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
69 * Bio::Cluster::SequenceFamily
70 - improved performance when using get_members with overlapping multiple
75 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
76 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
77 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
78 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
79 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
80 information was lost in a multi-result blast file [Paul Cantalupo]
81 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
82 total gaps [Paul Cantalupo]
83 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
84 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
85 when end of domain indicator is split across lines [Paul Cantalupo]
86 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
88 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
89 instances where blank lines are within sequences [cjfields]
90 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
92 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
93 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
95 * Various fixes for Stockholm file indexing and processing [bosborne]
96 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
97 breaks parsing [cjfields]
98 * Fix case where Bio::Seq::Meta* objects with no meta information could not
99 be reverse-complemented [fangly]
100 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
101 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
102 when unsure that values will be numerical [fangly]
103 * Fix undef warnings in Bio::SeqIO::embl [fangly]
104 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
105 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
106 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
108 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
109 source_tag and display_name must return a string, not undef [fangly]
110 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
111 add_SeqFeature takes a single argument [fangly]
112 * Use cross-platform filenames and temporary directory in
113 Bio::DB::Taxonomy::flatfile [fangly]
114 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
115 properly identified as existing taxa in the database [fangly]
116 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
117 without also passing a lineage to store [fangly]
118 * Prevent passing a directory to the gi2taxid option (-g) of
119 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
121 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
122 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
123 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
124 object before trying to access, and no longer returns repeated sequences.
131 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
132 modules using Ace will also be deprecated [lds, cjfields]
133 * Minor bug fix release
134 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
135 * Address Build.PL issues when DBI is not present [hartzell]
136 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
137 * Remove deprecated code for perl 5.14.0 compat [cjfields]
138 * Due to schema changes and lack of support for older versions, support
139 for NeXML 0.9 is only (very) partially implemented.
140 See: https://redmine.open-bio.org/issues/3207
144 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
145 docs [genehack, cjfields]
146 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
147 module version from dist_version (probably not the best way to do this,
148 but it seems to work) [rbuels, cjfields]
151 1.6.900 April 14, 201
155 * This will probably be the last release to add significant features to
156 core modules; subsequent releases will be for bug fixes alone.
157 We are planning on a restructuring of core for summer 2011, potentially
158 as part of the Google Summer of Code. This may become BioPerl 2.0.
159 * Version bump represents 'just prior to v 1.7'. We may have point
160 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
161 This code essentially is what is on the github master branch.
165 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
167 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
168 - removal of Scalar::Util::weaken code, which was causing odd headaches
169 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
170 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
172 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
175 - bug 2515 - new contribution [Ryan Golhar, jhannah]
177 - support for reading Maq, Sam and Bowtie files [maj]
178 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
179 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
180 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
181 - bug 2726: reading/writing granularity: whole scaffold or one contig
182 at a time [Joshua Udall, fangly]
184 - Added parsing of xrefs to OBO files, which are stored as secondary
185 dbxrefs of the cvterm [Naama Menda]
186 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
187 * PAML code updated to work with PAML 4.4d [DaveMessina]
191 * [3198] - sort tabular BLAST hits by score [DaveMessina]
192 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
193 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
194 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
196 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
197 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
198 * [3164] - TreeFunctionsI syntax bug [gjuggler]
199 * [3163] - AssemblyIO speedup [fangly]
200 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
202 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
203 * [3158] - fix EMBL file mis-parsing [cjfields]
204 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
206 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
207 * [3148] - URL change for UniProt [cjfields]
208 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
209 * [3136] - HMMer3 parser fixes [kblin]
210 * [3126] - catch description [Toshihiko Akiba]
211 * [3122] - Catch instances where non-seekable filehandles were being
212 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
213 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
214 [dukeleto, rbuels, cjfields]
215 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
217 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
218 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
220 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
221 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
222 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
223 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
224 * [3086] - EMBL misparsing long tags [kblin, cjfields]
225 * [3085] - CommandExts and array of files [maj, hyphaltip]
226 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
227 for alignment slices [Ha X. Dang, cjfields]
228 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
229 * [3073] - fix parsing of GenBank files from RDP [cjfields]
230 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
231 * [3064] - All-gap midline BLAST report issues [cjfields]
232 * [3063] - BLASt report RID [Razi Khaja, cjfields]
233 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
234 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
235 * [3039] - correct Newick output root node branch length [gjuggler,
237 * [3038] - SELEX alignment error [Bernd, cjfields]
238 * [3033] - PrimarySeq ID setting [Bernd, maj]
239 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
240 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
241 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
242 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
243 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
244 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
245 PAML 4.4d [DaveMessina]
246 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
248 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
249 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
250 * [3017] - using threads with Bio::DB::GenBank [cjfields]
251 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
252 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
253 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
254 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
255 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
257 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
258 * [2977] - TreeIO issues [DaveMessina]
259 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
260 * [2944] - Bio::Tools::GFF score [cjfields]
261 * [2942] - correct MapTiling output [maj]
262 * [2939] - PDB residue insertion codes [John May, maj]
263 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
264 * [2928] - GuessSeqFormat raw [maj]
265 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
266 * [2922] - open() directive issue [cjfields]
267 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
268 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
269 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
270 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
272 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
273 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
274 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
275 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
276 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
277 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
278 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
279 * [2758] - Bio::AssemblyIO ace problems [fangly]
280 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
281 * [2726] - ace file IO [Josh, fangly]
282 * [2700] - Refactor Build.PL [cjfields]
283 * [2673] - addition of simple Root-based clone() method [cjfields]
284 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
285 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
286 * [2594] - Bio::Species memory leak [cjfields]
287 * [2515] - GenBank XML parser [jhannah]
288 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
289 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
290 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
292 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
296 * Bio::Expression modules - these were originally designed to go with the
297 bioperl-microarray suite of tools, however they have never been completed
298 and so have been removed from the distribution. The original code has
299 been moved into the inactive bioperl-microarray suite. [cjfields]
303 * Repository moved from Subversion (SVN) to
304 http://github.com/bioperl/bioperl-live [cjfields]
305 * Bug database has moved to Redmine (https://redmine.open-bio.org)
