1 Summary of important user-visible changes for BioPerl
2 -----------------------------------------------------
5 * Add minimum dependency on base.pm v2.18. Fixes bug in some cases when
6 using SUPER::new() [#307].
7 * Fix test for BSML SAX by using lax parser XML::SAX::PurePerl since
8 the external DTD URL now 404s [#376].
10 1.7.8 2021-02-02 23:02:18-06:00 America/Chicago
11 * Bio::SeqIO::interpro has been moved to a separate repository to
12 deal with issues with XML::DOM::XPath bitrot [#347]
14 * Adjust Swiss-Prot FT A..B lines [#348] from @smoe
15 * Update %FTQUAL_NO_QUOTE: List of qualifiers without quote [#339] from
18 1.7.7 2019-12-07 13:41:36-06:00 America/Chicago
20 * The program bp_chaos_plot has been removed.
22 * GD is now no longer a dependency, suggestion or requirement.
24 * #321 - GenBank format fix for un-quoted features, text wrapping
26 * Bio::DB::Query::WebQuery now includes methods for delay(), delay_policy(),
27 and a 'private' _sleep() function that mirror those from
28 Bio::DB::WebDBSeqI, primarily for compliance with potential website
29 restrictions for the number and frequency of queries (e.g. NCBI eUtils).
31 * Fix bug #329, related to Bio::Tree::Statistics::transfer_bootstrap_expectation
34 1.7.6 2019-08-28 12:37:01+01:00 Europe/London
36 * The program bp_classify_hits_kingdom has been removed and is
37 now part of the examples documentation instead.
39 * GD is now listed as a suggestion instead of a requirement. The
40 bp_chaos_plot program will now work with the GD module.
42 * New method Bio::Tree::Statistics::transfer_bootstrap_expectation
43 to compute Transfer Bootstrap Expectation (TBE) for internal
44 nodes based on the methods outlined in Lemoine et al, Nature,
47 * New method Bio::SeqIO::fasta::next_seq_fast to retrieve next
48 sequence in the stream faster but not perfect.
51 1.7.5 2019-02-11 14:57:45+00:00 Europe/London
53 * The following modules have been removed from the BioPerl
54 distribution to be part of a separate distribution with
55 independent development:
59 * The Bio::Seq::SeqWithQuality module, which was deprecated since
60 2001, was finally removed.
62 * The deprecated() method has been deprecated. It is recommended
63 to use Carp::carp to warn.
65 * The following methods have been deprecated for a long while and
66 have now been removed:
68 Bio::Align::AlignI->no_residues
69 Bio::Align::AlignI->no_sequences
70 Bio::LocatableSeq->no_gap
71 Bio::LocatableSeq->no_sequences
72 Bio::SeqFeature::Generic->slurp_gff_file
73 Bio::SimpleAlign->no_residues
74 Bio::SimpleAlign->no_sequences
77 1.7.4 2019-02-05 16:23:53+00:00 Europe/London
79 * Fix Bio::Root::Test, and the testuite, to properly check for
80 internet connection and the NO_NETWORK_TESTING environment
81 variable. Previously, tests that required internet connection
82 were not being skipped, causing tests to fail.
85 1.7.3 2019-01-30 13:30:34+00:00 Europe/London
87 * The following modules have been removed from the BioPerl
88 distribution to be part of a separate distribution. They have
89 been integrated into other module distributions for independent
94 Bio::AlignIO::stockholm
104 Bio::DB::Expression::*
106 Bio::DB::GFF::Adaptor::*
107 Bio::DB::GFF::Aggregator::*
108 Bio::DB::GFF::Featname
109 Bio::DB::GFF::Feature
111 Bio::DB::GFF::RelSegment
112 Bio::DB::GFF::Segment
113 Bio::DB::GFF::Typename
119 Bio::DB::Query::GenBank
120 Bio::DB::Query::HIVQuery
122 Bio::DB::SeqFeature::*
123 Bio::DB::SeqVersion::*
126 Bio::DB::Taxonomy::entrez
127 Bio::DB::Taxonomy::sqlite
130 Bio::Factory::MapFactoryI
132 Bio::Index::Stockholm
136 Bio::MolEvol::CodonModel
145 Bio::Search::HSP::HMMERHSP
146 Bio::Search::HSP::HmmpfamHSP
147 Bio::Search::Hit::HMMERHit
148 Bio::Search::Hit::HmmpfamHit
149 Bio::Search::Hit::hmmer3Hit
150 Bio::Search::Result::HMMERResult
151 Bio::Search::Result::HmmpfamResult
152 Bio::Search::Result::hmmer3Result
155 Bio::SearchIO::hmmer2
156 Bio::SearchIO::hmmer3
157 Bio::SearchIO::hmmer_pull
159 Bio::SeqFeature::SiRNA::*
167 Bio::SeqIO::entrezgene
170 Bio::SeqIO::flybase_chadoxml
171 Bio::SeqIO::lasergene
178 Bio::Tools::AlignFactory
179 Bio::Tools::Analysis::* (except SimpleAnalysisBase)
183 Bio::Tools::Phylo::Gumby
184 Bio::Tools::Protparam
185 Bio::Tools::Run::RemoteBlast
189 Bio::Tree::AlleleNode
190 Bio::Tree::Draw::Cladogram
192 Bio::TreeIO::svggraph
195 * The following modules are new in the BioPerl distribution. They
196 have been previously released in the BioPerl-Run distribution.
197 This will enable smaller distributions that provide a
198 Bio::Tool::Run interface, to be only dependent on the BioPerl
199 distribution instead of the whole (very large) BioPerl-Run:
201 Bio::Tools::Run::Analysis
202 Bio::Tools::Run::AnalysisFactory
203 Bio::Tools::Run::Phylo::PhyloBase
204 Bio::Tools::Run::WrapperBase
205 Bio::Tools::Run::WrapperBase::CommandExts
207 * The following programs have been removed:
209 bp_biofetch_genbank_proxy
214 bp_download_query_genbank
218 bp_generate_histogram
219 bp_heterogeneity_test
233 * Because of the move of so many modules and programs into
234 separate distributions, the following modules are no longer
243 Bio::ASN1::EntrezGene
244 Bio::Expression::Contact
245 Bio::Expression::DataSet
246 Bio::Expression::Platform
247 Bio::Expression::Sample
249 Bio::GMOD::CMap::Utils
251 Bio::Phylo::Forest::Tree
254 Bio::Phylo::Matrices::Datum
255 Bio::Phylo::Matrices::Matrix
256 Bio::SeqFeature::Annotated
257 Bio::SeqIO::staden::read
258 Bio::Tools::Run::Alignment::Clustalw
259 Bio::Tools::Run::Ensembl
260 Bio::Tools::Run::Phylo::Molphy::ProtML
261 Bio::Tools::Run::Phylo::Phylip::Neighbor
262 Bio::Tools::Run::Phylo::Phylip::ProtDist
263 Bio::Tools::Run::Phylo::Phylip::ProtPars
264 Bio::Tools::Run::Samtools
272 Data::Stag::XMLWriter
288 PostScript::TextBlock
292 SVG::Graph::Data::Node
293 SVG::Graph::Data::Tree
295 Spreadsheet::ParseExcel
297 Text::NSP::Measures::2D::Fisher2::twotailed
305 * The following is a new prerequisite:
307 Test::RequiresInternet
309 * The deobfuscator has been removed.
311 * The emacs bioperl minor mode is no longer distributed as part of the
312 perl module distributions. See
313 https://github.com/bioperl/emacs-bioperl-mode
320 * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
321 * #245 - Code coverage fixes [zmughal,cjfields]
322 * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
323 * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
324 * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
325 * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
326 * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
327 * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
328 * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
329 * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
330 * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
331 * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
335 * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
341 * Minor release to incorporate fix for CPAN indexing, which
342 prevented proper updates [cjfields]
343 * Fix problem in managing Target attribute for gff3 [Jukes34]
344 * Minor bug fixes related to NCBI HTTPS support [cjfields]
350 * We have migrated to Github Pages. This was actually planned, but the
351 recent OBF server compromise forced our hand.
