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 ---------------------------------------------------------
22 * Address CPAN test failures [cjfields]
23 * Add BIOPROJECT support for Genbank files [hyphaltip]
24 * Better regex support for HMMER3 output [bosborne]
28 * Minor update to address CPAN test failures
32 * Remove Bio::Biblio and related files [carandraug]
33 - this cause version clashes with an independently-released
34 version of Bio::Biblio
40 * Hash randomization fixes for perl 5.18.x
41 - Note: at least one module (Bio::Map::Physical) still has a failing test;
42 this is documented in bug #3446 and has been TODO'd; we will be pulling
43 Bio::Map and similar modules out of core into separate distributions in the
44 1.7.x release series [cjfields]
48 * Bio::Seq::SimulatedRead
49 - New module to represent reads taken from other sequences [fangly]
51 - New regexp() method to create regular expressions from IUPAC sequences
53 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
54 - Code refresh [fangly]
56 - Added support for the Greengenes and Silva taxonomies [fangly]
57 * Bio::Tree::TreeFunctionsI
58 - get_lineage_string() represents a lineage as a string [fangly]
59 - add_trait() returns instead of reporting an error when the column
60 number is exceeded in add_trait() [fangly]
61 - Option to support tree leaves without trait [fangly]
62 - Allow ID of 0 in trait files [fangly]
63 * Bio::DB::Taxonomy::list
64 - Misc optimizations [fangly]
65 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
66 * Bio::DB::Taxonomy::*
67 - get_num_taxa() returns the number of taxa in the database [fangly]
68 * Bio::DB::Fasta and Bio::DB::Qual
69 - support indexing an arbitrary list of files [fangly]
70 - user can supply an arbitrary index file name [fangly]
71 - new option to remove index file at the end [fangly]
73 - now handles IUPAC degenerate residues [fangly]
74 * Bio::PrimarySeq and Bio::PrimarySeqI
75 - speed improvements for large sequences [Ben Woodcroft, fangly]
77 - tightened and optimized quality string validation [fangly]
79 - new method and option 'block', to create FASTA output with space
80 intervaled blocks (similar to genbank or EMBL) has been implemented.
81 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
82 in favour of the methods 'width' and 'preferred_id_type` respectively.
84 - moved from bioperl-live into the separate distribution Bio-FeatureIO
85 * Bio::SeqFeature::Annotated
86 - moved from bioperl-live into the separate distribution Bio-FeatureIO
87 * Bio::Cluster::SequenceFamily
88 - improved performance when using get_members with overlapping multiple
90 * Bio::SearchIO::hmmer3
91 - now supports nhmmer [bosborne]
95 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
96 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
97 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
98 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
99 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
100 information was lost in a multi-result blast file [Paul Cantalupo]
101 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
102 total gaps [Paul Cantalupo]
103 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
104 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
105 when end of domain indicator is split across lines [Paul Cantalupo]
106 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
108 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
109 instances where blank lines are within sequences [cjfields]
110 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
112 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
113 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
115 * Various fixes for Stockholm file indexing and processing [bosborne]
116 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
117 breaks parsing [cjfields]
118 * Fix case where Bio::Seq::Meta* objects with no meta information could not
119 be reverse-complemented [fangly]
120 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
121 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
122 when unsure that values will be numerical [fangly]
123 * Fix undef warnings in Bio::SeqIO::embl [fangly]
124 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
125 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
126 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
128 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
129 source_tag and display_name must return a string, not undef [fangly]
130 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
131 add_SeqFeature takes a single argument [fangly]
132 * Use cross-platform filenames and temporary directory in
133 Bio::DB::Taxonomy::flatfile [fangly]
134 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
135 properly identified as existing taxa in the database [fangly]
136 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
137 without also passing a lineage to store [fangly]
138 * Prevent passing a directory to the gi2taxid option (-g) of
139 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
141 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
142 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
143 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
144 object before trying to access, and no longer returns repeated sequences.
151 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
152 modules using Ace will also be deprecated [lds, cjfields]
153 * Minor bug fix release
154 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
155 * Address Build.PL issues when DBI is not present [hartzell]
156 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
157 * Remove deprecated code for perl 5.14.0 compat [cjfields]
158 * Due to schema changes and lack of support for older versions, support
159 for NeXML 0.9 is only (very) partially implemented.
160 See: https://redmine.open-bio.org/issues/3207
164 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
165 docs [genehack, cjfields]
166 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
167 module version from dist_version (probably not the best way to do this,
168 but it seems to work) [rbuels, cjfields]
171 1.6.900 April 14, 201
175 * This will probably be the last release to add significant features to
176 core modules; subsequent releases will be for bug fixes alone.
177 We are planning on a restructuring of core for summer 2011, potentially
178 as part of the Google Summer of Code. This may become BioPerl 2.0.
