1 Summary of important user-visible changes for BioPerl
2 -----------------------------------------------------
6 * The following modules have been removed from the BioPerl
7 distribution to be part of a separate distribution. They have
8 been integrated into other module distributions for independent
13 Bio::AlignIO::stockholm
23 Bio::DB::Expression::*
25 Bio::DB::GFF::Adaptor::*
26 Bio::DB::GFF::Aggregator::*
27 Bio::DB::GFF::Featname
30 Bio::DB::GFF::RelSegment
32 Bio::DB::GFF::Typename
38 Bio::DB::Query::GenBank
39 Bio::DB::Query::HIVQuery
41 Bio::DB::SeqFeature::*
42 Bio::DB::SeqVersion::*
45 Bio::DB::Taxonomy::entrez
46 Bio::DB::Taxonomy::sqlite
49 Bio::Factory::MapFactoryI
55 Bio::MolEvol::CodonModel
64 Bio::Search::HSP::HMMERHSP
65 Bio::Search::HSP::HmmpfamHSP
66 Bio::Search::Hit::HMMERHit
67 Bio::Search::Hit::HmmpfamHit
68 Bio::Search::Hit::hmmer3Hit
69 Bio::Search::Result::HMMERResult
70 Bio::Search::Result::HmmpfamResult
71 Bio::Search::Result::hmmer3Result
76 Bio::SearchIO::hmmer_pull
78 Bio::SeqFeature::SiRNA::*
86 Bio::SeqIO::entrezgene
89 Bio::SeqIO::flybase_chadoxml
96 Bio::Tools::AlignFactory
97 Bio::Tools::Analysis::* (except SimpleAnalysisBase)
101 Bio::Tools::Phylo::Gumby
102 Bio::Tools::Protparam
103 Bio::Tools::Run::RemoteBlast
107 Bio::Tree::AlleleNode
108 Bio::Tree::Draw::Cladogram
110 Bio::TreeIO::svggraph
113 * The following modules are new in the BioPerl distribution. They
114 have been previously released in the BioPerl-Run distribution.
115 This will enable smaller distributions that provide a
116 Bio::Tool::Run interface, to be only dependent on the BioPerl
117 distribution instead of the whole (very large) BioPerl-Run:
119 Bio::Tools::Run::Analysis
120 Bio::Tools::Run::AnalysisFactory
121 Bio::Tools::Run::Phylo::PhyloBase
122 Bio::Tools::Run::WrapperBase
123 Bio::Tools::Run::WrapperBase::CommandExts
125 * The following programs have been removed:
127 bp_biofetch_genbank_proxy
132 bp_download_query_genbank
136 bp_generate_histogram
137 bp_heterogeneity_test
151 * Because of the move of so many modules and programs into
152 separate distributions, the following modules are no longer
161 Bio::ASN1::EntrezGene
162 Bio::Expression::Contact
163 Bio::Expression::DataSet
164 Bio::Expression::Platform
165 Bio::Expression::Sample
167 Bio::GMOD::CMap::Utils
169 Bio::Phylo::Forest::Tree
172 Bio::Phylo::Matrices::Datum
173 Bio::Phylo::Matrices::Matrix
174 Bio::SeqFeature::Annotated
175 Bio::SeqIO::staden::read
176 Bio::Tools::Run::Alignment::Clustalw
177 Bio::Tools::Run::Ensembl
178 Bio::Tools::Run::Phylo::Molphy::ProtML
179 Bio::Tools::Run::Phylo::Phylip::Neighbor
180 Bio::Tools::Run::Phylo::Phylip::ProtDist
181 Bio::Tools::Run::Phylo::Phylip::ProtPars
182 Bio::Tools::Run::Samtools
190 Data::Stag::XMLWriter
206 PostScript::TextBlock
210 SVG::Graph::Data::Node
211 SVG::Graph::Data::Tree
213 Spreadsheet::ParseExcel
215 Text::NSP::Measures::2D::Fisher2::twotailed
223 * The following is a new prerequisite:
225 Test::RequiresInternet
227 * The deobfuscator has been removed.
229 * The emacs bioperl minor mode is no longer distributed as part of the
230 perl module distributions. See
231 https://github.com/bioperl/emacs-bioperl-mode
238 * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
239 * #245 - Code coverage fixes [zmughal,cjfields]
240 * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
241 * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
242 * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
243 * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
244 * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
245 * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
246 * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
247 * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
248 * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
249 * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
253 * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
259 * Minor release to incorporate fix for CPAN indexing, which
260 prevented proper updates [cjfields]
261 * Fix problem in managing Target attribute for gff3 [Jukes34]
262 * Minor bug fixes related to NCBI HTTPS support [cjfields]
268 * We have migrated to Github Pages. This was actually planned, but the
269 recent OBF server compromise forced our hand.
271 Brian Osborne [bosborne] took this under his wing to move docs and has
272 done a tremendous amount of work formatting the site and working out some
273 of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
274 Cantalupo and Franscison Ossandon also helped. Kudos!!
276 * Similarly, the official issue tracker is now Github Issues. This has
277 been updated in the relevant documentation bits (we hope!)
281 * Previously deprecated modules removed
282 * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
283 * Bio::DB::SeqHound has been removed due to the service no longer being
285 * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
286 reasons due to the server no longer having a valid cert
287 * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
288 * Bio::Coordinate, Bio::SearchIO::blastxml,
289 Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
294 * Docker instances of tagged releases are available! [hlapp]
295 * NCBI HTTPS support [mjohnson and others]
296 * Bio::SearchIO::infernal
297 - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
298 * Bio::Search::HSP::ModelHSP
299 - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
301 * Bio::Search::Result::INFERNALResult
302 - Added new module to represent features of Infernal reports [pcantalupo]
303 * Bio::DB::Taxonomy SQLite option [cjfields]
304 * WrapperBase quoted option values [majensen]
305 * Various documentation fixes and updates [bosborne]
309 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
310 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
311 * NeXML parser fixes [fjossandon]
312 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
313 * RT 103272 : SeqFeature database deletion skipped features with a decimal -
314 Joshua Fortriede (Xenbase)
315 * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
316 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
317 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
318 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
319 * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
320 * Issue #84: EMBL format wrapping problem [nyamned]
321 * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
322 * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
323 or compiled C code (when Inline::C is installed) [rocky]
324 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
325 * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
326 * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
327 * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
328 to be consistent with "$hit->bits" behaviour [fjossandon]
329 * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
330 aminoacids made "next_seq" confused and broke the parser [fjossandon]
331 * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
332 Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
333 to "complement(join(A..B,C..D))" [fjossandon]
334 * For the many many many fixes that weren't mentioned - blame the release guy!
338 [Significant changes]
340 * Bug/feature issue tracking has moved to GitHub Issues:
341 https://github.com/bioperl/bioperl-live/issues
342 * DB_File has been demoted from "required" to "recommended",
343 which should make easier for Windows users to install BioPerl
344 if they don't need that module.
