Prevent passing a directory to the gi2taxid option (-g) of
544 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
545 [fangly]
546 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
547 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
548 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
549 object before trying to access, and no longer returns repeated sequences.
552 1.6.901 May 18, 2011
554 [Notes]
556 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
557 modules using Ace will also be deprecated [lds, cjfields]
558 * Minor bug fix release
559 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
560 * Address Build.PL issues when DBI is not present [hartzell]
561 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
562 * Remove deprecated code for perl 5.14.0 compat [cjfields]
563 * Due to schema changes and lack of support for older versions, support
564 for NeXML 0.9 is only (very) partially implemented.
565 See: https://redmine.open-bio.org/issues/3207
567 [Bug fixes]
569 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
570 docs [genehack, cjfields]
571 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
572 module version from dist_version (probably not the best way to do this,
573 but it seems to work) [rbuels, cjfields]
576 1.6.900 April 14, 201
578 [Notes]
580 * This will probably be the last release to add significant features to
581 core modules; subsequent releases will be for bug fixes alone.
582 We are planning on a restructuring of core for summer 2011, potentially
583 as part of the Google Summer of Code. This may become BioPerl 2.0.
584 * Version bump represents 'just prior to v 1.7'. We may have point
585 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
586 This code essentially is what is on the github master branch.
588 [New features]
590 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
591 * Bio::Tree refactor
592 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
593 - removal of Scalar::Util::weaken code, which was causing odd headaches
594 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
595 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
596 many others]
597 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
598 [Warren Kretzschmar]
599 * Bio::SeqIO::gbxml
600 - bug 2515 - new contribution [Ryan Golhar, jhannah]
601 * Bio::Assembly::IO
602 - support for reading Maq, Sam and Bowtie files [maj]
603 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
604 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
605 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
606 - bug 2726: reading/writing granularity: whole scaffold or one contig
607 at a time [Joshua Udall, fangly]
608 * Bio::OntologyIO
609 - Added parsing of xrefs to OBO files, which are stored as secondary
610 dbxrefs of the cvterm [Naama Menda]
611 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
612 * PAML code updated to work with PAML 4.4d [DaveMessina]
614 [Bug fixes]
616 * [3198] - sort tabular BLAST hits by score [DaveMessina]
617 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
618 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
619 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
620 [cjfields]
621 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
622 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
623 * [3164] - TreeFunctionsI syntax bug [gjuggler]
624 * [3163] - AssemblyIO speedup [fangly]
625 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
626 hyphaltip]
627 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
628 * [3158] - fix EMBL file mis-parsing [cjfields]
629 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
630 cjfields]
631 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
632 * [3148] - URL change for UniProt [cjfields]
633 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
634 * [3136] - HMMer3 parser fixes [kblin]
635 * [3126] - catch description [Toshihiko Akiba]
636 * [3122] - Catch instances where non-seekable filehandles were being
637 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
638 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
639 [dukeleto, rbuels, cjfields]
640 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
641 jhannah]
642 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
643 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
644 cjfields]
645 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
646 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
647 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
648 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
649 * [3086] - EMBL misparsing long tags [kblin, cjfields]
650 * [3085] - CommandExts and array of files [maj, hyphaltip]
651 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
652 for alignment slices [Ha X. Dang, cjfields]
653 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
654 * [3073] - fix parsing of GenBank files from RDP [cjfields]
655 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
656 * [3064] - All-gap midline BLAST report issues [cjfields]
657 * [3063] - BLASt report RID [Razi Khaja, cjfields]
658 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
659 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
660 * [3039] - correct Newick output root node branch length [gjuggler,
661 DaveMessina]
662 * [3038] - SELEX alignment error [Bernd, cjfields]
663 * [3033] - PrimarySeq ID setting [Bernd, maj]
664 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
665 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
666 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
667 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
668 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
669 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
670 PAML 4.4d [DaveMessina]
671 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
672 DaveMessina]
673 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
674 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
675 * [3017] - using threads with Bio::DB::GenBank [cjfields]
676 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
677 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
678 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
679 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
680 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
681 cjfields]
682 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
683 * [2977] - TreeIO issues [DaveMessina]
684 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
685 * [2944] - Bio::Tools::GFF score [cjfields]
686 * [2942] - correct MapTiling output [maj]
687 * [2939] - PDB residue insertion codes [John May, maj]
688 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
689 * [2928] - GuessSeqFormat raw [maj]
690 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
691 * [2922] - open() directive issue [cjfields]
692 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
693 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
694 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
695 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
696 cjfields]
697 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
698 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
699 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
700 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
701 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
702 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
703 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
704 * [2758] - Bio::AssemblyIO ace problems [fangly]
705 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
706 * [2726] - ace file IO [Josh, fangly]
707 * [2700] - Refactor Build.PL [cjfields]
708 * [2673] - addition of simple Root-based clone() method [cjfields]
709 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
710 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
711 * [2594] - Bio::Species memory leak [cjfields]
712 * [2515] - GenBank XML parser [jhannah]
713 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
714 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
715 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
716 cjfields]
717 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
719 [Deprecated]
721 * Bio::Expression modules - these were originally designed to go with the
722 bioperl-microarray suite of tools, however they have never been completed
723 and so have been removed from the distribution. The original code has
724 been moved into the inactive bioperl-microarray suite. [cjfields]
726 [Other]
728 * Repository moved from Subversion (SVN) to
729 http://github.com/bioperl/bioperl-live [cjfields]
730 * Bug database has moved to Redmine (https://redmine.open-bio.org)
