1 ---------------------------------------------------------
2 Revision history for BioPerl core modules
3 ---------------------------------------------------------
4 The comprehensive history and ongoing development of BioPerl:
6 http://github.com/bioperl/bioperl-live
8 Some of that history is also highlighted on our wiki:
10 http://www.bioperl.org/wiki/Change_log
11 http://www.bioperl.org/wiki/History_of_BioPerl
13 Bugs and requested features list:
15 https://redmine.open-bio.org/projects/bioperl
17 CPAN releases are branched from 'master'.
18 ---------------------------------------------------------
24 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
25 modules using Ace will also be deprecated [lds, cjfields]
26 * Minor bug fix release
27 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
28 * Address Build.PL issues when DBI is not present [hartzell]
29 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
30 * Remove deprecated code for impending perl 5.14.0 release [cjfields]
31 * Due to schema changes and lack of support for older versions, support
32 for NeXML 0.9 is only (very) partially implemented.
33 See: https://redmine.open-bio.org/issues/3207
37 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
38 docs [genehack, cjfields]
45 * This will probably be the last release to add significant features to
46 core modules; subsequent releases will be for bug fixes alone.
47 We are planning on a restructuring of core for summer 2011, potentially
48 as part of the Google Summer of Code. This may become BioPerl 2.0.
49 * Version bump represents 'just prior to v 1.7'. We may have point
50 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
51 This code essentially is what is on the github master branch.
55 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
57 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
58 - removal of Scalar::Util::weaken code, which was causing odd headaches
59 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
60 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
62 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
65 - bug 2515 - new contribution [Ryan Golhar, jhannah]
67 - support for reading Maq, Sam and Bowtie files [maj]
68 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
69 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
70 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
71 - bug 2726: reading/writing granularity: whole scaffold or one contig
72 at a time [Joshua Udall, fangly]
74 - Added parsing of xrefs to OBO files, which are stored as secondary
75 dbxrefs of the cvterm [Naama Menda]
76 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
77 * PAML code updated to work with PAML 4.4d [DaveMessina]
81 * [3198] - sort tabular BLAST hits by score [DaveMessina]
82 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
83 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
84 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
86 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
87 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
88 * [3164] - TreeFunctionsI syntax bug [gjuggler]
89 * [3163] - AssemblyIO speedup [fangly]
90 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
92 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
93 * [3158] - fix EMBL file mis-parsing [cjfields]
94 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
96 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
97 * [3148] - URL change for UniProt [cjfields]
98 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
99 * [3136] - HMMer3 parser fixes [kblin]
100 * [3126] - catch description [Toshihiko Akiba]
101 * [3122] - Catch instances where non-seekable filehandles were being
102 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
103 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
104 [dukeleto, rbuels, cjfields]
105 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
107 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
108 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
110 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
111 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
112 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
113 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
114 * [3086] - EMBL misparsing long tags [kblin, cjfields]
115 * [3085] - CommandExts and array of files [maj, hyphaltip]
116 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
117 for alignment slices [Ha X. Dang, cjfields]
118 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
119 * [3073] - fix parsing of GenBank files from RDP [cjfields]
120 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
121 * [3064] - All-gap midline BLAST report issues [cjfields]
122 * [3063] - BLASt report RID [Razi Khaja, cjfields]
123 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
124 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
125 * [3039] - correct Newick output root node branch length [gjuggler,
127 * [3038] - SELEX alignment error [Bernd, cjfields]
128 * [3033] - PrimarySeq ID setting [Bernd, maj]
129 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
130 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
131 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
132 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
133 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
134 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
135 PAML 4.4d [DaveMessina]
136 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
138 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
139 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
140 * [3017] - using threads with Bio::DB::GenBank [cjfields]
141 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
142 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
143 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
144 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
145 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
147 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
148 * [2977] - TreeIO issues [DaveMessina]
149 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
150 * [2944] - Bio::Tools::GFF score [cjfields]
151 * [2942] - correct MapTiling output [maj]
152 * [2939] - PDB residue insertion codes [John May, maj]
153 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
154 * [2928] - GuessSeqFormat raw [maj]
155 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
156 * [2922] - open() directive issue [cjfields]
157 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
158 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
159 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
160 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
162 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
163 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
164 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
165 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
166 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
167 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
168 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
169 * [2758] - Bio::AssemblyIO ace problems [fangly]
170 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
171 * [2726] - ace file IO [Josh, fangly]
172 * [2700] - Refactor Build.PL [cjfields]
173 * [2673] - addition of simple Root-based clone() method [cjfields]
174 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
175 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
176 * [2594] - Bio::Species memory leak [cjfields]
177 * [2515] - GenBank XML parser [jhannah]
178 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
179 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
180 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
182 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
186 * Bio::Expression modules - these were originally designed to go with the
187 bioperl-microarray suite of tools, however they have never been completed
188 and so have been removed from the distribution. The original code has
189 been moved into the inactive bioperl-microarray suite. [cjfields]
193 * Repository moved from Subversion (SVN) to
194 http://github.com/bioperl/bioperl-live [cjfields]
195 * Bug database has moved to Redmine (https://redmine.open-bio.org)
