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://redmine.open-bio.org/projects/bioperl
17 CPAN releases are branched from 'master'.
18 ---------------------------------------------------------
24 * Bio::Seq::SimulatedRead
25 - New module to represent reads taken from other sequences [fangly]
27 - Support of Clone::Fast as a faster cloning alternative [fangly]
29 - Moved the format() and variant() methods from Bio::*IO modules to
30 Bio::Root::IO [fangly]
31 - Can now use format() to get the type of IO format in use [fangly]
33 - New regexp() method to create regular expressions from IUPAC sequences
35 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
36 - Code refresh [fangly]
38 - Added support for the Greengenes and Silva taxonomies [fangly]
39 * Bio::Tree::TreeFunctionsI
40 - get_lineage_string() represents a lineage as a string [fangly]
41 - add_trait() returns instead of reporting an error when the column
42 number is exceeded in add_trait() [fangly]
43 - Option to support tree leaves without trait [fangly]
44 - Allow ID of 0 in trait files [fangly]
45 * Bio::DB::Taxonomy::list
46 - Misc optimizations [fangly]
47 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
48 * Bio::DB::Taxonomy::*
49 - get_num_taxa() returns the number of taxa in the database [fangly]
50 * Bio::DB::Fasta and Bio::DB::Qual
51 - support indexing an arbitrary list of files [fangly]
52 - user can supply an arbitrary index file name [fangly]
53 - new option to remove index file at the end [fangly]
55 - now handles IUPAC degenerate residues [fangly]
56 * Bio::PrimarySeq and Bio::PrimarySeqI
57 - speed improvements for large sequences [Ben Woodcroft, fangly]
59 - tightened and optimized quality string validation [fangly]
61 - new method and option 'block', to create FASTA output with space
62 intervaled blocks (similar to genbank or EMBL) has been implemented.
63 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
64 in favour of the methods 'width' and 'preferred_id_type` respectively.
66 - moved from bioperl-live into the separate distribution Bio-FeatureIO
67 * Bio::SeqFeature::Annotated
68 - moved from bioperl-live into the separate distribution Bio-FeatureIO
72 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
73 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
74 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
75 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
76 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
77 information was lost in a multi-result blast file [Paul Cantalupo]
78 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
79 total gaps [Paul Cantalupo]
80 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
81 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
82 when end of domain indicator is split across lines [Paul Cantalupo]
83 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
85 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
86 instances where blank lines are within sequences [cjfields]
87 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
89 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
90 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
92 * Various fixes for Stockholm file indexing and processing [bosborne]
93 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
94 breaks parsing [cjfields]
95 * Fix case where Bio::Seq::Meta* objects with no meta information could not
96 be reverse-complemented [fangly]
97 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
98 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
99 when unsure that values will be numerical [fangly]
100 * Fix undef warnings in Bio::SeqIO::embl [fangly]
101 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
102 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
103 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
105 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
106 source_tag and display_name must return a string, not undef [fangly]
107 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
108 add_SeqFeature takes a single argument [fangly]
109 * Use cross-platform filenames and temporary directory in
110 Bio::DB::Taxonomy::flatfile [fangly]
111 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
112 properly identified as existing taxa in the database [fangly]
113 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
114 without also passing a lineage to store [fangly]
115 * Prevent passing a directory to the gi2taxid option (-g) of
116 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
118 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
119 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
126 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
127 modules using Ace will also be deprecated [lds, cjfields]
128 * Minor bug fix release
129 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
130 * Address Build.PL issues when DBI is not present [hartzell]
131 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
132 * Remove deprecated code for perl 5.14.0 compat [cjfields]
133 * Due to schema changes and lack of support for older versions, support
134 for NeXML 0.9 is only (very) partially implemented.
135 See: https://redmine.open-bio.org/issues/3207
139 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
140 docs [genehack, cjfields]
141 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
142 module version from dist_version (probably not the best way to do this,
143 but it seems to work) [rbuels, cjfields]
146 1.6.900 April 14, 201
150 * This will probably be the last release to add significant features to
151 core modules; subsequent releases will be for bug fixes alone.
152 We are planning on a restructuring of core for summer 2011, potentially
153 as part of the Google Summer of Code. This may become BioPerl 2.0.
154 * Version bump represents 'just prior to v 1.7'. We may have point
155 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
156 This code essentially is what is on the github master branch.
160 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
162 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
163 - removal of Scalar::Util::weaken code, which was causing odd headaches
164 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
165 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
167 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
170 - bug 2515 - new contribution [Ryan Golhar, jhannah]
172 - support for reading Maq, Sam and Bowtie files [maj]
173 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
174 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
175 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
176 - bug 2726: reading/writing granularity: whole scaffold or one contig
177 at a time [Joshua Udall, fangly]
179 - Added parsing of xrefs to OBO files, which are stored as secondary
180 dbxrefs of the cvterm [Naama Menda]
181 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
182 * PAML code updated to work with PAML 4.4d [DaveMessina]
186 * [3198] - sort tabular BLAST hits by score [DaveMessina]
187 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
188 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
189 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
191 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
192 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
193 * [3164] - TreeFunctionsI syntax bug [gjuggler]
194 * [3163] - AssemblyIO speedup [fangly]
195 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
197 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
198 * [3158] - fix EMBL file mis-parsing [cjfields]
199 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
201 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
202 * [3148] - URL change for UniProt [cjfields]
203 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
204 * [3136] - HMMer3 parser fixes [kblin]
205 * [3126] - catch description [Toshihiko Akiba]
206 * [3122] - Catch instances where non-seekable filehandles were being
207 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
208 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
209 [dukeleto, rbuels, cjfields]
210 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
212 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
213 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
215 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
216 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
217 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
218 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
219 * [3086] - EMBL misparsing long tags [kblin, cjfields]
220 * [3085] - CommandExts and array of files [maj, hyphaltip]
221 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
222 for alignment slices [Ha X. Dang, cjfields]
223 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
224 * [3073] - fix parsing of GenBank files from RDP [cjfields]
225 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
226 * [3064] - All-gap midline BLAST report issues [cjfields]
227 * [3063] - BLASt report RID [Razi Khaja, cjfields]
228 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
229 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
230 * [3039] - correct Newick output root node branch length [gjuggler,
232 * [3038] - SELEX alignment error [Bernd, cjfields]
233 * [3033] - PrimarySeq ID setting [Bernd, maj]
234 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
235 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
236 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
237 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
238 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
239 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
