1 ---------------------------------------------------------
2 Revision history for BioPerl core modules
3 ---------------------------------------------------------
4 The comprehensive history and ongoing development of BioPerl:
6 http://github.com/bioperl/bioperl-live
8 Some of that history is also highlighted on our wiki:
10 http://www.bioperl.org/wiki/Change_log
11 http://www.bioperl.org/wiki/History_of_BioPerl
13 Bugs and requested features list:
15 https://github.com/bioperl/bioperl-live/issues
17 CPAN releases are branched from 'master'.
18 ---------------------------------------------------------
22 In order to reduce the number of dependencies, we are actively encouraging
23 developers wanting to submit new code with additional dependencies to release
24 code in a separate repository and release it on CPAN. We can help assist in this
25 process and can also place this under the 'bioperl' Github organization (and
26 similarly under the bioperl umbrella account in CPAN), though this is not
29 We will also be moving additonal code to other repositories and will release
30 them separately on CPAN. Modules considered obsolute (relies on a dead web
31 service or utilizes strict dependencies that are also considered obsolete) will
36 * The following modules have been moved here from the BioPerl-Run
39 Bio::Tools::Run::Analysis
40 Bio::Tools::Run::AnalysisFactory
41 Bio::Tools::Run::WrapperBase
42 Bio::Tools::Run::WrapperBase::CommandExts
44 * The following modules have been removed from the BioPerl
45 distribution to be part of a separate distribution also
48 Bio::AlignIO::stockholm
50 Bio::DB::Expression::geo
53 Bio::Tools::AlignFactory
57 * The following programs have been removed:
64 * The deobfuscator has been removed.
66 * The script `bp_blast2tree` has been moved to the BioPerl-Run
67 distribution since it's mainly a wrapper to modules in there.
69 * The entire Bio::PopGen namespace, Bio::Tree::AlleleNode
70 module, and scripts bp_composite_LD and bp_heterogeneity_test
71 have been moved into a separate distribution named Bio-PopGen.
73 * All modules related to the NeXML format have been moved into a
74 separate distribution named Bio-NeXMLIO. These are:
82 This also means BioPerl is no longer dependent on Bio-Phylo.
84 * All modules interfacing to ACeDB servers have been moved into a
85 separate distribution named Bio-DB-Ace. These are:
88 * Bio::DB::GFF::Adaptor::ace
89 * Bio::DB::GFF::Adaptor::dbi::mysqlace
90 * Bio::DB::GFF::Adaptor::dbi::oracleace
92 This also means BioPerl is no longer dependent on AcePerl.
94 * The module Bio::Draw::Pictogram has been moved to a separate
95 distribution named Bio-Draw-Pictogram. This also means BioPerl
96 is no longer dependent on SVG.
98 * The module Bio::Tree::Draw::Cladogram has been moved to a
99 separate distribution named Bio-Tree-Draw-Cladogram. This also
100 means BioPerl is no longer dependent on PostScript.
102 * The module Bio::TreeIO::svggraph has been moved to a separate
103 distribution named Bio-TreeIO-svggraph. This also means that
104 BioPerl is no longer dependent on SVG-Graph and Tree-DAG_Node.
106 * The module Bio::SeqIO::excel has been moved to a separate
107 distribution named Bio-SeqIO-excel. This also means that
108 BioPerl is no longer dependent on Spreadsheet-ParseExcel.
110 * The entire Bio::PhyloNetwork namespace has been moved to a
111 separate distribution named Bio-PhyloNetwork. This also means
112 that BioPerl is no longer dependent on Algorithm::Munkres,
113 GraphViz, and Array::Compare.
115 * The entire Bio::Asembly namespace has been moved to a separate
116 distribution named Bio-Assembly. This also means that BioPerl
117 is no longer dependent on Bio-SamTools and Sort-Naturally.
119 * The entire Bio::Structure namespace has been moved to a
120 separate distribution named Bio-Structure.
122 * The entire Bio::SeqEvolution namespace has been moved to a
123 separate distribution named Bio-SeqEvolution.
125 * The Bio::Tools::Gel module has been moved into its own
126 distribution named Bio-Tools-Gel.
128 * The entire Bio::Restriction namespace has been moved to a
129 separate distribution named Bio-Restriction.
131 * The module Bio::SeqIO::entrezgene has been moved to the
132 Bio-ASN1-EntrezGene distribution.
134 * The module Bio::MolEvol::CodonModel has moved to a distribution
135 of its own, named after itself.
137 * The module Bio::Perl has moved to a new distribution named
140 * The module Bio::Tools::Run::RemoteBlast has moved to a new
141 distribution named after itself.
143 * The module Bio::Align::Graphics has been moved to a new distribution
144 named after itself. This also means that BioPerl is no longer
147 * The entire Bio::DB::HIV namespace, the Bio::DB::Query::HIVQuery
148 module, and the the bp_hivq program have been moved to their
149 own distribution named Bio-DB-HIV. This also drops the bioperl
150 dependency on XML-Simple and Term-ReadLine.
152 * The entire Bio::DB::TFBS namespace has been moved to its own
153 distribution named after itself.
155 * All modules to handle HMMER programs output have been moved to their
156 own distribution named Bio-SearchIO-hmmer. This also includes the
157 programs bp_hmmer_to_table and bp_parse_hmmsearch.
159 * Bio::DB::MeSH and related Bio::Phenotype::MeSH modules have moved
160 to their own distribution Bio-DB-MeSH.
162 * The Bio::DB::Universal module has been moved to its own distribution.
164 * The emacs bioperl minor mode is no longer distributed as part of the
165 perl module distributions. See
166 https://github.com/bioperl/emacs-bioperl-mode
172 * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
173 * #245 - Code coverage fixes [zmughal,cjfields]
174 * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
175 * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
176 * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
177 * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
178 * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
179 * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
180 * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
181 * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
182 * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
183 * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
187 * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
193 * Minor release to incorporate fix for CPAN indexing, which
194 prevented proper updates [cjfields]
195 * Fix problem in managing Target attribute for gff3 [Jukes34]
196 * Minor bug fixes related to NCBI HTTPS support [cjfields]
202 * We have migrated to Github Pages. This was actually planned, but the
203 recent OBF server compromise forced our hand.
205 Brian Osborne [bosborne] took this under his wing to move docs and has
206 done a tremendous amount of work formatting the site and working out some
207 of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
208 Cantalupo and Franscison Ossandon also helped. Kudos!!
210 * Similarly, the official issue tracker is now Github Issues. This has
211 been updated in the relevant documentation bits (we hope!)
215 * Previously deprecated modules removed
216 * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
217 * Bio::DB::SeqHound has been removed due to the service no longer being
219 * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
220 reasons due to the server no longer having a valid cert
221 * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
222 * Bio::Coordinate, Bio::SearchIO::blastxml,
223 Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
228 * Docker instances of tagged releases are available! [hlapp]
229 * NCBI HTTPS support [mjohnson and others]
230 * Bio::SearchIO::infernal
231 - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
232 * Bio::Search::HSP::ModelHSP
233 - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
235 * Bio::Search::Result::INFERNALResult
236 - Added new module to represent features of Infernal reports [pcantalupo]
237 * Bio::DB::Taxonomy SQLite option [cjfields]
238 * WrapperBase quoted option values [majensen]
239 * Various documentation fixes and updates [bosborne]
243 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
244 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
245 * NeXML parser fixes [fjossandon]
246 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
247 * RT 103272 : SeqFeature database deletion skipped features with a decimal -
248 Joshua Fortriede (Xenbase)
249 * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
250 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
251 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
252 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
253 * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
254 * Issue #84: EMBL format wrapping problem [nyamned]
255 * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
256 * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
257 or compiled C code (when Inline::C is installed) [rocky]
258 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
259 * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
260 * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
261 * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
262 to be consistent with "$hit->bits" behaviour [fjossandon]
263 * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
264 aminoacids made "next_seq" confused and broke the parser [fjossandon]
265 * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
266 Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
267 to "complement(join(A..B,C..D))" [fjossandon]
268 * For the many many many fixes that weren't mentioned - blame the release guy!