196 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
197 Thieme have been moved to their own distribution (Bio-Microarray).
200 1.6.1 Sept. 29, 2009 (point release)
201 * No change from last alpha except VERSION and doc updates [cjfields]
203 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
204 * Fix for silent OBDA bug related to FASTA validation [cjfields]
206 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
207 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
208 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
210 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
212 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
213 * WinXP test fixes [cjfields, maj]
214 * BioPerl.pod added for descriptive information, fixes CPAN indexing
216 * Minor doc fixes [cjfields]
218 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
219 * Fix tests failing due to merging issues [cjfields]
220 * More documentation updates for POD parsing [cjfields]
222 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
224 - fix YAML meta data generation [cjfields]
226 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
227 * Bio::Align::DNAStatistics
228 - fix divide by zero problem [jason]
230 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
231 * Bio::AlignIO::stockholm
232 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
233 * Bio::Assembly::Tools::ContigSpectrum
234 - function to score contig spectrum [fangly]
235 * Bio::DB::EUtilities
236 - small updates [cjfields]
238 - berkeleydb database now autoindexes wig files and locks correctly
241 - various small updates for stability; tracking changes to LANL
242 database interface [maj]
243 * Bio::DB::SeqFeature (lots of updates and changes)
244 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
245 - bug 2835 - patch [Dan Bolser]
246 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
248 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
249 * Bio::Factory::FTLocationFactory
250 - mailing list bug fix [cjfields]
252 - performance work on column_from_residue_number [hartzell]
253 * Bio::Matrix::IO::phylip
254 - bug 2800 - patch to fix phylip parsing [Wei Zou]
256 - Google Summer of Code project from Chase Miller - parsers for Nexml
257 file format [maj, chmille4]
259 - Make Individual, Population, Marker objects AnnotatableI [maj]
260 - simplify LD code [jason]
262 - deal with empty intersection [jason]
264 - significant overhaul of Bio::Restriction system: complete support for
265 external and non-palindromic cutters. [maj]
267 - CPANPLUS support, no automatic installation [sendu]
269 - allow IO::String (regression fix) [cjfields]
270 - catch unintentional undef values [cjfields]
271 - throw if non-fh is passed to -fh [maj]
272 * Bio::Root::Root/RootI
273 - small debugging and core fixes [cjfields]
275 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
276 * Bio::Root::Utilities
277 - bug 2737 - better warnings [cjfields]
279 - tiling completely refactored, HOWTO added [maj]
280 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
281 will deprecate usage of the older tiling code in the next BioPerl
283 - small fixes [cjfields]
285 - Infernal 1.0 output now parsed [cjfields]
286 - new parser for gmap -f9 output [hartzell]
287 - bug 2852 - fix infinite loop in some output [cjfields]
288 - blastxml output now passes all TODO tests [cjfields]
289 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
290 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
291 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
292 * Bio::Seq::LargePrimarySeq
293 - delete tempdirs [cjfields]
294 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
296 - extract regions based on quality threshold value [Dan Bolser, heikki]
297 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
298 * Bio::SeqFeature::Lite
299 - various Bio::DB::SeqFeature-related fixes [lstein]
300 * Bio::SeqFeature::Tools::TypeMapper
301 - additional terms for GenBank to SO map [scain]
302 * Bio::SeqIO::chadoxml
303 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
305 - support for CDS records [dave_messina, Sylvia]
307 - complete refactoring to handle all FASTQ variants, perform validation,
308 write output. API now conforms with other Bio* parsers and the rest of
309 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
311 * Bio::SeqIO::genbank
312 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
313 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
314 * Bio::SeqIO::largefasta
315 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
317 - add option for 'single' and 'multiple'
319 - bug 2881 - fix scf round-tripping [Adam Sj¿gren]
321 - bug 2766, 2810 - copy over tags from features, doc fixes [David
324 - bug 2793 - patch for add_seq index issue [jhannah, maj]
325 - bug 2801 - throw if args are required [cjfields]
326 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
327 [Tristan Lefebure, maj]
328 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
329 - fix POD and add get_SeqFeatures filter [maj]
330 * Bio::Tools::dpAlign
331 - add support for LocatableSeq [ymc]
332 - to be moved to a separate distribution [cjfields, rbuels]
333 * Bio::Tools::EUtilities
334 - fix for two bugs from mail list [Adam Whitney, cjfields]
335 - add generic ItemContainerI interface for containing same methods
338 - fix up code, add more warnings [cjfields]
339 - to be moved to a separate distribution [cjfields, rbuels]
340 * Bio::Tools::Primer3
341 - bug 2862 - fenceposting issue fixed [maj]
342 * Bio::Tools::Run::RemoteBlast
343 - tests for remote RPS-BLAST [mcook]
344 * Bio::Tools::SeqPattern
345 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
346 * Bio::Tools::tRNAscanSE
347 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
349 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
350 * Bio::Tree::Statistics
351 - several methods for calculating Fitch-based score, internal trait
352 values, statratio(), sum of leaf distances [heikki]
354 - bug 2869 - add docs indicating edge case where nodes can be
355 prematurely garbage-collected [cjfields]
356 - add as_text() function to create Tree as a string in specified format
358 * Bio::Tree::TreeFunctionsI
359 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
361 * Bio::TreeIO::newick
362 - fix small semicolon issue [cjfields]
364 - update to bp_seqfeature_load for SQLite [lstein]
365 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
366 - fastam9_to_table - fix for MPI output [jason]
367 - gccalc - total stats [jason]
369 - POD cleanup re: FEEDBACK section [maj, cjfields]
370 - cleanup or fix dead links [cjfields]
371 - Use of no_* methods (indicating 'number of something') is deprecated
372 in favor of num_* [cjfields]
373 - lots of new tests for the above bugs and refactors [everyone!]
374 - new template for Komodo text editor [cjfields]
377 * Feature/Annotation rollback
378 - Problematic changes introduced prior to the 1.5 release have been
379 rolled back. These changes led to subtle bugs involving operator
380 overloading and interface methods.
381 - Behavior is very similar to that for BioPerl 1.4, with tag values
382 being stored generically as simple scalars. Results in a modest
385 - Split into a separate distribution on CPAN, primarily so development
386 isn't reliant on a complete BioPerl release.
387 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
388 is only available via Subversion (via bioperl-live main trunk)
390 - Common test bed for all BioPerl modules
392 - Common Module::Build-based subclass for all BioPerl modules
393 * Bio::DB::EUtilities
394 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
395 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
396 and user agent request posting and retrieval
397 * Test implementation and reorganization
398 - Tests have been reorganized into groups based on classes or use
400 - Automated test coverage is now online:
401 http://www.bioperl.org/wiki/Test_Coverage
402 - After this release, untested modules will be moved into a
403 separate developer distribution until tests can be derived.
