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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 1.6.901 May 3, 2011
22 * Minor bug fix release
23 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
24 * Address Build.PL issues when DBI is not present [hartzell]
25 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
26 * Remove deprecated code for impending perl 5.14.0 release [cjfields]
27 * Due to schema changes and lack of support for older versions, support
28 for NeXML 0.9 is only (very) partially implemented.
29 See: https://redmine.open-bio.org/issues/3207
31 1.6.900 April 14, 201
33 [Notes]
35 * This will probably be the last release to add significant features to
36 core modules; subsequent releases will be for bug fixes alone.
37 We are planning on a restructuring of core for summer 2011, potentially
38 as part of the Google Summer of Code. This may become BioPerl 2.0.
39 * Version bump represents 'just prior to v 1.7'. We may have point
40 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
41 This code essentially is what is on the github master branch.
43 [New features]
45 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
46 * Bio::Tree refactor
47 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
48 - removal of Scalar::Util::weaken code, which was causing odd headaches
49 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
50 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
51 many others]
52 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
53 [Warren Kretzschmar]
54 * Bio::SeqIO::gbxml
55 - bug 2515 - new contribution [Ryan Golhar, jhannah]
56 * Bio::Assembly::IO
57 - support for reading Maq, Sam and Bowtie files [maj]
58 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
59 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
60 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
61 - bug 2726: reading/writing granularity: whole scaffold or one contig
62 at a time [Joshua Udall, fangly]
63 * Bio::OntologyIO
64 - Added parsing of xrefs to OBO files, which are stored as secondary
65 dbxrefs of the cvterm [Naama Menda]
66 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
67 * PAML code updated to work with PAML 4.4d [DaveMessina]
69 [Bug fixes]
71 * [3198] - sort tabular BLAST hits by score [DaveMessina]
72 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
73 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
74 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
75 [cjfields]
76 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
77 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
78 * [3164] - TreeFunctionsI syntax bug [gjuggler]
79 * [3163] - AssemblyIO speedup [fangly]
80 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
81 hyphaltip]
82 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
83 * [3158] - fix EMBL file mis-parsing [cjfields]
84 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
85 cjfields]
86 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
87 * [3148] - URL change for UniProt [cjfields]
88 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
89 * [3136] - HMMer3 parser fixes [kblin]
90 * [3126] - catch description [Toshihiko Akiba]
91 * [3122] - Catch instances where non-seekable filehandles were being
92 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
93 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
94 [dukeleto, rbuels, cjfields]
95 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
96 jhannah]
97 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
98 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
99 cjfields]
100 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
101 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
102 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
103 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
104 * [3086] - EMBL misparsing long tags [kblin, cjfields]
105 * [3085] - CommandExts and array of files [maj, hyphaltip]
106 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
107 for alignment slices [Ha X. Dang, cjfields]
108 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
109 * [3073] - fix parsing of GenBank files from RDP [cjfields]
110 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
111 * [3064] - All-gap midline BLAST report issues [cjfields]
112 * [3063] - BLASt report RID [Razi Khaja, cjfields]
113 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
114 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
115 * [3039] - correct Newick output root node branch length [gjuggler,
116 DaveMessina]
117 * [3038] - SELEX alignment error [Bernd, cjfields]
118 * [3033] - PrimarySeq ID setting [Bernd, maj]
119 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
120 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
121 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
122 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
123 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
124 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
125 PAML 4.4d [DaveMessina]
126 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
127 DaveMessina]
128 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
129 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
130 * [3017] - using threads with Bio::DB::GenBank [cjfields]
131 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
132 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
133 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
134 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
135 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
136 cjfields]
137 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
138 * [2977] - TreeIO issues [DaveMessina]
139 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
140 * [2944] - Bio::Tools::GFF score [cjfields]
141 * [2942] - correct MapTiling output [maj]
142 * [2939] - PDB residue insertion codes [John May, maj]
143 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
144 * [2928] - GuessSeqFormat raw [maj]
145 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
146 * [2922] - open() directive issue [cjfields]
147 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
148 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
149 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
150 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
151 cjfields]
152 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
153 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
154 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
155 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
156 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
157 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
158 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
159 * [2758] - Bio::AssemblyIO ace problems [fangly]
160 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
161 * [2726] - ace file IO [Josh, fangly]
162 * [2700] - Refactor Build.PL [cjfields]
163 * [2673] - addition of simple Root-based clone() method [cjfields]
164 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
165 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
166 * [2594] - Bio::Species memory leak [cjfields]
167 * [2515] - GenBank XML parser [jhannah]
168 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
169 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
170 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
171 cjfields]
172 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
174 [Deprecated]
176 * Bio::Expression modules - these were originally designed to go with the
177 bioperl-microarray suite of tools, however they have never been completed
178 and so have been removed from the distribution. The original code has
179 been moved into the inactive bioperl-microarray suite. [cjfields]
181 [Other]
183 * Repository moved from Subversion (SVN) to
184 http://github.com/bioperl/bioperl-live [cjfields]
185 * Bug database has moved to Redmine (https://redmine.open-bio.org)
