1 Summary of important user-visible changes for BioPerl
2 -----------------------------------------------------
6 * The program bp_classify_hits_kingdom has been removed and is
7 now part of the examples documentation instead.
10 1.7.5 2019-02-11 14:57:45+00:00 Europe/London
12 * The following modules have been removed from the BioPerl
13 distribution to be part of a separate distribution with
14 independent development:
18 * The Bio::Seq::SeqWithQuality module, which was deprecated since
19 2001, was finally removed.
21 * The deprecated() method has been deprecated. It is recommended
22 to use Carp::carp to warn.
24 * The following methods have been deprecated for a long while and
25 have now been removed:
27 Bio::Align::AlignI->no_residues
28 Bio::Align::AlignI->no_sequences
29 Bio::LocatableSeq->no_gap
30 Bio::LocatableSeq->no_sequences
31 Bio::SeqFeature::Generic->slurp_gff_file
32 Bio::SimpleAlign->no_residues
33 Bio::SimpleAlign->no_sequences
36 1.7.4 2019-02-05 16:23:53+00:00 Europe/London
38 * Fix Bio::Root::Test, and the testuite, to properly check for
39 internet connection and the NO_NETWORK_TESTING environment
40 variable. Previously, tests that required internet connection
41 were not being skipped, causing tests to fail.
44 1.7.3 2019-01-30 13:30:34+00:00 Europe/London
46 * The following modules have been removed from the BioPerl
47 distribution to be part of a separate distribution. They have
48 been integrated into other module distributions for independent
53 Bio::AlignIO::stockholm
63 Bio::DB::Expression::*
65 Bio::DB::GFF::Adaptor::*
66 Bio::DB::GFF::Aggregator::*
67 Bio::DB::GFF::Featname
70 Bio::DB::GFF::RelSegment
72 Bio::DB::GFF::Typename
78 Bio::DB::Query::GenBank
79 Bio::DB::Query::HIVQuery
81 Bio::DB::SeqFeature::*
82 Bio::DB::SeqVersion::*
85 Bio::DB::Taxonomy::entrez
86 Bio::DB::Taxonomy::sqlite
89 Bio::Factory::MapFactoryI
95 Bio::MolEvol::CodonModel
104 Bio::Search::HSP::HMMERHSP
105 Bio::Search::HSP::HmmpfamHSP
106 Bio::Search::Hit::HMMERHit
107 Bio::Search::Hit::HmmpfamHit
108 Bio::Search::Hit::hmmer3Hit
109 Bio::Search::Result::HMMERResult
110 Bio::Search::Result::HmmpfamResult
111 Bio::Search::Result::hmmer3Result
114 Bio::SearchIO::hmmer2
115 Bio::SearchIO::hmmer3
116 Bio::SearchIO::hmmer_pull
118 Bio::SeqFeature::SiRNA::*
126 Bio::SeqIO::entrezgene
129 Bio::SeqIO::flybase_chadoxml
130 Bio::SeqIO::lasergene
137 Bio::Tools::AlignFactory
138 Bio::Tools::Analysis::* (except SimpleAnalysisBase)
142 Bio::Tools::Phylo::Gumby
143 Bio::Tools::Protparam
144 Bio::Tools::Run::RemoteBlast
148 Bio::Tree::AlleleNode
149 Bio::Tree::Draw::Cladogram
151 Bio::TreeIO::svggraph
154 * The following modules are new in the BioPerl distribution. They
155 have been previously released in the BioPerl-Run distribution.
156 This will enable smaller distributions that provide a
157 Bio::Tool::Run interface, to be only dependent on the BioPerl
158 distribution instead of the whole (very large) BioPerl-Run:
160 Bio::Tools::Run::Analysis
161 Bio::Tools::Run::AnalysisFactory
162 Bio::Tools::Run::Phylo::PhyloBase
163 Bio::Tools::Run::WrapperBase
164 Bio::Tools::Run::WrapperBase::CommandExts
166 * The following programs have been removed:
168 bp_biofetch_genbank_proxy
173 bp_download_query_genbank
177 bp_generate_histogram
178 bp_heterogeneity_test
192 * Because of the move of so many modules and programs into
193 separate distributions, the following modules are no longer
202 Bio::ASN1::EntrezGene
203 Bio::Expression::Contact
204 Bio::Expression::DataSet
205 Bio::Expression::Platform
206 Bio::Expression::Sample
208 Bio::GMOD::CMap::Utils
210 Bio::Phylo::Forest::Tree
213 Bio::Phylo::Matrices::Datum
214 Bio::Phylo::Matrices::Matrix
215 Bio::SeqFeature::Annotated
216 Bio::SeqIO::staden::read
217 Bio::Tools::Run::Alignment::Clustalw
218 Bio::Tools::Run::Ensembl
219 Bio::Tools::Run::Phylo::Molphy::ProtML
220 Bio::Tools::Run::Phylo::Phylip::Neighbor
221 Bio::Tools::Run::Phylo::Phylip::ProtDist
222 Bio::Tools::Run::Phylo::Phylip::ProtPars
223 Bio::Tools::Run::Samtools
231 Data::Stag::XMLWriter
247 PostScript::TextBlock
251 SVG::Graph::Data::Node
252 SVG::Graph::Data::Tree
254 Spreadsheet::ParseExcel
256 Text::NSP::Measures::2D::Fisher2::twotailed
264 * The following is a new prerequisite:
266 Test::RequiresInternet
268 * The deobfuscator has been removed.
270 * The emacs bioperl minor mode is no longer distributed as part of the
271 perl module distributions. See
272 https://github.com/bioperl/emacs-bioperl-mode
279 * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
280 * #245 - Code coverage fixes [zmughal,cjfields]
281 * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
282 * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
283 * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
284 * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
285 * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
286 * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
287 * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
288 * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
289 * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
290 * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
294 * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
300 * Minor release to incorporate fix for CPAN indexing, which
301 prevented proper updates [cjfields]
302 * Fix problem in managing Target attribute for gff3 [Jukes34]
303 * Minor bug fixes related to NCBI HTTPS support [cjfields]
309 * We have migrated to Github Pages. This was actually planned, but the
310 recent OBF server compromise forced our hand.
312 Brian Osborne [bosborne] took this under his wing to move docs and has
313 done a tremendous amount of work formatting the site and working out some
314 of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
315 Cantalupo and Franscison Ossandon also helped. Kudos!!
317 * Similarly, the official issue tracker is now Github Issues. This has
318 been updated in the relevant documentation bits (we hope!)
322 * Previously deprecated modules removed
323 * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
324 * Bio::DB::SeqHound has been removed due to the service no longer being
326 * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
327 reasons due to the server no longer having a valid cert
328 * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
329 * Bio::Coordinate, Bio::SearchIO::blastxml,
330 Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
335 * Docker instances of tagged releases are available! [hlapp]
336 * NCBI HTTPS support [mjohnson and others]
337 * Bio::SearchIO::infernal
338 - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
339 * Bio::Search::HSP::ModelHSP
340 - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
342 * Bio::Search::Result::INFERNALResult
343 - Added new module to represent features of Infernal reports [pcantalupo]
344 * Bio::DB::Taxonomy SQLite option [cjfields]
345 * WrapperBase quoted option values [majensen]
346 * Various documentation fixes and updates [bosborne]
350 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
351 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
352 * NeXML parser fixes [fjossandon]
353 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
354 * RT 103272 : SeqFeature database deletion skipped features with a decimal -
355 Joshua Fortriede (Xenbase)
356 * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
357 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
358 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
359 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
360 * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
361 * Issue #84: EMBL format wrapping problem [nyamned]
362 * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
363 * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
364 or compiled C code (when Inline::C is installed) [rocky]
365 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
366 * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
367 * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
368 * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
369 to be consistent with "$hit->bits" behaviour [fjossandon]
370 * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
371 aminoacids made "next_seq" confused and broke the parser [fjossandon]
372 * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
373 Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
374 to "complement(join(A..B,C..D))" [fjossandon]
375 * For the many many many fixes that weren't mentioned - blame the release guy!