272 [Significant changes]
274 * Bug/feature issue tracking has moved to GitHub Issues:
275 https://github.com/bioperl/bioperl-live/issues
276 * DB_File has been demoted from "required" to "recommended",
277 which should make easier for Windows users to install BioPerl
278 if they don't need that module.
282 * Bio::Search::HSP::GenericHSP
283 - Bug #3370, added a "posterior_string" method to retrieve the
284 posterior probability lines (PP) from HMMER3 reports [fjossandon]
285 - Added a "consensus_string" method to retrieve the consensus
286 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
287 * Bio::SearchIO::hmmer2
288 - The number of identical and conserved residues are now calculated
289 directly from the homology line [fjossandon]
290 - Now the Query Length and Hit Length are reported when the alignment
291 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
292 - Implemented the capture of the consensus structure lines [fjossandon]
293 * Bio::SearchIO::hmmer3
294 - The number of identical and conserved residues are now calculated
295 directly from the homology line [fjossandon]
296 - Now the Hit Length is reported when the alignment runs until the end
297 of the sequence/model ('.]' or '[]') [fjossandon]
298 - Implemented the capture of the consensus structure lines [fjossandon]
299 - Implemented the capture of the posterior probability lines [fjossandon]
300 - Completed the development of NHMMER parsing, including alignments [fjossandon]
301 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
302 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
303 "min_score", "min_bits, and "hit_filter" methods from
304 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
305 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
306 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
307 besides Blast, instead of being ignored. Added tests for all moved methods
308 using HMMER outputs and run the full test suite and everything pass [fjossandon]
309 * Bio::SeqIO::MultiFile
310 - Autodetection of file format [fangly]
311 * Bio::Tools::GuessSeqFormat:
312 - Format detection from non-seekable filehandles such as STDIN [fangly]
316 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
317 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
318 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
319 * Abstract: Fixed ActivePerl incapability of removing temporary files
320 because of problems closing tied filehandles [fjossandon]
321 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
322 because ActivePerl were producing a ".index.pag" and ".index.dir"
323 files instead of a single ".index" file (like Strawberry Perl).
324 Now those temporary files are correctly considered and deleted. [fjossandon]
325 * Test files: Added missing module requirements (DB_File and Data::Stag)
326 to several tests files that were failing because those modules were
327 not present. Now those test files are correctly skipped instead. [fjossandon]
328 * Blast: Added support to changes in bl2seq from BLAST+ output, which
329 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
330 * Phylip: Return undef in "next_aln" at file end to avoid
331 an infinite loop [yschensandiego]
332 * HMMER3: When a hit description is too long, it is truncated in
333 the Scores table. In those cases, the more complete description from
334 the Annotation line (>>) will be used [fjossandon]
335 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
336 since it is now used by HMMER3 format in alignments [fjossandon]
337 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
338 to return undef if the query/hit length is unknown (like in some
339 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
340 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
341 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
342 added support to multi-query reports, reduced code redundancy,
343 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
344 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
345 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
346 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
347 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
348 * Double-quotes on paths are needed in some places [fjossandon]
349 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
350 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
351 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
352 with the latest changes made in their own repositories [fjossandon]
353 * General synching of files with the master branch [fjossandon]
354 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
355 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
356 * Fixed broken MeSH parser [fjossandon]
357 * Fixed missing detection of format in SeqIO when given a -string [fangly]
361 * Major Windows support updates! [fjossandon]
362 * MAKER update to allow for stricter standard codon table [cjfields]
363 * Better support for circular sequences [fjossandon]
364 * Fixes for some complex location types [fjossandon]
365 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
366 * Fix bug #2978 related to BLAST report type [fjossandon]
367 * Deobfuscator fixes [DaveMessina]
371 * Address CPAN test failures [cjfields]
372 * Add BIOPROJECT support for Genbank files [hyphaltip]
373 * Better regex support for HMMER3 output [bosborne]
377 * Minor update to address CPAN test failures
381 * Remove Bio::Biblio and related files [carandraug]
382 - this cause version clashes with an independently-released
383 version of Bio::Biblio
389 * Hash randomization fixes for perl 5.18.x
390 - Note: at least one module (Bio::Map::Physical) still has a failing test;
391 this is documented in bug #3446 and has been TODO'd; we will be pulling
392 Bio::Map and similar modules out of core into separate distributions in the
393 1.7.x release series [cjfields]
397 * Bio::Seq::SimulatedRead
398 - New module to represent reads taken from other sequences [fangly]
400 - Support of Clone::Fast as a faster cloning alternative [fangly]
402 - Moved the format() and variant() methods from Bio::*IO modules to
403 Bio::Root::IO [fangly]
404 - Can now use format() to get the type of IO format in use [fangly]
406 - New regexp() method to create regular expressions from IUPAC sequences
408 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
409 - Code refresh [fangly]
411 - Added support for the Greengenes and Silva taxonomies [fangly]
412 * Bio::Tree::TreeFunctionsI
413 - get_lineage_string() represents a lineage as a string [fangly]
414 - add_trait() returns instead of reporting an error when the column
415 number is exceeded in add_trait() [fangly]
416 - Option to support tree leaves without trait [fangly]
417 - Allow ID of 0 in trait files [fangly]
418 * Bio::DB::Taxonomy::list
419 - Misc optimizations [fangly]
420 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
421 * Bio::DB::Taxonomy::*
422 - get_num_taxa() returns the number of taxa in the database [fangly]
423 * Bio::DB::Fasta and Bio::DB::Qual
424 - support indexing an arbitrary list of files [fangly]
425 - user can supply an arbitrary index file name [fangly]
426 - new option to remove index file at the end [fangly]
428 - now handles IUPAC degenerate residues [fangly]
429 * Bio::PrimarySeq and Bio::PrimarySeqI
430 - speed improvements for large sequences [Ben Woodcroft, fangly]
432 - tightened and optimized quality string validation [fangly]
434 - new method and option 'block', to create FASTA output with space
435 intervaled blocks (similar to genbank or EMBL) has been implemented.
436 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
437 in favour of the methods 'width' and 'preferred_id_type` respectively.
439 - moved from bioperl-live into the separate distribution Bio-FeatureIO
440 * Bio::SeqFeature::Annotated
441 - moved from bioperl-live into the separate distribution Bio-FeatureIO
442 * Bio::Cluster::SequenceFamily
443 - improved performance when using get_members with overlapping multiple
445 * Bio::SearchIO::hmmer3
446 - now supports nhmmer [bosborne]
450 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
451 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
452 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
453 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
454 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
455 information was lost in a multi-result blast file [Paul Cantalupo]
456 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
457 total gaps [Paul Cantalupo]
458 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
459 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
460 when end of domain indicator is split across lines [Paul Cantalupo]
461 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
463 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
464 instances where blank lines are within sequences [cjfields]
465 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
467 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
468 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
470 * Various fixes for Stockholm file indexing and processing [bosborne]
471 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
472 breaks parsing [cjfields]
473 * Fix case where Bio::Seq::Meta* objects with no meta information could not
474 be reverse-complemented [fangly]
475 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
476 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
477 when unsure that values will be numerical [fangly]
478 * Fix undef warnings in Bio::SeqIO::embl [fangly]
479 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
480 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
481 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
483 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
484 source_tag and display_name must return a string, not undef [fangly]
485 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
486 add_SeqFeature takes a single argument [fangly]
487 * Use cross-platform filenames and temporary directory in
488 Bio::DB::Taxonomy::flatfile [fangly]
489 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
490 properly identified as existing taxa in the database [fangly]
491 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
492 without also passing a lineage to store [fangly]
493 * Prevent passing a directory to the gi2taxid option (-g) of
494 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
496 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
497 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
498 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
499 object before trying to access, and no longer returns repeated sequences.