404 Also, new modules to be added are expected to have a test suite
405 and adequate test coverage.
407 1.5.2 Developer release
409 Full details of changes since 1.5.1 are available online at:
410 http://www.bioperl.org/wiki/Change_log
411 The following represents a brief overview of the most important changes.
414 - Overhaul. Brand new system fully allows markers to have multiple
415 positions on multiple maps, and to have relative positions. Should be
419 - This module and all the modules in the Taxonomy directory now
420 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
425 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
427 * New methods ancestor(), each_Descendent() and _handle_internal_id().
429 * Allows for different database modules to create Bio::Taxon objects
430 with the same internal id when the same taxon is requested from each.
433 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
435 * No longer includes the fake root node 'root'; there are multiple roots
436 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
439 * get_node() has new option -full
441 * Caches data retrieved from website
444 - Now a Bio::Taxon. Carries out the species name -> specific name munging
445 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
446 backward compatability in species() method.
448 o Bio::Search and Bio::SearchIO
449 - Overhaul. The existing system has been sped up via some minor changes
450 (mostly gain-of-function to the API). Bio::PullParserI is introduced
451 as a potential eventual replacment for the existing system, though as
452 yet only a Hmmpfam parser exists written using it.
455 1.5.1 Developer release
457 o Major problem with how Annotations were written out with
458 Bio::Seq is fixed by reverting to old behavior for
459 Bio::Annotation objects.
464 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
465 expect at l east 9 spaces at the beginning of a line to
466 indicate line wrapping.
468 * Treat multi-line SOURCE sections correctly, this defect broke
469 both common_name() and classification()
471 * parse swissprot fields in genpept file
473 * parse WGS genbank records
476 * Changed regexp for ID line. The capturing parentheses are
477 the same, the difference is an optional repeated-not-semi-
478 colon expression following the captured \S+. This means the
479 regexp works when the division looks like /PRO;/ or when the
480 division looks like /ANG ;/ - the latter is from EMBL
483 * fix ID line parsing: the molecule string can have spaces in
484 it. Like: "genomic DNA"
486 - swiss.pm: bugs #1727, #1734
489 * Added parser for entrezgene ASN1 (text format) files.
490 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
494 - maf.pm coordinate problem fixed
496 o Bio::Taxonomy and Bio::DB::Taxonomy
498 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
499 can be done via Web without downloading all the sequence.
501 o Bio::Tools::Run::RemoteBlast supports more options and complies
502 to changes to the NCBI interface. It is reccomended that you
503 retrieve the data in XML instead of plain-text BLAST report to
504 insure proper parsing and retrieval of all information as NCBI
505 fully expects to change things in the future.
507 o Bio::Tree and Bio::TreeIO
509 - Fixes so that re-rooting a tree works properly
511 - Writing out nhx format from a newick/nexus file will properly output
512 bootstrap information. The use must move the internal node labels over
514 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
515 $node->bootstrap($node->id);
518 - Nexus parsing is much more flexible now, does not care about
521 - Cladogram drawing module in Bio::Tree::Draw
523 - Node height and depth now properly calculated
525 - fix tree pruning algorithm so that node with 1 child gets merged
527 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
528 bugs and improvements were added, see Gbrowse mailing list for most of
531 o Bio::DB::GFF partially supports GFF3. See information about
532 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
534 o Better location parsing in Bio::Factory::FTLocationFactory -
535 this is part of the engine for parsing EMBL/GenBank feature table
536 locations. Nested join/order-by/complement are allowed now
538 o Bio::PrimarySeqI->translate now takes named parameters
540 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
541 reconstruction) is now supported. Parsing different models and
542 branch specific parametes are now supported.
544 o Bio::Factory::FTLocationFactory - parse hierarchical locations
547 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
548 for getter/setter functions
552 - blast bug #1739; match scientific notation in score
553 and possible e+ values
555 - blast.pm reads more WU-BLAST parameters and parameters, match
556 a full database pathname,
558 - Handle NCBI WEB and newer BLAST formats specifically
559 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
561 - psl off-by-one error fixed
563 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
564 and HSPs can be constructed from them.
566 - HSPs query/hit now have a seqdesc field filled out (this was
567 always available via $hit->description and
568 $result->query_description
570 - hmmer.pm can parse -A0 hmmpfam files
572 - Writer::GbrowseGFF more customizeable.
574 o Bio::Tools::Hmmpfam
575 make e-value default score displayed in gff, rather than raw score
576 allow parse of multiple records
579 1.5 Developer release
581 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
582 provide Jukes-Cantor and Kimura pairwise distance methods,
585 o Bio::AlignIO support for "po" format of POA, and "maf";
586 Bio::AlignIO::largemultifasta is a new alternative to
587 Bio::AlignIO::fasta for temporary file-based manipulation of
588 particularly large multiple sequence alignments.
590 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
591 be treated similarly as an assembled contig.
593 o Bio::CodonUsage provides new rare_codon() and probable_codons()
594 methods for identifying particular codons that encode a given
597 o Bio::Coordinate::Utils provides new from_align() method to build
598 a Bio::Coordinate pair directly from a
599 Bio::Align::AlignI-conforming object.
601 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
602 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
603 web service using standard Pubmed query syntax, and retrieve
606 o Bio::DB::GFF has various sundry bug fixes.
608 o Bio::FeatureIO is a new SeqIO-style subsystem for
609 writing/reading genomic features to/from files. I/O classes
610 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
611 classes only read/write Bio::SeqFeature::Annotated objects.
612 Notably, the GFF v3 class requires features to be typed into the
615 o Bio::Graph namespace contains new modules for manipulation and
616 analysis of protein interaction graphs.