179 * Version bump represents 'just prior to v 1.7'. We may have point
180 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
181 This code essentially is what is on the github master branch.
185 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
187 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
188 - removal of Scalar::Util::weaken code, which was causing odd headaches
189 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
190 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
192 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
195 - bug 2515 - new contribution [Ryan Golhar, jhannah]
197 - support for reading Maq, Sam and Bowtie files [maj]
198 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
199 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
200 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
201 - bug 2726: reading/writing granularity: whole scaffold or one contig
202 at a time [Joshua Udall, fangly]
204 - Added parsing of xrefs to OBO files, which are stored as secondary
205 dbxrefs of the cvterm [Naama Menda]
206 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
207 * PAML code updated to work with PAML 4.4d [DaveMessina]
211 * [3198] - sort tabular BLAST hits by score [DaveMessina]
212 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
213 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
214 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
216 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
217 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
218 * [3164] - TreeFunctionsI syntax bug [gjuggler]
219 * [3163] - AssemblyIO speedup [fangly]
220 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
222 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
223 * [3158] - fix EMBL file mis-parsing [cjfields]
224 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
226 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
227 * [3148] - URL change for UniProt [cjfields]
228 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
229 * [3136] - HMMer3 parser fixes [kblin]
230 * [3126] - catch description [Toshihiko Akiba]
231 * [3122] - Catch instances where non-seekable filehandles were being
232 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
233 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
234 [dukeleto, rbuels, cjfields]
235 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
237 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
238 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
240 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
241 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
242 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
243 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
244 * [3086] - EMBL misparsing long tags [kblin, cjfields]
245 * [3085] - CommandExts and array of files [maj, hyphaltip]
246 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
247 for alignment slices [Ha X. Dang, cjfields]
248 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
249 * [3073] - fix parsing of GenBank files from RDP [cjfields]
250 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
251 * [3064] - All-gap midline BLAST report issues [cjfields]
252 * [3063] - BLASt report RID [Razi Khaja, cjfields]
253 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
254 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
255 * [3039] - correct Newick output root node branch length [gjuggler,
257 * [3038] - SELEX alignment error [Bernd, cjfields]
258 * [3033] - PrimarySeq ID setting [Bernd, maj]
259 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
260 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
261 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
262 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
263 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
264 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
265 PAML 4.4d [DaveMessina]
266 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
268 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
269 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
270 * [3017] - using threads with Bio::DB::GenBank [cjfields]
271 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
272 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
273 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
274 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
275 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
277 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
278 * [2977] - TreeIO issues [DaveMessina]
279 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
280 * [2944] - Bio::Tools::GFF score [cjfields]
281 * [2942] - correct MapTiling output [maj]
282 * [2939] - PDB residue insertion codes [John May, maj]
283 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
284 * [2928] - GuessSeqFormat raw [maj]
285 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
286 * [2922] - open() directive issue [cjfields]
287 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
288 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
289 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
290 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
292 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
293 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
294 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
295 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
296 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
297 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
298 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
299 * [2758] - Bio::AssemblyIO ace problems [fangly]
300 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
301 * [2726] - ace file IO [Josh, fangly]
302 * [2700] - Refactor Build.PL [cjfields]
303 * [2673] - addition of simple Root-based clone() method [cjfields]
304 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
305 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
306 * [2594] - Bio::Species memory leak [cjfields]
307 * [2515] - GenBank XML parser [jhannah]
308 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
309 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
310 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
312 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
316 * Bio::Expression modules - these were originally designed to go with the
317 bioperl-microarray suite of tools, however they have never been completed
318 and so have been removed from the distribution. The original code has
319 been moved into the inactive bioperl-microarray suite. [cjfields]
323 * Repository moved from Subversion (SVN) to
324 http://github.com/bioperl/bioperl-live [cjfields]
325 * Bug database has moved to Redmine (https://redmine.open-bio.org)
326 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
327 Thieme have been moved to their own distribution (Bio-Microarray).
330 1.6.1 Sept. 29, 2009 (point release)
331 * No change from last alpha except VERSION and doc updates [cjfields]
333 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
334 * Fix for silent OBDA bug related to FASTA validation [cjfields]
336 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
337 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
338 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
340 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
342 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
343 * WinXP test fixes [cjfields, maj]
344 * BioPerl.pod added for descriptive information, fixes CPAN indexing
346 * Minor doc fixes [cjfields]
348 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
349 * Fix tests failing due to merging issues [cjfields]
350 * More documentation updates for POD parsing [cjfields]
352 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
354 - fix YAML meta data generation [cjfields]
356 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
357 * Bio::Align::DNAStatistics
358 - fix divide by zero problem [jason]
360 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
361 * Bio::AlignIO::stockholm
362 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
363 * Bio::Assembly::Tools::ContigSpectrum
364 - function to score contig spectrum [fangly]
365 * Bio::DB::EUtilities
366 - small updates [cjfields]
368 - berkeleydb database now autoindexes wig files and locks correctly
371 - various small updates for stability; tracking changes to LANL
372 database interface [maj]
373 * Bio::DB::SeqFeature (lots of updates and changes)
374 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
375 - bug 2835 - patch [Dan Bolser]
376 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
378 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
379 * Bio::Factory::FTLocationFactory
380 - mailing list bug fix [cjfields]
382 - performance work on column_from_residue_number [hartzell]
383 * Bio::Matrix::IO::phylip
384 - bug 2800 - patch to fix phylip parsing [Wei Zou]
386 - Google Summer of Code project from Chase Miller - parsers for Nexml
387 file format [maj, chmille4]
389 - Make Individual, Population, Marker objects AnnotatableI [maj]
390 - simplify LD code [jason]
392 - deal with empty intersection [jason]
394 - significant overhaul of Bio::Restriction system: complete support for
395 external and non-palindromic cutters. [maj]
397 - CPANPLUS support, no automatic installation [sendu]
399 - allow IO::String (regression fix) [cjfields]
400 - catch unintentional undef values [cjfields]
401 - throw if non-fh is passed to -fh [maj]
402 * Bio::Root::Root/RootI
403 - small debugging and core fixes [cjfields]
405 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
406 * Bio::Root::Utilities
407 - bug 2737 - better warnings [cjfields]
409 - tiling completely refactored, HOWTO added [maj]
410 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
411 will deprecate usage of the older tiling code in the next BioPerl
413 - small fixes [cjfields]
415 - Infernal 1.0 output now parsed [cjfields]
416 - new parser for gmap -f9 output [hartzell]
417 - bug 2852 - fix infinite loop in some output [cjfields]
418 - blastxml output now passes all TODO tests [cjfields]
419 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
420 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
421 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
422 * Bio::Seq::LargePrimarySeq
423 - delete tempdirs [cjfields]
424 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
426 - extract regions based on quality threshold value [Dan Bolser, heikki]
427 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
428 * Bio::SeqFeature::Lite
429 - various Bio::DB::SeqFeature-related fixes [lstein]
430 * Bio::SeqFeature::Tools::TypeMapper
431 - additional terms for GenBank to SO map [scain]
432 * Bio::SeqIO::chadoxml
433 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
435 - support for CDS records [dave_messina, Sylvia]
437 - complete refactoring to handle all FASTQ variants, perform validation,
438 write output. API now conforms with other Bio* parsers and the rest of
439 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
441 * Bio::SeqIO::genbank
442 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
443 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
444 * Bio::SeqIO::largefasta
445 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
447 - add option for 'single' and 'multiple'
449 - bug 2881 - fix scf round-tripping [Adam Søgren]
451 - bug 2766, 2810 - copy over tags from features, doc fixes [David
454 - bug 2793 - patch for add_seq index issue [jhannah, maj]
455 - bug 2801 - throw if args are required [cjfields]
456 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
457 [Tristan Lefebure, maj]
458 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
459 - fix POD and add get_SeqFeatures filter [maj]
460 * Bio::Tools::dpAlign
461 - add support for LocatableSeq [ymc]
462 - to be moved to a separate distribution [cjfields, rbuels]
463 * Bio::Tools::EUtilities
464 - fix for two bugs from mail list [Adam Whitney, cjfields]
465 - add generic ItemContainerI interface for containing same methods
468 - fix up code, add more warnings [cjfields]
469 - to be moved to a separate distribution [cjfields, rbuels]
470 * Bio::Tools::Primer3
471 - bug 2862 - fenceposting issue fixed [maj]
472 * Bio::Tools::Run::RemoteBlast
473 - tests for remote RPS-BLAST [mcook]
474 * Bio::Tools::SeqPattern
475 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
476 * Bio::Tools::tRNAscanSE
477 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
479 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
480 * Bio::Tree::Statistics
481 - several methods for calculating Fitch-based score, internal trait
482 values, statratio(), sum of leaf distances [heikki]
484 - bug 2869 - add docs indicating edge case where nodes can be
485 prematurely garbage-collected [cjfields]
486 - add as_text() function to create Tree as a string in specified format
488 * Bio::Tree::TreeFunctionsI
489 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
491 * Bio::TreeIO::newick
492 - fix small semicolon issue [cjfields]
494 - update to bp_seqfeature_load for SQLite [lstein]
495 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
496 - fastam9_to_table - fix for MPI output [jason]
497 - gccalc - total stats [jason]
499 - POD cleanup re: FEEDBACK section [maj, cjfields]
500 - cleanup or fix dead links [cjfields]
501 - Use of no_* methods (indicating 'number of something') is deprecated
502 in favor of num_* [cjfields]
503 - lots of new tests for the above bugs and refactors [everyone!]