353 Brian Osborne [bosborne] took this under his wing to move docs and has
354 done a tremendous amount of work formatting the site and working out some
355 of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
356 Cantalupo and Franscison Ossandon also helped. Kudos!!
358 * Similarly, the official issue tracker is now Github Issues. This has
359 been updated in the relevant documentation bits (we hope!)
363 * Previously deprecated modules removed
364 * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
365 * Bio::DB::SeqHound has been removed due to the service no longer being
367 * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
368 reasons due to the server no longer having a valid cert
369 * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
370 * Bio::Coordinate, Bio::SearchIO::blastxml,
371 Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
376 * Docker instances of tagged releases are available! [hlapp]
377 * NCBI HTTPS support [mjohnson and others]
378 * Bio::SearchIO::infernal
379 - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
380 * Bio::Search::HSP::ModelHSP
381 - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
383 * Bio::Search::Result::INFERNALResult
384 - Added new module to represent features of Infernal reports [pcantalupo]
385 * Bio::DB::Taxonomy SQLite option [cjfields]
386 * WrapperBase quoted option values [majensen]
387 * Various documentation fixes and updates [bosborne]
391 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
392 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
393 * NeXML parser fixes [fjossandon]
394 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
395 * RT 103272 : SeqFeature database deletion skipped features with a decimal -
396 Joshua Fortriede (Xenbase)
397 * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
398 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
399 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
400 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
401 * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
402 * Issue #84: EMBL format wrapping problem [nyamned]
403 * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
404 * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
405 or compiled C code (when Inline::C is installed) [rocky]
406 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
407 * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
408 * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
409 * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
410 to be consistent with "$hit->bits" behaviour [fjossandon]
411 * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
412 aminoacids made "next_seq" confused and broke the parser [fjossandon]
413 * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
414 Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
415 to "complement(join(A..B,C..D))" [fjossandon]
416 * For the many many many fixes that weren't mentioned - blame the release guy!
420 [Significant changes]
422 * Bug/feature issue tracking has moved to GitHub Issues:
423 https://github.com/bioperl/bioperl-live/issues
424 * DB_File has been demoted from "required" to "recommended",
425 which should make easier for Windows users to install BioPerl
426 if they don't need that module.
430 * Bio::Search::HSP::GenericHSP
431 - Bug #3370, added a "posterior_string" method to retrieve the
432 posterior probability lines (PP) from HMMER3 reports [fjossandon]
433 - Added a "consensus_string" method to retrieve the consensus
434 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
435 * Bio::SearchIO::hmmer2
436 - The number of identical and conserved residues are now calculated
437 directly from the homology line [fjossandon]
438 - Now the Query Length and Hit Length are reported when the alignment
439 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
440 - Implemented the capture of the consensus structure lines [fjossandon]
441 * Bio::SearchIO::hmmer3
442 - The number of identical and conserved residues are now calculated
443 directly from the homology line [fjossandon]
444 - Now the Hit Length is reported when the alignment runs until the end
445 of the sequence/model ('.]' or '[]') [fjossandon]
446 - Implemented the capture of the consensus structure lines [fjossandon]
447 - Implemented the capture of the posterior probability lines [fjossandon]
448 - Completed the development of NHMMER parsing, including alignments [fjossandon]
449 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
450 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
451 "min_score", "min_bits, and "hit_filter" methods from
452 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
453 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
454 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
455 besides Blast, instead of being ignored. Added tests for all moved methods
456 using HMMER outputs and run the full test suite and everything pass [fjossandon]
457 * Bio::SeqIO::MultiFile
458 - Autodetection of file format [fangly]
459 * Bio::Tools::GuessSeqFormat:
460 - Format detection from non-seekable filehandles such as STDIN [fangly]
464 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
465 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
466 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
467 * Abstract: Fixed ActivePerl incapability of removing temporary files
468 because of problems closing tied filehandles [fjossandon]
469 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
470 because ActivePerl were producing a ".index.pag" and ".index.dir"
471 files instead of a single ".index" file (like Strawberry Perl).
472 Now those temporary files are correctly considered and deleted. [fjossandon]
473 * Test files: Added missing module requirements (DB_File and Data::Stag)
474 to several tests files that were failing because those modules were
475 not present. Now those test files are correctly skipped instead. [fjossandon]
476 * Blast: Added support to changes in bl2seq from BLAST+ output, which
477 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
478 * Phylip: Return undef in "next_aln" at file end to avoid
479 an infinite loop [yschensandiego]
480 * HMMER3: When a hit description is too long, it is truncated in
481 the Scores table. In those cases, the more complete description from
482 the Annotation line (>>) will be used [fjossandon]
483 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
484 since it is now used by HMMER3 format in alignments [fjossandon]
485 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
486 to return undef if the query/hit length is unknown (like in some
487 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
488 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
489 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
490 added support to multi-query reports, reduced code redundancy,
491 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
492 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
493 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
494 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
495 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
496 * Double-quotes on paths are needed in some places [fjossandon]
497 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
498 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
499 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
500 with the latest changes made in their own repositories [fjossandon]
501 * General synching of files with the master branch [fjossandon]
502 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
503 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
504 * Fixed broken MeSH parser [fjossandon]
505 * Fixed missing detection of format in SeqIO when given a -string [fangly]
509 * Major Windows support updates! [fjossandon]
510 * MAKER update to allow for stricter standard codon table [cjfields]
511 * Better support for circular sequences [fjossandon]
512 * Fixes for some complex location types [fjossandon]
513 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
514 * Fix bug #2978 related to BLAST report type [fjossandon]
515 * Deobfuscator fixes [DaveMessina]
519 * Address CPAN test failures [cjfields]
520 * Add BIOPROJECT support for Genbank files [hyphaltip]
521 * Better regex support for HMMER3 output [bosborne]
525 * Minor update to address CPAN test failures
529 * Remove Bio::Biblio and related files [carandraug]
530 - this cause version clashes with an independently-released
531 version of Bio::Biblio
537 * Hash randomization fixes for perl 5.18.x
538 - Note: at least one module (Bio::Map::Physical) still has a failing test;
539 this is documented in bug #3446 and has been TODO'd; we will be pulling
540 Bio::Map and similar modules out of core into separate distributions in the
541 1.7.x release series [cjfields]
545 * Bio::Seq::SimulatedRead
546 - New module to represent reads taken from other sequences [fangly]
548 - Support of Clone::Fast as a faster cloning alternative [fangly]
550 - Moved the format() and variant() methods from Bio::*IO modules to
551 Bio::Root::IO [fangly]
552 - Can now use format() to get the type of IO format in use [fangly]
554 - New regexp() method to create regular expressions from IUPAC sequences
556 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
557 - Code refresh [fangly]
559 - Added support for the Greengenes and Silva taxonomies [fangly]
560 * Bio::Tree::TreeFunctionsI
561 - get_lineage_string() represents a lineage as a string [fangly]
562 - add_trait() returns instead of reporting an error when the column
563 number is exceeded in add_trait() [fangly]
564 - Option to support tree leaves without trait [fangly]
565 - Allow ID of 0 in trait files [fangly]
566 * Bio::DB::Taxonomy::list
567 - Misc optimizations [fangly]
568 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
569 * Bio::DB::Taxonomy::*
570 - get_num_taxa() returns the number of taxa in the database [fangly]
571 * Bio::DB::Fasta and Bio::DB::Qual
572 - support indexing an arbitrary list of files [fangly]
573 - user can supply an arbitrary index file name [fangly]
574 - new option to remove index file at the end [fangly]
576 - now handles IUPAC degenerate residues [fangly]
577 * Bio::PrimarySeq and Bio::PrimarySeqI
578 - speed improvements for large sequences [Ben Woodcroft, fangly]
580 - tightened and optimized quality string validation [fangly]
582 - new method and option 'block', to create FASTA output with space
583 intervaled blocks (similar to genbank or EMBL) has been implemented.
584 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
585 in favour of the methods 'width' and 'preferred_id_type` respectively.