618 o Bio::Graphics has many bug fixes and shiny new glyphs.
620 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
621 indexing for HMMER reports and FASTA qual files, respectively.
623 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
624 new objects that can be placed within a Bio::Map::MapI-compliant
625 genetic/physical map; Bio::Map::Physical provides a new physical
626 map type; Bio::MapIO::fpc provides finger-printed clone mapping
629 o Bio::Matrix::PSM provide new support for postion-specific
630 (scoring) matrices (e.g. profiles, or "possums").
632 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
633 be instantiated without explicitly using Bio::OntologyIO. This
634 is possible through changes to Bio::Ontology::OntologyStore to
635 download ontology files from the web as necessary. Locations of
636 ontology files are hard-coded into
637 Bio::Ontology::DocumentRegistry.
639 o Bio::PopGen includes many new methods and data types for
640 population genetics analyses.
642 o New constructor to Bio::Range, unions(). Given a list of
643 ranges, returns another list of "flattened" ranges --
644 overlapping ranges are merged into a single range with the
645 mininum and maximum coordinates of the entire overlapping group.
647 o Bio::Root::IO now supports -url, in addition to -file and -fh.
648 The new -url argument allows one to specify the network address
649 of a file for input. -url currently only works for GET
650 requests, and thus is read-only.
652 o Bio::SearchIO::hmmer now returns individual Hit objects for each
653 domain alignment (thus containing only one HSP); previously
654 separate alignments would be merged into one hit if the domain
655 involved in the alignments was the same, but this only worked
656 when the repeated domain occured without interruption by any
657 other domain, leading to a confusing mixture of Hit and HSP
660 o Bio::Search::Result::ResultI-compliant report objects now
661 implement the "get_statistics" method to access
662 Bio::Search::StatisticsI objects that encapsulate any
663 statistical parameters associated with the search (e.g. Karlin's
664 lambda for BLAST/FASTA).
666 o Bio::Seq::LargeLocatableSeq combines the functionality already
667 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
669 o Bio::SeqFeature::Annotated is a replacement for
670 Bio::SeqFeature::Generic. It breaks compliance with the
671 Bio::SeqFeatureI interface because the author was sick of
672 dealing with untyped annotation tags. All
673 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
674 compliant, and accessible through Bio::Annotation::Collection.
676 o Bio::SeqFeature::Primer implements a Tm() method for primer
677 melting point predictions.
679 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
680 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
682 o Bio::Taxonomy::Node now implements the methods necessary for
683 Bio::Species interoperability.
685 o Bio::Tools::CodonTable has new reverse_translate_all() and
686 make_iupac_string() methods.
688 o Bio::Tools::dpAlign now provides sequence profile alignments.
690 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
692 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
695 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
696 for designing small inhibitory RNA.
698 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
699 methods based on a distance matrix.
701 o Bio::Tree::Statistics provides an assess_bootstrap() method to
702 calculate bootstrap support values on a guide tree topology,
703 based on provided bootstrap tree topologies.
705 o Bio::TreeIO now supports the Pagel (PAG) tree format.
711 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
713 o Bio::Graphics will work with gd1 or gd2
716 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
718 - blast.pm Parse multi-line query fields properly
719 - small speed improvements to blasttable.pm and others
721 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
722 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
723 supporting more complex queries
726 1.4. Stable major release
728 Since initial 1.2.0, 3000 separate changes have been made to make this release.
730 o installable scripts
732 o global module version from Bio::Root:Version
735 - major improvements; SVG support
738 - population genetics
739 - support several population genetics types of questions.
740 - Tests for statistical neutrality of mutations
741 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
742 Tests of population structure (Wright's F-statistic: Fst) is in
743 Bio::PopGen::PopStats. Calculating composite linkage
744 disequilibrium (LD) is available in Bio::PopGen::Statistics as
746 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
747 and csv (comma delimited formatted) data.
749 - a directory for implementing population simulations has
750 been added Bio::PopGen::Simulation and 2 simulations - a
751 Coalescent and a simple single-locus multi-allele genetic drift
752 simulation have been provided. This replaces the code in
753 Bio::Tree::RandomTree which has been deprecated until proper
754 methods for generating random phylogenetic trees are
758 - new restrion analysis modules
760 o Bio::Tools::Analysis
761 - web based DNA and Protein analysis framework and several
765 - per residue annotable sequences
768 - Bio::Matrix::PSM - Position Scoring Matrix
769 - Bio::Matrix::IO has been added for generalized parsing of
770 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
771 initial implementations for parsing BLOSUM/PAM and Phylip
772 Distance matricies respectively. A generic matrix
773 implementation for general use was added in
774 Bio::Matrix::Generic.
781 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
782 - small inhibitory RNA
784 o Bio::SeqFeature::Tools
785 - seqFeature mapping tools
786 - Bio::SeqFeature::Tools::Unflattener.pm
787 -- deal with mapping GenBank feature collections into
788 Chado/GFF3 processable feature sets (with SO term mappings)
790 o Bio::Tools::dpAlign
791 - pure perl dynamic programming sequence alignment
794 o new Bio::SearchIO formats
795 - axt and psl: UCSC formats.
796 - blasttable: NCBI -m 8 or -m 9 format from blastall
798 o new Bio::SeqIO formats
799 - chado, tab, kegg, tigr, game
800 - important fixes for old modules
804 o improved Bio::Tools::Genewise
806 o Bio::SeqIO now can recongnize sequence formats automatically from
809 o new parsers in Bio::Tools:
810 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
812 o Bio::DB::Registry bugs fixed
813 - BerkeleyDB-indexed flat files can be used by the OBDA system
814 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
815 used by the OBDA system
818 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
821 o hundreds of new and improved files
825 o Bio::Tree::AlleleNode has been updated to be a container of
826 an Bio::PopGen::Individual object for use in the Coalescent simulations.