186 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
187 Thieme have been moved to their own distribution (Bio-Microarray).
188 [cjfields]
190 1.6.1 Sept. 29, 2009 (point release)
191 * No change from last alpha except VERSION and doc updates [cjfields]
193 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
194 * Fix for silent OBDA bug related to FASTA validation [cjfields]
196 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
197 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
198 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
199 [cjfields]
200 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
202 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
203 * WinXP test fixes [cjfields, maj]
204 * BioPerl.pod added for descriptive information, fixes CPAN indexing
205 [cjfields]
206 * Minor doc fixes [cjfields]
208 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
209 * Fix tests failing due to merging issues [cjfields]
210 * More documentation updates for POD parsing [cjfields]
212 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
213 * Bio::Root::Build
214 - fix YAML meta data generation [cjfields]
216 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
217 * Bio::Align::DNAStatistics
218 - fix divide by zero problem [jason]
219 * Bio::AlignIO::*
220 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
221 * Bio::AlignIO::stockholm
222 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
223 * Bio::Assembly::Tools::ContigSpectrum
224 - function to score contig spectrum [fangly]
225 * Bio::DB::EUtilities
226 - small updates [cjfields]
227 * Bio::DB::Fasta
228 - berkeleydb database now autoindexes wig files and locks correctly
229 [lstein]
230 * Bio::DB::HIV
231 - various small updates for stability; tracking changes to LANL
232 database interface [maj]
233 * Bio::DB::SeqFeature (lots of updates and changes)
234 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
235 - bug 2835 - patch [Dan Bolser]
236 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
237 * Bio::DB::SwissProt
238 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
239 * Bio::Factory::FTLocationFactory
240 - mailing list bug fix [cjfields]
241 * Bio::LocatableSeq
242 - performance work on column_from_residue_number [hartzell]
243 * Bio::Matrix::IO::phylip
244 - bug 2800 - patch to fix phylip parsing [Wei Zou]
245 * Bio::Nexml
246 - Google Summer of Code project from Chase Miller - parsers for Nexml
247 file format [maj, chmille4]
248 * Bio::PopGen
249 - Make Individual, Population, Marker objects AnnotatableI [maj]
250 - simplify LD code [jason]
251 * Bio::RangeI
252 - deal with empty intersection [jason]
253 * Bio::Restriction
254 - significant overhaul of Bio::Restriction system: complete support for
255 external and non-palindromic cutters. [maj]
256 * Bio::Root::Build
257 - CPANPLUS support, no automatic installation [sendu]
258 * Bio::Root::IO
259 - allow IO::String (regression fix) [cjfields]
260 - catch unintentional undef values [cjfields]
261 - throw if non-fh is passed to -fh [maj]
262 * Bio::Root::Root/RootI
263 - small debugging and core fixes [cjfields]
264 * Bio::Root::Test
265 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
266 * Bio::Root::Utilities
267 - bug 2737 - better warnings [cjfields]
268 * Bio::Search
269 - tiling completely refactored, HOWTO added [maj]
270 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
271 will deprecate usage of the older tiling code in the next BioPerl
272 release
273 - small fixes [cjfields]
274 * Bio::SearchIO
275 - Infernal 1.0 output now parsed [cjfields]
276 - new parser for gmap -f9 output [hartzell]
277 - bug 2852 - fix infinite loop in some output [cjfields]
278 - blastxml output now passes all TODO tests [cjfields]
279 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
280 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
281 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
282 * Bio::Seq::LargePrimarySeq
283 - delete tempdirs [cjfields]
284 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
285 * Bio::Seq::Quality
286 - extract regions based on quality threshold value [Dan Bolser, heikki]
287 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
288 * Bio::SeqFeature::Lite
289 - various Bio::DB::SeqFeature-related fixes [lstein]
290 * Bio::SeqFeature::Tools::TypeMapper
291 - additional terms for GenBank to SO map [scain]
292 * Bio::SeqIO::chadoxml
293 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
294 * Bio::SeqIO::embl
295 - support for CDS records [dave_messina, Sylvia]
296 * Bio::SeqIO::fastq
297 - complete refactoring to handle all FASTQ variants, perform validation,
298 write output. API now conforms with other Bio* parsers and the rest of
299 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
300 [cjfields]
301 * Bio::SeqIO::genbank
302 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
303 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
304 * Bio::SeqIO::largefasta
305 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
306 * Bio::SeqIO::raw
307 - add option for 'single' and 'multiple'
308 * Bio::SeqIO::scf
309 - bug 2881 - fix scf round-tripping [Adam Sj¿gren]
310 * Bio::SeqUtils
311 - bug 2766, 2810 - copy over tags from features, doc fixes [David
312 Jackson]
313 * Bio::SimpleAlign
314 - bug 2793 - patch for add_seq index issue [jhannah, maj]
315 - bug 2801 - throw if args are required [cjfields]
316 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
317 [Tristan Lefebure, maj]
318 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
319 - fix POD and add get_SeqFeatures filter [maj]
320 * Bio::Tools::dpAlign
321 - add support for LocatableSeq [ymc]
322 - to be moved to a separate distribution [cjfields, rbuels]
323 * Bio::Tools::EUtilities
324 - fix for two bugs from mail list [Adam Whitney, cjfields]
325 - add generic ItemContainerI interface for containing same methods
326 [cjfields]
327 * Bio::Tools::HMM
328 - fix up code, add more warnings [cjfields]
329 - to be moved to a separate distribution [cjfields, rbuels]
330 * Bio::Tools::Primer3
331 - bug 2862 - fenceposting issue fixed [maj]
332 * Bio::Tools::Run::RemoteBlast
333 - tests for remote RPS-BLAST [mcook]
334 * Bio::Tools::SeqPattern
335 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
336 * Bio::Tools::tRNAscanSE
337 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
338 * Bio::Tree::*
339 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
340 * Bio::Tree::Statistics
341 - several methods for calculating Fitch-based score, internal trait
342 values, statratio(), sum of leaf distances [heikki]
343 * Bio::Tree::Tree
344 - bug 2869 - add docs indicating edge case where nodes can be
345 prematurely garbage-collected [cjfields]
346 - add as_text() function to create Tree as a string in specified format
347 [maj]
348 * Bio::Tree::TreeFunctionsI
349 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
350 Lefebure, maj]
351 * Bio::TreeIO::newick
352 - fix small semicolon issue [cjfields]
353 * scripts
354 - update to bp_seqfeature_load for SQLite [lstein]
355 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
356 - fastam9_to_table - fix for MPI output [jason]
357 - gccalc - total stats [jason]
358 * General Stuff
359 - POD cleanup re: FEEDBACK section [maj, cjfields]
360 - cleanup or fix dead links [cjfields]
361 - Use of no_* methods (indicating 'number of something') is deprecated
362 in favor of num_* [cjfields]
363 - lots of new tests for the above bugs and refactors [everyone!]
364 - new template for Komodo text editor [cjfields]
366 1.6.0 Winter 2009
367 * Feature/Annotation rollback
368 - Problematic changes introduced prior to the 1.5 release have been
369 rolled back. These changes led to subtle bugs involving operator
370 overloading and interface methods.
371 - Behavior is very similar to that for BioPerl 1.4, with tag values
372 being stored generically as simple scalars. Results in a modest
373 speedup.
374 * Bio::Graphics
375 - Split into a separate distribution on CPAN, primarily so development
376 isn't reliant on a complete BioPerl release.