587 - moved from bioperl-live into the separate distribution Bio-FeatureIO
588 * Bio::SeqFeature::Annotated
589 - moved from bioperl-live into the separate distribution Bio-FeatureIO
590 * Bio::Cluster::SequenceFamily
591 - improved performance when using get_members with overlapping multiple
593 * Bio::SearchIO::hmmer3
594 - now supports nhmmer [bosborne]
598 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
599 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
600 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
601 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
602 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
603 information was lost in a multi-result blast file [Paul Cantalupo]
604 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
605 total gaps [Paul Cantalupo]
606 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
607 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
608 when end of domain indicator is split across lines [Paul Cantalupo]
609 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
611 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
612 instances where blank lines are within sequences [cjfields]
613 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
615 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
616 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
618 * Various fixes for Stockholm file indexing and processing [bosborne]
619 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
620 breaks parsing [cjfields]
621 * Fix case where Bio::Seq::Meta* objects with no meta information could not
622 be reverse-complemented [fangly]
623 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
624 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
625 when unsure that values will be numerical [fangly]
626 * Fix undef warnings in Bio::SeqIO::embl [fangly]
627 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
628 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
629 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
631 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
632 source_tag and display_name must return a string, not undef [fangly]
633 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
634 add_SeqFeature takes a single argument [fangly]
635 * Use cross-platform filenames and temporary directory in
636 Bio::DB::Taxonomy::flatfile [fangly]
637 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
638 properly identified as existing taxa in the database [fangly]
639 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
640 without also passing a lineage to store [fangly]
641 * Prevent passing a directory to the gi2taxid option (-g) of
642 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
644 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
645 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
646 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
647 object before trying to access, and no longer returns repeated sequences.
654 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
655 modules using Ace will also be deprecated [lds, cjfields]
656 * Minor bug fix release
657 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
658 * Address Build.PL issues when DBI is not present [hartzell]
659 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
660 * Remove deprecated code for perl 5.14.0 compat [cjfields]
661 * Due to schema changes and lack of support for older versions, support
662 for NeXML 0.9 is only (very) partially implemented.
663 See: https://redmine.open-bio.org/issues/3207
667 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
668 docs [genehack, cjfields]
669 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
670 module version from dist_version (probably not the best way to do this,
671 but it seems to work) [rbuels, cjfields]
674 1.6.900 April 14, 201
678 * This will probably be the last release to add significant features to
679 core modules; subsequent releases will be for bug fixes alone.
680 We are planning on a restructuring of core for summer 2011, potentially
681 as part of the Google Summer of Code. This may become BioPerl 2.0.
682 * Version bump represents 'just prior to v 1.7'. We may have point
683 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
684 This code essentially is what is on the github master branch.
688 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
690 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
691 - removal of Scalar::Util::weaken code, which was causing odd headaches
692 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
693 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
695 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
698 - bug 2515 - new contribution [Ryan Golhar, jhannah]
700 - support for reading Maq, Sam and Bowtie files [maj]
701 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
702 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
703 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
704 - bug 2726: reading/writing granularity: whole scaffold or one contig
705 at a time [Joshua Udall, fangly]
707 - Added parsing of xrefs to OBO files, which are stored as secondary
708 dbxrefs of the cvterm [Naama Menda]
709 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
710 * PAML code updated to work with PAML 4.4d [DaveMessina]
714 * [3198] - sort tabular BLAST hits by score [DaveMessina]
715 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
716 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
717 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
719 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
720 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
721 * [3164] - TreeFunctionsI syntax bug [gjuggler]
722 * [3163] - AssemblyIO speedup [fangly]
723 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
725 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
726 * [3158] - fix EMBL file mis-parsing [cjfields]
727 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
729 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
730 * [3148] - URL change for UniProt [cjfields]
731 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
732 * [3136] - HMMer3 parser fixes [kblin]
733 * [3126] - catch description [Toshihiko Akiba]
734 * [3122] - Catch instances where non-seekable filehandles were being
735 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
736 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
737 [dukeleto, rbuels, cjfields]
738 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
740 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
741 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
743 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
744 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
745 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
746 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
747 * [3086] - EMBL misparsing long tags [kblin, cjfields]
748 * [3085] - CommandExts and array of files [maj, hyphaltip]
749 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
750 for alignment slices [Ha X. Dang, cjfields]
751 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
752 * [3073] - fix parsing of GenBank files from RDP [cjfields]
753 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
754 * [3064] - All-gap midline BLAST report issues [cjfields]
755 * [3063] - BLASt report RID [Razi Khaja, cjfields]
756 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
757 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
758 * [3039] - correct Newick output root node branch length [gjuggler,
760 * [3038] - SELEX alignment error [Bernd, cjfields]
761 * [3033] - PrimarySeq ID setting [Bernd, maj]
762 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
763 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
764 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
765 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
766 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
767 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
768 PAML 4.4d [DaveMessina]
769 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
771 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
772 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
773 * [3017] - using threads with Bio::DB::GenBank [cjfields]
774 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
775 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
776 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
777 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
778 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
780 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
781 * [2977] - TreeIO issues [DaveMessina]
782 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
783 * [2944] - Bio::Tools::GFF score [cjfields]
784 * [2942] - correct MapTiling output [maj]
785 * [2939] - PDB residue insertion codes [John May, maj]
786 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
787 * [2928] - GuessSeqFormat raw [maj]
788 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
789 * [2922] - open() directive issue [cjfields]
790 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
791 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
792 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
793 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
795 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
796 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
797 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
798 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
799 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
800 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
801 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
802 * [2758] - Bio::AssemblyIO ace problems [fangly]
803 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
804 * [2726] - ace file IO [Josh, fangly]
805 * [2700] - Refactor Build.PL [cjfields]
806 * [2673] - addition of simple Root-based clone() method [cjfields]
807 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
808 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
809 * [2594] - Bio::Species memory leak [cjfields]
810 * [2515] - GenBank XML parser [jhannah]
811 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
812 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
813 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
815 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
819 * Bio::Expression modules - these were originally designed to go with the
820 bioperl-microarray suite of tools, however they have never been completed
821 and so have been removed from the distribution. The original code has
822 been moved into the inactive bioperl-microarray suite. [cjfields]
826 * Repository moved from Subversion (SVN) to
827 http://github.com/bioperl/bioperl-live [cjfields]
828 * Bug database has moved to Redmine (https://redmine.open-bio.org)