831 1.2.3 Stable release update
832 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
834 o Bug #1477 - Sel --> Sec abbreviation fixed
835 o Fix bug #1487 where paring in-between locations when
836 end < start caused the FTLocationFactory logic to fail.
837 o Fix bug #1489 which was not dealing with keywords as an
838 arrayref properly (this is fixed on the main trunk because
839 keywords returns a string and the array is accessible via
841 o Bio::Tree::Tree memory leak (bug #1480) fixed
842 Added a new initialization option -nodelete which
843 won't try and cleanup the containing nodes if this
845 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
846 this was only present on the branch for the 1.2.1 and 1.2.2 series
847 - Also merged main trunk changes to the branch which make
848 newick -> nhx round tripping more effective (storing branch length
849 and bootstrap values in same locate for NodeNHX and Node
850 implementations.) Fixes to TreeIO parsing for labeled internal
851 also required small changes to TreeIO::nhx. Improved
852 tests for this module as well.
854 - Fixed bugs in BLAST parsing which couldn't parse NCBI
855 gapped blast properly (was losing hit significance values due to
856 the extra unexpeted column).
857 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
858 integer overflow (# of letters in nt seq dbs is > MAX_INT)
859 although doesn't try to correct it - will get the negative
860 number for you. Added a test for this as well.
861 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
862 has no top-level family classification scores but does have scores and
863 alignments for individual domains.
864 - Parsing FASTA reports where ungapped percent ID is < 10 and the
865 regular expression to match the line was missing the possibility of
866 an extra space. This is rare, which is why we probably did not
868 - BLAST parsing picks up more of the statistics/parameter fields
869 at the bottom of reports. Still not fully complete.
870 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
871 were fixed to include many improvements and added flexiblity
872 in outputting the files. Bug #1495 was also fixed in the process.
874 - Update for GFF3 compatibility.
875 - Added scripts for importing from UCSC and GenBank.
876 - Added a 1.2003 version number.
879 - Added a 1.2003 version number.
880 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
881 properly writing keywords out.
882 o Bio::SeqIO::genbank
883 - Fixed bug/enhancement #1513 where dates of
884 the form D-MMM-YYYY were not parsed. Even though this is
885 invalid format we can handle it - and also cleanup the date
886 string so it is properly formatted.
887 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
888 and written with Genbank format. Similarly bug #1515 is fixed to
889 parse in the ORIGIN text.
890 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
891 to specify the ID type, one of (accession accession.version
892 display primary). See Bio::SeqIO::preferred_id_type method
893 documentation for more information.
894 o Unigene parsing updated to handle file format changes by NCBI
896 1.2.2 Stable release update
898 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
899 - auto-discover ontology name
900 - bug in parsing relationships when certain characters are in the term
901 - fixed hard-coded prefix for term identifiers
902 - various smaller issues
904 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
905 of Bio::Ontology::TermI
907 o brought the OBDA Registry code up to latest specs
911 - accession number retrieval fixed
913 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
915 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
916 #1459 which now properly report alignment start/end info
917 for translated BLAST/FASTA searches.
919 o Bio::TreeIO::newick can parse labeled internal nodes
921 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
922 for BLASTX if if you provide -report_type => 'BLASTX' when
923 initializing a BPbl2seq object. Bioperl 1.3 will have better
924 support for bl2seq in the SearchIO system.
926 o Bio::Root::IO support a -noclose boolean flag which will not
927 close a filehandle upon object cleanup - useful when sharing
928 a filehandle among objects. Additionally code added s.t.
929 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
931 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
933 o Bio::SeqIO::genbank
934 - bug #1456 fixed which generated extra sequence lines
935 - write moltype correctly for genpept
937 1.2.1 Stable release update
939 o Inclusion of WrapperBase, a needed component for StandAloneBlast
941 o Addition from main trunk of Ontology objects, principly to allow
942 BioSQL releases against 1.2.1
944 o Fixes and cleanup of Bio::Coordinate modules
946 o A fix to Bio::Index::EMBL allowing retrieval of entries using
947 the primary accession number
949 o Other bug fixes, including bpindex GenBank fix
951 o Bio::SeqIO::genbank bug #1389 fixed
953 1.2 Stable major release
955 o More functionality added to Bio::Perl, the newbie module
957 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
958 Support for New Hampshire Extended (NHX) format parsing.
960 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
961 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
964 o New ontology parsing Bio::Ontology
966 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
967 multi-report (mlib) fasta reports, support for waba and exonerate.
969 o Bio::ClusterIO for parsing Unigene clusters
971 o Bio::Assembly added for representing phrap and ace assembly clusters.
973 o Rudimentary support for writing Chado XML (see
974 GMOD project: www.gmod.org for more information)
976 o Bio::Coordinate for mapping between different coordinate systems such
977 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
978 features into different coordinate systems.
980 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
981 with the get_Stream_by_query method and supports the latest
982 NCBI eutils interface.
984 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
985 object for extracting subsets of features : currently only
986 supports extraction by location.
988 1.1.1 Developer release
990 o Deprecated modules are now listed in the DEPRECATED file
992 o New HowTo documents located in doc/howto describing
995 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
996 and all old bugs are searchable through the bugzilla interface.
998 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1001 o Support for Genewise parsing in Bio::Tools::Genewise
1003 o Start of Ontology framework with Bio::Ontology
1005 o Speedup to the Bio::Root::Root object method _rearrange.
1006 A global _load_module method was implemented to simplify the
1007 dynamic loading of modules ala Bio::SeqIO::genbank. This
1008 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1011 o Several performance improvements to sequence parsing in Bio::SeqIO.
1012 Attempt to speedup by reducing object creation overhead.
1014 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1015 method for sequence retrieval with their E-utils CGI scripts.
1016 More work to support Entrez queries to their fullest is planned
1019 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1021 1.1 Developer release
1023 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1024 this separation removes some of the complexity in our test suite
1025 and separates the core modules in bioperl from those that need
1026 external programs to run.
