1 ---------------------------------------------------------
2 Revision history for BioPerl core modules
3 ---------------------------------------------------------
4 The comprehensive history and ongoing development of BioPerl:
6 http://github.com/bioperl/bioperl-live
8 Some of that history is also highlighted on our wiki:
10 http://www.bioperl.org/wiki/Change_log
11 http://www.bioperl.org/wiki/History_of_BioPerl
13 Bugs and requested features list:
15 https://redmine.open-bio.org/projects/bioperl
17 CPAN releases are branched from 'master'.
18 ---------------------------------------------------------
20 1.6.900 April 14, 2011
24 * This will probably be the last release to add significant features to
25 core modules; subsequent releases will be for bug fixes alone.
26 We are planning on a restructuring of core for summer 2011, potentially
27 as part of the Google Summer of Code. This may become BioPerl 2.0.
28 * Version bump represents 'just prior to v 1.7'. We may have point
29 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
30 This code essentially is what is on the github master branch.
34 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
36 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
37 - removal of Scalar::Util::weaken code, which was causing odd headaches
38 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
39 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
41 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
44 - bug 2515 - new contribution [Ryan Golhar, jhannah]
46 - support for reading Maq, Sam and Bowtie files [maj]
47 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
48 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
49 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
50 - bug 2726: reading/writing granularity: whole scaffold or one contig
51 at a time [Joshua Udall, fangly]
53 - Added parsing of xrefs to OBO files, which are stored as secondary
54 dbxrefs of the cvterm [Naama Menda]
55 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
56 * PAML code updated to work with PAML 4.4d [DaveMessina]
60 * [3198] - sort tabular BLAST hits by score [DaveMessina]
61 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
62 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
63 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
65 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
66 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
67 * [3164] - TreeFunctionsI syntax bug [gjuggler]
68 * [3163] - AssemblyIO speedup [fangly]
69 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
71 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
72 * [3158] - fix EMBL file mis-parsing [cjfields]
73 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
75 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
76 * [3148] - URL change for UniProt [cjfields]
77 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
78 * [3136] - HMMer3 parser fixes [kblin]
79 * [3126] - catch description [Toshihiko Akiba]
80 * [3122] - Catch instances where non-seekable filehandles were being
81 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
82 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
83 [dukeleto, rbuels, cjfields]
84 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
86 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
87 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
89 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
90 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
91 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
92 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
93 * [3086] - EMBL misparsing long tags [kblin, cjfields]
94 * [3085] - CommandExts and array of files [maj, hyphaltip]
95 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
96 for alignment slices [Ha X. Dang, cjfields]
97 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
98 * [3073] - fix parsing of GenBank files from RDP [cjfields]
99 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
100 * [3064] - All-gap midline BLAST report issues [cjfields]
101 * [3063] - BLASt report RID [Razi Khaja, cjfields]
102 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
103 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
104 * [3039] - correct Newick output root node branch length [gjuggler,
106 * [3038] - SELEX alignment error [Bernd, cjfields]
107 * [3033] - PrimarySeq ID setting [Bernd, maj]
108 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
109 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
110 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
111 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
112 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
113 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
114 PAML 4.4d [DaveMessina]
115 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
117 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
118 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
119 * [3017] - using threads with Bio::DB::GenBank [cjfields]
120 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
121 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
122 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
123 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
124 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
126 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
127 * [2977] - TreeIO issues [DaveMessina]
128 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
129 * [2944] - Bio::Tools::GFF score [cjfields]
130 * [2942] - correct MapTiling output [maj]
131 * [2939] - PDB residue insertion codes [John May, maj]
132 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
133 * [2928] - GuessSeqFormat raw [maj]
134 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
135 * [2922] - open() directive issue [cjfields]
136 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
137 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
138 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
139 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
141 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
142 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
143 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
144 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
145 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
146 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
147 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
148 * [2758] - Bio::AssemblyIO ace problems [fangly]
149 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
150 * [2726] - ace file IO [Josh, fangly]
151 * [2700] - Refactor Build.PL [cjfields]
152 * [2673] - addition of simple Root-based clone() method [cjfields]
153 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
154 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
155 * [2594] - Bio::Species memory leak [cjfields]
156 * [2515] - GenBank XML parser [jhannah]
157 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
158 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
159 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
161 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
165 * Bio::Expression modules - these were originally designed to go with the
166 bioperl-microarray suite of tools, however they have never been completed
167 and so have been removed from the distribution. The original code has
168 been moved into the inactive bioperl-microarray suite. [cjfields]
172 * Repository moved from Subversion (SVN) to
173 http://github.com/bioperl/bioperl-live [cjfields]
174 * Bug database has moved to Redmine (https://redmine.open-bio.org)