240 PAML 4.4d [DaveMessina]
241 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
243 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
244 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
245 * [3017] - using threads with Bio::DB::GenBank [cjfields]
246 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
247 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
248 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
249 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
250 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
252 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
253 * [2977] - TreeIO issues [DaveMessina]
254 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
255 * [2944] - Bio::Tools::GFF score [cjfields]
256 * [2942] - correct MapTiling output [maj]
257 * [2939] - PDB residue insertion codes [John May, maj]
258 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
259 * [2928] - GuessSeqFormat raw [maj]
260 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
261 * [2922] - open() directive issue [cjfields]
262 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
263 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
264 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
265 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
267 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
268 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
269 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
270 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
271 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
272 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
273 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
274 * [2758] - Bio::AssemblyIO ace problems [fangly]
275 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
276 * [2726] - ace file IO [Josh, fangly]
277 * [2700] - Refactor Build.PL [cjfields]
278 * [2673] - addition of simple Root-based clone() method [cjfields]
279 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
280 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
281 * [2594] - Bio::Species memory leak [cjfields]
282 * [2515] - GenBank XML parser [jhannah]
283 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
284 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
285 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
287 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
291 * Bio::Expression modules - these were originally designed to go with the
292 bioperl-microarray suite of tools, however they have never been completed
293 and so have been removed from the distribution. The original code has
294 been moved into the inactive bioperl-microarray suite. [cjfields]
298 * Repository moved from Subversion (SVN) to
299 http://github.com/bioperl/bioperl-live [cjfields]
300 * Bug database has moved to Redmine (https://redmine.open-bio.org)
301 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
302 Thieme have been moved to their own distribution (Bio-Microarray).
305 1.6.1 Sept. 29, 2009 (point release)
306 * No change from last alpha except VERSION and doc updates [cjfields]
308 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
309 * Fix for silent OBDA bug related to FASTA validation [cjfields]
311 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
312 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
313 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
315 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
317 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
318 * WinXP test fixes [cjfields, maj]
319 * BioPerl.pod added for descriptive information, fixes CPAN indexing
321 * Minor doc fixes [cjfields]
323 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
324 * Fix tests failing due to merging issues [cjfields]
325 * More documentation updates for POD parsing [cjfields]
327 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
329 - fix YAML meta data generation [cjfields]
331 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
332 * Bio::Align::DNAStatistics
333 - fix divide by zero problem [jason]
335 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
336 * Bio::AlignIO::stockholm
337 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
338 * Bio::Assembly::Tools::ContigSpectrum
339 - function to score contig spectrum [fangly]
340 * Bio::DB::EUtilities
341 - small updates [cjfields]
343 - berkeleydb database now autoindexes wig files and locks correctly
346 - various small updates for stability; tracking changes to LANL
347 database interface [maj]
348 * Bio::DB::SeqFeature (lots of updates and changes)
349 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
350 - bug 2835 - patch [Dan Bolser]
351 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
353 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
354 * Bio::Factory::FTLocationFactory
355 - mailing list bug fix [cjfields]
357 - performance work on column_from_residue_number [hartzell]
358 * Bio::Matrix::IO::phylip
359 - bug 2800 - patch to fix phylip parsing [Wei Zou]
361 - Google Summer of Code project from Chase Miller - parsers for Nexml
362 file format [maj, chmille4]
364 - Make Individual, Population, Marker objects AnnotatableI [maj]
365 - simplify LD code [jason]
367 - deal with empty intersection [jason]
369 - significant overhaul of Bio::Restriction system: complete support for
370 external and non-palindromic cutters. [maj]
372 - CPANPLUS support, no automatic installation [sendu]
374 - allow IO::String (regression fix) [cjfields]
375 - catch unintentional undef values [cjfields]
376 - throw if non-fh is passed to -fh [maj]
377 * Bio::Root::Root/RootI
378 - small debugging and core fixes [cjfields]
380 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
381 * Bio::Root::Utilities
382 - bug 2737 - better warnings [cjfields]
384 - tiling completely refactored, HOWTO added [maj]
385 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
386 will deprecate usage of the older tiling code in the next BioPerl
388 - small fixes [cjfields]
390 - Infernal 1.0 output now parsed [cjfields]
391 - new parser for gmap -f9 output [hartzell]
392 - bug 2852 - fix infinite loop in some output [cjfields]
393 - blastxml output now passes all TODO tests [cjfields]
394 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
395 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
396 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
397 * Bio::Seq::LargePrimarySeq
398 - delete tempdirs [cjfields]
399 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
401 - extract regions based on quality threshold value [Dan Bolser, heikki]
402 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
403 * Bio::SeqFeature::Lite
404 - various Bio::DB::SeqFeature-related fixes [lstein]
405 * Bio::SeqFeature::Tools::TypeMapper
406 - additional terms for GenBank to SO map [scain]
407 * Bio::SeqIO::chadoxml
408 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
410 - support for CDS records [dave_messina, Sylvia]
412 - complete refactoring to handle all FASTQ variants, perform validation,
413 write output. API now conforms with other Bio* parsers and the rest of
414 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
416 * Bio::SeqIO::genbank
417 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
418 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
419 * Bio::SeqIO::largefasta
420 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
422 - add option for 'single' and 'multiple'
424 - bug 2881 - fix scf round-tripping [Adam Søgren]
426 - bug 2766, 2810 - copy over tags from features, doc fixes [David
429 - bug 2793 - patch for add_seq index issue [jhannah, maj]
430 - bug 2801 - throw if args are required [cjfields]
431 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
432 [Tristan Lefebure, maj]
433 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
434 - fix POD and add get_SeqFeatures filter [maj]
435 * Bio::Tools::dpAlign
436 - add support for LocatableSeq [ymc]
437 - to be moved to a separate distribution [cjfields, rbuels]
438 * Bio::Tools::EUtilities
439 - fix for two bugs from mail list [Adam Whitney, cjfields]
440 - add generic ItemContainerI interface for containing same methods
443 - fix up code, add more warnings [cjfields]
444 - to be moved to a separate distribution [cjfields, rbuels]
445 * Bio::Tools::Primer3
446 - bug 2862 - fenceposting issue fixed [maj]
447 * Bio::Tools::Run::RemoteBlast
448 - tests for remote RPS-BLAST [mcook]
449 * Bio::Tools::SeqPattern
450 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
451 * Bio::Tools::tRNAscanSE
452 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
454 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
455 * Bio::Tree::Statistics
456 - several methods for calculating Fitch-based score, internal trait
457 values, statratio(), sum of leaf distances [heikki]
459 - bug 2869 - add docs indicating edge case where nodes can be
460 prematurely garbage-collected [cjfields]
461 - add as_text() function to create Tree as a string in specified format
463 * Bio::Tree::TreeFunctionsI
464 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
466 * Bio::TreeIO::newick
467 - fix small semicolon issue [cjfields]
469 - update to bp_seqfeature_load for SQLite [lstein]
470 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
471 - fastam9_to_table - fix for MPI output [jason]
472 - gccalc - total stats [jason]
474 - POD cleanup re: FEEDBACK section [maj, cjfields]
475 - cleanup or fix dead links [cjfields]
476 - Use of no_* methods (indicating 'number of something') is deprecated
477 in favor of num_* [cjfields]
478 - lots of new tests for the above bugs and refactors [everyone!]
