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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::DB::Taxonomy::sqlite
69 Bio::Index::Stockholm
70 Bio::LiveSeq::*
71 Bio::Phenotype::*
72 Bio::Root::Build
73 Bio::SearchDist
74 Bio::SeqIO::abi
75 Bio::SeqIO::alf
76 Bio::SeqIO::ctf
77 Bio::SeqIO::exp
78 Bio::SeqIO::pln
79 Bio::SeqIO::ztr
80 Bio::Tools::AlignFactory
81 Bio::Tools::Phylo::Gumby
82 Bio::Tools::dpAlign
83 Bio::Tools::pSW
84 Bio::Variation::*
86 * The following programs have been removed:
88 bp_bulk_load_gff
89 bp_das_server
90 bp_fast_load_gff
91 bp_flanks
92 bp_genbank2gff
93 bp_generate_histogram
94 bp_load_gff
95 bp_meta_gff
96 bp_netinstall
97 bp_process_wormbase
98 bp_seqfeature_delete
99 bp_seqfeature_gff3
100 bp_seqfeature_load
102 * The following modules are no longer dependencies:
104 Bio::SeqIO::staden::read
105 DBD::Pg
106 DBD::SQLite
107 MIME::Base64
108 Memoize
109 Text::ParseWords
111 [Code changes]
113 * The deobfuscator has been removed.
115 * The script `bp_blast2tree` has been moved to the BioPerl-Run
116 distribution since it's mainly a wrapper to modules in there.
118 * The entire Bio::PopGen namespace, Bio::Tree::AlleleNode
119 module, and scripts bp_composite_LD and bp_heterogeneity_test
120 have been moved into a separate distribution named Bio-PopGen.
122 * All modules related to the NeXML format have been moved into a
123 separate distribution named Bio-NeXMLIO. These are:
125 * Bio::AlignIO::nexml
126 * Bio::Nexml::Factory
127 * Bio::NexmlIO
128 * Bio::SeqIO::nexml
129 * Bio::TreeIO::nexml
131 This also means BioPerl is no longer dependent on Bio-Phylo.
133 * All modules interfacing to ACeDB servers have been moved into a
134 separate distribution named Bio-DB-Ace. These are:
136 * Bio::DB::Ace
137 * Bio::DB::GFF::Adaptor::ace
138 * Bio::DB::GFF::Adaptor::dbi::mysqlace
139 * Bio::DB::GFF::Adaptor::dbi::oracleace
141 This also means BioPerl is no longer dependent on AcePerl.
143 * The module Bio::Draw::Pictogram has been moved to a separate
144 distribution named Bio-Draw-Pictogram. This also means BioPerl
145 is no longer dependent on SVG.
147 * The module Bio::Tree::Draw::Cladogram has been moved to a
148 separate distribution named Bio-Tree-Draw-Cladogram. This also
149 means BioPerl is no longer dependent on PostScript.
151 * The module Bio::TreeIO::svggraph has been moved to a separate
152 distribution named Bio-TreeIO-svggraph. This also means that
153 BioPerl is no longer dependent on SVG-Graph and Tree-DAG_Node.
155 * The module Bio::SeqIO::excel has been moved to a separate
156 distribution named Bio-SeqIO-excel. This also means that
157 BioPerl is no longer dependent on Spreadsheet-ParseExcel.
159 * The entire Bio::PhyloNetwork namespace has been moved to a
160 separate distribution named Bio-PhyloNetwork. This also means
161 that BioPerl is no longer dependent on Algorithm::Munkres,
162 GraphViz, and Array::Compare.
164 * The entire Bio::Asembly namespace has been moved to a separate
165 distribution named Bio-Assembly. This also means that BioPerl
166 is no longer dependent on Bio-SamTools and Sort-Naturally.
168 * The entire Bio::Structure namespace has been moved to a
169 separate distribution named Bio-Structure.
171 * The entire Bio::SeqEvolution namespace has been moved to a
172 separate distribution named Bio-SeqEvolution.
174 * The Bio::Tools::Gel module has been moved into its own
175 distribution named Bio-Tools-Gel.
177 * The entire Bio::Restriction namespace has been moved to a
178 separate distribution named Bio-Restriction.
180 * The module Bio::SeqIO::entrezgene has been moved to the
181 Bio-ASN1-EntrezGene distribution.
183 * The module Bio::MolEvol::CodonModel has moved to a distribution
184 of its own, named after itself.
186 * The module Bio::Perl has moved to a new distribution named
187 Bio-Procedural.
189 * The module Bio::Tools::Run::RemoteBlast has moved to a new
190 distribution named after itself.
192 * The module Bio::Align::Graphics has been moved to a new distribution
193 named after itself. This also means that BioPerl is no longer
194 dependent on GD.
196 * The entire Bio::DB::HIV namespace, the Bio::DB::Query::HIVQuery
197 module, and the the bp_hivq program have been moved to their
198 own distribution named Bio-DB-HIV. This also drops the bioperl
199 dependency on XML-Simple and Term-ReadLine.
201 * The entire Bio::DB::TFBS namespace has been moved to its own
202 distribution named after itself.
204 * All modules to handle HMMER programs output have been moved to their
205 own distribution named Bio-SearchIO-hmmer. This also includes the
206 programs bp_hmmer_to_table and bp_parse_hmmsearch.
208 * Bio::DB::MeSH and related Bio::Phenotype::MeSH modules have moved
209 to their own distribution Bio-DB-MeSH.
211 * The Bio::DB::Universal module has been moved to its own distribution.
213 * The emacs bioperl minor mode is no longer distributed as part of the
214 perl module distributions. See
215 https://github.com/bioperl/emacs-bioperl-mode
217 1.7.2 - "Entebbe"
219 [Bugs]
221 * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
222 * #245 - Code coverage fixes [zmughal,cjfields]
223 * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
224 * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
225 * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
226 * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
227 * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
228 * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
229 * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
230 * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
231 * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
232 * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
234 [Code changes]
236 * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
238 1.7.1 - "Election"
240 [Bugs]
242 * Minor release to incorporate fix for CPAN indexing, which
243 prevented proper updates [cjfields]
244 * Fix problem in managing Target attribute for gff3 [Jukes34]
245 * Minor bug fixes related to NCBI HTTPS support [cjfields]
247 1.7.0 - "Disney"
249 [New site]
251 * We have migrated to Github Pages. This was actually planned, but the
252 recent OBF server compromise forced our hand.
254 Brian Osborne [bosborne] took this under his wing to move docs and has
255 done a tremendous amount of work formatting the site and working out some
256 of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
257 Cantalupo and Franscison Ossandon also helped. Kudos!!
259 * Similarly, the official issue tracker is now Github Issues. This has
260 been updated in the relevant documentation bits (we hope!)
262 [Code changes]
264 * Previously deprecated modules removed
265 * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
266 * Bio::DB::SeqHound has been removed due to the service no longer being
267 available
268 * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
269 reasons due to the server no longer having a valid cert
270 * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
271 * Bio::Coordinate, Bio::SearchIO::blastxml,
272 Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
273 added on CPAN
275 [New features]
277 * Docker instances of tagged releases are available! [hlapp]
278 * NCBI HTTPS support [mjohnson and others]
279 * Bio::SearchIO::infernal
280 - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
281 * Bio::Search::HSP::ModelHSP
282 - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
283 reports [pcantalupo]
284 * Bio::Search::Result::INFERNALResult
285 - Added new module to represent features of Infernal reports [pcantalupo]
286 * Bio::DB::Taxonomy SQLite option [cjfields]
287 * WrapperBase quoted option values [majensen]
288 * Various documentation fixes and updates [bosborne]
290 [Bug Fixes]
292 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
293 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
294 * NeXML parser fixes [fjossandon]
295 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
296 * RT 103272 : SeqFeature database deletion skipped features with a decimal -
297 Joshua Fortriede (Xenbase)
298 * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
299 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
300 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
301 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
302 * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
303 * Issue #84: EMBL format wrapping problem [nyamned]
304 * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
305 * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
306 or compiled C code (when Inline::C is installed) [rocky]
307 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
308 * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
309 * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
310 * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
311 to be consistent with "$hit->bits" behaviour [fjossandon]
312 * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
313 aminoacids made "next_seq" confused and broke the parser [fjossandon]
314 * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
315 Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
316 to "complement(join(A..B,C..D))" [fjossandon]
317 * For the many many many fixes that weren't mentioned - blame the release guy!