175 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
176 Thieme have been moved to their own distribution (Bio-Microarray).
179 1.6.1 Sept. 29, 2009 (point release)
180 * No change from last alpha except VERSION and doc updates [cjfields]
182 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
183 * Fix for silent OBDA bug related to FASTA validation [cjfields]
185 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
186 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
187 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
189 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
191 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
192 * WinXP test fixes [cjfields, maj]
193 * BioPerl.pod added for descriptive information, fixes CPAN indexing
195 * Minor doc fixes [cjfields]
197 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
198 * Fix tests failing due to merging issues [cjfields]
199 * More documentation updates for POD parsing [cjfields]
201 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
203 - fix YAML meta data generation [cjfields]
205 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
206 * Bio::Align::DNAStatistics
207 - fix divide by zero problem [jason]
209 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
210 * Bio::AlignIO::stockholm
211 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
212 * Bio::Assembly::Tools::ContigSpectrum
213 - function to score contig spectrum [fangly]
214 * Bio::DB::EUtilities
215 - small updates [cjfields]
217 - berkeleydb database now autoindexes wig files and locks correctly
220 - various small updates for stability; tracking changes to LANL
221 database interface [maj]
222 * Bio::DB::SeqFeature (lots of updates and changes)
223 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
224 - bug 2835 - patch [Dan Bolser]
225 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
227 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
228 * Bio::Factory::FTLocationFactory
229 - mailing list bug fix [cjfields]
231 - performance work on column_from_residue_number [hartzell]
232 * Bio::Matrix::IO::phylip
233 - bug 2800 - patch to fix phylip parsing [Wei Zou]
235 - Google Summer of Code project from Chase Miller - parsers for Nexml
236 file format [maj, chmille4]
238 - Make Individual, Population, Marker objects AnnotatableI [maj]
239 - simplify LD code [jason]
241 - deal with empty intersection [jason]
243 - significant overhaul of Bio::Restriction system: complete support for
244 external and non-palindromic cutters. [maj]
246 - CPANPLUS support, no automatic installation [sendu]
248 - allow IO::String (regression fix) [cjfields]
249 - catch unintentional undef values [cjfields]
250 - throw if non-fh is passed to -fh [maj]
251 * Bio::Root::Root/RootI
252 - small debugging and core fixes [cjfields]
254 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
255 * Bio::Root::Utilities
256 - bug 2737 - better warnings [cjfields]
258 - tiling completely refactored, HOWTO added [maj]
259 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
260 will deprecate usage of the older tiling code in the next BioPerl
262 - small fixes [cjfields]
264 - Infernal 1.0 output now parsed [cjfields]
265 - new parser for gmap -f9 output [hartzell]
266 - bug 2852 - fix infinite loop in some output [cjfields]
267 - blastxml output now passes all TODO tests [cjfields]
268 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
269 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
270 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
271 * Bio::Seq::LargePrimarySeq
272 - delete tempdirs [cjfields]
273 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
275 - extract regions based on quality threshold value [Dan Bolser, heikki]
276 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
277 * Bio::SeqFeature::Lite
278 - various Bio::DB::SeqFeature-related fixes [lstein]
279 * Bio::SeqFeature::Tools::TypeMapper
280 - additional terms for GenBank to SO map [scain]
281 * Bio::SeqIO::chadoxml
282 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
284 - support for CDS records [dave_messina, Sylvia]
286 - complete refactoring to handle all FASTQ variants, perform validation,
287 write output. API now conforms with other Bio* parsers and the rest of
288 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
290 * Bio::SeqIO::genbank
291 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
292 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
293 * Bio::SeqIO::largefasta
294 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
296 - add option for 'single' and 'multiple'
298 - bug 2881 - fix scf round-tripping [Adam Sj¿gren]
300 - bug 2766, 2810 - copy over tags from features, doc fixes [David
303 - bug 2793 - patch for add_seq index issue [jhannah, maj]
304 - bug 2801 - throw if args are required [cjfields]
305 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
306 [Tristan Lefebure, maj]
307 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
308 - fix POD and add get_SeqFeatures filter [maj]
309 * Bio::Tools::dpAlign
310 - add support for LocatableSeq [ymc]
311 - to be moved to a separate distribution [cjfields, rbuels]
312 * Bio::Tools::EUtilities
313 - fix for two bugs from mail list [Adam Whitney, cjfields]
314 - add generic ItemContainerI interface for containing same methods
317 - fix up code, add more warnings [cjfields]
318 - to be moved to a separate distribution [cjfields, rbuels]
319 * Bio::Tools::Primer3
320 - bug 2862 - fenceposting issue fixed [maj]
321 * Bio::Tools::Run::RemoteBlast
322 - tests for remote RPS-BLAST [mcook]
323 * Bio::Tools::SeqPattern
324 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
325 * Bio::Tools::tRNAscanSE
326 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
328 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
329 * Bio::Tree::Statistics
330 - several methods for calculating Fitch-based score, internal trait
331 values, statratio(), sum of leaf distances [heikki]
333 - bug 2869 - add docs indicating edge case where nodes can be
334 prematurely garbage-collected [cjfields]
335 - add as_text() function to create Tree as a string in specified format
337 * Bio::Tree::TreeFunctionsI
338 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
340 * Bio::TreeIO::newick
341 - fix small semicolon issue [cjfields]
343 - update to bp_seqfeature_load for SQLite [lstein]
344 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
345 - fastam9_to_table - fix for MPI output [jason]
346 - gccalc - total stats [jason]
348 - POD cleanup re: FEEDBACK section [maj, cjfields]
349 - cleanup or fix dead links [cjfields]
350 - Use of no_* methods (indicating 'number of something') is deprecated
351 in favor of num_* [cjfields]
352 - lots of new tests for the above bugs and refactors [everyone!]
353 - new template for Komodo text editor [cjfields]
356 * Feature/Annotation rollback
357 - Problematic changes introduced prior to the 1.5 release have been
358 rolled back. These changes led to subtle bugs involving operator
359 overloading and interface methods.
360 - Behavior is very similar to that for BioPerl 1.4, with tag values
361 being stored generically as simple scalars. Results in a modest
364 - Split into a separate distribution on CPAN, primarily so development
365 isn't reliant on a complete BioPerl release.
366 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
367 is only available via Subversion (via bioperl-live main trunk)
369 - Common test bed for all BioPerl modules
371 - Common Module::Build-based subclass for all BioPerl modules
372 * Bio::DB::EUtilities
373 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
374 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
375 and user agent request posting and retrieval
376 * Test implementation and reorganization
377 - Tests have been reorganized into groups based on classes or use
379 - Automated test coverage is now online:
380 http://www.bioperl.org/wiki/Test_Coverage
381 - After this release, untested modules will be moved into a
382 separate developer distribution until tests can be derived.
383 Also, new modules to be added are expected to have a test suite
384 and adequate test coverage.
