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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 ---------------------------------------------------------
20 1.?.?
22 [New features]
24 * Bio::Seq::SimulatedRead
25 - New module to represent reads taken from other sequences [fangly]
26 * Bio::Root::Root
27 - Support of Clone::Fast as a faster cloning alternative [fangly]
28 * Bio::Root::IO
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]
32 * Bio::Tools::IUPAC
33 - New regexp() method to create regular expressions from IUPAC sequences
34 [fangly]
35 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
36 - Code refresh [fangly]
37 * Bio::DB::Taxonomy
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]
54 * Bio::DB::Fasta
55 - now handles IUPAC degenerate residues [fangly]
56 * Bio::PrimarySeq and Bio::PrimarySeqI
57 - speed improvements for large sequences [Ben Woodcroft, fangly]
58 * Bio::PrimaryQual
59 - tightened and optimized quality string validation [fangly]
61 [Bug fixes]
63 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
64 cjfields]
65 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
66 instances where blank lines are within sequences [cjfields]
67 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
68 types [fangly]
69 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
70 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
71 cjfields]
72 * Various fixes for Stockholm file indexing and processing [bosborne]
73 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
74 breaks parsing [cjfields]
75 * Fix case where Bio::Seq::Meta* objects with no meta information could not
76 be reverse-complemented [fangly]
77 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
78 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
79 when unsure that values will be numerical [fangly]
80 * Fix undef warnings in Bio::SeqIO::embl [fangly]
81 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
82 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
83 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
84 Sallou]
85 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
86 source_tag and display_name must return a string, not undef [fangly]
87 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
88 add_SeqFeature takes a single argument [fangly]
89 * Use cross-platform filenames and temporary directory in
90 Bio::DB::Taxonomy::flatfile [fangly]
91 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
92 properly identified as existing taxa in the database [fangly]
93 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
94 without also passing a lineage to store [fangly]
95 * Prevent passing a directory to the gi2taxid option (-g) of
96 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
97 [fangly]
98 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
99 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
102 1.6.901 May 18, 2011
104 [Notes]
106 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
107 modules using Ace will also be deprecated [lds, cjfields]
108 * Minor bug fix release
109 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
110 * Address Build.PL issues when DBI is not present [hartzell]
111 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
112 * Remove deprecated code for perl 5.14.0 compat [cjfields]
113 * Due to schema changes and lack of support for older versions, support
114 for NeXML 0.9 is only (very) partially implemented.
115 See: https://redmine.open-bio.org/issues/3207
117 [Bug fixes]
119 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
120 docs [genehack, cjfields]
121 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
122 module version from dist_version (probably not the best way to do this,
123 but it seems to work) [rbuels, cjfields]
126 1.6.900 April 14, 201
128 [Notes]
130 * This will probably be the last release to add significant features to
131 core modules; subsequent releases will be for bug fixes alone.
132 We are planning on a restructuring of core for summer 2011, potentially
133 as part of the Google Summer of Code. This may become BioPerl 2.0.
134 * Version bump represents 'just prior to v 1.7'. We may have point
135 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
136 This code essentially is what is on the github master branch.
138 [New features]
140 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
141 * Bio::Tree refactor
142 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
143 - removal of Scalar::Util::weaken code, which was causing odd headaches
144 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
145 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
146 many others]
147 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
148 [Warren Kretzschmar]
149 * Bio::SeqIO::gbxml
150 - bug 2515 - new contribution [Ryan Golhar, jhannah]
151 * Bio::Assembly::IO
152 - support for reading Maq, Sam and Bowtie files [maj]
153 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
154 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
155 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
156 - bug 2726: reading/writing granularity: whole scaffold or one contig
157 at a time [Joshua Udall, fangly]
158 * Bio::OntologyIO
159 - Added parsing of xrefs to OBO files, which are stored as secondary
160 dbxrefs of the cvterm [Naama Menda]
161 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
162 * PAML code updated to work with PAML 4.4d [DaveMessina]
164 [Bug fixes]
166 * [3198] - sort tabular BLAST hits by score [DaveMessina]
167 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
168 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
169 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
170 [cjfields]
171 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
172 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
173 * [3164] - TreeFunctionsI syntax bug [gjuggler]
174 * [3163] - AssemblyIO speedup [fangly]
175 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
176 hyphaltip]
177 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
178 * [3158] - fix EMBL file mis-parsing [cjfields]
179 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
180 cjfields]
181 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
182 * [3148] - URL change for UniProt [cjfields]
183 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
184 * [3136] - HMMer3 parser fixes [kblin]
185 * [3126] - catch description [Toshihiko Akiba]
186 * [3122] - Catch instances where non-seekable filehandles were being
187 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
188 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
189 [dukeleto, rbuels, cjfields]
190 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
191 jhannah]
192 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
193 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
194 cjfields]
195 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
196 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
197 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
198 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
199 * [3086] - EMBL misparsing long tags [kblin, cjfields]
200 * [3085] - CommandExts and array of files [maj, hyphaltip]
201 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
202 for alignment slices [Ha X. Dang, cjfields]
203 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
204 * [3073] - fix parsing of GenBank files from RDP [cjfields]
205 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
206 * [3064] - All-gap midline BLAST report issues [cjfields]
207 * [3063] - BLASt report RID [Razi Khaja, cjfields]
208 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
209 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
210 * [3039] - correct Newick output root node branch length [gjuggler,
211 DaveMessina]
212 * [3038] - SELEX alignment error [Bernd, cjfields]
213 * [3033] - PrimarySeq ID setting [Bernd, maj]
214 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
215 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
216 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
217 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
218 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
219 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
220 PAML 4.4d [DaveMessina]
221 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
222 DaveMessina]
223 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
224 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
225 * [3017] - using threads with Bio::DB::GenBank [cjfields]
226 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
227 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
228 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
229 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
230 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
231 cjfields]
232 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
233 * [2977] - TreeIO issues [DaveMessina]
234 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
235 * [2944] - Bio::Tools::GFF score [cjfields]
236 * [2942] - correct MapTiling output [maj]
237 * [2939] - PDB residue insertion codes [John May, maj]
238 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
239 * [2928] - GuessSeqFormat raw [maj]
240 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
241 * [2922] - open() directive issue [cjfields]
242 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
243 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
244 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
245 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
246 cjfields]
247 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
248 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
249 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
250 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
251 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
252 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
253 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
254 * [2758] - Bio::AssemblyIO ace problems [fangly]
255 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
256 * [2726] - ace file IO [Josh, fangly]
257 * [2700] - Refactor Build.PL [cjfields]
258 * [2673] - addition of simple Root-based clone() method [cjfields]
259 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
260 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
261 * [2594] - Bio::Species memory leak [cjfields]
262 * [2515] - GenBank XML parser [jhannah]
263 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
264 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
265 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
266 cjfields]
267 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
269 [Deprecated]
271 * Bio::Expression modules - these were originally designed to go with the
272 bioperl-microarray suite of tools, however they have never been completed
273 and so have been removed from the distribution. The original code has
274 been moved into the inactive bioperl-microarray suite. [cjfields]
276 [Other]
278 * Repository moved from Subversion (SVN) to
279 http://github.com/bioperl/bioperl-live [cjfields]
280 * Bug database has moved to Redmine (https://redmine.open-bio.org)