504 - new template for Komodo text editor [cjfields]
507 * Feature/Annotation rollback
508 - Problematic changes introduced prior to the 1.5 release have been
509 rolled back. These changes led to subtle bugs involving operator
510 overloading and interface methods.
511 - Behavior is very similar to that for BioPerl 1.4, with tag values
512 being stored generically as simple scalars. Results in a modest
515 - Split into a separate distribution on CPAN, primarily so development
516 isn't reliant on a complete BioPerl release.
517 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
518 is only available via Subversion (via bioperl-live main trunk)
520 - Common test bed for all BioPerl modules
522 - Common Module::Build-based subclass for all BioPerl modules
523 * Bio::DB::EUtilities
524 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
525 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
526 and user agent request posting and retrieval
527 * Test implementation and reorganization
528 - Tests have been reorganized into groups based on classes or use
530 - Automated test coverage is now online:
531 http://www.bioperl.org/wiki/Test_Coverage
532 - After this release, untested modules will be moved into a
533 separate developer distribution until tests can be derived.
534 Also, new modules to be added are expected to have a test suite
535 and adequate test coverage.
537 1.5.2 Developer release
539 Full details of changes since 1.5.1 are available online at:
540 http://www.bioperl.org/wiki/Change_log
541 The following represents a brief overview of the most important changes.
544 - Overhaul. Brand new system fully allows markers to have multiple
545 positions on multiple maps, and to have relative positions. Should be
549 - This module and all the modules in the Taxonomy directory now
550 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
555 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
557 * New methods ancestor(), each_Descendent() and _handle_internal_id().
559 * Allows for different database modules to create Bio::Taxon objects
560 with the same internal id when the same taxon is requested from each.
563 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
565 * No longer includes the fake root node 'root'; there are multiple roots
566 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
569 * get_node() has new option -full
571 * Caches data retrieved from website
574 - Now a Bio::Taxon. Carries out the species name -> specific name munging
575 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
576 backward compatability in species() method.
578 o Bio::Search and Bio::SearchIO
579 - Overhaul. The existing system has been sped up via some minor changes
580 (mostly gain-of-function to the API). Bio::PullParserI is introduced
581 as a potential eventual replacment for the existing system, though as
582 yet only a Hmmpfam parser exists written using it.
585 1.5.1 Developer release
587 o Major problem with how Annotations were written out with
588 Bio::Seq is fixed by reverting to old behavior for
589 Bio::Annotation objects.
594 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
595 expect at l east 9 spaces at the beginning of a line to
596 indicate line wrapping.
598 * Treat multi-line SOURCE sections correctly, this defect broke
599 both common_name() and classification()
601 * parse swissprot fields in genpept file
603 * parse WGS genbank records
606 * Changed regexp for ID line. The capturing parentheses are
607 the same, the difference is an optional repeated-not-semi-
608 colon expression following the captured \S+. This means the
609 regexp works when the division looks like /PRO;/ or when the
610 division looks like /ANG ;/ - the latter is from EMBL
613 * fix ID line parsing: the molecule string can have spaces in
614 it. Like: "genomic DNA"
616 - swiss.pm: bugs #1727, #1734
619 * Added parser for entrezgene ASN1 (text format) files.
620 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
624 - maf.pm coordinate problem fixed
626 o Bio::Taxonomy and Bio::DB::Taxonomy
628 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
629 can be done via Web without downloading all the sequence.
631 o Bio::Tools::Run::RemoteBlast supports more options and complies
632 to changes to the NCBI interface. It is reccomended that you
633 retrieve the data in XML instead of plain-text BLAST report to
634 insure proper parsing and retrieval of all information as NCBI
635 fully expects to change things in the future.
637 o Bio::Tree and Bio::TreeIO
639 - Fixes so that re-rooting a tree works properly
641 - Writing out nhx format from a newick/nexus file will properly output
642 bootstrap information. The use must move the internal node labels over
644 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
645 $node->bootstrap($node->id);
648 - Nexus parsing is much more flexible now, does not care about
651 - Cladogram drawing module in Bio::Tree::Draw
653 - Node height and depth now properly calculated
655 - fix tree pruning algorithm so that node with 1 child gets merged
657 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
658 bugs and improvements were added, see Gbrowse mailing list for most of
661 o Bio::DB::GFF partially supports GFF3. See information about
662 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
664 o Better location parsing in Bio::Factory::FTLocationFactory -
665 this is part of the engine for parsing EMBL/GenBank feature table
666 locations. Nested join/order-by/complement are allowed now
668 o Bio::PrimarySeqI->translate now takes named parameters
670 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
671 reconstruction) is now supported. Parsing different models and
672 branch specific parametes are now supported.