319 1.6.924
321 [Significant changes]
323 * Bug/feature issue tracking has moved to GitHub Issues:
324 https://github.com/bioperl/bioperl-live/issues
325 * DB_File has been demoted from "required" to "recommended",
326 which should make easier for Windows users to install BioPerl
327 if they don't need that module.
329 [New features]
331 * Bio::Search::HSP::GenericHSP
332 - Bug #3370, added a "posterior_string" method to retrieve the
333 posterior probability lines (PP) from HMMER3 reports [fjossandon]
334 - Added a "consensus_string" method to retrieve the consensus
335 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
336 * Bio::SearchIO::hmmer2
337 - The number of identical and conserved residues are now calculated
338 directly from the homology line [fjossandon]
339 - Now the Query Length and Hit Length are reported when the alignment
340 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
341 - Implemented the capture of the consensus structure lines [fjossandon]
342 * Bio::SearchIO::hmmer3
343 - The number of identical and conserved residues are now calculated
344 directly from the homology line [fjossandon]
345 - Now the Hit Length is reported when the alignment runs until the end
346 of the sequence/model ('.]' or '[]') [fjossandon]
347 - Implemented the capture of the consensus structure lines [fjossandon]
348 - Implemented the capture of the posterior probability lines [fjossandon]
349 - Completed the development of NHMMER parsing, including alignments [fjossandon]
350 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
351 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
352 "min_score", "min_bits, and "hit_filter" methods from
353 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
354 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
355 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
356 besides Blast, instead of being ignored. Added tests for all moved methods
357 using HMMER outputs and run the full test suite and everything pass [fjossandon]
358 * Bio::SeqIO::MultiFile
359 - Autodetection of file format [fangly]
360 * Bio::Tools::GuessSeqFormat:
361 - Format detection from non-seekable filehandles such as STDIN [fangly]
363 [Bug fixes]
365 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
366 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
367 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
368 * Abstract: Fixed ActivePerl incapability of removing temporary files
369 because of problems closing tied filehandles [fjossandon]
370 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
371 because ActivePerl were producing a ".index.pag" and ".index.dir"
372 files instead of a single ".index" file (like Strawberry Perl).
373 Now those temporary files are correctly considered and deleted. [fjossandon]
374 * Test files: Added missing module requirements (DB_File and Data::Stag)
375 to several tests files that were failing because those modules were
376 not present. Now those test files are correctly skipped instead. [fjossandon]
377 * Blast: Added support to changes in bl2seq from BLAST+ output, which
378 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
379 * Phylip: Return undef in "next_aln" at file end to avoid
380 an infinite loop [yschensandiego]
381 * HMMER3: When a hit description is too long, it is truncated in
382 the Scores table. In those cases, the more complete description from
383 the Annotation line (>>) will be used [fjossandon]
384 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
385 since it is now used by HMMER3 format in alignments [fjossandon]
386 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
387 to return undef if the query/hit length is unknown (like in some
388 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
389 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
390 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
391 added support to multi-query reports, reduced code redundancy,
392 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
393 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
394 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
395 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
396 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
397 * Double-quotes on paths are needed in some places [fjossandon]
398 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
399 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
400 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
401 with the latest changes made in their own repositories [fjossandon]
402 * General synching of files with the master branch [fjossandon]
403 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
404 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
405 * Fixed broken MeSH parser [fjossandon]
406 * Fixed missing detection of format in SeqIO when given a -string [fangly]
408 1.6.923
410 * Major Windows support updates! [fjossandon]
411 * MAKER update to allow for stricter standard codon table [cjfields]
412 * Better support for circular sequences [fjossandon]
413 * Fixes for some complex location types [fjossandon]
414 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
415 * Fix bug #2978 related to BLAST report type [fjossandon]
416 * Deobfuscator fixes [DaveMessina]
418 1.6.922
420 * Address CPAN test failures [cjfields]
421 * Add BIOPROJECT support for Genbank files [hyphaltip]
422 * Better regex support for HMMER3 output [bosborne]
424 1.6.921
426 * Minor update to address CPAN test failures
428 1.6.920
430 * Remove Bio::Biblio and related files [carandraug]
431 - this cause version clashes with an independently-released
432 version of Bio::Biblio
434 1.6.910
436 [New features]
438 * Hash randomization fixes for perl 5.18.x
439 - Note: at least one module (Bio::Map::Physical) still has a failing test;
440 this is documented in bug #3446 and has been TODO'd; we will be pulling
441 Bio::Map and similar modules out of core into separate distributions in the
442 1.7.x release series [cjfields]
444 [New features]
446 * Bio::Seq::SimulatedRead
447 - New module to represent reads taken from other sequences [fangly]
448 * Bio::Root::Root
449 - Support of Clone::Fast as a faster cloning alternative [fangly]
450 * Bio::Root::IO
451 - Moved the format() and variant() methods from Bio::*IO modules to
452 Bio::Root::IO [fangly]
453 - Can now use format() to get the type of IO format in use [fangly]
454 * Bio::Tools::IUPAC
455 - New regexp() method to create regular expressions from IUPAC sequences
456 [fangly]
457 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
458 - Code refresh [fangly]
459 * Bio::DB::Taxonomy
460 - Added support for the Greengenes and Silva taxonomies [fangly]
461 * Bio::Tree::TreeFunctionsI
462 - get_lineage_string() represents a lineage as a string [fangly]
463 - add_trait() returns instead of reporting an error when the column
464 number is exceeded in add_trait() [fangly]
465 - Option to support tree leaves without trait [fangly]
466 - Allow ID of 0 in trait files [fangly]
467 * Bio::DB::Taxonomy::list
468 - Misc optimizations [fangly]
469 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
470 * Bio::DB::Taxonomy::*
471 - get_num_taxa() returns the number of taxa in the database [fangly]
472 * Bio::DB::Fasta and Bio::DB::Qual
473 - support indexing an arbitrary list of files [fangly]
474 - user can supply an arbitrary index file name [fangly]
475 - new option to remove index file at the end [fangly]
476 * Bio::DB::Fasta
477 - now handles IUPAC degenerate residues [fangly]
478 * Bio::PrimarySeq and Bio::PrimarySeqI
479 - speed improvements for large sequences [Ben Woodcroft, fangly]
480 * Bio::PrimaryQual
481 - tightened and optimized quality string validation [fangly]
482 * Bio::SeqIO::fasta
483 - new method and option 'block', to create FASTA output with space
484 intervaled blocks (similar to genbank or EMBL) has been implemented.
485 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
486 in favour of the methods 'width' and 'preferred_id_type` respectively.
487 * Bio::FeatureIO::*
488 - moved from bioperl-live into the separate distribution Bio-FeatureIO
489 * Bio::SeqFeature::Annotated
490 - moved from bioperl-live into the separate distribution Bio-FeatureIO
491 * Bio::Cluster::SequenceFamily
492 - improved performance when using get_members with overlapping multiple
493 criteria
494 * Bio::SearchIO::hmmer3
495 - now supports nhmmer [bosborne]
497 [Bug fixes]
499 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
500 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
501 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
502 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
503 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
504 information was lost in a multi-result blast file [Paul Cantalupo]
505 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
506 total gaps [Paul Cantalupo]
507 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
508 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
509 when end of domain indicator is split across lines [Paul Cantalupo]
510 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
511 cjfields]
512 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
513 instances where blank lines are within sequences [cjfields]
514 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
515 types [fangly]
516 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
517 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
518 cjfields]
519 * Various fixes for Stockholm file indexing and processing [bosborne]
520 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
521 breaks parsing [cjfields]
522 * Fix case where Bio::Seq::Meta* objects with no meta information could not
523 be reverse-complemented [fangly]
524 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
525 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
526 when unsure that values will be numerical [fangly]
527 * Fix undef warnings in Bio::SeqIO::embl [fangly]
528 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
529 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
530 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
531 Sallou]
532 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
533 source_tag and display_name must return a string, not undef [fangly]
534 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
535 add_SeqFeature takes a single argument [fangly]
536 * Use cross-platform filenames and temporary directory in
537 Bio::DB::Taxonomy::flatfile [fangly]
538 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
539 properly identified as existing taxa in the database [fangly]
540 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
541 without also passing a lineage to store [fangly]
542 * Prevent passing a directory to the gi2taxid option (-g) of
543 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
544 [fangly]
545 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
546 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
547 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
548 object before trying to access, and no longer returns repeated sequences.