506 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
507 modules using Ace will also be deprecated [lds, cjfields]
508 * Minor bug fix release
509 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
510 * Address Build.PL issues when DBI is not present [hartzell]
511 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
512 * Remove deprecated code for perl 5.14.0 compat [cjfields]
513 * Due to schema changes and lack of support for older versions, support
514 for NeXML 0.9 is only (very) partially implemented.
515 See: https://redmine.open-bio.org/issues/3207
519 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
520 docs [genehack, cjfields]
521 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
522 module version from dist_version (probably not the best way to do this,
523 but it seems to work) [rbuels, cjfields]
526 1.6.900 April 14, 201
530 * This will probably be the last release to add significant features to
531 core modules; subsequent releases will be for bug fixes alone.
532 We are planning on a restructuring of core for summer 2011, potentially
533 as part of the Google Summer of Code. This may become BioPerl 2.0.
534 * Version bump represents 'just prior to v 1.7'. We may have point
535 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
536 This code essentially is what is on the github master branch.
540 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
542 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
543 - removal of Scalar::Util::weaken code, which was causing odd headaches
544 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
545 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
547 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
550 - bug 2515 - new contribution [Ryan Golhar, jhannah]
552 - support for reading Maq, Sam and Bowtie files [maj]
553 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
554 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
555 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
556 - bug 2726: reading/writing granularity: whole scaffold or one contig
557 at a time [Joshua Udall, fangly]
559 - Added parsing of xrefs to OBO files, which are stored as secondary
560 dbxrefs of the cvterm [Naama Menda]
561 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
562 * PAML code updated to work with PAML 4.4d [DaveMessina]
566 * [3198] - sort tabular BLAST hits by score [DaveMessina]
567 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
568 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
569 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
571 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
572 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
573 * [3164] - TreeFunctionsI syntax bug [gjuggler]
574 * [3163] - AssemblyIO speedup [fangly]
575 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
577 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
578 * [3158] - fix EMBL file mis-parsing [cjfields]
579 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
581 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
582 * [3148] - URL change for UniProt [cjfields]
583 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
584 * [3136] - HMMer3 parser fixes [kblin]
585 * [3126] - catch description [Toshihiko Akiba]
586 * [3122] - Catch instances where non-seekable filehandles were being
587 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
588 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
589 [dukeleto, rbuels, cjfields]
590 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
592 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
593 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
595 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
596 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
597 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
598 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
599 * [3086] - EMBL misparsing long tags [kblin, cjfields]
600 * [3085] - CommandExts and array of files [maj, hyphaltip]
601 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
602 for alignment slices [Ha X. Dang, cjfields]
603 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
604 * [3073] - fix parsing of GenBank files from RDP [cjfields]
605 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
606 * [3064] - All-gap midline BLAST report issues [cjfields]
607 * [3063] - BLASt report RID [Razi Khaja, cjfields]
608 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
609 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
610 * [3039] - correct Newick output root node branch length [gjuggler,
612 * [3038] - SELEX alignment error [Bernd, cjfields]
613 * [3033] - PrimarySeq ID setting [Bernd, maj]
614 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
615 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
616 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
617 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
618 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
619 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
620 PAML 4.4d [DaveMessina]
621 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
623 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
624 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
625 * [3017] - using threads with Bio::DB::GenBank [cjfields]
626 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
627 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
628 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
629 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
630 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
632 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
633 * [2977] - TreeIO issues [DaveMessina]
634 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
635 * [2944] - Bio::Tools::GFF score [cjfields]
636 * [2942] - correct MapTiling output [maj]
637 * [2939] - PDB residue insertion codes [John May, maj]
638 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
639 * [2928] - GuessSeqFormat raw [maj]
640 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
641 * [2922] - open() directive issue [cjfields]
642 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
643 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
644 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
645 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
647 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
648 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
649 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
650 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
651 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
652 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
653 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
654 * [2758] - Bio::AssemblyIO ace problems [fangly]
655 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
656 * [2726] - ace file IO [Josh, fangly]
657 * [2700] - Refactor Build.PL [cjfields]
658 * [2673] - addition of simple Root-based clone() method [cjfields]
659 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
660 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
661 * [2594] - Bio::Species memory leak [cjfields]
662 * [2515] - GenBank XML parser [jhannah]
663 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
664 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
665 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
667 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
671 * Bio::Expression modules - these were originally designed to go with the
672 bioperl-microarray suite of tools, however they have never been completed
673 and so have been removed from the distribution. The original code has
674 been moved into the inactive bioperl-microarray suite. [cjfields]
678 * Repository moved from Subversion (SVN) to
679 http://github.com/bioperl/bioperl-live [cjfields]
680 * Bug database has moved to Redmine (https://redmine.open-bio.org)
681 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
682 Thieme have been moved to their own distribution (Bio-Microarray).
685 1.6.1 Sept. 29, 2009 (point release)
686 * No change from last alpha except VERSION and doc updates [cjfields]
688 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
689 * Fix for silent OBDA bug related to FASTA validation [cjfields]
691 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
692 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
693 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
695 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
697 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
698 * WinXP test fixes [cjfields, maj]
699 * BioPerl.pod added for descriptive information, fixes CPAN indexing
701 * Minor doc fixes [cjfields]
703 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
704 * Fix tests failing due to merging issues [cjfields]
705 * More documentation updates for POD parsing [cjfields]
707 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
709 - fix YAML meta data generation [cjfields]
711 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
712 * Bio::Align::DNAStatistics
713 - fix divide by zero problem [jason]
715 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
716 * Bio::AlignIO::stockholm
717 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
718 * Bio::Assembly::Tools::ContigSpectrum
719 - function to score contig spectrum [fangly]
720 * Bio::DB::EUtilities
721 - small updates [cjfields]
723 - berkeleydb database now autoindexes wig files and locks correctly
726 - various small updates for stability; tracking changes to LANL
727 database interface [maj]
728 * Bio::DB::SeqFeature (lots of updates and changes)
729 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
730 - bug 2835 - patch [Dan Bolser]
731 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
733 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
734 * Bio::Factory::FTLocationFactory
735 - mailing list bug fix [cjfields]
737 - performance work on column_from_residue_number [hartzell]
738 * Bio::Matrix::IO::phylip
739 - bug 2800 - patch to fix phylip parsing [Wei Zou]
741 - Google Summer of Code project from Chase Miller - parsers for Nexml
742 file format [maj, chmille4]
744 - Make Individual, Population, Marker objects AnnotatableI [maj]
745 - simplify LD code [jason]
747 - deal with empty intersection [jason]
749 - significant overhaul of Bio::Restriction system: complete support for
750 external and non-palindromic cutters. [maj]
752 - CPANPLUS support, no automatic installation [sendu]