674 o Bio::Factory::FTLocationFactory - parse hierarchical locations
677 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
678 for getter/setter functions
682 - blast bug #1739; match scientific notation in score
683 and possible e+ values
685 - blast.pm reads more WU-BLAST parameters and parameters, match
686 a full database pathname,
688 - Handle NCBI WEB and newer BLAST formats specifically
689 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
691 - psl off-by-one error fixed
693 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
694 and HSPs can be constructed from them.
696 - HSPs query/hit now have a seqdesc field filled out (this was
697 always available via $hit->description and
698 $result->query_description
700 - hmmer.pm can parse -A0 hmmpfam files
702 - Writer::GbrowseGFF more customizeable.
704 o Bio::Tools::Hmmpfam
705 make e-value default score displayed in gff, rather than raw score
706 allow parse of multiple records
709 1.5 Developer release
711 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
712 provide Jukes-Cantor and Kimura pairwise distance methods,
715 o Bio::AlignIO support for "po" format of POA, and "maf";
716 Bio::AlignIO::largemultifasta is a new alternative to
717 Bio::AlignIO::fasta for temporary file-based manipulation of
718 particularly large multiple sequence alignments.
720 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
721 be treated similarly as an assembled contig.
723 o Bio::CodonUsage provides new rare_codon() and probable_codons()
724 methods for identifying particular codons that encode a given
727 o Bio::Coordinate::Utils provides new from_align() method to build
728 a Bio::Coordinate pair directly from a
729 Bio::Align::AlignI-conforming object.
731 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
732 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
733 web service using standard Pubmed query syntax, and retrieve
736 o Bio::DB::GFF has various sundry bug fixes.
738 o Bio::FeatureIO is a new SeqIO-style subsystem for
739 writing/reading genomic features to/from files. I/O classes
740 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
741 classes only read/write Bio::SeqFeature::Annotated objects.
742 Notably, the GFF v3 class requires features to be typed into the
745 o Bio::Graph namespace contains new modules for manipulation and
746 analysis of protein interaction graphs.
748 o Bio::Graphics has many bug fixes and shiny new glyphs.
750 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
751 indexing for HMMER reports and FASTA qual files, respectively.
753 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
754 new objects that can be placed within a Bio::Map::MapI-compliant
755 genetic/physical map; Bio::Map::Physical provides a new physical
756 map type; Bio::MapIO::fpc provides finger-printed clone mapping
759 o Bio::Matrix::PSM provide new support for postion-specific
760 (scoring) matrices (e.g. profiles, or "possums").
762 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
763 be instantiated without explicitly using Bio::OntologyIO. This
764 is possible through changes to Bio::Ontology::OntologyStore to
765 download ontology files from the web as necessary. Locations of
766 ontology files are hard-coded into
767 Bio::Ontology::DocumentRegistry.
769 o Bio::PopGen includes many new methods and data types for
770 population genetics analyses.
772 o New constructor to Bio::Range, unions(). Given a list of
773 ranges, returns another list of "flattened" ranges --
774 overlapping ranges are merged into a single range with the
775 mininum and maximum coordinates of the entire overlapping group.
777 o Bio::Root::IO now supports -url, in addition to -file and -fh.
778 The new -url argument allows one to specify the network address
779 of a file for input. -url currently only works for GET
780 requests, and thus is read-only.
782 o Bio::SearchIO::hmmer now returns individual Hit objects for each
783 domain alignment (thus containing only one HSP); previously
784 separate alignments would be merged into one hit if the domain
785 involved in the alignments was the same, but this only worked
786 when the repeated domain occured without interruption by any
787 other domain, leading to a confusing mixture of Hit and HSP
790 o Bio::Search::Result::ResultI-compliant report objects now
791 implement the "get_statistics" method to access
792 Bio::Search::StatisticsI objects that encapsulate any
793 statistical parameters associated with the search (e.g. Karlin's
794 lambda for BLAST/FASTA).
796 o Bio::Seq::LargeLocatableSeq combines the functionality already
797 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
799 o Bio::SeqFeature::Annotated is a replacement for
800 Bio::SeqFeature::Generic. It breaks compliance with the
801 Bio::SeqFeatureI interface because the author was sick of
802 dealing with untyped annotation tags. All
803 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
804 compliant, and accessible through Bio::Annotation::Collection.
806 o Bio::SeqFeature::Primer implements a Tm() method for primer
807 melting point predictions.
809 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
810 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
812 o Bio::Taxonomy::Node now implements the methods necessary for
813 Bio::Species interoperability.
815 o Bio::Tools::CodonTable has new reverse_translate_all() and
816 make_iupac_string() methods.
818 o Bio::Tools::dpAlign now provides sequence profile alignments.
820 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
822 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
825 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
826 for designing small inhibitory RNA.
828 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
829 methods based on a distance matrix.
831 o Bio::Tree::Statistics provides an assess_bootstrap() method to
832 calculate bootstrap support values on a guide tree topology,
833 based on provided bootstrap tree topologies.
835 o Bio::TreeIO now supports the Pagel (PAG) tree format.
841 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
843 o Bio::Graphics will work with gd1 or gd2
846 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
848 - blast.pm Parse multi-line query fields properly
849 - small speed improvements to blasttable.pm and others
851 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
852 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
853 supporting more complex queries
856 1.4. Stable major release
858 Since initial 1.2.0, 3000 separate changes have been made to make this release.
860 o installable scripts
862 o global module version from Bio::Root:Version
865 - major improvements; SVG support
868 - population genetics
869 - support several population genetics types of questions.
870 - Tests for statistical neutrality of mutations
871 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
872 Tests of population structure (Wright's F-statistic: Fst) is in
873 Bio::PopGen::PopStats. Calculating composite linkage
874 disequilibrium (LD) is available in Bio::PopGen::Statistics as
876 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
877 and csv (comma delimited formatted) data.