551 1.6.901 May 18, 2011
553 [Notes]
555 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
556 modules using Ace will also be deprecated [lds, cjfields]
557 * Minor bug fix release
558 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
559 * Address Build.PL issues when DBI is not present [hartzell]
560 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
561 * Remove deprecated code for perl 5.14.0 compat [cjfields]
562 * Due to schema changes and lack of support for older versions, support
563 for NeXML 0.9 is only (very) partially implemented.
564 See: https://redmine.open-bio.org/issues/3207
566 [Bug fixes]
568 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
569 docs [genehack, cjfields]
570 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
571 module version from dist_version (probably not the best way to do this,
572 but it seems to work) [rbuels, cjfields]
575 1.6.900 April 14, 201
577 [Notes]
579 * This will probably be the last release to add significant features to
580 core modules; subsequent releases will be for bug fixes alone.
581 We are planning on a restructuring of core for summer 2011, potentially
582 as part of the Google Summer of Code. This may become BioPerl 2.0.
583 * Version bump represents 'just prior to v 1.7'. We may have point
584 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
585 This code essentially is what is on the github master branch.
587 [New features]
589 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
590 * Bio::Tree refactor
591 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
592 - removal of Scalar::Util::weaken code, which was causing odd headaches
593 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
594 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
595 many others]
596 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
597 [Warren Kretzschmar]
598 * Bio::SeqIO::gbxml
599 - bug 2515 - new contribution [Ryan Golhar, jhannah]
600 * Bio::Assembly::IO
601 - support for reading Maq, Sam and Bowtie files [maj]
602 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
603 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
604 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
605 - bug 2726: reading/writing granularity: whole scaffold or one contig
606 at a time [Joshua Udall, fangly]
607 * Bio::OntologyIO
608 - Added parsing of xrefs to OBO files, which are stored as secondary
609 dbxrefs of the cvterm [Naama Menda]
610 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
611 * PAML code updated to work with PAML 4.4d [DaveMessina]
613 [Bug fixes]
615 * [3198] - sort tabular BLAST hits by score [DaveMessina]
616 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
617 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
618 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
619 [cjfields]
620 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
621 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
622 * [3164] - TreeFunctionsI syntax bug [gjuggler]
623 * [3163] - AssemblyIO speedup [fangly]
624 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
625 hyphaltip]
626 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
627 * [3158] - fix EMBL file mis-parsing [cjfields]
628 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
629 cjfields]
630 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
631 * [3148] - URL change for UniProt [cjfields]
632 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
633 * [3136] - HMMer3 parser fixes [kblin]
634 * [3126] - catch description [Toshihiko Akiba]
635 * [3122] - Catch instances where non-seekable filehandles were being
636 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
637 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
638 [dukeleto, rbuels, cjfields]
639 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
640 jhannah]
641 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
642 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
643 cjfields]
644 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
645 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
646 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
647 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
648 * [3086] - EMBL misparsing long tags [kblin, cjfields]
649 * [3085] - CommandExts and array of files [maj, hyphaltip]
650 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
651 for alignment slices [Ha X. Dang, cjfields]
652 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
653 * [3073] - fix parsing of GenBank files from RDP [cjfields]
654 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
655 * [3064] - All-gap midline BLAST report issues [cjfields]
656 * [3063] - BLASt report RID [Razi Khaja, cjfields]
657 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
658 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
659 * [3039] - correct Newick output root node branch length [gjuggler,
660 DaveMessina]
661 * [3038] - SELEX alignment error [Bernd, cjfields]
662 * [3033] - PrimarySeq ID setting [Bernd, maj]
663 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
664 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
665 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
666 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
667 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
668 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
669 PAML 4.4d [DaveMessina]
670 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
671 DaveMessina]
672 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
673 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
674 * [3017] - using threads with Bio::DB::GenBank [cjfields]
675 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
676 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
677 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
678 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
679 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
680 cjfields]
681 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
682 * [2977] - TreeIO issues [DaveMessina]
683 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
684 * [2944] - Bio::Tools::GFF score [cjfields]
685 * [2942] - correct MapTiling output [maj]
686 * [2939] - PDB residue insertion codes [John May, maj]
687 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
688 * [2928] - GuessSeqFormat raw [maj]
689 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
690 * [2922] - open() directive issue [cjfields]
691 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
692 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
693 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
694 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
695 cjfields]
696 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
697 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
698 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
699 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
700 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
701 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
702 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
703 * [2758] - Bio::AssemblyIO ace problems [fangly]
704 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
705 * [2726] - ace file IO [Josh, fangly]
706 * [2700] - Refactor Build.PL [cjfields]
707 * [2673] - addition of simple Root-based clone() method [cjfields]
708 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
709 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
710 * [2594] - Bio::Species memory leak [cjfields]
711 * [2515] - GenBank XML parser [jhannah]
712 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
713 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
714 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
715 cjfields]
716 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
718 [Deprecated]
720 * Bio::Expression modules - these were originally designed to go with the
721 bioperl-microarray suite of tools, however they have never been completed
722 and so have been removed from the distribution. The original code has
723 been moved into the inactive bioperl-microarray suite. [cjfields]
725 [Other]
727 * Repository moved from Subversion (SVN) to
728 http://github.com/bioperl/bioperl-live [cjfields]
729 * Bug database has moved to Redmine (https://redmine.open-bio.org)
730 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
731 Thieme have been moved to their own distribution (Bio-Microarray).
732 [cjfields]
734 1.6.1 Sept. 29, 2009 (point release)
735 * No change from last alpha except VERSION and doc updates [cjfields]
737 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
738 * Fix for silent OBDA bug related to FASTA validation [cjfields]
740 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
741 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
742 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
743 [cjfields]
744 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
746 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
747 * WinXP test fixes [cjfields, maj]
748 * BioPerl.pod added for descriptive information, fixes CPAN indexing
749 [cjfields]
750 * Minor doc fixes [cjfields]
752 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
753 * Fix tests failing due to merging issues [cjfields]
754 * More documentation updates for POD parsing [cjfields]
756 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
757 * Bio::Root::Build
758 - fix YAML meta data generation [cjfields]
760 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
761 * Bio::Align::DNAStatistics
762 - fix divide by zero problem [jason]
763 * Bio::AlignIO::*
764 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
765 * Bio::AlignIO::stockholm
766 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
767 * Bio::Assembly::Tools::ContigSpectrum
768 - function to score contig spectrum [fangly]
769 * Bio::DB::EUtilities
770 - small updates [cjfields]
771 * Bio::DB::Fasta
772 - berkeleydb database now autoindexes wig files and locks correctly
773 [lstein]
774 * Bio::DB::HIV
775 - various small updates for stability; tracking changes to LANL
776 database interface [maj]
777 * Bio::DB::SeqFeature (lots of updates and changes)
778 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
779 - bug 2835 - patch [Dan Bolser]
780 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
781 * Bio::DB::SwissProt
782 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
783 * Bio::Factory::FTLocationFactory
784 - mailing list bug fix [cjfields]
785 * Bio::LocatableSeq
786 - performance work on column_from_residue_number [hartzell]
787 * Bio::Matrix::IO::phylip
788 - bug 2800 - patch to fix phylip parsing [Wei Zou]
789 * Bio::Nexml