829 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
830 Thieme have been moved to their own distribution (Bio-Microarray).
833 1.6.1 Sept. 29, 2009 (point release)
834 * No change from last alpha except VERSION and doc updates [cjfields]
836 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
837 * Fix for silent OBDA bug related to FASTA validation [cjfields]
839 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
840 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
841 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
843 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
845 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
846 * WinXP test fixes [cjfields, maj]
847 * BioPerl.pod added for descriptive information, fixes CPAN indexing
849 * Minor doc fixes [cjfields]
851 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
852 * Fix tests failing due to merging issues [cjfields]
853 * More documentation updates for POD parsing [cjfields]
855 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
857 - fix YAML meta data generation [cjfields]
859 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
860 * Bio::Align::DNAStatistics
861 - fix divide by zero problem [jason]
863 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
864 * Bio::AlignIO::stockholm
865 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
866 * Bio::Assembly::Tools::ContigSpectrum
867 - function to score contig spectrum [fangly]
868 * Bio::DB::EUtilities
869 - small updates [cjfields]
871 - berkeleydb database now autoindexes wig files and locks correctly
874 - various small updates for stability; tracking changes to LANL
875 database interface [maj]
876 * Bio::DB::SeqFeature (lots of updates and changes)
877 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
878 - bug 2835 - patch [Dan Bolser]
879 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
881 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
882 * Bio::Factory::FTLocationFactory
883 - mailing list bug fix [cjfields]
885 - performance work on column_from_residue_number [hartzell]
886 * Bio::Matrix::IO::phylip
887 - bug 2800 - patch to fix phylip parsing [Wei Zou]
889 - Google Summer of Code project from Chase Miller - parsers for Nexml
890 file format [maj, chmille4]
892 - Make Individual, Population, Marker objects AnnotatableI [maj]
893 - simplify LD code [jason]
895 - deal with empty intersection [jason]
897 - significant overhaul of Bio::Restriction system: complete support for
898 external and non-palindromic cutters. [maj]
900 - CPANPLUS support, no automatic installation [sendu]
902 - allow IO::String (regression fix) [cjfields]
903 - catch unintentional undef values [cjfields]
904 - throw if non-fh is passed to -fh [maj]
905 * Bio::Root::Root/RootI
906 - small debugging and core fixes [cjfields]
908 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
909 * Bio::Root::Utilities
910 - bug 2737 - better warnings [cjfields]
912 - tiling completely refactored, HOWTO added [maj]
913 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
914 will deprecate usage of the older tiling code in the next BioPerl
916 - small fixes [cjfields]
918 - Infernal 1.0 output now parsed [cjfields]
919 - new parser for gmap -f9 output [hartzell]
920 - bug 2852 - fix infinite loop in some output [cjfields]
921 - blastxml output now passes all TODO tests [cjfields]
922 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
923 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
924 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
925 * Bio::Seq::LargePrimarySeq
926 - delete tempdirs [cjfields]
927 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
929 - extract regions based on quality threshold value [Dan Bolser, heikki]
930 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
931 * Bio::SeqFeature::Lite
932 - various Bio::DB::SeqFeature-related fixes [lstein]
933 * Bio::SeqFeature::Tools::TypeMapper
934 - additional terms for GenBank to SO map [scain]
935 * Bio::SeqIO::chadoxml
936 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
938 - support for CDS records [dave_messina, Sylvia]
940 - complete refactoring to handle all FASTQ variants, perform validation,
941 write output. API now conforms with other Bio* parsers and the rest of
942 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
944 * Bio::SeqIO::genbank
945 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
946 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
947 * Bio::SeqIO::largefasta
948 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
950 - add option for 'single' and 'multiple'
952 - bug 2881 - fix scf round-tripping [Adam Søgren]
954 - bug 2766, 2810 - copy over tags from features, doc fixes [David
957 - bug 2793 - patch for add_seq index issue [jhannah, maj]
958 - bug 2801 - throw if args are required [cjfields]
959 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
960 [Tristan Lefebure, maj]
961 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
962 - fix POD and add get_SeqFeatures filter [maj]
963 * Bio::Tools::dpAlign
964 - add support for LocatableSeq [ymc]
965 - to be moved to a separate distribution [cjfields, rbuels]
966 * Bio::Tools::EUtilities
967 - fix for two bugs from mail list [Adam Whitney, cjfields]
968 - add generic ItemContainerI interface for containing same methods
971 - fix up code, add more warnings [cjfields]
972 - to be moved to a separate distribution [cjfields, rbuels]
973 * Bio::Tools::Primer3
974 - bug 2862 - fenceposting issue fixed [maj]
975 * Bio::Tools::Run::RemoteBlast
976 - tests for remote RPS-BLAST [mcook]
977 * Bio::Tools::SeqPattern
978 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
979 * Bio::Tools::tRNAscanSE
980 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
982 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
983 * Bio::Tree::Statistics
984 - several methods for calculating Fitch-based score, internal trait
985 values, statratio(), sum of leaf distances [heikki]
987 - bug 2869 - add docs indicating edge case where nodes can be
988 prematurely garbage-collected [cjfields]
989 - add as_text() function to create Tree as a string in specified format
991 * Bio::Tree::TreeFunctionsI
992 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
994 * Bio::TreeIO::newick
995 - fix small semicolon issue [cjfields]
997 - update to bp_seqfeature_load for SQLite [lstein]
998 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
999 - fastam9_to_table - fix for MPI output [jason]
1000 - gccalc - total stats [jason]
1002 - POD cleanup re: FEEDBACK section [maj, cjfields]
1003 - cleanup or fix dead links [cjfields]
1004 - Use of no_* methods (indicating 'number of something') is deprecated
1005 in favor of num_* [cjfields]
1006 - lots of new tests for the above bugs and refactors [everyone!]
1007 - new template for Komodo text editor [cjfields]
1010 * Feature/Annotation rollback
1011 - Problematic changes introduced prior to the 1.5 release have been
1012 rolled back. These changes led to subtle bugs involving operator
1013 overloading and interface methods.
1014 - Behavior is very similar to that for BioPerl 1.4, with tag values
1015 being stored generically as simple scalars. Results in a modest
1018 - Split into a separate distribution on CPAN, primarily so development
1019 isn't reliant on a complete BioPerl release.
1020 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
1021 is only available via Subversion (via bioperl-live main trunk)
1023 - Common test bed for all BioPerl modules
1025 - Common Module::Build-based subclass for all BioPerl modules
1026 * Bio::DB::EUtilities
1027 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
1028 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
1029 and user agent request posting and retrieval
1030 * Test implementation and reorganization
1031 - Tests have been reorganized into groups based on classes or use
1033 - Automated test coverage is now online:
1034 http://www.bioperl.org/wiki/Test_Coverage
1035 - After this release, untested modules will be moved into a
1036 separate developer distribution until tests can be derived.
1037 Also, new modules to be added are expected to have a test suite
1038 and adequate test coverage.
1040 1.5.2 Developer release
1042 Full details of changes since 1.5.1 are available online at:
1043 http://www.bioperl.org/wiki/Change_log
1044 The following represents a brief overview of the most important changes.
1047 - Overhaul. Brand new system fully allows markers to have multiple
1048 positions on multiple maps, and to have relative positions. Should be
1049 backward compatible.
1052 - This module and all the modules in the Taxonomy directory now
1053 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
1058 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
1060 * New methods ancestor(), each_Descendent() and _handle_internal_id().
1062 * Allows for different database modules to create Bio::Taxon objects
1063 with the same internal id when the same taxon is requested from each.
1066 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
1068 * No longer includes the fake root node 'root'; there are multiple roots
1069 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
1072 * get_node() has new option -full
1074 * Caches data retrieved from website
1077 - Now a Bio::Taxon. Carries out the species name -> specific name munging
1078 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
1079 backward compatability in species() method.
1081 o Bio::Search and Bio::SearchIO
1082 - Overhaul. The existing system has been sped up via some minor changes
1083 (mostly gain-of-function to the API). Bio::PullParserI is introduced
1084 as a potential eventual replacment for the existing system, though as
1085 yet only a Hmmpfam parser exists written using it.
1088 1.5.1 Developer release
1090 o Major problem with how Annotations were written out with
1091 Bio::Seq is fixed by reverting to old behavior for
1092 Bio::Annotation objects.
1097 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
1098 expect at l east 9 spaces at the beginning of a line to
1099 indicate line wrapping.
1101 * Treat multi-line SOURCE sections correctly, this defect broke
1102 both common_name() and classification()
1104 * parse swissprot fields in genpept file
1106 * parse WGS genbank records
1109 * Changed regexp for ID line. The capturing parentheses are
1110 the same, the difference is an optional repeated-not-semi-
1111 colon expression following the captured \S+. This means the
1112 regexp works when the division looks like /PRO;/ or when the
1113 division looks like /ANG ;/ - the latter is from EMBL
1116 * fix ID line parsing: the molecule string can have spaces in
1117 it. Like: "genomic DNA"
1119 - swiss.pm: bugs #1727, #1734
1122 * Added parser for entrezgene ASN1 (text format) files.
1123 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
1127 - maf.pm coordinate problem fixed
1129 o Bio::Taxonomy and Bio::DB::Taxonomy
1131 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
1132 can be done via Web without downloading all the sequence.
1134 o Bio::Tools::Run::RemoteBlast supports more options and complies
1135 to changes to the NCBI interface. It is reccomended that you
1136 retrieve the data in XML instead of plain-text BLAST report to
1137 insure proper parsing and retrieval of all information as NCBI
1138 fully expects to change things in the future.