281 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
282 Thieme have been moved to their own distribution (Bio-Microarray).
283 [cjfields]
285 1.6.1 Sept. 29, 2009 (point release)
286 * No change from last alpha except VERSION and doc updates [cjfields]
288 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
289 * Fix for silent OBDA bug related to FASTA validation [cjfields]
291 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
292 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
293 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
294 [cjfields]
295 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
297 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
298 * WinXP test fixes [cjfields, maj]
299 * BioPerl.pod added for descriptive information, fixes CPAN indexing
300 [cjfields]
301 * Minor doc fixes [cjfields]
303 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
304 * Fix tests failing due to merging issues [cjfields]
305 * More documentation updates for POD parsing [cjfields]
307 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
308 * Bio::Root::Build
309 - fix YAML meta data generation [cjfields]
311 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
312 * Bio::Align::DNAStatistics
313 - fix divide by zero problem [jason]
314 * Bio::AlignIO::*
315 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
316 * Bio::AlignIO::stockholm
317 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
318 * Bio::Assembly::Tools::ContigSpectrum
319 - function to score contig spectrum [fangly]
320 * Bio::DB::EUtilities
321 - small updates [cjfields]
322 * Bio::DB::Fasta
323 - berkeleydb database now autoindexes wig files and locks correctly
324 [lstein]
325 * Bio::DB::HIV
326 - various small updates for stability; tracking changes to LANL
327 database interface [maj]
328 * Bio::DB::SeqFeature (lots of updates and changes)
329 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
330 - bug 2835 - patch [Dan Bolser]
331 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
332 * Bio::DB::SwissProt
333 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
334 * Bio::Factory::FTLocationFactory
335 - mailing list bug fix [cjfields]
336 * Bio::LocatableSeq
337 - performance work on column_from_residue_number [hartzell]
338 * Bio::Matrix::IO::phylip
339 - bug 2800 - patch to fix phylip parsing [Wei Zou]
340 * Bio::Nexml
341 - Google Summer of Code project from Chase Miller - parsers for Nexml
342 file format [maj, chmille4]
343 * Bio::PopGen
344 - Make Individual, Population, Marker objects AnnotatableI [maj]
345 - simplify LD code [jason]
346 * Bio::RangeI
347 - deal with empty intersection [jason]
348 * Bio::Restriction
349 - significant overhaul of Bio::Restriction system: complete support for
350 external and non-palindromic cutters. [maj]
351 * Bio::Root::Build
352 - CPANPLUS support, no automatic installation [sendu]
353 * Bio::Root::IO
354 - allow IO::String (regression fix) [cjfields]
355 - catch unintentional undef values [cjfields]
356 - throw if non-fh is passed to -fh [maj]
357 * Bio::Root::Root/RootI
358 - small debugging and core fixes [cjfields]
359 * Bio::Root::Test
360 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
361 * Bio::Root::Utilities
362 - bug 2737 - better warnings [cjfields]
363 * Bio::Search
364 - tiling completely refactored, HOWTO added [maj]
365 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
366 will deprecate usage of the older tiling code in the next BioPerl
367 release
368 - small fixes [cjfields]
369 * Bio::SearchIO
370 - Infernal 1.0 output now parsed [cjfields]
371 - new parser for gmap -f9 output [hartzell]
372 - bug 2852 - fix infinite loop in some output [cjfields]
373 - blastxml output now passes all TODO tests [cjfields]
374 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
375 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
376 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
377 * Bio::Seq::LargePrimarySeq
378 - delete tempdirs [cjfields]
379 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
380 * Bio::Seq::Quality
381 - extract regions based on quality threshold value [Dan Bolser, heikki]
382 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
383 * Bio::SeqFeature::Lite
384 - various Bio::DB::SeqFeature-related fixes [lstein]
385 * Bio::SeqFeature::Tools::TypeMapper
386 - additional terms for GenBank to SO map [scain]
387 * Bio::SeqIO::chadoxml
388 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
389 * Bio::SeqIO::embl
390 - support for CDS records [dave_messina, Sylvia]
391 * Bio::SeqIO::fastq
392 - complete refactoring to handle all FASTQ variants, perform validation,
393 write output. API now conforms with other Bio* parsers and the rest of
394 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
395 [cjfields]
396 * Bio::SeqIO::genbank
397 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
398 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
399 * Bio::SeqIO::largefasta
400 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
401 * Bio::SeqIO::raw
402 - add option for 'single' and 'multiple'
403 * Bio::SeqIO::scf
404 - bug 2881 - fix scf round-tripping [Adam Sj¿gren]
405 * Bio::SeqUtils
406 - bug 2766, 2810 - copy over tags from features, doc fixes [David
407 Jackson]
408 * Bio::SimpleAlign
409 - bug 2793 - patch for add_seq index issue [jhannah, maj]
410 - bug 2801 - throw if args are required [cjfields]
411 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
412 [Tristan Lefebure, maj]
413 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
414 - fix POD and add get_SeqFeatures filter [maj]
415 * Bio::Tools::dpAlign
416 - add support for LocatableSeq [ymc]
417 - to be moved to a separate distribution [cjfields, rbuels]
418 * Bio::Tools::EUtilities
419 - fix for two bugs from mail list [Adam Whitney, cjfields]
420 - add generic ItemContainerI interface for containing same methods
421 [cjfields]
422 * Bio::Tools::HMM
423 - fix up code, add more warnings [cjfields]
424 - to be moved to a separate distribution [cjfields, rbuels]
425 * Bio::Tools::Primer3
426 - bug 2862 - fenceposting issue fixed [maj]
427 * Bio::Tools::Run::RemoteBlast
428 - tests for remote RPS-BLAST [mcook]
429 * Bio::Tools::SeqPattern
430 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
431 * Bio::Tools::tRNAscanSE
432 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
433 * Bio::Tree::*
434 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
435 * Bio::Tree::Statistics
436 - several methods for calculating Fitch-based score, internal trait
437 values, statratio(), sum of leaf distances [heikki]
438 * Bio::Tree::Tree
439 - bug 2869 - add docs indicating edge case where nodes can be
440 prematurely garbage-collected [cjfields]
441 - add as_text() function to create Tree as a string in specified format
442 [maj]
443 * Bio::Tree::TreeFunctionsI
444 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
445 Lefebure, maj]
446 * Bio::TreeIO::newick
447 - fix small semicolon issue [cjfields]
448 * scripts
449 - update to bp_seqfeature_load for SQLite [lstein]
450 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
451 - fastam9_to_table - fix for MPI output [jason]
452 - gccalc - total stats [jason]
453 * General Stuff
454 - POD cleanup re: FEEDBACK section [maj, cjfields]
455 - cleanup or fix dead links [cjfields]
456 - Use of no_* methods (indicating 'number of something') is deprecated
457 in favor of num_* [cjfields]
458 - lots of new tests for the above bugs and refactors [everyone!]