754 - allow IO::String (regression fix) [cjfields]
755 - catch unintentional undef values [cjfields]
756 - throw if non-fh is passed to -fh [maj]
757 * Bio::Root::Root/RootI
758 - small debugging and core fixes [cjfields]
760 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
761 * Bio::Root::Utilities
762 - bug 2737 - better warnings [cjfields]
764 - tiling completely refactored, HOWTO added [maj]
765 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
766 will deprecate usage of the older tiling code in the next BioPerl
768 - small fixes [cjfields]
770 - Infernal 1.0 output now parsed [cjfields]
771 - new parser for gmap -f9 output [hartzell]
772 - bug 2852 - fix infinite loop in some output [cjfields]
773 - blastxml output now passes all TODO tests [cjfields]
774 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
775 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
776 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
777 * Bio::Seq::LargePrimarySeq
778 - delete tempdirs [cjfields]
779 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
781 - extract regions based on quality threshold value [Dan Bolser, heikki]
782 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
783 * Bio::SeqFeature::Lite
784 - various Bio::DB::SeqFeature-related fixes [lstein]
785 * Bio::SeqFeature::Tools::TypeMapper
786 - additional terms for GenBank to SO map [scain]
787 * Bio::SeqIO::chadoxml
788 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
790 - support for CDS records [dave_messina, Sylvia]
792 - complete refactoring to handle all FASTQ variants, perform validation,
793 write output. API now conforms with other Bio* parsers and the rest of
794 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
796 * Bio::SeqIO::genbank
797 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
798 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
799 * Bio::SeqIO::largefasta
800 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
802 - add option for 'single' and 'multiple'
804 - bug 2881 - fix scf round-tripping [Adam Søgren]
806 - bug 2766, 2810 - copy over tags from features, doc fixes [David
809 - bug 2793 - patch for add_seq index issue [jhannah, maj]
810 - bug 2801 - throw if args are required [cjfields]
811 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
812 [Tristan Lefebure, maj]
813 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
814 - fix POD and add get_SeqFeatures filter [maj]
815 * Bio::Tools::dpAlign
816 - add support for LocatableSeq [ymc]
817 - to be moved to a separate distribution [cjfields, rbuels]
818 * Bio::Tools::EUtilities
819 - fix for two bugs from mail list [Adam Whitney, cjfields]
820 - add generic ItemContainerI interface for containing same methods
823 - fix up code, add more warnings [cjfields]
824 - to be moved to a separate distribution [cjfields, rbuels]
825 * Bio::Tools::Primer3
826 - bug 2862 - fenceposting issue fixed [maj]
827 * Bio::Tools::Run::RemoteBlast
828 - tests for remote RPS-BLAST [mcook]
829 * Bio::Tools::SeqPattern
830 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
831 * Bio::Tools::tRNAscanSE
832 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
834 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
835 * Bio::Tree::Statistics
836 - several methods for calculating Fitch-based score, internal trait
837 values, statratio(), sum of leaf distances [heikki]
839 - bug 2869 - add docs indicating edge case where nodes can be
840 prematurely garbage-collected [cjfields]
841 - add as_text() function to create Tree as a string in specified format
843 * Bio::Tree::TreeFunctionsI
844 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
846 * Bio::TreeIO::newick
847 - fix small semicolon issue [cjfields]
849 - update to bp_seqfeature_load for SQLite [lstein]
850 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
851 - fastam9_to_table - fix for MPI output [jason]
852 - gccalc - total stats [jason]
854 - POD cleanup re: FEEDBACK section [maj, cjfields]
855 - cleanup or fix dead links [cjfields]
856 - Use of no_* methods (indicating 'number of something') is deprecated
857 in favor of num_* [cjfields]
858 - lots of new tests for the above bugs and refactors [everyone!]
859 - new template for Komodo text editor [cjfields]
862 * Feature/Annotation rollback
863 - Problematic changes introduced prior to the 1.5 release have been
864 rolled back. These changes led to subtle bugs involving operator
865 overloading and interface methods.
866 - Behavior is very similar to that for BioPerl 1.4, with tag values
867 being stored generically as simple scalars. Results in a modest
870 - Split into a separate distribution on CPAN, primarily so development
871 isn't reliant on a complete BioPerl release.
872 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
873 is only available via Subversion (via bioperl-live main trunk)
875 - Common test bed for all BioPerl modules
877 - Common Module::Build-based subclass for all BioPerl modules
878 * Bio::DB::EUtilities
879 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
880 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
881 and user agent request posting and retrieval
882 * Test implementation and reorganization
883 - Tests have been reorganized into groups based on classes or use
885 - Automated test coverage is now online:
886 http://www.bioperl.org/wiki/Test_Coverage
887 - After this release, untested modules will be moved into a
888 separate developer distribution until tests can be derived.
889 Also, new modules to be added are expected to have a test suite
890 and adequate test coverage.
892 1.5.2 Developer release
894 Full details of changes since 1.5.1 are available online at:
895 http://www.bioperl.org/wiki/Change_log
896 The following represents a brief overview of the most important changes.
899 - Overhaul. Brand new system fully allows markers to have multiple
900 positions on multiple maps, and to have relative positions. Should be
904 - This module and all the modules in the Taxonomy directory now
905 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
910 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
912 * New methods ancestor(), each_Descendent() and _handle_internal_id().
914 * Allows for different database modules to create Bio::Taxon objects
915 with the same internal id when the same taxon is requested from each.
918 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
920 * No longer includes the fake root node 'root'; there are multiple roots
921 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
924 * get_node() has new option -full
926 * Caches data retrieved from website
929 - Now a Bio::Taxon. Carries out the species name -> specific name munging
930 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
931 backward compatability in species() method.
933 o Bio::Search and Bio::SearchIO
934 - Overhaul. The existing system has been sped up via some minor changes
935 (mostly gain-of-function to the API). Bio::PullParserI is introduced
936 as a potential eventual replacment for the existing system, though as
937 yet only a Hmmpfam parser exists written using it.
940 1.5.1 Developer release
942 o Major problem with how Annotations were written out with
943 Bio::Seq is fixed by reverting to old behavior for
944 Bio::Annotation objects.
949 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
950 expect at l east 9 spaces at the beginning of a line to
951 indicate line wrapping.
953 * Treat multi-line SOURCE sections correctly, this defect broke
954 both common_name() and classification()
956 * parse swissprot fields in genpept file
958 * parse WGS genbank records
961 * Changed regexp for ID line. The capturing parentheses are
962 the same, the difference is an optional repeated-not-semi-
963 colon expression following the captured \S+. This means the
964 regexp works when the division looks like /PRO;/ or when the
965 division looks like /ANG ;/ - the latter is from EMBL
968 * fix ID line parsing: the molecule string can have spaces in
969 it. Like: "genomic DNA"
971 - swiss.pm: bugs #1727, #1734
974 * Added parser for entrezgene ASN1 (text format) files.
975 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
979 - maf.pm coordinate problem fixed
981 o Bio::Taxonomy and Bio::DB::Taxonomy
983 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
984 can be done via Web without downloading all the sequence.
986 o Bio::Tools::Run::RemoteBlast supports more options and complies
987 to changes to the NCBI interface. It is reccomended that you
988 retrieve the data in XML instead of plain-text BLAST report to
989 insure proper parsing and retrieval of all information as NCBI
990 fully expects to change things in the future.
992 o Bio::Tree and Bio::TreeIO
994 - Fixes so that re-rooting a tree works properly
996 - Writing out nhx format from a newick/nexus file will properly output
997 bootstrap information. The use must move the internal node labels over
999 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
1000 $node->bootstrap($node->id);
1003 - Nexus parsing is much more flexible now, does not care about
1006 - Cladogram drawing module in Bio::Tree::Draw
1008 - Node height and depth now properly calculated
1010 - fix tree pruning algorithm so that node with 1 child gets merged
1012 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
1013 bugs and improvements were added, see Gbrowse mailing list for most of
1016 o Bio::DB::GFF partially supports GFF3. See information about
1017 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
1019 o Better location parsing in Bio::Factory::FTLocationFactory -
1020 this is part of the engine for parsing EMBL/GenBank feature table
1021 locations. Nested join/order-by/complement are allowed now
1023 o Bio::PrimarySeqI->translate now takes named parameters
1025 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
1026 reconstruction) is now supported. Parsing different models and
1027 branch specific parametes are now supported.
1029 o Bio::Factory::FTLocationFactory - parse hierarchical locations
1032 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
1033 for getter/setter functions
1037 - blast bug #1739; match scientific notation in score
1038 and possible e+ values
1040 - blast.pm reads more WU-BLAST parameters and parameters, match
1041 a full database pathname,
1043 - Handle NCBI WEB and newer BLAST formats specifically
1044 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
1046 - psl off-by-one error fixed
1048 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
1049 and HSPs can be constructed from them.