479 - new template for Komodo text editor [cjfields]
482 * Feature/Annotation rollback
483 - Problematic changes introduced prior to the 1.5 release have been
484 rolled back. These changes led to subtle bugs involving operator
485 overloading and interface methods.
486 - Behavior is very similar to that for BioPerl 1.4, with tag values
487 being stored generically as simple scalars. Results in a modest
490 - Split into a separate distribution on CPAN, primarily so development
491 isn't reliant on a complete BioPerl release.
492 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
493 is only available via Subversion (via bioperl-live main trunk)
495 - Common test bed for all BioPerl modules
497 - Common Module::Build-based subclass for all BioPerl modules
498 * Bio::DB::EUtilities
499 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
500 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
501 and user agent request posting and retrieval
502 * Test implementation and reorganization
503 - Tests have been reorganized into groups based on classes or use
505 - Automated test coverage is now online:
506 http://www.bioperl.org/wiki/Test_Coverage
507 - After this release, untested modules will be moved into a
508 separate developer distribution until tests can be derived.
509 Also, new modules to be added are expected to have a test suite
510 and adequate test coverage.
512 1.5.2 Developer release
514 Full details of changes since 1.5.1 are available online at:
515 http://www.bioperl.org/wiki/Change_log
516 The following represents a brief overview of the most important changes.
519 - Overhaul. Brand new system fully allows markers to have multiple
520 positions on multiple maps, and to have relative positions. Should be
524 - This module and all the modules in the Taxonomy directory now
525 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
530 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
532 * New methods ancestor(), each_Descendent() and _handle_internal_id().
534 * Allows for different database modules to create Bio::Taxon objects
535 with the same internal id when the same taxon is requested from each.
538 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
540 * No longer includes the fake root node 'root'; there are multiple roots
541 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
544 * get_node() has new option -full
546 * Caches data retrieved from website
549 - Now a Bio::Taxon. Carries out the species name -> specific name munging
550 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
551 backward compatability in species() method.
553 o Bio::Search and Bio::SearchIO
554 - Overhaul. The existing system has been sped up via some minor changes
555 (mostly gain-of-function to the API). Bio::PullParserI is introduced
556 as a potential eventual replacment for the existing system, though as
557 yet only a Hmmpfam parser exists written using it.
560 1.5.1 Developer release
562 o Major problem with how Annotations were written out with
563 Bio::Seq is fixed by reverting to old behavior for
564 Bio::Annotation objects.
569 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
570 expect at l east 9 spaces at the beginning of a line to
571 indicate line wrapping.
573 * Treat multi-line SOURCE sections correctly, this defect broke
574 both common_name() and classification()
576 * parse swissprot fields in genpept file
578 * parse WGS genbank records
581 * Changed regexp for ID line. The capturing parentheses are
582 the same, the difference is an optional repeated-not-semi-
583 colon expression following the captured \S+. This means the
584 regexp works when the division looks like /PRO;/ or when the
585 division looks like /ANG ;/ - the latter is from EMBL
588 * fix ID line parsing: the molecule string can have spaces in
589 it. Like: "genomic DNA"
591 - swiss.pm: bugs #1727, #1734
594 * Added parser for entrezgene ASN1 (text format) files.
595 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
599 - maf.pm coordinate problem fixed
601 o Bio::Taxonomy and Bio::DB::Taxonomy
603 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
604 can be done via Web without downloading all the sequence.
606 o Bio::Tools::Run::RemoteBlast supports more options and complies
607 to changes to the NCBI interface. It is reccomended that you
608 retrieve the data in XML instead of plain-text BLAST report to
609 insure proper parsing and retrieval of all information as NCBI
610 fully expects to change things in the future.
612 o Bio::Tree and Bio::TreeIO
614 - Fixes so that re-rooting a tree works properly
616 - Writing out nhx format from a newick/nexus file will properly output
617 bootstrap information. The use must move the internal node labels over
619 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
620 $node->bootstrap($node->id);
623 - Nexus parsing is much more flexible now, does not care about
626 - Cladogram drawing module in Bio::Tree::Draw
628 - Node height and depth now properly calculated
630 - fix tree pruning algorithm so that node with 1 child gets merged
632 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
633 bugs and improvements were added, see Gbrowse mailing list for most of
636 o Bio::DB::GFF partially supports GFF3. See information about
637 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
639 o Better location parsing in Bio::Factory::FTLocationFactory -
640 this is part of the engine for parsing EMBL/GenBank feature table
641 locations. Nested join/order-by/complement are allowed now
643 o Bio::PrimarySeqI->translate now takes named parameters
645 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
646 reconstruction) is now supported. Parsing different models and
647 branch specific parametes are now supported.