379 [Significant changes]
381 * Bug/feature issue tracking has moved to GitHub Issues:
382 https://github.com/bioperl/bioperl-live/issues
383 * DB_File has been demoted from "required" to "recommended",
384 which should make easier for Windows users to install BioPerl
385 if they don't need that module.
389 * Bio::Search::HSP::GenericHSP
390 - Bug #3370, added a "posterior_string" method to retrieve the
391 posterior probability lines (PP) from HMMER3 reports [fjossandon]
392 - Added a "consensus_string" method to retrieve the consensus
393 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
394 * Bio::SearchIO::hmmer2
395 - The number of identical and conserved residues are now calculated
396 directly from the homology line [fjossandon]
397 - Now the Query Length and Hit Length are reported when the alignment
398 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
399 - Implemented the capture of the consensus structure lines [fjossandon]
400 * Bio::SearchIO::hmmer3
401 - The number of identical and conserved residues are now calculated
402 directly from the homology line [fjossandon]
403 - Now the Hit Length is reported when the alignment runs until the end
404 of the sequence/model ('.]' or '[]') [fjossandon]
405 - Implemented the capture of the consensus structure lines [fjossandon]
406 - Implemented the capture of the posterior probability lines [fjossandon]
407 - Completed the development of NHMMER parsing, including alignments [fjossandon]
408 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
409 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
410 "min_score", "min_bits, and "hit_filter" methods from
411 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
412 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
413 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
414 besides Blast, instead of being ignored. Added tests for all moved methods
415 using HMMER outputs and run the full test suite and everything pass [fjossandon]
416 * Bio::SeqIO::MultiFile
417 - Autodetection of file format [fangly]
418 * Bio::Tools::GuessSeqFormat:
419 - Format detection from non-seekable filehandles such as STDIN [fangly]
423 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
424 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
425 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
426 * Abstract: Fixed ActivePerl incapability of removing temporary files
427 because of problems closing tied filehandles [fjossandon]
428 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
429 because ActivePerl were producing a ".index.pag" and ".index.dir"
430 files instead of a single ".index" file (like Strawberry Perl).
431 Now those temporary files are correctly considered and deleted. [fjossandon]
432 * Test files: Added missing module requirements (DB_File and Data::Stag)
433 to several tests files that were failing because those modules were
434 not present. Now those test files are correctly skipped instead. [fjossandon]
435 * Blast: Added support to changes in bl2seq from BLAST+ output, which
436 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
437 * Phylip: Return undef in "next_aln" at file end to avoid
438 an infinite loop [yschensandiego]
439 * HMMER3: When a hit description is too long, it is truncated in
440 the Scores table. In those cases, the more complete description from
441 the Annotation line (>>) will be used [fjossandon]
442 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
443 since it is now used by HMMER3 format in alignments [fjossandon]
444 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
445 to return undef if the query/hit length is unknown (like in some
446 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
447 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
448 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
449 added support to multi-query reports, reduced code redundancy,
450 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
451 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
452 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
453 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
454 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
455 * Double-quotes on paths are needed in some places [fjossandon]
456 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
457 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
458 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
459 with the latest changes made in their own repositories [fjossandon]
460 * General synching of files with the master branch [fjossandon]
461 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
462 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
463 * Fixed broken MeSH parser [fjossandon]
464 * Fixed missing detection of format in SeqIO when given a -string [fangly]
468 * Major Windows support updates! [fjossandon]
469 * MAKER update to allow for stricter standard codon table [cjfields]
470 * Better support for circular sequences [fjossandon]
471 * Fixes for some complex location types [fjossandon]
472 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
473 * Fix bug #2978 related to BLAST report type [fjossandon]
474 * Deobfuscator fixes [DaveMessina]
478 * Address CPAN test failures [cjfields]
479 * Add BIOPROJECT support for Genbank files [hyphaltip]
480 * Better regex support for HMMER3 output [bosborne]
484 * Minor update to address CPAN test failures
488 * Remove Bio::Biblio and related files [carandraug]
489 - this cause version clashes with an independently-released
490 version of Bio::Biblio
496 * Hash randomization fixes for perl 5.18.x
497 - Note: at least one module (Bio::Map::Physical) still has a failing test;
498 this is documented in bug #3446 and has been TODO'd; we will be pulling
499 Bio::Map and similar modules out of core into separate distributions in the
500 1.7.x release series [cjfields]
504 * Bio::Seq::SimulatedRead
505 - New module to represent reads taken from other sequences [fangly]
507 - Support of Clone::Fast as a faster cloning alternative [fangly]
509 - Moved the format() and variant() methods from Bio::*IO modules to
510 Bio::Root::IO [fangly]
511 - Can now use format() to get the type of IO format in use [fangly]
513 - New regexp() method to create regular expressions from IUPAC sequences
515 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
516 - Code refresh [fangly]
518 - Added support for the Greengenes and Silva taxonomies [fangly]
519 * Bio::Tree::TreeFunctionsI
520 - get_lineage_string() represents a lineage as a string [fangly]
521 - add_trait() returns instead of reporting an error when the column
522 number is exceeded in add_trait() [fangly]
523 - Option to support tree leaves without trait [fangly]
524 - Allow ID of 0 in trait files [fangly]
525 * Bio::DB::Taxonomy::list
526 - Misc optimizations [fangly]
527 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
528 * Bio::DB::Taxonomy::*
529 - get_num_taxa() returns the number of taxa in the database [fangly]
530 * Bio::DB::Fasta and Bio::DB::Qual
531 - support indexing an arbitrary list of files [fangly]
532 - user can supply an arbitrary index file name [fangly]
533 - new option to remove index file at the end [fangly]
535 - now handles IUPAC degenerate residues [fangly]
536 * Bio::PrimarySeq and Bio::PrimarySeqI
537 - speed improvements for large sequences [Ben Woodcroft, fangly]
539 - tightened and optimized quality string validation [fangly]
541 - new method and option 'block', to create FASTA output with space
542 intervaled blocks (similar to genbank or EMBL) has been implemented.
543 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
544 in favour of the methods 'width' and 'preferred_id_type` respectively.
546 - moved from bioperl-live into the separate distribution Bio-FeatureIO
547 * Bio::SeqFeature::Annotated
548 - moved from bioperl-live into the separate distribution Bio-FeatureIO
549 * Bio::Cluster::SequenceFamily
550 - improved performance when using get_members with overlapping multiple
552 * Bio::SearchIO::hmmer3
553 - now supports nhmmer [bosborne]
557 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
558 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
559 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
560 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
561 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
562 information was lost in a multi-result blast file [Paul Cantalupo]
563 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
564 total gaps [Paul Cantalupo]
565 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
566 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
567 when end of domain indicator is split across lines [Paul Cantalupo]
568 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
570 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
571 instances where blank lines are within sequences [cjfields]
572 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
574 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
575 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
577 * Various fixes for Stockholm file indexing and processing [bosborne]
578 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
579 breaks parsing [cjfields]
580 * Fix case where Bio::Seq::Meta* objects with no meta information could not
581 be reverse-complemented [fangly]
582 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
583 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
584 when unsure that values will be numerical [fangly]
585 * Fix undef warnings in Bio::SeqIO::embl [fangly]
586 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
587 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
588 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
590 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
591 source_tag and display_name must return a string, not undef [fangly]
592 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
593 add_SeqFeature takes a single argument [fangly]
594 * Use cross-platform filenames and temporary directory in
595 Bio::DB::Taxonomy::flatfile [fangly]
596 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
597 properly identified as existing taxa in the database [fangly]
598 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
599 without also passing a lineage to store [fangly]
600 * Prevent passing a directory to the gi2taxid option (-g) of
601 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
603 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
604 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
605 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
606 object before trying to access, and no longer returns repeated sequences.