386 1.5.2 Developer release
388 Full details of changes since 1.5.1 are available online at:
389 http://www.bioperl.org/wiki/Change_log
390 The following represents a brief overview of the most important changes.
393 - Overhaul. Brand new system fully allows markers to have multiple
394 positions on multiple maps, and to have relative positions. Should be
398 - This module and all the modules in the Taxonomy directory now
399 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
404 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
406 * New methods ancestor(), each_Descendent() and _handle_internal_id().
408 * Allows for different database modules to create Bio::Taxon objects
409 with the same internal id when the same taxon is requested from each.
412 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
414 * No longer includes the fake root node 'root'; there are multiple roots
415 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
418 * get_node() has new option -full
420 * Caches data retrieved from website
423 - Now a Bio::Taxon. Carries out the species name -> specific name munging
424 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
425 backward compatability in species() method.
427 o Bio::Search and Bio::SearchIO
428 - Overhaul. The existing system has been sped up via some minor changes
429 (mostly gain-of-function to the API). Bio::PullParserI is introduced
430 as a potential eventual replacment for the existing system, though as
431 yet only a Hmmpfam parser exists written using it.
434 1.5.1 Developer release
436 o Major problem with how Annotations were written out with
437 Bio::Seq is fixed by reverting to old behavior for
438 Bio::Annotation objects.
443 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
444 expect at l east 9 spaces at the beginning of a line to
445 indicate line wrapping.
447 * Treat multi-line SOURCE sections correctly, this defect broke
448 both common_name() and classification()
450 * parse swissprot fields in genpept file
452 * parse WGS genbank records
455 * Changed regexp for ID line. The capturing parentheses are
456 the same, the difference is an optional repeated-not-semi-
457 colon expression following the captured \S+. This means the
458 regexp works when the division looks like /PRO;/ or when the
459 division looks like /ANG ;/ - the latter is from EMBL
462 * fix ID line parsing: the molecule string can have spaces in
463 it. Like: "genomic DNA"
465 - swiss.pm: bugs #1727, #1734
468 * Added parser for entrezgene ASN1 (text format) files.
469 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
473 - maf.pm coordinate problem fixed
475 o Bio::Taxonomy and Bio::DB::Taxonomy
477 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
478 can be done via Web without downloading all the sequence.
480 o Bio::Tools::Run::RemoteBlast supports more options and complies
481 to changes to the NCBI interface. It is reccomended that you
482 retrieve the data in XML instead of plain-text BLAST report to
483 insure proper parsing and retrieval of all information as NCBI
484 fully expects to change things in the future.
486 o Bio::Tree and Bio::TreeIO
488 - Fixes so that re-rooting a tree works properly
490 - Writing out nhx format from a newick/nexus file will properly output
491 bootstrap information. The use must move the internal node labels over
493 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
494 $node->bootstrap($node->id);
497 - Nexus parsing is much more flexible now, does not care about
500 - Cladogram drawing module in Bio::Tree::Draw
502 - Node height and depth now properly calculated
504 - fix tree pruning algorithm so that node with 1 child gets merged
506 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
507 bugs and improvements were added, see Gbrowse mailing list for most of
510 o Bio::DB::GFF partially supports GFF3. See information about
511 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
513 o Better location parsing in Bio::Factory::FTLocationFactory -
514 this is part of the engine for parsing EMBL/GenBank feature table
515 locations. Nested join/order-by/complement are allowed now
517 o Bio::PrimarySeqI->translate now takes named parameters
519 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
520 reconstruction) is now supported. Parsing different models and
521 branch specific parametes are now supported.
523 o Bio::Factory::FTLocationFactory - parse hierarchical locations
526 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
527 for getter/setter functions
531 - blast bug #1739; match scientific notation in score
532 and possible e+ values
534 - blast.pm reads more WU-BLAST parameters and parameters, match
535 a full database pathname,
537 - Handle NCBI WEB and newer BLAST formats specifically
538 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
540 - psl off-by-one error fixed
542 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
543 and HSPs can be constructed from them.
545 - HSPs query/hit now have a seqdesc field filled out (this was
546 always available via $hit->description and
547 $result->query_description
549 - hmmer.pm can parse -A0 hmmpfam files
551 - Writer::GbrowseGFF more customizeable.
553 o Bio::Tools::Hmmpfam
554 make e-value default score displayed in gff, rather than raw score
555 allow parse of multiple records
558 1.5 Developer release
560 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
561 provide Jukes-Cantor and Kimura pairwise distance methods,
564 o Bio::AlignIO support for "po" format of POA, and "maf";
565 Bio::AlignIO::largemultifasta is a new alternative to
566 Bio::AlignIO::fasta for temporary file-based manipulation of
567 particularly large multiple sequence alignments.
569 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
570 be treated similarly as an assembled contig.
572 o Bio::CodonUsage provides new rare_codon() and probable_codons()
573 methods for identifying particular codons that encode a given
576 o Bio::Coordinate::Utils provides new from_align() method to build
577 a Bio::Coordinate pair directly from a
578 Bio::Align::AlignI-conforming object.
580 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
581 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
582 web service using standard Pubmed query syntax, and retrieve
585 o Bio::DB::GFF has various sundry bug fixes.
587 o Bio::FeatureIO is a new SeqIO-style subsystem for
588 writing/reading genomic features to/from files. I/O classes
589 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
590 classes only read/write Bio::SeqFeature::Annotated objects.
591 Notably, the GFF v3 class requires features to be typed into the
594 o Bio::Graph namespace contains new modules for manipulation and
595 analysis of protein interaction graphs.
597 o Bio::Graphics has many bug fixes and shiny new glyphs.
599 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
600 indexing for HMMER reports and FASTA qual files, respectively.