649 o Bio::Factory::FTLocationFactory - parse hierarchical locations
652 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
653 for getter/setter functions
657 - blast bug #1739; match scientific notation in score
658 and possible e+ values
660 - blast.pm reads more WU-BLAST parameters and parameters, match
661 a full database pathname,
663 - Handle NCBI WEB and newer BLAST formats specifically
664 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
666 - psl off-by-one error fixed
668 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
669 and HSPs can be constructed from them.
671 - HSPs query/hit now have a seqdesc field filled out (this was
672 always available via $hit->description and
673 $result->query_description
675 - hmmer.pm can parse -A0 hmmpfam files
677 - Writer::GbrowseGFF more customizeable.
679 o Bio::Tools::Hmmpfam
680 make e-value default score displayed in gff, rather than raw score
681 allow parse of multiple records
684 1.5 Developer release
686 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
687 provide Jukes-Cantor and Kimura pairwise distance methods,
690 o Bio::AlignIO support for "po" format of POA, and "maf";
691 Bio::AlignIO::largemultifasta is a new alternative to
692 Bio::AlignIO::fasta for temporary file-based manipulation of
693 particularly large multiple sequence alignments.
695 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
696 be treated similarly as an assembled contig.
698 o Bio::CodonUsage provides new rare_codon() and probable_codons()
699 methods for identifying particular codons that encode a given
702 o Bio::Coordinate::Utils provides new from_align() method to build
703 a Bio::Coordinate pair directly from a
704 Bio::Align::AlignI-conforming object.
706 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
707 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
708 web service using standard Pubmed query syntax, and retrieve
711 o Bio::DB::GFF has various sundry bug fixes.
713 o Bio::FeatureIO is a new SeqIO-style subsystem for
714 writing/reading genomic features to/from files. I/O classes
715 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
716 classes only read/write Bio::SeqFeature::Annotated objects.
717 Notably, the GFF v3 class requires features to be typed into the
720 o Bio::Graph namespace contains new modules for manipulation and
721 analysis of protein interaction graphs.
723 o Bio::Graphics has many bug fixes and shiny new glyphs.
725 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
726 indexing for HMMER reports and FASTA qual files, respectively.
728 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
729 new objects that can be placed within a Bio::Map::MapI-compliant
730 genetic/physical map; Bio::Map::Physical provides a new physical
731 map type; Bio::MapIO::fpc provides finger-printed clone mapping
734 o Bio::Matrix::PSM provide new support for postion-specific
735 (scoring) matrices (e.g. profiles, or "possums").
737 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
738 be instantiated without explicitly using Bio::OntologyIO. This
739 is possible through changes to Bio::Ontology::OntologyStore to
740 download ontology files from the web as necessary. Locations of
741 ontology files are hard-coded into
742 Bio::Ontology::DocumentRegistry.
744 o Bio::PopGen includes many new methods and data types for
745 population genetics analyses.
747 o New constructor to Bio::Range, unions(). Given a list of
748 ranges, returns another list of "flattened" ranges --
749 overlapping ranges are merged into a single range with the
750 mininum and maximum coordinates of the entire overlapping group.
752 o Bio::Root::IO now supports -url, in addition to -file and -fh.
753 The new -url argument allows one to specify the network address
754 of a file for input. -url currently only works for GET
755 requests, and thus is read-only.
757 o Bio::SearchIO::hmmer now returns individual Hit objects for each
758 domain alignment (thus containing only one HSP); previously
759 separate alignments would be merged into one hit if the domain
760 involved in the alignments was the same, but this only worked
761 when the repeated domain occured without interruption by any
762 other domain, leading to a confusing mixture of Hit and HSP
765 o Bio::Search::Result::ResultI-compliant report objects now
766 implement the "get_statistics" method to access
767 Bio::Search::StatisticsI objects that encapsulate any
768 statistical parameters associated with the search (e.g. Karlin's
769 lambda for BLAST/FASTA).
771 o Bio::Seq::LargeLocatableSeq combines the functionality already
772 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
774 o Bio::SeqFeature::Annotated is a replacement for
775 Bio::SeqFeature::Generic. It breaks compliance with the
776 Bio::SeqFeatureI interface because the author was sick of
777 dealing with untyped annotation tags. All
778 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
779 compliant, and accessible through Bio::Annotation::Collection.
781 o Bio::SeqFeature::Primer implements a Tm() method for primer
782 melting point predictions.
784 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
785 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
787 o Bio::Taxonomy::Node now implements the methods necessary for
788 Bio::Species interoperability.
790 o Bio::Tools::CodonTable has new reverse_translate_all() and
791 make_iupac_string() methods.
793 o Bio::Tools::dpAlign now provides sequence profile alignments.
795 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
797 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
800 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
801 for designing small inhibitory RNA.
803 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
804 methods based on a distance matrix.
806 o Bio::Tree::Statistics provides an assess_bootstrap() method to
807 calculate bootstrap support values on a guide tree topology,
808 based on provided bootstrap tree topologies.
810 o Bio::TreeIO now supports the Pagel (PAG) tree format.
816 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
818 o Bio::Graphics will work with gd1 or gd2
821 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
823 - blast.pm Parse multi-line query fields properly
824 - small speed improvements to blasttable.pm and others
826 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
827 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
828 supporting more complex queries
831 1.4. Stable major release
833 Since initial 1.2.0, 3000 separate changes have been made to make this release.
835 o installable scripts
837 o global module version from Bio::Root:Version
840 - major improvements; SVG support
843 - population genetics
844 - support several population genetics types of questions.
845 - Tests for statistical neutrality of mutations
846 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
847 Tests of population structure (Wright's F-statistic: Fst) is in
848 Bio::PopGen::PopStats. Calculating composite linkage
849 disequilibrium (LD) is available in Bio::PopGen::Statistics as
851 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
852 and csv (comma delimited formatted) data.