377 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
378 is only available via Subversion (via bioperl-live main trunk)
379 * Bio::Root::Test
380 - Common test bed for all BioPerl modules
381 * Bio::Root::Build
382 - Common Module::Build-based subclass for all BioPerl modules
383 * Bio::DB::EUtilities
384 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
385 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
386 and user agent request posting and retrieval
387 * Test implementation and reorganization
388 - Tests have been reorganized into groups based on classes or use
389 cases.
390 - Automated test coverage is now online:
391 http://www.bioperl.org/wiki/Test_Coverage
392 - After this release, untested modules will be moved into a
393 separate developer distribution until tests can be derived.
394 Also, new modules to be added are expected to have a test suite
395 and adequate test coverage.
397 1.5.2 Developer release
399 Full details of changes since 1.5.1 are available online at:
400 http://www.bioperl.org/wiki/Change_log
401 The following represents a brief overview of the most important changes.
403 o Bio::Map
404 - Overhaul. Brand new system fully allows markers to have multiple
405 positions on multiple maps, and to have relative positions. Should be
406 backward compatible.
408 o Bio::Taxonomy
409 - This module and all the modules in the Taxonomy directory now
410 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
412 o Bio::DB::Taxonomy
414 - Taxonomy.pm
415 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
417 * New methods ancestor(), each_Descendent() and _handle_internal_id().
419 * Allows for different database modules to create Bio::Taxon objects
420 with the same internal id when the same taxon is requested from each.
422 - flatfile.pm
423 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
425 * No longer includes the fake root node 'root'; there are multiple roots
426 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
428 - entrez.pm
429 * get_node() has new option -full
431 * Caches data retrieved from website
433 o Bio::Species
434 - Now a Bio::Taxon. Carries out the species name -> specific name munging
435 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
436 backward compatability in species() method.
438 o Bio::Search and Bio::SearchIO
439 - Overhaul. The existing system has been sped up via some minor changes
440 (mostly gain-of-function to the API). Bio::PullParserI is introduced
441 as a potential eventual replacment for the existing system, though as
442 yet only a Hmmpfam parser exists written using it.
445 1.5.1 Developer release
447 o Major problem with how Annotations were written out with
448 Bio::Seq is fixed by reverting to old behavior for
449 Bio::Annotation objects.
451 o Bio::SeqIO
453 - genbank.pm
454 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
455 expect at l east 9 spaces at the beginning of a line to
456 indicate line wrapping.
458 * Treat multi-line SOURCE sections correctly, this defect broke
459 both common_name() and classification()
461 * parse swissprot fields in genpept file
463 * parse WGS genbank records
465 - embl.pm
466 * Changed regexp for ID line. The capturing parentheses are
467 the same, the difference is an optional repeated-not-semi-
468 colon expression following the captured \S+. This means the
469 regexp works when the division looks like /PRO;/ or when the
470 division looks like /ANG ;/ - the latter is from EMBL
471 repbase
473 * fix ID line parsing: the molecule string can have spaces in
474 it. Like: "genomic DNA"
476 - swiss.pm: bugs #1727, #1734
478 - entrezgene.pm
479 * Added parser for entrezgene ASN1 (text format) files.
480 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
482 o Bio::AlignIO
484 - maf.pm coordinate problem fixed
486 o Bio::Taxonomy and Bio::DB::Taxonomy
488 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
489 can be done via Web without downloading all the sequence.
491 o Bio::Tools::Run::RemoteBlast supports more options and complies
492 to changes to the NCBI interface. It is reccomended that you
493 retrieve the data in XML instead of plain-text BLAST report to
494 insure proper parsing and retrieval of all information as NCBI
495 fully expects to change things in the future.
497 o Bio::Tree and Bio::TreeIO
499 - Fixes so that re-rooting a tree works properly
501 - Writing out nhx format from a newick/nexus file will properly output
502 bootstrap information. The use must move the internal node labels over
503 to bootstraps.
504 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
505 $node->bootstrap($node->id);
506 $node->id('');
507 }
508 - Nexus parsing is much more flexible now, does not care about
509 LF.
511 - Cladogram drawing module in Bio::Tree::Draw
513 - Node height and depth now properly calculated
515 - fix tree pruning algorithm so that node with 1 child gets merged
517 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
518 bugs and improvements were added, see Gbrowse mailing list for most of
519 these.
521 o Bio::DB::GFF partially supports GFF3. See information about
522 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
524 o Better location parsing in Bio::Factory::FTLocationFactory -
525 this is part of the engine for parsing EMBL/GenBank feature table
526 locations. Nested join/order-by/complement are allowed now
528 o Bio::PrimarySeqI->translate now takes named parameters
530 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
531 reconstruction) is now supported. Parsing different models and
532 branch specific parametes are now supported.
534 o Bio::Factory::FTLocationFactory - parse hierarchical locations
535 (joins of joins)
537 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
538 for getter/setter functions
540 o Bio::SearchIO
542 - blast bug #1739; match scientific notation in score
543 and possible e+ values
545 - blast.pm reads more WU-BLAST parameters and parameters, match
546 a full database pathname,
548 - Handle NCBI WEB and newer BLAST formats specifically
549 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
551 - psl off-by-one error fixed
553 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
554 and HSPs can be constructed from them.
556 - HSPs query/hit now have a seqdesc field filled out (this was
557 always available via $hit->description and
558 $result->query_description
560 - hmmer.pm can parse -A0 hmmpfam files
562 - Writer::GbrowseGFF more customizeable.
564 o Bio::Tools::Hmmpfam
565 make e-value default score displayed in gff, rather than raw score
566 allow parse of multiple records
569 1.5 Developer release
571 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
572 provide Jukes-Cantor and Kimura pairwise distance methods,
573 respectively.
575 o Bio::AlignIO support for "po" format of POA, and "maf";
576 Bio::AlignIO::largemultifasta is a new alternative to
577 Bio::AlignIO::fasta for temporary file-based manipulation of
578 particularly large multiple sequence alignments.
580 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
581 be treated similarly as an assembled contig.
583 o Bio::CodonUsage provides new rare_codon() and probable_codons()
584 methods for identifying particular codons that encode a given
585 amino acid.
587 o Bio::Coordinate::Utils provides new from_align() method to build
588 a Bio::Coordinate pair directly from a
589 Bio::Align::AlignI-conforming object.
591 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
592 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
593 web service using standard Pubmed query syntax, and retrieve
594 results as XML.