731 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
732 Thieme have been moved to their own distribution (Bio-Microarray).
733 [cjfields]
735 1.6.1 Sept. 29, 2009 (point release)
736 * No change from last alpha except VERSION and doc updates [cjfields]
738 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
739 * Fix for silent OBDA bug related to FASTA validation [cjfields]
741 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
742 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
743 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
744 [cjfields]
745 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
747 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
748 * WinXP test fixes [cjfields, maj]
749 * BioPerl.pod added for descriptive information, fixes CPAN indexing
750 [cjfields]
751 * Minor doc fixes [cjfields]
753 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
754 * Fix tests failing due to merging issues [cjfields]
755 * More documentation updates for POD parsing [cjfields]
757 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
758 * Bio::Root::Build
759 - fix YAML meta data generation [cjfields]
761 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
762 * Bio::Align::DNAStatistics
763 - fix divide by zero problem [jason]
764 * Bio::AlignIO::*
765 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
766 * Bio::AlignIO::stockholm
767 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
768 * Bio::Assembly::Tools::ContigSpectrum
769 - function to score contig spectrum [fangly]
770 * Bio::DB::EUtilities
771 - small updates [cjfields]
772 * Bio::DB::Fasta
773 - berkeleydb database now autoindexes wig files and locks correctly
774 [lstein]
775 * Bio::DB::HIV
776 - various small updates for stability; tracking changes to LANL
777 database interface [maj]
778 * Bio::DB::SeqFeature (lots of updates and changes)
779 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
780 - bug 2835 - patch [Dan Bolser]
781 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
782 * Bio::DB::SwissProt
783 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
784 * Bio::Factory::FTLocationFactory
785 - mailing list bug fix [cjfields]
786 * Bio::LocatableSeq
787 - performance work on column_from_residue_number [hartzell]
788 * Bio::Matrix::IO::phylip
789 - bug 2800 - patch to fix phylip parsing [Wei Zou]
790 * Bio::Nexml
791 - Google Summer of Code project from Chase Miller - parsers for Nexml
792 file format [maj, chmille4]
793 * Bio::PopGen
794 - Make Individual, Population, Marker objects AnnotatableI [maj]
795 - simplify LD code [jason]
796 * Bio::RangeI
797 - deal with empty intersection [jason]
798 * Bio::Restriction
799 - significant overhaul of Bio::Restriction system: complete support for
800 external and non-palindromic cutters. [maj]
801 * Bio::Root::Build
802 - CPANPLUS support, no automatic installation [sendu]
803 * Bio::Root::IO
804 - allow IO::String (regression fix) [cjfields]
805 - catch unintentional undef values [cjfields]
806 - throw if non-fh is passed to -fh [maj]
807 * Bio::Root::Root/RootI
808 - small debugging and core fixes [cjfields]
809 * Bio::Root::Test
810 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
811 * Bio::Root::Utilities
812 - bug 2737 - better warnings [cjfields]
813 * Bio::Search
814 - tiling completely refactored, HOWTO added [maj]
815 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
816 will deprecate usage of the older tiling code in the next BioPerl
817 release
818 - small fixes [cjfields]
819 * Bio::SearchIO
820 - Infernal 1.0 output now parsed [cjfields]
821 - new parser for gmap -f9 output [hartzell]
822 - bug 2852 - fix infinite loop in some output [cjfields]
823 - blastxml output now passes all TODO tests [cjfields]
824 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
825 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
826 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
827 * Bio::Seq::LargePrimarySeq
828 - delete tempdirs [cjfields]
829 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
830 * Bio::Seq::Quality
831 - extract regions based on quality threshold value [Dan Bolser, heikki]
832 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
833 * Bio::SeqFeature::Lite
834 - various Bio::DB::SeqFeature-related fixes [lstein]
835 * Bio::SeqFeature::Tools::TypeMapper
836 - additional terms for GenBank to SO map [scain]
837 * Bio::SeqIO::chadoxml
838 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
839 * Bio::SeqIO::embl
840 - support for CDS records [dave_messina, Sylvia]
841 * Bio::SeqIO::fastq
842 - complete refactoring to handle all FASTQ variants, perform validation,
843 write output. API now conforms with other Bio* parsers and the rest of
844 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
845 [cjfields]
846 * Bio::SeqIO::genbank
847 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
848 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
849 * Bio::SeqIO::largefasta
850 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
851 * Bio::SeqIO::raw
852 - add option for 'single' and 'multiple'
853 * Bio::SeqIO::scf
854 - bug 2881 - fix scf round-tripping [Adam Søgren]
855 * Bio::SeqUtils
856 - bug 2766, 2810 - copy over tags from features, doc fixes [David
857 Jackson]
858 * Bio::SimpleAlign
859 - bug 2793 - patch for add_seq index issue [jhannah, maj]
860 - bug 2801 - throw if args are required [cjfields]
861 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
862 [Tristan Lefebure, maj]
863 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
864 - fix POD and add get_SeqFeatures filter [maj]
865 * Bio::Tools::dpAlign
866 - add support for LocatableSeq [ymc]
867 - to be moved to a separate distribution [cjfields, rbuels]
868 * Bio::Tools::EUtilities
869 - fix for two bugs from mail list [Adam Whitney, cjfields]
870 - add generic ItemContainerI interface for containing same methods
871 [cjfields]
872 * Bio::Tools::HMM
873 - fix up code, add more warnings [cjfields]
874 - to be moved to a separate distribution [cjfields, rbuels]
875 * Bio::Tools::Primer3
876 - bug 2862 - fenceposting issue fixed [maj]
877 * Bio::Tools::Run::RemoteBlast
878 - tests for remote RPS-BLAST [mcook]
879 * Bio::Tools::SeqPattern
880 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
881 * Bio::Tools::tRNAscanSE
882 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
883 * Bio::Tree::*
884 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
885 * Bio::Tree::Statistics
886 - several methods for calculating Fitch-based score, internal trait
887 values, statratio(), sum of leaf distances [heikki]
888 * Bio::Tree::Tree
889 - bug 2869 - add docs indicating edge case where nodes can be
890 prematurely garbage-collected [cjfields]
891 - add as_text() function to create Tree as a string in specified format
892 [maj]
893 * Bio::Tree::TreeFunctionsI
894 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
895 Lefebure, maj]
896 * Bio::TreeIO::newick
897 - fix small semicolon issue [cjfields]
898 * scripts
899 - update to bp_seqfeature_load for SQLite [lstein]
900 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
901 - fastam9_to_table - fix for MPI output [jason]
902 - gccalc - total stats [jason]
903 * General Stuff
904 - POD cleanup re: FEEDBACK section [maj, cjfields]
905 - cleanup or fix dead links [cjfields]
906 - Use of no_* methods (indicating 'number of something') is deprecated
907 in favor of num_* [cjfields]
908 - lots of new tests for the above bugs and refactors [everyone!]
909 - new template for Komodo text editor [cjfields]
911 1.6.0 Winter 2009
912 * Feature/Annotation rollback
913 - Problematic changes introduced prior to the 1.5 release have been
914 rolled back. These changes led to subtle bugs involving operator
915 overloading and interface methods.
916 - Behavior is very similar to that for BioPerl 1.4, with tag values
917 being stored generically as simple scalars. Results in a modest
918 speedup.