790 - Google Summer of Code project from Chase Miller - parsers for Nexml
791 file format [maj, chmille4]
792 * Bio::PopGen
793 - Make Individual, Population, Marker objects AnnotatableI [maj]
794 - simplify LD code [jason]
795 * Bio::RangeI
796 - deal with empty intersection [jason]
797 * Bio::Restriction
798 - significant overhaul of Bio::Restriction system: complete support for
799 external and non-palindromic cutters. [maj]
800 * Bio::Root::Build
801 - CPANPLUS support, no automatic installation [sendu]
802 * Bio::Root::IO
803 - allow IO::String (regression fix) [cjfields]
804 - catch unintentional undef values [cjfields]
805 - throw if non-fh is passed to -fh [maj]
806 * Bio::Root::Root/RootI
807 - small debugging and core fixes [cjfields]
808 * Bio::Root::Test
809 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
810 * Bio::Root::Utilities
811 - bug 2737 - better warnings [cjfields]
812 * Bio::Search
813 - tiling completely refactored, HOWTO added [maj]
814 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
815 will deprecate usage of the older tiling code in the next BioPerl
816 release
817 - small fixes [cjfields]
818 * Bio::SearchIO
819 - Infernal 1.0 output now parsed [cjfields]
820 - new parser for gmap -f9 output [hartzell]
821 - bug 2852 - fix infinite loop in some output [cjfields]
822 - blastxml output now passes all TODO tests [cjfields]
823 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
824 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
825 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
826 * Bio::Seq::LargePrimarySeq
827 - delete tempdirs [cjfields]
828 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
829 * Bio::Seq::Quality
830 - extract regions based on quality threshold value [Dan Bolser, heikki]
831 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
832 * Bio::SeqFeature::Lite
833 - various Bio::DB::SeqFeature-related fixes [lstein]
834 * Bio::SeqFeature::Tools::TypeMapper
835 - additional terms for GenBank to SO map [scain]
836 * Bio::SeqIO::chadoxml
837 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
838 * Bio::SeqIO::embl
839 - support for CDS records [dave_messina, Sylvia]
840 * Bio::SeqIO::fastq
841 - complete refactoring to handle all FASTQ variants, perform validation,
842 write output. API now conforms with other Bio* parsers and the rest of
843 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
844 [cjfields]
845 * Bio::SeqIO::genbank
846 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
847 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
848 * Bio::SeqIO::largefasta
849 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
850 * Bio::SeqIO::raw
851 - add option for 'single' and 'multiple'
852 * Bio::SeqIO::scf
853 - bug 2881 - fix scf round-tripping [Adam Søgren]
854 * Bio::SeqUtils
855 - bug 2766, 2810 - copy over tags from features, doc fixes [David
856 Jackson]
857 * Bio::SimpleAlign
858 - bug 2793 - patch for add_seq index issue [jhannah, maj]
859 - bug 2801 - throw if args are required [cjfields]
860 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
861 [Tristan Lefebure, maj]
862 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
863 - fix POD and add get_SeqFeatures filter [maj]
864 * Bio::Tools::dpAlign
865 - add support for LocatableSeq [ymc]
866 - to be moved to a separate distribution [cjfields, rbuels]
867 * Bio::Tools::EUtilities
868 - fix for two bugs from mail list [Adam Whitney, cjfields]
869 - add generic ItemContainerI interface for containing same methods
870 [cjfields]
871 * Bio::Tools::HMM
872 - fix up code, add more warnings [cjfields]
873 - to be moved to a separate distribution [cjfields, rbuels]
874 * Bio::Tools::Primer3
875 - bug 2862 - fenceposting issue fixed [maj]
876 * Bio::Tools::Run::RemoteBlast
877 - tests for remote RPS-BLAST [mcook]
878 * Bio::Tools::SeqPattern
879 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
880 * Bio::Tools::tRNAscanSE
881 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
882 * Bio::Tree::*
883 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
884 * Bio::Tree::Statistics
885 - several methods for calculating Fitch-based score, internal trait
886 values, statratio(), sum of leaf distances [heikki]
887 * Bio::Tree::Tree
888 - bug 2869 - add docs indicating edge case where nodes can be
889 prematurely garbage-collected [cjfields]
890 - add as_text() function to create Tree as a string in specified format
891 [maj]
892 * Bio::Tree::TreeFunctionsI
893 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
894 Lefebure, maj]
895 * Bio::TreeIO::newick
896 - fix small semicolon issue [cjfields]
897 * scripts
898 - update to bp_seqfeature_load for SQLite [lstein]
899 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
900 - fastam9_to_table - fix for MPI output [jason]
901 - gccalc - total stats [jason]
902 * General Stuff
903 - POD cleanup re: FEEDBACK section [maj, cjfields]
904 - cleanup or fix dead links [cjfields]
905 - Use of no_* methods (indicating 'number of something') is deprecated
906 in favor of num_* [cjfields]
907 - lots of new tests for the above bugs and refactors [everyone!]
908 - new template for Komodo text editor [cjfields]
910 1.6.0 Winter 2009
911 * Feature/Annotation rollback
912 - Problematic changes introduced prior to the 1.5 release have been
913 rolled back. These changes led to subtle bugs involving operator
914 overloading and interface methods.
915 - Behavior is very similar to that for BioPerl 1.4, with tag values
916 being stored generically as simple scalars. Results in a modest
917 speedup.
918 * Bio::Graphics
919 - Split into a separate distribution on CPAN, primarily so development
920 isn't reliant on a complete BioPerl release.
921 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
922 is only available via Subversion (via bioperl-live main trunk)
923 * Bio::Root::Test
924 - Common test bed for all BioPerl modules
925 * Bio::Root::Build
926 - Common Module::Build-based subclass for all BioPerl modules
927 * Bio::DB::EUtilities
928 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
929 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
930 and user agent request posting and retrieval
931 * Test implementation and reorganization
932 - Tests have been reorganized into groups based on classes or use
933 cases.
934 - Automated test coverage is now online:
935 http://www.bioperl.org/wiki/Test_Coverage
936 - After this release, untested modules will be moved into a
937 separate developer distribution until tests can be derived.
938 Also, new modules to be added are expected to have a test suite
939 and adequate test coverage.
941 1.5.2 Developer release
943 Full details of changes since 1.5.1 are available online at:
944 http://www.bioperl.org/wiki/Change_log
945 The following represents a brief overview of the most important changes.
947 o Bio::Map
948 - Overhaul. Brand new system fully allows markers to have multiple
949 positions on multiple maps, and to have relative positions. Should be
950 backward compatible.
952 o Bio::Taxonomy
953 - This module and all the modules in the Taxonomy directory now
954 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
956 o Bio::DB::Taxonomy
958 - Taxonomy.pm
959 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
961 * New methods ancestor(), each_Descendent() and _handle_internal_id().
963 * Allows for different database modules to create Bio::Taxon objects
964 with the same internal id when the same taxon is requested from each.
966 - flatfile.pm
967 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
969 * No longer includes the fake root node 'root'; there are multiple roots
970 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
972 - entrez.pm
973 * get_node() has new option -full
975 * Caches data retrieved from website
977 o Bio::Species
978 - Now a Bio::Taxon. Carries out the species name -> specific name munging
979 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
980 backward compatability in species() method.
982 o Bio::Search and Bio::SearchIO
983 - Overhaul. The existing system has been sped up via some minor changes
984 (mostly gain-of-function to the API). Bio::PullParserI is introduced
985 as a potential eventual replacment for the existing system, though as
986 yet only a Hmmpfam parser exists written using it.
989 1.5.1 Developer release
991 o Major problem with how Annotations were written out with
992 Bio::Seq is fixed by reverting to old behavior for
993 Bio::Annotation objects.
995 o Bio::SeqIO
997 - genbank.pm
998 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
999 expect at l east 9 spaces at the beginning of a line to
1000 indicate line wrapping.
1002 * Treat multi-line SOURCE sections correctly, this defect broke
1003 both common_name() and classification()
1005 * parse swissprot fields in genpept file
1007 * parse WGS genbank records
1009 - embl.pm
1010 * Changed regexp for ID line. The capturing parentheses are
1011 the same, the difference is an optional repeated-not-semi-
1012 colon expression following the captured \S+. This means the
1013 regexp works when the division looks like /PRO;/ or when the
1014 division looks like /ANG ;/ - the latter is from EMBL
1015 repbase
1017 * fix ID line parsing: the molecule string can have spaces in
1018 it. Like: "genomic DNA"
1020 - swiss.pm: bugs #1727, #1734
1022 - entrezgene.pm
1023 * Added parser for entrezgene ASN1 (text format) files.
1024 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
1026 o Bio::AlignIO
1028 - maf.pm coordinate problem fixed
1030 o Bio::Taxonomy and Bio::DB::Taxonomy
1032 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
1033 can be done via Web without downloading all the sequence.
1035 o Bio::Tools::Run::RemoteBlast supports more options and complies
1036 to changes to the NCBI interface. It is reccomended that you
1037 retrieve the data in XML instead of plain-text BLAST report to
1038 insure proper parsing and retrieval of all information as NCBI
1039 fully expects to change things in the future.
1041 o Bio::Tree and Bio::TreeIO
1043 - Fixes so that re-rooting a tree works properly
1045 - Writing out nhx format from a newick/nexus file will properly output
1046 bootstrap information. The use must move the internal node labels over
1047 to bootstraps.
1048 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
1049 $node->bootstrap($node->id);
1050 $node->id('');
1051 }
1052 - Nexus parsing is much more flexible now, does not care about
1053 LF.
1055 - Cladogram drawing module in Bio::Tree::Draw
1057 - Node height and depth now properly calculated
1059 - fix tree pruning algorithm so that node with 1 child gets merged
1061 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
1062 bugs and improvements were added, see Gbrowse mailing list for most of
1063 these.