459 - new template for Komodo text editor [cjfields]
461 1.6.0 Winter 2009
462 * Feature/Annotation rollback
463 - Problematic changes introduced prior to the 1.5 release have been
464 rolled back. These changes led to subtle bugs involving operator
465 overloading and interface methods.
466 - Behavior is very similar to that for BioPerl 1.4, with tag values
467 being stored generically as simple scalars. Results in a modest
468 speedup.
469 * Bio::Graphics
470 - Split into a separate distribution on CPAN, primarily so development
471 isn't reliant on a complete BioPerl release.
472 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
473 is only available via Subversion (via bioperl-live main trunk)
474 * Bio::Root::Test
475 - Common test bed for all BioPerl modules
476 * Bio::Root::Build
477 - Common Module::Build-based subclass for all BioPerl modules
478 * Bio::DB::EUtilities
479 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
480 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
481 and user agent request posting and retrieval
482 * Test implementation and reorganization
483 - Tests have been reorganized into groups based on classes or use
484 cases.
485 - Automated test coverage is now online:
486 http://www.bioperl.org/wiki/Test_Coverage
487 - After this release, untested modules will be moved into a
488 separate developer distribution until tests can be derived.
489 Also, new modules to be added are expected to have a test suite
490 and adequate test coverage.
492 1.5.2 Developer release
494 Full details of changes since 1.5.1 are available online at:
495 http://www.bioperl.org/wiki/Change_log
496 The following represents a brief overview of the most important changes.
498 o Bio::Map
499 - Overhaul. Brand new system fully allows markers to have multiple
500 positions on multiple maps, and to have relative positions. Should be
501 backward compatible.
503 o Bio::Taxonomy
504 - This module and all the modules in the Taxonomy directory now
505 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
507 o Bio::DB::Taxonomy
509 - Taxonomy.pm
510 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
512 * New methods ancestor(), each_Descendent() and _handle_internal_id().
514 * Allows for different database modules to create Bio::Taxon objects
515 with the same internal id when the same taxon is requested from each.
517 - flatfile.pm
518 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
520 * No longer includes the fake root node 'root'; there are multiple roots
521 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
523 - entrez.pm
524 * get_node() has new option -full
526 * Caches data retrieved from website
528 o Bio::Species
529 - Now a Bio::Taxon. Carries out the species name -> specific name munging
530 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
531 backward compatability in species() method.
533 o Bio::Search and Bio::SearchIO
534 - Overhaul. The existing system has been sped up via some minor changes
535 (mostly gain-of-function to the API). Bio::PullParserI is introduced
536 as a potential eventual replacment for the existing system, though as
537 yet only a Hmmpfam parser exists written using it.
540 1.5.1 Developer release
542 o Major problem with how Annotations were written out with
543 Bio::Seq is fixed by reverting to old behavior for
544 Bio::Annotation objects.
546 o Bio::SeqIO
548 - genbank.pm
549 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
550 expect at l east 9 spaces at the beginning of a line to
551 indicate line wrapping.
553 * Treat multi-line SOURCE sections correctly, this defect broke
554 both common_name() and classification()
556 * parse swissprot fields in genpept file
558 * parse WGS genbank records
560 - embl.pm
561 * Changed regexp for ID line. The capturing parentheses are
562 the same, the difference is an optional repeated-not-semi-
563 colon expression following the captured \S+. This means the
564 regexp works when the division looks like /PRO;/ or when the
565 division looks like /ANG ;/ - the latter is from EMBL
566 repbase
568 * fix ID line parsing: the molecule string can have spaces in
569 it. Like: "genomic DNA"
571 - swiss.pm: bugs #1727, #1734
573 - entrezgene.pm
574 * Added parser for entrezgene ASN1 (text format) files.
575 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
577 o Bio::AlignIO
579 - maf.pm coordinate problem fixed
581 o Bio::Taxonomy and Bio::DB::Taxonomy
583 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
584 can be done via Web without downloading all the sequence.
586 o Bio::Tools::Run::RemoteBlast supports more options and complies
587 to changes to the NCBI interface. It is reccomended that you
588 retrieve the data in XML instead of plain-text BLAST report to
589 insure proper parsing and retrieval of all information as NCBI
590 fully expects to change things in the future.
592 o Bio::Tree and Bio::TreeIO
594 - Fixes so that re-rooting a tree works properly
596 - Writing out nhx format from a newick/nexus file will properly output
597 bootstrap information. The use must move the internal node labels over
598 to bootstraps.
599 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
600 $node->bootstrap($node->id);
601 $node->id('');
602 }
603 - Nexus parsing is much more flexible now, does not care about
604 LF.
606 - Cladogram drawing module in Bio::Tree::Draw
608 - Node height and depth now properly calculated
610 - fix tree pruning algorithm so that node with 1 child gets merged
612 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
613 bugs and improvements were added, see Gbrowse mailing list for most of
614 these.
616 o Bio::DB::GFF partially supports GFF3. See information about
617 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
619 o Better location parsing in Bio::Factory::FTLocationFactory -
620 this is part of the engine for parsing EMBL/GenBank feature table
621 locations. Nested join/order-by/complement are allowed now
623 o Bio::PrimarySeqI->translate now takes named parameters
625 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
626 reconstruction) is now supported. Parsing different models and
627 branch specific parametes are now supported.