879 - a directory for implementing population simulations has
880 been added Bio::PopGen::Simulation and 2 simulations - a
881 Coalescent and a simple single-locus multi-allele genetic drift
882 simulation have been provided. This replaces the code in
883 Bio::Tree::RandomTree which has been deprecated until proper
884 methods for generating random phylogenetic trees are
888 - new restrion analysis modules
890 o Bio::Tools::Analysis
891 - web based DNA and Protein analysis framework and several
895 - per residue annotable sequences
898 - Bio::Matrix::PSM - Position Scoring Matrix
899 - Bio::Matrix::IO has been added for generalized parsing of
900 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
901 initial implementations for parsing BLOSUM/PAM and Phylip
902 Distance matricies respectively. A generic matrix
903 implementation for general use was added in
904 Bio::Matrix::Generic.
911 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
912 - small inhibitory RNA
914 o Bio::SeqFeature::Tools
915 - seqFeature mapping tools
916 - Bio::SeqFeature::Tools::Unflattener.pm
917 -- deal with mapping GenBank feature collections into
918 Chado/GFF3 processable feature sets (with SO term mappings)
920 o Bio::Tools::dpAlign
921 - pure perl dynamic programming sequence alignment
924 o new Bio::SearchIO formats
925 - axt and psl: UCSC formats.
926 - blasttable: NCBI -m 8 or -m 9 format from blastall
928 o new Bio::SeqIO formats
929 - chado, tab, kegg, tigr, game
930 - important fixes for old modules
934 o improved Bio::Tools::Genewise
936 o Bio::SeqIO now can recongnize sequence formats automatically from
939 o new parsers in Bio::Tools:
940 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
942 o Bio::DB::Registry bugs fixed
943 - BerkeleyDB-indexed flat files can be used by the OBDA system
944 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
945 used by the OBDA system
948 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
951 o hundreds of new and improved files
955 o Bio::Tree::AlleleNode has been updated to be a container of
956 an Bio::PopGen::Individual object for use in the Coalescent simulations.
961 1.2.3 Stable release update
962 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
964 o Bug #1477 - Sel --> Sec abbreviation fixed
965 o Fix bug #1487 where paring in-between locations when
966 end < start caused the FTLocationFactory logic to fail.
967 o Fix bug #1489 which was not dealing with keywords as an
968 arrayref properly (this is fixed on the main trunk because
969 keywords returns a string and the array is accessible via
971 o Bio::Tree::Tree memory leak (bug #1480) fixed
972 Added a new initialization option -nodelete which
973 won't try and cleanup the containing nodes if this
975 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
976 this was only present on the branch for the 1.2.1 and 1.2.2 series
977 - Also merged main trunk changes to the branch which make
978 newick -> nhx round tripping more effective (storing branch length
979 and bootstrap values in same locate for NodeNHX and Node
980 implementations.) Fixes to TreeIO parsing for labeled internal
981 also required small changes to TreeIO::nhx. Improved
982 tests for this module as well.
984 - Fixed bugs in BLAST parsing which couldn't parse NCBI
985 gapped blast properly (was losing hit significance values due to
986 the extra unexpeted column).
987 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
988 integer overflow (# of letters in nt seq dbs is > MAX_INT)
989 although doesn't try to correct it - will get the negative
990 number for you. Added a test for this as well.
991 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
992 has no top-level family classification scores but does have scores and
993 alignments for individual domains.
994 - Parsing FASTA reports where ungapped percent ID is < 10 and the
995 regular expression to match the line was missing the possibility of
996 an extra space. This is rare, which is why we probably did not
998 - BLAST parsing picks up more of the statistics/parameter fields
999 at the bottom of reports. Still not fully complete.
1000 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1001 were fixed to include many improvements and added flexiblity
1002 in outputting the files. Bug #1495 was also fixed in the process.
1004 - Update for GFF3 compatibility.
1005 - Added scripts for importing from UCSC and GenBank.
1006 - Added a 1.2003 version number.
1009 - Added a 1.2003 version number.
1010 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1011 properly writing keywords out.
1012 o Bio::SeqIO::genbank
1013 - Fixed bug/enhancement #1513 where dates of
1014 the form D-MMM-YYYY were not parsed. Even though this is
1015 invalid format we can handle it - and also cleanup the date
1016 string so it is properly formatted.
1017 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1018 and written with Genbank format. Similarly bug #1515 is fixed to
1019 parse in the ORIGIN text.
1020 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1021 to specify the ID type, one of (accession accession.version
1022 display primary). See Bio::SeqIO::preferred_id_type method
1023 documentation for more information.
1024 o Unigene parsing updated to handle file format changes by NCBI
1026 1.2.2 Stable release update
1028 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1029 - auto-discover ontology name
1030 - bug in parsing relationships when certain characters are in the term
1031 - fixed hard-coded prefix for term identifiers
1032 - various smaller issues
1034 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1035 of Bio::Ontology::TermI
1037 o brought the OBDA Registry code up to latest specs
1041 - accession number retrieval fixed
1043 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1045 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1046 #1459 which now properly report alignment start/end info
1047 for translated BLAST/FASTA searches.
1049 o Bio::TreeIO::newick can parse labeled internal nodes
1051 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1052 for BLASTX if if you provide -report_type => 'BLASTX' when
1053 initializing a BPbl2seq object. Bioperl 1.3 will have better
1054 support for bl2seq in the SearchIO system.
1056 o Bio::Root::IO support a -noclose boolean flag which will not
1057 close a filehandle upon object cleanup - useful when sharing
1058 a filehandle among objects. Additionally code added s.t.
1059 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1061 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1063 o Bio::SeqIO::genbank
1064 - bug #1456 fixed which generated extra sequence lines
1065 - write moltype correctly for genpept
1067 1.2.1 Stable release update
1069 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1071 o Addition from main trunk of Ontology objects, principly to allow
1072 BioSQL releases against 1.2.1
1074 o Fixes and cleanup of Bio::Coordinate modules
1076 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1077 the primary accession number
1079 o Other bug fixes, including bpindex GenBank fix
1081 o Bio::SeqIO::genbank bug #1389 fixed
1083 1.2 Stable major release
1085 o More functionality added to Bio::Perl, the newbie module
1087 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1088 Support for New Hampshire Extended (NHX) format parsing.
1090 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1091 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1094 o New ontology parsing Bio::Ontology
1096 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1097 multi-report (mlib) fasta reports, support for waba and exonerate.
1099 o Bio::ClusterIO for parsing Unigene clusters
1101 o Bio::Assembly added for representing phrap and ace assembly clusters.