596 o Bio::DB::GFF has various sundry bug fixes.
598 o Bio::FeatureIO is a new SeqIO-style subsystem for
599 writing/reading genomic features to/from files. I/O classes
600 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
601 classes only read/write Bio::SeqFeature::Annotated objects.
602 Notably, the GFF v3 class requires features to be typed into the
603 Sequence Ontology.
605 o Bio::Graph namespace contains new modules for manipulation and
606 analysis of protein interaction graphs.
608 o Bio::Graphics has many bug fixes and shiny new glyphs.
610 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
611 indexing for HMMER reports and FASTA qual files, respectively.
613 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
614 new objects that can be placed within a Bio::Map::MapI-compliant
615 genetic/physical map; Bio::Map::Physical provides a new physical
616 map type; Bio::MapIO::fpc provides finger-printed clone mapping
617 import.
619 o Bio::Matrix::PSM provide new support for postion-specific
620 (scoring) matrices (e.g. profiles, or "possums").
622 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
623 be instantiated without explicitly using Bio::OntologyIO. This
624 is possible through changes to Bio::Ontology::OntologyStore to
625 download ontology files from the web as necessary. Locations of
626 ontology files are hard-coded into
627 Bio::Ontology::DocumentRegistry.
629 o Bio::PopGen includes many new methods and data types for
630 population genetics analyses.
632 o New constructor to Bio::Range, unions(). Given a list of
633 ranges, returns another list of "flattened" ranges --
634 overlapping ranges are merged into a single range with the
635 mininum and maximum coordinates of the entire overlapping group.
637 o Bio::Root::IO now supports -url, in addition to -file and -fh.
638 The new -url argument allows one to specify the network address
639 of a file for input. -url currently only works for GET
640 requests, and thus is read-only.
642 o Bio::SearchIO::hmmer now returns individual Hit objects for each
643 domain alignment (thus containing only one HSP); previously
644 separate alignments would be merged into one hit if the domain
645 involved in the alignments was the same, but this only worked
646 when the repeated domain occured without interruption by any
647 other domain, leading to a confusing mixture of Hit and HSP
648 objects.
650 o Bio::Search::Result::ResultI-compliant report objects now
651 implement the "get_statistics" method to access
652 Bio::Search::StatisticsI objects that encapsulate any
653 statistical parameters associated with the search (e.g. Karlin's
654 lambda for BLAST/FASTA).
656 o Bio::Seq::LargeLocatableSeq combines the functionality already
657 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
659 o Bio::SeqFeature::Annotated is a replacement for
660 Bio::SeqFeature::Generic. It breaks compliance with the
661 Bio::SeqFeatureI interface because the author was sick of
662 dealing with untyped annotation tags. All
663 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
664 compliant, and accessible through Bio::Annotation::Collection.
666 o Bio::SeqFeature::Primer implements a Tm() method for primer
667 melting point predictions.
669 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
670 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
672 o Bio::Taxonomy::Node now implements the methods necessary for
673 Bio::Species interoperability.
675 o Bio::Tools::CodonTable has new reverse_translate_all() and
676 make_iupac_string() methods.
678 o Bio::Tools::dpAlign now provides sequence profile alignments.
680 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
682 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
683 parsers.
685 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
686 for designing small inhibitory RNA.
688 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
689 methods based on a distance matrix.
691 o Bio::Tree::Statistics provides an assess_bootstrap() method to
692 calculate bootstrap support values on a guide tree topology,
693 based on provided bootstrap tree topologies.
695 o Bio::TreeIO now supports the Pagel (PAG) tree format.
697 1.4 branch
699 1.4.1
701 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
703 o Bio::Graphics will work with gd1 or gd2
705 o Bio::SearchIO
706 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
707 (RF lines alone)
708 - blast.pm Parse multi-line query fields properly
709 - small speed improvements to blasttable.pm and others
711 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
712 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
713 supporting more complex queries
716 1.4. Stable major release
718 Since initial 1.2.0, 3000 separate changes have been made to make this release.
720 o installable scripts
722 o global module version from Bio::Root:Version
724 o Bio::Graphics
725 - major improvements; SVG support
727 o Bio::Popgen
728 - population genetics
729 - support several population genetics types of questions.
730 - Tests for statistical neutrality of mutations
731 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
732 Tests of population structure (Wright's F-statistic: Fst) is in
733 Bio::PopGen::PopStats. Calculating composite linkage
734 disequilibrium (LD) is available in Bio::PopGen::Statistics as
735 well.
736 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
737 and csv (comma delimited formatted) data.
739 - a directory for implementing population simulations has
740 been added Bio::PopGen::Simulation and 2 simulations - a
741 Coalescent and a simple single-locus multi-allele genetic drift
742 simulation have been provided. This replaces the code in
743 Bio::Tree::RandomTree which has been deprecated until proper
744 methods for generating random phylogenetic trees are
745 implemented.
747 o Bio::Restriction
748 - new restrion analysis modules
750 o Bio::Tools::Analysis
751 - web based DNA and Protein analysis framework and several
752 implementations
754 o Bio::Seq::Meta
755 - per residue annotable sequences
757 o Bio::Matrix
758 - Bio::Matrix::PSM - Position Scoring Matrix
759 - Bio::Matrix::IO has been added for generalized parsing of
760 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
761 initial implementations for parsing BLOSUM/PAM and Phylip
762 Distance matricies respectively. A generic matrix
763 implementation for general use was added in
764 Bio::Matrix::Generic.
766 o Bio::Ontology
767 - major changes
769 o Bio:Tree
771 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
772 - small inhibitory RNA
774 o Bio::SeqFeature::Tools
775 - seqFeature mapping tools
776 - Bio::SeqFeature::Tools::Unflattener.pm
777 -- deal with mapping GenBank feature collections into
778 Chado/GFF3 processable feature sets (with SO term mappings)
780 o Bio::Tools::dpAlign
781 - pure perl dynamic programming sequence alignment
782 - needs Bioperl-ext
784 o new Bio::SearchIO formats
785 - axt and psl: UCSC formats.