919 * Bio::Graphics
920 - Split into a separate distribution on CPAN, primarily so development
921 isn't reliant on a complete BioPerl release.
922 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
923 is only available via Subversion (via bioperl-live main trunk)
924 * Bio::Root::Test
925 - Common test bed for all BioPerl modules
926 * Bio::Root::Build
927 - Common Module::Build-based subclass for all BioPerl modules
928 * Bio::DB::EUtilities
929 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
930 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
931 and user agent request posting and retrieval
932 * Test implementation and reorganization
933 - Tests have been reorganized into groups based on classes or use
934 cases.
935 - Automated test coverage is now online:
936 http://www.bioperl.org/wiki/Test_Coverage
937 - After this release, untested modules will be moved into a
938 separate developer distribution until tests can be derived.
939 Also, new modules to be added are expected to have a test suite
940 and adequate test coverage.
942 1.5.2 Developer release
944 Full details of changes since 1.5.1 are available online at:
945 http://www.bioperl.org/wiki/Change_log
946 The following represents a brief overview of the most important changes.
948 o Bio::Map
949 - Overhaul. Brand new system fully allows markers to have multiple
950 positions on multiple maps, and to have relative positions. Should be
951 backward compatible.
953 o Bio::Taxonomy
954 - This module and all the modules in the Taxonomy directory now
955 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
957 o Bio::DB::Taxonomy
959 - Taxonomy.pm
960 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
962 * New methods ancestor(), each_Descendent() and _handle_internal_id().
964 * Allows for different database modules to create Bio::Taxon objects
965 with the same internal id when the same taxon is requested from each.
967 - flatfile.pm
968 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
970 * No longer includes the fake root node 'root'; there are multiple roots
971 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
973 - entrez.pm
974 * get_node() has new option -full
976 * Caches data retrieved from website
978 o Bio::Species
979 - Now a Bio::Taxon. Carries out the species name -> specific name munging
980 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
981 backward compatability in species() method.
983 o Bio::Search and Bio::SearchIO
984 - Overhaul. The existing system has been sped up via some minor changes
985 (mostly gain-of-function to the API). Bio::PullParserI is introduced
986 as a potential eventual replacment for the existing system, though as
987 yet only a Hmmpfam parser exists written using it.
990 1.5.1 Developer release
992 o Major problem with how Annotations were written out with
993 Bio::Seq is fixed by reverting to old behavior for
994 Bio::Annotation objects.
996 o Bio::SeqIO
998 - genbank.pm
999 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
1000 expect at l east 9 spaces at the beginning of a line to
1001 indicate line wrapping.
1003 * Treat multi-line SOURCE sections correctly, this defect broke
1004 both common_name() and classification()
1006 * parse swissprot fields in genpept file
1008 * parse WGS genbank records
1010 - embl.pm
1011 * Changed regexp for ID line. The capturing parentheses are
1012 the same, the difference is an optional repeated-not-semi-
1013 colon expression following the captured \S+. This means the
1014 regexp works when the division looks like /PRO;/ or when the
1015 division looks like /ANG ;/ - the latter is from EMBL
1016 repbase
1018 * fix ID line parsing: the molecule string can have spaces in
1019 it. Like: "genomic DNA"
1021 - swiss.pm: bugs #1727, #1734
1023 - entrezgene.pm
1024 * Added parser for entrezgene ASN1 (text format) files.
1025 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
1027 o Bio::AlignIO
1029 - maf.pm coordinate problem fixed
1031 o Bio::Taxonomy and Bio::DB::Taxonomy
1033 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
1034 can be done via Web without downloading all the sequence.
1036 o Bio::Tools::Run::RemoteBlast supports more options and complies
1037 to changes to the NCBI interface. It is reccomended that you
1038 retrieve the data in XML instead of plain-text BLAST report to
1039 insure proper parsing and retrieval of all information as NCBI
1040 fully expects to change things in the future.
1042 o Bio::Tree and Bio::TreeIO
1044 - Fixes so that re-rooting a tree works properly
1046 - Writing out nhx format from a newick/nexus file will properly output
1047 bootstrap information. The use must move the internal node labels over
1048 to bootstraps.
1049 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
1050 $node->bootstrap($node->id);
1051 $node->id('');
1052 }
1053 - Nexus parsing is much more flexible now, does not care about
1054 LF.
1056 - Cladogram drawing module in Bio::Tree::Draw
1058 - Node height and depth now properly calculated
1060 - fix tree pruning algorithm so that node with 1 child gets merged
1062 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
1063 bugs and improvements were added, see Gbrowse mailing list for most of
1064 these.
1066 o Bio::DB::GFF partially supports GFF3. See information about
1067 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
1069 o Better location parsing in Bio::Factory::FTLocationFactory -
1070 this is part of the engine for parsing EMBL/GenBank feature table
1071 locations. Nested join/order-by/complement are allowed now
1073 o Bio::PrimarySeqI->translate now takes named parameters
1075 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
1076 reconstruction) is now supported. Parsing different models and
1077 branch specific parametes are now supported.
1079 o Bio::Factory::FTLocationFactory - parse hierarchical locations
1080 (joins of joins)
1082 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
1083 for getter/setter functions
1085 o Bio::SearchIO
1087 - blast bug #1739; match scientific notation in score
1088 and possible e+ values
1090 - blast.pm reads more WU-BLAST parameters and parameters, match
1091 a full database pathname,
1093 - Handle NCBI WEB and newer BLAST formats specifically
1094 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
1096 - psl off-by-one error fixed
1098 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
1099 and HSPs can be constructed from them.
1101 - HSPs query/hit now have a seqdesc field filled out (this was
1102 always available via $hit->description and
1103 $result->query_description
1105 - hmmer.pm can parse -A0 hmmpfam files
1107 - Writer::GbrowseGFF more customizeable.
1109 o Bio::Tools::Hmmpfam
1110 make e-value default score displayed in gff, rather than raw score
1111 allow parse of multiple records
1114 1.5 Developer release
1116 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
1117 provide Jukes-Cantor and Kimura pairwise distance methods,
1118 respectively.
1120 o Bio::AlignIO support for "po" format of POA, and "maf";
1121 Bio::AlignIO::largemultifasta is a new alternative to
1122 Bio::AlignIO::fasta for temporary file-based manipulation of
1123 particularly large multiple sequence alignments.
1125 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
1126 be treated similarly as an assembled contig.
1128 o Bio::CodonUsage provides new rare_codon() and probable_codons()
1129 methods for identifying particular codons that encode a given
1130 amino acid.