306 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
307 Thieme have been moved to their own distribution (Bio-Microarray).
310 1.6.1 Sept. 29, 2009 (point release)
311 * No change from last alpha except VERSION and doc updates [cjfields]
313 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
314 * Fix for silent OBDA bug related to FASTA validation [cjfields]
316 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
317 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
318 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
320 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
322 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
323 * WinXP test fixes [cjfields, maj]
324 * BioPerl.pod added for descriptive information, fixes CPAN indexing
326 * Minor doc fixes [cjfields]
328 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
329 * Fix tests failing due to merging issues [cjfields]
330 * More documentation updates for POD parsing [cjfields]
332 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
334 - fix YAML meta data generation [cjfields]
336 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
337 * Bio::Align::DNAStatistics
338 - fix divide by zero problem [jason]
340 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
341 * Bio::AlignIO::stockholm
342 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
343 * Bio::Assembly::Tools::ContigSpectrum
344 - function to score contig spectrum [fangly]
345 * Bio::DB::EUtilities
346 - small updates [cjfields]
348 - berkeleydb database now autoindexes wig files and locks correctly
351 - various small updates for stability; tracking changes to LANL
352 database interface [maj]
353 * Bio::DB::SeqFeature (lots of updates and changes)
354 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
355 - bug 2835 - patch [Dan Bolser]
356 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
358 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
359 * Bio::Factory::FTLocationFactory
360 - mailing list bug fix [cjfields]
362 - performance work on column_from_residue_number [hartzell]
363 * Bio::Matrix::IO::phylip
364 - bug 2800 - patch to fix phylip parsing [Wei Zou]
366 - Google Summer of Code project from Chase Miller - parsers for Nexml
367 file format [maj, chmille4]
369 - Make Individual, Population, Marker objects AnnotatableI [maj]
370 - simplify LD code [jason]
372 - deal with empty intersection [jason]
374 - significant overhaul of Bio::Restriction system: complete support for
375 external and non-palindromic cutters. [maj]
377 - CPANPLUS support, no automatic installation [sendu]
379 - allow IO::String (regression fix) [cjfields]
380 - catch unintentional undef values [cjfields]
381 - throw if non-fh is passed to -fh [maj]
382 * Bio::Root::Root/RootI
383 - small debugging and core fixes [cjfields]
385 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
386 * Bio::Root::Utilities
387 - bug 2737 - better warnings [cjfields]
389 - tiling completely refactored, HOWTO added [maj]
390 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
391 will deprecate usage of the older tiling code in the next BioPerl
393 - small fixes [cjfields]
395 - Infernal 1.0 output now parsed [cjfields]
396 - new parser for gmap -f9 output [hartzell]
397 - bug 2852 - fix infinite loop in some output [cjfields]
398 - blastxml output now passes all TODO tests [cjfields]
399 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
400 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
401 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
402 * Bio::Seq::LargePrimarySeq
403 - delete tempdirs [cjfields]
404 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
406 - extract regions based on quality threshold value [Dan Bolser, heikki]
407 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
408 * Bio::SeqFeature::Lite
409 - various Bio::DB::SeqFeature-related fixes [lstein]
410 * Bio::SeqFeature::Tools::TypeMapper
411 - additional terms for GenBank to SO map [scain]
412 * Bio::SeqIO::chadoxml
413 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
415 - support for CDS records [dave_messina, Sylvia]
417 - complete refactoring to handle all FASTQ variants, perform validation,
418 write output. API now conforms with other Bio* parsers and the rest of
419 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
421 * Bio::SeqIO::genbank
422 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
423 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
424 * Bio::SeqIO::largefasta
425 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
427 - add option for 'single' and 'multiple'
429 - bug 2881 - fix scf round-tripping [Adam Søgren]
431 - bug 2766, 2810 - copy over tags from features, doc fixes [David
434 - bug 2793 - patch for add_seq index issue [jhannah, maj]
435 - bug 2801 - throw if args are required [cjfields]
436 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
437 [Tristan Lefebure, maj]
438 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
439 - fix POD and add get_SeqFeatures filter [maj]
440 * Bio::Tools::dpAlign
441 - add support for LocatableSeq [ymc]
442 - to be moved to a separate distribution [cjfields, rbuels]
443 * Bio::Tools::EUtilities
444 - fix for two bugs from mail list [Adam Whitney, cjfields]
445 - add generic ItemContainerI interface for containing same methods
448 - fix up code, add more warnings [cjfields]
449 - to be moved to a separate distribution [cjfields, rbuels]
450 * Bio::Tools::Primer3
451 - bug 2862 - fenceposting issue fixed [maj]
452 * Bio::Tools::Run::RemoteBlast
453 - tests for remote RPS-BLAST [mcook]
454 * Bio::Tools::SeqPattern
455 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
456 * Bio::Tools::tRNAscanSE
457 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
459 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
460 * Bio::Tree::Statistics
461 - several methods for calculating Fitch-based score, internal trait
462 values, statratio(), sum of leaf distances [heikki]
464 - bug 2869 - add docs indicating edge case where nodes can be
465 prematurely garbage-collected [cjfields]
466 - add as_text() function to create Tree as a string in specified format
468 * Bio::Tree::TreeFunctionsI
469 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
471 * Bio::TreeIO::newick
472 - fix small semicolon issue [cjfields]
474 - update to bp_seqfeature_load for SQLite [lstein]
475 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
476 - fastam9_to_table - fix for MPI output [jason]
477 - gccalc - total stats [jason]
479 - POD cleanup re: FEEDBACK section [maj, cjfields]
480 - cleanup or fix dead links [cjfields]
481 - Use of no_* methods (indicating 'number of something') is deprecated
482 in favor of num_* [cjfields]
483 - lots of new tests for the above bugs and refactors [everyone!]