348 * Bio::Search::HSP::GenericHSP
349 - Bug #3370, added a "posterior_string" method to retrieve the
350 posterior probability lines (PP) from HMMER3 reports [fjossandon]
351 - Added a "consensus_string" method to retrieve the consensus
352 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
353 * Bio::SearchIO::hmmer2
354 - The number of identical and conserved residues are now calculated
355 directly from the homology line [fjossandon]
356 - Now the Query Length and Hit Length are reported when the alignment
357 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
358 - Implemented the capture of the consensus structure lines [fjossandon]
359 * Bio::SearchIO::hmmer3
360 - The number of identical and conserved residues are now calculated
361 directly from the homology line [fjossandon]
362 - Now the Hit Length is reported when the alignment runs until the end
363 of the sequence/model ('.]' or '[]') [fjossandon]
364 - Implemented the capture of the consensus structure lines [fjossandon]
365 - Implemented the capture of the posterior probability lines [fjossandon]
366 - Completed the development of NHMMER parsing, including alignments [fjossandon]
367 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
368 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
369 "min_score", "min_bits, and "hit_filter" methods from
370 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
371 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
372 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
373 besides Blast, instead of being ignored. Added tests for all moved methods
374 using HMMER outputs and run the full test suite and everything pass [fjossandon]
375 * Bio::SeqIO::MultiFile
376 - Autodetection of file format [fangly]
377 * Bio::Tools::GuessSeqFormat:
378 - Format detection from non-seekable filehandles such as STDIN [fangly]
382 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
383 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
384 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
385 * Abstract: Fixed ActivePerl incapability of removing temporary files
386 because of problems closing tied filehandles [fjossandon]
387 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
388 because ActivePerl were producing a ".index.pag" and ".index.dir"
389 files instead of a single ".index" file (like Strawberry Perl).
390 Now those temporary files are correctly considered and deleted. [fjossandon]
391 * Test files: Added missing module requirements (DB_File and Data::Stag)
392 to several tests files that were failing because those modules were
393 not present. Now those test files are correctly skipped instead. [fjossandon]
394 * Blast: Added support to changes in bl2seq from BLAST+ output, which
395 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
396 * Phylip: Return undef in "next_aln" at file end to avoid
397 an infinite loop [yschensandiego]
398 * HMMER3: When a hit description is too long, it is truncated in
399 the Scores table. In those cases, the more complete description from
400 the Annotation line (>>) will be used [fjossandon]
401 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
402 since it is now used by HMMER3 format in alignments [fjossandon]
403 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
404 to return undef if the query/hit length is unknown (like in some
405 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
406 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
407 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
408 added support to multi-query reports, reduced code redundancy,
409 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
410 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
411 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
412 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
413 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
414 * Double-quotes on paths are needed in some places [fjossandon]
415 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
416 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
417 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
418 with the latest changes made in their own repositories [fjossandon]
419 * General synching of files with the master branch [fjossandon]
420 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
421 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
422 * Fixed broken MeSH parser [fjossandon]
423 * Fixed missing detection of format in SeqIO when given a -string [fangly]
427 * Major Windows support updates! [fjossandon]
428 * MAKER update to allow for stricter standard codon table [cjfields]
429 * Better support for circular sequences [fjossandon]
430 * Fixes for some complex location types [fjossandon]
431 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
432 * Fix bug #2978 related to BLAST report type [fjossandon]
433 * Deobfuscator fixes [DaveMessina]
437 * Address CPAN test failures [cjfields]
438 * Add BIOPROJECT support for Genbank files [hyphaltip]
439 * Better regex support for HMMER3 output [bosborne]
443 * Minor update to address CPAN test failures
447 * Remove Bio::Biblio and related files [carandraug]
448 - this cause version clashes with an independently-released
449 version of Bio::Biblio
455 * Hash randomization fixes for perl 5.18.x
456 - Note: at least one module (Bio::Map::Physical) still has a failing test;
457 this is documented in bug #3446 and has been TODO'd; we will be pulling
458 Bio::Map and similar modules out of core into separate distributions in the
459 1.7.x release series [cjfields]
463 * Bio::Seq::SimulatedRead
464 - New module to represent reads taken from other sequences [fangly]
466 - Support of Clone::Fast as a faster cloning alternative [fangly]
468 - Moved the format() and variant() methods from Bio::*IO modules to
469 Bio::Root::IO [fangly]
470 - Can now use format() to get the type of IO format in use [fangly]
472 - New regexp() method to create regular expressions from IUPAC sequences
474 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
475 - Code refresh [fangly]
477 - Added support for the Greengenes and Silva taxonomies [fangly]
478 * Bio::Tree::TreeFunctionsI
479 - get_lineage_string() represents a lineage as a string [fangly]
480 - add_trait() returns instead of reporting an error when the column
481 number is exceeded in add_trait() [fangly]
482 - Option to support tree leaves without trait [fangly]
483 - Allow ID of 0 in trait files [fangly]
484 * Bio::DB::Taxonomy::list
485 - Misc optimizations [fangly]
486 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
487 * Bio::DB::Taxonomy::*
488 - get_num_taxa() returns the number of taxa in the database [fangly]
489 * Bio::DB::Fasta and Bio::DB::Qual
490 - support indexing an arbitrary list of files [fangly]
491 - user can supply an arbitrary index file name [fangly]
492 - new option to remove index file at the end [fangly]
494 - now handles IUPAC degenerate residues [fangly]
495 * Bio::PrimarySeq and Bio::PrimarySeqI
496 - speed improvements for large sequences [Ben Woodcroft, fangly]
498 - tightened and optimized quality string validation [fangly]
500 - new method and option 'block', to create FASTA output with space
501 intervaled blocks (similar to genbank or EMBL) has been implemented.
502 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
503 in favour of the methods 'width' and 'preferred_id_type` respectively.
505 - moved from bioperl-live into the separate distribution Bio-FeatureIO
506 * Bio::SeqFeature::Annotated
507 - moved from bioperl-live into the separate distribution Bio-FeatureIO
508 * Bio::Cluster::SequenceFamily
509 - improved performance when using get_members with overlapping multiple
511 * Bio::SearchIO::hmmer3
512 - now supports nhmmer [bosborne]
516 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
517 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
518 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
519 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
520 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
521 information was lost in a multi-result blast file [Paul Cantalupo]
522 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
523 total gaps [Paul Cantalupo]
524 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
525 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
526 when end of domain indicator is split across lines [Paul Cantalupo]
527 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
529 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
530 instances where blank lines are within sequences [cjfields]
531 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
533 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
534 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
536 * Various fixes for Stockholm file indexing and processing [bosborne]
537 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
538 breaks parsing [cjfields]
539 * Fix case where Bio::Seq::Meta* objects with no meta information could not
540 be reverse-complemented [fangly]
541 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
542 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
543 when unsure that values will be numerical [fangly]
544 * Fix undef warnings in Bio::SeqIO::embl [fangly]
545 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
546 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
547 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
549 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
550 source_tag and display_name must return a string, not undef [fangly]
551 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
552 add_SeqFeature takes a single argument [fangly]
553 * Use cross-platform filenames and temporary directory in
554 Bio::DB::Taxonomy::flatfile [fangly]
555 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
556 properly identified as existing taxa in the database [fangly]
557 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
558 without also passing a lineage to store [fangly]
559 * Prevent passing a directory to the gi2taxid option (-g) of
560 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
562 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
563 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
564 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
565 object before trying to access, and no longer returns repeated sequences.
572 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
573 modules using Ace will also be deprecated [lds, cjfields]
574 * Minor bug fix release
575 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
576 * Address Build.PL issues when DBI is not present [hartzell]
577 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
578 * Remove deprecated code for perl 5.14.0 compat [cjfields]
579 * Due to schema changes and lack of support for older versions, support
580 for NeXML 0.9 is only (very) partially implemented.
581 See: https://redmine.open-bio.org/issues/3207
585 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
586 docs [genehack, cjfields]
587 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
588 module version from dist_version (probably not the best way to do this,
589 but it seems to work) [rbuels, cjfields]
592 1.6.900 April 14, 201
596 * This will probably be the last release to add significant features to
597 core modules; subsequent releases will be for bug fixes alone.
598 We are planning on a restructuring of core for summer 2011, potentially
599 as part of the Google Summer of Code. This may become BioPerl 2.0.