1132 o Bio::Coordinate::Utils provides new from_align() method to build
1133 a Bio::Coordinate pair directly from a
1134 Bio::Align::AlignI-conforming object.
1136 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
1137 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
1138 web service using standard Pubmed query syntax, and retrieve
1139 results as XML.
1141 o Bio::DB::GFF has various sundry bug fixes.
1143 o Bio::FeatureIO is a new SeqIO-style subsystem for
1144 writing/reading genomic features to/from files. I/O classes
1145 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
1146 classes only read/write Bio::SeqFeature::Annotated objects.
1147 Notably, the GFF v3 class requires features to be typed into the
1148 Sequence Ontology.
1150 o Bio::Graph namespace contains new modules for manipulation and
1151 analysis of protein interaction graphs.
1153 o Bio::Graphics has many bug fixes and shiny new glyphs.
1155 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
1156 indexing for HMMER reports and FASTA qual files, respectively.
1158 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
1159 new objects that can be placed within a Bio::Map::MapI-compliant
1160 genetic/physical map; Bio::Map::Physical provides a new physical
1161 map type; Bio::MapIO::fpc provides finger-printed clone mapping
1162 import.
1164 o Bio::Matrix::PSM provide new support for postion-specific
1165 (scoring) matrices (e.g. profiles, or "possums").
1167 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
1168 be instantiated without explicitly using Bio::OntologyIO. This
1169 is possible through changes to Bio::Ontology::OntologyStore to
1170 download ontology files from the web as necessary. Locations of
1171 ontology files are hard-coded into
1172 Bio::Ontology::DocumentRegistry.
1174 o Bio::PopGen includes many new methods and data types for
1175 population genetics analyses.
1177 o New constructor to Bio::Range, unions(). Given a list of
1178 ranges, returns another list of "flattened" ranges --
1179 overlapping ranges are merged into a single range with the
1180 mininum and maximum coordinates of the entire overlapping group.
1182 o Bio::Root::IO now supports -url, in addition to -file and -fh.
1183 The new -url argument allows one to specify the network address
1184 of a file for input. -url currently only works for GET
1185 requests, and thus is read-only.
1187 o Bio::SearchIO::hmmer now returns individual Hit objects for each
1188 domain alignment (thus containing only one HSP); previously
1189 separate alignments would be merged into one hit if the domain
1190 involved in the alignments was the same, but this only worked
1191 when the repeated domain occured without interruption by any
1192 other domain, leading to a confusing mixture of Hit and HSP
1193 objects.
1195 o Bio::Search::Result::ResultI-compliant report objects now
1196 implement the "get_statistics" method to access
1197 Bio::Search::StatisticsI objects that encapsulate any
1198 statistical parameters associated with the search (e.g. Karlin's
1199 lambda for BLAST/FASTA).
1201 o Bio::Seq::LargeLocatableSeq combines the functionality already
1202 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
1204 o Bio::SeqFeature::Annotated is a replacement for
1205 Bio::SeqFeature::Generic. It breaks compliance with the
1206 Bio::SeqFeatureI interface because the author was sick of
1207 dealing with untyped annotation tags. All
1208 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
1209 compliant, and accessible through Bio::Annotation::Collection.
1211 o Bio::SeqFeature::Primer implements a Tm() method for primer
1212 melting point predictions.
1214 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
1215 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
1217 o Bio::Taxonomy::Node now implements the methods necessary for
1218 Bio::Species interoperability.
1220 o Bio::Tools::CodonTable has new reverse_translate_all() and
1221 make_iupac_string() methods.
1223 o Bio::Tools::dpAlign now provides sequence profile alignments.
1225 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
1227 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
1228 parsers.
1230 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
1231 for designing small inhibitory RNA.
1233 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
1234 methods based on a distance matrix.
1236 o Bio::Tree::Statistics provides an assess_bootstrap() method to
1237 calculate bootstrap support values on a guide tree topology,
1238 based on provided bootstrap tree topologies.
1240 o Bio::TreeIO now supports the Pagel (PAG) tree format.
1242 1.4 branch
1244 1.4.1
1246 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
1248 o Bio::Graphics will work with gd1 or gd2
1250 o Bio::SearchIO
1251 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
1252 (RF lines alone)
1253 - blast.pm Parse multi-line query fields properly
1254 - small speed improvements to blasttable.pm and others
1256 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
1257 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
1258 supporting more complex queries
1261 1.4. Stable major release
1263 Since initial 1.2.0, 3000 separate changes have been made to make this release.
1265 o installable scripts
1267 o global module version from Bio::Root:Version
1269 o Bio::Graphics
1270 - major improvements; SVG support
1272 o Bio::Popgen
1273 - population genetics
1274 - support several population genetics types of questions.
1275 - Tests for statistical neutrality of mutations
1276 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
1277 Tests of population structure (Wright's F-statistic: Fst) is in
1278 Bio::PopGen::PopStats. Calculating composite linkage
1279 disequilibrium (LD) is available in Bio::PopGen::Statistics as
1280 well.
1281 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1282 and csv (comma delimited formatted) data.
1284 - a directory for implementing population simulations has
1285 been added Bio::PopGen::Simulation and 2 simulations - a
1286 Coalescent and a simple single-locus multi-allele genetic drift
1287 simulation have been provided. This replaces the code in
1288 Bio::Tree::RandomTree which has been deprecated until proper
1289 methods for generating random phylogenetic trees are
1290 implemented.
1292 o Bio::Restriction
1293 - new restrion analysis modules
1295 o Bio::Tools::Analysis
1296 - web based DNA and Protein analysis framework and several
1297 implementations
1299 o Bio::Seq::Meta
1300 - per residue annotable sequences
1302 o Bio::Matrix
1303 - Bio::Matrix::PSM - Position Scoring Matrix
1304 - Bio::Matrix::IO has been added for generalized parsing of
1305 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1306 initial implementations for parsing BLOSUM/PAM and Phylip
1307 Distance matricies respectively. A generic matrix
1308 implementation for general use was added in
1309 Bio::Matrix::Generic.
1311 o Bio::Ontology
1312 - major changes
1314 o Bio:Tree
1316 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1317 - small inhibitory RNA
1319 o Bio::SeqFeature::Tools
1320 - seqFeature mapping tools
1321 - Bio::SeqFeature::Tools::Unflattener.pm
1322 -- deal with mapping GenBank feature collections into
1323 Chado/GFF3 processable feature sets (with SO term mappings)
1325 o Bio::Tools::dpAlign
1326 - pure perl dynamic programming sequence alignment
1327 - needs Bioperl-ext
1329 o new Bio::SearchIO formats
1330 - axt and psl: UCSC formats.