484 - new template for Komodo text editor [cjfields]
487 * Feature/Annotation rollback
488 - Problematic changes introduced prior to the 1.5 release have been
489 rolled back. These changes led to subtle bugs involving operator
490 overloading and interface methods.
491 - Behavior is very similar to that for BioPerl 1.4, with tag values
492 being stored generically as simple scalars. Results in a modest
495 - Split into a separate distribution on CPAN, primarily so development
496 isn't reliant on a complete BioPerl release.
497 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
498 is only available via Subversion (via bioperl-live main trunk)
500 - Common test bed for all BioPerl modules
502 - Common Module::Build-based subclass for all BioPerl modules
503 * Bio::DB::EUtilities
504 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
505 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
506 and user agent request posting and retrieval
507 * Test implementation and reorganization
508 - Tests have been reorganized into groups based on classes or use
510 - Automated test coverage is now online:
511 http://www.bioperl.org/wiki/Test_Coverage
512 - After this release, untested modules will be moved into a
513 separate developer distribution until tests can be derived.
514 Also, new modules to be added are expected to have a test suite
515 and adequate test coverage.
517 1.5.2 Developer release
519 Full details of changes since 1.5.1 are available online at:
520 http://www.bioperl.org/wiki/Change_log
521 The following represents a brief overview of the most important changes.
524 - Overhaul. Brand new system fully allows markers to have multiple
525 positions on multiple maps, and to have relative positions. Should be
529 - This module and all the modules in the Taxonomy directory now
530 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
535 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
537 * New methods ancestor(), each_Descendent() and _handle_internal_id().
539 * Allows for different database modules to create Bio::Taxon objects
540 with the same internal id when the same taxon is requested from each.
543 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
545 * No longer includes the fake root node 'root'; there are multiple roots
546 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
549 * get_node() has new option -full
551 * Caches data retrieved from website
554 - Now a Bio::Taxon. Carries out the species name -> specific name munging
555 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
556 backward compatability in species() method.
558 o Bio::Search and Bio::SearchIO
559 - Overhaul. The existing system has been sped up via some minor changes
560 (mostly gain-of-function to the API). Bio::PullParserI is introduced
561 as a potential eventual replacment for the existing system, though as
562 yet only a Hmmpfam parser exists written using it.
565 1.5.1 Developer release
567 o Major problem with how Annotations were written out with
568 Bio::Seq is fixed by reverting to old behavior for
569 Bio::Annotation objects.
574 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
575 expect at l east 9 spaces at the beginning of a line to
576 indicate line wrapping.
578 * Treat multi-line SOURCE sections correctly, this defect broke
579 both common_name() and classification()
581 * parse swissprot fields in genpept file
583 * parse WGS genbank records
586 * Changed regexp for ID line. The capturing parentheses are
587 the same, the difference is an optional repeated-not-semi-
588 colon expression following the captured \S+. This means the
589 regexp works when the division looks like /PRO;/ or when the
590 division looks like /ANG ;/ - the latter is from EMBL
593 * fix ID line parsing: the molecule string can have spaces in
594 it. Like: "genomic DNA"
596 - swiss.pm: bugs #1727, #1734
599 * Added parser for entrezgene ASN1 (text format) files.
600 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
604 - maf.pm coordinate problem fixed
606 o Bio::Taxonomy and Bio::DB::Taxonomy
608 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
609 can be done via Web without downloading all the sequence.
611 o Bio::Tools::Run::RemoteBlast supports more options and complies
612 to changes to the NCBI interface. It is reccomended that you
613 retrieve the data in XML instead of plain-text BLAST report to
614 insure proper parsing and retrieval of all information as NCBI
615 fully expects to change things in the future.
617 o Bio::Tree and Bio::TreeIO
619 - Fixes so that re-rooting a tree works properly
621 - Writing out nhx format from a newick/nexus file will properly output
622 bootstrap information. The use must move the internal node labels over
624 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
625 $node->bootstrap($node->id);
628 - Nexus parsing is much more flexible now, does not care about
631 - Cladogram drawing module in Bio::Tree::Draw
633 - Node height and depth now properly calculated
635 - fix tree pruning algorithm so that node with 1 child gets merged
637 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
638 bugs and improvements were added, see Gbrowse mailing list for most of
641 o Bio::DB::GFF partially supports GFF3. See information about
642 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
644 o Better location parsing in Bio::Factory::FTLocationFactory -
645 this is part of the engine for parsing EMBL/GenBank feature table
646 locations. Nested join/order-by/complement are allowed now
648 o Bio::PrimarySeqI->translate now takes named parameters
650 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
651 reconstruction) is now supported. Parsing different models and
652 branch specific parametes are now supported.
654 o Bio::Factory::FTLocationFactory - parse hierarchical locations
657 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
658 for getter/setter functions
662 - blast bug #1739; match scientific notation in score
663 and possible e+ values
665 - blast.pm reads more WU-BLAST parameters and parameters, match
666 a full database pathname,
668 - Handle NCBI WEB and newer BLAST formats specifically
669 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
671 - psl off-by-one error fixed
673 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
674 and HSPs can be constructed from them.
676 - HSPs query/hit now have a seqdesc field filled out (this was
677 always available via $hit->description and
678 $result->query_description
680 - hmmer.pm can parse -A0 hmmpfam files
682 - Writer::GbrowseGFF more customizeable.
684 o Bio::Tools::Hmmpfam
685 make e-value default score displayed in gff, rather than raw score
686 allow parse of multiple records
689 1.5 Developer release
691 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
692 provide Jukes-Cantor and Kimura pairwise distance methods,
695 o Bio::AlignIO support for "po" format of POA, and "maf";
696 Bio::AlignIO::largemultifasta is a new alternative to
697 Bio::AlignIO::fasta for temporary file-based manipulation of
698 particularly large multiple sequence alignments.
700 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
701 be treated similarly as an assembled contig.