1065 o Bio::DB::GFF partially supports GFF3. See information about
1066 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
1068 o Better location parsing in Bio::Factory::FTLocationFactory -
1069 this is part of the engine for parsing EMBL/GenBank feature table
1070 locations. Nested join/order-by/complement are allowed now
1072 o Bio::PrimarySeqI->translate now takes named parameters
1074 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
1075 reconstruction) is now supported. Parsing different models and
1076 branch specific parametes are now supported.
1078 o Bio::Factory::FTLocationFactory - parse hierarchical locations
1079 (joins of joins)
1081 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
1082 for getter/setter functions
1084 o Bio::SearchIO
1086 - blast bug #1739; match scientific notation in score
1087 and possible e+ values
1089 - blast.pm reads more WU-BLAST parameters and parameters, match
1090 a full database pathname,
1092 - Handle NCBI WEB and newer BLAST formats specifically
1093 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
1095 - psl off-by-one error fixed
1097 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
1098 and HSPs can be constructed from them.
1100 - HSPs query/hit now have a seqdesc field filled out (this was
1101 always available via $hit->description and
1102 $result->query_description
1104 - hmmer.pm can parse -A0 hmmpfam files
1106 - Writer::GbrowseGFF more customizeable.
1108 o Bio::Tools::Hmmpfam
1109 make e-value default score displayed in gff, rather than raw score
1110 allow parse of multiple records
1113 1.5 Developer release
1115 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
1116 provide Jukes-Cantor and Kimura pairwise distance methods,
1117 respectively.
1119 o Bio::AlignIO support for "po" format of POA, and "maf";
1120 Bio::AlignIO::largemultifasta is a new alternative to
1121 Bio::AlignIO::fasta for temporary file-based manipulation of
1122 particularly large multiple sequence alignments.
1124 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
1125 be treated similarly as an assembled contig.
1127 o Bio::CodonUsage provides new rare_codon() and probable_codons()
1128 methods for identifying particular codons that encode a given
1129 amino acid.
1131 o Bio::Coordinate::Utils provides new from_align() method to build
1132 a Bio::Coordinate pair directly from a
1133 Bio::Align::AlignI-conforming object.
1135 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
1136 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
1137 web service using standard Pubmed query syntax, and retrieve
1138 results as XML.
1140 o Bio::DB::GFF has various sundry bug fixes.
1142 o Bio::FeatureIO is a new SeqIO-style subsystem for
1143 writing/reading genomic features to/from files. I/O classes
1144 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
1145 classes only read/write Bio::SeqFeature::Annotated objects.
1146 Notably, the GFF v3 class requires features to be typed into the
1147 Sequence Ontology.
1149 o Bio::Graph namespace contains new modules for manipulation and
1150 analysis of protein interaction graphs.
1152 o Bio::Graphics has many bug fixes and shiny new glyphs.
1154 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
1155 indexing for HMMER reports and FASTA qual files, respectively.
1157 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
1158 new objects that can be placed within a Bio::Map::MapI-compliant
1159 genetic/physical map; Bio::Map::Physical provides a new physical
1160 map type; Bio::MapIO::fpc provides finger-printed clone mapping
1161 import.
1163 o Bio::Matrix::PSM provide new support for postion-specific
1164 (scoring) matrices (e.g. profiles, or "possums").
1166 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
1167 be instantiated without explicitly using Bio::OntologyIO. This
1168 is possible through changes to Bio::Ontology::OntologyStore to
1169 download ontology files from the web as necessary. Locations of
1170 ontology files are hard-coded into
1171 Bio::Ontology::DocumentRegistry.
1173 o Bio::PopGen includes many new methods and data types for
1174 population genetics analyses.
1176 o New constructor to Bio::Range, unions(). Given a list of
1177 ranges, returns another list of "flattened" ranges --
1178 overlapping ranges are merged into a single range with the
1179 mininum and maximum coordinates of the entire overlapping group.
1181 o Bio::Root::IO now supports -url, in addition to -file and -fh.
1182 The new -url argument allows one to specify the network address
1183 of a file for input. -url currently only works for GET
1184 requests, and thus is read-only.
1186 o Bio::SearchIO::hmmer now returns individual Hit objects for each
1187 domain alignment (thus containing only one HSP); previously
1188 separate alignments would be merged into one hit if the domain
1189 involved in the alignments was the same, but this only worked
1190 when the repeated domain occured without interruption by any
1191 other domain, leading to a confusing mixture of Hit and HSP
1192 objects.
1194 o Bio::Search::Result::ResultI-compliant report objects now
1195 implement the "get_statistics" method to access
1196 Bio::Search::StatisticsI objects that encapsulate any
1197 statistical parameters associated with the search (e.g. Karlin's
1198 lambda for BLAST/FASTA).
1200 o Bio::Seq::LargeLocatableSeq combines the functionality already
1201 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
1203 o Bio::SeqFeature::Annotated is a replacement for
1204 Bio::SeqFeature::Generic. It breaks compliance with the
1205 Bio::SeqFeatureI interface because the author was sick of
1206 dealing with untyped annotation tags. All
1207 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
1208 compliant, and accessible through Bio::Annotation::Collection.
1210 o Bio::SeqFeature::Primer implements a Tm() method for primer
1211 melting point predictions.
1213 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
1214 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
1216 o Bio::Taxonomy::Node now implements the methods necessary for
1217 Bio::Species interoperability.
1219 o Bio::Tools::CodonTable has new reverse_translate_all() and
1220 make_iupac_string() methods.
1222 o Bio::Tools::dpAlign now provides sequence profile alignments.
1224 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
1226 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
1227 parsers.
1229 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
1230 for designing small inhibitory RNA.
1232 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
1233 methods based on a distance matrix.
1235 o Bio::Tree::Statistics provides an assess_bootstrap() method to
1236 calculate bootstrap support values on a guide tree topology,
1237 based on provided bootstrap tree topologies.
1239 o Bio::TreeIO now supports the Pagel (PAG) tree format.
1241 1.4 branch
1243 1.4.1
1245 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
1247 o Bio::Graphics will work with gd1 or gd2
1249 o Bio::SearchIO
1250 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
1251 (RF lines alone)
1252 - blast.pm Parse multi-line query fields properly
1253 - small speed improvements to blasttable.pm and others
1255 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
1256 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
1257 supporting more complex queries
1260 1.4. Stable major release
1262 Since initial 1.2.0, 3000 separate changes have been made to make this release.
1264 o installable scripts
1266 o global module version from Bio::Root:Version
1268 o Bio::Graphics
1269 - major improvements; SVG support
1271 o Bio::Popgen
1272 - population genetics
1273 - support several population genetics types of questions.
1274 - Tests for statistical neutrality of mutations
1275 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
1276 Tests of population structure (Wright's F-statistic: Fst) is in
1277 Bio::PopGen::PopStats. Calculating composite linkage
1278 disequilibrium (LD) is available in Bio::PopGen::Statistics as
1279 well.
1280 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1281 and csv (comma delimited formatted) data.
1283 - a directory for implementing population simulations has
1284 been added Bio::PopGen::Simulation and 2 simulations - a
1285 Coalescent and a simple single-locus multi-allele genetic drift
1286 simulation have been provided. This replaces the code in
1287 Bio::Tree::RandomTree which has been deprecated until proper
1288 methods for generating random phylogenetic trees are
1289 implemented.
1291 o Bio::Restriction
1292 - new restrion analysis modules
1294 o Bio::Tools::Analysis
1295 - web based DNA and Protein analysis framework and several
1296 implementations
1298 o Bio::Seq::Meta
1299 - per residue annotable sequences
1301 o Bio::Matrix
1302 - Bio::Matrix::PSM - Position Scoring Matrix
1303 - Bio::Matrix::IO has been added for generalized parsing of
1304 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1305 initial implementations for parsing BLOSUM/PAM and Phylip
1306 Distance matricies respectively. A generic matrix
1307 implementation for general use was added in
1308 Bio::Matrix::Generic.
1310 o Bio::Ontology
1311 - major changes
1313 o Bio:Tree
1315 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1316 - small inhibitory RNA
1318 o Bio::SeqFeature::Tools
1319 - seqFeature mapping tools
1320 - Bio::SeqFeature::Tools::Unflattener.pm
1321 -- deal with mapping GenBank feature collections into
1322 Chado/GFF3 processable feature sets (with SO term mappings)
1324 o Bio::Tools::dpAlign
1325 - pure perl dynamic programming sequence alignment
1326 - needs Bioperl-ext
1328 o new Bio::SearchIO formats
1329 - axt and psl: UCSC formats.