786 - blasttable: NCBI -m 8 or -m 9 format from blastall
788 o new Bio::SeqIO formats
789 - chado, tab, kegg, tigr, game
790 - important fixes for old modules
792 o Bio::AlignIO: maf
794 o improved Bio::Tools::Genewise
796 o Bio::SeqIO now can recongnize sequence formats automatically from
797 stream
799 o new parsers in Bio::Tools:
800 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
802 o Bio::DB::Registry bugs fixed
803 - BerkeleyDB-indexed flat files can be used by the OBDA system
804 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
805 used by the OBDA system
807 o several new HOWTOs
808 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
809 Databases
811 o hundreds of new and improved files
814 o
815 o Bio::Tree::AlleleNode has been updated to be a container of
816 an Bio::PopGen::Individual object for use in the Coalescent simulations.
819 1.2 Branch
821 1.2.3 Stable release update
822 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
823 handling.
824 o Bug #1477 - Sel --> Sec abbreviation fixed
825 o Fix bug #1487 where paring in-between locations when
826 end < start caused the FTLocationFactory logic to fail.
827 o Fix bug #1489 which was not dealing with keywords as an
828 arrayref properly (this is fixed on the main trunk because
829 keywords returns a string and the array is accessible via
830 get_keywords).
831 o Bio::Tree::Tree memory leak (bug #1480) fixed
832 Added a new initialization option -nodelete which
833 won't try and cleanup the containing nodes if this
834 is true.
835 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
836 this was only present on the branch for the 1.2.1 and 1.2.2 series
837 - Also merged main trunk changes to the branch which make
838 newick -> nhx round tripping more effective (storing branch length
839 and bootstrap values in same locate for NodeNHX and Node
840 implementations.) Fixes to TreeIO parsing for labeled internal
841 also required small changes to TreeIO::nhx. Improved
842 tests for this module as well.
843 o Bio::SearchIO
844 - Fixed bugs in BLAST parsing which couldn't parse NCBI
845 gapped blast properly (was losing hit significance values due to
846 the extra unexpeted column).
847 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
848 integer overflow (# of letters in nt seq dbs is > MAX_INT)
849 although doesn't try to correct it - will get the negative
850 number for you. Added a test for this as well.
851 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
852 has no top-level family classification scores but does have scores and
853 alignments for individual domains.
854 - Parsing FASTA reports where ungapped percent ID is < 10 and the
855 regular expression to match the line was missing the possibility of
856 an extra space. This is rare, which is why we probably did not
857 catch it before.
858 - BLAST parsing picks up more of the statistics/parameter fields
859 at the bottom of reports. Still not fully complete.
860 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
861 were fixed to include many improvements and added flexiblity
862 in outputting the files. Bug #1495 was also fixed in the process.
863 o Bio::DB::GFF
864 - Update for GFF3 compatibility.
865 - Added scripts for importing from UCSC and GenBank.
866 - Added a 1.2003 version number.
867 o Bio::Graphics
868 - Updated tutorial.
869 - Added a 1.2003 version number.
870 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
871 properly writing keywords out.
872 o Bio::SeqIO::genbank
873 - Fixed bug/enhancement #1513 where dates of
874 the form D-MMM-YYYY were not parsed. Even though this is
875 invalid format we can handle it - and also cleanup the date
876 string so it is properly formatted.
877 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
878 and written with Genbank format. Similarly bug #1515 is fixed to
879 parse in the ORIGIN text.
880 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
881 to specify the ID type, one of (accession accession.version
882 display primary). See Bio::SeqIO::preferred_id_type method
883 documentation for more information.
884 o Unigene parsing updated to handle file format changes by NCBI
886 1.2.2 Stable release update
888 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
889 - auto-discover ontology name
890 - bug in parsing relationships when certain characters are in the term
891 - fixed hard-coded prefix for term identifiers
892 - various smaller issues
894 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
895 of Bio::Ontology::TermI
897 o brought the OBDA Registry code up to latest specs
899 o Bio::DB::GenBank
900 - eutils URL change
901 - accession number retrieval fixed
903 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
905 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
906 #1459 which now properly report alignment start/end info
907 for translated BLAST/FASTA searches.
909 o Bio::TreeIO::newick can parse labeled internal nodes
911 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
912 for BLASTX if if you provide -report_type => 'BLASTX' when
913 initializing a BPbl2seq object. Bioperl 1.3 will have better
914 support for bl2seq in the SearchIO system.
916 o Bio::Root::IO support a -noclose boolean flag which will not
917 close a filehandle upon object cleanup - useful when sharing
918 a filehandle among objects. Additionally code added s.t.
919 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
921 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
923 o Bio::SeqIO::genbank
924 - bug #1456 fixed which generated extra sequence lines
925 - write moltype correctly for genpept
927 1.2.1 Stable release update
929 o Inclusion of WrapperBase, a needed component for StandAloneBlast
931 o Addition from main trunk of Ontology objects, principly to allow
932 BioSQL releases against 1.2.1
934 o Fixes and cleanup of Bio::Coordinate modules
936 o A fix to Bio::Index::EMBL allowing retrieval of entries using
937 the primary accession number
939 o Other bug fixes, including bpindex GenBank fix
941 o Bio::SeqIO::genbank bug #1389 fixed
943 1.2 Stable major release
945 o More functionality added to Bio::Perl, the newbie module
947 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
948 Support for New Hampshire Extended (NHX) format parsing.
950 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
951 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
952 Hmmpfam parser.
954 o New ontology parsing Bio::Ontology
956 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
957 multi-report (mlib) fasta reports, support for waba and exonerate.
959 o Bio::ClusterIO for parsing Unigene clusters
961 o Bio::Assembly added for representing phrap and ace assembly clusters.
963 o Rudimentary support for writing Chado XML (see
964 GMOD project: www.gmod.org for more information)
966 o Bio::Coordinate for mapping between different coordinate systems such
967 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
968 features into different coordinate systems.
970 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
971 with the get_Stream_by_query method and supports the latest
972 NCBI eutils interface.
974 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
975 object for extracting subsets of features : currently only
976 supports extraction by location.
978 1.1.1 Developer release
980 o Deprecated modules are now listed in the DEPRECATED file
982 o New HowTo documents located in doc/howto describing
983 a domain of Bioperl.
985 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
986 and all old bugs are searchable through the bugzilla interface.
988 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
989 have been addressed.