703 o Bio::CodonUsage provides new rare_codon() and probable_codons()
704 methods for identifying particular codons that encode a given
707 o Bio::Coordinate::Utils provides new from_align() method to build
708 a Bio::Coordinate pair directly from a
709 Bio::Align::AlignI-conforming object.
711 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
712 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
713 web service using standard Pubmed query syntax, and retrieve
716 o Bio::DB::GFF has various sundry bug fixes.
718 o Bio::FeatureIO is a new SeqIO-style subsystem for
719 writing/reading genomic features to/from files. I/O classes
720 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
721 classes only read/write Bio::SeqFeature::Annotated objects.
722 Notably, the GFF v3 class requires features to be typed into the
725 o Bio::Graph namespace contains new modules for manipulation and
726 analysis of protein interaction graphs.
728 o Bio::Graphics has many bug fixes and shiny new glyphs.
730 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
731 indexing for HMMER reports and FASTA qual files, respectively.
733 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
734 new objects that can be placed within a Bio::Map::MapI-compliant
735 genetic/physical map; Bio::Map::Physical provides a new physical
736 map type; Bio::MapIO::fpc provides finger-printed clone mapping
739 o Bio::Matrix::PSM provide new support for postion-specific
740 (scoring) matrices (e.g. profiles, or "possums").
742 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
743 be instantiated without explicitly using Bio::OntologyIO. This
744 is possible through changes to Bio::Ontology::OntologyStore to
745 download ontology files from the web as necessary. Locations of
746 ontology files are hard-coded into
747 Bio::Ontology::DocumentRegistry.
749 o Bio::PopGen includes many new methods and data types for
750 population genetics analyses.
752 o New constructor to Bio::Range, unions(). Given a list of
753 ranges, returns another list of "flattened" ranges --
754 overlapping ranges are merged into a single range with the
755 mininum and maximum coordinates of the entire overlapping group.
757 o Bio::Root::IO now supports -url, in addition to -file and -fh.
758 The new -url argument allows one to specify the network address
759 of a file for input. -url currently only works for GET
760 requests, and thus is read-only.
762 o Bio::SearchIO::hmmer now returns individual Hit objects for each
763 domain alignment (thus containing only one HSP); previously
764 separate alignments would be merged into one hit if the domain
765 involved in the alignments was the same, but this only worked
766 when the repeated domain occured without interruption by any
767 other domain, leading to a confusing mixture of Hit and HSP
770 o Bio::Search::Result::ResultI-compliant report objects now
771 implement the "get_statistics" method to access
772 Bio::Search::StatisticsI objects that encapsulate any
773 statistical parameters associated with the search (e.g. Karlin's
774 lambda for BLAST/FASTA).
776 o Bio::Seq::LargeLocatableSeq combines the functionality already
777 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
779 o Bio::SeqFeature::Annotated is a replacement for
780 Bio::SeqFeature::Generic. It breaks compliance with the
781 Bio::SeqFeatureI interface because the author was sick of
782 dealing with untyped annotation tags. All
783 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
784 compliant, and accessible through Bio::Annotation::Collection.
786 o Bio::SeqFeature::Primer implements a Tm() method for primer
787 melting point predictions.
789 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
790 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
792 o Bio::Taxonomy::Node now implements the methods necessary for
793 Bio::Species interoperability.
795 o Bio::Tools::CodonTable has new reverse_translate_all() and
796 make_iupac_string() methods.
798 o Bio::Tools::dpAlign now provides sequence profile alignments.
800 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
802 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
805 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
806 for designing small inhibitory RNA.
808 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
809 methods based on a distance matrix.
811 o Bio::Tree::Statistics provides an assess_bootstrap() method to
812 calculate bootstrap support values on a guide tree topology,
813 based on provided bootstrap tree topologies.
815 o Bio::TreeIO now supports the Pagel (PAG) tree format.
821 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
823 o Bio::Graphics will work with gd1 or gd2
826 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
828 - blast.pm Parse multi-line query fields properly
829 - small speed improvements to blasttable.pm and others
831 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
832 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
833 supporting more complex queries
836 1.4. Stable major release
838 Since initial 1.2.0, 3000 separate changes have been made to make this release.
840 o installable scripts
842 o global module version from Bio::Root:Version
845 - major improvements; SVG support
848 - population genetics
849 - support several population genetics types of questions.
850 - Tests for statistical neutrality of mutations
851 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
852 Tests of population structure (Wright's F-statistic: Fst) is in
853 Bio::PopGen::PopStats. Calculating composite linkage
854 disequilibrium (LD) is available in Bio::PopGen::Statistics as
856 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
857 and csv (comma delimited formatted) data.
859 - a directory for implementing population simulations has
860 been added Bio::PopGen::Simulation and 2 simulations - a
861 Coalescent and a simple single-locus multi-allele genetic drift
862 simulation have been provided. This replaces the code in
863 Bio::Tree::RandomTree which has been deprecated until proper
864 methods for generating random phylogenetic trees are
868 - new restrion analysis modules
870 o Bio::Tools::Analysis
871 - web based DNA and Protein analysis framework and several
875 - per residue annotable sequences
878 - Bio::Matrix::PSM - Position Scoring Matrix
879 - Bio::Matrix::IO has been added for generalized parsing of
880 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
881 initial implementations for parsing BLOSUM/PAM and Phylip
882 Distance matricies respectively. A generic matrix
883 implementation for general use was added in
884 Bio::Matrix::Generic.
891 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
892 - small inhibitory RNA
894 o Bio::SeqFeature::Tools
895 - seqFeature mapping tools
896 - Bio::SeqFeature::Tools::Unflattener.pm
897 -- deal with mapping GenBank feature collections into
898 Chado/GFF3 processable feature sets (with SO term mappings)
900 o Bio::Tools::dpAlign
901 - pure perl dynamic programming sequence alignment
904 o new Bio::SearchIO formats
905 - axt and psl: UCSC formats.