1330 - blasttable: NCBI -m 8 or -m 9 format from blastall
1332 o new Bio::SeqIO formats
1333 - chado, tab, kegg, tigr, game
1334 - important fixes for old modules
1336 o Bio::AlignIO: maf
1338 o improved Bio::Tools::Genewise
1340 o Bio::SeqIO now can recongnize sequence formats automatically from
1341 stream
1343 o new parsers in Bio::Tools:
1344 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1346 o Bio::DB::Registry bugs fixed
1347 - BerkeleyDB-indexed flat files can be used by the OBDA system
1348 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1349 used by the OBDA system
1351 o several new HOWTOs
1352 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1353 Databases
1355 o hundreds of new and improved files
1358 o
1359 o Bio::Tree::AlleleNode has been updated to be a container of
1360 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1363 1.2 Branch
1365 1.2.3 Stable release update
1366 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1367 handling.
1368 o Bug #1477 - Sel --> Sec abbreviation fixed
1369 o Fix bug #1487 where paring in-between locations when
1370 end < start caused the FTLocationFactory logic to fail.
1371 o Fix bug #1489 which was not dealing with keywords as an
1372 arrayref properly (this is fixed on the main trunk because
1373 keywords returns a string and the array is accessible via
1374 get_keywords).
1375 o Bio::Tree::Tree memory leak (bug #1480) fixed
1376 Added a new initialization option -nodelete which
1377 won't try and cleanup the containing nodes if this
1378 is true.
1379 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1380 this was only present on the branch for the 1.2.1 and 1.2.2 series
1381 - Also merged main trunk changes to the branch which make
1382 newick -> nhx round tripping more effective (storing branch length
1383 and bootstrap values in same locate for NodeNHX and Node
1384 implementations.) Fixes to TreeIO parsing for labeled internal
1385 also required small changes to TreeIO::nhx. Improved
1386 tests for this module as well.
1387 o Bio::SearchIO
1388 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1389 gapped blast properly (was losing hit significance values due to
1390 the extra unexpeted column).
1391 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1392 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1393 although doesn't try to correct it - will get the negative
1394 number for you. Added a test for this as well.
1395 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1396 has no top-level family classification scores but does have scores and
1397 alignments for individual domains.
1398 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1399 regular expression to match the line was missing the possibility of
1400 an extra space. This is rare, which is why we probably did not
1401 catch it before.
1402 - BLAST parsing picks up more of the statistics/parameter fields
1403 at the bottom of reports. Still not fully complete.
1404 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1405 were fixed to include many improvements and added flexiblity
1406 in outputting the files. Bug #1495 was also fixed in the process.
1407 o Bio::DB::GFF
1408 - Update for GFF3 compatibility.
1409 - Added scripts for importing from UCSC and GenBank.
1410 - Added a 1.2003 version number.
1411 o Bio::Graphics
1412 - Updated tutorial.
1413 - Added a 1.2003 version number.
1414 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1415 properly writing keywords out.
1416 o Bio::SeqIO::genbank
1417 - Fixed bug/enhancement #1513 where dates of
1418 the form D-MMM-YYYY were not parsed. Even though this is
1419 invalid format we can handle it - and also cleanup the date
1420 string so it is properly formatted.
1421 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1422 and written with Genbank format. Similarly bug #1515 is fixed to
1423 parse in the ORIGIN text.
1424 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1425 to specify the ID type, one of (accession accession.version
1426 display primary). See Bio::SeqIO::preferred_id_type method
1427 documentation for more information.
1428 o Unigene parsing updated to handle file format changes by NCBI
1430 1.2.2 Stable release update
1432 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1433 - auto-discover ontology name
1434 - bug in parsing relationships when certain characters are in the term
1435 - fixed hard-coded prefix for term identifiers
1436 - various smaller issues
1438 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1439 of Bio::Ontology::TermI
1441 o brought the OBDA Registry code up to latest specs
1443 o Bio::DB::GenBank
1444 - eutils URL change
1445 - accession number retrieval fixed
1447 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1449 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1450 #1459 which now properly report alignment start/end info
1451 for translated BLAST/FASTA searches.
1453 o Bio::TreeIO::newick can parse labeled internal nodes
1455 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1456 for BLASTX if if you provide -report_type => 'BLASTX' when
1457 initializing a BPbl2seq object. Bioperl 1.3 will have better
1458 support for bl2seq in the SearchIO system.
1460 o Bio::Root::IO support a -noclose boolean flag which will not
1461 close a filehandle upon object cleanup - useful when sharing
1462 a filehandle among objects. Additionally code added s.t.
1463 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1465 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1467 o Bio::SeqIO::genbank
1468 - bug #1456 fixed which generated extra sequence lines
1469 - write moltype correctly for genpept
1471 1.2.1 Stable release update
1473 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1475 o Addition from main trunk of Ontology objects, principly to allow
1476 BioSQL releases against 1.2.1
1478 o Fixes and cleanup of Bio::Coordinate modules
1480 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1481 the primary accession number
1483 o Other bug fixes, including bpindex GenBank fix
1485 o Bio::SeqIO::genbank bug #1389 fixed
1487 1.2 Stable major release
1489 o More functionality added to Bio::Perl, the newbie module
1491 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1492 Support for New Hampshire Extended (NHX) format parsing.
1494 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1495 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1496 Hmmpfam parser.
1498 o New ontology parsing Bio::Ontology
1500 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1501 multi-report (mlib) fasta reports, support for waba and exonerate.
1503 o Bio::ClusterIO for parsing Unigene clusters
1505 o Bio::Assembly added for representing phrap and ace assembly clusters.
1507 o Rudimentary support for writing Chado XML (see
1508 GMOD project: www.gmod.org for more information)
1510 o Bio::Coordinate for mapping between different coordinate systems such
1511 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1512 features into different coordinate systems.
1514 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1515 with the get_Stream_by_query method and supports the latest
1516 NCBI eutils interface.
1518 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1519 object for extracting subsets of features : currently only
1520 supports extraction by location.
1522 1.1.1 Developer release
1524 o Deprecated modules are now listed in the DEPRECATED file
1526 o New HowTo documents located in doc/howto describing
1527 a domain of Bioperl.
1529 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1530 and all old bugs are searchable through the bugzilla interface.
1532 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1533 have been addressed.
1535 o Support for Genewise parsing in Bio::Tools::Genewise
1537 o Start of Ontology framework with Bio::Ontology
1539 o Speedup to the Bio::Root::Root object method _rearrange.
1540 A global _load_module method was implemented to simplify the
1541 dynamic loading of modules ala Bio::SeqIO::genbank. This
1542 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1543 etc).
1545 o Several performance improvements to sequence parsing in Bio::SeqIO.
1546 Attempt to speedup by reducing object creation overhead.
1548 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1549 method for sequence retrieval with their E-utils CGI scripts.
1550 More work to support Entrez queries to their fullest is planned
1551 before 1.2 release.
1553 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1555 1.1 Developer release
1557 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1558 this separation removes some of the complexity in our test suite
1559 and separates the core modules in bioperl from those that need
1560 external programs to run.
1562 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1563 not run into trouble running the makefile
1565 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1566 read,create,and write locations for grouped/split locations
1567 (like mRNA features on genomic sequence).
1569 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1570 and PAML (codeml,aaml, etc) parsing.
1572 o Bio::Tree:: objects expanded to handle testing monophyly,
1573 paraphyly, least common ancestor, etc.
1575 o Bio::Coordinate for mapping locations from different coordinate spaces
1577 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1578 added for parsing hmmpfam and hmmsearch output.
1580 o Bio::SearchIO::Writer::TextResultWriter for outputting
1581 a pseudo-blast textfile format
1584 1.0.2 Bug fix release
1586 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1587 in this release will not work after December 2002 when NCBI
1588 shuts off the old Entrez cgi scripts. We have already fixed
1589 on our main development branch and the functionality will be
1590 available in the next stable bioperl release (1.2) slated for
1591 Fall 2002.
1593 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1594 testset by Robin Emig. These were fixed as was the get_aln
1595 method in Bio::Search::HSP::GenericHSP to handle the extra
1596 context sequence that is provided with a FastA alignment.