1051 - HSPs query/hit now have a seqdesc field filled out (this was
1052 always available via $hit->description and
1053 $result->query_description
1055 - hmmer.pm can parse -A0 hmmpfam files
1057 - Writer::GbrowseGFF more customizeable.
1059 o Bio::Tools::Hmmpfam
1060 make e-value default score displayed in gff, rather than raw score
1061 allow parse of multiple records
1064 1.5 Developer release
1066 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
1067 provide Jukes-Cantor and Kimura pairwise distance methods,
1070 o Bio::AlignIO support for "po" format of POA, and "maf";
1071 Bio::AlignIO::largemultifasta is a new alternative to
1072 Bio::AlignIO::fasta for temporary file-based manipulation of
1073 particularly large multiple sequence alignments.
1075 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
1076 be treated similarly as an assembled contig.
1078 o Bio::CodonUsage provides new rare_codon() and probable_codons()
1079 methods for identifying particular codons that encode a given
1082 o Bio::Coordinate::Utils provides new from_align() method to build
1083 a Bio::Coordinate pair directly from a
1084 Bio::Align::AlignI-conforming object.
1086 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
1087 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
1088 web service using standard Pubmed query syntax, and retrieve
1091 o Bio::DB::GFF has various sundry bug fixes.
1093 o Bio::FeatureIO is a new SeqIO-style subsystem for
1094 writing/reading genomic features to/from files. I/O classes
1095 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
1096 classes only read/write Bio::SeqFeature::Annotated objects.
1097 Notably, the GFF v3 class requires features to be typed into the
1100 o Bio::Graph namespace contains new modules for manipulation and
1101 analysis of protein interaction graphs.
1103 o Bio::Graphics has many bug fixes and shiny new glyphs.
1105 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
1106 indexing for HMMER reports and FASTA qual files, respectively.
1108 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
1109 new objects that can be placed within a Bio::Map::MapI-compliant
1110 genetic/physical map; Bio::Map::Physical provides a new physical
1111 map type; Bio::MapIO::fpc provides finger-printed clone mapping
1114 o Bio::Matrix::PSM provide new support for postion-specific
1115 (scoring) matrices (e.g. profiles, or "possums").
1117 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
1118 be instantiated without explicitly using Bio::OntologyIO. This
1119 is possible through changes to Bio::Ontology::OntologyStore to
1120 download ontology files from the web as necessary. Locations of
1121 ontology files are hard-coded into
1122 Bio::Ontology::DocumentRegistry.
1124 o Bio::PopGen includes many new methods and data types for
1125 population genetics analyses.
1127 o New constructor to Bio::Range, unions(). Given a list of
1128 ranges, returns another list of "flattened" ranges --
1129 overlapping ranges are merged into a single range with the
1130 mininum and maximum coordinates of the entire overlapping group.
1132 o Bio::Root::IO now supports -url, in addition to -file and -fh.
1133 The new -url argument allows one to specify the network address
1134 of a file for input. -url currently only works for GET
1135 requests, and thus is read-only.
1137 o Bio::SearchIO::hmmer now returns individual Hit objects for each
1138 domain alignment (thus containing only one HSP); previously
1139 separate alignments would be merged into one hit if the domain
1140 involved in the alignments was the same, but this only worked
1141 when the repeated domain occured without interruption by any
1142 other domain, leading to a confusing mixture of Hit and HSP
1145 o Bio::Search::Result::ResultI-compliant report objects now
1146 implement the "get_statistics" method to access
1147 Bio::Search::StatisticsI objects that encapsulate any
1148 statistical parameters associated with the search (e.g. Karlin's
1149 lambda for BLAST/FASTA).
1151 o Bio::Seq::LargeLocatableSeq combines the functionality already
1152 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
1154 o Bio::SeqFeature::Annotated is a replacement for
1155 Bio::SeqFeature::Generic. It breaks compliance with the
1156 Bio::SeqFeatureI interface because the author was sick of
1157 dealing with untyped annotation tags. All
1158 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
1159 compliant, and accessible through Bio::Annotation::Collection.
1161 o Bio::SeqFeature::Primer implements a Tm() method for primer
1162 melting point predictions.
1164 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
1165 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
1167 o Bio::Taxonomy::Node now implements the methods necessary for
1168 Bio::Species interoperability.
1170 o Bio::Tools::CodonTable has new reverse_translate_all() and
1171 make_iupac_string() methods.
1173 o Bio::Tools::dpAlign now provides sequence profile alignments.
1175 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
1177 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
1180 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
1181 for designing small inhibitory RNA.
1183 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
1184 methods based on a distance matrix.
1186 o Bio::Tree::Statistics provides an assess_bootstrap() method to
1187 calculate bootstrap support values on a guide tree topology,
1188 based on provided bootstrap tree topologies.
1190 o Bio::TreeIO now supports the Pagel (PAG) tree format.
1196 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
1198 o Bio::Graphics will work with gd1 or gd2
1201 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
1203 - blast.pm Parse multi-line query fields properly
1204 - small speed improvements to blasttable.pm and others
1206 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
1207 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
1208 supporting more complex queries
1211 1.4. Stable major release
1213 Since initial 1.2.0, 3000 separate changes have been made to make this release.
1215 o installable scripts
1217 o global module version from Bio::Root:Version
1220 - major improvements; SVG support
1223 - population genetics
1224 - support several population genetics types of questions.
1225 - Tests for statistical neutrality of mutations
1226 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
1227 Tests of population structure (Wright's F-statistic: Fst) is in
1228 Bio::PopGen::PopStats. Calculating composite linkage
1229 disequilibrium (LD) is available in Bio::PopGen::Statistics as
1231 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1232 and csv (comma delimited formatted) data.
1234 - a directory for implementing population simulations has
1235 been added Bio::PopGen::Simulation and 2 simulations - a
1236 Coalescent and a simple single-locus multi-allele genetic drift
1237 simulation have been provided. This replaces the code in
1238 Bio::Tree::RandomTree which has been deprecated until proper
1239 methods for generating random phylogenetic trees are
1243 - new restrion analysis modules
1245 o Bio::Tools::Analysis
1246 - web based DNA and Protein analysis framework and several
1250 - per residue annotable sequences
1253 - Bio::Matrix::PSM - Position Scoring Matrix
1254 - Bio::Matrix::IO has been added for generalized parsing of
1255 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1256 initial implementations for parsing BLOSUM/PAM and Phylip
1257 Distance matricies respectively. A generic matrix
1258 implementation for general use was added in
1259 Bio::Matrix::Generic.
1266 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1267 - small inhibitory RNA
1269 o Bio::SeqFeature::Tools
1270 - seqFeature mapping tools
1271 - Bio::SeqFeature::Tools::Unflattener.pm
1272 -- deal with mapping GenBank feature collections into
1273 Chado/GFF3 processable feature sets (with SO term mappings)
1275 o Bio::Tools::dpAlign
1276 - pure perl dynamic programming sequence alignment
1279 o new Bio::SearchIO formats
1280 - axt and psl: UCSC formats.
1281 - blasttable: NCBI -m 8 or -m 9 format from blastall
1283 o new Bio::SeqIO formats
1284 - chado, tab, kegg, tigr, game
1285 - important fixes for old modules
1289 o improved Bio::Tools::Genewise
1291 o Bio::SeqIO now can recongnize sequence formats automatically from
1294 o new parsers in Bio::Tools:
1295 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1297 o Bio::DB::Registry bugs fixed
1298 - BerkeleyDB-indexed flat files can be used by the OBDA system
1299 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1300 used by the OBDA system
1302 o several new HOWTOs
1303 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1306 o hundreds of new and improved files
1310 o Bio::Tree::AlleleNode has been updated to be a container of
1311 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1316 1.2.3 Stable release update
1317 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1319 o Bug #1477 - Sel --> Sec abbreviation fixed
1320 o Fix bug #1487 where paring in-between locations when
1321 end < start caused the FTLocationFactory logic to fail.