991 o Support for Genewise parsing in Bio::Tools::Genewise
993 o Start of Ontology framework with Bio::Ontology
995 o Speedup to the Bio::Root::Root object method _rearrange.
996 A global _load_module method was implemented to simplify the
997 dynamic loading of modules ala Bio::SeqIO::genbank. This
998 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
999 etc).
1001 o Several performance improvements to sequence parsing in Bio::SeqIO.
1002 Attempt to speedup by reducing object creation overhead.
1004 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1005 method for sequence retrieval with their E-utils CGI scripts.
1006 More work to support Entrez queries to their fullest is planned
1007 before 1.2 release.
1009 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1011 1.1 Developer release
1013 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1014 this separation removes some of the complexity in our test suite
1015 and separates the core modules in bioperl from those that need
1016 external programs to run.
1018 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1019 not run into trouble running the makefile
1021 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1022 read,create,and write locations for grouped/split locations
1023 (like mRNA features on genomic sequence).
1025 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1026 and PAML (codeml,aaml, etc) parsing.
1028 o Bio::Tree:: objects expanded to handle testing monophyly,
1029 paraphyly, least common ancestor, etc.
1031 o Bio::Coordinate for mapping locations from different coordinate spaces
1033 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1034 added for parsing hmmpfam and hmmsearch output.
1036 o Bio::SearchIO::Writer::TextResultWriter for outputting
1037 a pseudo-blast textfile format
1040 1.0.2 Bug fix release
1042 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1043 in this release will not work after December 2002 when NCBI
1044 shuts off the old Entrez cgi scripts. We have already fixed
1045 on our main development branch and the functionality will be
1046 available in the next stable bioperl release (1.2) slated for
1047 Fall 2002.
1049 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1050 testset by Robin Emig. These were fixed as was the get_aln
1051 method in Bio::Search::HSP::GenericHSP to handle the extra
1052 context sequence that is provided with a FastA alignment.
1054 o Migrating differences between Bio::Search::XX::BlastXX to
1055 Bio::Search::XX::GenericXX objects. This included mechanism
1056 to retrieve whole list of HSPs from Hits and whole list of Hits from
1057 Results in addition to the current next_XX iterator methods that
1058 are available. Added seq_inds() method to GenericHSP which identifies
1059 indexes in the query or hit sequences where conserved,identical,gaps,
1060 or mismatch residues are located (adapted from Steve Chervitz's
1061 implementation in BlastHSP).
1063 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1064 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1066 o Bio::Graphics glyph set improved and extended for GBrowse release
1068 o Bio::Tree::Tree get_nodes implementation improvement thanks
1069 to Howard Ross notice performance problem when writing out
1070 unbalanced trees.
1072 o Bio::Location::Fuzzy::new named parameter -loc_type became
1073 -location_type, Bio::Location::Simple::new named parameter
1074 -seqid becamse -seq_id.
1076 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1077 was mis-detecting that gaps should be placed at the beginning of
1078 the alignment when the best alignment starts internally in the
1079 sequence.
1081 1.0.1 Bug fix release
1083 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1085 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1086 and mixed (3.3 - 3.4) versions of FASTA.
1088 o Small API change to add methods for completeness across
1089 implementations of Bio::Search objects. These new methods
1090 in the interface are implemented by the GenericXX object as well
1091 as the BlastXX objects.
1092 * Bio::Search::Result::ResultI
1093 - hits() method returns list of all Hits (next_hit is an
1094 iterator method)
1096 * Bio::Search::Hit::HitI
1097 - hsps() method returns list of all HSPs (next_hsp is an
1098 iterator method)
1100 o The Bio::SearchIO::Writer classes have been fixed to handle results
1101 created from either psiblast (Search::BlastXX objects) or
1102 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1103 has to be done here to make it work properly and will nee major
1104 API changes.
1106 o Bugs in Bio::Tools::HMMER fixed, including
1107 * #1178 - Root::IO destructor wasn't being called
1108 * #1034 - filter_on_cutoff now behaves properly
1110 o Bio::SeqFeature::Computation initialization args fixed and
1111 tests added.
1113 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1115 o Updated FAQ with more example based answers to typical questions
1117 o Bug #1202 was fixed which would improperly join together qual values
1118 parsed by Bio::SeqIO::qual when a trailing space was not present before
1119 the newline.
1121 1.0.0 Major Stable Release
1123 This represents a major release of bioperl with significant
1124 improvements over the 0.7.x series of releases.
1126 o Bio::Tools::Blast is officially deprecated. Please see
1127 Bio::SearchIO for BLAST and FastA parsing.
1129 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1130 Bio::LocationI objects as well as start/end.
1132 o Bio::Biblio contains modules for Bibliographic data.
1133 Bio::DB::Biblio contains the query modules. Additionally one can
1134 parse medlinexml from the ebi bibliographic query service (BQS)
1135 system and Pubmed xml from NCBI. See Martin Senger's
1136 documentation in Bio::Biblio for more information.
1138 o Bio::DB::Registry is a sequence database registry part of
1139 Open Bioinformatics Database Access. See
1140 http://obda.open-bio.org for more information.
1142 o File-based and In-Memory Sequence caching is provided by
1143 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1144 local database.
1146 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1147 been added by Lincoln Stein.
1149 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1151 o A FAQ has been started and is included in the release to provide
1152 a starting point for frequent questions and issues.
1154 0.9.3 Developer's release
1156 o Event based parsing system improved (SearchIO). With parsers for
1157 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1158 Additionally a lazy parsing system for text and html blast reports was
1159 added and is called psiblast (name subject to change in future releases).
1161 o Bio::Search objects improved and standardized with associated Interfaces
1162 written. The concept of a search "Hit" was standardized to be called
1163 "hit" consistently and the use of "subject" was deprecated in all active
1164 modules.
1166 o Bio::Structure added (since 0.9.1) for Protein structure objects
1167 and PDB parser to retrieve and write these structures from data files.
1169 o Several important Bio::DB::GFF bug fixes for handling features that
1170 are mapped to multiple reference points. Updated mysql adaptor
1171 so as to be able to store large (>100 megabase) chunks of DNA into
1172 Bio::DB::GFF databases.
1174 0.9.2 Developer's release
1176 o Bio::Search and Bio::SearchIO system introduced for event based
1177 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1178 in text and XML and FASTA reports in standard output format.