600 * Version bump represents 'just prior to v 1.7'. We may have point
601 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
602 This code essentially is what is on the github master branch.
606 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
608 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
609 - removal of Scalar::Util::weaken code, which was causing odd headaches
610 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
611 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
613 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
616 - bug 2515 - new contribution [Ryan Golhar, jhannah]
618 - support for reading Maq, Sam and Bowtie files [maj]
619 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
620 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
621 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
622 - bug 2726: reading/writing granularity: whole scaffold or one contig
623 at a time [Joshua Udall, fangly]
625 - Added parsing of xrefs to OBO files, which are stored as secondary
626 dbxrefs of the cvterm [Naama Menda]
627 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
628 * PAML code updated to work with PAML 4.4d [DaveMessina]
632 * [3198] - sort tabular BLAST hits by score [DaveMessina]
633 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
634 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
635 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
637 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
638 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
639 * [3164] - TreeFunctionsI syntax bug [gjuggler]
640 * [3163] - AssemblyIO speedup [fangly]
641 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
643 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
644 * [3158] - fix EMBL file mis-parsing [cjfields]
645 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
647 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
648 * [3148] - URL change for UniProt [cjfields]
649 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
650 * [3136] - HMMer3 parser fixes [kblin]
651 * [3126] - catch description [Toshihiko Akiba]
652 * [3122] - Catch instances where non-seekable filehandles were being
653 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
654 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
655 [dukeleto, rbuels, cjfields]
656 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
658 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
659 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
661 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
662 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
663 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
664 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
665 * [3086] - EMBL misparsing long tags [kblin, cjfields]
666 * [3085] - CommandExts and array of files [maj, hyphaltip]
667 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
668 for alignment slices [Ha X. Dang, cjfields]
669 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
670 * [3073] - fix parsing of GenBank files from RDP [cjfields]
671 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
672 * [3064] - All-gap midline BLAST report issues [cjfields]
673 * [3063] - BLASt report RID [Razi Khaja, cjfields]
674 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
675 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
676 * [3039] - correct Newick output root node branch length [gjuggler,
678 * [3038] - SELEX alignment error [Bernd, cjfields]
679 * [3033] - PrimarySeq ID setting [Bernd, maj]
680 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
681 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
682 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
683 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
684 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
685 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
686 PAML 4.4d [DaveMessina]
687 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
689 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
690 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
691 * [3017] - using threads with Bio::DB::GenBank [cjfields]
692 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
693 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
694 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
695 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
696 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
698 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
699 * [2977] - TreeIO issues [DaveMessina]
700 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
701 * [2944] - Bio::Tools::GFF score [cjfields]
702 * [2942] - correct MapTiling output [maj]
703 * [2939] - PDB residue insertion codes [John May, maj]
704 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
705 * [2928] - GuessSeqFormat raw [maj]
706 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
707 * [2922] - open() directive issue [cjfields]
708 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
709 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
710 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
711 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
713 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
714 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
715 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
716 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
717 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
718 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
719 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
720 * [2758] - Bio::AssemblyIO ace problems [fangly]
721 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
722 * [2726] - ace file IO [Josh, fangly]
723 * [2700] - Refactor Build.PL [cjfields]
724 * [2673] - addition of simple Root-based clone() method [cjfields]
725 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
726 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
727 * [2594] - Bio::Species memory leak [cjfields]
728 * [2515] - GenBank XML parser [jhannah]
729 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
730 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
731 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
733 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
737 * Bio::Expression modules - these were originally designed to go with the
738 bioperl-microarray suite of tools, however they have never been completed
739 and so have been removed from the distribution. The original code has
740 been moved into the inactive bioperl-microarray suite. [cjfields]
744 * Repository moved from Subversion (SVN) to
745 http://github.com/bioperl/bioperl-live [cjfields]
746 * Bug database has moved to Redmine (https://redmine.open-bio.org)
747 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
748 Thieme have been moved to their own distribution (Bio-Microarray).
751 1.6.1 Sept. 29, 2009 (point release)
752 * No change from last alpha except VERSION and doc updates [cjfields]
754 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
755 * Fix for silent OBDA bug related to FASTA validation [cjfields]
757 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
758 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
759 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
761 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
763 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
764 * WinXP test fixes [cjfields, maj]
765 * BioPerl.pod added for descriptive information, fixes CPAN indexing
767 * Minor doc fixes [cjfields]
769 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
770 * Fix tests failing due to merging issues [cjfields]
771 * More documentation updates for POD parsing [cjfields]
773 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
775 - fix YAML meta data generation [cjfields]
777 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
778 * Bio::Align::DNAStatistics
779 - fix divide by zero problem [jason]
781 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
782 * Bio::AlignIO::stockholm
783 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
784 * Bio::Assembly::Tools::ContigSpectrum
785 - function to score contig spectrum [fangly]
786 * Bio::DB::EUtilities
787 - small updates [cjfields]
789 - berkeleydb database now autoindexes wig files and locks correctly
792 - various small updates for stability; tracking changes to LANL
793 database interface [maj]
794 * Bio::DB::SeqFeature (lots of updates and changes)
795 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
796 - bug 2835 - patch [Dan Bolser]
797 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
799 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
800 * Bio::Factory::FTLocationFactory
801 - mailing list bug fix [cjfields]
803 - performance work on column_from_residue_number [hartzell]
804 * Bio::Matrix::IO::phylip
805 - bug 2800 - patch to fix phylip parsing [Wei Zou]
807 - Google Summer of Code project from Chase Miller - parsers for Nexml
808 file format [maj, chmille4]
810 - Make Individual, Population, Marker objects AnnotatableI [maj]
811 - simplify LD code [jason]
813 - deal with empty intersection [jason]
815 - significant overhaul of Bio::Restriction system: complete support for
816 external and non-palindromic cutters. [maj]
818 - CPANPLUS support, no automatic installation [sendu]
820 - allow IO::String (regression fix) [cjfields]
821 - catch unintentional undef values [cjfields]
822 - throw if non-fh is passed to -fh [maj]
823 * Bio::Root::Root/RootI
824 - small debugging and core fixes [cjfields]
826 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
827 * Bio::Root::Utilities
828 - bug 2737 - better warnings [cjfields]
830 - tiling completely refactored, HOWTO added [maj]
831 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
832 will deprecate usage of the older tiling code in the next BioPerl
834 - small fixes [cjfields]
836 - Infernal 1.0 output now parsed [cjfields]
837 - new parser for gmap -f9 output [hartzell]
838 - bug 2852 - fix infinite loop in some output [cjfields]
839 - blastxml output now passes all TODO tests [cjfields]
840 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
841 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
842 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
843 * Bio::Seq::LargePrimarySeq
844 - delete tempdirs [cjfields]
845 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
847 - extract regions based on quality threshold value [Dan Bolser, heikki]
848 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
849 * Bio::SeqFeature::Lite
850 - various Bio::DB::SeqFeature-related fixes [lstein]
851 * Bio::SeqFeature::Tools::TypeMapper
852 - additional terms for GenBank to SO map [scain]
853 * Bio::SeqIO::chadoxml
854 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
856 - support for CDS records [dave_messina, Sylvia]
858 - complete refactoring to handle all FASTQ variants, perform validation,
859 write output. API now conforms with other Bio* parsers and the rest of
860 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
862 * Bio::SeqIO::genbank
863 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
864 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
865 * Bio::SeqIO::largefasta
866 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
868 - add option for 'single' and 'multiple'
870 - bug 2881 - fix scf round-tripping [Adam Søgren]
872 - bug 2766, 2810 - copy over tags from features, doc fixes [David
875 - bug 2793 - patch for add_seq index issue [jhannah, maj]
876 - bug 2801 - throw if args are required [cjfields]
877 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
878 [Tristan Lefebure, maj]
879 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
880 - fix POD and add get_SeqFeatures filter [maj]
881 * Bio::Tools::dpAlign
882 - add support for LocatableSeq [ymc]
883 - to be moved to a separate distribution [cjfields, rbuels]
884 * Bio::Tools::EUtilities
885 - fix for two bugs from mail list [Adam Whitney, cjfields]
886 - add generic ItemContainerI interface for containing same methods
889 - fix up code, add more warnings [cjfields]
890 - to be moved to a separate distribution [cjfields, rbuels]
891 * Bio::Tools::Primer3
892 - bug 2862 - fenceposting issue fixed [maj]
893 * Bio::Tools::Run::RemoteBlast
894 - tests for remote RPS-BLAST [mcook]
895 * Bio::Tools::SeqPattern
896 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
897 * Bio::Tools::tRNAscanSE
898 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
900 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
901 * Bio::Tree::Statistics
902 - several methods for calculating Fitch-based score, internal trait
903 values, statratio(), sum of leaf distances [heikki]
905 - bug 2869 - add docs indicating edge case where nodes can be
906 prematurely garbage-collected [cjfields]
907 - add as_text() function to create Tree as a string in specified format
909 * Bio::Tree::TreeFunctionsI
910 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
912 * Bio::TreeIO::newick
913 - fix small semicolon issue [cjfields]
915 - update to bp_seqfeature_load for SQLite [lstein]
916 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
917 - fastam9_to_table - fix for MPI output [jason]
918 - gccalc - total stats [jason]
920 - POD cleanup re: FEEDBACK section [maj, cjfields]
921 - cleanup or fix dead links [cjfields]
922 - Use of no_* methods (indicating 'number of something') is deprecated
923 in favor of num_* [cjfields]
924 - lots of new tests for the above bugs and refactors [everyone!]