1322 o Fix bug #1489 which was not dealing with keywords as an
1323 arrayref properly (this is fixed on the main trunk because
1324 keywords returns a string and the array is accessible via
1326 o Bio::Tree::Tree memory leak (bug #1480) fixed
1327 Added a new initialization option -nodelete which
1328 won't try and cleanup the containing nodes if this
1330 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1331 this was only present on the branch for the 1.2.1 and 1.2.2 series
1332 - Also merged main trunk changes to the branch which make
1333 newick -> nhx round tripping more effective (storing branch length
1334 and bootstrap values in same locate for NodeNHX and Node
1335 implementations.) Fixes to TreeIO parsing for labeled internal
1336 also required small changes to TreeIO::nhx. Improved
1337 tests for this module as well.
1339 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1340 gapped blast properly (was losing hit significance values due to
1341 the extra unexpeted column).
1342 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1343 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1344 although doesn't try to correct it - will get the negative
1345 number for you. Added a test for this as well.
1346 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1347 has no top-level family classification scores but does have scores and
1348 alignments for individual domains.
1349 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1350 regular expression to match the line was missing the possibility of
1351 an extra space. This is rare, which is why we probably did not
1353 - BLAST parsing picks up more of the statistics/parameter fields
1354 at the bottom of reports. Still not fully complete.
1355 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1356 were fixed to include many improvements and added flexiblity
1357 in outputting the files. Bug #1495 was also fixed in the process.
1359 - Update for GFF3 compatibility.
1360 - Added scripts for importing from UCSC and GenBank.
1361 - Added a 1.2003 version number.
1364 - Added a 1.2003 version number.
1365 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1366 properly writing keywords out.
1367 o Bio::SeqIO::genbank
1368 - Fixed bug/enhancement #1513 where dates of
1369 the form D-MMM-YYYY were not parsed. Even though this is
1370 invalid format we can handle it - and also cleanup the date
1371 string so it is properly formatted.
1372 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1373 and written with Genbank format. Similarly bug #1515 is fixed to
1374 parse in the ORIGIN text.
1375 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1376 to specify the ID type, one of (accession accession.version
1377 display primary). See Bio::SeqIO::preferred_id_type method
1378 documentation for more information.
1379 o Unigene parsing updated to handle file format changes by NCBI
1381 1.2.2 Stable release update
1383 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1384 - auto-discover ontology name
1385 - bug in parsing relationships when certain characters are in the term
1386 - fixed hard-coded prefix for term identifiers
1387 - various smaller issues
1389 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1390 of Bio::Ontology::TermI
1392 o brought the OBDA Registry code up to latest specs
1396 - accession number retrieval fixed
1398 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1400 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1401 #1459 which now properly report alignment start/end info
1402 for translated BLAST/FASTA searches.
1404 o Bio::TreeIO::newick can parse labeled internal nodes
1406 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1407 for BLASTX if if you provide -report_type => 'BLASTX' when
1408 initializing a BPbl2seq object. Bioperl 1.3 will have better
1409 support for bl2seq in the SearchIO system.
1411 o Bio::Root::IO support a -noclose boolean flag which will not
1412 close a filehandle upon object cleanup - useful when sharing
1413 a filehandle among objects. Additionally code added s.t.
1414 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1416 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1418 o Bio::SeqIO::genbank
1419 - bug #1456 fixed which generated extra sequence lines
1420 - write moltype correctly for genpept
1422 1.2.1 Stable release update
1424 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1426 o Addition from main trunk of Ontology objects, principly to allow
1427 BioSQL releases against 1.2.1
1429 o Fixes and cleanup of Bio::Coordinate modules
1431 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1432 the primary accession number
1434 o Other bug fixes, including bpindex GenBank fix
1436 o Bio::SeqIO::genbank bug #1389 fixed
1438 1.2 Stable major release
1440 o More functionality added to Bio::Perl, the newbie module
1442 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1443 Support for New Hampshire Extended (NHX) format parsing.
1445 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1446 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1449 o New ontology parsing Bio::Ontology
1451 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1452 multi-report (mlib) fasta reports, support for waba and exonerate.
1454 o Bio::ClusterIO for parsing Unigene clusters
1456 o Bio::Assembly added for representing phrap and ace assembly clusters.
1458 o Rudimentary support for writing Chado XML (see
1459 GMOD project: www.gmod.org for more information)
1461 o Bio::Coordinate for mapping between different coordinate systems such
1462 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1463 features into different coordinate systems.
1465 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1466 with the get_Stream_by_query method and supports the latest
1467 NCBI eutils interface.
1469 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1470 object for extracting subsets of features : currently only
1471 supports extraction by location.
1473 1.1.1 Developer release
1475 o Deprecated modules are now listed in the DEPRECATED file
1477 o New HowTo documents located in doc/howto describing
1478 a domain of Bioperl.
1480 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1481 and all old bugs are searchable through the bugzilla interface.
1483 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1484 have been addressed.
1486 o Support for Genewise parsing in Bio::Tools::Genewise
1488 o Start of Ontology framework with Bio::Ontology
1490 o Speedup to the Bio::Root::Root object method _rearrange.
1491 A global _load_module method was implemented to simplify the
1492 dynamic loading of modules ala Bio::SeqIO::genbank. This
1493 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1496 o Several performance improvements to sequence parsing in Bio::SeqIO.
1497 Attempt to speedup by reducing object creation overhead.
1499 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1500 method for sequence retrieval with their E-utils CGI scripts.
1501 More work to support Entrez queries to their fullest is planned
1504 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1506 1.1 Developer release
1508 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1509 this separation removes some of the complexity in our test suite
1510 and separates the core modules in bioperl from those that need
1511 external programs to run.
1513 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1514 not run into trouble running the makefile
1516 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1517 read,create,and write locations for grouped/split locations
1518 (like mRNA features on genomic sequence).
1520 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1521 and PAML (codeml,aaml, etc) parsing.
1523 o Bio::Tree:: objects expanded to handle testing monophyly,
1524 paraphyly, least common ancestor, etc.
1526 o Bio::Coordinate for mapping locations from different coordinate spaces
1528 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1529 added for parsing hmmpfam and hmmsearch output.
1531 o Bio::SearchIO::Writer::TextResultWriter for outputting
1532 a pseudo-blast textfile format
1535 1.0.2 Bug fix release
1537 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1538 in this release will not work after December 2002 when NCBI
1539 shuts off the old Entrez cgi scripts. We have already fixed
1540 on our main development branch and the functionality will be
1541 available in the next stable bioperl release (1.2) slated for
1544 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1545 testset by Robin Emig. These were fixed as was the get_aln
1546 method in Bio::Search::HSP::GenericHSP to handle the extra
1547 context sequence that is provided with a FastA alignment.
1549 o Migrating differences between Bio::Search::XX::BlastXX to
1550 Bio::Search::XX::GenericXX objects. This included mechanism
1551 to retrieve whole list of HSPs from Hits and whole list of Hits from
1552 Results in addition to the current next_XX iterator methods that
1553 are available. Added seq_inds() method to GenericHSP which identifies
1554 indexes in the query or hit sequences where conserved,identical,gaps,
1555 or mismatch residues are located (adapted from Steve Chervitz's
1556 implementation in BlastHSP).
1558 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1559 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1561 o Bio::Graphics glyph set improved and extended for GBrowse release
1563 o Bio::Tree::Tree get_nodes implementation improvement thanks
1564 to Howard Ross notice performance problem when writing out
1567 o Bio::Location::Fuzzy::new named parameter -loc_type became
1568 -location_type, Bio::Location::Simple::new named parameter
1569 -seqid becamse -seq_id.