1598 o Migrating differences between Bio::Search::XX::BlastXX to
1599 Bio::Search::XX::GenericXX objects. This included mechanism
1600 to retrieve whole list of HSPs from Hits and whole list of Hits from
1601 Results in addition to the current next_XX iterator methods that
1602 are available. Added seq_inds() method to GenericHSP which identifies
1603 indexes in the query or hit sequences where conserved,identical,gaps,
1604 or mismatch residues are located (adapted from Steve Chervitz's
1605 implementation in BlastHSP).
1607 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1608 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1610 o Bio::Graphics glyph set improved and extended for GBrowse release
1612 o Bio::Tree::Tree get_nodes implementation improvement thanks
1613 to Howard Ross notice performance problem when writing out
1614 unbalanced trees.
1616 o Bio::Location::Fuzzy::new named parameter -loc_type became
1617 -location_type, Bio::Location::Simple::new named parameter
1618 -seqid becamse -seq_id.
1620 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1621 was mis-detecting that gaps should be placed at the beginning of
1622 the alignment when the best alignment starts internally in the
1623 sequence.
1625 1.0.1 Bug fix release
1627 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1629 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1630 and mixed (3.3 - 3.4) versions of FASTA.
1632 o Small API change to add methods for completeness across
1633 implementations of Bio::Search objects. These new methods
1634 in the interface are implemented by the GenericXX object as well
1635 as the BlastXX objects.
1636 * Bio::Search::Result::ResultI
1637 - hits() method returns list of all Hits (next_hit is an
1638 iterator method)
1640 * Bio::Search::Hit::HitI
1641 - hsps() method returns list of all HSPs (next_hsp is an
1642 iterator method)
1644 o The Bio::SearchIO::Writer classes have been fixed to handle results
1645 created from either psiblast (Search::BlastXX objects) or
1646 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1647 has to be done here to make it work properly and will nee major
1648 API changes.
1650 o Bugs in Bio::Tools::HMMER fixed, including
1651 * #1178 - Root::IO destructor wasn't being called
1652 * #1034 - filter_on_cutoff now behaves properly
1654 o Bio::SeqFeature::Computation initialization args fixed and
1655 tests added.
1657 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1659 o Updated FAQ with more example based answers to typical questions
1661 o Bug #1202 was fixed which would improperly join together qual values
1662 parsed by Bio::SeqIO::qual when a trailing space was not present before
1663 the newline.
1665 1.0.0 Major Stable Release
1667 This represents a major release of bioperl with significant
1668 improvements over the 0.7.x series of releases.
1670 o Bio::Tools::Blast is officially deprecated. Please see
1671 Bio::SearchIO for BLAST and FastA parsing.
1673 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1674 Bio::LocationI objects as well as start/end.
1676 o Bio::Biblio contains modules for Bibliographic data.
1677 Bio::DB::Biblio contains the query modules. Additionally one can
1678 parse medlinexml from the ebi bibliographic query service (BQS)
1679 system and Pubmed xml from NCBI. See Martin Senger's
1680 documentation in Bio::Biblio for more information.
1682 o Bio::DB::Registry is a sequence database registry part of
1683 Open Bioinformatics Database Access. See
1684 http://obda.open-bio.org for more information.
1686 o File-based and In-Memory Sequence caching is provided by
1687 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1688 local database.
1690 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1691 been added by Lincoln Stein.
1693 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1695 o A FAQ has been started and is included in the release to provide
1696 a starting point for frequent questions and issues.
1698 0.9.3 Developer's release
1700 o Event based parsing system improved (SearchIO). With parsers for
1701 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1702 Additionally a lazy parsing system for text and html blast reports was
1703 added and is called psiblast (name subject to change in future releases).
1705 o Bio::Search objects improved and standardized with associated Interfaces
1706 written. The concept of a search "Hit" was standardized to be called
1707 "hit" consistently and the use of "subject" was deprecated in all active
1708 modules.
1710 o Bio::Structure added (since 0.9.1) for Protein structure objects
1711 and PDB parser to retrieve and write these structures from data files.
1713 o Several important Bio::DB::GFF bug fixes for handling features that
1714 are mapped to multiple reference points. Updated mysql adaptor
1715 so as to be able to store large (>100 megabase) chunks of DNA into
1716 Bio::DB::GFF databases.
1718 0.9.2 Developer's release
1720 o Bio::Search and Bio::SearchIO system introduced for event based
1721 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1722 in text and XML and FASTA reports in standard output format.
1724 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1725 generator is included in Bio::TreeIO::RandomTrees and a
1726 statistics module for evaluating.
1728 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1729 server for DAS servers.
1731 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1732 files. The entire BPlite system migrated to using Bio::Root::IO
1733 for the data stream.
1735 o Bio::Tools::Alignment for Consed and sequence Trimming
1736 functionality.
1738 o Bio::Structure for Protein structure information and parsing
1740 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1741 cgi-bin entry point which should be more reliable.
1743 o Bio::Map and Bio::MapIO for biological map navigation and a
1744 framework afor parsing them in. Only preliminary work here.
1746 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1747 Future work will integrate Pise and allow submission of analysis on
1748 remote servers.
1750 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1751 introduced as new objects for handling Sequence Annotation
1752 information (dblinks, references, etc) and is more robust that
1753 previous system.
1755 o Bio::Tools::FASTAParser introduced.
1757 o Scripts from the bioperl script submission project and new
1758 scripts from bioperl authors are included in "scripts" directory.
1760 o Factory objects and interfaces are being introduced and are more
1761 strictly enforced.
1763 o Bio::Root::Root introduced as the base object while
1764 Bio::Root::RootI is now simply an interface.
1766 o Bio::DB::RefSeq provides database access to copy of the NCBI
1767 RefSeq database using the EBI dbfetch script.
1769 0.9.0 Developer's release
1771 o perl version at least 5.005 is now required instead of perl 5.004
1773 o Bio::Tools::Run::RemoteBlast is available for running remote
1774 blast jobs at NCBI.
1776 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1778 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1779 Also added are related modules UTR3, UTR5, Exon, Intron,
1780 Promotor, PolyA and Transcript.
1782 o Speedup of translate method in PrimarySeq
1784 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1785 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1787 o Various fixes to Variation toolkit
1789 o Bio::DB::EMBL provides database access to EMBL sequence data.
1790 Bio::DB::Universal provides a central way to point to indexes
1791 and dbs in a single interface.
1793 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1795 o Bio::Factory::EMBOSS is still in design phase as is
1796 Bio::Factory::ApplicationFactoryI
1798 o Dia models for bioperl design are provided in the models/ directory
1800 0.7.2 Bug fix release
1802 o documentation fixes in many modules - SYNOPSIS code verified
1803 to be runnable in many (but not all modules)
1805 o corrected MANIFEST file from 0.7.1 release
1807 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1808 split locations
1810 o Bio::SeqIO::genbank
1811 * Correct parsing and writing of genbank format with protein data
1812 * moltype and molecule separation
1814 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1816 o Bio::SimpleAlign fixed to correctly handle consensus
1817 sequence calculation
1819 o Bio::Tools::HMMER supports hmmer 2.2g
1821 o Bio::Tools::BPlite to support report type specific parsing. Most
1822 major changes are not on the 0.7 branch.
1824 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1825 with File::Spec
1827 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1828 in several types of mutations:
1829 1.) AA level: deletion, complex
1830 2.) AA level: complex, inframe
1831 3.) RNA level: silent
1833 o BPbl2seq parsing of empty reports will not die, but will return
1834 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1835 $report->query() and $report->subject() methods. So an easy
1836 way to test if report was empty is to see if
1837 $report->query->seqname is undefined.
1839 0.7.1 Bug fix release
1841 o Better parsing of genbank/EMBL files especially fixing bugs
1842 related to Feature table parsing and locations on remote
1843 sequences. Additionally, species name parsing was better.
1845 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1846 which include a number of header lines.
1848 o More strict genbank and EMBL format writing (corrected number of
1849 spaces where appropriate).
1851 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1852 for related BPlite BUGS that are unresolved in this release.
1854 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1855 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1856 use expasy mirrors or EBI dbfetch cgi-script.
1858 o A moderate number of documentation improvements were made as
1859 well to provide a better code synopsis in each module.
1862 0.7 Large number of changes, including refactoring of the
1863 Object system, new parsers, new functionality and
1864 all round better system. Highlights are:
1867 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1868 Bio::Root::IO for I/O and file/handle capabilities.
1870 o Imported BPlite modules from Ian Korf for BLAST
1871 parsing. This is considered the supported BLAST parser;
1872 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1874 o Improved Sequence Feature model. Added complete location
1875 modelling (with fuzzy and compound locations). See
1876 Bio::LocationI and the modules under Bio/Location. Added
1877 support in Genbank/EMBL format parsing to completely parse
1878 feature tables for complex locations.