602 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
603 new objects that can be placed within a Bio::Map::MapI-compliant
604 genetic/physical map; Bio::Map::Physical provides a new physical
605 map type; Bio::MapIO::fpc provides finger-printed clone mapping
608 o Bio::Matrix::PSM provide new support for postion-specific
609 (scoring) matrices (e.g. profiles, or "possums").
611 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
612 be instantiated without explicitly using Bio::OntologyIO. This
613 is possible through changes to Bio::Ontology::OntologyStore to
614 download ontology files from the web as necessary. Locations of
615 ontology files are hard-coded into
616 Bio::Ontology::DocumentRegistry.
618 o Bio::PopGen includes many new methods and data types for
619 population genetics analyses.
621 o New constructor to Bio::Range, unions(). Given a list of
622 ranges, returns another list of "flattened" ranges --
623 overlapping ranges are merged into a single range with the
624 mininum and maximum coordinates of the entire overlapping group.
626 o Bio::Root::IO now supports -url, in addition to -file and -fh.
627 The new -url argument allows one to specify the network address
628 of a file for input. -url currently only works for GET
629 requests, and thus is read-only.
631 o Bio::SearchIO::hmmer now returns individual Hit objects for each
632 domain alignment (thus containing only one HSP); previously
633 separate alignments would be merged into one hit if the domain
634 involved in the alignments was the same, but this only worked
635 when the repeated domain occured without interruption by any
636 other domain, leading to a confusing mixture of Hit and HSP
639 o Bio::Search::Result::ResultI-compliant report objects now
640 implement the "get_statistics" method to access
641 Bio::Search::StatisticsI objects that encapsulate any
642 statistical parameters associated with the search (e.g. Karlin's
643 lambda for BLAST/FASTA).
645 o Bio::Seq::LargeLocatableSeq combines the functionality already
646 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
648 o Bio::SeqFeature::Annotated is a replacement for
649 Bio::SeqFeature::Generic. It breaks compliance with the
650 Bio::SeqFeatureI interface because the author was sick of
651 dealing with untyped annotation tags. All
652 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
653 compliant, and accessible through Bio::Annotation::Collection.
655 o Bio::SeqFeature::Primer implements a Tm() method for primer
656 melting point predictions.
658 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
659 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
661 o Bio::Taxonomy::Node now implements the methods necessary for
662 Bio::Species interoperability.
664 o Bio::Tools::CodonTable has new reverse_translate_all() and
665 make_iupac_string() methods.
667 o Bio::Tools::dpAlign now provides sequence profile alignments.
669 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
671 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
674 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
675 for designing small inhibitory RNA.
677 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
678 methods based on a distance matrix.
680 o Bio::Tree::Statistics provides an assess_bootstrap() method to
681 calculate bootstrap support values on a guide tree topology,
682 based on provided bootstrap tree topologies.
684 o Bio::TreeIO now supports the Pagel (PAG) tree format.
690 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
692 o Bio::Graphics will work with gd1 or gd2
695 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
697 - blast.pm Parse multi-line query fields properly
698 - small speed improvements to blasttable.pm and others
700 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
701 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
702 supporting more complex queries
705 1.4. Stable major release
707 Since initial 1.2.0, 3000 separate changes have been made to make this release.
709 o installable scripts
711 o global module version from Bio::Root:Version
714 - major improvements; SVG support
717 - population genetics
718 - support several population genetics types of questions.
719 - Tests for statistical neutrality of mutations
720 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
721 Tests of population structure (Wright's F-statistic: Fst) is in
722 Bio::PopGen::PopStats. Calculating composite linkage
723 disequilibrium (LD) is available in Bio::PopGen::Statistics as
725 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
726 and csv (comma delimited formatted) data.
728 - a directory for implementing population simulations has
729 been added Bio::PopGen::Simulation and 2 simulations - a
730 Coalescent and a simple single-locus multi-allele genetic drift
731 simulation have been provided. This replaces the code in
732 Bio::Tree::RandomTree which has been deprecated until proper
733 methods for generating random phylogenetic trees are
737 - new restrion analysis modules
739 o Bio::Tools::Analysis
740 - web based DNA and Protein analysis framework and several
744 - per residue annotable sequences
747 - Bio::Matrix::PSM - Position Scoring Matrix
748 - Bio::Matrix::IO has been added for generalized parsing of
749 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
750 initial implementations for parsing BLOSUM/PAM and Phylip
751 Distance matricies respectively. A generic matrix
752 implementation for general use was added in
753 Bio::Matrix::Generic.
760 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
761 - small inhibitory RNA
763 o Bio::SeqFeature::Tools
764 - seqFeature mapping tools
765 - Bio::SeqFeature::Tools::Unflattener.pm
766 -- deal with mapping GenBank feature collections into
767 Chado/GFF3 processable feature sets (with SO term mappings)
769 o Bio::Tools::dpAlign
770 - pure perl dynamic programming sequence alignment
773 o new Bio::SearchIO formats
774 - axt and psl: UCSC formats.
775 - blasttable: NCBI -m 8 or -m 9 format from blastall
777 o new Bio::SeqIO formats
778 - chado, tab, kegg, tigr, game
779 - important fixes for old modules
783 o improved Bio::Tools::Genewise
785 o Bio::SeqIO now can recongnize sequence formats automatically from
788 o new parsers in Bio::Tools:
789 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
791 o Bio::DB::Registry bugs fixed
792 - BerkeleyDB-indexed flat files can be used by the OBDA system
793 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
794 used by the OBDA system
797 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
800 o hundreds of new and improved files
804 o Bio::Tree::AlleleNode has been updated to be a container of
805 an Bio::PopGen::Individual object for use in the Coalescent simulations.
810 1.2.3 Stable release update
811 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
813 o Bug #1477 - Sel --> Sec abbreviation fixed
814 o Fix bug #1487 where paring in-between locations when
815 end < start caused the FTLocationFactory logic to fail.