925 - new template for Komodo text editor [cjfields]
928 * Feature/Annotation rollback
929 - Problematic changes introduced prior to the 1.5 release have been
930 rolled back. These changes led to subtle bugs involving operator
931 overloading and interface methods.
932 - Behavior is very similar to that for BioPerl 1.4, with tag values
933 being stored generically as simple scalars. Results in a modest
936 - Split into a separate distribution on CPAN, primarily so development
937 isn't reliant on a complete BioPerl release.
938 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
939 is only available via Subversion (via bioperl-live main trunk)
941 - Common test bed for all BioPerl modules
943 - Common Module::Build-based subclass for all BioPerl modules
944 * Bio::DB::EUtilities
945 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
946 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
947 and user agent request posting and retrieval
948 * Test implementation and reorganization
949 - Tests have been reorganized into groups based on classes or use
951 - Automated test coverage is now online:
952 http://www.bioperl.org/wiki/Test_Coverage
953 - After this release, untested modules will be moved into a
954 separate developer distribution until tests can be derived.
955 Also, new modules to be added are expected to have a test suite
956 and adequate test coverage.
958 1.5.2 Developer release
960 Full details of changes since 1.5.1 are available online at:
961 http://www.bioperl.org/wiki/Change_log
962 The following represents a brief overview of the most important changes.
965 - Overhaul. Brand new system fully allows markers to have multiple
966 positions on multiple maps, and to have relative positions. Should be
970 - This module and all the modules in the Taxonomy directory now
971 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
976 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
978 * New methods ancestor(), each_Descendent() and _handle_internal_id().
980 * Allows for different database modules to create Bio::Taxon objects
981 with the same internal id when the same taxon is requested from each.
984 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
986 * No longer includes the fake root node 'root'; there are multiple roots
987 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
990 * get_node() has new option -full
992 * Caches data retrieved from website
995 - Now a Bio::Taxon. Carries out the species name -> specific name munging
996 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
997 backward compatability in species() method.
999 o Bio::Search and Bio::SearchIO
1000 - Overhaul. The existing system has been sped up via some minor changes
1001 (mostly gain-of-function to the API). Bio::PullParserI is introduced
1002 as a potential eventual replacment for the existing system, though as
1003 yet only a Hmmpfam parser exists written using it.
1006 1.5.1 Developer release
1008 o Major problem with how Annotations were written out with
1009 Bio::Seq is fixed by reverting to old behavior for
1010 Bio::Annotation objects.
1015 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
1016 expect at l east 9 spaces at the beginning of a line to
1017 indicate line wrapping.
1019 * Treat multi-line SOURCE sections correctly, this defect broke
1020 both common_name() and classification()
1022 * parse swissprot fields in genpept file
1024 * parse WGS genbank records
1027 * Changed regexp for ID line. The capturing parentheses are
1028 the same, the difference is an optional repeated-not-semi-
1029 colon expression following the captured \S+. This means the
1030 regexp works when the division looks like /PRO;/ or when the
1031 division looks like /ANG ;/ - the latter is from EMBL
1034 * fix ID line parsing: the molecule string can have spaces in
1035 it. Like: "genomic DNA"
1037 - swiss.pm: bugs #1727, #1734
1040 * Added parser for entrezgene ASN1 (text format) files.
1041 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
1045 - maf.pm coordinate problem fixed
1047 o Bio::Taxonomy and Bio::DB::Taxonomy
1049 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
1050 can be done via Web without downloading all the sequence.
1052 o Bio::Tools::Run::RemoteBlast supports more options and complies
1053 to changes to the NCBI interface. It is reccomended that you
1054 retrieve the data in XML instead of plain-text BLAST report to
1055 insure proper parsing and retrieval of all information as NCBI
1056 fully expects to change things in the future.
1058 o Bio::Tree and Bio::TreeIO
1060 - Fixes so that re-rooting a tree works properly
1062 - Writing out nhx format from a newick/nexus file will properly output
1063 bootstrap information. The use must move the internal node labels over
1065 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
1066 $node->bootstrap($node->id);
1069 - Nexus parsing is much more flexible now, does not care about
1072 - Cladogram drawing module in Bio::Tree::Draw
1074 - Node height and depth now properly calculated
1076 - fix tree pruning algorithm so that node with 1 child gets merged
1078 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
1079 bugs and improvements were added, see Gbrowse mailing list for most of
1082 o Bio::DB::GFF partially supports GFF3. See information about
1083 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
1085 o Better location parsing in Bio::Factory::FTLocationFactory -
1086 this is part of the engine for parsing EMBL/GenBank feature table
1087 locations. Nested join/order-by/complement are allowed now
1089 o Bio::PrimarySeqI->translate now takes named parameters
1091 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
1092 reconstruction) is now supported. Parsing different models and
1093 branch specific parametes are now supported.
1095 o Bio::Factory::FTLocationFactory - parse hierarchical locations
1098 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
1099 for getter/setter functions
1103 - blast bug #1739; match scientific notation in score
1104 and possible e+ values
1106 - blast.pm reads more WU-BLAST parameters and parameters, match
1107 a full database pathname,
1109 - Handle NCBI WEB and newer BLAST formats specifically
1110 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
1112 - psl off-by-one error fixed
1114 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
1115 and HSPs can be constructed from them.
1117 - HSPs query/hit now have a seqdesc field filled out (this was
1118 always available via $hit->description and
1119 $result->query_description
1121 - hmmer.pm can parse -A0 hmmpfam files
1123 - Writer::GbrowseGFF more customizeable.
1125 o Bio::Tools::Hmmpfam
1126 make e-value default score displayed in gff, rather than raw score
1127 allow parse of multiple records
1130 1.5 Developer release
1132 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
1133 provide Jukes-Cantor and Kimura pairwise distance methods,
1136 o Bio::AlignIO support for "po" format of POA, and "maf";
1137 Bio::AlignIO::largemultifasta is a new alternative to
1138 Bio::AlignIO::fasta for temporary file-based manipulation of
1139 particularly large multiple sequence alignments.