906 - blasttable: NCBI -m 8 or -m 9 format from blastall
908 o new Bio::SeqIO formats
909 - chado, tab, kegg, tigr, game
910 - important fixes for old modules
914 o improved Bio::Tools::Genewise
916 o Bio::SeqIO now can recongnize sequence formats automatically from
919 o new parsers in Bio::Tools:
920 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
922 o Bio::DB::Registry bugs fixed
923 - BerkeleyDB-indexed flat files can be used by the OBDA system
924 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
925 used by the OBDA system
928 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
931 o hundreds of new and improved files
935 o Bio::Tree::AlleleNode has been updated to be a container of
936 an Bio::PopGen::Individual object for use in the Coalescent simulations.
941 1.2.3 Stable release update
942 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
944 o Bug #1477 - Sel --> Sec abbreviation fixed
945 o Fix bug #1487 where paring in-between locations when
946 end < start caused the FTLocationFactory logic to fail.
947 o Fix bug #1489 which was not dealing with keywords as an
948 arrayref properly (this is fixed on the main trunk because
949 keywords returns a string and the array is accessible via
951 o Bio::Tree::Tree memory leak (bug #1480) fixed
952 Added a new initialization option -nodelete which
953 won't try and cleanup the containing nodes if this
955 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
956 this was only present on the branch for the 1.2.1 and 1.2.2 series
957 - Also merged main trunk changes to the branch which make
958 newick -> nhx round tripping more effective (storing branch length
959 and bootstrap values in same locate for NodeNHX and Node
960 implementations.) Fixes to TreeIO parsing for labeled internal
961 also required small changes to TreeIO::nhx. Improved
962 tests for this module as well.
964 - Fixed bugs in BLAST parsing which couldn't parse NCBI
965 gapped blast properly (was losing hit significance values due to
966 the extra unexpeted column).
967 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
968 integer overflow (# of letters in nt seq dbs is > MAX_INT)
969 although doesn't try to correct it - will get the negative
970 number for you. Added a test for this as well.
971 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
972 has no top-level family classification scores but does have scores and
973 alignments for individual domains.
974 - Parsing FASTA reports where ungapped percent ID is < 10 and the
975 regular expression to match the line was missing the possibility of
976 an extra space. This is rare, which is why we probably did not
978 - BLAST parsing picks up more of the statistics/parameter fields
979 at the bottom of reports. Still not fully complete.
980 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
981 were fixed to include many improvements and added flexiblity
982 in outputting the files. Bug #1495 was also fixed in the process.
984 - Update for GFF3 compatibility.
985 - Added scripts for importing from UCSC and GenBank.
986 - Added a 1.2003 version number.
989 - Added a 1.2003 version number.
990 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
991 properly writing keywords out.
992 o Bio::SeqIO::genbank
993 - Fixed bug/enhancement #1513 where dates of
994 the form D-MMM-YYYY were not parsed. Even though this is
995 invalid format we can handle it - and also cleanup the date
996 string so it is properly formatted.
997 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
998 and written with Genbank format. Similarly bug #1515 is fixed to
999 parse in the ORIGIN text.
1000 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1001 to specify the ID type, one of (accession accession.version
1002 display primary). See Bio::SeqIO::preferred_id_type method
1003 documentation for more information.
1004 o Unigene parsing updated to handle file format changes by NCBI
1006 1.2.2 Stable release update
1008 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1009 - auto-discover ontology name
1010 - bug in parsing relationships when certain characters are in the term
1011 - fixed hard-coded prefix for term identifiers
1012 - various smaller issues
1014 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1015 of Bio::Ontology::TermI
1017 o brought the OBDA Registry code up to latest specs
1021 - accession number retrieval fixed
1023 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1025 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1026 #1459 which now properly report alignment start/end info
1027 for translated BLAST/FASTA searches.
1029 o Bio::TreeIO::newick can parse labeled internal nodes
1031 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1032 for BLASTX if if you provide -report_type => 'BLASTX' when
1033 initializing a BPbl2seq object. Bioperl 1.3 will have better
1034 support for bl2seq in the SearchIO system.
1036 o Bio::Root::IO support a -noclose boolean flag which will not
1037 close a filehandle upon object cleanup - useful when sharing
1038 a filehandle among objects. Additionally code added s.t.
1039 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1041 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1043 o Bio::SeqIO::genbank
1044 - bug #1456 fixed which generated extra sequence lines
1045 - write moltype correctly for genpept
1047 1.2.1 Stable release update
1049 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1051 o Addition from main trunk of Ontology objects, principly to allow
1052 BioSQL releases against 1.2.1
1054 o Fixes and cleanup of Bio::Coordinate modules
1056 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1057 the primary accession number
1059 o Other bug fixes, including bpindex GenBank fix
1061 o Bio::SeqIO::genbank bug #1389 fixed
1063 1.2 Stable major release
1065 o More functionality added to Bio::Perl, the newbie module
1067 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1068 Support for New Hampshire Extended (NHX) format parsing.
1070 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1071 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1074 o New ontology parsing Bio::Ontology
1076 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1077 multi-report (mlib) fasta reports, support for waba and exonerate.
1079 o Bio::ClusterIO for parsing Unigene clusters
1081 o Bio::Assembly added for representing phrap and ace assembly clusters.
1083 o Rudimentary support for writing Chado XML (see
1084 GMOD project: www.gmod.org for more information)
1086 o Bio::Coordinate for mapping between different coordinate systems such
1087 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1088 features into different coordinate systems.
1090 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1091 with the get_Stream_by_query method and supports the latest
1092 NCBI eutils interface.
1094 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1095 object for extracting subsets of features : currently only
1096 supports extraction by location.
1098 1.1.1 Developer release
1100 o Deprecated modules are now listed in the DEPRECATED file
1102 o New HowTo documents located in doc/howto describing
1103 a domain of Bioperl.
1105 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1106 and all old bugs are searchable through the bugzilla interface.
1108 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1109 have been addressed.
1111 o Support for Genewise parsing in Bio::Tools::Genewise
1113 o Start of Ontology framework with Bio::Ontology
1115 o Speedup to the Bio::Root::Root object method _rearrange.