613 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
614 modules using Ace will also be deprecated [lds, cjfields]
615 * Minor bug fix release
616 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
617 * Address Build.PL issues when DBI is not present [hartzell]
618 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
619 * Remove deprecated code for perl 5.14.0 compat [cjfields]
620 * Due to schema changes and lack of support for older versions, support
621 for NeXML 0.9 is only (very) partially implemented.
622 See: https://redmine.open-bio.org/issues/3207
626 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
627 docs [genehack, cjfields]
628 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
629 module version from dist_version (probably not the best way to do this,
630 but it seems to work) [rbuels, cjfields]
633 1.6.900 April 14, 201
637 * This will probably be the last release to add significant features to
638 core modules; subsequent releases will be for bug fixes alone.
639 We are planning on a restructuring of core for summer 2011, potentially
640 as part of the Google Summer of Code. This may become BioPerl 2.0.
641 * Version bump represents 'just prior to v 1.7'. We may have point
642 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
643 This code essentially is what is on the github master branch.
647 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
649 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
650 - removal of Scalar::Util::weaken code, which was causing odd headaches
651 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
652 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
654 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
657 - bug 2515 - new contribution [Ryan Golhar, jhannah]
659 - support for reading Maq, Sam and Bowtie files [maj]
660 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
661 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
662 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
663 - bug 2726: reading/writing granularity: whole scaffold or one contig
664 at a time [Joshua Udall, fangly]
666 - Added parsing of xrefs to OBO files, which are stored as secondary
667 dbxrefs of the cvterm [Naama Menda]
668 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
669 * PAML code updated to work with PAML 4.4d [DaveMessina]
673 * [3198] - sort tabular BLAST hits by score [DaveMessina]
674 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
675 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
676 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
678 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
679 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
680 * [3164] - TreeFunctionsI syntax bug [gjuggler]
681 * [3163] - AssemblyIO speedup [fangly]
682 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
684 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
685 * [3158] - fix EMBL file mis-parsing [cjfields]
686 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
688 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
689 * [3148] - URL change for UniProt [cjfields]
690 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
691 * [3136] - HMMer3 parser fixes [kblin]
692 * [3126] - catch description [Toshihiko Akiba]
693 * [3122] - Catch instances where non-seekable filehandles were being
694 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
695 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
696 [dukeleto, rbuels, cjfields]
697 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
699 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
700 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
702 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
703 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
704 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
705 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
706 * [3086] - EMBL misparsing long tags [kblin, cjfields]
707 * [3085] - CommandExts and array of files [maj, hyphaltip]
708 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
709 for alignment slices [Ha X. Dang, cjfields]
710 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
711 * [3073] - fix parsing of GenBank files from RDP [cjfields]
712 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
713 * [3064] - All-gap midline BLAST report issues [cjfields]
714 * [3063] - BLASt report RID [Razi Khaja, cjfields]
715 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
716 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
717 * [3039] - correct Newick output root node branch length [gjuggler,
719 * [3038] - SELEX alignment error [Bernd, cjfields]
720 * [3033] - PrimarySeq ID setting [Bernd, maj]
721 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
722 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
723 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
724 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
725 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
726 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
727 PAML 4.4d [DaveMessina]
728 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
730 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
731 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
732 * [3017] - using threads with Bio::DB::GenBank [cjfields]
733 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
734 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
735 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
736 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
737 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
739 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
740 * [2977] - TreeIO issues [DaveMessina]
741 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
742 * [2944] - Bio::Tools::GFF score [cjfields]
743 * [2942] - correct MapTiling output [maj]
744 * [2939] - PDB residue insertion codes [John May, maj]
745 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
746 * [2928] - GuessSeqFormat raw [maj]
747 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
748 * [2922] - open() directive issue [cjfields]
749 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
750 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
751 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
752 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
754 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
755 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
756 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
757 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
758 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
759 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
760 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
761 * [2758] - Bio::AssemblyIO ace problems [fangly]
762 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
763 * [2726] - ace file IO [Josh, fangly]
764 * [2700] - Refactor Build.PL [cjfields]
765 * [2673] - addition of simple Root-based clone() method [cjfields]
766 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
767 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
768 * [2594] - Bio::Species memory leak [cjfields]
769 * [2515] - GenBank XML parser [jhannah]
770 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
771 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
772 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
774 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
778 * Bio::Expression modules - these were originally designed to go with the
779 bioperl-microarray suite of tools, however they have never been completed
780 and so have been removed from the distribution. The original code has
781 been moved into the inactive bioperl-microarray suite. [cjfields]
785 * Repository moved from Subversion (SVN) to
786 http://github.com/bioperl/bioperl-live [cjfields]
787 * Bug database has moved to Redmine (https://redmine.open-bio.org)
788 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
789 Thieme have been moved to their own distribution (Bio-Microarray).
792 1.6.1 Sept. 29, 2009 (point release)
793 * No change from last alpha except VERSION and doc updates [cjfields]
795 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
796 * Fix for silent OBDA bug related to FASTA validation [cjfields]
798 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
799 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
800 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
802 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
804 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
805 * WinXP test fixes [cjfields, maj]
806 * BioPerl.pod added for descriptive information, fixes CPAN indexing
808 * Minor doc fixes [cjfields]
810 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
811 * Fix tests failing due to merging issues [cjfields]
812 * More documentation updates for POD parsing [cjfields]
814 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
816 - fix YAML meta data generation [cjfields]
818 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
819 * Bio::Align::DNAStatistics
820 - fix divide by zero problem [jason]
822 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
823 * Bio::AlignIO::stockholm
824 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
825 * Bio::Assembly::Tools::ContigSpectrum
826 - function to score contig spectrum [fangly]
827 * Bio::DB::EUtilities
828 - small updates [cjfields]
830 - berkeleydb database now autoindexes wig files and locks correctly
833 - various small updates for stability; tracking changes to LANL
834 database interface [maj]
835 * Bio::DB::SeqFeature (lots of updates and changes)
836 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
837 - bug 2835 - patch [Dan Bolser]
838 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
840 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
841 * Bio::Factory::FTLocationFactory
842 - mailing list bug fix [cjfields]
844 - performance work on column_from_residue_number [hartzell]
845 * Bio::Matrix::IO::phylip
846 - bug 2800 - patch to fix phylip parsing [Wei Zou]
848 - Google Summer of Code project from Chase Miller - parsers for Nexml
849 file format [maj, chmille4]
851 - Make Individual, Population, Marker objects AnnotatableI [maj]
852 - simplify LD code [jason]
854 - deal with empty intersection [jason]
856 - significant overhaul of Bio::Restriction system: complete support for
857 external and non-palindromic cutters. [maj]
859 - CPANPLUS support, no automatic installation [sendu]
861 - allow IO::String (regression fix) [cjfields]