1331 - blasttable: NCBI -m 8 or -m 9 format from blastall
1333 o new Bio::SeqIO formats
1334 - chado, tab, kegg, tigr, game
1335 - important fixes for old modules
1337 o Bio::AlignIO: maf
1339 o improved Bio::Tools::Genewise
1341 o Bio::SeqIO now can recongnize sequence formats automatically from
1342 stream
1344 o new parsers in Bio::Tools:
1345 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1347 o Bio::DB::Registry bugs fixed
1348 - BerkeleyDB-indexed flat files can be used by the OBDA system
1349 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1350 used by the OBDA system
1352 o several new HOWTOs
1353 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1354 Databases
1356 o hundreds of new and improved files
1359 o
1360 o Bio::Tree::AlleleNode has been updated to be a container of
1361 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1364 1.2 Branch
1366 1.2.3 Stable release update
1367 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1368 handling.
1369 o Bug #1477 - Sel --> Sec abbreviation fixed
1370 o Fix bug #1487 where paring in-between locations when
1371 end < start caused the FTLocationFactory logic to fail.
1372 o Fix bug #1489 which was not dealing with keywords as an
1373 arrayref properly (this is fixed on the main trunk because
1374 keywords returns a string and the array is accessible via
1375 get_keywords).
1376 o Bio::Tree::Tree memory leak (bug #1480) fixed
1377 Added a new initialization option -nodelete which
1378 won't try and cleanup the containing nodes if this
1379 is true.
1380 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1381 this was only present on the branch for the 1.2.1 and 1.2.2 series
1382 - Also merged main trunk changes to the branch which make
1383 newick -> nhx round tripping more effective (storing branch length
1384 and bootstrap values in same locate for NodeNHX and Node
1385 implementations.) Fixes to TreeIO parsing for labeled internal
1386 also required small changes to TreeIO::nhx. Improved
1387 tests for this module as well.
1388 o Bio::SearchIO
1389 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1390 gapped blast properly (was losing hit significance values due to
1391 the extra unexpeted column).
1392 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1393 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1394 although doesn't try to correct it - will get the negative
1395 number for you. Added a test for this as well.
1396 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1397 has no top-level family classification scores but does have scores and
1398 alignments for individual domains.
1399 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1400 regular expression to match the line was missing the possibility of
1401 an extra space. This is rare, which is why we probably did not
1402 catch it before.
1403 - BLAST parsing picks up more of the statistics/parameter fields
1404 at the bottom of reports. Still not fully complete.
1405 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1406 were fixed to include many improvements and added flexiblity
1407 in outputting the files. Bug #1495 was also fixed in the process.
1408 o Bio::DB::GFF
1409 - Update for GFF3 compatibility.
1410 - Added scripts for importing from UCSC and GenBank.
1411 - Added a 1.2003 version number.
1412 o Bio::Graphics
1413 - Updated tutorial.
1414 - Added a 1.2003 version number.
1415 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1416 properly writing keywords out.
1417 o Bio::SeqIO::genbank
1418 - Fixed bug/enhancement #1513 where dates of
1419 the form D-MMM-YYYY were not parsed. Even though this is
1420 invalid format we can handle it - and also cleanup the date
1421 string so it is properly formatted.
1422 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1423 and written with Genbank format. Similarly bug #1515 is fixed to
1424 parse in the ORIGIN text.
1425 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1426 to specify the ID type, one of (accession accession.version
1427 display primary). See Bio::SeqIO::preferred_id_type method
1428 documentation for more information.
1429 o Unigene parsing updated to handle file format changes by NCBI
1431 1.2.2 Stable release update
1433 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1434 - auto-discover ontology name
1435 - bug in parsing relationships when certain characters are in the term
1436 - fixed hard-coded prefix for term identifiers
1437 - various smaller issues
1439 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1440 of Bio::Ontology::TermI
1442 o brought the OBDA Registry code up to latest specs
1444 o Bio::DB::GenBank
1445 - eutils URL change
1446 - accession number retrieval fixed
1448 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1450 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1451 #1459 which now properly report alignment start/end info
1452 for translated BLAST/FASTA searches.
1454 o Bio::TreeIO::newick can parse labeled internal nodes
1456 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1457 for BLASTX if if you provide -report_type => 'BLASTX' when
1458 initializing a BPbl2seq object. Bioperl 1.3 will have better
1459 support for bl2seq in the SearchIO system.
1461 o Bio::Root::IO support a -noclose boolean flag which will not
1462 close a filehandle upon object cleanup - useful when sharing
1463 a filehandle among objects. Additionally code added s.t.
1464 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1466 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1468 o Bio::SeqIO::genbank
1469 - bug #1456 fixed which generated extra sequence lines
1470 - write moltype correctly for genpept
1472 1.2.1 Stable release update
1474 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1476 o Addition from main trunk of Ontology objects, principly to allow
1477 BioSQL releases against 1.2.1
1479 o Fixes and cleanup of Bio::Coordinate modules
1481 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1482 the primary accession number
1484 o Other bug fixes, including bpindex GenBank fix
1486 o Bio::SeqIO::genbank bug #1389 fixed
1488 1.2 Stable major release
1490 o More functionality added to Bio::Perl, the newbie module
1492 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1493 Support for New Hampshire Extended (NHX) format parsing.
1495 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1496 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1497 Hmmpfam parser.
1499 o New ontology parsing Bio::Ontology
1501 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1502 multi-report (mlib) fasta reports, support for waba and exonerate.
1504 o Bio::ClusterIO for parsing Unigene clusters
1506 o Bio::Assembly added for representing phrap and ace assembly clusters.
1508 o Rudimentary support for writing Chado XML (see
1509 GMOD project: www.gmod.org for more information)
1511 o Bio::Coordinate for mapping between different coordinate systems such
1512 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1513 features into different coordinate systems.
1515 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1516 with the get_Stream_by_query method and supports the latest
1517 NCBI eutils interface.
1519 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1520 object for extracting subsets of features : currently only
1521 supports extraction by location.
1523 1.1.1 Developer release
1525 o Deprecated modules are now listed in the DEPRECATED file
1527 o New HowTo documents located in doc/howto describing
1528 a domain of Bioperl.