1116 A global _load_module method was implemented to simplify the
1117 dynamic loading of modules ala Bio::SeqIO::genbank. This
1118 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1121 o Several performance improvements to sequence parsing in Bio::SeqIO.
1122 Attempt to speedup by reducing object creation overhead.
1124 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1125 method for sequence retrieval with their E-utils CGI scripts.
1126 More work to support Entrez queries to their fullest is planned
1129 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1131 1.1 Developer release
1133 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1134 this separation removes some of the complexity in our test suite
1135 and separates the core modules in bioperl from those that need
1136 external programs to run.
1138 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1139 not run into trouble running the makefile
1141 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1142 read,create,and write locations for grouped/split locations
1143 (like mRNA features on genomic sequence).
1145 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1146 and PAML (codeml,aaml, etc) parsing.
1148 o Bio::Tree:: objects expanded to handle testing monophyly,
1149 paraphyly, least common ancestor, etc.
1151 o Bio::Coordinate for mapping locations from different coordinate spaces
1153 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1154 added for parsing hmmpfam and hmmsearch output.
1156 o Bio::SearchIO::Writer::TextResultWriter for outputting
1157 a pseudo-blast textfile format
1160 1.0.2 Bug fix release
1162 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1163 in this release will not work after December 2002 when NCBI
1164 shuts off the old Entrez cgi scripts. We have already fixed
1165 on our main development branch and the functionality will be
1166 available in the next stable bioperl release (1.2) slated for
1169 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1170 testset by Robin Emig. These were fixed as was the get_aln
1171 method in Bio::Search::HSP::GenericHSP to handle the extra
1172 context sequence that is provided with a FastA alignment.
1174 o Migrating differences between Bio::Search::XX::BlastXX to
1175 Bio::Search::XX::GenericXX objects. This included mechanism
1176 to retrieve whole list of HSPs from Hits and whole list of Hits from
1177 Results in addition to the current next_XX iterator methods that
1178 are available. Added seq_inds() method to GenericHSP which identifies
1179 indexes in the query or hit sequences where conserved,identical,gaps,
1180 or mismatch residues are located (adapted from Steve Chervitz's
1181 implementation in BlastHSP).
1183 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1184 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1186 o Bio::Graphics glyph set improved and extended for GBrowse release
1188 o Bio::Tree::Tree get_nodes implementation improvement thanks
1189 to Howard Ross notice performance problem when writing out
1192 o Bio::Location::Fuzzy::new named parameter -loc_type became
1193 -location_type, Bio::Location::Simple::new named parameter
1194 -seqid becamse -seq_id.
1196 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1197 was mis-detecting that gaps should be placed at the beginning of
1198 the alignment when the best alignment starts internally in the
1201 1.0.1 Bug fix release
1203 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1205 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1206 and mixed (3.3 - 3.4) versions of FASTA.
1208 o Small API change to add methods for completeness across
1209 implementations of Bio::Search objects. These new methods
1210 in the interface are implemented by the GenericXX object as well
1211 as the BlastXX objects.
1212 * Bio::Search::Result::ResultI
1213 - hits() method returns list of all Hits (next_hit is an
1216 * Bio::Search::Hit::HitI
1217 - hsps() method returns list of all HSPs (next_hsp is an
1220 o The Bio::SearchIO::Writer classes have been fixed to handle results
1221 created from either psiblast (Search::BlastXX objects) or
1222 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1223 has to be done here to make it work properly and will nee major
1226 o Bugs in Bio::Tools::HMMER fixed, including
1227 * #1178 - Root::IO destructor wasn't being called
1228 * #1034 - filter_on_cutoff now behaves properly
1230 o Bio::SeqFeature::Computation initialization args fixed and
1233 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1235 o Updated FAQ with more example based answers to typical questions
1237 o Bug #1202 was fixed which would improperly join together qual values
1238 parsed by Bio::SeqIO::qual when a trailing space was not present before
1241 1.0.0 Major Stable Release
1243 This represents a major release of bioperl with significant
1244 improvements over the 0.7.x series of releases.
1246 o Bio::Tools::Blast is officially deprecated. Please see
1247 Bio::SearchIO for BLAST and FastA parsing.
1249 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1250 Bio::LocationI objects as well as start/end.
1252 o Bio::Biblio contains modules for Bibliographic data.
1253 Bio::DB::Biblio contains the query modules. Additionally one can
1254 parse medlinexml from the ebi bibliographic query service (BQS)
1255 system and Pubmed xml from NCBI. See Martin Senger's
1256 documentation in Bio::Biblio for more information.
1258 o Bio::DB::Registry is a sequence database registry part of
1259 Open Bioinformatics Database Access. See
1260 http://obda.open-bio.org for more information.
1262 o File-based and In-Memory Sequence caching is provided by
1263 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1266 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1267 been added by Lincoln Stein.
1269 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1271 o A FAQ has been started and is included in the release to provide
1272 a starting point for frequent questions and issues.
1274 0.9.3 Developer's release
1276 o Event based parsing system improved (SearchIO). With parsers for
1277 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1278 Additionally a lazy parsing system for text and html blast reports was
1279 added and is called psiblast (name subject to change in future releases).
1281 o Bio::Search objects improved and standardized with associated Interfaces
1282 written. The concept of a search "Hit" was standardized to be called
1283 "hit" consistently and the use of "subject" was deprecated in all active
1286 o Bio::Structure added (since 0.9.1) for Protein structure objects
1287 and PDB parser to retrieve and write these structures from data files.
1289 o Several important Bio::DB::GFF bug fixes for handling features that
1290 are mapped to multiple reference points. Updated mysql adaptor
1291 so as to be able to store large (>100 megabase) chunks of DNA into
1292 Bio::DB::GFF databases.
1294 0.9.2 Developer's release
1296 o Bio::Search and Bio::SearchIO system introduced for event based
1297 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1298 in text and XML and FASTA reports in standard output format.
1300 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1301 generator is included in Bio::TreeIO::RandomTrees and a
1302 statistics module for evaluating.
1304 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1305 server for DAS servers.