1028 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1029 not run into trouble running the makefile
1031 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1032 read,create,and write locations for grouped/split locations
1033 (like mRNA features on genomic sequence).
1035 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1036 and PAML (codeml,aaml, etc) parsing.
1038 o Bio::Tree:: objects expanded to handle testing monophyly,
1039 paraphyly, least common ancestor, etc.
1041 o Bio::Coordinate for mapping locations from different coordinate spaces
1043 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1044 added for parsing hmmpfam and hmmsearch output.
1046 o Bio::SearchIO::Writer::TextResultWriter for outputting
1047 a pseudo-blast textfile format
1050 1.0.2 Bug fix release
1052 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1053 in this release will not work after December 2002 when NCBI
1054 shuts off the old Entrez cgi scripts. We have already fixed
1055 on our main development branch and the functionality will be
1056 available in the next stable bioperl release (1.2) slated for
1059 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1060 testset by Robin Emig. These were fixed as was the get_aln
1061 method in Bio::Search::HSP::GenericHSP to handle the extra
1062 context sequence that is provided with a FastA alignment.
1064 o Migrating differences between Bio::Search::XX::BlastXX to
1065 Bio::Search::XX::GenericXX objects. This included mechanism
1066 to retrieve whole list of HSPs from Hits and whole list of Hits from
1067 Results in addition to the current next_XX iterator methods that
1068 are available. Added seq_inds() method to GenericHSP which identifies
1069 indexes in the query or hit sequences where conserved,identical,gaps,
1070 or mismatch residues are located (adapted from Steve Chervitz's
1071 implementation in BlastHSP).
1073 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1074 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1076 o Bio::Graphics glyph set improved and extended for GBrowse release
1078 o Bio::Tree::Tree get_nodes implementation improvement thanks
1079 to Howard Ross notice performance problem when writing out
1082 o Bio::Location::Fuzzy::new named parameter -loc_type became
1083 -location_type, Bio::Location::Simple::new named parameter
1084 -seqid becamse -seq_id.
1086 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1087 was mis-detecting that gaps should be placed at the beginning of
1088 the alignment when the best alignment starts internally in the
1091 1.0.1 Bug fix release
1093 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1095 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1096 and mixed (3.3 - 3.4) versions of FASTA.
1098 o Small API change to add methods for completeness across
1099 implementations of Bio::Search objects. These new methods
1100 in the interface are implemented by the GenericXX object as well
1101 as the BlastXX objects.
1102 * Bio::Search::Result::ResultI
1103 - hits() method returns list of all Hits (next_hit is an
1106 * Bio::Search::Hit::HitI
1107 - hsps() method returns list of all HSPs (next_hsp is an
1110 o The Bio::SearchIO::Writer classes have been fixed to handle results
1111 created from either psiblast (Search::BlastXX objects) or
1112 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1113 has to be done here to make it work properly and will nee major
1116 o Bugs in Bio::Tools::HMMER fixed, including
1117 * #1178 - Root::IO destructor wasn't being called
1118 * #1034 - filter_on_cutoff now behaves properly
1120 o Bio::SeqFeature::Computation initialization args fixed and
1123 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1125 o Updated FAQ with more example based answers to typical questions
1127 o Bug #1202 was fixed which would improperly join together qual values
1128 parsed by Bio::SeqIO::qual when a trailing space was not present before
1131 1.0.0 Major Stable Release
1133 This represents a major release of bioperl with significant
1134 improvements over the 0.7.x series of releases.
1136 o Bio::Tools::Blast is officially deprecated. Please see
1137 Bio::SearchIO for BLAST and FastA parsing.
1139 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1140 Bio::LocationI objects as well as start/end.
1142 o Bio::Biblio contains modules for Bibliographic data.
1143 Bio::DB::Biblio contains the query modules. Additionally one can
1144 parse medlinexml from the ebi bibliographic query service (BQS)
1145 system and Pubmed xml from NCBI. See Martin Senger's
1146 documentation in Bio::Biblio for more information.
1148 o Bio::DB::Registry is a sequence database registry part of
1149 Open Bioinformatics Database Access. See
1150 http://obda.open-bio.org for more information.
1152 o File-based and In-Memory Sequence caching is provided by
1153 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1156 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1157 been added by Lincoln Stein.
1159 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1161 o A FAQ has been started and is included in the release to provide
1162 a starting point for frequent questions and issues.
1164 0.9.3 Developer's release
1166 o Event based parsing system improved (SearchIO). With parsers for
1167 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1168 Additionally a lazy parsing system for text and html blast reports was
1169 added and is called psiblast (name subject to change in future releases).
1171 o Bio::Search objects improved and standardized with associated Interfaces
1172 written. The concept of a search "Hit" was standardized to be called
1173 "hit" consistently and the use of "subject" was deprecated in all active
1176 o Bio::Structure added (since 0.9.1) for Protein structure objects
1177 and PDB parser to retrieve and write these structures from data files.
1179 o Several important Bio::DB::GFF bug fixes for handling features that
1180 are mapped to multiple reference points. Updated mysql adaptor
1181 so as to be able to store large (>100 megabase) chunks of DNA into
1182 Bio::DB::GFF databases.
1184 0.9.2 Developer's release
1186 o Bio::Search and Bio::SearchIO system introduced for event based
1187 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1188 in text and XML and FASTA reports in standard output format.
1190 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1191 generator is included in Bio::TreeIO::RandomTrees and a
1192 statistics module for evaluating.
1194 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1195 server for DAS servers.
1197 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1198 files. The entire BPlite system migrated to using Bio::Root::IO
1199 for the data stream.
1201 o Bio::Tools::Alignment for Consed and sequence Trimming
1204 o Bio::Structure for Protein structure information and parsing
1206 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1207 cgi-bin entry point which should be more reliable.