1141 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
1142 be treated similarly as an assembled contig.
1144 o Bio::CodonUsage provides new rare_codon() and probable_codons()
1145 methods for identifying particular codons that encode a given
1148 o Bio::Coordinate::Utils provides new from_align() method to build
1149 a Bio::Coordinate pair directly from a
1150 Bio::Align::AlignI-conforming object.
1152 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
1153 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
1154 web service using standard Pubmed query syntax, and retrieve
1157 o Bio::DB::GFF has various sundry bug fixes.
1159 o Bio::FeatureIO is a new SeqIO-style subsystem for
1160 writing/reading genomic features to/from files. I/O classes
1161 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
1162 classes only read/write Bio::SeqFeature::Annotated objects.
1163 Notably, the GFF v3 class requires features to be typed into the
1166 o Bio::Graph namespace contains new modules for manipulation and
1167 analysis of protein interaction graphs.
1169 o Bio::Graphics has many bug fixes and shiny new glyphs.
1171 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
1172 indexing for HMMER reports and FASTA qual files, respectively.
1174 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
1175 new objects that can be placed within a Bio::Map::MapI-compliant
1176 genetic/physical map; Bio::Map::Physical provides a new physical
1177 map type; Bio::MapIO::fpc provides finger-printed clone mapping
1180 o Bio::Matrix::PSM provide new support for postion-specific
1181 (scoring) matrices (e.g. profiles, or "possums").
1183 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
1184 be instantiated without explicitly using Bio::OntologyIO. This
1185 is possible through changes to Bio::Ontology::OntologyStore to
1186 download ontology files from the web as necessary. Locations of
1187 ontology files are hard-coded into
1188 Bio::Ontology::DocumentRegistry.
1190 o Bio::PopGen includes many new methods and data types for
1191 population genetics analyses.
1193 o New constructor to Bio::Range, unions(). Given a list of
1194 ranges, returns another list of "flattened" ranges --
1195 overlapping ranges are merged into a single range with the
1196 mininum and maximum coordinates of the entire overlapping group.
1198 o Bio::Root::IO now supports -url, in addition to -file and -fh.
1199 The new -url argument allows one to specify the network address
1200 of a file for input. -url currently only works for GET
1201 requests, and thus is read-only.
1203 o Bio::SearchIO::hmmer now returns individual Hit objects for each
1204 domain alignment (thus containing only one HSP); previously
1205 separate alignments would be merged into one hit if the domain
1206 involved in the alignments was the same, but this only worked
1207 when the repeated domain occured without interruption by any
1208 other domain, leading to a confusing mixture of Hit and HSP
1211 o Bio::Search::Result::ResultI-compliant report objects now
1212 implement the "get_statistics" method to access
1213 Bio::Search::StatisticsI objects that encapsulate any
1214 statistical parameters associated with the search (e.g. Karlin's
1215 lambda for BLAST/FASTA).
1217 o Bio::Seq::LargeLocatableSeq combines the functionality already
1218 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
1220 o Bio::SeqFeature::Annotated is a replacement for
1221 Bio::SeqFeature::Generic. It breaks compliance with the
1222 Bio::SeqFeatureI interface because the author was sick of
1223 dealing with untyped annotation tags. All
1224 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
1225 compliant, and accessible through Bio::Annotation::Collection.
1227 o Bio::SeqFeature::Primer implements a Tm() method for primer
1228 melting point predictions.
1230 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
1231 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
1233 o Bio::Taxonomy::Node now implements the methods necessary for
1234 Bio::Species interoperability.
1236 o Bio::Tools::CodonTable has new reverse_translate_all() and
1237 make_iupac_string() methods.
1239 o Bio::Tools::dpAlign now provides sequence profile alignments.
1241 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
1243 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
1246 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
1247 for designing small inhibitory RNA.
1249 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
1250 methods based on a distance matrix.
1252 o Bio::Tree::Statistics provides an assess_bootstrap() method to
1253 calculate bootstrap support values on a guide tree topology,
1254 based on provided bootstrap tree topologies.
1256 o Bio::TreeIO now supports the Pagel (PAG) tree format.
1262 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
1264 o Bio::Graphics will work with gd1 or gd2
1267 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
1269 - blast.pm Parse multi-line query fields properly
1270 - small speed improvements to blasttable.pm and others
1272 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
1273 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
1274 supporting more complex queries
1277 1.4. Stable major release
1279 Since initial 1.2.0, 3000 separate changes have been made to make this release.
1281 o installable scripts
1283 o global module version from Bio::Root:Version
1286 - major improvements; SVG support
1289 - population genetics
1290 - support several population genetics types of questions.
1291 - Tests for statistical neutrality of mutations
1292 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
1293 Tests of population structure (Wright's F-statistic: Fst) is in
1294 Bio::PopGen::PopStats. Calculating composite linkage
1295 disequilibrium (LD) is available in Bio::PopGen::Statistics as
1297 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1298 and csv (comma delimited formatted) data.
1300 - a directory for implementing population simulations has
1301 been added Bio::PopGen::Simulation and 2 simulations - a
1302 Coalescent and a simple single-locus multi-allele genetic drift
1303 simulation have been provided. This replaces the code in
1304 Bio::Tree::RandomTree which has been deprecated until proper
1305 methods for generating random phylogenetic trees are
1309 - new restrion analysis modules
1311 o Bio::Tools::Analysis
1312 - web based DNA and Protein analysis framework and several
1316 - per residue annotable sequences
1319 - Bio::Matrix::PSM - Position Scoring Matrix
1320 - Bio::Matrix::IO has been added for generalized parsing of
1321 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1322 initial implementations for parsing BLOSUM/PAM and Phylip
1323 Distance matricies respectively. A generic matrix
1324 implementation for general use was added in
1325 Bio::Matrix::Generic.
1332 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1333 - small inhibitory RNA
1335 o Bio::SeqFeature::Tools
1336 - seqFeature mapping tools
1337 - Bio::SeqFeature::Tools::Unflattener.pm
1338 -- deal with mapping GenBank feature collections into
1339 Chado/GFF3 processable feature sets (with SO term mappings)
1341 o Bio::Tools::dpAlign
1342 - pure perl dynamic programming sequence alignment
1345 o new Bio::SearchIO formats
1346 - axt and psl: UCSC formats.
1347 - blasttable: NCBI -m 8 or -m 9 format from blastall
1349 o new Bio::SeqIO formats
1350 - chado, tab, kegg, tigr, game
1351 - important fixes for old modules
1355 o improved Bio::Tools::Genewise
1357 o Bio::SeqIO now can recongnize sequence formats automatically from
1360 o new parsers in Bio::Tools:
1361 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1363 o Bio::DB::Registry bugs fixed
1364 - BerkeleyDB-indexed flat files can be used by the OBDA system
1365 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1366 used by the OBDA system
1368 o several new HOWTOs
1369 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1372 o hundreds of new and improved files
1376 o Bio::Tree::AlleleNode has been updated to be a container of
1377 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1382 1.2.3 Stable release update
1383 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1385 o Bug #1477 - Sel --> Sec abbreviation fixed
1386 o Fix bug #1487 where paring in-between locations when
1387 end < start caused the FTLocationFactory logic to fail.