1103 o Rudimentary support for writing Chado XML (see
1104 GMOD project: www.gmod.org for more information)
1106 o Bio::Coordinate for mapping between different coordinate systems such
1107 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1108 features into different coordinate systems.
1110 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1111 with the get_Stream_by_query method and supports the latest
1112 NCBI eutils interface.
1114 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1115 object for extracting subsets of features : currently only
1116 supports extraction by location.
1118 1.1.1 Developer release
1120 o Deprecated modules are now listed in the DEPRECATED file
1122 o New HowTo documents located in doc/howto describing
1123 a domain of Bioperl.
1125 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1126 and all old bugs are searchable through the bugzilla interface.
1128 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1129 have been addressed.
1131 o Support for Genewise parsing in Bio::Tools::Genewise
1133 o Start of Ontology framework with Bio::Ontology
1135 o Speedup to the Bio::Root::Root object method _rearrange.
1136 A global _load_module method was implemented to simplify the
1137 dynamic loading of modules ala Bio::SeqIO::genbank. This
1138 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1141 o Several performance improvements to sequence parsing in Bio::SeqIO.
1142 Attempt to speedup by reducing object creation overhead.
1144 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1145 method for sequence retrieval with their E-utils CGI scripts.
1146 More work to support Entrez queries to their fullest is planned
1149 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1151 1.1 Developer release
1153 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1154 this separation removes some of the complexity in our test suite
1155 and separates the core modules in bioperl from those that need
1156 external programs to run.
1158 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1159 not run into trouble running the makefile
1161 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1162 read,create,and write locations for grouped/split locations
1163 (like mRNA features on genomic sequence).
1165 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1166 and PAML (codeml,aaml, etc) parsing.
1168 o Bio::Tree:: objects expanded to handle testing monophyly,
1169 paraphyly, least common ancestor, etc.
1171 o Bio::Coordinate for mapping locations from different coordinate spaces
1173 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1174 added for parsing hmmpfam and hmmsearch output.
1176 o Bio::SearchIO::Writer::TextResultWriter for outputting
1177 a pseudo-blast textfile format
1180 1.0.2 Bug fix release
1182 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1183 in this release will not work after December 2002 when NCBI
1184 shuts off the old Entrez cgi scripts. We have already fixed
1185 on our main development branch and the functionality will be
1186 available in the next stable bioperl release (1.2) slated for
1189 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1190 testset by Robin Emig. These were fixed as was the get_aln
1191 method in Bio::Search::HSP::GenericHSP to handle the extra
1192 context sequence that is provided with a FastA alignment.
1194 o Migrating differences between Bio::Search::XX::BlastXX to
1195 Bio::Search::XX::GenericXX objects. This included mechanism
1196 to retrieve whole list of HSPs from Hits and whole list of Hits from
1197 Results in addition to the current next_XX iterator methods that
1198 are available. Added seq_inds() method to GenericHSP which identifies
1199 indexes in the query or hit sequences where conserved,identical,gaps,
1200 or mismatch residues are located (adapted from Steve Chervitz's
1201 implementation in BlastHSP).
1203 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1204 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1206 o Bio::Graphics glyph set improved and extended for GBrowse release
1208 o Bio::Tree::Tree get_nodes implementation improvement thanks
1209 to Howard Ross notice performance problem when writing out
1212 o Bio::Location::Fuzzy::new named parameter -loc_type became
1213 -location_type, Bio::Location::Simple::new named parameter
1214 -seqid becamse -seq_id.
1216 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1217 was mis-detecting that gaps should be placed at the beginning of
1218 the alignment when the best alignment starts internally in the
1221 1.0.1 Bug fix release
1223 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1225 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1226 and mixed (3.3 - 3.4) versions of FASTA.
1228 o Small API change to add methods for completeness across
1229 implementations of Bio::Search objects. These new methods
1230 in the interface are implemented by the GenericXX object as well
1231 as the BlastXX objects.
1232 * Bio::Search::Result::ResultI
1233 - hits() method returns list of all Hits (next_hit is an
1236 * Bio::Search::Hit::HitI
1237 - hsps() method returns list of all HSPs (next_hsp is an
1240 o The Bio::SearchIO::Writer classes have been fixed to handle results
1241 created from either psiblast (Search::BlastXX objects) or
1242 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1243 has to be done here to make it work properly and will nee major
1246 o Bugs in Bio::Tools::HMMER fixed, including
1247 * #1178 - Root::IO destructor wasn't being called
1248 * #1034 - filter_on_cutoff now behaves properly
1250 o Bio::SeqFeature::Computation initialization args fixed and
1253 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1255 o Updated FAQ with more example based answers to typical questions
1257 o Bug #1202 was fixed which would improperly join together qual values
1258 parsed by Bio::SeqIO::qual when a trailing space was not present before
1261 1.0.0 Major Stable Release
1263 This represents a major release of bioperl with significant
1264 improvements over the 0.7.x series of releases.
1266 o Bio::Tools::Blast is officially deprecated. Please see
1267 Bio::SearchIO for BLAST and FastA parsing.
1269 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1270 Bio::LocationI objects as well as start/end.
1272 o Bio::Biblio contains modules for Bibliographic data.
1273 Bio::DB::Biblio contains the query modules. Additionally one can
1274 parse medlinexml from the ebi bibliographic query service (BQS)
1275 system and Pubmed xml from NCBI. See Martin Senger's
1276 documentation in Bio::Biblio for more information.
1278 o Bio::DB::Registry is a sequence database registry part of
1279 Open Bioinformatics Database Access. See
1280 http://obda.open-bio.org for more information.
1282 o File-based and In-Memory Sequence caching is provided by
1283 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1286 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1287 been added by Lincoln Stein.
1289 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1291 o A FAQ has been started and is included in the release to provide
1292 a starting point for frequent questions and issues.
1294 0.9.3 Developer's release
1296 o Event based parsing system improved (SearchIO). With parsers for
1297 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1298 Additionally a lazy parsing system for text and html blast reports was
1299 added and is called psiblast (name subject to change in future releases).
1301 o Bio::Search objects improved and standardized with associated Interfaces
1302 written. The concept of a search "Hit" was standardized to be called
1303 "hit" consistently and the use of "subject" was deprecated in all active
1306 o Bio::Structure added (since 0.9.1) for Protein structure objects
1307 and PDB parser to retrieve and write these structures from data files.