1180 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1181 generator is included in Bio::TreeIO::RandomTrees and a
1182 statistics module for evaluating.
1184 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1185 server for DAS servers.
1187 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1188 files. The entire BPlite system migrated to using Bio::Root::IO
1189 for the data stream.
1191 o Bio::Tools::Alignment for Consed and sequence Trimming
1192 functionality.
1194 o Bio::Structure for Protein structure information and parsing
1196 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1197 cgi-bin entry point which should be more reliable.
1199 o Bio::Map and Bio::MapIO for biological map navigation and a
1200 framework afor parsing them in. Only preliminary work here.
1202 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1203 Future work will integrate Pise and allow submission of analysis on
1204 remote servers.
1206 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1207 introduced as new objects for handling Sequence Annotation
1208 information (dblinks, references, etc) and is more robust that
1209 previous system.
1211 o Bio::Tools::FASTAParser introduced.
1213 o Scripts from the bioperl script submission project and new
1214 scripts from bioperl authors are included in "scripts" directory.
1216 o Factory objects and interfaces are being introduced and are more
1217 strictly enforced.
1219 o Bio::Root::Root introduced as the base object while
1220 Bio::Root::RootI is now simply an interface.
1222 o Bio::DB::RefSeq provides database access to copy of the NCBI
1223 RefSeq database using the EBI dbfetch script.
1225 0.9.0 Developer's release
1227 o perl version at least 5.005 is now required instead of perl 5.004
1229 o Bio::Tools::Run::RemoteBlast is available for running remote
1230 blast jobs at NCBI.
1232 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1234 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1235 Also added are related modules UTR3, UTR5, Exon, Intron,
1236 Promotor, PolyA and Transcript.
1238 o Speedup of translate method in PrimarySeq
1240 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1241 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1243 o Various fixes to Variation toolkit
1245 o Bio::DB::EMBL provides database access to EMBL sequence data.
1246 Bio::DB::Universal provides a central way to point to indexes
1247 and dbs in a single interface.
1249 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1251 o Bio::Factory::EMBOSS is still in design phase as is
1252 Bio::Factory::ApplicationFactoryI
1254 o Dia models for bioperl design are provided in the models/ directory
1256 0.7.2 Bug fix release
1258 o documentation fixes in many modules - SYNOPSIS code verified
1259 to be runnable in many (but not all modules)
1261 o corrected MANIFEST file from 0.7.1 release
1263 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1264 split locations
1266 o Bio::SeqIO::genbank
1267 * Correct parsing and writing of genbank format with protein data
1268 * moltype and molecule separation
1270 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1272 o Bio::SimpleAlign fixed to correctly handle consensus
1273 sequence calculation
1275 o Bio::Tools::HMMER supports hmmer 2.2g
1277 o Bio::Tools::BPlite to support report type specific parsing. Most
1278 major changes are not on the 0.7 branch.
1280 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1281 with File::Spec
1283 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1284 in several types of mutations:
1285 1.) AA level: deletion, complex
1286 2.) AA level: complex, inframe
1287 3.) RNA level: silent
1289 o BPbl2seq parsing of empty reports will not die, but will return
1290 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1291 $report->query() and $report->subject() methods. So an easy
1292 way to test if report was empty is to see if
1293 $report->query->seqname is undefined.
1295 0.7.1 Bug fix release
1297 o Better parsing of genbank/EMBL files especially fixing bugs
1298 related to Feature table parsing and locations on remote
1299 sequences. Additionally, species name parsing was better.
1301 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1302 which include a number of header lines.
1304 o More strict genbank and EMBL format writing (corrected number of
1305 spaces where appropriate).
1307 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1308 for related BPlite BUGS that are unresolved in this release.
1310 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1311 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1312 use expasy mirrors or EBI dbfetch cgi-script.
1314 o A moderate number of documentation improvements were made as
1315 well to provide a better code synopsis in each module.
1318 0.7 Large number of changes, including refactoring of the
1319 Object system, new parsers, new functionality and
1320 all round better system. Highlights are:
1323 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1324 Bio::Root::IO for I/O and file/handle capabilities.
1326 o Imported BPlite modules from Ian Korf for BLAST
1327 parsing. This is considered the supported BLAST parser;
1328 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1330 o Improved Sequence Feature model. Added complete location
1331 modelling (with fuzzy and compound locations). See
1332 Bio::LocationI and the modules under Bio/Location. Added
1333 support in Genbank/EMBL format parsing to completely parse
1334 feature tables for complex locations.
1336 o Moved special support for databanks etc to specialized modules under
1337 Bio/Seq/. One of these supports very large sequences through
1338 a temporary file as a backend.
1340 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1341 CDS retrieval and exon shuffling.
1343 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1345 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1346 DB/GDB (the latter has platform-specific limitations).
1348 o New analysis parser framework for HT sequence annotation (see
1349 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1351 o New Alignment IO framework
1353 o New Index modules (Swissprot)
1355 o New modules for running Blast within perl
1356 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1357 Multiple Sequence Alignment tools ClustalW and TCoffee
1358 (Bio::Tools::Run::Alignment).
1360 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1361 documentation across the package.
1363 o Much improved cross platform support. Many known incompatibilities
1364 have been fixed; however, NT and Mac do not work across the entire
1365 setup (see PLATFORMS).
1367 o Many bug fixes, code restructuring, etc. Overall stability and
1368 maintainability benefit a lot.
1370 o A total of 957 automatic tests
1373 0.6.2
1375 There are very few functionality changes but a large
1376 number of software improvements/bug fixes across the package.
1378 o The EMBL/GenBank parsing are improved.
1380 o The Swissprot reading is improved. Swissprot writing
1381 is disabled as it doesn't work at all. This needs to
1382 wait for 0.7 release
1384 o BLAST reports with no hits are correctly parsed.
1386 o Several other bugs of the BLAST parser (regular expressions, ...)
1387 fixed.
1389 o Old syntax calls have been replaced with more modern syntax
1391 o Modules that did not work at all, in particular the Sim4
1392 set have been removed
1394 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1395 have improved compliance with interface specs and documentation
1397 o Mailing list documentation updated throughout the distribution
1399 o Most minor bug fixes have happened.