1388 o Fix bug #1489 which was not dealing with keywords as an
1389 arrayref properly (this is fixed on the main trunk because
1390 keywords returns a string and the array is accessible via
1392 o Bio::Tree::Tree memory leak (bug #1480) fixed
1393 Added a new initialization option -nodelete which
1394 won't try and cleanup the containing nodes if this
1396 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1397 this was only present on the branch for the 1.2.1 and 1.2.2 series
1398 - Also merged main trunk changes to the branch which make
1399 newick -> nhx round tripping more effective (storing branch length
1400 and bootstrap values in same locate for NodeNHX and Node
1401 implementations.) Fixes to TreeIO parsing for labeled internal
1402 also required small changes to TreeIO::nhx. Improved
1403 tests for this module as well.
1405 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1406 gapped blast properly (was losing hit significance values due to
1407 the extra unexpeted column).
1408 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1409 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1410 although doesn't try to correct it - will get the negative
1411 number for you. Added a test for this as well.
1412 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1413 has no top-level family classification scores but does have scores and
1414 alignments for individual domains.
1415 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1416 regular expression to match the line was missing the possibility of
1417 an extra space. This is rare, which is why we probably did not
1419 - BLAST parsing picks up more of the statistics/parameter fields
1420 at the bottom of reports. Still not fully complete.
1421 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1422 were fixed to include many improvements and added flexiblity
1423 in outputting the files. Bug #1495 was also fixed in the process.
1425 - Update for GFF3 compatibility.
1426 - Added scripts for importing from UCSC and GenBank.
1427 - Added a 1.2003 version number.
1430 - Added a 1.2003 version number.
1431 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1432 properly writing keywords out.
1433 o Bio::SeqIO::genbank
1434 - Fixed bug/enhancement #1513 where dates of
1435 the form D-MMM-YYYY were not parsed. Even though this is
1436 invalid format we can handle it - and also cleanup the date
1437 string so it is properly formatted.
1438 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1439 and written with Genbank format. Similarly bug #1515 is fixed to
1440 parse in the ORIGIN text.
1441 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1442 to specify the ID type, one of (accession accession.version
1443 display primary). See Bio::SeqIO::preferred_id_type method
1444 documentation for more information.
1445 o Unigene parsing updated to handle file format changes by NCBI
1447 1.2.2 Stable release update
1449 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1450 - auto-discover ontology name
1451 - bug in parsing relationships when certain characters are in the term
1452 - fixed hard-coded prefix for term identifiers
1453 - various smaller issues
1455 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1456 of Bio::Ontology::TermI
1458 o brought the OBDA Registry code up to latest specs
1462 - accession number retrieval fixed
1464 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1466 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1467 #1459 which now properly report alignment start/end info
1468 for translated BLAST/FASTA searches.
1470 o Bio::TreeIO::newick can parse labeled internal nodes
1472 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1473 for BLASTX if if you provide -report_type => 'BLASTX' when
1474 initializing a BPbl2seq object. Bioperl 1.3 will have better
1475 support for bl2seq in the SearchIO system.
1477 o Bio::Root::IO support a -noclose boolean flag which will not
1478 close a filehandle upon object cleanup - useful when sharing
1479 a filehandle among objects. Additionally code added s.t.
1480 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1482 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1484 o Bio::SeqIO::genbank
1485 - bug #1456 fixed which generated extra sequence lines
1486 - write moltype correctly for genpept
1488 1.2.1 Stable release update
1490 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1492 o Addition from main trunk of Ontology objects, principly to allow
1493 BioSQL releases against 1.2.1
1495 o Fixes and cleanup of Bio::Coordinate modules
1497 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1498 the primary accession number
1500 o Other bug fixes, including bpindex GenBank fix
1502 o Bio::SeqIO::genbank bug #1389 fixed
1504 1.2 Stable major release
1506 o More functionality added to Bio::Perl, the newbie module
1508 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1509 Support for New Hampshire Extended (NHX) format parsing.
1511 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1512 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1515 o New ontology parsing Bio::Ontology
1517 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1518 multi-report (mlib) fasta reports, support for waba and exonerate.
1520 o Bio::ClusterIO for parsing Unigene clusters
1522 o Bio::Assembly added for representing phrap and ace assembly clusters.
1524 o Rudimentary support for writing Chado XML (see
1525 GMOD project: www.gmod.org for more information)
1527 o Bio::Coordinate for mapping between different coordinate systems such
1528 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1529 features into different coordinate systems.
1531 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1532 with the get_Stream_by_query method and supports the latest
1533 NCBI eutils interface.
1535 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1536 object for extracting subsets of features : currently only
1537 supports extraction by location.
1539 1.1.1 Developer release
1541 o Deprecated modules are now listed in the DEPRECATED file
1543 o New HowTo documents located in doc/howto describing
1544 a domain of Bioperl.
1546 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1547 and all old bugs are searchable through the bugzilla interface.
1549 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1550 have been addressed.
1552 o Support for Genewise parsing in Bio::Tools::Genewise
1554 o Start of Ontology framework with Bio::Ontology
1556 o Speedup to the Bio::Root::Root object method _rearrange.
1557 A global _load_module method was implemented to simplify the
1558 dynamic loading of modules ala Bio::SeqIO::genbank. This
1559 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1562 o Several performance improvements to sequence parsing in Bio::SeqIO.
1563 Attempt to speedup by reducing object creation overhead.
1565 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1566 method for sequence retrieval with their E-utils CGI scripts.
1567 More work to support Entrez queries to their fullest is planned
1570 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1572 1.1 Developer release
1574 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1575 this separation removes some of the complexity in our test suite
1576 and separates the core modules in bioperl from those that need
1577 external programs to run.
1579 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1580 not run into trouble running the makefile
1582 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1583 read,create,and write locations for grouped/split locations
1584 (like mRNA features on genomic sequence).
1586 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1587 and PAML (codeml,aaml, etc) parsing.
1589 o Bio::Tree:: objects expanded to handle testing monophyly,
1590 paraphyly, least common ancestor, etc.
1592 o Bio::Coordinate for mapping locations from different coordinate spaces
1594 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1595 added for parsing hmmpfam and hmmsearch output.
1597 o Bio::SearchIO::Writer::TextResultWriter for outputting
1598 a pseudo-blast textfile format
1601 1.0.2 Bug fix release
1603 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1604 in this release will not work after December 2002 when NCBI
1605 shuts off the old Entrez cgi scripts. We have already fixed
1606 on our main development branch and the functionality will be
1607 available in the next stable bioperl release (1.2) slated for
1610 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1611 testset by Robin Emig. These were fixed as was the get_aln
1612 method in Bio::Search::HSP::GenericHSP to handle the extra
1613 context sequence that is provided with a FastA alignment.
1615 o Migrating differences between Bio::Search::XX::BlastXX to
1616 Bio::Search::XX::GenericXX objects. This included mechanism
1617 to retrieve whole list of HSPs from Hits and whole list of Hits from
1618 Results in addition to the current next_XX iterator methods that
1619 are available. Added seq_inds() method to GenericHSP which identifies
1620 indexes in the query or hit sequences where conserved,identical,gaps,
1621 or mismatch residues are located (adapted from Steve Chervitz's
1622 implementation in BlastHSP).
1624 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1625 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1627 o Bio::Graphics glyph set improved and extended for GBrowse release
1629 o Bio::Tree::Tree get_nodes implementation improvement thanks
1630 to Howard Ross notice performance problem when writing out
1633 o Bio::Location::Fuzzy::new named parameter -loc_type became
1634 -location_type, Bio::Location::Simple::new named parameter
1635 -seqid becamse -seq_id.
1637 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1638 was mis-detecting that gaps should be placed at the beginning of
1639 the alignment when the best alignment starts internally in the
1642 1.0.1 Bug fix release
1644 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1646 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1647 and mixed (3.3 - 3.4) versions of FASTA.