854 - a directory for implementing population simulations has
855 been added Bio::PopGen::Simulation and 2 simulations - a
856 Coalescent and a simple single-locus multi-allele genetic drift
857 simulation have been provided. This replaces the code in
858 Bio::Tree::RandomTree which has been deprecated until proper
859 methods for generating random phylogenetic trees are
863 - new restrion analysis modules
865 o Bio::Tools::Analysis
866 - web based DNA and Protein analysis framework and several
870 - per residue annotable sequences
873 - Bio::Matrix::PSM - Position Scoring Matrix
874 - Bio::Matrix::IO has been added for generalized parsing of
875 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
876 initial implementations for parsing BLOSUM/PAM and Phylip
877 Distance matricies respectively. A generic matrix
878 implementation for general use was added in
879 Bio::Matrix::Generic.
886 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
887 - small inhibitory RNA
889 o Bio::SeqFeature::Tools
890 - seqFeature mapping tools
891 - Bio::SeqFeature::Tools::Unflattener.pm
892 -- deal with mapping GenBank feature collections into
893 Chado/GFF3 processable feature sets (with SO term mappings)
895 o Bio::Tools::dpAlign
896 - pure perl dynamic programming sequence alignment
899 o new Bio::SearchIO formats
900 - axt and psl: UCSC formats.
901 - blasttable: NCBI -m 8 or -m 9 format from blastall
903 o new Bio::SeqIO formats
904 - chado, tab, kegg, tigr, game
905 - important fixes for old modules
909 o improved Bio::Tools::Genewise
911 o Bio::SeqIO now can recongnize sequence formats automatically from
914 o new parsers in Bio::Tools:
915 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
917 o Bio::DB::Registry bugs fixed
918 - BerkeleyDB-indexed flat files can be used by the OBDA system
919 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
920 used by the OBDA system
923 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
926 o hundreds of new and improved files
930 o Bio::Tree::AlleleNode has been updated to be a container of
931 an Bio::PopGen::Individual object for use in the Coalescent simulations.
936 1.2.3 Stable release update
937 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
939 o Bug #1477 - Sel --> Sec abbreviation fixed
940 o Fix bug #1487 where paring in-between locations when
941 end < start caused the FTLocationFactory logic to fail.
942 o Fix bug #1489 which was not dealing with keywords as an
943 arrayref properly (this is fixed on the main trunk because
944 keywords returns a string and the array is accessible via
946 o Bio::Tree::Tree memory leak (bug #1480) fixed
947 Added a new initialization option -nodelete which
948 won't try and cleanup the containing nodes if this
950 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
951 this was only present on the branch for the 1.2.1 and 1.2.2 series
952 - Also merged main trunk changes to the branch which make
953 newick -> nhx round tripping more effective (storing branch length
954 and bootstrap values in same locate for NodeNHX and Node
955 implementations.) Fixes to TreeIO parsing for labeled internal
956 also required small changes to TreeIO::nhx. Improved
957 tests for this module as well.
959 - Fixed bugs in BLAST parsing which couldn't parse NCBI
960 gapped blast properly (was losing hit significance values due to
961 the extra unexpeted column).
962 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
963 integer overflow (# of letters in nt seq dbs is > MAX_INT)
964 although doesn't try to correct it - will get the negative
965 number for you. Added a test for this as well.
966 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
967 has no top-level family classification scores but does have scores and
968 alignments for individual domains.
969 - Parsing FASTA reports where ungapped percent ID is < 10 and the
970 regular expression to match the line was missing the possibility of
971 an extra space. This is rare, which is why we probably did not
973 - BLAST parsing picks up more of the statistics/parameter fields
974 at the bottom of reports. Still not fully complete.
975 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
976 were fixed to include many improvements and added flexiblity
977 in outputting the files. Bug #1495 was also fixed in the process.
979 - Update for GFF3 compatibility.
980 - Added scripts for importing from UCSC and GenBank.
981 - Added a 1.2003 version number.
984 - Added a 1.2003 version number.
985 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
986 properly writing keywords out.
987 o Bio::SeqIO::genbank
988 - Fixed bug/enhancement #1513 where dates of
989 the form D-MMM-YYYY were not parsed. Even though this is
990 invalid format we can handle it - and also cleanup the date
991 string so it is properly formatted.
992 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
993 and written with Genbank format. Similarly bug #1515 is fixed to
994 parse in the ORIGIN text.
995 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
996 to specify the ID type, one of (accession accession.version
997 display primary). See Bio::SeqIO::preferred_id_type method
998 documentation for more information.
999 o Unigene parsing updated to handle file format changes by NCBI
1001 1.2.2 Stable release update
1003 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1004 - auto-discover ontology name
1005 - bug in parsing relationships when certain characters are in the term
1006 - fixed hard-coded prefix for term identifiers
1007 - various smaller issues
1009 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1010 of Bio::Ontology::TermI
1012 o brought the OBDA Registry code up to latest specs
1016 - accession number retrieval fixed
1018 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1020 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1021 #1459 which now properly report alignment start/end info
1022 for translated BLAST/FASTA searches.
1024 o Bio::TreeIO::newick can parse labeled internal nodes
1026 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1027 for BLASTX if if you provide -report_type => 'BLASTX' when
1028 initializing a BPbl2seq object. Bioperl 1.3 will have better
1029 support for bl2seq in the SearchIO system.
1031 o Bio::Root::IO support a -noclose boolean flag which will not
1032 close a filehandle upon object cleanup - useful when sharing
1033 a filehandle among objects. Additionally code added s.t.
1034 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1036 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1038 o Bio::SeqIO::genbank
1039 - bug #1456 fixed which generated extra sequence lines
1040 - write moltype correctly for genpept
1042 1.2.1 Stable release update
1044 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1046 o Addition from main trunk of Ontology objects, principly to allow
1047 BioSQL releases against 1.2.1
1049 o Fixes and cleanup of Bio::Coordinate modules
1051 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1052 the primary accession number
1054 o Other bug fixes, including bpindex GenBank fix
1056 o Bio::SeqIO::genbank bug #1389 fixed
1058 1.2 Stable major release
1060 o More functionality added to Bio::Perl, the newbie module
1062 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1063 Support for New Hampshire Extended (NHX) format parsing.
1065 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1066 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1069 o New ontology parsing Bio::Ontology
1071 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1072 multi-report (mlib) fasta reports, support for waba and exonerate.
1074 o Bio::ClusterIO for parsing Unigene clusters
1076 o Bio::Assembly added for representing phrap and ace assembly clusters.
1078 o Rudimentary support for writing Chado XML (see
1079 GMOD project: www.gmod.org for more information)
1081 o Bio::Coordinate for mapping between different coordinate systems such
1082 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1083 features into different coordinate systems.