862 - catch unintentional undef values [cjfields]
863 - throw if non-fh is passed to -fh [maj]
864 * Bio::Root::Root/RootI
865 - small debugging and core fixes [cjfields]
867 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
868 * Bio::Root::Utilities
869 - bug 2737 - better warnings [cjfields]
871 - tiling completely refactored, HOWTO added [maj]
872 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
873 will deprecate usage of the older tiling code in the next BioPerl
875 - small fixes [cjfields]
877 - Infernal 1.0 output now parsed [cjfields]
878 - new parser for gmap -f9 output [hartzell]
879 - bug 2852 - fix infinite loop in some output [cjfields]
880 - blastxml output now passes all TODO tests [cjfields]
881 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
882 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
883 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
884 * Bio::Seq::LargePrimarySeq
885 - delete tempdirs [cjfields]
886 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
888 - extract regions based on quality threshold value [Dan Bolser, heikki]
889 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
890 * Bio::SeqFeature::Lite
891 - various Bio::DB::SeqFeature-related fixes [lstein]
892 * Bio::SeqFeature::Tools::TypeMapper
893 - additional terms for GenBank to SO map [scain]
894 * Bio::SeqIO::chadoxml
895 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
897 - support for CDS records [dave_messina, Sylvia]
899 - complete refactoring to handle all FASTQ variants, perform validation,
900 write output. API now conforms with other Bio* parsers and the rest of
901 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
903 * Bio::SeqIO::genbank
904 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
905 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
906 * Bio::SeqIO::largefasta
907 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
909 - add option for 'single' and 'multiple'
911 - bug 2881 - fix scf round-tripping [Adam Søgren]
913 - bug 2766, 2810 - copy over tags from features, doc fixes [David
916 - bug 2793 - patch for add_seq index issue [jhannah, maj]
917 - bug 2801 - throw if args are required [cjfields]
918 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
919 [Tristan Lefebure, maj]
920 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
921 - fix POD and add get_SeqFeatures filter [maj]
922 * Bio::Tools::dpAlign
923 - add support for LocatableSeq [ymc]
924 - to be moved to a separate distribution [cjfields, rbuels]
925 * Bio::Tools::EUtilities
926 - fix for two bugs from mail list [Adam Whitney, cjfields]
927 - add generic ItemContainerI interface for containing same methods
930 - fix up code, add more warnings [cjfields]
931 - to be moved to a separate distribution [cjfields, rbuels]
932 * Bio::Tools::Primer3
933 - bug 2862 - fenceposting issue fixed [maj]
934 * Bio::Tools::Run::RemoteBlast
935 - tests for remote RPS-BLAST [mcook]
936 * Bio::Tools::SeqPattern
937 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
938 * Bio::Tools::tRNAscanSE
939 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
941 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
942 * Bio::Tree::Statistics
943 - several methods for calculating Fitch-based score, internal trait
944 values, statratio(), sum of leaf distances [heikki]
946 - bug 2869 - add docs indicating edge case where nodes can be
947 prematurely garbage-collected [cjfields]
948 - add as_text() function to create Tree as a string in specified format
950 * Bio::Tree::TreeFunctionsI
951 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
953 * Bio::TreeIO::newick
954 - fix small semicolon issue [cjfields]
956 - update to bp_seqfeature_load for SQLite [lstein]
957 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
958 - fastam9_to_table - fix for MPI output [jason]
959 - gccalc - total stats [jason]
961 - POD cleanup re: FEEDBACK section [maj, cjfields]
962 - cleanup or fix dead links [cjfields]
963 - Use of no_* methods (indicating 'number of something') is deprecated
964 in favor of num_* [cjfields]
965 - lots of new tests for the above bugs and refactors [everyone!]
966 - new template for Komodo text editor [cjfields]
969 * Feature/Annotation rollback
970 - Problematic changes introduced prior to the 1.5 release have been
971 rolled back. These changes led to subtle bugs involving operator
972 overloading and interface methods.
973 - Behavior is very similar to that for BioPerl 1.4, with tag values
974 being stored generically as simple scalars. Results in a modest
977 - Split into a separate distribution on CPAN, primarily so development
978 isn't reliant on a complete BioPerl release.
979 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
980 is only available via Subversion (via bioperl-live main trunk)
982 - Common test bed for all BioPerl modules
984 - Common Module::Build-based subclass for all BioPerl modules
985 * Bio::DB::EUtilities
986 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
987 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
988 and user agent request posting and retrieval
989 * Test implementation and reorganization
990 - Tests have been reorganized into groups based on classes or use
992 - Automated test coverage is now online:
993 http://www.bioperl.org/wiki/Test_Coverage
994 - After this release, untested modules will be moved into a
995 separate developer distribution until tests can be derived.
996 Also, new modules to be added are expected to have a test suite
997 and adequate test coverage.
999 1.5.2 Developer release
1001 Full details of changes since 1.5.1 are available online at:
1002 http://www.bioperl.org/wiki/Change_log
1003 The following represents a brief overview of the most important changes.
1006 - Overhaul. Brand new system fully allows markers to have multiple
1007 positions on multiple maps, and to have relative positions. Should be
1008 backward compatible.
1011 - This module and all the modules in the Taxonomy directory now
1012 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
1017 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
1019 * New methods ancestor(), each_Descendent() and _handle_internal_id().
1021 * Allows for different database modules to create Bio::Taxon objects
1022 with the same internal id when the same taxon is requested from each.
1025 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
1027 * No longer includes the fake root node 'root'; there are multiple roots
1028 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
1031 * get_node() has new option -full
1033 * Caches data retrieved from website
1036 - Now a Bio::Taxon. Carries out the species name -> specific name munging
1037 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
1038 backward compatability in species() method.
1040 o Bio::Search and Bio::SearchIO
1041 - Overhaul. The existing system has been sped up via some minor changes
1042 (mostly gain-of-function to the API). Bio::PullParserI is introduced
1043 as a potential eventual replacment for the existing system, though as
1044 yet only a Hmmpfam parser exists written using it.
1047 1.5.1 Developer release
1049 o Major problem with how Annotations were written out with
1050 Bio::Seq is fixed by reverting to old behavior for
1051 Bio::Annotation objects.
1056 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
1057 expect at l east 9 spaces at the beginning of a line to
1058 indicate line wrapping.
1060 * Treat multi-line SOURCE sections correctly, this defect broke
1061 both common_name() and classification()
1063 * parse swissprot fields in genpept file
1065 * parse WGS genbank records
1068 * Changed regexp for ID line. The capturing parentheses are
1069 the same, the difference is an optional repeated-not-semi-
1070 colon expression following the captured \S+. This means the
1071 regexp works when the division looks like /PRO;/ or when the
1072 division looks like /ANG ;/ - the latter is from EMBL
1075 * fix ID line parsing: the molecule string can have spaces in
1076 it. Like: "genomic DNA"
1078 - swiss.pm: bugs #1727, #1734
1081 * Added parser for entrezgene ASN1 (text format) files.
1082 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
1086 - maf.pm coordinate problem fixed
1088 o Bio::Taxonomy and Bio::DB::Taxonomy
1090 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
1091 can be done via Web without downloading all the sequence.
1093 o Bio::Tools::Run::RemoteBlast supports more options and complies
1094 to changes to the NCBI interface. It is reccomended that you
1095 retrieve the data in XML instead of plain-text BLAST report to
1096 insure proper parsing and retrieval of all information as NCBI
1097 fully expects to change things in the future.
1099 o Bio::Tree and Bio::TreeIO
1101 - Fixes so that re-rooting a tree works properly
1103 - Writing out nhx format from a newick/nexus file will properly output
1104 bootstrap information. The use must move the internal node labels over
1106 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
1107 $node->bootstrap($node->id);
1110 - Nexus parsing is much more flexible now, does not care about
1113 - Cladogram drawing module in Bio::Tree::Draw
1115 - Node height and depth now properly calculated
1117 - fix tree pruning algorithm so that node with 1 child gets merged
1119 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
1120 bugs and improvements were added, see Gbrowse mailing list for most of
1123 o Bio::DB::GFF partially supports GFF3. See information about
1124 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
1126 o Better location parsing in Bio::Factory::FTLocationFactory -
1127 this is part of the engine for parsing EMBL/GenBank feature table
1128 locations. Nested join/order-by/complement are allowed now
1130 o Bio::PrimarySeqI->translate now takes named parameters
1132 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
1133 reconstruction) is now supported. Parsing different models and
1134 branch specific parametes are now supported.
1136 o Bio::Factory::FTLocationFactory - parse hierarchical locations
1139 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
1140 for getter/setter functions
1144 - blast bug #1739; match scientific notation in score
1145 and possible e+ values
1147 - blast.pm reads more WU-BLAST parameters and parameters, match
1148 a full database pathname,
1150 - Handle NCBI WEB and newer BLAST formats specifically
1151 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
1153 - psl off-by-one error fixed
1155 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
1156 and HSPs can be constructed from them.