1649 o Small API change to add methods for completeness across
1650 implementations of Bio::Search objects. These new methods
1651 in the interface are implemented by the GenericXX object as well
1652 as the BlastXX objects.
1653 * Bio::Search::Result::ResultI
1654 - hits() method returns list of all Hits (next_hit is an
1657 * Bio::Search::Hit::HitI
1658 - hsps() method returns list of all HSPs (next_hsp is an
1661 o The Bio::SearchIO::Writer classes have been fixed to handle results
1662 created from either psiblast (Search::BlastXX objects) or
1663 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1664 has to be done here to make it work properly and will nee major
1667 o Bugs in Bio::Tools::HMMER fixed, including
1668 * #1178 - Root::IO destructor wasn't being called
1669 * #1034 - filter_on_cutoff now behaves properly
1671 o Bio::SeqFeature::Computation initialization args fixed and
1674 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1676 o Updated FAQ with more example based answers to typical questions
1678 o Bug #1202 was fixed which would improperly join together qual values
1679 parsed by Bio::SeqIO::qual when a trailing space was not present before
1682 1.0.0 Major Stable Release
1684 This represents a major release of bioperl with significant
1685 improvements over the 0.7.x series of releases.
1687 o Bio::Tools::Blast is officially deprecated. Please see
1688 Bio::SearchIO for BLAST and FastA parsing.
1690 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1691 Bio::LocationI objects as well as start/end.
1693 o Bio::Biblio contains modules for Bibliographic data.
1694 Bio::DB::Biblio contains the query modules. Additionally one can
1695 parse medlinexml from the ebi bibliographic query service (BQS)
1696 system and Pubmed xml from NCBI. See Martin Senger's
1697 documentation in Bio::Biblio for more information.
1699 o Bio::DB::Registry is a sequence database registry part of
1700 Open Bioinformatics Database Access. See
1701 http://obda.open-bio.org for more information.
1703 o File-based and In-Memory Sequence caching is provided by
1704 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1707 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1708 been added by Lincoln Stein.
1710 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1712 o A FAQ has been started and is included in the release to provide
1713 a starting point for frequent questions and issues.
1715 0.9.3 Developer's release
1717 o Event based parsing system improved (SearchIO). With parsers for
1718 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1719 Additionally a lazy parsing system for text and html blast reports was
1720 added and is called psiblast (name subject to change in future releases).
1722 o Bio::Search objects improved and standardized with associated Interfaces
1723 written. The concept of a search "Hit" was standardized to be called
1724 "hit" consistently and the use of "subject" was deprecated in all active
1727 o Bio::Structure added (since 0.9.1) for Protein structure objects
1728 and PDB parser to retrieve and write these structures from data files.
1730 o Several important Bio::DB::GFF bug fixes for handling features that
1731 are mapped to multiple reference points. Updated mysql adaptor
1732 so as to be able to store large (>100 megabase) chunks of DNA into
1733 Bio::DB::GFF databases.
1735 0.9.2 Developer's release
1737 o Bio::Search and Bio::SearchIO system introduced for event based
1738 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1739 in text and XML and FASTA reports in standard output format.
1741 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1742 generator is included in Bio::TreeIO::RandomTrees and a
1743 statistics module for evaluating.
1745 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1746 server for DAS servers.
1748 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1749 files. The entire BPlite system migrated to using Bio::Root::IO
1750 for the data stream.
1752 o Bio::Tools::Alignment for Consed and sequence Trimming
1755 o Bio::Structure for Protein structure information and parsing
1757 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1758 cgi-bin entry point which should be more reliable.
1760 o Bio::Map and Bio::MapIO for biological map navigation and a
1761 framework afor parsing them in. Only preliminary work here.
1763 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1764 Future work will integrate Pise and allow submission of analysis on
1767 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1768 introduced as new objects for handling Sequence Annotation
1769 information (dblinks, references, etc) and is more robust that
1772 o Bio::Tools::FASTAParser introduced.
1774 o Scripts from the bioperl script submission project and new
1775 scripts from bioperl authors are included in "scripts" directory.
1777 o Factory objects and interfaces are being introduced and are more
1780 o Bio::Root::Root introduced as the base object while
1781 Bio::Root::RootI is now simply an interface.
1783 o Bio::DB::RefSeq provides database access to copy of the NCBI
1784 RefSeq database using the EBI dbfetch script.
1786 0.9.0 Developer's release
1788 o perl version at least 5.005 is now required instead of perl 5.004
1790 o Bio::Tools::Run::RemoteBlast is available for running remote
1793 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1795 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1796 Also added are related modules UTR3, UTR5, Exon, Intron,
1797 Promotor, PolyA and Transcript.
1799 o Speedup of translate method in PrimarySeq
1801 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1802 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1804 o Various fixes to Variation toolkit
1806 o Bio::DB::EMBL provides database access to EMBL sequence data.
1807 Bio::DB::Universal provides a central way to point to indexes
1808 and dbs in a single interface.
1810 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1812 o Bio::Factory::EMBOSS is still in design phase as is
1813 Bio::Factory::ApplicationFactoryI
1815 o Dia models for bioperl design are provided in the models/ directory
1817 0.7.2 Bug fix release
1819 o documentation fixes in many modules - SYNOPSIS code verified
1820 to be runnable in many (but not all modules)
1822 o corrected MANIFEST file from 0.7.1 release
1824 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1827 o Bio::SeqIO::genbank
1828 * Correct parsing and writing of genbank format with protein data
1829 * moltype and molecule separation
1831 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1833 o Bio::SimpleAlign fixed to correctly handle consensus
1834 sequence calculation
1836 o Bio::Tools::HMMER supports hmmer 2.2g
1838 o Bio::Tools::BPlite to support report type specific parsing. Most
1839 major changes are not on the 0.7 branch.
1841 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1844 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1845 in several types of mutations:
1846 1.) AA level: deletion, complex
1847 2.) AA level: complex, inframe
1848 3.) RNA level: silent
1850 o BPbl2seq parsing of empty reports will not die, but will return
1851 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1852 $report->query() and $report->subject() methods. So an easy
1853 way to test if report was empty is to see if
1854 $report->query->seqname is undefined.
1856 0.7.1 Bug fix release
1858 o Better parsing of genbank/EMBL files especially fixing bugs
1859 related to Feature table parsing and locations on remote
1860 sequences. Additionally, species name parsing was better.
1862 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1863 which include a number of header lines.
1865 o More strict genbank and EMBL format writing (corrected number of
1866 spaces where appropriate).
1868 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1869 for related BPlite BUGS that are unresolved in this release.
1871 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1872 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1873 use expasy mirrors or EBI dbfetch cgi-script.
1875 o A moderate number of documentation improvements were made as
1876 well to provide a better code synopsis in each module.
1879 0.7 Large number of changes, including refactoring of the
1880 Object system, new parsers, new functionality and
1881 all round better system. Highlights are:
1884 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1885 Bio::Root::IO for I/O and file/handle capabilities.
1887 o Imported BPlite modules from Ian Korf for BLAST
1888 parsing. This is considered the supported BLAST parser;
1889 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1891 o Improved Sequence Feature model. Added complete location
1892 modelling (with fuzzy and compound locations). See
1893 Bio::LocationI and the modules under Bio/Location. Added
1894 support in Genbank/EMBL format parsing to completely parse
1895 feature tables for complex locations.
1897 o Moved special support for databanks etc to specialized modules under
1898 Bio/Seq/. One of these supports very large sequences through
1899 a temporary file as a backend.
1901 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1902 CDS retrieval and exon shuffling.
1904 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1906 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1907 DB/GDB (the latter has platform-specific limitations).