1307 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1308 files. The entire BPlite system migrated to using Bio::Root::IO
1309 for the data stream.
1311 o Bio::Tools::Alignment for Consed and sequence Trimming
1314 o Bio::Structure for Protein structure information and parsing
1316 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1317 cgi-bin entry point which should be more reliable.
1319 o Bio::Map and Bio::MapIO for biological map navigation and a
1320 framework afor parsing them in. Only preliminary work here.
1322 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1323 Future work will integrate Pise and allow submission of analysis on
1326 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1327 introduced as new objects for handling Sequence Annotation
1328 information (dblinks, references, etc) and is more robust that
1331 o Bio::Tools::FASTAParser introduced.
1333 o Scripts from the bioperl script submission project and new
1334 scripts from bioperl authors are included in "scripts" directory.
1336 o Factory objects and interfaces are being introduced and are more
1339 o Bio::Root::Root introduced as the base object while
1340 Bio::Root::RootI is now simply an interface.
1342 o Bio::DB::RefSeq provides database access to copy of the NCBI
1343 RefSeq database using the EBI dbfetch script.
1345 0.9.0 Developer's release
1347 o perl version at least 5.005 is now required instead of perl 5.004
1349 o Bio::Tools::Run::RemoteBlast is available for running remote
1352 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1354 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1355 Also added are related modules UTR3, UTR5, Exon, Intron,
1356 Promotor, PolyA and Transcript.
1358 o Speedup of translate method in PrimarySeq
1360 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1361 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1363 o Various fixes to Variation toolkit
1365 o Bio::DB::EMBL provides database access to EMBL sequence data.
1366 Bio::DB::Universal provides a central way to point to indexes
1367 and dbs in a single interface.
1369 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1371 o Bio::Factory::EMBOSS is still in design phase as is
1372 Bio::Factory::ApplicationFactoryI
1374 o Dia models for bioperl design are provided in the models/ directory
1376 0.7.2 Bug fix release
1378 o documentation fixes in many modules - SYNOPSIS code verified
1379 to be runnable in many (but not all modules)
1381 o corrected MANIFEST file from 0.7.1 release
1383 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1386 o Bio::SeqIO::genbank
1387 * Correct parsing and writing of genbank format with protein data
1388 * moltype and molecule separation
1390 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1392 o Bio::SimpleAlign fixed to correctly handle consensus
1393 sequence calculation
1395 o Bio::Tools::HMMER supports hmmer 2.2g
1397 o Bio::Tools::BPlite to support report type specific parsing. Most
1398 major changes are not on the 0.7 branch.
1400 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1403 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1404 in several types of mutations:
1405 1.) AA level: deletion, complex
1406 2.) AA level: complex, inframe
1407 3.) RNA level: silent
1409 o BPbl2seq parsing of empty reports will not die, but will return
1410 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1411 $report->query() and $report->subject() methods. So an easy
1412 way to test if report was empty is to see if
1413 $report->query->seqname is undefined.
1415 0.7.1 Bug fix release
1417 o Better parsing of genbank/EMBL files especially fixing bugs
1418 related to Feature table parsing and locations on remote
1419 sequences. Additionally, species name parsing was better.
1421 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1422 which include a number of header lines.
1424 o More strict genbank and EMBL format writing (corrected number of
1425 spaces where appropriate).
1427 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1428 for related BPlite BUGS that are unresolved in this release.
1430 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1431 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1432 use expasy mirrors or EBI dbfetch cgi-script.
1434 o A moderate number of documentation improvements were made as
1435 well to provide a better code synopsis in each module.
1438 0.7 Large number of changes, including refactoring of the
1439 Object system, new parsers, new functionality and
1440 all round better system. Highlights are:
1443 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1444 Bio::Root::IO for I/O and file/handle capabilities.
1446 o Imported BPlite modules from Ian Korf for BLAST
1447 parsing. This is considered the supported BLAST parser;
1448 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1450 o Improved Sequence Feature model. Added complete location
1451 modelling (with fuzzy and compound locations). See
1452 Bio::LocationI and the modules under Bio/Location. Added
1453 support in Genbank/EMBL format parsing to completely parse
1454 feature tables for complex locations.
1456 o Moved special support for databanks etc to specialized modules under
1457 Bio/Seq/. One of these supports very large sequences through
1458 a temporary file as a backend.
1460 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1461 CDS retrieval and exon shuffling.
1463 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1465 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1466 DB/GDB (the latter has platform-specific limitations).
1468 o New analysis parser framework for HT sequence annotation (see
1469 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1471 o New Alignment IO framework
1473 o New Index modules (Swissprot)
1475 o New modules for running Blast within perl
1476 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1477 Multiple Sequence Alignment tools ClustalW and TCoffee
1478 (Bio::Tools::Run::Alignment).
1480 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1481 documentation across the package.
1483 o Much improved cross platform support. Many known incompatibilities
1484 have been fixed; however, NT and Mac do not work across the entire
1485 setup (see PLATFORMS).
1487 o Many bug fixes, code restructuring, etc. Overall stability and
1488 maintainability benefit a lot.
1490 o A total of 957 automatic tests
1495 There are very few functionality changes but a large
1496 number of software improvements/bug fixes across the package.
1498 o The EMBL/GenBank parsing are improved.
1500 o The Swissprot reading is improved. Swissprot writing
1501 is disabled as it doesn't work at all. This needs to
1502 wait for 0.7 release
1504 o BLAST reports with no hits are correctly parsed.
1506 o Several other bugs of the BLAST parser (regular expressions, ...)
1509 o Old syntax calls have been replaced with more modern syntax
1511 o Modules that did not work at all, in particular the Sim4
1512 set have been removed
1514 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1515 have improved compliance with interface specs and documentation
1517 o Mailing list documentation updated throughout the distribution
1519 o Most minor bug fixes have happened.