1140 o Bio::Tree and Bio::TreeIO
1142 - Fixes so that re-rooting a tree works properly
1144 - Writing out nhx format from a newick/nexus file will properly output
1145 bootstrap information. The use must move the internal node labels over
1147 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
1148 $node->bootstrap($node->id);
1151 - Nexus parsing is much more flexible now, does not care about
1154 - Cladogram drawing module in Bio::Tree::Draw
1156 - Node height and depth now properly calculated
1158 - fix tree pruning algorithm so that node with 1 child gets merged
1160 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
1161 bugs and improvements were added, see Gbrowse mailing list for most of
1164 o Bio::DB::GFF partially supports GFF3. See information about
1165 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
1167 o Better location parsing in Bio::Factory::FTLocationFactory -
1168 this is part of the engine for parsing EMBL/GenBank feature table
1169 locations. Nested join/order-by/complement are allowed now
1171 o Bio::PrimarySeqI->translate now takes named parameters
1173 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
1174 reconstruction) is now supported. Parsing different models and
1175 branch specific parametes are now supported.
1177 o Bio::Factory::FTLocationFactory - parse hierarchical locations
1180 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
1181 for getter/setter functions
1185 - blast bug #1739; match scientific notation in score
1186 and possible e+ values
1188 - blast.pm reads more WU-BLAST parameters and parameters, match
1189 a full database pathname,
1191 - Handle NCBI WEB and newer BLAST formats specifically
1192 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
1194 - psl off-by-one error fixed
1196 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
1197 and HSPs can be constructed from them.
1199 - HSPs query/hit now have a seqdesc field filled out (this was
1200 always available via $hit->description and
1201 $result->query_description
1203 - hmmer.pm can parse -A0 hmmpfam files
1205 - Writer::GbrowseGFF more customizeable.
1207 o Bio::Tools::Hmmpfam
1208 make e-value default score displayed in gff, rather than raw score
1209 allow parse of multiple records
1212 1.5 Developer release
1214 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
1215 provide Jukes-Cantor and Kimura pairwise distance methods,
1218 o Bio::AlignIO support for "po" format of POA, and "maf";
1219 Bio::AlignIO::largemultifasta is a new alternative to
1220 Bio::AlignIO::fasta for temporary file-based manipulation of
1221 particularly large multiple sequence alignments.
1223 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
1224 be treated similarly as an assembled contig.
1226 o Bio::CodonUsage provides new rare_codon() and probable_codons()
1227 methods for identifying particular codons that encode a given
1230 o Bio::Coordinate::Utils provides new from_align() method to build
1231 a Bio::Coordinate pair directly from a
1232 Bio::Align::AlignI-conforming object.
1234 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
1235 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
1236 web service using standard Pubmed query syntax, and retrieve
1239 o Bio::DB::GFF has various sundry bug fixes.
1241 o Bio::FeatureIO is a new SeqIO-style subsystem for
1242 writing/reading genomic features to/from files. I/O classes
1243 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
1244 classes only read/write Bio::SeqFeature::Annotated objects.
1245 Notably, the GFF v3 class requires features to be typed into the
1248 o Bio::Graph namespace contains new modules for manipulation and
1249 analysis of protein interaction graphs.
1251 o Bio::Graphics has many bug fixes and shiny new glyphs.
1253 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
1254 indexing for HMMER reports and FASTA qual files, respectively.
1256 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
1257 new objects that can be placed within a Bio::Map::MapI-compliant
1258 genetic/physical map; Bio::Map::Physical provides a new physical
1259 map type; Bio::MapIO::fpc provides finger-printed clone mapping
1262 o Bio::Matrix::PSM provide new support for postion-specific
1263 (scoring) matrices (e.g. profiles, or "possums").
1265 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
1266 be instantiated without explicitly using Bio::OntologyIO. This
1267 is possible through changes to Bio::Ontology::OntologyStore to
1268 download ontology files from the web as necessary. Locations of
1269 ontology files are hard-coded into
1270 Bio::Ontology::DocumentRegistry.
1272 o Bio::PopGen includes many new methods and data types for
1273 population genetics analyses.
1275 o New constructor to Bio::Range, unions(). Given a list of
1276 ranges, returns another list of "flattened" ranges --
1277 overlapping ranges are merged into a single range with the
1278 mininum and maximum coordinates of the entire overlapping group.
1280 o Bio::Root::IO now supports -url, in addition to -file and -fh.
1281 The new -url argument allows one to specify the network address
1282 of a file for input. -url currently only works for GET
1283 requests, and thus is read-only.
1285 o Bio::SearchIO::hmmer now returns individual Hit objects for each
1286 domain alignment (thus containing only one HSP); previously
1287 separate alignments would be merged into one hit if the domain
1288 involved in the alignments was the same, but this only worked
1289 when the repeated domain occured without interruption by any
1290 other domain, leading to a confusing mixture of Hit and HSP
1293 o Bio::Search::Result::ResultI-compliant report objects now
1294 implement the "get_statistics" method to access
1295 Bio::Search::StatisticsI objects that encapsulate any
1296 statistical parameters associated with the search (e.g. Karlin's
1297 lambda for BLAST/FASTA).
1299 o Bio::Seq::LargeLocatableSeq combines the functionality already
1300 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
1302 o Bio::SeqFeature::Annotated is a replacement for
1303 Bio::SeqFeature::Generic. It breaks compliance with the
1304 Bio::SeqFeatureI interface because the author was sick of
1305 dealing with untyped annotation tags. All
1306 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
1307 compliant, and accessible through Bio::Annotation::Collection.
1309 o Bio::SeqFeature::Primer implements a Tm() method for primer
1310 melting point predictions.
1312 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
1313 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
1315 o Bio::Taxonomy::Node now implements the methods necessary for
1316 Bio::Species interoperability.
1318 o Bio::Tools::CodonTable has new reverse_translate_all() and
1319 make_iupac_string() methods.
1321 o Bio::Tools::dpAlign now provides sequence profile alignments.
1323 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
1325 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
1328 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
1329 for designing small inhibitory RNA.
1331 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
1332 methods based on a distance matrix.
1334 o Bio::Tree::Statistics provides an assess_bootstrap() method to
1335 calculate bootstrap support values on a guide tree topology,
1336 based on provided bootstrap tree topologies.
1338 o Bio::TreeIO now supports the Pagel (PAG) tree format.
1344 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
1346 o Bio::Graphics will work with gd1 or gd2
1349 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
1351 - blast.pm Parse multi-line query fields properly
1352 - small speed improvements to blasttable.pm and others
1354 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
1355 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
1356 supporting more complex queries
1359 1.4. Stable major release
1361 Since initial 1.2.0, 3000 separate changes have been made to make this release.
1363 o installable scripts
1365 o global module version from Bio::Root:Version
1368 - major improvements; SVG support
1371 - population genetics
1372 - support several population genetics types of questions.
1373 - Tests for statistical neutrality of mutations
1374 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
1375 Tests of population structure (Wright's F-statistic: Fst) is in
1376 Bio::PopGen::PopStats. Calculating composite linkage
1377 disequilibrium (LD) is available in Bio::PopGen::Statistics as
1379 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1380 and csv (comma delimited formatted) data.
1382 - a directory for implementing population simulations has
1383 been added Bio::PopGen::Simulation and 2 simulations - a
1384 Coalescent and a simple single-locus multi-allele genetic drift
1385 simulation have been provided. This replaces the code in
1386 Bio::Tree::RandomTree which has been deprecated until proper
1387 methods for generating random phylogenetic trees are
1391 - new restrion analysis modules
1393 o Bio::Tools::Analysis
1394 - web based DNA and Protein analysis framework and several
1398 - per residue annotable sequences
1401 - Bio::Matrix::PSM - Position Scoring Matrix
1402 - Bio::Matrix::IO has been added for generalized parsing of
1403 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1404 initial implementations for parsing BLOSUM/PAM and Phylip
1405 Distance matricies respectively. A generic matrix
1406 implementation for general use was added in
1407 Bio::Matrix::Generic.
1414 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1415 - small inhibitory RNA
1417 o Bio::SeqFeature::Tools
1418 - seqFeature mapping tools
1419 - Bio::SeqFeature::Tools::Unflattener.pm
1420 -- deal with mapping GenBank feature collections into
1421 Chado/GFF3 processable feature sets (with SO term mappings)
1423 o Bio::Tools::dpAlign
1424 - pure perl dynamic programming sequence alignment
1427 o new Bio::SearchIO formats
1428 - axt and psl: UCSC formats.