1309 o Several important Bio::DB::GFF bug fixes for handling features that
1310 are mapped to multiple reference points. Updated mysql adaptor
1311 so as to be able to store large (>100 megabase) chunks of DNA into
1312 Bio::DB::GFF databases.
1314 0.9.2 Developer's release
1316 o Bio::Search and Bio::SearchIO system introduced for event based
1317 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1318 in text and XML and FASTA reports in standard output format.
1320 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1321 generator is included in Bio::TreeIO::RandomTrees and a
1322 statistics module for evaluating.
1324 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1325 server for DAS servers.
1327 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1328 files. The entire BPlite system migrated to using Bio::Root::IO
1329 for the data stream.
1331 o Bio::Tools::Alignment for Consed and sequence Trimming
1334 o Bio::Structure for Protein structure information and parsing
1336 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1337 cgi-bin entry point which should be more reliable.
1339 o Bio::Map and Bio::MapIO for biological map navigation and a
1340 framework afor parsing them in. Only preliminary work here.
1342 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1343 Future work will integrate Pise and allow submission of analysis on
1346 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1347 introduced as new objects for handling Sequence Annotation
1348 information (dblinks, references, etc) and is more robust that
1351 o Bio::Tools::FASTAParser introduced.
1353 o Scripts from the bioperl script submission project and new
1354 scripts from bioperl authors are included in "scripts" directory.
1356 o Factory objects and interfaces are being introduced and are more
1359 o Bio::Root::Root introduced as the base object while
1360 Bio::Root::RootI is now simply an interface.
1362 o Bio::DB::RefSeq provides database access to copy of the NCBI
1363 RefSeq database using the EBI dbfetch script.
1365 0.9.0 Developer's release
1367 o perl version at least 5.005 is now required instead of perl 5.004
1369 o Bio::Tools::Run::RemoteBlast is available for running remote
1372 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1374 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1375 Also added are related modules UTR3, UTR5, Exon, Intron,
1376 Promotor, PolyA and Transcript.
1378 o Speedup of translate method in PrimarySeq
1380 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1381 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1383 o Various fixes to Variation toolkit
1385 o Bio::DB::EMBL provides database access to EMBL sequence data.
1386 Bio::DB::Universal provides a central way to point to indexes
1387 and dbs in a single interface.
1389 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1391 o Bio::Factory::EMBOSS is still in design phase as is
1392 Bio::Factory::ApplicationFactoryI
1394 o Dia models for bioperl design are provided in the models/ directory
1396 0.7.2 Bug fix release
1398 o documentation fixes in many modules - SYNOPSIS code verified
1399 to be runnable in many (but not all modules)
1401 o corrected MANIFEST file from 0.7.1 release
1403 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1406 o Bio::SeqIO::genbank
1407 * Correct parsing and writing of genbank format with protein data
1408 * moltype and molecule separation
1410 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1412 o Bio::SimpleAlign fixed to correctly handle consensus
1413 sequence calculation
1415 o Bio::Tools::HMMER supports hmmer 2.2g
1417 o Bio::Tools::BPlite to support report type specific parsing. Most
1418 major changes are not on the 0.7 branch.
1420 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1423 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1424 in several types of mutations:
1425 1.) AA level: deletion, complex
1426 2.) AA level: complex, inframe
1427 3.) RNA level: silent
1429 o BPbl2seq parsing of empty reports will not die, but will return
1430 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1431 $report->query() and $report->subject() methods. So an easy
1432 way to test if report was empty is to see if
1433 $report->query->seqname is undefined.
1435 0.7.1 Bug fix release
1437 o Better parsing of genbank/EMBL files especially fixing bugs
1438 related to Feature table parsing and locations on remote
1439 sequences. Additionally, species name parsing was better.
1441 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1442 which include a number of header lines.
1444 o More strict genbank and EMBL format writing (corrected number of
1445 spaces where appropriate).
1447 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1448 for related BPlite BUGS that are unresolved in this release.
1450 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1451 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1452 use expasy mirrors or EBI dbfetch cgi-script.
1454 o A moderate number of documentation improvements were made as
1455 well to provide a better code synopsis in each module.
1458 0.7 Large number of changes, including refactoring of the
1459 Object system, new parsers, new functionality and
1460 all round better system. Highlights are:
1463 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1464 Bio::Root::IO for I/O and file/handle capabilities.
1466 o Imported BPlite modules from Ian Korf for BLAST
1467 parsing. This is considered the supported BLAST parser;
1468 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1470 o Improved Sequence Feature model. Added complete location
1471 modelling (with fuzzy and compound locations). See
1472 Bio::LocationI and the modules under Bio/Location. Added
1473 support in Genbank/EMBL format parsing to completely parse
1474 feature tables for complex locations.
1476 o Moved special support for databanks etc to specialized modules under
1477 Bio/Seq/. One of these supports very large sequences through
1478 a temporary file as a backend.
1480 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1481 CDS retrieval and exon shuffling.
1483 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1485 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1486 DB/GDB (the latter has platform-specific limitations).
1488 o New analysis parser framework for HT sequence annotation (see
1489 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1491 o New Alignment IO framework
1493 o New Index modules (Swissprot)
1495 o New modules for running Blast within perl
1496 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1497 Multiple Sequence Alignment tools ClustalW and TCoffee
1498 (Bio::Tools::Run::Alignment).
1500 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1501 documentation across the package.
1503 o Much improved cross platform support. Many known incompatibilities
1504 have been fixed; however, NT and Mac do not work across the entire
1505 setup (see PLATFORMS).
1507 o Many bug fixes, code restructuring, etc. Overall stability and
1508 maintainability benefit a lot.
1510 o A total of 957 automatic tests
1515 There are very few functionality changes but a large
1516 number of software improvements/bug fixes across the package.
1518 o The EMBL/GenBank parsing are improved.
1520 o The Swissprot reading is improved. Swissprot writing
1521 is disabled as it doesn't work at all. This needs to
1522 wait for 0.7 release
1524 o BLAST reports with no hits are correctly parsed.
1526 o Several other bugs of the BLAST parser (regular expressions, ...)
1529 o Old syntax calls have been replaced with more modern syntax
1531 o Modules that did not work at all, in particular the Sim4
1532 set have been removed
1534 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1535 have improved compliance with interface specs and documentation
1537 o Mailing list documentation updated throughout the distribution
1539 o Most minor bug fixes have happened.