1530 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1531 and all old bugs are searchable through the bugzilla interface.
1533 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1534 have been addressed.
1536 o Support for Genewise parsing in Bio::Tools::Genewise
1538 o Start of Ontology framework with Bio::Ontology
1540 o Speedup to the Bio::Root::Root object method _rearrange.
1541 A global _load_module method was implemented to simplify the
1542 dynamic loading of modules ala Bio::SeqIO::genbank. This
1543 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1544 etc).
1546 o Several performance improvements to sequence parsing in Bio::SeqIO.
1547 Attempt to speedup by reducing object creation overhead.
1549 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1550 method for sequence retrieval with their E-utils CGI scripts.
1551 More work to support Entrez queries to their fullest is planned
1552 before 1.2 release.
1554 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1556 1.1 Developer release
1558 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1559 this separation removes some of the complexity in our test suite
1560 and separates the core modules in bioperl from those that need
1561 external programs to run.
1563 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1564 not run into trouble running the makefile
1566 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1567 read,create,and write locations for grouped/split locations
1568 (like mRNA features on genomic sequence).
1570 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1571 and PAML (codeml,aaml, etc) parsing.
1573 o Bio::Tree:: objects expanded to handle testing monophyly,
1574 paraphyly, least common ancestor, etc.
1576 o Bio::Coordinate for mapping locations from different coordinate spaces
1578 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1579 added for parsing hmmpfam and hmmsearch output.
1581 o Bio::SearchIO::Writer::TextResultWriter for outputting
1582 a pseudo-blast textfile format
1585 1.0.2 Bug fix release
1587 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1588 in this release will not work after December 2002 when NCBI
1589 shuts off the old Entrez cgi scripts. We have already fixed
1590 on our main development branch and the functionality will be
1591 available in the next stable bioperl release (1.2) slated for
1592 Fall 2002.
1594 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1595 testset by Robin Emig. These were fixed as was the get_aln
1596 method in Bio::Search::HSP::GenericHSP to handle the extra
1597 context sequence that is provided with a FastA alignment.
1599 o Migrating differences between Bio::Search::XX::BlastXX to
1600 Bio::Search::XX::GenericXX objects. This included mechanism
1601 to retrieve whole list of HSPs from Hits and whole list of Hits from
1602 Results in addition to the current next_XX iterator methods that
1603 are available. Added seq_inds() method to GenericHSP which identifies
1604 indexes in the query or hit sequences where conserved,identical,gaps,
1605 or mismatch residues are located (adapted from Steve Chervitz's
1606 implementation in BlastHSP).
1608 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1609 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1611 o Bio::Graphics glyph set improved and extended for GBrowse release
1613 o Bio::Tree::Tree get_nodes implementation improvement thanks
1614 to Howard Ross notice performance problem when writing out
1615 unbalanced trees.
1617 o Bio::Location::Fuzzy::new named parameter -loc_type became
1618 -location_type, Bio::Location::Simple::new named parameter
1619 -seqid becamse -seq_id.
1621 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1622 was mis-detecting that gaps should be placed at the beginning of
1623 the alignment when the best alignment starts internally in the
1624 sequence.
1626 1.0.1 Bug fix release
1628 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1630 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1631 and mixed (3.3 - 3.4) versions of FASTA.
1633 o Small API change to add methods for completeness across
1634 implementations of Bio::Search objects. These new methods
1635 in the interface are implemented by the GenericXX object as well
1636 as the BlastXX objects.
1637 * Bio::Search::Result::ResultI
1638 - hits() method returns list of all Hits (next_hit is an
1639 iterator method)
1641 * Bio::Search::Hit::HitI
1642 - hsps() method returns list of all HSPs (next_hsp is an
1643 iterator method)
1645 o The Bio::SearchIO::Writer classes have been fixed to handle results
1646 created from either psiblast (Search::BlastXX objects) or
1647 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1648 has to be done here to make it work properly and will nee major
1649 API changes.
1651 o Bugs in Bio::Tools::HMMER fixed, including
1652 * #1178 - Root::IO destructor wasn't being called
1653 * #1034 - filter_on_cutoff now behaves properly
1655 o Bio::SeqFeature::Computation initialization args fixed and
1656 tests added.
1658 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1660 o Updated FAQ with more example based answers to typical questions
1662 o Bug #1202 was fixed which would improperly join together qual values
1663 parsed by Bio::SeqIO::qual when a trailing space was not present before
1664 the newline.
1666 1.0.0 Major Stable Release
1668 This represents a major release of bioperl with significant
1669 improvements over the 0.7.x series of releases.
1671 o Bio::Tools::Blast is officially deprecated. Please see
1672 Bio::SearchIO for BLAST and FastA parsing.
1674 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1675 Bio::LocationI objects as well as start/end.
1677 o Bio::Biblio contains modules for Bibliographic data.
1678 Bio::DB::Biblio contains the query modules. Additionally one can
1679 parse medlinexml from the ebi bibliographic query service (BQS)
1680 system and Pubmed xml from NCBI. See Martin Senger's
1681 documentation in Bio::Biblio for more information.
1683 o Bio::DB::Registry is a sequence database registry part of
1684 Open Bioinformatics Database Access. See
1685 http://obda.open-bio.org for more information.
1687 o File-based and In-Memory Sequence caching is provided by
1688 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1689 local database.
1691 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1692 been added by Lincoln Stein.
1694 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1696 o A FAQ has been started and is included in the release to provide
1697 a starting point for frequent questions and issues.
1699 0.9.3 Developer's release
1701 o Event based parsing system improved (SearchIO). With parsers for
1702 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1703 Additionally a lazy parsing system for text and html blast reports was
1704 added and is called psiblast (name subject to change in future releases).
1706 o Bio::Search objects improved and standardized with associated Interfaces
1707 written. The concept of a search "Hit" was standardized to be called
1708 "hit" consistently and the use of "subject" was deprecated in all active
1709 modules.
1711 o Bio::Structure added (since 0.9.1) for Protein structure objects
1712 and PDB parser to retrieve and write these structures from data files.
1714 o Several important Bio::DB::GFF bug fixes for handling features that
1715 are mapped to multiple reference points. Updated mysql adaptor
1716 so as to be able to store large (>100 megabase) chunks of DNA into
1717 Bio::DB::GFF databases.
1719 0.9.2 Developer's release
1721 o Bio::Search and Bio::SearchIO system introduced for event based
1722 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1723 in text and XML and FASTA reports in standard output format.