1571 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1572 was mis-detecting that gaps should be placed at the beginning of
1573 the alignment when the best alignment starts internally in the
1576 1.0.1 Bug fix release
1578 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1580 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1581 and mixed (3.3 - 3.4) versions of FASTA.
1583 o Small API change to add methods for completeness across
1584 implementations of Bio::Search objects. These new methods
1585 in the interface are implemented by the GenericXX object as well
1586 as the BlastXX objects.
1587 * Bio::Search::Result::ResultI
1588 - hits() method returns list of all Hits (next_hit is an
1591 * Bio::Search::Hit::HitI
1592 - hsps() method returns list of all HSPs (next_hsp is an
1595 o The Bio::SearchIO::Writer classes have been fixed to handle results
1596 created from either psiblast (Search::BlastXX objects) or
1597 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1598 has to be done here to make it work properly and will nee major
1601 o Bugs in Bio::Tools::HMMER fixed, including
1602 * #1178 - Root::IO destructor wasn't being called
1603 * #1034 - filter_on_cutoff now behaves properly
1605 o Bio::SeqFeature::Computation initialization args fixed and
1608 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1610 o Updated FAQ with more example based answers to typical questions
1612 o Bug #1202 was fixed which would improperly join together qual values
1613 parsed by Bio::SeqIO::qual when a trailing space was not present before
1616 1.0.0 Major Stable Release
1618 This represents a major release of bioperl with significant
1619 improvements over the 0.7.x series of releases.
1621 o Bio::Tools::Blast is officially deprecated. Please see
1622 Bio::SearchIO for BLAST and FastA parsing.
1624 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1625 Bio::LocationI objects as well as start/end.
1627 o Bio::Biblio contains modules for Bibliographic data.
1628 Bio::DB::Biblio contains the query modules. Additionally one can
1629 parse medlinexml from the ebi bibliographic query service (BQS)
1630 system and Pubmed xml from NCBI. See Martin Senger's
1631 documentation in Bio::Biblio for more information.
1633 o Bio::DB::Registry is a sequence database registry part of
1634 Open Bioinformatics Database Access. See
1635 http://obda.open-bio.org for more information.
1637 o File-based and In-Memory Sequence caching is provided by
1638 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1641 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1642 been added by Lincoln Stein.
1644 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1646 o A FAQ has been started and is included in the release to provide
1647 a starting point for frequent questions and issues.
1649 0.9.3 Developer's release
1651 o Event based parsing system improved (SearchIO). With parsers for
1652 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1653 Additionally a lazy parsing system for text and html blast reports was
1654 added and is called psiblast (name subject to change in future releases).
1656 o Bio::Search objects improved and standardized with associated Interfaces
1657 written. The concept of a search "Hit" was standardized to be called
1658 "hit" consistently and the use of "subject" was deprecated in all active
1661 o Bio::Structure added (since 0.9.1) for Protein structure objects
1662 and PDB parser to retrieve and write these structures from data files.
1664 o Several important Bio::DB::GFF bug fixes for handling features that
1665 are mapped to multiple reference points. Updated mysql adaptor
1666 so as to be able to store large (>100 megabase) chunks of DNA into
1667 Bio::DB::GFF databases.
1669 0.9.2 Developer's release
1671 o Bio::Search and Bio::SearchIO system introduced for event based
1672 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1673 in text and XML and FASTA reports in standard output format.
1675 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1676 generator is included in Bio::TreeIO::RandomTrees and a
1677 statistics module for evaluating.
1679 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1680 server for DAS servers.
1682 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1683 files. The entire BPlite system migrated to using Bio::Root::IO
1684 for the data stream.
1686 o Bio::Tools::Alignment for Consed and sequence Trimming
1689 o Bio::Structure for Protein structure information and parsing
1691 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1692 cgi-bin entry point which should be more reliable.
1694 o Bio::Map and Bio::MapIO for biological map navigation and a
1695 framework afor parsing them in. Only preliminary work here.
1697 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1698 Future work will integrate Pise and allow submission of analysis on
1701 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1702 introduced as new objects for handling Sequence Annotation
1703 information (dblinks, references, etc) and is more robust that
1706 o Bio::Tools::FASTAParser introduced.
1708 o Scripts from the bioperl script submission project and new
1709 scripts from bioperl authors are included in "scripts" directory.
1711 o Factory objects and interfaces are being introduced and are more
1714 o Bio::Root::Root introduced as the base object while
1715 Bio::Root::RootI is now simply an interface.
1717 o Bio::DB::RefSeq provides database access to copy of the NCBI
1718 RefSeq database using the EBI dbfetch script.
1720 0.9.0 Developer's release
1722 o perl version at least 5.005 is now required instead of perl 5.004
1724 o Bio::Tools::Run::RemoteBlast is available for running remote
1727 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1729 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1730 Also added are related modules UTR3, UTR5, Exon, Intron,
1731 Promotor, PolyA and Transcript.
1733 o Speedup of translate method in PrimarySeq
1735 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1736 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1738 o Various fixes to Variation toolkit
1740 o Bio::DB::EMBL provides database access to EMBL sequence data.
1741 Bio::DB::Universal provides a central way to point to indexes
1742 and dbs in a single interface.
1744 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1746 o Bio::Factory::EMBOSS is still in design phase as is
1747 Bio::Factory::ApplicationFactoryI
1749 o Dia models for bioperl design are provided in the models/ directory
1751 0.7.2 Bug fix release
1753 o documentation fixes in many modules - SYNOPSIS code verified
1754 to be runnable in many (but not all modules)
1756 o corrected MANIFEST file from 0.7.1 release
1758 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1761 o Bio::SeqIO::genbank
1762 * Correct parsing and writing of genbank format with protein data
1763 * moltype and molecule separation
1765 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1767 o Bio::SimpleAlign fixed to correctly handle consensus
1768 sequence calculation
1770 o Bio::Tools::HMMER supports hmmer 2.2g
1772 o Bio::Tools::BPlite to support report type specific parsing. Most
1773 major changes are not on the 0.7 branch.
1775 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1778 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1779 in several types of mutations:
1780 1.) AA level: deletion, complex
1781 2.) AA level: complex, inframe
1782 3.) RNA level: silent
1784 o BPbl2seq parsing of empty reports will not die, but will return
1785 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1786 $report->query() and $report->subject() methods. So an easy
1787 way to test if report was empty is to see if
1788 $report->query->seqname is undefined.
1790 0.7.1 Bug fix release
1792 o Better parsing of genbank/EMBL files especially fixing bugs
1793 related to Feature table parsing and locations on remote
1794 sequences. Additionally, species name parsing was better.
1796 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1797 which include a number of header lines.
1799 o More strict genbank and EMBL format writing (corrected number of
1800 spaces where appropriate).
1802 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1803 for related BPlite BUGS that are unresolved in this release.
1805 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1806 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1807 use expasy mirrors or EBI dbfetch cgi-script.
1809 o A moderate number of documentation improvements were made as
1810 well to provide a better code synopsis in each module.
1813 0.7 Large number of changes, including refactoring of the
1814 Object system, new parsers, new functionality and
1815 all round better system. Highlights are:
1818 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1819 Bio::Root::IO for I/O and file/handle capabilities.
1821 o Imported BPlite modules from Ian Korf for BLAST
1822 parsing. This is considered the supported BLAST parser;
1823 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1825 o Improved Sequence Feature model. Added complete location
1826 modelling (with fuzzy and compound locations). See
1827 Bio::LocationI and the modules under Bio/Location. Added
1828 support in Genbank/EMBL format parsing to completely parse
1829 feature tables for complex locations.
1831 o Moved special support for databanks etc to specialized modules under
1832 Bio/Seq/. One of these supports very large sequences through
1833 a temporary file as a backend.
1835 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1836 CDS retrieval and exon shuffling.