1429 - blasttable: NCBI -m 8 or -m 9 format from blastall
1431 o new Bio::SeqIO formats
1432 - chado, tab, kegg, tigr, game
1433 - important fixes for old modules
1437 o improved Bio::Tools::Genewise
1439 o Bio::SeqIO now can recongnize sequence formats automatically from
1442 o new parsers in Bio::Tools:
1443 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1445 o Bio::DB::Registry bugs fixed
1446 - BerkeleyDB-indexed flat files can be used by the OBDA system
1447 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1448 used by the OBDA system
1450 o several new HOWTOs
1451 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1454 o hundreds of new and improved files
1458 o Bio::Tree::AlleleNode has been updated to be a container of
1459 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1464 1.2.3 Stable release update
1465 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1467 o Bug #1477 - Sel --> Sec abbreviation fixed
1468 o Fix bug #1487 where paring in-between locations when
1469 end < start caused the FTLocationFactory logic to fail.
1470 o Fix bug #1489 which was not dealing with keywords as an
1471 arrayref properly (this is fixed on the main trunk because
1472 keywords returns a string and the array is accessible via
1474 o Bio::Tree::Tree memory leak (bug #1480) fixed
1475 Added a new initialization option -nodelete which
1476 won't try and cleanup the containing nodes if this
1478 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1479 this was only present on the branch for the 1.2.1 and 1.2.2 series
1480 - Also merged main trunk changes to the branch which make
1481 newick -> nhx round tripping more effective (storing branch length
1482 and bootstrap values in same locate for NodeNHX and Node
1483 implementations.) Fixes to TreeIO parsing for labeled internal
1484 also required small changes to TreeIO::nhx. Improved
1485 tests for this module as well.
1487 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1488 gapped blast properly (was losing hit significance values due to
1489 the extra unexpeted column).
1490 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1491 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1492 although doesn't try to correct it - will get the negative
1493 number for you. Added a test for this as well.
1494 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1495 has no top-level family classification scores but does have scores and
1496 alignments for individual domains.
1497 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1498 regular expression to match the line was missing the possibility of
1499 an extra space. This is rare, which is why we probably did not
1501 - BLAST parsing picks up more of the statistics/parameter fields
1502 at the bottom of reports. Still not fully complete.
1503 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1504 were fixed to include many improvements and added flexiblity
1505 in outputting the files. Bug #1495 was also fixed in the process.
1507 - Update for GFF3 compatibility.
1508 - Added scripts for importing from UCSC and GenBank.
1509 - Added a 1.2003 version number.
1512 - Added a 1.2003 version number.
1513 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1514 properly writing keywords out.
1515 o Bio::SeqIO::genbank
1516 - Fixed bug/enhancement #1513 where dates of
1517 the form D-MMM-YYYY were not parsed. Even though this is
1518 invalid format we can handle it - and also cleanup the date
1519 string so it is properly formatted.
1520 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1521 and written with Genbank format. Similarly bug #1515 is fixed to
1522 parse in the ORIGIN text.
1523 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1524 to specify the ID type, one of (accession accession.version
1525 display primary). See Bio::SeqIO::preferred_id_type method
1526 documentation for more information.
1527 o Unigene parsing updated to handle file format changes by NCBI
1529 1.2.2 Stable release update
1531 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1532 - auto-discover ontology name
1533 - bug in parsing relationships when certain characters are in the term
1534 - fixed hard-coded prefix for term identifiers
1535 - various smaller issues
1537 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1538 of Bio::Ontology::TermI
1540 o brought the OBDA Registry code up to latest specs
1544 - accession number retrieval fixed
1546 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1548 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1549 #1459 which now properly report alignment start/end info
1550 for translated BLAST/FASTA searches.
1552 o Bio::TreeIO::newick can parse labeled internal nodes
1554 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1555 for BLASTX if if you provide -report_type => 'BLASTX' when
1556 initializing a BPbl2seq object. Bioperl 1.3 will have better
1557 support for bl2seq in the SearchIO system.
1559 o Bio::Root::IO support a -noclose boolean flag which will not
1560 close a filehandle upon object cleanup - useful when sharing
1561 a filehandle among objects. Additionally code added s.t.
1562 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1564 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1566 o Bio::SeqIO::genbank
1567 - bug #1456 fixed which generated extra sequence lines
1568 - write moltype correctly for genpept
1570 1.2.1 Stable release update
1572 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1574 o Addition from main trunk of Ontology objects, principly to allow
1575 BioSQL releases against 1.2.1
1577 o Fixes and cleanup of Bio::Coordinate modules
1579 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1580 the primary accession number
1582 o Other bug fixes, including bpindex GenBank fix
1584 o Bio::SeqIO::genbank bug #1389 fixed
1586 1.2 Stable major release
1588 o More functionality added to Bio::Perl, the newbie module
1590 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1591 Support for New Hampshire Extended (NHX) format parsing.
1593 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1594 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1597 o New ontology parsing Bio::Ontology
1599 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1600 multi-report (mlib) fasta reports, support for waba and exonerate.
1602 o Bio::ClusterIO for parsing Unigene clusters
1604 o Bio::Assembly added for representing phrap and ace assembly clusters.
1606 o Rudimentary support for writing Chado XML (see
1607 GMOD project: www.gmod.org for more information)
1609 o Bio::Coordinate for mapping between different coordinate systems such
1610 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1611 features into different coordinate systems.
1613 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1614 with the get_Stream_by_query method and supports the latest
1615 NCBI eutils interface.
1617 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1618 object for extracting subsets of features : currently only
1619 supports extraction by location.
1621 1.1.1 Developer release
1623 o Deprecated modules are now listed in the DEPRECATED file
1625 o New HowTo documents located in doc/howto describing
1626 a domain of Bioperl.
1628 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1629 and all old bugs are searchable through the bugzilla interface.
1631 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1632 have been addressed.
1634 o Support for Genewise parsing in Bio::Tools::Genewise
1636 o Start of Ontology framework with Bio::Ontology
1638 o Speedup to the Bio::Root::Root object method _rearrange.
1639 A global _load_module method was implemented to simplify the
1640 dynamic loading of modules ala Bio::SeqIO::genbank. This
1641 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1644 o Several performance improvements to sequence parsing in Bio::SeqIO.
1645 Attempt to speedup by reducing object creation overhead.
1647 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1648 method for sequence retrieval with their E-utils CGI scripts.
1649 More work to support Entrez queries to their fullest is planned
1652 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1654 1.1 Developer release
1656 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1657 this separation removes some of the complexity in our test suite
1658 and separates the core modules in bioperl from those that need
1659 external programs to run.
1661 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1662 not run into trouble running the makefile
1664 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1665 read,create,and write locations for grouped/split locations
1666 (like mRNA features on genomic sequence).
1668 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1669 and PAML (codeml,aaml, etc) parsing.
1671 o Bio::Tree:: objects expanded to handle testing monophyly,
1672 paraphyly, least common ancestor, etc.
1674 o Bio::Coordinate for mapping locations from different coordinate spaces
1676 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1677 added for parsing hmmpfam and hmmsearch output.
1679 o Bio::SearchIO::Writer::TextResultWriter for outputting
1680 a pseudo-blast textfile format
1683 1.0.2 Bug fix release
1685 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1686 in this release will not work after December 2002 when NCBI
1687 shuts off the old Entrez cgi scripts. We have already fixed
1688 on our main development branch and the functionality will be
1689 available in the next stable bioperl release (1.2) slated for
1692 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1693 testset by Robin Emig. These were fixed as was the get_aln
1694 method in Bio::Search::HSP::GenericHSP to handle the extra
1695 context sequence that is provided with a FastA alignment.
1697 o Migrating differences between Bio::Search::XX::BlastXX to
1698 Bio::Search::XX::GenericXX objects. This included mechanism
1699 to retrieve whole list of HSPs from Hits and whole list of Hits from
1700 Results in addition to the current next_XX iterator methods that
1701 are available. Added seq_inds() method to GenericHSP which identifies
1702 indexes in the query or hit sequences where conserved,identical,gaps,
1703 or mismatch residues are located (adapted from Steve Chervitz's
1704 implementation in BlastHSP).