1209 o Bio::Map and Bio::MapIO for biological map navigation and a
1210 framework afor parsing them in. Only preliminary work here.
1212 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1213 Future work will integrate Pise and allow submission of analysis on
1216 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1217 introduced as new objects for handling Sequence Annotation
1218 information (dblinks, references, etc) and is more robust that
1221 o Bio::Tools::FASTAParser introduced.
1223 o Scripts from the bioperl script submission project and new
1224 scripts from bioperl authors are included in "scripts" directory.
1226 o Factory objects and interfaces are being introduced and are more
1229 o Bio::Root::Root introduced as the base object while
1230 Bio::Root::RootI is now simply an interface.
1232 o Bio::DB::RefSeq provides database access to copy of the NCBI
1233 RefSeq database using the EBI dbfetch script.
1235 0.9.0 Developer's release
1237 o perl version at least 5.005 is now required instead of perl 5.004
1239 o Bio::Tools::Run::RemoteBlast is available for running remote
1242 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1244 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1245 Also added are related modules UTR3, UTR5, Exon, Intron,
1246 Promotor, PolyA and Transcript.
1248 o Speedup of translate method in PrimarySeq
1250 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1251 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1253 o Various fixes to Variation toolkit
1255 o Bio::DB::EMBL provides database access to EMBL sequence data.
1256 Bio::DB::Universal provides a central way to point to indexes
1257 and dbs in a single interface.
1259 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1261 o Bio::Factory::EMBOSS is still in design phase as is
1262 Bio::Factory::ApplicationFactoryI
1264 o Dia models for bioperl design are provided in the models/ directory
1266 0.7.2 Bug fix release
1268 o documentation fixes in many modules - SYNOPSIS code verified
1269 to be runnable in many (but not all modules)
1271 o corrected MANIFEST file from 0.7.1 release
1273 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1276 o Bio::SeqIO::genbank
1277 * Correct parsing and writing of genbank format with protein data
1278 * moltype and molecule separation
1280 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1282 o Bio::SimpleAlign fixed to correctly handle consensus
1283 sequence calculation
1285 o Bio::Tools::HMMER supports hmmer 2.2g
1287 o Bio::Tools::BPlite to support report type specific parsing. Most
1288 major changes are not on the 0.7 branch.
1290 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1293 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1294 in several types of mutations:
1295 1.) AA level: deletion, complex
1296 2.) AA level: complex, inframe
1297 3.) RNA level: silent
1299 o BPbl2seq parsing of empty reports will not die, but will return
1300 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1301 $report->query() and $report->subject() methods. So an easy
1302 way to test if report was empty is to see if
1303 $report->query->seqname is undefined.
1305 0.7.1 Bug fix release
1307 o Better parsing of genbank/EMBL files especially fixing bugs
1308 related to Feature table parsing and locations on remote
1309 sequences. Additionally, species name parsing was better.
1311 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1312 which include a number of header lines.
1314 o More strict genbank and EMBL format writing (corrected number of
1315 spaces where appropriate).
1317 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1318 for related BPlite BUGS that are unresolved in this release.
1320 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1321 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1322 use expasy mirrors or EBI dbfetch cgi-script.
1324 o A moderate number of documentation improvements were made as
1325 well to provide a better code synopsis in each module.
1328 0.7 Large number of changes, including refactoring of the
1329 Object system, new parsers, new functionality and
1330 all round better system. Highlights are:
1333 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1334 Bio::Root::IO for I/O and file/handle capabilities.
1336 o Imported BPlite modules from Ian Korf for BLAST
1337 parsing. This is considered the supported BLAST parser;
1338 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1340 o Improved Sequence Feature model. Added complete location
1341 modelling (with fuzzy and compound locations). See
1342 Bio::LocationI and the modules under Bio/Location. Added
1343 support in Genbank/EMBL format parsing to completely parse
1344 feature tables for complex locations.
1346 o Moved special support for databanks etc to specialized modules under
1347 Bio/Seq/. One of these supports very large sequences through
1348 a temporary file as a backend.
1350 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1351 CDS retrieval and exon shuffling.
1353 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1355 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1356 DB/GDB (the latter has platform-specific limitations).
1358 o New analysis parser framework for HT sequence annotation (see
1359 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1361 o New Alignment IO framework
1363 o New Index modules (Swissprot)
1365 o New modules for running Blast within perl
1366 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1367 Multiple Sequence Alignment tools ClustalW and TCoffee
1368 (Bio::Tools::Run::Alignment).
1370 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1371 documentation across the package.
1373 o Much improved cross platform support. Many known incompatibilities
1374 have been fixed; however, NT and Mac do not work across the entire
1375 setup (see PLATFORMS).
1377 o Many bug fixes, code restructuring, etc. Overall stability and
1378 maintainability benefit a lot.
1380 o A total of 957 automatic tests
1385 There are very few functionality changes but a large
1386 number of software improvements/bug fixes across the package.
1388 o The EMBL/GenBank parsing are improved.
1390 o The Swissprot reading is improved. Swissprot writing
1391 is disabled as it doesn't work at all. This needs to
1392 wait for 0.7 release
1394 o BLAST reports with no hits are correctly parsed.
1396 o Several other bugs of the BLAST parser (regular expressions, ...)
1399 o Old syntax calls have been replaced with more modern syntax
1401 o Modules that did not work at all, in particular the Sim4
1402 set have been removed
1404 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1405 have improved compliance with interface specs and documentation
1407 o Mailing list documentation updated throughout the distribution
1409 o Most minor bug fixes have happened.
1411 o The scripts in /examples now work and have the modern syntax
1412 rather than the deprecated syntax
1415 0.6.1 Sun April 2 2000
1417 o Sequences can have Sequence Features attached to them
1418 - The sequence features can be read from or written to
1419 EMBL and GenBank style flat files
1421 o Objects for Annotation, including References (but not
1422 full medline abstracts), Database links and Comments are
1425 o A Species object to represent nodes on a taxonomy tree
1428 o The ability to parse HMMER and Sim4 output has been added
1430 o The Blast parsing has been improved, with better PSI-BLAST
1431 support and better overall behaviour.