1725 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1726 generator is included in Bio::TreeIO::RandomTrees and a
1727 statistics module for evaluating.
1729 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1730 server for DAS servers.
1732 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1733 files. The entire BPlite system migrated to using Bio::Root::IO
1734 for the data stream.
1736 o Bio::Tools::Alignment for Consed and sequence Trimming
1737 functionality.
1739 o Bio::Structure for Protein structure information and parsing
1741 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1742 cgi-bin entry point which should be more reliable.
1744 o Bio::Map and Bio::MapIO for biological map navigation and a
1745 framework afor parsing them in. Only preliminary work here.
1747 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1748 Future work will integrate Pise and allow submission of analysis on
1749 remote servers.
1751 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1752 introduced as new objects for handling Sequence Annotation
1753 information (dblinks, references, etc) and is more robust that
1754 previous system.
1756 o Bio::Tools::FASTAParser introduced.
1758 o Scripts from the bioperl script submission project and new
1759 scripts from bioperl authors are included in "scripts" directory.
1761 o Factory objects and interfaces are being introduced and are more
1762 strictly enforced.
1764 o Bio::Root::Root introduced as the base object while
1765 Bio::Root::RootI is now simply an interface.
1767 o Bio::DB::RefSeq provides database access to copy of the NCBI
1768 RefSeq database using the EBI dbfetch script.
1770 0.9.0 Developer's release
1772 o perl version at least 5.005 is now required instead of perl 5.004
1774 o Bio::Tools::Run::RemoteBlast is available for running remote
1775 blast jobs at NCBI.
1777 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1779 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1780 Also added are related modules UTR3, UTR5, Exon, Intron,
1781 Promotor, PolyA and Transcript.
1783 o Speedup of translate method in PrimarySeq
1785 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1786 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1788 o Various fixes to Variation toolkit
1790 o Bio::DB::EMBL provides database access to EMBL sequence data.
1791 Bio::DB::Universal provides a central way to point to indexes
1792 and dbs in a single interface.
1794 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1796 o Bio::Factory::EMBOSS is still in design phase as is
1797 Bio::Factory::ApplicationFactoryI
1799 o Dia models for bioperl design are provided in the models/ directory
1801 0.7.2 Bug fix release
1803 o documentation fixes in many modules - SYNOPSIS code verified
1804 to be runnable in many (but not all modules)
1806 o corrected MANIFEST file from 0.7.1 release
1808 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1809 split locations
1811 o Bio::SeqIO::genbank
1812 * Correct parsing and writing of genbank format with protein data
1813 * moltype and molecule separation
1815 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1817 o Bio::SimpleAlign fixed to correctly handle consensus
1818 sequence calculation
1820 o Bio::Tools::HMMER supports hmmer 2.2g
1822 o Bio::Tools::BPlite to support report type specific parsing. Most
1823 major changes are not on the 0.7 branch.
1825 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1826 with File::Spec
1828 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1829 in several types of mutations:
1830 1.) AA level: deletion, complex
1831 2.) AA level: complex, inframe
1832 3.) RNA level: silent
1834 o BPbl2seq parsing of empty reports will not die, but will return
1835 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1836 $report->query() and $report->subject() methods. So an easy
1837 way to test if report was empty is to see if
1838 $report->query->seqname is undefined.
1840 0.7.1 Bug fix release
1842 o Better parsing of genbank/EMBL files especially fixing bugs
1843 related to Feature table parsing and locations on remote
1844 sequences. Additionally, species name parsing was better.
1846 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1847 which include a number of header lines.
1849 o More strict genbank and EMBL format writing (corrected number of
1850 spaces where appropriate).
1852 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1853 for related BPlite BUGS that are unresolved in this release.
1855 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1856 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1857 use expasy mirrors or EBI dbfetch cgi-script.
1859 o A moderate number of documentation improvements were made as
1860 well to provide a better code synopsis in each module.
1863 0.7 Large number of changes, including refactoring of the
1864 Object system, new parsers, new functionality and
1865 all round better system. Highlights are:
1868 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1869 Bio::Root::IO for I/O and file/handle capabilities.
1871 o Imported BPlite modules from Ian Korf for BLAST
1872 parsing. This is considered the supported BLAST parser;
1873 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1875 o Improved Sequence Feature model. Added complete location
1876 modelling (with fuzzy and compound locations). See
1877 Bio::LocationI and the modules under Bio/Location. Added
1878 support in Genbank/EMBL format parsing to completely parse
1879 feature tables for complex locations.
1881 o Moved special support for databanks etc to specialized modules under
1882 Bio/Seq/. One of these supports very large sequences through
1883 a temporary file as a backend.
1885 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1886 CDS retrieval and exon shuffling.
1888 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1890 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1891 DB/GDB (the latter has platform-specific limitations).
1893 o New analysis parser framework for HT sequence annotation (see
1894 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1896 o New Alignment IO framework
1898 o New Index modules (Swissprot)
1900 o New modules for running Blast within perl
1901 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1902 Multiple Sequence Alignment tools ClustalW and TCoffee
1903 (Bio::Tools::Run::Alignment).
1905 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1906 documentation across the package.
1908 o Much improved cross platform support. Many known incompatibilities
1909 have been fixed; however, NT and Mac do not work across the entire
1910 setup (see PLATFORMS).
1912 o Many bug fixes, code restructuring, etc. Overall stability and
1913 maintainability benefit a lot.
1915 o A total of 957 automatic tests
1918 0.6.2
1920 There are very few functionality changes but a large
1921 number of software improvements/bug fixes across the package.
1923 o The EMBL/GenBank parsing are improved.
1925 o The Swissprot reading is improved. Swissprot writing
1926 is disabled as it doesn't work at all. This needs to
1927 wait for 0.7 release
1929 o BLAST reports with no hits are correctly parsed.
1931 o Several other bugs of the BLAST parser (regular expressions, ...)
1932 fixed.
1934 o Old syntax calls have been replaced with more modern syntax
1936 o Modules that did not work at all, in particular the Sim4
1937 set have been removed
1939 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1940 have improved compliance with interface specs and documentation
1942 o Mailing list documentation updated throughout the distribution
1944 o Most minor bug fixes have happened.