816 o Fix bug #1489 which was not dealing with keywords as an
817 arrayref properly (this is fixed on the main trunk because
818 keywords returns a string and the array is accessible via
820 o Bio::Tree::Tree memory leak (bug #1480) fixed
821 Added a new initialization option -nodelete which
822 won't try and cleanup the containing nodes if this
824 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
825 this was only present on the branch for the 1.2.1 and 1.2.2 series
826 - Also merged main trunk changes to the branch which make
827 newick -> nhx round tripping more effective (storing branch length
828 and bootstrap values in same locate for NodeNHX and Node
829 implementations.) Fixes to TreeIO parsing for labeled internal
830 also required small changes to TreeIO::nhx. Improved
831 tests for this module as well.
833 - Fixed bugs in BLAST parsing which couldn't parse NCBI
834 gapped blast properly (was losing hit significance values due to
835 the extra unexpeted column).
836 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
837 integer overflow (# of letters in nt seq dbs is > MAX_INT)
838 although doesn't try to correct it - will get the negative
839 number for you. Added a test for this as well.
840 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
841 has no top-level family classification scores but does have scores and
842 alignments for individual domains.
843 - Parsing FASTA reports where ungapped percent ID is < 10 and the
844 regular expression to match the line was missing the possibility of
845 an extra space. This is rare, which is why we probably did not
847 - BLAST parsing picks up more of the statistics/parameter fields
848 at the bottom of reports. Still not fully complete.
849 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
850 were fixed to include many improvements and added flexiblity
851 in outputting the files. Bug #1495 was also fixed in the process.
853 - Update for GFF3 compatibility.
854 - Added scripts for importing from UCSC and GenBank.
855 - Added a 1.2003 version number.
858 - Added a 1.2003 version number.
859 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
860 properly writing keywords out.
861 o Bio::SeqIO::genbank
862 - Fixed bug/enhancement #1513 where dates of
863 the form D-MMM-YYYY were not parsed. Even though this is
864 invalid format we can handle it - and also cleanup the date
865 string so it is properly formatted.
866 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
867 and written with Genbank format. Similarly bug #1515 is fixed to
868 parse in the ORIGIN text.
869 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
870 to specify the ID type, one of (accession accession.version
871 display primary). See Bio::SeqIO::preferred_id_type method
872 documentation for more information.
873 o Unigene parsing updated to handle file format changes by NCBI
875 1.2.2 Stable release update
877 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
878 - auto-discover ontology name
879 - bug in parsing relationships when certain characters are in the term
880 - fixed hard-coded prefix for term identifiers
881 - various smaller issues
883 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
884 of Bio::Ontology::TermI
886 o brought the OBDA Registry code up to latest specs
890 - accession number retrieval fixed
892 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
894 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
895 #1459 which now properly report alignment start/end info
896 for translated BLAST/FASTA searches.
898 o Bio::TreeIO::newick can parse labeled internal nodes
900 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
901 for BLASTX if if you provide -report_type => 'BLASTX' when
902 initializing a BPbl2seq object. Bioperl 1.3 will have better
903 support for bl2seq in the SearchIO system.
905 o Bio::Root::IO support a -noclose boolean flag which will not
906 close a filehandle upon object cleanup - useful when sharing
907 a filehandle among objects. Additionally code added s.t.
908 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
910 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
912 o Bio::SeqIO::genbank
913 - bug #1456 fixed which generated extra sequence lines
914 - write moltype correctly for genpept
916 1.2.1 Stable release update
918 o Inclusion of WrapperBase, a needed component for StandAloneBlast
920 o Addition from main trunk of Ontology objects, principly to allow
921 BioSQL releases against 1.2.1
923 o Fixes and cleanup of Bio::Coordinate modules
925 o A fix to Bio::Index::EMBL allowing retrieval of entries using
926 the primary accession number
928 o Other bug fixes, including bpindex GenBank fix
930 o Bio::SeqIO::genbank bug #1389 fixed
932 1.2 Stable major release
934 o More functionality added to Bio::Perl, the newbie module
936 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
937 Support for New Hampshire Extended (NHX) format parsing.
939 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
940 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
943 o New ontology parsing Bio::Ontology
945 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
946 multi-report (mlib) fasta reports, support for waba and exonerate.
948 o Bio::ClusterIO for parsing Unigene clusters
950 o Bio::Assembly added for representing phrap and ace assembly clusters.
952 o Rudimentary support for writing Chado XML (see
953 GMOD project: www.gmod.org for more information)
955 o Bio::Coordinate for mapping between different coordinate systems such
956 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
957 features into different coordinate systems.
959 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
960 with the get_Stream_by_query method and supports the latest
961 NCBI eutils interface.
963 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
964 object for extracting subsets of features : currently only
965 supports extraction by location.
967 1.1.1 Developer release
969 o Deprecated modules are now listed in the DEPRECATED file
971 o New HowTo documents located in doc/howto describing
974 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
975 and all old bugs are searchable through the bugzilla interface.
977 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
980 o Support for Genewise parsing in Bio::Tools::Genewise
982 o Start of Ontology framework with Bio::Ontology
984 o Speedup to the Bio::Root::Root object method _rearrange.
985 A global _load_module method was implemented to simplify the
986 dynamic loading of modules ala Bio::SeqIO::genbank. This
987 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
990 o Several performance improvements to sequence parsing in Bio::SeqIO.
991 Attempt to speedup by reducing object creation overhead.
993 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
994 method for sequence retrieval with their E-utils CGI scripts.
995 More work to support Entrez queries to their fullest is planned
998 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1000 1.1 Developer release
1002 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1003 this separation removes some of the complexity in our test suite
1004 and separates the core modules in bioperl from those that need
1005 external programs to run.
1007 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1008 not run into trouble running the makefile
1010 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1011 read,create,and write locations for grouped/split locations
1012 (like mRNA features on genomic sequence).