629 o Bio::Factory::FTLocationFactory - parse hierarchical locations
630 (joins of joins)
632 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
633 for getter/setter functions
635 o Bio::SearchIO
637 - blast bug #1739; match scientific notation in score
638 and possible e+ values
640 - blast.pm reads more WU-BLAST parameters and parameters, match
641 a full database pathname,
643 - Handle NCBI WEB and newer BLAST formats specifically
644 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
646 - psl off-by-one error fixed
648 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
649 and HSPs can be constructed from them.
651 - HSPs query/hit now have a seqdesc field filled out (this was
652 always available via $hit->description and
653 $result->query_description
655 - hmmer.pm can parse -A0 hmmpfam files
657 - Writer::GbrowseGFF more customizeable.
659 o Bio::Tools::Hmmpfam
660 make e-value default score displayed in gff, rather than raw score
661 allow parse of multiple records
664 1.5 Developer release
666 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
667 provide Jukes-Cantor and Kimura pairwise distance methods,
668 respectively.
670 o Bio::AlignIO support for "po" format of POA, and "maf";
671 Bio::AlignIO::largemultifasta is a new alternative to
672 Bio::AlignIO::fasta for temporary file-based manipulation of
673 particularly large multiple sequence alignments.
675 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
676 be treated similarly as an assembled contig.
678 o Bio::CodonUsage provides new rare_codon() and probable_codons()
679 methods for identifying particular codons that encode a given
680 amino acid.
682 o Bio::Coordinate::Utils provides new from_align() method to build
683 a Bio::Coordinate pair directly from a
684 Bio::Align::AlignI-conforming object.
686 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
687 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
688 web service using standard Pubmed query syntax, and retrieve
689 results as XML.
691 o Bio::DB::GFF has various sundry bug fixes.
693 o Bio::FeatureIO is a new SeqIO-style subsystem for
694 writing/reading genomic features to/from files. I/O classes
695 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
696 classes only read/write Bio::SeqFeature::Annotated objects.
697 Notably, the GFF v3 class requires features to be typed into the
698 Sequence Ontology.
700 o Bio::Graph namespace contains new modules for manipulation and
701 analysis of protein interaction graphs.
703 o Bio::Graphics has many bug fixes and shiny new glyphs.
705 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
706 indexing for HMMER reports and FASTA qual files, respectively.
708 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
709 new objects that can be placed within a Bio::Map::MapI-compliant
710 genetic/physical map; Bio::Map::Physical provides a new physical
711 map type; Bio::MapIO::fpc provides finger-printed clone mapping
712 import.
714 o Bio::Matrix::PSM provide new support for postion-specific
715 (scoring) matrices (e.g. profiles, or "possums").
717 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
718 be instantiated without explicitly using Bio::OntologyIO. This
719 is possible through changes to Bio::Ontology::OntologyStore to
720 download ontology files from the web as necessary. Locations of
721 ontology files are hard-coded into
722 Bio::Ontology::DocumentRegistry.
724 o Bio::PopGen includes many new methods and data types for
725 population genetics analyses.
727 o New constructor to Bio::Range, unions(). Given a list of
728 ranges, returns another list of "flattened" ranges --
729 overlapping ranges are merged into a single range with the
730 mininum and maximum coordinates of the entire overlapping group.
732 o Bio::Root::IO now supports -url, in addition to -file and -fh.
733 The new -url argument allows one to specify the network address
734 of a file for input. -url currently only works for GET
735 requests, and thus is read-only.
737 o Bio::SearchIO::hmmer now returns individual Hit objects for each
738 domain alignment (thus containing only one HSP); previously
739 separate alignments would be merged into one hit if the domain
740 involved in the alignments was the same, but this only worked
741 when the repeated domain occured without interruption by any
742 other domain, leading to a confusing mixture of Hit and HSP
743 objects.
745 o Bio::Search::Result::ResultI-compliant report objects now
746 implement the "get_statistics" method to access
747 Bio::Search::StatisticsI objects that encapsulate any
748 statistical parameters associated with the search (e.g. Karlin's
749 lambda for BLAST/FASTA).
751 o Bio::Seq::LargeLocatableSeq combines the functionality already
752 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
754 o Bio::SeqFeature::Annotated is a replacement for
755 Bio::SeqFeature::Generic. It breaks compliance with the
756 Bio::SeqFeatureI interface because the author was sick of
757 dealing with untyped annotation tags. All
758 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
759 compliant, and accessible through Bio::Annotation::Collection.
761 o Bio::SeqFeature::Primer implements a Tm() method for primer
762 melting point predictions.
764 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
765 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
767 o Bio::Taxonomy::Node now implements the methods necessary for
768 Bio::Species interoperability.
770 o Bio::Tools::CodonTable has new reverse_translate_all() and
771 make_iupac_string() methods.
773 o Bio::Tools::dpAlign now provides sequence profile alignments.
775 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
777 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
778 parsers.
780 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
781 for designing small inhibitory RNA.
783 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
784 methods based on a distance matrix.
786 o Bio::Tree::Statistics provides an assess_bootstrap() method to
787 calculate bootstrap support values on a guide tree topology,
788 based on provided bootstrap tree topologies.
790 o Bio::TreeIO now supports the Pagel (PAG) tree format.
792 1.4 branch
794 1.4.1
796 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
798 o Bio::Graphics will work with gd1 or gd2
800 o Bio::SearchIO
801 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
802 (RF lines alone)
803 - blast.pm Parse multi-line query fields properly
804 - small speed improvements to blasttable.pm and others
806 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
807 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
808 supporting more complex queries
811 1.4. Stable major release
813 Since initial 1.2.0, 3000 separate changes have been made to make this release.
815 o installable scripts
817 o global module version from Bio::Root:Version
819 o Bio::Graphics
820 - major improvements; SVG support
822 o Bio::Popgen
823 - population genetics
824 - support several population genetics types of questions.
825 - Tests for statistical neutrality of mutations
826 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
827 Tests of population structure (Wright's F-statistic: Fst) is in
828 Bio::PopGen::PopStats. Calculating composite linkage
829 disequilibrium (LD) is available in Bio::PopGen::Statistics as
830 well.
831 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
832 and csv (comma delimited formatted) data.
834 - a directory for implementing population simulations has
835 been added Bio::PopGen::Simulation and 2 simulations - a
836 Coalescent and a simple single-locus multi-allele genetic drift
837 simulation have been provided. This replaces the code in
838 Bio::Tree::RandomTree which has been deprecated until proper
839 methods for generating random phylogenetic trees are
840 implemented.