1085 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1086 with the get_Stream_by_query method and supports the latest
1087 NCBI eutils interface.
1089 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1090 object for extracting subsets of features : currently only
1091 supports extraction by location.
1093 1.1.1 Developer release
1095 o Deprecated modules are now listed in the DEPRECATED file
1097 o New HowTo documents located in doc/howto describing
1098 a domain of Bioperl.
1100 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1101 and all old bugs are searchable through the bugzilla interface.
1103 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1104 have been addressed.
1106 o Support for Genewise parsing in Bio::Tools::Genewise
1108 o Start of Ontology framework with Bio::Ontology
1110 o Speedup to the Bio::Root::Root object method _rearrange.
1111 A global _load_module method was implemented to simplify the
1112 dynamic loading of modules ala Bio::SeqIO::genbank. This
1113 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1116 o Several performance improvements to sequence parsing in Bio::SeqIO.
1117 Attempt to speedup by reducing object creation overhead.
1119 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1120 method for sequence retrieval with their E-utils CGI scripts.
1121 More work to support Entrez queries to their fullest is planned
1124 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1126 1.1 Developer release
1128 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1129 this separation removes some of the complexity in our test suite
1130 and separates the core modules in bioperl from those that need
1131 external programs to run.
1133 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1134 not run into trouble running the makefile
1136 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1137 read,create,and write locations for grouped/split locations
1138 (like mRNA features on genomic sequence).
1140 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1141 and PAML (codeml,aaml, etc) parsing.
1143 o Bio::Tree:: objects expanded to handle testing monophyly,
1144 paraphyly, least common ancestor, etc.
1146 o Bio::Coordinate for mapping locations from different coordinate spaces
1148 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1149 added for parsing hmmpfam and hmmsearch output.
1151 o Bio::SearchIO::Writer::TextResultWriter for outputting
1152 a pseudo-blast textfile format
1155 1.0.2 Bug fix release
1157 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1158 in this release will not work after December 2002 when NCBI
1159 shuts off the old Entrez cgi scripts. We have already fixed
1160 on our main development branch and the functionality will be
1161 available in the next stable bioperl release (1.2) slated for
1164 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1165 testset by Robin Emig. These were fixed as was the get_aln
1166 method in Bio::Search::HSP::GenericHSP to handle the extra
1167 context sequence that is provided with a FastA alignment.
1169 o Migrating differences between Bio::Search::XX::BlastXX to
1170 Bio::Search::XX::GenericXX objects. This included mechanism
1171 to retrieve whole list of HSPs from Hits and whole list of Hits from
1172 Results in addition to the current next_XX iterator methods that
1173 are available. Added seq_inds() method to GenericHSP which identifies
1174 indexes in the query or hit sequences where conserved,identical,gaps,
1175 or mismatch residues are located (adapted from Steve Chervitz's
1176 implementation in BlastHSP).
1178 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1179 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1181 o Bio::Graphics glyph set improved and extended for GBrowse release
1183 o Bio::Tree::Tree get_nodes implementation improvement thanks
1184 to Howard Ross notice performance problem when writing out
1187 o Bio::Location::Fuzzy::new named parameter -loc_type became
1188 -location_type, Bio::Location::Simple::new named parameter
1189 -seqid becamse -seq_id.
1191 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1192 was mis-detecting that gaps should be placed at the beginning of
1193 the alignment when the best alignment starts internally in the
1196 1.0.1 Bug fix release
1198 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1200 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1201 and mixed (3.3 - 3.4) versions of FASTA.
1203 o Small API change to add methods for completeness across
1204 implementations of Bio::Search objects. These new methods
1205 in the interface are implemented by the GenericXX object as well
1206 as the BlastXX objects.
1207 * Bio::Search::Result::ResultI
1208 - hits() method returns list of all Hits (next_hit is an
1211 * Bio::Search::Hit::HitI
1212 - hsps() method returns list of all HSPs (next_hsp is an
1215 o The Bio::SearchIO::Writer classes have been fixed to handle results
1216 created from either psiblast (Search::BlastXX objects) or
1217 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1218 has to be done here to make it work properly and will nee major
1221 o Bugs in Bio::Tools::HMMER fixed, including
1222 * #1178 - Root::IO destructor wasn't being called
1223 * #1034 - filter_on_cutoff now behaves properly
1225 o Bio::SeqFeature::Computation initialization args fixed and
1228 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1230 o Updated FAQ with more example based answers to typical questions
1232 o Bug #1202 was fixed which would improperly join together qual values
1233 parsed by Bio::SeqIO::qual when a trailing space was not present before
1236 1.0.0 Major Stable Release
1238 This represents a major release of bioperl with significant
1239 improvements over the 0.7.x series of releases.
1241 o Bio::Tools::Blast is officially deprecated. Please see
1242 Bio::SearchIO for BLAST and FastA parsing.
1244 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1245 Bio::LocationI objects as well as start/end.
1247 o Bio::Biblio contains modules for Bibliographic data.
1248 Bio::DB::Biblio contains the query modules. Additionally one can
1249 parse medlinexml from the ebi bibliographic query service (BQS)
1250 system and Pubmed xml from NCBI. See Martin Senger's
1251 documentation in Bio::Biblio for more information.
1253 o Bio::DB::Registry is a sequence database registry part of
1254 Open Bioinformatics Database Access. See
1255 http://obda.open-bio.org for more information.
1257 o File-based and In-Memory Sequence caching is provided by
1258 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1261 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1262 been added by Lincoln Stein.
1264 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1266 o A FAQ has been started and is included in the release to provide
1267 a starting point for frequent questions and issues.
1269 0.9.3 Developer's release
1271 o Event based parsing system improved (SearchIO). With parsers for
1272 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1273 Additionally a lazy parsing system for text and html blast reports was
1274 added and is called psiblast (name subject to change in future releases).
1276 o Bio::Search objects improved and standardized with associated Interfaces
1277 written. The concept of a search "Hit" was standardized to be called
1278 "hit" consistently and the use of "subject" was deprecated in all active
1281 o Bio::Structure added (since 0.9.1) for Protein structure objects
1282 and PDB parser to retrieve and write these structures from data files.