1158 - HSPs query/hit now have a seqdesc field filled out (this was
1159 always available via $hit->description and
1160 $result->query_description
1162 - hmmer.pm can parse -A0 hmmpfam files
1164 - Writer::GbrowseGFF more customizeable.
1166 o Bio::Tools::Hmmpfam
1167 make e-value default score displayed in gff, rather than raw score
1168 allow parse of multiple records
1171 1.5 Developer release
1173 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
1174 provide Jukes-Cantor and Kimura pairwise distance methods,
1177 o Bio::AlignIO support for "po" format of POA, and "maf";
1178 Bio::AlignIO::largemultifasta is a new alternative to
1179 Bio::AlignIO::fasta for temporary file-based manipulation of
1180 particularly large multiple sequence alignments.
1182 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
1183 be treated similarly as an assembled contig.
1185 o Bio::CodonUsage provides new rare_codon() and probable_codons()
1186 methods for identifying particular codons that encode a given
1189 o Bio::Coordinate::Utils provides new from_align() method to build
1190 a Bio::Coordinate pair directly from a
1191 Bio::Align::AlignI-conforming object.
1193 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
1194 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
1195 web service using standard Pubmed query syntax, and retrieve
1198 o Bio::DB::GFF has various sundry bug fixes.
1200 o Bio::FeatureIO is a new SeqIO-style subsystem for
1201 writing/reading genomic features to/from files. I/O classes
1202 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
1203 classes only read/write Bio::SeqFeature::Annotated objects.
1204 Notably, the GFF v3 class requires features to be typed into the
1207 o Bio::Graph namespace contains new modules for manipulation and
1208 analysis of protein interaction graphs.
1210 o Bio::Graphics has many bug fixes and shiny new glyphs.
1212 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
1213 indexing for HMMER reports and FASTA qual files, respectively.
1215 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
1216 new objects that can be placed within a Bio::Map::MapI-compliant
1217 genetic/physical map; Bio::Map::Physical provides a new physical
1218 map type; Bio::MapIO::fpc provides finger-printed clone mapping
1221 o Bio::Matrix::PSM provide new support for postion-specific
1222 (scoring) matrices (e.g. profiles, or "possums").
1224 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
1225 be instantiated without explicitly using Bio::OntologyIO. This
1226 is possible through changes to Bio::Ontology::OntologyStore to
1227 download ontology files from the web as necessary. Locations of
1228 ontology files are hard-coded into
1229 Bio::Ontology::DocumentRegistry.
1231 o Bio::PopGen includes many new methods and data types for
1232 population genetics analyses.
1234 o New constructor to Bio::Range, unions(). Given a list of
1235 ranges, returns another list of "flattened" ranges --
1236 overlapping ranges are merged into a single range with the
1237 mininum and maximum coordinates of the entire overlapping group.
1239 o Bio::Root::IO now supports -url, in addition to -file and -fh.
1240 The new -url argument allows one to specify the network address
1241 of a file for input. -url currently only works for GET
1242 requests, and thus is read-only.
1244 o Bio::SearchIO::hmmer now returns individual Hit objects for each
1245 domain alignment (thus containing only one HSP); previously
1246 separate alignments would be merged into one hit if the domain
1247 involved in the alignments was the same, but this only worked
1248 when the repeated domain occured without interruption by any
1249 other domain, leading to a confusing mixture of Hit and HSP
1252 o Bio::Search::Result::ResultI-compliant report objects now
1253 implement the "get_statistics" method to access
1254 Bio::Search::StatisticsI objects that encapsulate any
1255 statistical parameters associated with the search (e.g. Karlin's
1256 lambda for BLAST/FASTA).
1258 o Bio::Seq::LargeLocatableSeq combines the functionality already
1259 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
1261 o Bio::SeqFeature::Annotated is a replacement for
1262 Bio::SeqFeature::Generic. It breaks compliance with the
1263 Bio::SeqFeatureI interface because the author was sick of
1264 dealing with untyped annotation tags. All
1265 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
1266 compliant, and accessible through Bio::Annotation::Collection.
1268 o Bio::SeqFeature::Primer implements a Tm() method for primer
1269 melting point predictions.
1271 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
1272 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
1274 o Bio::Taxonomy::Node now implements the methods necessary for
1275 Bio::Species interoperability.
1277 o Bio::Tools::CodonTable has new reverse_translate_all() and
1278 make_iupac_string() methods.
1280 o Bio::Tools::dpAlign now provides sequence profile alignments.
1282 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
1284 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
1287 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
1288 for designing small inhibitory RNA.
1290 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
1291 methods based on a distance matrix.
1293 o Bio::Tree::Statistics provides an assess_bootstrap() method to
1294 calculate bootstrap support values on a guide tree topology,
1295 based on provided bootstrap tree topologies.
1297 o Bio::TreeIO now supports the Pagel (PAG) tree format.
1303 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
1305 o Bio::Graphics will work with gd1 or gd2
1308 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
1310 - blast.pm Parse multi-line query fields properly
1311 - small speed improvements to blasttable.pm and others
1313 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
1314 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
1315 supporting more complex queries
1318 1.4. Stable major release
1320 Since initial 1.2.0, 3000 separate changes have been made to make this release.
1322 o installable scripts
1324 o global module version from Bio::Root:Version
1327 - major improvements; SVG support
1330 - population genetics
1331 - support several population genetics types of questions.
1332 - Tests for statistical neutrality of mutations
1333 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
1334 Tests of population structure (Wright's F-statistic: Fst) is in
1335 Bio::PopGen::PopStats. Calculating composite linkage
1336 disequilibrium (LD) is available in Bio::PopGen::Statistics as
1338 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1339 and csv (comma delimited formatted) data.
1341 - a directory for implementing population simulations has
1342 been added Bio::PopGen::Simulation and 2 simulations - a
1343 Coalescent and a simple single-locus multi-allele genetic drift
1344 simulation have been provided. This replaces the code in
1345 Bio::Tree::RandomTree which has been deprecated until proper
1346 methods for generating random phylogenetic trees are
1350 - new restrion analysis modules
1352 o Bio::Tools::Analysis
1353 - web based DNA and Protein analysis framework and several
1357 - per residue annotable sequences
1360 - Bio::Matrix::PSM - Position Scoring Matrix
1361 - Bio::Matrix::IO has been added for generalized parsing of
1362 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1363 initial implementations for parsing BLOSUM/PAM and Phylip
1364 Distance matricies respectively. A generic matrix
1365 implementation for general use was added in
1366 Bio::Matrix::Generic.
1373 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1374 - small inhibitory RNA
1376 o Bio::SeqFeature::Tools
1377 - seqFeature mapping tools
1378 - Bio::SeqFeature::Tools::Unflattener.pm
1379 -- deal with mapping GenBank feature collections into
1380 Chado/GFF3 processable feature sets (with SO term mappings)
1382 o Bio::Tools::dpAlign
1383 - pure perl dynamic programming sequence alignment
1386 o new Bio::SearchIO formats
1387 - axt and psl: UCSC formats.
1388 - blasttable: NCBI -m 8 or -m 9 format from blastall
1390 o new Bio::SeqIO formats
1391 - chado, tab, kegg, tigr, game
1392 - important fixes for old modules
1396 o improved Bio::Tools::Genewise
1398 o Bio::SeqIO now can recongnize sequence formats automatically from
1401 o new parsers in Bio::Tools:
1402 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1404 o Bio::DB::Registry bugs fixed
1405 - BerkeleyDB-indexed flat files can be used by the OBDA system
1406 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1407 used by the OBDA system
1409 o several new HOWTOs
1410 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1413 o hundreds of new and improved files
1417 o Bio::Tree::AlleleNode has been updated to be a container of
1418 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1423 1.2.3 Stable release update
1424 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1426 o Bug #1477 - Sel --> Sec abbreviation fixed
1427 o Fix bug #1487 where paring in-between locations when
1428 end < start caused the FTLocationFactory logic to fail.