842 o Bio::Restriction
843 - new restrion analysis modules
845 o Bio::Tools::Analysis
846 - web based DNA and Protein analysis framework and several
847 implementations
849 o Bio::Seq::Meta
850 - per residue annotable sequences
852 o Bio::Matrix
853 - Bio::Matrix::PSM - Position Scoring Matrix
854 - Bio::Matrix::IO has been added for generalized parsing of
855 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
856 initial implementations for parsing BLOSUM/PAM and Phylip
857 Distance matricies respectively. A generic matrix
858 implementation for general use was added in
859 Bio::Matrix::Generic.
861 o Bio::Ontology
862 - major changes
864 o Bio:Tree
866 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
867 - small inhibitory RNA
869 o Bio::SeqFeature::Tools
870 - seqFeature mapping tools
871 - Bio::SeqFeature::Tools::Unflattener.pm
872 -- deal with mapping GenBank feature collections into
873 Chado/GFF3 processable feature sets (with SO term mappings)
875 o Bio::Tools::dpAlign
876 - pure perl dynamic programming sequence alignment
877 - needs Bioperl-ext
879 o new Bio::SearchIO formats
880 - axt and psl: UCSC formats.
881 - blasttable: NCBI -m 8 or -m 9 format from blastall
883 o new Bio::SeqIO formats
884 - chado, tab, kegg, tigr, game
885 - important fixes for old modules
887 o Bio::AlignIO: maf
889 o improved Bio::Tools::Genewise
891 o Bio::SeqIO now can recongnize sequence formats automatically from
892 stream
894 o new parsers in Bio::Tools:
895 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
897 o Bio::DB::Registry bugs fixed
898 - BerkeleyDB-indexed flat files can be used by the OBDA system
899 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
900 used by the OBDA system
902 o several new HOWTOs
903 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
904 Databases
906 o hundreds of new and improved files
909 o
910 o Bio::Tree::AlleleNode has been updated to be a container of
911 an Bio::PopGen::Individual object for use in the Coalescent simulations.
914 1.2 Branch
916 1.2.3 Stable release update
917 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
918 handling.
919 o Bug #1477 - Sel --> Sec abbreviation fixed
920 o Fix bug #1487 where paring in-between locations when
921 end < start caused the FTLocationFactory logic to fail.
922 o Fix bug #1489 which was not dealing with keywords as an
923 arrayref properly (this is fixed on the main trunk because
924 keywords returns a string and the array is accessible via
925 get_keywords).
926 o Bio::Tree::Tree memory leak (bug #1480) fixed
927 Added a new initialization option -nodelete which
928 won't try and cleanup the containing nodes if this
929 is true.
930 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
931 this was only present on the branch for the 1.2.1 and 1.2.2 series
932 - Also merged main trunk changes to the branch which make
933 newick -> nhx round tripping more effective (storing branch length
934 and bootstrap values in same locate for NodeNHX and Node
935 implementations.) Fixes to TreeIO parsing for labeled internal
936 also required small changes to TreeIO::nhx. Improved
937 tests for this module as well.
938 o Bio::SearchIO
939 - Fixed bugs in BLAST parsing which couldn't parse NCBI
940 gapped blast properly (was losing hit significance values due to
941 the extra unexpeted column).
942 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
943 integer overflow (# of letters in nt seq dbs is > MAX_INT)
944 although doesn't try to correct it - will get the negative
945 number for you. Added a test for this as well.
946 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
947 has no top-level family classification scores but does have scores and
948 alignments for individual domains.
949 - Parsing FASTA reports where ungapped percent ID is < 10 and the
950 regular expression to match the line was missing the possibility of
951 an extra space. This is rare, which is why we probably did not
952 catch it before.
953 - BLAST parsing picks up more of the statistics/parameter fields
954 at the bottom of reports. Still not fully complete.
955 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
956 were fixed to include many improvements and added flexiblity
957 in outputting the files. Bug #1495 was also fixed in the process.
958 o Bio::DB::GFF
959 - Update for GFF3 compatibility.
960 - Added scripts for importing from UCSC and GenBank.
961 - Added a 1.2003 version number.
962 o Bio::Graphics
963 - Updated tutorial.
964 - Added a 1.2003 version number.
965 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
966 properly writing keywords out.
967 o Bio::SeqIO::genbank
968 - Fixed bug/enhancement #1513 where dates of
969 the form D-MMM-YYYY were not parsed. Even though this is
970 invalid format we can handle it - and also cleanup the date
971 string so it is properly formatted.
972 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
973 and written with Genbank format. Similarly bug #1515 is fixed to
974 parse in the ORIGIN text.
975 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
976 to specify the ID type, one of (accession accession.version
977 display primary). See Bio::SeqIO::preferred_id_type method
978 documentation for more information.
979 o Unigene parsing updated to handle file format changes by NCBI
981 1.2.2 Stable release update
983 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
984 - auto-discover ontology name
985 - bug in parsing relationships when certain characters are in the term
986 - fixed hard-coded prefix for term identifiers
987 - various smaller issues
989 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
990 of Bio::Ontology::TermI
992 o brought the OBDA Registry code up to latest specs
994 o Bio::DB::GenBank
995 - eutils URL change
996 - accession number retrieval fixed
998 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1000 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1001 #1459 which now properly report alignment start/end info
1002 for translated BLAST/FASTA searches.
1004 o Bio::TreeIO::newick can parse labeled internal nodes
1006 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1007 for BLASTX if if you provide -report_type => 'BLASTX' when
1008 initializing a BPbl2seq object. Bioperl 1.3 will have better
1009 support for bl2seq in the SearchIO system.
1011 o Bio::Root::IO support a -noclose boolean flag which will not
1012 close a filehandle upon object cleanup - useful when sharing
1013 a filehandle among objects. Additionally code added s.t.
1014 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1016 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1018 o Bio::SeqIO::genbank
1019 - bug #1456 fixed which generated extra sequence lines
1020 - write moltype correctly for genpept
1022 1.2.1 Stable release update
1024 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1026 o Addition from main trunk of Ontology objects, principly to allow
1027 BioSQL releases against 1.2.1
1029 o Fixes and cleanup of Bio::Coordinate modules
1031 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1032 the primary accession number
1034 o Other bug fixes, including bpindex GenBank fix
1036 o Bio::SeqIO::genbank bug #1389 fixed
1038 1.2 Stable major release
1040 o More functionality added to Bio::Perl, the newbie module
1042 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1043 Support for New Hampshire Extended (NHX) format parsing.
1045 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1046 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1047 Hmmpfam parser.
1049 o New ontology parsing Bio::Ontology
1051 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1052 multi-report (mlib) fasta reports, support for waba and exonerate.
1054 o Bio::ClusterIO for parsing Unigene clusters
1056 o Bio::Assembly added for representing phrap and ace assembly clusters.