1706 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1707 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1709 o Bio::Graphics glyph set improved and extended for GBrowse release
1711 o Bio::Tree::Tree get_nodes implementation improvement thanks
1712 to Howard Ross notice performance problem when writing out
1715 o Bio::Location::Fuzzy::new named parameter -loc_type became
1716 -location_type, Bio::Location::Simple::new named parameter
1717 -seqid becamse -seq_id.
1719 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1720 was mis-detecting that gaps should be placed at the beginning of
1721 the alignment when the best alignment starts internally in the
1724 1.0.1 Bug fix release
1726 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1728 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1729 and mixed (3.3 - 3.4) versions of FASTA.
1731 o Small API change to add methods for completeness across
1732 implementations of Bio::Search objects. These new methods
1733 in the interface are implemented by the GenericXX object as well
1734 as the BlastXX objects.
1735 * Bio::Search::Result::ResultI
1736 - hits() method returns list of all Hits (next_hit is an
1739 * Bio::Search::Hit::HitI
1740 - hsps() method returns list of all HSPs (next_hsp is an
1743 o The Bio::SearchIO::Writer classes have been fixed to handle results
1744 created from either psiblast (Search::BlastXX objects) or
1745 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1746 has to be done here to make it work properly and will nee major
1749 o Bugs in Bio::Tools::HMMER fixed, including
1750 * #1178 - Root::IO destructor wasn't being called
1751 * #1034 - filter_on_cutoff now behaves properly
1753 o Bio::SeqFeature::Computation initialization args fixed and
1756 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1758 o Updated FAQ with more example based answers to typical questions
1760 o Bug #1202 was fixed which would improperly join together qual values
1761 parsed by Bio::SeqIO::qual when a trailing space was not present before
1764 1.0.0 Major Stable Release
1766 This represents a major release of bioperl with significant
1767 improvements over the 0.7.x series of releases.
1769 o Bio::Tools::Blast is officially deprecated. Please see
1770 Bio::SearchIO for BLAST and FastA parsing.
1772 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1773 Bio::LocationI objects as well as start/end.
1775 o Bio::Biblio contains modules for Bibliographic data.
1776 Bio::DB::Biblio contains the query modules. Additionally one can
1777 parse medlinexml from the ebi bibliographic query service (BQS)
1778 system and Pubmed xml from NCBI. See Martin Senger's
1779 documentation in Bio::Biblio for more information.
1781 o Bio::DB::Registry is a sequence database registry part of
1782 Open Bioinformatics Database Access. See
1783 http://obda.open-bio.org for more information.
1785 o File-based and In-Memory Sequence caching is provided by
1786 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1789 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1790 been added by Lincoln Stein.
1792 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1794 o A FAQ has been started and is included in the release to provide
1795 a starting point for frequent questions and issues.
1797 0.9.3 Developer's release
1799 o Event based parsing system improved (SearchIO). With parsers for
1800 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1801 Additionally a lazy parsing system for text and html blast reports was
1802 added and is called psiblast (name subject to change in future releases).
1804 o Bio::Search objects improved and standardized with associated Interfaces
1805 written. The concept of a search "Hit" was standardized to be called
1806 "hit" consistently and the use of "subject" was deprecated in all active
1809 o Bio::Structure added (since 0.9.1) for Protein structure objects
1810 and PDB parser to retrieve and write these structures from data files.
1812 o Several important Bio::DB::GFF bug fixes for handling features that
1813 are mapped to multiple reference points. Updated mysql adaptor
1814 so as to be able to store large (>100 megabase) chunks of DNA into
1815 Bio::DB::GFF databases.
1817 0.9.2 Developer's release
1819 o Bio::Search and Bio::SearchIO system introduced for event based
1820 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1821 in text and XML and FASTA reports in standard output format.
1823 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1824 generator is included in Bio::TreeIO::RandomTrees and a
1825 statistics module for evaluating.
1827 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1828 server for DAS servers.
1830 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1831 files. The entire BPlite system migrated to using Bio::Root::IO
1832 for the data stream.
1834 o Bio::Tools::Alignment for Consed and sequence Trimming
1837 o Bio::Structure for Protein structure information and parsing
1839 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1840 cgi-bin entry point which should be more reliable.
1842 o Bio::Map and Bio::MapIO for biological map navigation and a
1843 framework afor parsing them in. Only preliminary work here.
1845 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1846 Future work will integrate Pise and allow submission of analysis on
1849 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1850 introduced as new objects for handling Sequence Annotation
1851 information (dblinks, references, etc) and is more robust that
1854 o Bio::Tools::FASTAParser introduced.
1856 o Scripts from the bioperl script submission project and new
1857 scripts from bioperl authors are included in "scripts" directory.
1859 o Factory objects and interfaces are being introduced and are more
1862 o Bio::Root::Root introduced as the base object while
1863 Bio::Root::RootI is now simply an interface.
1865 o Bio::DB::RefSeq provides database access to copy of the NCBI
1866 RefSeq database using the EBI dbfetch script.
1868 0.9.0 Developer's release
1870 o perl version at least 5.005 is now required instead of perl 5.004
1872 o Bio::Tools::Run::RemoteBlast is available for running remote
1875 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1877 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1878 Also added are related modules UTR3, UTR5, Exon, Intron,
1879 Promotor, PolyA and Transcript.
1881 o Speedup of translate method in PrimarySeq
1883 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1884 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1886 o Various fixes to Variation toolkit
1888 o Bio::DB::EMBL provides database access to EMBL sequence data.
1889 Bio::DB::Universal provides a central way to point to indexes
1890 and dbs in a single interface.
1892 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1894 o Bio::Factory::EMBOSS is still in design phase as is
1895 Bio::Factory::ApplicationFactoryI
1897 o Dia models for bioperl design are provided in the models/ directory
1899 0.7.2 Bug fix release
1901 o documentation fixes in many modules - SYNOPSIS code verified
1902 to be runnable in many (but not all modules)
1904 o corrected MANIFEST file from 0.7.1 release
1906 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1909 o Bio::SeqIO::genbank
1910 * Correct parsing and writing of genbank format with protein data
1911 * moltype and molecule separation
1913 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1915 o Bio::SimpleAlign fixed to correctly handle consensus
1916 sequence calculation
1918 o Bio::Tools::HMMER supports hmmer 2.2g
1920 o Bio::Tools::BPlite to support report type specific parsing. Most
1921 major changes are not on the 0.7 branch.
1923 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1926 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1927 in several types of mutations:
1928 1.) AA level: deletion, complex
1929 2.) AA level: complex, inframe
1930 3.) RNA level: silent
1932 o BPbl2seq parsing of empty reports will not die, but will return
1933 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1934 $report->query() and $report->subject() methods. So an easy
1935 way to test if report was empty is to see if
1936 $report->query->seqname is undefined.
1938 0.7.1 Bug fix release
1940 o Better parsing of genbank/EMBL files especially fixing bugs
1941 related to Feature table parsing and locations on remote
1942 sequences. Additionally, species name parsing was better.
1944 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1945 which include a number of header lines.
1947 o More strict genbank and EMBL format writing (corrected number of
1948 spaces where appropriate).
1950 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1951 for related BPlite BUGS that are unresolved in this release.
1953 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1954 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1955 use expasy mirrors or EBI dbfetch cgi-script.
1957 o A moderate number of documentation improvements were made as
1958 well to provide a better code synopsis in each module.
1961 0.7 Large number of changes, including refactoring of the
1962 Object system, new parsers, new functionality and
1963 all round better system. Highlights are:
1966 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1967 Bio::Root::IO for I/O and file/handle capabilities.
1969 o Imported BPlite modules from Ian Korf for BLAST
1970 parsing. This is considered the supported BLAST parser;
1971 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1973 o Improved Sequence Feature model. Added complete location
1974 modelling (with fuzzy and compound locations). See
1975 Bio::LocationI and the modules under Bio/Location. Added
1976 support in Genbank/EMBL format parsing to completely parse
1977 feature tables for complex locations.