1284 o Several important Bio::DB::GFF bug fixes for handling features that
1285 are mapped to multiple reference points. Updated mysql adaptor
1286 so as to be able to store large (>100 megabase) chunks of DNA into
1287 Bio::DB::GFF databases.
1289 0.9.2 Developer's release
1291 o Bio::Search and Bio::SearchIO system introduced for event based
1292 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1293 in text and XML and FASTA reports in standard output format.
1295 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1296 generator is included in Bio::TreeIO::RandomTrees and a
1297 statistics module for evaluating.
1299 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1300 server for DAS servers.
1302 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1303 files. The entire BPlite system migrated to using Bio::Root::IO
1304 for the data stream.
1306 o Bio::Tools::Alignment for Consed and sequence Trimming
1309 o Bio::Structure for Protein structure information and parsing
1311 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1312 cgi-bin entry point which should be more reliable.
1314 o Bio::Map and Bio::MapIO for biological map navigation and a
1315 framework afor parsing them in. Only preliminary work here.
1317 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1318 Future work will integrate Pise and allow submission of analysis on
1321 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1322 introduced as new objects for handling Sequence Annotation
1323 information (dblinks, references, etc) and is more robust that
1326 o Bio::Tools::FASTAParser introduced.
1328 o Scripts from the bioperl script submission project and new
1329 scripts from bioperl authors are included in "scripts" directory.
1331 o Factory objects and interfaces are being introduced and are more
1334 o Bio::Root::Root introduced as the base object while
1335 Bio::Root::RootI is now simply an interface.
1337 o Bio::DB::RefSeq provides database access to copy of the NCBI
1338 RefSeq database using the EBI dbfetch script.
1340 0.9.0 Developer's release
1342 o perl version at least 5.005 is now required instead of perl 5.004
1344 o Bio::Tools::Run::RemoteBlast is available for running remote
1347 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1349 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1350 Also added are related modules UTR3, UTR5, Exon, Intron,
1351 Promotor, PolyA and Transcript.
1353 o Speedup of translate method in PrimarySeq
1355 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1356 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1358 o Various fixes to Variation toolkit
1360 o Bio::DB::EMBL provides database access to EMBL sequence data.
1361 Bio::DB::Universal provides a central way to point to indexes
1362 and dbs in a single interface.
1364 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1366 o Bio::Factory::EMBOSS is still in design phase as is
1367 Bio::Factory::ApplicationFactoryI
1369 o Dia models for bioperl design are provided in the models/ directory
1371 0.7.2 Bug fix release
1373 o documentation fixes in many modules - SYNOPSIS code verified
1374 to be runnable in many (but not all modules)
1376 o corrected MANIFEST file from 0.7.1 release
1378 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1381 o Bio::SeqIO::genbank
1382 * Correct parsing and writing of genbank format with protein data
1383 * moltype and molecule separation
1385 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1387 o Bio::SimpleAlign fixed to correctly handle consensus
1388 sequence calculation
1390 o Bio::Tools::HMMER supports hmmer 2.2g
1392 o Bio::Tools::BPlite to support report type specific parsing. Most
1393 major changes are not on the 0.7 branch.
1395 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1398 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1399 in several types of mutations:
1400 1.) AA level: deletion, complex
1401 2.) AA level: complex, inframe
1402 3.) RNA level: silent
1404 o BPbl2seq parsing of empty reports will not die, but will return
1405 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1406 $report->query() and $report->subject() methods. So an easy
1407 way to test if report was empty is to see if
1408 $report->query->seqname is undefined.
1410 0.7.1 Bug fix release
1412 o Better parsing of genbank/EMBL files especially fixing bugs
1413 related to Feature table parsing and locations on remote
1414 sequences. Additionally, species name parsing was better.
1416 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1417 which include a number of header lines.
1419 o More strict genbank and EMBL format writing (corrected number of
1420 spaces where appropriate).
1422 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1423 for related BPlite BUGS that are unresolved in this release.
1425 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1426 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1427 use expasy mirrors or EBI dbfetch cgi-script.
1429 o A moderate number of documentation improvements were made as
1430 well to provide a better code synopsis in each module.
1433 0.7 Large number of changes, including refactoring of the
1434 Object system, new parsers, new functionality and
1435 all round better system. Highlights are:
1438 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1439 Bio::Root::IO for I/O and file/handle capabilities.
1441 o Imported BPlite modules from Ian Korf for BLAST
1442 parsing. This is considered the supported BLAST parser;
1443 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1445 o Improved Sequence Feature model. Added complete location
1446 modelling (with fuzzy and compound locations). See
1447 Bio::LocationI and the modules under Bio/Location. Added
1448 support in Genbank/EMBL format parsing to completely parse
1449 feature tables for complex locations.
1451 o Moved special support for databanks etc to specialized modules under
1452 Bio/Seq/. One of these supports very large sequences through
1453 a temporary file as a backend.
1455 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1456 CDS retrieval and exon shuffling.
1458 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1460 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1461 DB/GDB (the latter has platform-specific limitations).
1463 o New analysis parser framework for HT sequence annotation (see
1464 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1466 o New Alignment IO framework
1468 o New Index modules (Swissprot)
1470 o New modules for running Blast within perl
1471 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1472 Multiple Sequence Alignment tools ClustalW and TCoffee
1473 (Bio::Tools::Run::Alignment).
1475 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1476 documentation across the package.
1478 o Much improved cross platform support. Many known incompatibilities
1479 have been fixed; however, NT and Mac do not work across the entire
1480 setup (see PLATFORMS).
1482 o Many bug fixes, code restructuring, etc. Overall stability and
1483 maintainability benefit a lot.
1485 o A total of 957 automatic tests
1490 There are very few functionality changes but a large
1491 number of software improvements/bug fixes across the package.
1493 o The EMBL/GenBank parsing are improved.
1495 o The Swissprot reading is improved. Swissprot writing
1496 is disabled as it doesn't work at all. This needs to
1497 wait for 0.7 release
1499 o BLAST reports with no hits are correctly parsed.
1501 o Several other bugs of the BLAST parser (regular expressions, ...)
1504 o Old syntax calls have been replaced with more modern syntax
1506 o Modules that did not work at all, in particular the Sim4
1507 set have been removed
1509 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1510 have improved compliance with interface specs and documentation
1512 o Mailing list documentation updated throughout the distribution
1514 o Most minor bug fixes have happened.