1058 o Rudimentary support for writing Chado XML (see
1059 GMOD project: www.gmod.org for more information)
1061 o Bio::Coordinate for mapping between different coordinate systems such
1062 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1063 features into different coordinate systems.
1065 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1066 with the get_Stream_by_query method and supports the latest
1067 NCBI eutils interface.
1069 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1070 object for extracting subsets of features : currently only
1071 supports extraction by location.
1073 1.1.1 Developer release
1075 o Deprecated modules are now listed in the DEPRECATED file
1077 o New HowTo documents located in doc/howto describing
1078 a domain of Bioperl.
1080 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1081 and all old bugs are searchable through the bugzilla interface.
1083 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1084 have been addressed.
1086 o Support for Genewise parsing in Bio::Tools::Genewise
1088 o Start of Ontology framework with Bio::Ontology
1090 o Speedup to the Bio::Root::Root object method _rearrange.
1091 A global _load_module method was implemented to simplify the
1092 dynamic loading of modules ala Bio::SeqIO::genbank. This
1093 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1094 etc).
1096 o Several performance improvements to sequence parsing in Bio::SeqIO.
1097 Attempt to speedup by reducing object creation overhead.
1099 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1100 method for sequence retrieval with their E-utils CGI scripts.
1101 More work to support Entrez queries to their fullest is planned
1102 before 1.2 release.
1104 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1106 1.1 Developer release
1108 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1109 this separation removes some of the complexity in our test suite
1110 and separates the core modules in bioperl from those that need
1111 external programs to run.
1113 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1114 not run into trouble running the makefile
1116 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1117 read,create,and write locations for grouped/split locations
1118 (like mRNA features on genomic sequence).
1120 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1121 and PAML (codeml,aaml, etc) parsing.
1123 o Bio::Tree:: objects expanded to handle testing monophyly,
1124 paraphyly, least common ancestor, etc.
1126 o Bio::Coordinate for mapping locations from different coordinate spaces
1128 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1129 added for parsing hmmpfam and hmmsearch output.
1131 o Bio::SearchIO::Writer::TextResultWriter for outputting
1132 a pseudo-blast textfile format
1135 1.0.2 Bug fix release
1137 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1138 in this release will not work after December 2002 when NCBI
1139 shuts off the old Entrez cgi scripts. We have already fixed
1140 on our main development branch and the functionality will be
1141 available in the next stable bioperl release (1.2) slated for
1142 Fall 2002.
1144 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1145 testset by Robin Emig. These were fixed as was the get_aln
1146 method in Bio::Search::HSP::GenericHSP to handle the extra
1147 context sequence that is provided with a FastA alignment.
1149 o Migrating differences between Bio::Search::XX::BlastXX to
1150 Bio::Search::XX::GenericXX objects. This included mechanism
1151 to retrieve whole list of HSPs from Hits and whole list of Hits from
1152 Results in addition to the current next_XX iterator methods that
1153 are available. Added seq_inds() method to GenericHSP which identifies
1154 indexes in the query or hit sequences where conserved,identical,gaps,
1155 or mismatch residues are located (adapted from Steve Chervitz's
1156 implementation in BlastHSP).
1158 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1159 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1161 o Bio::Graphics glyph set improved and extended for GBrowse release
1163 o Bio::Tree::Tree get_nodes implementation improvement thanks
1164 to Howard Ross notice performance problem when writing out
1165 unbalanced trees.
1167 o Bio::Location::Fuzzy::new named parameter -loc_type became
1168 -location_type, Bio::Location::Simple::new named parameter
1169 -seqid becamse -seq_id.
1171 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1172 was mis-detecting that gaps should be placed at the beginning of
1173 the alignment when the best alignment starts internally in the
1174 sequence.
1176 1.0.1 Bug fix release
1178 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1180 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1181 and mixed (3.3 - 3.4) versions of FASTA.
1183 o Small API change to add methods for completeness across
1184 implementations of Bio::Search objects. These new methods
1185 in the interface are implemented by the GenericXX object as well
1186 as the BlastXX objects.
1187 * Bio::Search::Result::ResultI
1188 - hits() method returns list of all Hits (next_hit is an
1189 iterator method)
1191 * Bio::Search::Hit::HitI
1192 - hsps() method returns list of all HSPs (next_hsp is an
1193 iterator method)
1195 o The Bio::SearchIO::Writer classes have been fixed to handle results
1196 created from either psiblast (Search::BlastXX objects) or
1197 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1198 has to be done here to make it work properly and will nee major
1199 API changes.
1201 o Bugs in Bio::Tools::HMMER fixed, including
1202 * #1178 - Root::IO destructor wasn't being called
1203 * #1034 - filter_on_cutoff now behaves properly
1205 o Bio::SeqFeature::Computation initialization args fixed and
1206 tests added.
1208 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1210 o Updated FAQ with more example based answers to typical questions
1212 o Bug #1202 was fixed which would improperly join together qual values
1213 parsed by Bio::SeqIO::qual when a trailing space was not present before
1214 the newline.
1216 1.0.0 Major Stable Release
1218 This represents a major release of bioperl with significant
1219 improvements over the 0.7.x series of releases.
1221 o Bio::Tools::Blast is officially deprecated. Please see
1222 Bio::SearchIO for BLAST and FastA parsing.
1224 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1225 Bio::LocationI objects as well as start/end.
1227 o Bio::Biblio contains modules for Bibliographic data.
1228 Bio::DB::Biblio contains the query modules. Additionally one can
1229 parse medlinexml from the ebi bibliographic query service (BQS)
1230 system and Pubmed xml from NCBI. See Martin Senger's
1231 documentation in Bio::Biblio for more information.
1233 o Bio::DB::Registry is a sequence database registry part of
1234 Open Bioinformatics Database Access. See
1235 http://obda.open-bio.org for more information.
1237 o File-based and In-Memory Sequence caching is provided by
1238 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1239 local database.
1241 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1242 been added by Lincoln Stein.
1244 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1246 o A FAQ has been started and is included in the release to provide
1247 a starting point for frequent questions and issues.
1249 0.9.3 Developer's release
1251 o Event based parsing system improved (SearchIO). With parsers for
1252 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1253 Additionally a lazy parsing system for text and html blast reports was
1254 added and is called psiblast (name subject to change in future releases).
1256 o Bio::Search objects improved and standardized with associated Interfaces
1257 written. The concept of a search "Hit" was standardized to be called
1258 "hit" consistently and the use of "subject" was deprecated in all active
1259 modules.