1014 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1015 and PAML (codeml,aaml, etc) parsing.
1017 o Bio::Tree:: objects expanded to handle testing monophyly,
1018 paraphyly, least common ancestor, etc.
1020 o Bio::Coordinate for mapping locations from different coordinate spaces
1022 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1023 added for parsing hmmpfam and hmmsearch output.
1025 o Bio::SearchIO::Writer::TextResultWriter for outputting
1026 a pseudo-blast textfile format
1029 1.0.2 Bug fix release
1031 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1032 in this release will not work after December 2002 when NCBI
1033 shuts off the old Entrez cgi scripts. We have already fixed
1034 on our main development branch and the functionality will be
1035 available in the next stable bioperl release (1.2) slated for
1038 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1039 testset by Robin Emig. These were fixed as was the get_aln
1040 method in Bio::Search::HSP::GenericHSP to handle the extra
1041 context sequence that is provided with a FastA alignment.
1043 o Migrating differences between Bio::Search::XX::BlastXX to
1044 Bio::Search::XX::GenericXX objects. This included mechanism
1045 to retrieve whole list of HSPs from Hits and whole list of Hits from
1046 Results in addition to the current next_XX iterator methods that
1047 are available. Added seq_inds() method to GenericHSP which identifies
1048 indexes in the query or hit sequences where conserved,identical,gaps,
1049 or mismatch residues are located (adapted from Steve Chervitz's
1050 implementation in BlastHSP).
1052 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1053 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1055 o Bio::Graphics glyph set improved and extended for GBrowse release
1057 o Bio::Tree::Tree get_nodes implementation improvement thanks
1058 to Howard Ross notice performance problem when writing out
1061 o Bio::Location::Fuzzy::new named parameter -loc_type became
1062 -location_type, Bio::Location::Simple::new named parameter
1063 -seqid becamse -seq_id.
1065 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1066 was mis-detecting that gaps should be placed at the beginning of
1067 the alignment when the best alignment starts internally in the
1070 1.0.1 Bug fix release
1072 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1074 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1075 and mixed (3.3 - 3.4) versions of FASTA.
1077 o Small API change to add methods for completeness across
1078 implementations of Bio::Search objects. These new methods
1079 in the interface are implemented by the GenericXX object as well
1080 as the BlastXX objects.
1081 * Bio::Search::Result::ResultI
1082 - hits() method returns list of all Hits (next_hit is an
1085 * Bio::Search::Hit::HitI
1086 - hsps() method returns list of all HSPs (next_hsp is an
1089 o The Bio::SearchIO::Writer classes have been fixed to handle results
1090 created from either psiblast (Search::BlastXX objects) or
1091 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1092 has to be done here to make it work properly and will nee major
1095 o Bugs in Bio::Tools::HMMER fixed, including
1096 * #1178 - Root::IO destructor wasn't being called
1097 * #1034 - filter_on_cutoff now behaves properly
1099 o Bio::SeqFeature::Computation initialization args fixed and
1102 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1104 o Updated FAQ with more example based answers to typical questions
1106 o Bug #1202 was fixed which would improperly join together qual values
1107 parsed by Bio::SeqIO::qual when a trailing space was not present before
1110 1.0.0 Major Stable Release
1112 This represents a major release of bioperl with significant
1113 improvements over the 0.7.x series of releases.
1115 o Bio::Tools::Blast is officially deprecated. Please see
1116 Bio::SearchIO for BLAST and FastA parsing.
1118 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1119 Bio::LocationI objects as well as start/end.
1121 o Bio::Biblio contains modules for Bibliographic data.
1122 Bio::DB::Biblio contains the query modules. Additionally one can
1123 parse medlinexml from the ebi bibliographic query service (BQS)
1124 system and Pubmed xml from NCBI. See Martin Senger's
1125 documentation in Bio::Biblio for more information.
1127 o Bio::DB::Registry is a sequence database registry part of
1128 Open Bioinformatics Database Access. See
1129 http://obda.open-bio.org for more information.
1131 o File-based and In-Memory Sequence caching is provided by
1132 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1135 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1136 been added by Lincoln Stein.
1138 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1140 o A FAQ has been started and is included in the release to provide
1141 a starting point for frequent questions and issues.
1143 0.9.3 Developer's release
1145 o Event based parsing system improved (SearchIO). With parsers for
1146 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1147 Additionally a lazy parsing system for text and html blast reports was
1148 added and is called psiblast (name subject to change in future releases).
1150 o Bio::Search objects improved and standardized with associated Interfaces
1151 written. The concept of a search "Hit" was standardized to be called
1152 "hit" consistently and the use of "subject" was deprecated in all active
1155 o Bio::Structure added (since 0.9.1) for Protein structure objects
1156 and PDB parser to retrieve and write these structures from data files.
1158 o Several important Bio::DB::GFF bug fixes for handling features that
1159 are mapped to multiple reference points. Updated mysql adaptor
1160 so as to be able to store large (>100 megabase) chunks of DNA into
1161 Bio::DB::GFF databases.
1163 0.9.2 Developer's release
1165 o Bio::Search and Bio::SearchIO system introduced for event based
1166 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1167 in text and XML and FASTA reports in standard output format.
1169 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1170 generator is included in Bio::TreeIO::RandomTrees and a
1171 statistics module for evaluating.
1173 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1174 server for DAS servers.
1176 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1177 files. The entire BPlite system migrated to using Bio::Root::IO
1178 for the data stream.
1180 o Bio::Tools::Alignment for Consed and sequence Trimming
1183 o Bio::Structure for Protein structure information and parsing
1185 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1186 cgi-bin entry point which should be more reliable.
1188 o Bio::Map and Bio::MapIO for biological map navigation and a
1189 framework afor parsing them in. Only preliminary work here.