1541 o The scripts in /examples now work and have the modern syntax
1542 rather than the deprecated syntax
1545 0.6.1 Sun April 2 2000
1547 o Sequences can have Sequence Features attached to them
1548 - The sequence features can be read from or written to
1549 EMBL and GenBank style flat files
1551 o Objects for Annotation, including References (but not
1552 full medline abstracts), Database links and Comments are
1555 o A Species object to represent nodes on a taxonomy tree
1558 o The ability to parse HMMER and Sim4 output has been added
1560 o The Blast parsing has been improved, with better PSI-BLAST
1561 support and better overall behaviour.
1563 o Flat file indexed databases provide both random access
1564 and sequential access to their component sequences.
1566 o A CodonTable object has been written with all known
1567 CodonTables accessible.
1569 o A number of new lightweight analysis tools have been
1570 added, such as molecular weight determination.
1572 The 0.6 release also has improved software engineering
1574 o The sequence objects have been rewritten, providing more
1575 maintainable and easier to implement objects. These
1576 objects are backwardly compatible with the 0.05.1 objects
1578 o Many objects are defined in terms of interfaces and then
1579 a Perl implementation has been provided. The interfaces
1580 are found in the 'I' files (module names ending in 'I').
1582 This means that it is possible to wrap C/CORBA/SQL access
1583 as true "bioperl" objects, compatible with the rest of
1586 o The SeqIO system has been overhauled to provide better
1587 processing and perl-like automatic interpretation of <>
1590 o Many more tests have been added (a total of 172 automatic
1591 tests are now run before release).
1595 0.05.1 Tue Jun 29 05:30:44 1999
1596 - Central distribution now requires Perl 5.004. This was
1597 done to get around 5.003-based problems in Bio/Index/*
1599 - Various bug fixes in the Bio::Tools::Blast modules
1600 including better exception handling and PSI-Blast
1601 support. See Bio/Tools/Blast/CHANGES for more.
1602 - Fixed the Parse mechanism in Seq.pm to use readseq.
1603 Follow the instructions in README for how to install
1604 it (basically, you have to edit Parse.pm).
1605 - Improved documentation of Seq.pm, indicating where
1606 objects are returned and where strings are returned.
1607 - Fixed uninitialized warnings in Bio::Root::Object.pm
1608 and Bio::Tools::SeqPattern.pm.
1609 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1611 0.05 Sun Apr 25 01:14:11 1999
1612 - Bio::Tools::Blast modules have less memory problems
1613 and faster parsing. Webblast uses LWP and supports
1614 more functionality. See Bio/Tools/Blast/CHANGES for more.
1615 - The Bio::SeqIO system has been started, moving the
1616 sequence reformatting code out of the sequence object
1617 - The Bio::Index:: system has been started, providing
1618 generic index capabilities and specifically works for
1619 Fasta formatted databases and EMBL .dat formatted
1621 - The Bio::DB:: system started, providing access to
1622 databases, both via flat file + index (see above) and
1624 - The scripts/ directory, where industrial strength scripts
1625 are put has been started.
1626 - Many changes - a better distribution all round.
1628 0.04.4 Wed Feb 17 02:20:13 1999
1629 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1630 (see Bio::Tools::Blast::CHANGES).
1631 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1632 - Beefed up the t/Fasta.t test script.
1633 - Small fix in Bio::Seq::type() (now always returns a string).
1634 - Changed Bio::Root::Utilities::get_newline_char() to
1635 get_newline() since it could return more than one char.
1636 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1637 - Changed default timeout to 20 seconds (was 3).
1638 - Moved lengthy modification notes to the bottom of some files.
1639 - Fixed SimpleAlign write_fasta bug.
1640 - Beefed up SimpleAlign.t test
1642 0.04.3 Thu Feb 4 07:48:53 1999
1643 - Bio::Root::Object.pm and Global.pm now detect when
1644 script is run as a CGI and suppress output that is only
1645 appropriate when running interactively.
1646 - Bio::Root::Err::_set_context() adds name of script ($0).
1647 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1648 regarding the use of the static objects via the qw(:obj) tag.
1649 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1650 CORE::reverse, avoiding Perl warnings.
1651 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1652 example scripts (see Bio::Tools::Blast::CHANGES).
1653 - examples/seq/seqtools.pl no longer always warns about using
1654 -prot or -nucl command-line arguments; only when using the
1656 - Methods added to Bio::Root::Utilities: create_filehandle(),
1657 get_newline_char(), and taste_file() to generalize filehandle
1658 creation and autodetect newline characters in files/streams
1659 (see bug report #19).
1660 - Bio::Root::IOManager::read() now handles timeouts and uses
1661 Utilities::create_filehandle().
1662 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1663 of hardwiring in "\n".
1664 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1666 0.04.2 Wed Dec 30 02:27:36 1998
1667 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1668 (see Bio::Tools::Blast::CHANGES).
1669 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1670 to CORE::reverse (prevents ambiguous warnings with 5.005).
1671 - Appending '.tmp.bioperl' to temporary files created by
1672 Bio::Root::Utilities::compress() or uncompress() to
1673 make it easy to identify & cleanup these files as needed.
1674 - Developers: Created CVS branch release-0-04-bug from
1675 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1676 be sure to cvs checkout this branch into a clean area.
1678 0.04.1 Wed Dec 16 05:39:15 1998
1679 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1680 (see Bio::Tools::Blast::CHANGES).
1681 - Compile/SW/Makefile.PL now removes *.o and *.a files
1684 0.04 Tue Dec 8 07:49:19 1998
1685 - Lots of new modules added including:
1686 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1687 and Bio/Compile directory containing XS-linked C code for
1688 creating Smith-Waterman sequence alignments from within Perl.
1689 * Steve Chervitz's Blast distribution has been incorporated.
1690 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1691 - Bio/examples directory for demo scripts for all included modules.
1692 - Bio/t directory containing test suit for all included modules.
1693 - For changes specific to the Blast-related modules prior to
1694 incorporation in this central distribution, see the CHANGES
1695 file in the Bio/Tools/Blast directory.
1697 0.01 Tue Sep 8 14:23:22 1998
1698 - original version from central CVS tree; created by h2xs 1.18