1429 o Fix bug #1489 which was not dealing with keywords as an
1430 arrayref properly (this is fixed on the main trunk because
1431 keywords returns a string and the array is accessible via
1433 o Bio::Tree::Tree memory leak (bug #1480) fixed
1434 Added a new initialization option -nodelete which
1435 won't try and cleanup the containing nodes if this
1437 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1438 this was only present on the branch for the 1.2.1 and 1.2.2 series
1439 - Also merged main trunk changes to the branch which make
1440 newick -> nhx round tripping more effective (storing branch length
1441 and bootstrap values in same locate for NodeNHX and Node
1442 implementations.) Fixes to TreeIO parsing for labeled internal
1443 also required small changes to TreeIO::nhx. Improved
1444 tests for this module as well.
1446 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1447 gapped blast properly (was losing hit significance values due to
1448 the extra unexpeted column).
1449 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1450 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1451 although doesn't try to correct it - will get the negative
1452 number for you. Added a test for this as well.
1453 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1454 has no top-level family classification scores but does have scores and
1455 alignments for individual domains.
1456 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1457 regular expression to match the line was missing the possibility of
1458 an extra space. This is rare, which is why we probably did not
1460 - BLAST parsing picks up more of the statistics/parameter fields
1461 at the bottom of reports. Still not fully complete.
1462 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1463 were fixed to include many improvements and added flexiblity
1464 in outputting the files. Bug #1495 was also fixed in the process.
1466 - Update for GFF3 compatibility.
1467 - Added scripts for importing from UCSC and GenBank.
1468 - Added a 1.2003 version number.
1471 - Added a 1.2003 version number.
1472 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1473 properly writing keywords out.
1474 o Bio::SeqIO::genbank
1475 - Fixed bug/enhancement #1513 where dates of
1476 the form D-MMM-YYYY were not parsed. Even though this is
1477 invalid format we can handle it - and also cleanup the date
1478 string so it is properly formatted.
1479 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1480 and written with Genbank format. Similarly bug #1515 is fixed to
1481 parse in the ORIGIN text.
1482 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1483 to specify the ID type, one of (accession accession.version
1484 display primary). See Bio::SeqIO::preferred_id_type method
1485 documentation for more information.
1486 o Unigene parsing updated to handle file format changes by NCBI
1488 1.2.2 Stable release update
1490 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1491 - auto-discover ontology name
1492 - bug in parsing relationships when certain characters are in the term
1493 - fixed hard-coded prefix for term identifiers
1494 - various smaller issues
1496 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1497 of Bio::Ontology::TermI
1499 o brought the OBDA Registry code up to latest specs
1503 - accession number retrieval fixed
1505 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1507 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1508 #1459 which now properly report alignment start/end info
1509 for translated BLAST/FASTA searches.
1511 o Bio::TreeIO::newick can parse labeled internal nodes
1513 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1514 for BLASTX if if you provide -report_type => 'BLASTX' when
1515 initializing a BPbl2seq object. Bioperl 1.3 will have better
1516 support for bl2seq in the SearchIO system.
1518 o Bio::Root::IO support a -noclose boolean flag which will not
1519 close a filehandle upon object cleanup - useful when sharing
1520 a filehandle among objects. Additionally code added s.t.
1521 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1523 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1525 o Bio::SeqIO::genbank
1526 - bug #1456 fixed which generated extra sequence lines
1527 - write moltype correctly for genpept
1529 1.2.1 Stable release update
1531 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1533 o Addition from main trunk of Ontology objects, principly to allow
1534 BioSQL releases against 1.2.1
1536 o Fixes and cleanup of Bio::Coordinate modules
1538 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1539 the primary accession number
1541 o Other bug fixes, including bpindex GenBank fix
1543 o Bio::SeqIO::genbank bug #1389 fixed
1545 1.2 Stable major release
1547 o More functionality added to Bio::Perl, the newbie module
1549 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1550 Support for New Hampshire Extended (NHX) format parsing.
1552 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1553 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1556 o New ontology parsing Bio::Ontology
1558 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1559 multi-report (mlib) fasta reports, support for waba and exonerate.
1561 o Bio::ClusterIO for parsing Unigene clusters
1563 o Bio::Assembly added for representing phrap and ace assembly clusters.
1565 o Rudimentary support for writing Chado XML (see
1566 GMOD project: www.gmod.org for more information)
1568 o Bio::Coordinate for mapping between different coordinate systems such
1569 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1570 features into different coordinate systems.
1572 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1573 with the get_Stream_by_query method and supports the latest
1574 NCBI eutils interface.
1576 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1577 object for extracting subsets of features : currently only
1578 supports extraction by location.
1580 1.1.1 Developer release
1582 o Deprecated modules are now listed in the DEPRECATED file
1584 o New HowTo documents located in doc/howto describing
1585 a domain of Bioperl.
1587 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1588 and all old bugs are searchable through the bugzilla interface.
1590 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1591 have been addressed.
1593 o Support for Genewise parsing in Bio::Tools::Genewise
1595 o Start of Ontology framework with Bio::Ontology
1597 o Speedup to the Bio::Root::Root object method _rearrange.
1598 A global _load_module method was implemented to simplify the
1599 dynamic loading of modules ala Bio::SeqIO::genbank. This
1600 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1603 o Several performance improvements to sequence parsing in Bio::SeqIO.
1604 Attempt to speedup by reducing object creation overhead.
1606 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1607 method for sequence retrieval with their E-utils CGI scripts.
1608 More work to support Entrez queries to their fullest is planned
1611 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1613 1.1 Developer release
1615 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1616 this separation removes some of the complexity in our test suite
1617 and separates the core modules in bioperl from those that need
1618 external programs to run.
1620 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1621 not run into trouble running the makefile
1623 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1624 read,create,and write locations for grouped/split locations
1625 (like mRNA features on genomic sequence).
1627 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1628 and PAML (codeml,aaml, etc) parsing.
1630 o Bio::Tree:: objects expanded to handle testing monophyly,
1631 paraphyly, least common ancestor, etc.
1633 o Bio::Coordinate for mapping locations from different coordinate spaces
1635 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1636 added for parsing hmmpfam and hmmsearch output.
1638 o Bio::SearchIO::Writer::TextResultWriter for outputting
1639 a pseudo-blast textfile format
1642 1.0.2 Bug fix release
1644 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1645 in this release will not work after December 2002 when NCBI
1646 shuts off the old Entrez cgi scripts. We have already fixed
1647 on our main development branch and the functionality will be
1648 available in the next stable bioperl release (1.2) slated for
1651 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1652 testset by Robin Emig. These were fixed as was the get_aln
1653 method in Bio::Search::HSP::GenericHSP to handle the extra
1654 context sequence that is provided with a FastA alignment.
1656 o Migrating differences between Bio::Search::XX::BlastXX to
1657 Bio::Search::XX::GenericXX objects. This included mechanism
1658 to retrieve whole list of HSPs from Hits and whole list of Hits from
1659 Results in addition to the current next_XX iterator methods that
1660 are available. Added seq_inds() method to GenericHSP which identifies
1661 indexes in the query or hit sequences where conserved,identical,gaps,
1662 or mismatch residues are located (adapted from Steve Chervitz's
1663 implementation in BlastHSP).
1665 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1666 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1668 o Bio::Graphics glyph set improved and extended for GBrowse release
1670 o Bio::Tree::Tree get_nodes implementation improvement thanks
1671 to Howard Ross notice performance problem when writing out
1674 o Bio::Location::Fuzzy::new named parameter -loc_type became
1675 -location_type, Bio::Location::Simple::new named parameter
1676 -seqid becamse -seq_id.