1261 o Bio::Structure added (since 0.9.1) for Protein structure objects
1262 and PDB parser to retrieve and write these structures from data files.
1264 o Several important Bio::DB::GFF bug fixes for handling features that
1265 are mapped to multiple reference points. Updated mysql adaptor
1266 so as to be able to store large (>100 megabase) chunks of DNA into
1267 Bio::DB::GFF databases.
1269 0.9.2 Developer's release
1271 o Bio::Search and Bio::SearchIO system introduced for event based
1272 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1273 in text and XML and FASTA reports in standard output format.
1275 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1276 generator is included in Bio::TreeIO::RandomTrees and a
1277 statistics module for evaluating.
1279 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1280 server for DAS servers.
1282 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1283 files. The entire BPlite system migrated to using Bio::Root::IO
1284 for the data stream.
1286 o Bio::Tools::Alignment for Consed and sequence Trimming
1287 functionality.
1289 o Bio::Structure for Protein structure information and parsing
1291 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1292 cgi-bin entry point which should be more reliable.
1294 o Bio::Map and Bio::MapIO for biological map navigation and a
1295 framework afor parsing them in. Only preliminary work here.
1297 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1298 Future work will integrate Pise and allow submission of analysis on
1299 remote servers.
1301 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1302 introduced as new objects for handling Sequence Annotation
1303 information (dblinks, references, etc) and is more robust that
1304 previous system.
1306 o Bio::Tools::FASTAParser introduced.
1308 o Scripts from the bioperl script submission project and new
1309 scripts from bioperl authors are included in "scripts" directory.
1311 o Factory objects and interfaces are being introduced and are more
1312 strictly enforced.
1314 o Bio::Root::Root introduced as the base object while
1315 Bio::Root::RootI is now simply an interface.
1317 o Bio::DB::RefSeq provides database access to copy of the NCBI
1318 RefSeq database using the EBI dbfetch script.
1320 0.9.0 Developer's release
1322 o perl version at least 5.005 is now required instead of perl 5.004
1324 o Bio::Tools::Run::RemoteBlast is available for running remote
1325 blast jobs at NCBI.
1327 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1329 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1330 Also added are related modules UTR3, UTR5, Exon, Intron,
1331 Promotor, PolyA and Transcript.
1333 o Speedup of translate method in PrimarySeq
1335 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1336 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1338 o Various fixes to Variation toolkit
1340 o Bio::DB::EMBL provides database access to EMBL sequence data.
1341 Bio::DB::Universal provides a central way to point to indexes
1342 and dbs in a single interface.
1344 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1346 o Bio::Factory::EMBOSS is still in design phase as is
1347 Bio::Factory::ApplicationFactoryI
1349 o Dia models for bioperl design are provided in the models/ directory
1351 0.7.2 Bug fix release
1353 o documentation fixes in many modules - SYNOPSIS code verified
1354 to be runnable in many (but not all modules)
1356 o corrected MANIFEST file from 0.7.1 release
1358 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1359 split locations
1361 o Bio::SeqIO::genbank
1362 * Correct parsing and writing of genbank format with protein data
1363 * moltype and molecule separation
1365 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1367 o Bio::SimpleAlign fixed to correctly handle consensus
1368 sequence calculation
1370 o Bio::Tools::HMMER supports hmmer 2.2g
1372 o Bio::Tools::BPlite to support report type specific parsing. Most
1373 major changes are not on the 0.7 branch.
1375 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1376 with File::Spec
1378 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1379 in several types of mutations:
1380 1.) AA level: deletion, complex
1381 2.) AA level: complex, inframe
1382 3.) RNA level: silent
1384 o BPbl2seq parsing of empty reports will not die, but will return
1385 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1386 $report->query() and $report->subject() methods. So an easy
1387 way to test if report was empty is to see if
1388 $report->query->seqname is undefined.
1390 0.7.1 Bug fix release
1392 o Better parsing of genbank/EMBL files especially fixing bugs
1393 related to Feature table parsing and locations on remote
1394 sequences. Additionally, species name parsing was better.
1396 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1397 which include a number of header lines.
1399 o More strict genbank and EMBL format writing (corrected number of
1400 spaces where appropriate).
1402 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1403 for related BPlite BUGS that are unresolved in this release.
1405 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1406 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1407 use expasy mirrors or EBI dbfetch cgi-script.
1409 o A moderate number of documentation improvements were made as
1410 well to provide a better code synopsis in each module.
1413 0.7 Large number of changes, including refactoring of the
1414 Object system, new parsers, new functionality and
1415 all round better system. Highlights are:
1418 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1419 Bio::Root::IO for I/O and file/handle capabilities.
1421 o Imported BPlite modules from Ian Korf for BLAST
1422 parsing. This is considered the supported BLAST parser;
1423 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1425 o Improved Sequence Feature model. Added complete location
1426 modelling (with fuzzy and compound locations). See
1427 Bio::LocationI and the modules under Bio/Location. Added
1428 support in Genbank/EMBL format parsing to completely parse
1429 feature tables for complex locations.
1431 o Moved special support for databanks etc to specialized modules under
1432 Bio/Seq/. One of these supports very large sequences through
1433 a temporary file as a backend.
1435 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1436 CDS retrieval and exon shuffling.
1438 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1440 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1441 DB/GDB (the latter has platform-specific limitations).
1443 o New analysis parser framework for HT sequence annotation (see
1444 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1446 o New Alignment IO framework
1448 o New Index modules (Swissprot)
1450 o New modules for running Blast within perl
1451 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1452 Multiple Sequence Alignment tools ClustalW and TCoffee
1453 (Bio::Tools::Run::Alignment).
1455 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1456 documentation across the package.
1458 o Much improved cross platform support. Many known incompatibilities
1459 have been fixed; however, NT and Mac do not work across the entire
1460 setup (see PLATFORMS).
1462 o Many bug fixes, code restructuring, etc. Overall stability and
1463 maintainability benefit a lot.
1465 o A total of 957 automatic tests
1468 0.6.2
1470 There are very few functionality changes but a large
1471 number of software improvements/bug fixes across the package.
1473 o The EMBL/GenBank parsing are improved.
1475 o The Swissprot reading is improved. Swissprot writing
1476 is disabled as it doesn't work at all. This needs to
1477 wait for 0.7 release
1479 o BLAST reports with no hits are correctly parsed.
1481 o Several other bugs of the BLAST parser (regular expressions, ...)
1482 fixed.