1401 o The scripts in /examples now work and have the modern syntax
1402 rather than the deprecated syntax
1405 0.6.1 Sun April 2 2000
1407 o Sequences can have Sequence Features attached to them
1408 - The sequence features can be read from or written to
1409 EMBL and GenBank style flat files
1411 o Objects for Annotation, including References (but not
1412 full medline abstracts), Database links and Comments are
1413 provided
1415 o A Species object to represent nodes on a taxonomy tree
1416 is provided
1418 o The ability to parse HMMER and Sim4 output has been added
1420 o The Blast parsing has been improved, with better PSI-BLAST
1421 support and better overall behaviour.
1423 o Flat file indexed databases provide both random access
1424 and sequential access to their component sequences.
1426 o A CodonTable object has been written with all known
1427 CodonTables accessible.
1429 o A number of new lightweight analysis tools have been
1430 added, such as molecular weight determination.
1432 The 0.6 release also has improved software engineering
1434 o The sequence objects have been rewritten, providing more
1435 maintainable and easier to implement objects. These
1436 objects are backwardly compatible with the 0.05.1 objects
1438 o Many objects are defined in terms of interfaces and then
1439 a Perl implementation has been provided. The interfaces
1440 are found in the 'I' files (module names ending in 'I').
1442 This means that it is possible to wrap C/CORBA/SQL access
1443 as true "bioperl" objects, compatible with the rest of
1444 bioperl.
1446 o The SeqIO system has been overhauled to provide better
1447 processing and perl-like automatic interpretation of <>
1448 over arguments.
1450 o Many more tests have been added (a total of 172 automatic
1451 tests are now run before release).
1455 0.05.1 Tue Jun 29 05:30:44 1999
1456 - Central distribution now requires Perl 5.004. This was
1457 done to get around 5.003-based problems in Bio/Index/*
1458 and SimpleAlign.
1459 - Various bug fixes in the Bio::Tools::Blast modules
1460 including better exception handling and PSI-Blast
1461 support. See Bio/Tools/Blast/CHANGES for more.
1462 - Fixed the Parse mechanism in Seq.pm to use readseq.
1463 Follow the instructions in README for how to install
1464 it (basically, you have to edit Parse.pm).
1465 - Improved documentation of Seq.pm, indicating where
1466 objects are returned and where strings are returned.
1467 - Fixed uninitialized warnings in Bio::Root::Object.pm
1468 and Bio::Tools::SeqPattern.pm.
1469 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1471 0.05 Sun Apr 25 01:14:11 1999
1472 - Bio::Tools::Blast modules have less memory problems
1473 and faster parsing. Webblast uses LWP and supports
1474 more functionality. See Bio/Tools/Blast/CHANGES for more.
1475 - The Bio::SeqIO system has been started, moving the
1476 sequence reformatting code out of the sequence object
1477 - The Bio::Index:: system has been started, providing
1478 generic index capabilities and specifically works for
1479 Fasta formatted databases and EMBL .dat formatted
1480 databases
1481 - The Bio::DB:: system started, providing access to
1482 databases, both via flat file + index (see above) and
1483 via http to NCBI
1484 - The scripts/ directory, where industrial strength scripts
1485 are put has been started.
1486 - Many changes - a better distribution all round.
1488 0.04.4 Wed Feb 17 02:20:13 1999
1489 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1490 (see Bio::Tools::Blast::CHANGES).
1491 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1492 - Beefed up the t/Fasta.t test script.
1493 - Small fix in Bio::Seq::type() (now always returns a string).
1494 - Changed Bio::Root::Utilities::get_newline_char() to
1495 get_newline() since it could return more than one char.
1496 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1497 - Changed default timeout to 20 seconds (was 3).
1498 - Moved lengthy modification notes to the bottom of some files.
1499 - Fixed SimpleAlign write_fasta bug.
1500 - Beefed up SimpleAlign.t test
1502 0.04.3 Thu Feb 4 07:48:53 1999
1503 - Bio::Root::Object.pm and Global.pm now detect when
1504 script is run as a CGI and suppress output that is only
1505 appropriate when running interactively.
1506 - Bio::Root::Err::_set_context() adds name of script ($0).
1507 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1508 regarding the use of the static objects via the qw(:obj) tag.
1509 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1510 CORE::reverse, avoiding Perl warnings.
1511 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1512 example scripts (see Bio::Tools::Blast::CHANGES).
1513 - examples/seq/seqtools.pl no longer always warns about using
1514 -prot or -nucl command-line arguments; only when using the
1515 -debug argument.
1516 - Methods added to Bio::Root::Utilities: create_filehandle(),
1517 get_newline_char(), and taste_file() to generalize filehandle
1518 creation and autodetect newline characters in files/streams
1519 (see bug report #19).
1520 - Bio::Root::IOManager::read() now handles timeouts and uses
1521 Utilities::create_filehandle().
1522 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1523 of hardwiring in "\n".
1524 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1526 0.04.2 Wed Dec 30 02:27:36 1998
1527 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1528 (see Bio::Tools::Blast::CHANGES).
1529 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1530 to CORE::reverse (prevents ambiguous warnings with 5.005).
1531 - Appending '.tmp.bioperl' to temporary files created by
1532 Bio::Root::Utilities::compress() or uncompress() to
1533 make it easy to identify & cleanup these files as needed.
1534 - Developers: Created CVS branch release-0-04-bug from
1535 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1536 be sure to cvs checkout this branch into a clean area.
1538 0.04.1 Wed Dec 16 05:39:15 1998
1539 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1540 (see Bio::Tools::Blast::CHANGES).
1541 - Compile/SW/Makefile.PL now removes *.o and *.a files
1542 with make clean.
1544 0.04 Tue Dec 8 07:49:19 1998
1545 - Lots of new modules added including:
1546 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1547 and Bio/Compile directory containing XS-linked C code for
1548 creating Smith-Waterman sequence alignments from within Perl.
1549 * Steve Chervitz's Blast distribution has been incorporated.
1550 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1551 - Bio/examples directory for demo scripts for all included modules.
1552 - Bio/t directory containing test suit for all included modules.
1553 - For changes specific to the Blast-related modules prior to
1554 incorporation in this central distribution, see the CHANGES
1555 file in the Bio/Tools/Blast directory.
1557 0.01 Tue Sep 8 14:23:22 1998
1558 - original version from central CVS tree; created by h2xs 1.18