1979 o Moved special support for databanks etc to specialized modules under
1980 Bio/Seq/. One of these supports very large sequences through
1981 a temporary file as a backend.
1983 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1984 CDS retrieval and exon shuffling.
1986 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1988 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1989 DB/GDB (the latter has platform-specific limitations).
1991 o New analysis parser framework for HT sequence annotation (see
1992 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1994 o New Alignment IO framework
1996 o New Index modules (Swissprot)
1998 o New modules for running Blast within perl
1999 (Bio::Tools::Run::StandAloneBlast). Added modules for running
2000 Multiple Sequence Alignment tools ClustalW and TCoffee
2001 (Bio::Tools::Run::Alignment).
2003 o New Cookbook-style tutorial (see bptutorial.pl). Improved
2004 documentation across the package.
2006 o Much improved cross platform support. Many known incompatibilities
2007 have been fixed; however, NT and Mac do not work across the entire
2008 setup (see PLATFORMS).
2010 o Many bug fixes, code restructuring, etc. Overall stability and
2011 maintainability benefit a lot.
2013 o A total of 957 automatic tests
2018 There are very few functionality changes but a large
2019 number of software improvements/bug fixes across the package.
2021 o The EMBL/GenBank parsing are improved.
2023 o The Swissprot reading is improved. Swissprot writing
2024 is disabled as it doesn't work at all. This needs to
2025 wait for 0.7 release
2027 o BLAST reports with no hits are correctly parsed.
2029 o Several other bugs of the BLAST parser (regular expressions, ...)
2032 o Old syntax calls have been replaced with more modern syntax
2034 o Modules that did not work at all, in particular the Sim4
2035 set have been removed
2037 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
2038 have improved compliance with interface specs and documentation
2040 o Mailing list documentation updated throughout the distribution
2042 o Most minor bug fixes have happened.
2044 o The scripts in /examples now work and have the modern syntax
2045 rather than the deprecated syntax
2048 0.6.1 Sun April 2 2000
2050 o Sequences can have Sequence Features attached to them
2051 - The sequence features can be read from or written to
2052 EMBL and GenBank style flat files
2054 o Objects for Annotation, including References (but not
2055 full medline abstracts), Database links and Comments are
2058 o A Species object to represent nodes on a taxonomy tree
2061 o The ability to parse HMMER and Sim4 output has been added
2063 o The Blast parsing has been improved, with better PSI-BLAST
2064 support and better overall behaviour.
2066 o Flat file indexed databases provide both random access
2067 and sequential access to their component sequences.
2069 o A CodonTable object has been written with all known
2070 CodonTables accessible.
2072 o A number of new lightweight analysis tools have been
2073 added, such as molecular weight determination.
2075 The 0.6 release also has improved software engineering
2077 o The sequence objects have been rewritten, providing more
2078 maintainable and easier to implement objects. These
2079 objects are backwardly compatible with the 0.05.1 objects
2081 o Many objects are defined in terms of interfaces and then
2082 a Perl implementation has been provided. The interfaces
2083 are found in the 'I' files (module names ending in 'I').
2085 This means that it is possible to wrap C/CORBA/SQL access
2086 as true "bioperl" objects, compatible with the rest of
2089 o The SeqIO system has been overhauled to provide better
2090 processing and perl-like automatic interpretation of <>
2093 o Many more tests have been added (a total of 172 automatic
2094 tests are now run before release).
2098 0.05.1 Tue Jun 29 05:30:44 1999
2099 - Central distribution now requires Perl 5.004. This was
2100 done to get around 5.003-based problems in Bio/Index/*
2102 - Various bug fixes in the Bio::Tools::Blast modules
2103 including better exception handling and PSI-Blast
2104 support. See Bio/Tools/Blast/CHANGES for more.
2105 - Fixed the Parse mechanism in Seq.pm to use readseq.
2106 Follow the instructions in README for how to install
2107 it (basically, you have to edit Parse.pm).
2108 - Improved documentation of Seq.pm, indicating where
2109 objects are returned and where strings are returned.
2110 - Fixed uninitialized warnings in Bio::Root::Object.pm
2111 and Bio::Tools::SeqPattern.pm.
2112 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
2114 0.05 Sun Apr 25 01:14:11 1999
2115 - Bio::Tools::Blast modules have less memory problems
2116 and faster parsing. Webblast uses LWP and supports
2117 more functionality. See Bio/Tools/Blast/CHANGES for more.
2118 - The Bio::SeqIO system has been started, moving the
2119 sequence reformatting code out of the sequence object
2120 - The Bio::Index:: system has been started, providing
2121 generic index capabilities and specifically works for
2122 Fasta formatted databases and EMBL .dat formatted
2124 - The Bio::DB:: system started, providing access to
2125 databases, both via flat file + index (see above) and
2127 - The scripts/ directory, where industrial strength scripts
2128 are put has been started.
2129 - Many changes - a better distribution all round.
2131 0.04.4 Wed Feb 17 02:20:13 1999
2132 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
2133 (see Bio::Tools::Blast::CHANGES).
2134 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
2135 - Beefed up the t/Fasta.t test script.
2136 - Small fix in Bio::Seq::type() (now always returns a string).
2137 - Changed Bio::Root::Utilities::get_newline_char() to
2138 get_newline() since it could return more than one char.
2139 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
2140 - Changed default timeout to 20 seconds (was 3).
2141 - Moved lengthy modification notes to the bottom of some files.
2142 - Fixed SimpleAlign write_fasta bug.
2143 - Beefed up SimpleAlign.t test
2145 0.04.3 Thu Feb 4 07:48:53 1999
2146 - Bio::Root::Object.pm and Global.pm now detect when
2147 script is run as a CGI and suppress output that is only
2148 appropriate when running interactively.
2149 - Bio::Root::Err::_set_context() adds name of script ($0).
2150 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
2151 regarding the use of the static objects via the qw(:obj) tag.
2152 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
2153 CORE::reverse, avoiding Perl warnings.
2154 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
2155 example scripts (see Bio::Tools::Blast::CHANGES).
2156 - examples/seq/seqtools.pl no longer always warns about using
2157 -prot or -nucl command-line arguments; only when using the
2159 - Methods added to Bio::Root::Utilities: create_filehandle(),
2160 get_newline_char(), and taste_file() to generalize filehandle
2161 creation and autodetect newline characters in files/streams
2162 (see bug report #19).
2163 - Bio::Root::IOManager::read() now handles timeouts and uses
2164 Utilities::create_filehandle().
2165 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
2166 of hardwiring in "\n".
2167 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
2169 0.04.2 Wed Dec 30 02:27:36 1998
2170 - Bug fixes in Bio::Tools::Blast modules, version 0.073
2171 (see Bio::Tools::Blast::CHANGES).
2172 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
2173 to CORE::reverse (prevents ambiguous warnings with 5.005).
2174 - Appending '.tmp.bioperl' to temporary files created by
2175 Bio::Root::Utilities::compress() or uncompress() to
2176 make it easy to identify & cleanup these files as needed.
2177 - Developers: Created CVS branch release-0-04-bug from
2178 release-0-04-1. Before making bug fixes to the 0.04.1 release,
2179 be sure to cvs checkout this branch into a clean area.
2181 0.04.1 Wed Dec 16 05:39:15 1998
2182 - Bug fixes in Bio::Tools::Blast modules, version 0.072
2183 (see Bio::Tools::Blast::CHANGES).
2184 - Compile/SW/Makefile.PL now removes *.o and *.a files
2187 0.04 Tue Dec 8 07:49:19 1998
2188 - Lots of new modules added including:
2189 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
2190 and Bio/Compile directory containing XS-linked C code for
2191 creating Smith-Waterman sequence alignments from within Perl.
2192 * Steve Chervitz's Blast distribution has been incorporated.
2193 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
2194 - Bio/examples directory for demo scripts for all included modules.
2195 - Bio/t directory containing test suit for all included modules.
2196 - For changes specific to the Blast-related modules prior to
2197 incorporation in this central distribution, see the CHANGES
2198 file in the Bio/Tools/Blast directory.
2200 0.01 Tue Sep 8 14:23:22 1998
2201 - original version from central CVS tree; created by h2xs 1.18