1521 o The scripts in /examples now work and have the modern syntax
1522 rather than the deprecated syntax
1525 0.6.1 Sun April 2 2000
1527 o Sequences can have Sequence Features attached to them
1528 - The sequence features can be read from or written to
1529 EMBL and GenBank style flat files
1531 o Objects for Annotation, including References (but not
1532 full medline abstracts), Database links and Comments are
1535 o A Species object to represent nodes on a taxonomy tree
1538 o The ability to parse HMMER and Sim4 output has been added
1540 o The Blast parsing has been improved, with better PSI-BLAST
1541 support and better overall behaviour.
1543 o Flat file indexed databases provide both random access
1544 and sequential access to their component sequences.
1546 o A CodonTable object has been written with all known
1547 CodonTables accessible.
1549 o A number of new lightweight analysis tools have been
1550 added, such as molecular weight determination.
1552 The 0.6 release also has improved software engineering
1554 o The sequence objects have been rewritten, providing more
1555 maintainable and easier to implement objects. These
1556 objects are backwardly compatible with the 0.05.1 objects
1558 o Many objects are defined in terms of interfaces and then
1559 a Perl implementation has been provided. The interfaces
1560 are found in the 'I' files (module names ending in 'I').
1562 This means that it is possible to wrap C/CORBA/SQL access
1563 as true "bioperl" objects, compatible with the rest of
1566 o The SeqIO system has been overhauled to provide better
1567 processing and perl-like automatic interpretation of <>
1570 o Many more tests have been added (a total of 172 automatic
1571 tests are now run before release).
1575 0.05.1 Tue Jun 29 05:30:44 1999
1576 - Central distribution now requires Perl 5.004. This was
1577 done to get around 5.003-based problems in Bio/Index/*
1579 - Various bug fixes in the Bio::Tools::Blast modules
1580 including better exception handling and PSI-Blast
1581 support. See Bio/Tools/Blast/CHANGES for more.
1582 - Fixed the Parse mechanism in Seq.pm to use readseq.
1583 Follow the instructions in README for how to install
1584 it (basically, you have to edit Parse.pm).
1585 - Improved documentation of Seq.pm, indicating where
1586 objects are returned and where strings are returned.
1587 - Fixed uninitialized warnings in Bio::Root::Object.pm
1588 and Bio::Tools::SeqPattern.pm.
1589 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1591 0.05 Sun Apr 25 01:14:11 1999
1592 - Bio::Tools::Blast modules have less memory problems
1593 and faster parsing. Webblast uses LWP and supports
1594 more functionality. See Bio/Tools/Blast/CHANGES for more.
1595 - The Bio::SeqIO system has been started, moving the
1596 sequence reformatting code out of the sequence object
1597 - The Bio::Index:: system has been started, providing
1598 generic index capabilities and specifically works for
1599 Fasta formatted databases and EMBL .dat formatted
1601 - The Bio::DB:: system started, providing access to
1602 databases, both via flat file + index (see above) and
1604 - The scripts/ directory, where industrial strength scripts
1605 are put has been started.
1606 - Many changes - a better distribution all round.
1608 0.04.4 Wed Feb 17 02:20:13 1999
1609 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1610 (see Bio::Tools::Blast::CHANGES).
1611 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1612 - Beefed up the t/Fasta.t test script.
1613 - Small fix in Bio::Seq::type() (now always returns a string).
1614 - Changed Bio::Root::Utilities::get_newline_char() to
1615 get_newline() since it could return more than one char.
1616 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1617 - Changed default timeout to 20 seconds (was 3).
1618 - Moved lengthy modification notes to the bottom of some files.
1619 - Fixed SimpleAlign write_fasta bug.
1620 - Beefed up SimpleAlign.t test
1622 0.04.3 Thu Feb 4 07:48:53 1999
1623 - Bio::Root::Object.pm and Global.pm now detect when
1624 script is run as a CGI and suppress output that is only
1625 appropriate when running interactively.
1626 - Bio::Root::Err::_set_context() adds name of script ($0).
1627 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1628 regarding the use of the static objects via the qw(:obj) tag.
1629 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1630 CORE::reverse, avoiding Perl warnings.
1631 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1632 example scripts (see Bio::Tools::Blast::CHANGES).
1633 - examples/seq/seqtools.pl no longer always warns about using
1634 -prot or -nucl command-line arguments; only when using the
1636 - Methods added to Bio::Root::Utilities: create_filehandle(),
1637 get_newline_char(), and taste_file() to generalize filehandle
1638 creation and autodetect newline characters in files/streams
1639 (see bug report #19).
1640 - Bio::Root::IOManager::read() now handles timeouts and uses
1641 Utilities::create_filehandle().
1642 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1643 of hardwiring in "\n".
1644 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1646 0.04.2 Wed Dec 30 02:27:36 1998
1647 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1648 (see Bio::Tools::Blast::CHANGES).
1649 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1650 to CORE::reverse (prevents ambiguous warnings with 5.005).
1651 - Appending '.tmp.bioperl' to temporary files created by
1652 Bio::Root::Utilities::compress() or uncompress() to
1653 make it easy to identify & cleanup these files as needed.
1654 - Developers: Created CVS branch release-0-04-bug from
1655 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1656 be sure to cvs checkout this branch into a clean area.
1658 0.04.1 Wed Dec 16 05:39:15 1998
1659 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1660 (see Bio::Tools::Blast::CHANGES).
1661 - Compile/SW/Makefile.PL now removes *.o and *.a files
1664 0.04 Tue Dec 8 07:49:19 1998
1665 - Lots of new modules added including:
1666 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1667 and Bio/Compile directory containing XS-linked C code for
1668 creating Smith-Waterman sequence alignments from within Perl.
1669 * Steve Chervitz's Blast distribution has been incorporated.
1670 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1671 - Bio/examples directory for demo scripts for all included modules.
1672 - Bio/t directory containing test suit for all included modules.
1673 - For changes specific to the Blast-related modules prior to
1674 incorporation in this central distribution, see the CHANGES
1675 file in the Bio/Tools/Blast directory.
1677 0.01 Tue Sep 8 14:23:22 1998
1678 - original version from central CVS tree; created by h2xs 1.18