1946 o The scripts in /examples now work and have the modern syntax
1947 rather than the deprecated syntax
1950 0.6.1 Sun April 2 2000
1952 o Sequences can have Sequence Features attached to them
1953 - The sequence features can be read from or written to
1954 EMBL and GenBank style flat files
1956 o Objects for Annotation, including References (but not
1957 full medline abstracts), Database links and Comments are
1958 provided
1960 o A Species object to represent nodes on a taxonomy tree
1961 is provided
1963 o The ability to parse HMMER and Sim4 output has been added
1965 o The Blast parsing has been improved, with better PSI-BLAST
1966 support and better overall behaviour.
1968 o Flat file indexed databases provide both random access
1969 and sequential access to their component sequences.
1971 o A CodonTable object has been written with all known
1972 CodonTables accessible.
1974 o A number of new lightweight analysis tools have been
1975 added, such as molecular weight determination.
1977 The 0.6 release also has improved software engineering
1979 o The sequence objects have been rewritten, providing more
1980 maintainable and easier to implement objects. These
1981 objects are backwardly compatible with the 0.05.1 objects
1983 o Many objects are defined in terms of interfaces and then
1984 a Perl implementation has been provided. The interfaces
1985 are found in the 'I' files (module names ending in 'I').
1987 This means that it is possible to wrap C/CORBA/SQL access
1988 as true "bioperl" objects, compatible with the rest of
1989 bioperl.
1991 o The SeqIO system has been overhauled to provide better
1992 processing and perl-like automatic interpretation of <>
1993 over arguments.
1995 o Many more tests have been added (a total of 172 automatic
1996 tests are now run before release).
2000 0.05.1 Tue Jun 29 05:30:44 1999
2001 - Central distribution now requires Perl 5.004. This was
2002 done to get around 5.003-based problems in Bio/Index/*
2003 and SimpleAlign.
2004 - Various bug fixes in the Bio::Tools::Blast modules
2005 including better exception handling and PSI-Blast
2006 support. See Bio/Tools/Blast/CHANGES for more.
2007 - Fixed the Parse mechanism in Seq.pm to use readseq.
2008 Follow the instructions in README for how to install
2009 it (basically, you have to edit Parse.pm).
2010 - Improved documentation of Seq.pm, indicating where
2011 objects are returned and where strings are returned.
2012 - Fixed uninitialized warnings in Bio::Root::Object.pm
2013 and Bio::Tools::SeqPattern.pm.
2014 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
2016 0.05 Sun Apr 25 01:14:11 1999
2017 - Bio::Tools::Blast modules have less memory problems
2018 and faster parsing. Webblast uses LWP and supports
2019 more functionality. See Bio/Tools/Blast/CHANGES for more.
2020 - The Bio::SeqIO system has been started, moving the
2021 sequence reformatting code out of the sequence object
2022 - The Bio::Index:: system has been started, providing
2023 generic index capabilities and specifically works for
2024 Fasta formatted databases and EMBL .dat formatted
2025 databases
2026 - The Bio::DB:: system started, providing access to
2027 databases, both via flat file + index (see above) and
2028 via http to NCBI
2029 - The scripts/ directory, where industrial strength scripts
2030 are put has been started.
2031 - Many changes - a better distribution all round.
2033 0.04.4 Wed Feb 17 02:20:13 1999
2034 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
2035 (see Bio::Tools::Blast::CHANGES).
2036 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
2037 - Beefed up the t/Fasta.t test script.
2038 - Small fix in Bio::Seq::type() (now always returns a string).
2039 - Changed Bio::Root::Utilities::get_newline_char() to
2040 get_newline() since it could return more than one char.
2041 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
2042 - Changed default timeout to 20 seconds (was 3).
2043 - Moved lengthy modification notes to the bottom of some files.
2044 - Fixed SimpleAlign write_fasta bug.
2045 - Beefed up SimpleAlign.t test
2047 0.04.3 Thu Feb 4 07:48:53 1999
2048 - Bio::Root::Object.pm and Global.pm now detect when
2049 script is run as a CGI and suppress output that is only
2050 appropriate when running interactively.
2051 - Bio::Root::Err::_set_context() adds name of script ($0).
2052 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
2053 regarding the use of the static objects via the qw(:obj) tag.
2054 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
2055 CORE::reverse, avoiding Perl warnings.
2056 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
2057 example scripts (see Bio::Tools::Blast::CHANGES).
2058 - examples/seq/seqtools.pl no longer always warns about using
2059 -prot or -nucl command-line arguments; only when using the
2060 -debug argument.
2061 - Methods added to Bio::Root::Utilities: create_filehandle(),
2062 get_newline_char(), and taste_file() to generalize filehandle
2063 creation and autodetect newline characters in files/streams
2064 (see bug report #19).
2065 - Bio::Root::IOManager::read() now handles timeouts and uses
2066 Utilities::create_filehandle().
2067 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
2068 of hardwiring in "\n".
2069 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
2071 0.04.2 Wed Dec 30 02:27:36 1998
2072 - Bug fixes in Bio::Tools::Blast modules, version 0.073
2073 (see Bio::Tools::Blast::CHANGES).
2074 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
2075 to CORE::reverse (prevents ambiguous warnings with 5.005).
2076 - Appending '.tmp.bioperl' to temporary files created by
2077 Bio::Root::Utilities::compress() or uncompress() to
2078 make it easy to identify & cleanup these files as needed.
2079 - Developers: Created CVS branch release-0-04-bug from
2080 release-0-04-1. Before making bug fixes to the 0.04.1 release,
2081 be sure to cvs checkout this branch into a clean area.
2083 0.04.1 Wed Dec 16 05:39:15 1998
2084 - Bug fixes in Bio::Tools::Blast modules, version 0.072
2085 (see Bio::Tools::Blast::CHANGES).
2086 - Compile/SW/Makefile.PL now removes *.o and *.a files
2087 with make clean.
2089 0.04 Tue Dec 8 07:49:19 1998
2090 - Lots of new modules added including:
2091 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
2092 and Bio/Compile directory containing XS-linked C code for
2093 creating Smith-Waterman sequence alignments from within Perl.
2094 * Steve Chervitz's Blast distribution has been incorporated.
2095 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
2096 - Bio/examples directory for demo scripts for all included modules.
2097 - Bio/t directory containing test suit for all included modules.
2098 - For changes specific to the Blast-related modules prior to
2099 incorporation in this central distribution, see the CHANGES
2100 file in the Bio/Tools/Blast directory.
2102 0.01 Tue Sep 8 14:23:22 1998
2103 - original version from central CVS tree; created by h2xs 1.18