1433 o Flat file indexed databases provide both random access
1434 and sequential access to their component sequences.
1436 o A CodonTable object has been written with all known
1437 CodonTables accessible.
1439 o A number of new lightweight analysis tools have been
1440 added, such as molecular weight determination.
1442 The 0.6 release also has improved software engineering
1444 o The sequence objects have been rewritten, providing more
1445 maintainable and easier to implement objects. These
1446 objects are backwardly compatible with the 0.05.1 objects
1448 o Many objects are defined in terms of interfaces and then
1449 a Perl implementation has been provided. The interfaces
1450 are found in the 'I' files (module names ending in 'I').
1452 This means that it is possible to wrap C/CORBA/SQL access
1453 as true "bioperl" objects, compatible with the rest of
1456 o The SeqIO system has been overhauled to provide better
1457 processing and perl-like automatic interpretation of <>
1460 o Many more tests have been added (a total of 172 automatic
1461 tests are now run before release).
1465 0.05.1 Tue Jun 29 05:30:44 1999
1466 - Central distribution now requires Perl 5.004. This was
1467 done to get around 5.003-based problems in Bio/Index/*
1469 - Various bug fixes in the Bio::Tools::Blast modules
1470 including better exception handling and PSI-Blast
1471 support. See Bio/Tools/Blast/CHANGES for more.
1472 - Fixed the Parse mechanism in Seq.pm to use readseq.
1473 Follow the instructions in README for how to install
1474 it (basically, you have to edit Parse.pm).
1475 - Improved documentation of Seq.pm, indicating where
1476 objects are returned and where strings are returned.
1477 - Fixed uninitialized warnings in Bio::Root::Object.pm
1478 and Bio::Tools::SeqPattern.pm.
1479 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1481 0.05 Sun Apr 25 01:14:11 1999
1482 - Bio::Tools::Blast modules have less memory problems
1483 and faster parsing. Webblast uses LWP and supports
1484 more functionality. See Bio/Tools/Blast/CHANGES for more.
1485 - The Bio::SeqIO system has been started, moving the
1486 sequence reformatting code out of the sequence object
1487 - The Bio::Index:: system has been started, providing
1488 generic index capabilities and specifically works for
1489 Fasta formatted databases and EMBL .dat formatted
1491 - The Bio::DB:: system started, providing access to
1492 databases, both via flat file + index (see above) and
1494 - The scripts/ directory, where industrial strength scripts
1495 are put has been started.
1496 - Many changes - a better distribution all round.
1498 0.04.4 Wed Feb 17 02:20:13 1999
1499 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1500 (see Bio::Tools::Blast::CHANGES).
1501 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1502 - Beefed up the t/Fasta.t test script.
1503 - Small fix in Bio::Seq::type() (now always returns a string).
1504 - Changed Bio::Root::Utilities::get_newline_char() to
1505 get_newline() since it could return more than one char.
1506 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1507 - Changed default timeout to 20 seconds (was 3).
1508 - Moved lengthy modification notes to the bottom of some files.
1509 - Fixed SimpleAlign write_fasta bug.
1510 - Beefed up SimpleAlign.t test
1512 0.04.3 Thu Feb 4 07:48:53 1999
1513 - Bio::Root::Object.pm and Global.pm now detect when
1514 script is run as a CGI and suppress output that is only
1515 appropriate when running interactively.
1516 - Bio::Root::Err::_set_context() adds name of script ($0).
1517 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1518 regarding the use of the static objects via the qw(:obj) tag.
1519 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1520 CORE::reverse, avoiding Perl warnings.
1521 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1522 example scripts (see Bio::Tools::Blast::CHANGES).
1523 - examples/seq/seqtools.pl no longer always warns about using
1524 -prot or -nucl command-line arguments; only when using the
1526 - Methods added to Bio::Root::Utilities: create_filehandle(),
1527 get_newline_char(), and taste_file() to generalize filehandle
1528 creation and autodetect newline characters in files/streams
1529 (see bug report #19).
1530 - Bio::Root::IOManager::read() now handles timeouts and uses
1531 Utilities::create_filehandle().
1532 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1533 of hardwiring in "\n".
1534 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1536 0.04.2 Wed Dec 30 02:27:36 1998
1537 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1538 (see Bio::Tools::Blast::CHANGES).
1539 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1540 to CORE::reverse (prevents ambiguous warnings with 5.005).
1541 - Appending '.tmp.bioperl' to temporary files created by
1542 Bio::Root::Utilities::compress() or uncompress() to
1543 make it easy to identify & cleanup these files as needed.
1544 - Developers: Created CVS branch release-0-04-bug from
1545 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1546 be sure to cvs checkout this branch into a clean area.
1548 0.04.1 Wed Dec 16 05:39:15 1998
1549 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1550 (see Bio::Tools::Blast::CHANGES).
1551 - Compile/SW/Makefile.PL now removes *.o and *.a files
1554 0.04 Tue Dec 8 07:49:19 1998
1555 - Lots of new modules added including:
1556 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1557 and Bio/Compile directory containing XS-linked C code for
1558 creating Smith-Waterman sequence alignments from within Perl.
1559 * Steve Chervitz's Blast distribution has been incorporated.
1560 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1561 - Bio/examples directory for demo scripts for all included modules.
1562 - Bio/t directory containing test suit for all included modules.
1563 - For changes specific to the Blast-related modules prior to
1564 incorporation in this central distribution, see the CHANGES
1565 file in the Bio/Tools/Blast directory.
1567 0.01 Tue Sep 8 14:23:22 1998
1568 - original version from central CVS tree; created by h2xs 1.18