1191 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1192 Future work will integrate Pise and allow submission of analysis on
1195 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1196 introduced as new objects for handling Sequence Annotation
1197 information (dblinks, references, etc) and is more robust that
1200 o Bio::Tools::FASTAParser introduced.
1202 o Scripts from the bioperl script submission project and new
1203 scripts from bioperl authors are included in "scripts" directory.
1205 o Factory objects and interfaces are being introduced and are more
1208 o Bio::Root::Root introduced as the base object while
1209 Bio::Root::RootI is now simply an interface.
1211 o Bio::DB::RefSeq provides database access to copy of the NCBI
1212 RefSeq database using the EBI dbfetch script.
1214 0.9.0 Developer's release
1216 o perl version at least 5.005 is now required instead of perl 5.004
1218 o Bio::Tools::Run::RemoteBlast is available for running remote
1221 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1223 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1224 Also added are related modules UTR3, UTR5, Exon, Intron,
1225 Promotor, PolyA and Transcript.
1227 o Speedup of translate method in PrimarySeq
1229 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1230 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1232 o Various fixes to Variation toolkit
1234 o Bio::DB::EMBL provides database access to EMBL sequence data.
1235 Bio::DB::Universal provides a central way to point to indexes
1236 and dbs in a single interface.
1238 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1240 o Bio::Factory::EMBOSS is still in design phase as is
1241 Bio::Factory::ApplicationFactoryI
1243 o Dia models for bioperl design are provided in the models/ directory
1245 0.7.2 Bug fix release
1247 o documentation fixes in many modules - SYNOPSIS code verified
1248 to be runnable in many (but not all modules)
1250 o corrected MANIFEST file from 0.7.1 release
1252 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1255 o Bio::SeqIO::genbank
1256 * Correct parsing and writing of genbank format with protein data
1257 * moltype and molecule separation
1259 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1261 o Bio::SimpleAlign fixed to correctly handle consensus
1262 sequence calculation
1264 o Bio::Tools::HMMER supports hmmer 2.2g
1266 o Bio::Tools::BPlite to support report type specific parsing. Most
1267 major changes are not on the 0.7 branch.
1269 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1272 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1273 in several types of mutations:
1274 1.) AA level: deletion, complex
1275 2.) AA level: complex, inframe
1276 3.) RNA level: silent
1278 o BPbl2seq parsing of empty reports will not die, but will return
1279 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1280 $report->query() and $report->subject() methods. So an easy
1281 way to test if report was empty is to see if
1282 $report->query->seqname is undefined.
1284 0.7.1 Bug fix release
1286 o Better parsing of genbank/EMBL files especially fixing bugs
1287 related to Feature table parsing and locations on remote
1288 sequences. Additionally, species name parsing was better.
1290 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1291 which include a number of header lines.
1293 o More strict genbank and EMBL format writing (corrected number of
1294 spaces where appropriate).
1296 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1297 for related BPlite BUGS that are unresolved in this release.
1299 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1300 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1301 use expasy mirrors or EBI dbfetch cgi-script.
1303 o A moderate number of documentation improvements were made as
1304 well to provide a better code synopsis in each module.
1307 0.7 Large number of changes, including refactoring of the
1308 Object system, new parsers, new functionality and
1309 all round better system. Highlights are:
1312 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1313 Bio::Root::IO for I/O and file/handle capabilities.
1315 o Imported BPlite modules from Ian Korf for BLAST
1316 parsing. This is considered the supported BLAST parser;
1317 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1319 o Improved Sequence Feature model. Added complete location
1320 modelling (with fuzzy and compound locations). See
1321 Bio::LocationI and the modules under Bio/Location. Added
1322 support in Genbank/EMBL format parsing to completely parse
1323 feature tables for complex locations.
1325 o Moved special support for databanks etc to specialized modules under
1326 Bio/Seq/. One of these supports very large sequences through
1327 a temporary file as a backend.
1329 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1330 CDS retrieval and exon shuffling.
1332 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1334 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1335 DB/GDB (the latter has platform-specific limitations).
1337 o New analysis parser framework for HT sequence annotation (see
1338 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1340 o New Alignment IO framework
1342 o New Index modules (Swissprot)
1344 o New modules for running Blast within perl
1345 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1346 Multiple Sequence Alignment tools ClustalW and TCoffee
1347 (Bio::Tools::Run::Alignment).
1349 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1350 documentation across the package.
1352 o Much improved cross platform support. Many known incompatibilities
1353 have been fixed; however, NT and Mac do not work across the entire
1354 setup (see PLATFORMS).
1356 o Many bug fixes, code restructuring, etc. Overall stability and
1357 maintainability benefit a lot.
1359 o A total of 957 automatic tests
1364 There are very few functionality changes but a large
1365 number of software improvements/bug fixes across the package.
1367 o The EMBL/GenBank parsing are improved.
1369 o The Swissprot reading is improved. Swissprot writing
1370 is disabled as it doesn't work at all. This needs to
1371 wait for 0.7 release
1373 o BLAST reports with no hits are correctly parsed.
1375 o Several other bugs of the BLAST parser (regular expressions, ...)
1378 o Old syntax calls have been replaced with more modern syntax
1380 o Modules that did not work at all, in particular the Sim4
1381 set have been removed
1383 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1384 have improved compliance with interface specs and documentation
1386 o Mailing list documentation updated throughout the distribution
1388 o Most minor bug fixes have happened.
1390 o The scripts in /examples now work and have the modern syntax
1391 rather than the deprecated syntax
1394 0.6.1 Sun April 2 2000
1396 o Sequences can have Sequence Features attached to them
1397 - The sequence features can be read from or written to
1398 EMBL and GenBank style flat files
1400 o Objects for Annotation, including References (but not
1401 full medline abstracts), Database links and Comments are
1404 o A Species object to represent nodes on a taxonomy tree
1407 o The ability to parse HMMER and Sim4 output has been added
1409 o The Blast parsing has been improved, with better PSI-BLAST
1410 support and better overall behaviour.