1838 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1840 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1841 DB/GDB (the latter has platform-specific limitations).
1843 o New analysis parser framework for HT sequence annotation (see
1844 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1846 o New Alignment IO framework
1848 o New Index modules (Swissprot)
1850 o New modules for running Blast within perl
1851 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1852 Multiple Sequence Alignment tools ClustalW and TCoffee
1853 (Bio::Tools::Run::Alignment).
1855 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1856 documentation across the package.
1858 o Much improved cross platform support. Many known incompatibilities
1859 have been fixed; however, NT and Mac do not work across the entire
1860 setup (see PLATFORMS).
1862 o Many bug fixes, code restructuring, etc. Overall stability and
1863 maintainability benefit a lot.
1865 o A total of 957 automatic tests
1870 There are very few functionality changes but a large
1871 number of software improvements/bug fixes across the package.
1873 o The EMBL/GenBank parsing are improved.
1875 o The Swissprot reading is improved. Swissprot writing
1876 is disabled as it doesn't work at all. This needs to
1877 wait for 0.7 release
1879 o BLAST reports with no hits are correctly parsed.
1881 o Several other bugs of the BLAST parser (regular expressions, ...)
1884 o Old syntax calls have been replaced with more modern syntax
1886 o Modules that did not work at all, in particular the Sim4
1887 set have been removed
1889 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1890 have improved compliance with interface specs and documentation
1892 o Mailing list documentation updated throughout the distribution
1894 o Most minor bug fixes have happened.
1896 o The scripts in /examples now work and have the modern syntax
1897 rather than the deprecated syntax
1900 0.6.1 Sun April 2 2000
1902 o Sequences can have Sequence Features attached to them
1903 - The sequence features can be read from or written to
1904 EMBL and GenBank style flat files
1906 o Objects for Annotation, including References (but not
1907 full medline abstracts), Database links and Comments are
1910 o A Species object to represent nodes on a taxonomy tree
1913 o The ability to parse HMMER and Sim4 output has been added
1915 o The Blast parsing has been improved, with better PSI-BLAST
1916 support and better overall behaviour.
1918 o Flat file indexed databases provide both random access
1919 and sequential access to their component sequences.
1921 o A CodonTable object has been written with all known
1922 CodonTables accessible.
1924 o A number of new lightweight analysis tools have been
1925 added, such as molecular weight determination.
1927 The 0.6 release also has improved software engineering
1929 o The sequence objects have been rewritten, providing more
1930 maintainable and easier to implement objects. These
1931 objects are backwardly compatible with the 0.05.1 objects
1933 o Many objects are defined in terms of interfaces and then
1934 a Perl implementation has been provided. The interfaces
1935 are found in the 'I' files (module names ending in 'I').
1937 This means that it is possible to wrap C/CORBA/SQL access
1938 as true "bioperl" objects, compatible with the rest of
1941 o The SeqIO system has been overhauled to provide better
1942 processing and perl-like automatic interpretation of <>
1945 o Many more tests have been added (a total of 172 automatic
1946 tests are now run before release).
1950 0.05.1 Tue Jun 29 05:30:44 1999
1951 - Central distribution now requires Perl 5.004. This was
1952 done to get around 5.003-based problems in Bio/Index/*
1954 - Various bug fixes in the Bio::Tools::Blast modules
1955 including better exception handling and PSI-Blast
1956 support. See Bio/Tools/Blast/CHANGES for more.
1957 - Fixed the Parse mechanism in Seq.pm to use readseq.
1958 Follow the instructions in README for how to install
1959 it (basically, you have to edit Parse.pm).
1960 - Improved documentation of Seq.pm, indicating where
1961 objects are returned and where strings are returned.
1962 - Fixed uninitialized warnings in Bio::Root::Object.pm
1963 and Bio::Tools::SeqPattern.pm.
1964 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1966 0.05 Sun Apr 25 01:14:11 1999
1967 - Bio::Tools::Blast modules have less memory problems
1968 and faster parsing. Webblast uses LWP and supports
1969 more functionality. See Bio/Tools/Blast/CHANGES for more.
1970 - The Bio::SeqIO system has been started, moving the
1971 sequence reformatting code out of the sequence object
1972 - The Bio::Index:: system has been started, providing
1973 generic index capabilities and specifically works for
1974 Fasta formatted databases and EMBL .dat formatted
1976 - The Bio::DB:: system started, providing access to
1977 databases, both via flat file + index (see above) and
1979 - The scripts/ directory, where industrial strength scripts
1980 are put has been started.
1981 - Many changes - a better distribution all round.
1983 0.04.4 Wed Feb 17 02:20:13 1999
1984 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1985 (see Bio::Tools::Blast::CHANGES).
1986 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1987 - Beefed up the t/Fasta.t test script.
1988 - Small fix in Bio::Seq::type() (now always returns a string).
1989 - Changed Bio::Root::Utilities::get_newline_char() to
1990 get_newline() since it could return more than one char.
1991 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1992 - Changed default timeout to 20 seconds (was 3).
1993 - Moved lengthy modification notes to the bottom of some files.
1994 - Fixed SimpleAlign write_fasta bug.
1995 - Beefed up SimpleAlign.t test
1997 0.04.3 Thu Feb 4 07:48:53 1999
1998 - Bio::Root::Object.pm and Global.pm now detect when
1999 script is run as a CGI and suppress output that is only
2000 appropriate when running interactively.
2001 - Bio::Root::Err::_set_context() adds name of script ($0).
2002 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
2003 regarding the use of the static objects via the qw(:obj) tag.
2004 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
2005 CORE::reverse, avoiding Perl warnings.
2006 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
2007 example scripts (see Bio::Tools::Blast::CHANGES).
2008 - examples/seq/seqtools.pl no longer always warns about using
2009 -prot or -nucl command-line arguments; only when using the
2011 - Methods added to Bio::Root::Utilities: create_filehandle(),
2012 get_newline_char(), and taste_file() to generalize filehandle
2013 creation and autodetect newline characters in files/streams
2014 (see bug report #19).
2015 - Bio::Root::IOManager::read() now handles timeouts and uses
2016 Utilities::create_filehandle().
2017 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
2018 of hardwiring in "\n".
2019 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
2021 0.04.2 Wed Dec 30 02:27:36 1998
2022 - Bug fixes in Bio::Tools::Blast modules, version 0.073
2023 (see Bio::Tools::Blast::CHANGES).
2024 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
2025 to CORE::reverse (prevents ambiguous warnings with 5.005).
2026 - Appending '.tmp.bioperl' to temporary files created by
2027 Bio::Root::Utilities::compress() or uncompress() to
2028 make it easy to identify & cleanup these files as needed.
2029 - Developers: Created CVS branch release-0-04-bug from
2030 release-0-04-1. Before making bug fixes to the 0.04.1 release,
2031 be sure to cvs checkout this branch into a clean area.
2033 0.04.1 Wed Dec 16 05:39:15 1998
2034 - Bug fixes in Bio::Tools::Blast modules, version 0.072
2035 (see Bio::Tools::Blast::CHANGES).
2036 - Compile/SW/Makefile.PL now removes *.o and *.a files
2039 0.04 Tue Dec 8 07:49:19 1998
2040 - Lots of new modules added including:
2041 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
2042 and Bio/Compile directory containing XS-linked C code for
2043 creating Smith-Waterman sequence alignments from within Perl.
2044 * Steve Chervitz's Blast distribution has been incorporated.
2045 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
2046 - Bio/examples directory for demo scripts for all included modules.
2047 - Bio/t directory containing test suit for all included modules.
2048 - For changes specific to the Blast-related modules prior to
2049 incorporation in this central distribution, see the CHANGES
2050 file in the Bio/Tools/Blast directory.
2052 0.01 Tue Sep 8 14:23:22 1998
2053 - original version from central CVS tree; created by h2xs 1.18