1880 o Moved special support for databanks etc to specialized modules under
1881 Bio/Seq/. One of these supports very large sequences through
1882 a temporary file as a backend.
1884 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1885 CDS retrieval and exon shuffling.
1887 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1889 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1890 DB/GDB (the latter has platform-specific limitations).
1892 o New analysis parser framework for HT sequence annotation (see
1893 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1895 o New Alignment IO framework
1897 o New Index modules (Swissprot)
1899 o New modules for running Blast within perl
1900 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1901 Multiple Sequence Alignment tools ClustalW and TCoffee
1902 (Bio::Tools::Run::Alignment).
1904 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1905 documentation across the package.
1907 o Much improved cross platform support. Many known incompatibilities
1908 have been fixed; however, NT and Mac do not work across the entire
1909 setup (see PLATFORMS).
1911 o Many bug fixes, code restructuring, etc. Overall stability and
1912 maintainability benefit a lot.
1914 o A total of 957 automatic tests
1917 0.6.2
1919 There are very few functionality changes but a large
1920 number of software improvements/bug fixes across the package.
1922 o The EMBL/GenBank parsing are improved.
1924 o The Swissprot reading is improved. Swissprot writing
1925 is disabled as it doesn't work at all. This needs to
1926 wait for 0.7 release
1928 o BLAST reports with no hits are correctly parsed.
1930 o Several other bugs of the BLAST parser (regular expressions, ...)
1931 fixed.
1933 o Old syntax calls have been replaced with more modern syntax
1935 o Modules that did not work at all, in particular the Sim4
1936 set have been removed
1938 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1939 have improved compliance with interface specs and documentation
1941 o Mailing list documentation updated throughout the distribution
1943 o Most minor bug fixes have happened.
1945 o The scripts in /examples now work and have the modern syntax
1946 rather than the deprecated syntax
1949 0.6.1 Sun April 2 2000
1951 o Sequences can have Sequence Features attached to them
1952 - The sequence features can be read from or written to
1953 EMBL and GenBank style flat files
1955 o Objects for Annotation, including References (but not
1956 full medline abstracts), Database links and Comments are
1957 provided
1959 o A Species object to represent nodes on a taxonomy tree
1960 is provided
1962 o The ability to parse HMMER and Sim4 output has been added
1964 o The Blast parsing has been improved, with better PSI-BLAST
1965 support and better overall behaviour.
1967 o Flat file indexed databases provide both random access
1968 and sequential access to their component sequences.
1970 o A CodonTable object has been written with all known
1971 CodonTables accessible.
1973 o A number of new lightweight analysis tools have been
1974 added, such as molecular weight determination.
1976 The 0.6 release also has improved software engineering
1978 o The sequence objects have been rewritten, providing more
1979 maintainable and easier to implement objects. These
1980 objects are backwardly compatible with the 0.05.1 objects
1982 o Many objects are defined in terms of interfaces and then
1983 a Perl implementation has been provided. The interfaces
1984 are found in the 'I' files (module names ending in 'I').
1986 This means that it is possible to wrap C/CORBA/SQL access
1987 as true "bioperl" objects, compatible with the rest of
1988 bioperl.
1990 o The SeqIO system has been overhauled to provide better
1991 processing and perl-like automatic interpretation of <>
1992 over arguments.
1994 o Many more tests have been added (a total of 172 automatic
1995 tests are now run before release).
1999 0.05.1 Tue Jun 29 05:30:44 1999
2000 - Central distribution now requires Perl 5.004. This was
2001 done to get around 5.003-based problems in Bio/Index/*
2002 and SimpleAlign.
2003 - Various bug fixes in the Bio::Tools::Blast modules
2004 including better exception handling and PSI-Blast
2005 support. See Bio/Tools/Blast/CHANGES for more.
2006 - Fixed the Parse mechanism in Seq.pm to use readseq.
2007 Follow the instructions in README for how to install
2008 it (basically, you have to edit Parse.pm).
2009 - Improved documentation of Seq.pm, indicating where
2010 objects are returned and where strings are returned.
2011 - Fixed uninitialized warnings in Bio::Root::Object.pm
2012 and Bio::Tools::SeqPattern.pm.
2013 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
2015 0.05 Sun Apr 25 01:14:11 1999
2016 - Bio::Tools::Blast modules have less memory problems
2017 and faster parsing. Webblast uses LWP and supports
2018 more functionality. See Bio/Tools/Blast/CHANGES for more.
2019 - The Bio::SeqIO system has been started, moving the
2020 sequence reformatting code out of the sequence object
2021 - The Bio::Index:: system has been started, providing
2022 generic index capabilities and specifically works for
2023 Fasta formatted databases and EMBL .dat formatted
2024 databases
2025 - The Bio::DB:: system started, providing access to
2026 databases, both via flat file + index (see above) and
2027 via http to NCBI
2028 - The scripts/ directory, where industrial strength scripts
2029 are put has been started.
2030 - Many changes - a better distribution all round.
2032 0.04.4 Wed Feb 17 02:20:13 1999
2033 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
2034 (see Bio::Tools::Blast::CHANGES).
2035 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
2036 - Beefed up the t/Fasta.t test script.
2037 - Small fix in Bio::Seq::type() (now always returns a string).
2038 - Changed Bio::Root::Utilities::get_newline_char() to
2039 get_newline() since it could return more than one char.
2040 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
2041 - Changed default timeout to 20 seconds (was 3).
2042 - Moved lengthy modification notes to the bottom of some files.
2043 - Fixed SimpleAlign write_fasta bug.
2044 - Beefed up SimpleAlign.t test
2046 0.04.3 Thu Feb 4 07:48:53 1999
2047 - Bio::Root::Object.pm and Global.pm now detect when
2048 script is run as a CGI and suppress output that is only
2049 appropriate when running interactively.
2050 - Bio::Root::Err::_set_context() adds name of script ($0).
2051 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
2052 regarding the use of the static objects via the qw(:obj) tag.
2053 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
2054 CORE::reverse, avoiding Perl warnings.
2055 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
2056 example scripts (see Bio::Tools::Blast::CHANGES).
2057 - examples/seq/seqtools.pl no longer always warns about using
2058 -prot or -nucl command-line arguments; only when using the
2059 -debug argument.
2060 - Methods added to Bio::Root::Utilities: create_filehandle(),
2061 get_newline_char(), and taste_file() to generalize filehandle
2062 creation and autodetect newline characters in files/streams
2063 (see bug report #19).
2064 - Bio::Root::IOManager::read() now handles timeouts and uses
2065 Utilities::create_filehandle().
2066 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
2067 of hardwiring in "\n".
2068 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
2070 0.04.2 Wed Dec 30 02:27:36 1998
2071 - Bug fixes in Bio::Tools::Blast modules, version 0.073
2072 (see Bio::Tools::Blast::CHANGES).
2073 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
2074 to CORE::reverse (prevents ambiguous warnings with 5.005).
2075 - Appending '.tmp.bioperl' to temporary files created by
2076 Bio::Root::Utilities::compress() or uncompress() to
2077 make it easy to identify & cleanup these files as needed.
2078 - Developers: Created CVS branch release-0-04-bug from
2079 release-0-04-1. Before making bug fixes to the 0.04.1 release,
2080 be sure to cvs checkout this branch into a clean area.
2082 0.04.1 Wed Dec 16 05:39:15 1998
2083 - Bug fixes in Bio::Tools::Blast modules, version 0.072
2084 (see Bio::Tools::Blast::CHANGES).
2085 - Compile/SW/Makefile.PL now removes *.o and *.a files
2086 with make clean.
2088 0.04 Tue Dec 8 07:49:19 1998
2089 - Lots of new modules added including:
2090 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
2091 and Bio/Compile directory containing XS-linked C code for
2092 creating Smith-Waterman sequence alignments from within Perl.
2093 * Steve Chervitz's Blast distribution has been incorporated.
2094 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
2095 - Bio/examples directory for demo scripts for all included modules.
2096 - Bio/t directory containing test suit for all included modules.
2097 - For changes specific to the Blast-related modules prior to
2098 incorporation in this central distribution, see the CHANGES
2099 file in the Bio/Tools/Blast directory.
2101 0.01 Tue Sep 8 14:23:22 1998
2102 - original version from central CVS tree; created by h2xs 1.18