1516 o The scripts in /examples now work and have the modern syntax
1517 rather than the deprecated syntax
1520 0.6.1 Sun April 2 2000
1522 o Sequences can have Sequence Features attached to them
1523 - The sequence features can be read from or written to
1524 EMBL and GenBank style flat files
1526 o Objects for Annotation, including References (but not
1527 full medline abstracts), Database links and Comments are
1530 o A Species object to represent nodes on a taxonomy tree
1533 o The ability to parse HMMER and Sim4 output has been added
1535 o The Blast parsing has been improved, with better PSI-BLAST
1536 support and better overall behaviour.
1538 o Flat file indexed databases provide both random access
1539 and sequential access to their component sequences.
1541 o A CodonTable object has been written with all known
1542 CodonTables accessible.
1544 o A number of new lightweight analysis tools have been
1545 added, such as molecular weight determination.
1547 The 0.6 release also has improved software engineering
1549 o The sequence objects have been rewritten, providing more
1550 maintainable and easier to implement objects. These
1551 objects are backwardly compatible with the 0.05.1 objects
1553 o Many objects are defined in terms of interfaces and then
1554 a Perl implementation has been provided. The interfaces
1555 are found in the 'I' files (module names ending in 'I').
1557 This means that it is possible to wrap C/CORBA/SQL access
1558 as true "bioperl" objects, compatible with the rest of
1561 o The SeqIO system has been overhauled to provide better
1562 processing and perl-like automatic interpretation of <>
1565 o Many more tests have been added (a total of 172 automatic
1566 tests are now run before release).
1570 0.05.1 Tue Jun 29 05:30:44 1999
1571 - Central distribution now requires Perl 5.004. This was
1572 done to get around 5.003-based problems in Bio/Index/*
1574 - Various bug fixes in the Bio::Tools::Blast modules
1575 including better exception handling and PSI-Blast
1576 support. See Bio/Tools/Blast/CHANGES for more.
1577 - Fixed the Parse mechanism in Seq.pm to use readseq.
1578 Follow the instructions in README for how to install
1579 it (basically, you have to edit Parse.pm).
1580 - Improved documentation of Seq.pm, indicating where
1581 objects are returned and where strings are returned.
1582 - Fixed uninitialized warnings in Bio::Root::Object.pm
1583 and Bio::Tools::SeqPattern.pm.
1584 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1586 0.05 Sun Apr 25 01:14:11 1999
1587 - Bio::Tools::Blast modules have less memory problems
1588 and faster parsing. Webblast uses LWP and supports
1589 more functionality. See Bio/Tools/Blast/CHANGES for more.
1590 - The Bio::SeqIO system has been started, moving the
1591 sequence reformatting code out of the sequence object
1592 - The Bio::Index:: system has been started, providing
1593 generic index capabilities and specifically works for
1594 Fasta formatted databases and EMBL .dat formatted
1596 - The Bio::DB:: system started, providing access to
1597 databases, both via flat file + index (see above) and
1599 - The scripts/ directory, where industrial strength scripts
1600 are put has been started.
1601 - Many changes - a better distribution all round.
1603 0.04.4 Wed Feb 17 02:20:13 1999
1604 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1605 (see Bio::Tools::Blast::CHANGES).
1606 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1607 - Beefed up the t/Fasta.t test script.
1608 - Small fix in Bio::Seq::type() (now always returns a string).
1609 - Changed Bio::Root::Utilities::get_newline_char() to
1610 get_newline() since it could return more than one char.
1611 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1612 - Changed default timeout to 20 seconds (was 3).
1613 - Moved lengthy modification notes to the bottom of some files.
1614 - Fixed SimpleAlign write_fasta bug.
1615 - Beefed up SimpleAlign.t test
1617 0.04.3 Thu Feb 4 07:48:53 1999
1618 - Bio::Root::Object.pm and Global.pm now detect when
1619 script is run as a CGI and suppress output that is only
1620 appropriate when running interactively.
1621 - Bio::Root::Err::_set_context() adds name of script ($0).
1622 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1623 regarding the use of the static objects via the qw(:obj) tag.
1624 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1625 CORE::reverse, avoiding Perl warnings.
1626 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1627 example scripts (see Bio::Tools::Blast::CHANGES).
1628 - examples/seq/seqtools.pl no longer always warns about using
1629 -prot or -nucl command-line arguments; only when using the
1631 - Methods added to Bio::Root::Utilities: create_filehandle(),
1632 get_newline_char(), and taste_file() to generalize filehandle
1633 creation and autodetect newline characters in files/streams
1634 (see bug report #19).
1635 - Bio::Root::IOManager::read() now handles timeouts and uses
1636 Utilities::create_filehandle().
1637 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1638 of hardwiring in "\n".
1639 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1641 0.04.2 Wed Dec 30 02:27:36 1998
1642 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1643 (see Bio::Tools::Blast::CHANGES).
1644 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1645 to CORE::reverse (prevents ambiguous warnings with 5.005).
1646 - Appending '.tmp.bioperl' to temporary files created by
1647 Bio::Root::Utilities::compress() or uncompress() to
1648 make it easy to identify & cleanup these files as needed.
1649 - Developers: Created CVS branch release-0-04-bug from
1650 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1651 be sure to cvs checkout this branch into a clean area.
1653 0.04.1 Wed Dec 16 05:39:15 1998
1654 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1655 (see Bio::Tools::Blast::CHANGES).
1656 - Compile/SW/Makefile.PL now removes *.o and *.a files
1659 0.04 Tue Dec 8 07:49:19 1998
1660 - Lots of new modules added including:
1661 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1662 and Bio/Compile directory containing XS-linked C code for
1663 creating Smith-Waterman sequence alignments from within Perl.
1664 * Steve Chervitz's Blast distribution has been incorporated.
1665 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1666 - Bio/examples directory for demo scripts for all included modules.
1667 - Bio/t directory containing test suit for all included modules.
1668 - For changes specific to the Blast-related modules prior to
1669 incorporation in this central distribution, see the CHANGES
1670 file in the Bio/Tools/Blast directory.
1672 0.01 Tue Sep 8 14:23:22 1998
1673 - original version from central CVS tree; created by h2xs 1.18