1678 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1679 was mis-detecting that gaps should be placed at the beginning of
1680 the alignment when the best alignment starts internally in the
1683 1.0.1 Bug fix release
1685 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1687 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1688 and mixed (3.3 - 3.4) versions of FASTA.
1690 o Small API change to add methods for completeness across
1691 implementations of Bio::Search objects. These new methods
1692 in the interface are implemented by the GenericXX object as well
1693 as the BlastXX objects.
1694 * Bio::Search::Result::ResultI
1695 - hits() method returns list of all Hits (next_hit is an
1698 * Bio::Search::Hit::HitI
1699 - hsps() method returns list of all HSPs (next_hsp is an
1702 o The Bio::SearchIO::Writer classes have been fixed to handle results
1703 created from either psiblast (Search::BlastXX objects) or
1704 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1705 has to be done here to make it work properly and will nee major
1708 o Bugs in Bio::Tools::HMMER fixed, including
1709 * #1178 - Root::IO destructor wasn't being called
1710 * #1034 - filter_on_cutoff now behaves properly
1712 o Bio::SeqFeature::Computation initialization args fixed and
1715 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1717 o Updated FAQ with more example based answers to typical questions
1719 o Bug #1202 was fixed which would improperly join together qual values
1720 parsed by Bio::SeqIO::qual when a trailing space was not present before
1723 1.0.0 Major Stable Release
1725 This represents a major release of bioperl with significant
1726 improvements over the 0.7.x series of releases.
1728 o Bio::Tools::Blast is officially deprecated. Please see
1729 Bio::SearchIO for BLAST and FastA parsing.
1731 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1732 Bio::LocationI objects as well as start/end.
1734 o Bio::Biblio contains modules for Bibliographic data.
1735 Bio::DB::Biblio contains the query modules. Additionally one can
1736 parse medlinexml from the ebi bibliographic query service (BQS)
1737 system and Pubmed xml from NCBI. See Martin Senger's
1738 documentation in Bio::Biblio for more information.
1740 o Bio::DB::Registry is a sequence database registry part of
1741 Open Bioinformatics Database Access. See
1742 http://obda.open-bio.org for more information.
1744 o File-based and In-Memory Sequence caching is provided by
1745 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1748 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1749 been added by Lincoln Stein.
1751 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1753 o A FAQ has been started and is included in the release to provide
1754 a starting point for frequent questions and issues.
1756 0.9.3 Developer's release
1758 o Event based parsing system improved (SearchIO). With parsers for
1759 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1760 Additionally a lazy parsing system for text and html blast reports was
1761 added and is called psiblast (name subject to change in future releases).
1763 o Bio::Search objects improved and standardized with associated Interfaces
1764 written. The concept of a search "Hit" was standardized to be called
1765 "hit" consistently and the use of "subject" was deprecated in all active
1768 o Bio::Structure added (since 0.9.1) for Protein structure objects
1769 and PDB parser to retrieve and write these structures from data files.
1771 o Several important Bio::DB::GFF bug fixes for handling features that
1772 are mapped to multiple reference points. Updated mysql adaptor
1773 so as to be able to store large (>100 megabase) chunks of DNA into
1774 Bio::DB::GFF databases.
1776 0.9.2 Developer's release
1778 o Bio::Search and Bio::SearchIO system introduced for event based
1779 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1780 in text and XML and FASTA reports in standard output format.
1782 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1783 generator is included in Bio::TreeIO::RandomTrees and a
1784 statistics module for evaluating.
1786 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1787 server for DAS servers.
1789 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1790 files. The entire BPlite system migrated to using Bio::Root::IO
1791 for the data stream.
1793 o Bio::Tools::Alignment for Consed and sequence Trimming
1796 o Bio::Structure for Protein structure information and parsing
1798 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1799 cgi-bin entry point which should be more reliable.
1801 o Bio::Map and Bio::MapIO for biological map navigation and a
1802 framework afor parsing them in. Only preliminary work here.
1804 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1805 Future work will integrate Pise and allow submission of analysis on
1808 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1809 introduced as new objects for handling Sequence Annotation
1810 information (dblinks, references, etc) and is more robust that
1813 o Bio::Tools::FASTAParser introduced.
1815 o Scripts from the bioperl script submission project and new
1816 scripts from bioperl authors are included in "scripts" directory.
1818 o Factory objects and interfaces are being introduced and are more
1821 o Bio::Root::Root introduced as the base object while
1822 Bio::Root::RootI is now simply an interface.
1824 o Bio::DB::RefSeq provides database access to copy of the NCBI
1825 RefSeq database using the EBI dbfetch script.
1827 0.9.0 Developer's release
1829 o perl version at least 5.005 is now required instead of perl 5.004
1831 o Bio::Tools::Run::RemoteBlast is available for running remote
1834 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1836 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1837 Also added are related modules UTR3, UTR5, Exon, Intron,
1838 Promotor, PolyA and Transcript.
1840 o Speedup of translate method in PrimarySeq
1842 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1843 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1845 o Various fixes to Variation toolkit
1847 o Bio::DB::EMBL provides database access to EMBL sequence data.
1848 Bio::DB::Universal provides a central way to point to indexes
1849 and dbs in a single interface.
1851 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1853 o Bio::Factory::EMBOSS is still in design phase as is
1854 Bio::Factory::ApplicationFactoryI
1856 o Dia models for bioperl design are provided in the models/ directory
1858 0.7.2 Bug fix release
1860 o documentation fixes in many modules - SYNOPSIS code verified
1861 to be runnable in many (but not all modules)
1863 o corrected MANIFEST file from 0.7.1 release
1865 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1868 o Bio::SeqIO::genbank
1869 * Correct parsing and writing of genbank format with protein data
1870 * moltype and molecule separation
1872 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1874 o Bio::SimpleAlign fixed to correctly handle consensus
1875 sequence calculation
1877 o Bio::Tools::HMMER supports hmmer 2.2g
1879 o Bio::Tools::BPlite to support report type specific parsing. Most
1880 major changes are not on the 0.7 branch.
1882 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1885 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1886 in several types of mutations:
1887 1.) AA level: deletion, complex
1888 2.) AA level: complex, inframe
1889 3.) RNA level: silent
1891 o BPbl2seq parsing of empty reports will not die, but will return
1892 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1893 $report->query() and $report->subject() methods. So an easy
1894 way to test if report was empty is to see if
1895 $report->query->seqname is undefined.
1897 0.7.1 Bug fix release
1899 o Better parsing of genbank/EMBL files especially fixing bugs
1900 related to Feature table parsing and locations on remote
1901 sequences. Additionally, species name parsing was better.
1903 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1904 which include a number of header lines.
1906 o More strict genbank and EMBL format writing (corrected number of
1907 spaces where appropriate).
1909 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1910 for related BPlite BUGS that are unresolved in this release.
1912 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1913 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1914 use expasy mirrors or EBI dbfetch cgi-script.
1916 o A moderate number of documentation improvements were made as
1917 well to provide a better code synopsis in each module.
1920 0.7 Large number of changes, including refactoring of the
1921 Object system, new parsers, new functionality and
1922 all round better system. Highlights are:
1925 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1926 Bio::Root::IO for I/O and file/handle capabilities.
1928 o Imported BPlite modules from Ian Korf for BLAST
1929 parsing. This is considered the supported BLAST parser;
1930 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1932 o Improved Sequence Feature model. Added complete location
1933 modelling (with fuzzy and compound locations). See
1934 Bio::LocationI and the modules under Bio/Location. Added
1935 support in Genbank/EMBL format parsing to completely parse
1936 feature tables for complex locations.
1938 o Moved special support for databanks etc to specialized modules under
1939 Bio/Seq/. One of these supports very large sequences through
1940 a temporary file as a backend.
1942 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1943 CDS retrieval and exon shuffling.