1484 o Old syntax calls have been replaced with more modern syntax
1486 o Modules that did not work at all, in particular the Sim4
1487 set have been removed
1489 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1490 have improved compliance with interface specs and documentation
1492 o Mailing list documentation updated throughout the distribution
1494 o Most minor bug fixes have happened.
1496 o The scripts in /examples now work and have the modern syntax
1497 rather than the deprecated syntax
1500 0.6.1 Sun April 2 2000
1502 o Sequences can have Sequence Features attached to them
1503 - The sequence features can be read from or written to
1504 EMBL and GenBank style flat files
1506 o Objects for Annotation, including References (but not
1507 full medline abstracts), Database links and Comments are
1508 provided
1510 o A Species object to represent nodes on a taxonomy tree
1511 is provided
1513 o The ability to parse HMMER and Sim4 output has been added
1515 o The Blast parsing has been improved, with better PSI-BLAST
1516 support and better overall behaviour.
1518 o Flat file indexed databases provide both random access
1519 and sequential access to their component sequences.
1521 o A CodonTable object has been written with all known
1522 CodonTables accessible.
1524 o A number of new lightweight analysis tools have been
1525 added, such as molecular weight determination.
1527 The 0.6 release also has improved software engineering
1529 o The sequence objects have been rewritten, providing more
1530 maintainable and easier to implement objects. These
1531 objects are backwardly compatible with the 0.05.1 objects
1533 o Many objects are defined in terms of interfaces and then
1534 a Perl implementation has been provided. The interfaces
1535 are found in the 'I' files (module names ending in 'I').
1537 This means that it is possible to wrap C/CORBA/SQL access
1538 as true "bioperl" objects, compatible with the rest of
1539 bioperl.
1541 o The SeqIO system has been overhauled to provide better
1542 processing and perl-like automatic interpretation of <>
1543 over arguments.
1545 o Many more tests have been added (a total of 172 automatic
1546 tests are now run before release).
1550 0.05.1 Tue Jun 29 05:30:44 1999
1551 - Central distribution now requires Perl 5.004. This was
1552 done to get around 5.003-based problems in Bio/Index/*
1553 and SimpleAlign.
1554 - Various bug fixes in the Bio::Tools::Blast modules
1555 including better exception handling and PSI-Blast
1556 support. See Bio/Tools/Blast/CHANGES for more.
1557 - Fixed the Parse mechanism in Seq.pm to use readseq.
1558 Follow the instructions in README for how to install
1559 it (basically, you have to edit Parse.pm).
1560 - Improved documentation of Seq.pm, indicating where
1561 objects are returned and where strings are returned.
1562 - Fixed uninitialized warnings in Bio::Root::Object.pm
1563 and Bio::Tools::SeqPattern.pm.
1564 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1566 0.05 Sun Apr 25 01:14:11 1999
1567 - Bio::Tools::Blast modules have less memory problems
1568 and faster parsing. Webblast uses LWP and supports
1569 more functionality. See Bio/Tools/Blast/CHANGES for more.
1570 - The Bio::SeqIO system has been started, moving the
1571 sequence reformatting code out of the sequence object
1572 - The Bio::Index:: system has been started, providing
1573 generic index capabilities and specifically works for
1574 Fasta formatted databases and EMBL .dat formatted
1575 databases
1576 - The Bio::DB:: system started, providing access to
1577 databases, both via flat file + index (see above) and
1578 via http to NCBI
1579 - The scripts/ directory, where industrial strength scripts
1580 are put has been started.
1581 - Many changes - a better distribution all round.
1583 0.04.4 Wed Feb 17 02:20:13 1999
1584 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1585 (see Bio::Tools::Blast::CHANGES).
1586 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1587 - Beefed up the t/Fasta.t test script.
1588 - Small fix in Bio::Seq::type() (now always returns a string).
1589 - Changed Bio::Root::Utilities::get_newline_char() to
1590 get_newline() since it could return more than one char.
1591 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1592 - Changed default timeout to 20 seconds (was 3).
1593 - Moved lengthy modification notes to the bottom of some files.
1594 - Fixed SimpleAlign write_fasta bug.
1595 - Beefed up SimpleAlign.t test
1597 0.04.3 Thu Feb 4 07:48:53 1999
1598 - Bio::Root::Object.pm and Global.pm now detect when
1599 script is run as a CGI and suppress output that is only
1600 appropriate when running interactively.
1601 - Bio::Root::Err::_set_context() adds name of script ($0).
1602 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1603 regarding the use of the static objects via the qw(:obj) tag.
1604 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1605 CORE::reverse, avoiding Perl warnings.
1606 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1607 example scripts (see Bio::Tools::Blast::CHANGES).
1608 - examples/seq/seqtools.pl no longer always warns about using
1609 -prot or -nucl command-line arguments; only when using the
1610 -debug argument.
1611 - Methods added to Bio::Root::Utilities: create_filehandle(),
1612 get_newline_char(), and taste_file() to generalize filehandle
1613 creation and autodetect newline characters in files/streams
1614 (see bug report #19).
1615 - Bio::Root::IOManager::read() now handles timeouts and uses
1616 Utilities::create_filehandle().
1617 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1618 of hardwiring in "\n".
1619 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1621 0.04.2 Wed Dec 30 02:27:36 1998
1622 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1623 (see Bio::Tools::Blast::CHANGES).
1624 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1625 to CORE::reverse (prevents ambiguous warnings with 5.005).
1626 - Appending '.tmp.bioperl' to temporary files created by
1627 Bio::Root::Utilities::compress() or uncompress() to
1628 make it easy to identify & cleanup these files as needed.
1629 - Developers: Created CVS branch release-0-04-bug from
1630 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1631 be sure to cvs checkout this branch into a clean area.
1633 0.04.1 Wed Dec 16 05:39:15 1998
1634 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1635 (see Bio::Tools::Blast::CHANGES).
1636 - Compile/SW/Makefile.PL now removes *.o and *.a files
1637 with make clean.
1639 0.04 Tue Dec 8 07:49:19 1998
1640 - Lots of new modules added including:
1641 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1642 and Bio/Compile directory containing XS-linked C code for
1643 creating Smith-Waterman sequence alignments from within Perl.
1644 * Steve Chervitz's Blast distribution has been incorporated.
1645 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1646 - Bio/examples directory for demo scripts for all included modules.
1647 - Bio/t directory containing test suit for all included modules.
1648 - For changes specific to the Blast-related modules prior to
1649 incorporation in this central distribution, see the CHANGES
1650 file in the Bio/Tools/Blast directory.
1652 0.01 Tue Sep 8 14:23:22 1998
1653 - original version from central CVS tree; created by h2xs 1.18