1909 o New analysis parser framework for HT sequence annotation (see
1910 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1912 o New Alignment IO framework
1914 o New Index modules (Swissprot)
1916 o New modules for running Blast within perl
1917 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1918 Multiple Sequence Alignment tools ClustalW and TCoffee
1919 (Bio::Tools::Run::Alignment).
1921 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1922 documentation across the package.
1924 o Much improved cross platform support. Many known incompatibilities
1925 have been fixed; however, NT and Mac do not work across the entire
1926 setup (see PLATFORMS).
1928 o Many bug fixes, code restructuring, etc. Overall stability and
1929 maintainability benefit a lot.
1931 o A total of 957 automatic tests
1936 There are very few functionality changes but a large
1937 number of software improvements/bug fixes across the package.
1939 o The EMBL/GenBank parsing are improved.
1941 o The Swissprot reading is improved. Swissprot writing
1942 is disabled as it doesn't work at all. This needs to
1943 wait for 0.7 release
1945 o BLAST reports with no hits are correctly parsed.
1947 o Several other bugs of the BLAST parser (regular expressions, ...)
1950 o Old syntax calls have been replaced with more modern syntax
1952 o Modules that did not work at all, in particular the Sim4
1953 set have been removed
1955 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1956 have improved compliance with interface specs and documentation
1958 o Mailing list documentation updated throughout the distribution
1960 o Most minor bug fixes have happened.
1962 o The scripts in /examples now work and have the modern syntax
1963 rather than the deprecated syntax
1966 0.6.1 Sun April 2 2000
1968 o Sequences can have Sequence Features attached to them
1969 - The sequence features can be read from or written to
1970 EMBL and GenBank style flat files
1972 o Objects for Annotation, including References (but not
1973 full medline abstracts), Database links and Comments are
1976 o A Species object to represent nodes on a taxonomy tree
1979 o The ability to parse HMMER and Sim4 output has been added
1981 o The Blast parsing has been improved, with better PSI-BLAST
1982 support and better overall behaviour.
1984 o Flat file indexed databases provide both random access
1985 and sequential access to their component sequences.
1987 o A CodonTable object has been written with all known
1988 CodonTables accessible.
1990 o A number of new lightweight analysis tools have been
1991 added, such as molecular weight determination.
1993 The 0.6 release also has improved software engineering
1995 o The sequence objects have been rewritten, providing more
1996 maintainable and easier to implement objects. These
1997 objects are backwardly compatible with the 0.05.1 objects
1999 o Many objects are defined in terms of interfaces and then
2000 a Perl implementation has been provided. The interfaces
2001 are found in the 'I' files (module names ending in 'I').
2003 This means that it is possible to wrap C/CORBA/SQL access
2004 as true "bioperl" objects, compatible with the rest of
2007 o The SeqIO system has been overhauled to provide better
2008 processing and perl-like automatic interpretation of <>
2011 o Many more tests have been added (a total of 172 automatic
2012 tests are now run before release).
2016 0.05.1 Tue Jun 29 05:30:44 1999
2017 - Central distribution now requires Perl 5.004. This was
2018 done to get around 5.003-based problems in Bio/Index/*
2020 - Various bug fixes in the Bio::Tools::Blast modules
2021 including better exception handling and PSI-Blast
2022 support. See Bio/Tools/Blast/CHANGES for more.
2023 - Fixed the Parse mechanism in Seq.pm to use readseq.
2024 Follow the instructions in README for how to install
2025 it (basically, you have to edit Parse.pm).
2026 - Improved documentation of Seq.pm, indicating where
2027 objects are returned and where strings are returned.
2028 - Fixed uninitialized warnings in Bio::Root::Object.pm
2029 and Bio::Tools::SeqPattern.pm.
2030 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
2032 0.05 Sun Apr 25 01:14:11 1999
2033 - Bio::Tools::Blast modules have less memory problems
2034 and faster parsing. Webblast uses LWP and supports
2035 more functionality. See Bio/Tools/Blast/CHANGES for more.
2036 - The Bio::SeqIO system has been started, moving the
2037 sequence reformatting code out of the sequence object
2038 - The Bio::Index:: system has been started, providing
2039 generic index capabilities and specifically works for
2040 Fasta formatted databases and EMBL .dat formatted
2042 - The Bio::DB:: system started, providing access to
2043 databases, both via flat file + index (see above) and
2045 - The scripts/ directory, where industrial strength scripts
2046 are put has been started.
2047 - Many changes - a better distribution all round.
2049 0.04.4 Wed Feb 17 02:20:13 1999
2050 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
2051 (see Bio::Tools::Blast::CHANGES).
2052 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
2053 - Beefed up the t/Fasta.t test script.
2054 - Small fix in Bio::Seq::type() (now always returns a string).
2055 - Changed Bio::Root::Utilities::get_newline_char() to
2056 get_newline() since it could return more than one char.
2057 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
2058 - Changed default timeout to 20 seconds (was 3).
2059 - Moved lengthy modification notes to the bottom of some files.
2060 - Fixed SimpleAlign write_fasta bug.
2061 - Beefed up SimpleAlign.t test
2063 0.04.3 Thu Feb 4 07:48:53 1999
2064 - Bio::Root::Object.pm and Global.pm now detect when
2065 script is run as a CGI and suppress output that is only
2066 appropriate when running interactively.
2067 - Bio::Root::Err::_set_context() adds name of script ($0).
2068 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
2069 regarding the use of the static objects via the qw(:obj) tag.
2070 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
2071 CORE::reverse, avoiding Perl warnings.
2072 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
2073 example scripts (see Bio::Tools::Blast::CHANGES).
2074 - examples/seq/seqtools.pl no longer always warns about using
2075 -prot or -nucl command-line arguments; only when using the
2077 - Methods added to Bio::Root::Utilities: create_filehandle(),
2078 get_newline_char(), and taste_file() to generalize filehandle
2079 creation and autodetect newline characters in files/streams
2080 (see bug report #19).
2081 - Bio::Root::IOManager::read() now handles timeouts and uses
2082 Utilities::create_filehandle().
2083 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
2084 of hardwiring in "\n".
2085 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
2087 0.04.2 Wed Dec 30 02:27:36 1998
2088 - Bug fixes in Bio::Tools::Blast modules, version 0.073
2089 (see Bio::Tools::Blast::CHANGES).
2090 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
2091 to CORE::reverse (prevents ambiguous warnings with 5.005).
2092 - Appending '.tmp.bioperl' to temporary files created by
2093 Bio::Root::Utilities::compress() or uncompress() to
2094 make it easy to identify & cleanup these files as needed.
2095 - Developers: Created CVS branch release-0-04-bug from
2096 release-0-04-1. Before making bug fixes to the 0.04.1 release,
2097 be sure to cvs checkout this branch into a clean area.
2099 0.04.1 Wed Dec 16 05:39:15 1998
2100 - Bug fixes in Bio::Tools::Blast modules, version 0.072
2101 (see Bio::Tools::Blast::CHANGES).
2102 - Compile/SW/Makefile.PL now removes *.o and *.a files
2105 0.04 Tue Dec 8 07:49:19 1998
2106 - Lots of new modules added including:
2107 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
2108 and Bio/Compile directory containing XS-linked C code for
2109 creating Smith-Waterman sequence alignments from within Perl.
2110 * Steve Chervitz's Blast distribution has been incorporated.
2111 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
2112 - Bio/examples directory for demo scripts for all included modules.
2113 - Bio/t directory containing test suit for all included modules.
2114 - For changes specific to the Blast-related modules prior to
2115 incorporation in this central distribution, see the CHANGES
2116 file in the Bio/Tools/Blast directory.
2118 0.01 Tue Sep 8 14:23:22 1998
2119 - original version from central CVS tree; created by h2xs 1.18