1412 o Flat file indexed databases provide both random access
1413 and sequential access to their component sequences.
1415 o A CodonTable object has been written with all known
1416 CodonTables accessible.
1418 o A number of new lightweight analysis tools have been
1419 added, such as molecular weight determination.
1421 The 0.6 release also has improved software engineering
1423 o The sequence objects have been rewritten, providing more
1424 maintainable and easier to implement objects. These
1425 objects are backwardly compatible with the 0.05.1 objects
1427 o Many objects are defined in terms of interfaces and then
1428 a Perl implementation has been provided. The interfaces
1429 are found in the 'I' files (module names ending in 'I').
1431 This means that it is possible to wrap C/CORBA/SQL access
1432 as true "bioperl" objects, compatible with the rest of
1435 o The SeqIO system has been overhauled to provide better
1436 processing and perl-like automatic interpretation of <>
1439 o Many more tests have been added (a total of 172 automatic
1440 tests are now run before release).
1444 0.05.1 Tue Jun 29 05:30:44 1999
1445 - Central distribution now requires Perl 5.004. This was
1446 done to get around 5.003-based problems in Bio/Index/*
1448 - Various bug fixes in the Bio::Tools::Blast modules
1449 including better exception handling and PSI-Blast
1450 support. See Bio/Tools/Blast/CHANGES for more.
1451 - Fixed the Parse mechanism in Seq.pm to use readseq.
1452 Follow the instructions in README for how to install
1453 it (basically, you have to edit Parse.pm).
1454 - Improved documentation of Seq.pm, indicating where
1455 objects are returned and where strings are returned.
1456 - Fixed uninitialized warnings in Bio::Root::Object.pm
1457 and Bio::Tools::SeqPattern.pm.
1458 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1460 0.05 Sun Apr 25 01:14:11 1999
1461 - Bio::Tools::Blast modules have less memory problems
1462 and faster parsing. Webblast uses LWP and supports
1463 more functionality. See Bio/Tools/Blast/CHANGES for more.
1464 - The Bio::SeqIO system has been started, moving the
1465 sequence reformatting code out of the sequence object
1466 - The Bio::Index:: system has been started, providing
1467 generic index capabilities and specifically works for
1468 Fasta formatted databases and EMBL .dat formatted
1470 - The Bio::DB:: system started, providing access to
1471 databases, both via flat file + index (see above) and
1473 - The scripts/ directory, where industrial strength scripts
1474 are put has been started.
1475 - Many changes - a better distribution all round.
1477 0.04.4 Wed Feb 17 02:20:13 1999
1478 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1479 (see Bio::Tools::Blast::CHANGES).
1480 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1481 - Beefed up the t/Fasta.t test script.
1482 - Small fix in Bio::Seq::type() (now always returns a string).
1483 - Changed Bio::Root::Utilities::get_newline_char() to
1484 get_newline() since it could return more than one char.
1485 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1486 - Changed default timeout to 20 seconds (was 3).
1487 - Moved lengthy modification notes to the bottom of some files.
1488 - Fixed SimpleAlign write_fasta bug.
1489 - Beefed up SimpleAlign.t test
1491 0.04.3 Thu Feb 4 07:48:53 1999
1492 - Bio::Root::Object.pm and Global.pm now detect when
1493 script is run as a CGI and suppress output that is only
1494 appropriate when running interactively.
1495 - Bio::Root::Err::_set_context() adds name of script ($0).
1496 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1497 regarding the use of the static objects via the qw(:obj) tag.
1498 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1499 CORE::reverse, avoiding Perl warnings.
1500 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1501 example scripts (see Bio::Tools::Blast::CHANGES).
1502 - examples/seq/seqtools.pl no longer always warns about using
1503 -prot or -nucl command-line arguments; only when using the
1505 - Methods added to Bio::Root::Utilities: create_filehandle(),
1506 get_newline_char(), and taste_file() to generalize filehandle
1507 creation and autodetect newline characters in files/streams
1508 (see bug report #19).
1509 - Bio::Root::IOManager::read() now handles timeouts and uses
1510 Utilities::create_filehandle().
1511 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1512 of hardwiring in "\n".
1513 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1515 0.04.2 Wed Dec 30 02:27:36 1998
1516 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1517 (see Bio::Tools::Blast::CHANGES).
1518 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1519 to CORE::reverse (prevents ambiguous warnings with 5.005).
1520 - Appending '.tmp.bioperl' to temporary files created by
1521 Bio::Root::Utilities::compress() or uncompress() to
1522 make it easy to identify & cleanup these files as needed.
1523 - Developers: Created CVS branch release-0-04-bug from
1524 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1525 be sure to cvs checkout this branch into a clean area.
1527 0.04.1 Wed Dec 16 05:39:15 1998
1528 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1529 (see Bio::Tools::Blast::CHANGES).
1530 - Compile/SW/Makefile.PL now removes *.o and *.a files
1533 0.04 Tue Dec 8 07:49:19 1998
1534 - Lots of new modules added including:
1535 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1536 and Bio/Compile directory containing XS-linked C code for
1537 creating Smith-Waterman sequence alignments from within Perl.
1538 * Steve Chervitz's Blast distribution has been incorporated.
1539 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1540 - Bio/examples directory for demo scripts for all included modules.
1541 - Bio/t directory containing test suit for all included modules.
1542 - For changes specific to the Blast-related modules prior to
1543 incorporation in this central distribution, see the CHANGES
1544 file in the Bio/Tools/Blast directory.
1546 0.01 Tue Sep 8 14:23:22 1998
1547 - original version from central CVS tree; created by h2xs 1.18