1945 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1947 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1948 DB/GDB (the latter has platform-specific limitations).
1950 o New analysis parser framework for HT sequence annotation (see
1951 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1953 o New Alignment IO framework
1955 o New Index modules (Swissprot)
1957 o New modules for running Blast within perl
1958 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1959 Multiple Sequence Alignment tools ClustalW and TCoffee
1960 (Bio::Tools::Run::Alignment).
1962 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1963 documentation across the package.
1965 o Much improved cross platform support. Many known incompatibilities
1966 have been fixed; however, NT and Mac do not work across the entire
1967 setup (see PLATFORMS).
1969 o Many bug fixes, code restructuring, etc. Overall stability and
1970 maintainability benefit a lot.
1972 o A total of 957 automatic tests
1977 There are very few functionality changes but a large
1978 number of software improvements/bug fixes across the package.
1980 o The EMBL/GenBank parsing are improved.
1982 o The Swissprot reading is improved. Swissprot writing
1983 is disabled as it doesn't work at all. This needs to
1984 wait for 0.7 release
1986 o BLAST reports with no hits are correctly parsed.
1988 o Several other bugs of the BLAST parser (regular expressions, ...)
1991 o Old syntax calls have been replaced with more modern syntax
1993 o Modules that did not work at all, in particular the Sim4
1994 set have been removed
1996 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1997 have improved compliance with interface specs and documentation
1999 o Mailing list documentation updated throughout the distribution
2001 o Most minor bug fixes have happened.
2003 o The scripts in /examples now work and have the modern syntax
2004 rather than the deprecated syntax
2007 0.6.1 Sun April 2 2000
2009 o Sequences can have Sequence Features attached to them
2010 - The sequence features can be read from or written to
2011 EMBL and GenBank style flat files
2013 o Objects for Annotation, including References (but not
2014 full medline abstracts), Database links and Comments are
2017 o A Species object to represent nodes on a taxonomy tree
2020 o The ability to parse HMMER and Sim4 output has been added
2022 o The Blast parsing has been improved, with better PSI-BLAST
2023 support and better overall behaviour.
2025 o Flat file indexed databases provide both random access
2026 and sequential access to their component sequences.
2028 o A CodonTable object has been written with all known
2029 CodonTables accessible.
2031 o A number of new lightweight analysis tools have been
2032 added, such as molecular weight determination.
2034 The 0.6 release also has improved software engineering
2036 o The sequence objects have been rewritten, providing more
2037 maintainable and easier to implement objects. These
2038 objects are backwardly compatible with the 0.05.1 objects
2040 o Many objects are defined in terms of interfaces and then
2041 a Perl implementation has been provided. The interfaces
2042 are found in the 'I' files (module names ending in 'I').
2044 This means that it is possible to wrap C/CORBA/SQL access
2045 as true "bioperl" objects, compatible with the rest of
2048 o The SeqIO system has been overhauled to provide better
2049 processing and perl-like automatic interpretation of <>
2052 o Many more tests have been added (a total of 172 automatic
2053 tests are now run before release).
2057 0.05.1 Tue Jun 29 05:30:44 1999
2058 - Central distribution now requires Perl 5.004. This was
2059 done to get around 5.003-based problems in Bio/Index/*
2061 - Various bug fixes in the Bio::Tools::Blast modules
2062 including better exception handling and PSI-Blast
2063 support. See Bio/Tools/Blast/CHANGES for more.
2064 - Fixed the Parse mechanism in Seq.pm to use readseq.
2065 Follow the instructions in README for how to install
2066 it (basically, you have to edit Parse.pm).
2067 - Improved documentation of Seq.pm, indicating where
2068 objects are returned and where strings are returned.
2069 - Fixed uninitialized warnings in Bio::Root::Object.pm
2070 and Bio::Tools::SeqPattern.pm.
2071 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
2073 0.05 Sun Apr 25 01:14:11 1999
2074 - Bio::Tools::Blast modules have less memory problems
2075 and faster parsing. Webblast uses LWP and supports
2076 more functionality. See Bio/Tools/Blast/CHANGES for more.
2077 - The Bio::SeqIO system has been started, moving the
2078 sequence reformatting code out of the sequence object
2079 - The Bio::Index:: system has been started, providing
2080 generic index capabilities and specifically works for
2081 Fasta formatted databases and EMBL .dat formatted
2083 - The Bio::DB:: system started, providing access to
2084 databases, both via flat file + index (see above) and
2086 - The scripts/ directory, where industrial strength scripts
2087 are put has been started.
2088 - Many changes - a better distribution all round.
2090 0.04.4 Wed Feb 17 02:20:13 1999
2091 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
2092 (see Bio::Tools::Blast::CHANGES).
2093 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
2094 - Beefed up the t/Fasta.t test script.
2095 - Small fix in Bio::Seq::type() (now always returns a string).
2096 - Changed Bio::Root::Utilities::get_newline_char() to
2097 get_newline() since it could return more than one char.
2098 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
2099 - Changed default timeout to 20 seconds (was 3).
2100 - Moved lengthy modification notes to the bottom of some files.
2101 - Fixed SimpleAlign write_fasta bug.
2102 - Beefed up SimpleAlign.t test
2104 0.04.3 Thu Feb 4 07:48:53 1999
2105 - Bio::Root::Object.pm and Global.pm now detect when
2106 script is run as a CGI and suppress output that is only
2107 appropriate when running interactively.
2108 - Bio::Root::Err::_set_context() adds name of script ($0).
2109 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
2110 regarding the use of the static objects via the qw(:obj) tag.
2111 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
2112 CORE::reverse, avoiding Perl warnings.
2113 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
2114 example scripts (see Bio::Tools::Blast::CHANGES).
2115 - examples/seq/seqtools.pl no longer always warns about using
2116 -prot or -nucl command-line arguments; only when using the
2118 - Methods added to Bio::Root::Utilities: create_filehandle(),
2119 get_newline_char(), and taste_file() to generalize filehandle
2120 creation and autodetect newline characters in files/streams
2121 (see bug report #19).
2122 - Bio::Root::IOManager::read() now handles timeouts and uses
2123 Utilities::create_filehandle().
2124 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
2125 of hardwiring in "\n".
2126 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
2128 0.04.2 Wed Dec 30 02:27:36 1998
2129 - Bug fixes in Bio::Tools::Blast modules, version 0.073
2130 (see Bio::Tools::Blast::CHANGES).
2131 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
2132 to CORE::reverse (prevents ambiguous warnings with 5.005).
2133 - Appending '.tmp.bioperl' to temporary files created by
2134 Bio::Root::Utilities::compress() or uncompress() to
2135 make it easy to identify & cleanup these files as needed.
2136 - Developers: Created CVS branch release-0-04-bug from
2137 release-0-04-1. Before making bug fixes to the 0.04.1 release,
2138 be sure to cvs checkout this branch into a clean area.
2140 0.04.1 Wed Dec 16 05:39:15 1998
2141 - Bug fixes in Bio::Tools::Blast modules, version 0.072
2142 (see Bio::Tools::Blast::CHANGES).
2143 - Compile/SW/Makefile.PL now removes *.o and *.a files
2146 0.04 Tue Dec 8 07:49:19 1998
2147 - Lots of new modules added including:
2148 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
2149 and Bio/Compile directory containing XS-linked C code for
2150 creating Smith-Waterman sequence alignments from within Perl.
2151 * Steve Chervitz's Blast distribution has been incorporated.
2152 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
2153 - Bio/examples directory for demo scripts for all included modules.
2154 - Bio/t directory containing test suit for all included modules.
2155 - For changes specific to the Blast-related modules prior to
2156 incorporation in this central distribution, see the CHANGES
2157 file in the Bio/Tools/Blast directory.
2159 0.01 Tue Sep 8 14:23:22 1998
2160 - original version from central CVS tree; created by h2xs 1.18