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 * Minor bug fix release
25 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
26 * Address Build.PL issues when DBI is not present [hartzell]
27 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
28 * Remove deprecated code for impending perl 5.14.0 release [cjfields]
30 1.6.900 April 14, 2011
34 * This will probably be the last release to add significant features to
35 core modules; subsequent releases will be for bug fixes alone.
36 We are planning on a restructuring of core for summer 2011, potentially
37 as part of the Google Summer of Code. This may become BioPerl 2.0.
38 * Version bump represents 'just prior to v 1.7'. We may have point
39 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
40 This code essentially is what is on the github master branch.
44 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
46 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
47 - removal of Scalar::Util::weaken code, which was causing odd headaches
48 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
49 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
51 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
54 - bug 2515 - new contribution [Ryan Golhar, jhannah]
56 - support for reading Maq, Sam and Bowtie files [maj]
57 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
58 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
59 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
60 - bug 2726: reading/writing granularity: whole scaffold or one contig
61 at a time [Joshua Udall, fangly]
63 - Added parsing of xrefs to OBO files, which are stored as secondary
64 dbxrefs of the cvterm [Naama Menda]
65 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
66 * PAML code updated to work with PAML 4.4d [DaveMessina]
70 * [3198] - sort tabular BLAST hits by score [DaveMessina]
71 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
72 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
73 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
75 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
76 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
77 * [3164] - TreeFunctionsI syntax bug [gjuggler]
78 * [3163] - AssemblyIO speedup [fangly]
79 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
81 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
82 * [3158] - fix EMBL file mis-parsing [cjfields]
83 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
85 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
86 * [3148] - URL change for UniProt [cjfields]
87 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
88 * [3136] - HMMer3 parser fixes [kblin]
89 * [3126] - catch description [Toshihiko Akiba]
90 * [3122] - Catch instances where non-seekable filehandles were being
91 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
92 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
93 [dukeleto, rbuels, cjfields]
94 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
96 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
97 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
99 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
100 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
101 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
102 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
103 * [3086] - EMBL misparsing long tags [kblin, cjfields]
104 * [3085] - CommandExts and array of files [maj, hyphaltip]
105 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
106 for alignment slices [Ha X. Dang, cjfields]
107 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
108 * [3073] - fix parsing of GenBank files from RDP [cjfields]
109 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
110 * [3064] - All-gap midline BLAST report issues [cjfields]
111 * [3063] - BLASt report RID [Razi Khaja, cjfields]
112 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
113 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
114 * [3039] - correct Newick output root node branch length [gjuggler,
116 * [3038] - SELEX alignment error [Bernd, cjfields]
117 * [3033] - PrimarySeq ID setting [Bernd, maj]
118 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
119 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
120 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
121 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
122 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
123 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
124 PAML 4.4d [DaveMessina]
125 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
127 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
128 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
129 * [3017] - using threads with Bio::DB::GenBank [cjfields]
130 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
131 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
132 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
133 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
134 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
136 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
137 * [2977] - TreeIO issues [DaveMessina]
138 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
139 * [2944] - Bio::Tools::GFF score [cjfields]
140 * [2942] - correct MapTiling output [maj]
141 * [2939] - PDB residue insertion codes [John May, maj]
142 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
143 * [2928] - GuessSeqFormat raw [maj]
144 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
145 * [2922] - open() directive issue [cjfields]
146 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
147 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
148 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
149 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
151 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
152 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
153 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
154 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
155 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
156 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
157 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
158 * [2758] - Bio::AssemblyIO ace problems [fangly]
159 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
160 * [2726] - ace file IO [Josh, fangly]
161 * [2700] - Refactor Build.PL [cjfields]
162 * [2673] - addition of simple Root-based clone() method [cjfields]
163 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
164 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
165 * [2594] - Bio::Species memory leak [cjfields]
166 * [2515] - GenBank XML parser [jhannah]
167 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
168 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
169 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
171 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
175 * Bio::Expression modules - these were originally designed to go with the
176 bioperl-microarray suite of tools, however they have never been completed
177 and so have been removed from the distribution. The original code has
178 been moved into the inactive bioperl-microarray suite. [cjfields]
182 * Repository moved from Subversion (SVN) to
183 http://github.com/bioperl/bioperl-live [cjfields]
184 * Bug database has moved to Redmine (https://redmine.open-bio.org)
185 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
186 Thieme have been moved to their own distribution (Bio-Microarray).
189 1.6.1 Sept. 29, 2009 (point release)
190 * No change from last alpha except VERSION and doc updates [cjfields]
192 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
193 * Fix for silent OBDA bug related to FASTA validation [cjfields]
195 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
196 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
197 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
199 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
201 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
202 * WinXP test fixes [cjfields, maj]
203 * BioPerl.pod added for descriptive information, fixes CPAN indexing
205 * Minor doc fixes [cjfields]
207 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
208 * Fix tests failing due to merging issues [cjfields]
209 * More documentation updates for POD parsing [cjfields]
211 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
213 - fix YAML meta data generation [cjfields]
215 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
216 * Bio::Align::DNAStatistics
217 - fix divide by zero problem [jason]
219 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
220 * Bio::AlignIO::stockholm
221 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
222 * Bio::Assembly::Tools::ContigSpectrum
223 - function to score contig spectrum [fangly]
224 * Bio::DB::EUtilities
225 - small updates [cjfields]
227 - berkeleydb database now autoindexes wig files and locks correctly
230 - various small updates for stability; tracking changes to LANL
231 database interface [maj]
232 * Bio::DB::SeqFeature (lots of updates and changes)
233 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
234 - bug 2835 - patch [Dan Bolser]
235 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
237 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
238 * Bio::Factory::FTLocationFactory
239 - mailing list bug fix [cjfields]
241 - performance work on column_from_residue_number [hartzell]
242 * Bio::Matrix::IO::phylip
243 - bug 2800 - patch to fix phylip parsing [Wei Zou]
245 - Google Summer of Code project from Chase Miller - parsers for Nexml
246 file format [maj, chmille4]
248 - Make Individual, Population, Marker objects AnnotatableI [maj]
249 - simplify LD code [jason]
251 - deal with empty intersection [jason]
253 - significant overhaul of Bio::Restriction system: complete support for
254 external and non-palindromic cutters. [maj]
256 - CPANPLUS support, no automatic installation [sendu]
258 - allow IO::String (regression fix) [cjfields]
259 - catch unintentional undef values [cjfields]
260 - throw if non-fh is passed to -fh [maj]
261 * Bio::Root::Root/RootI
262 - small debugging and core fixes [cjfields]
264 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
265 * Bio::Root::Utilities
266 - bug 2737 - better warnings [cjfields]
268 - tiling completely refactored, HOWTO added [maj]
269 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
270 will deprecate usage of the older tiling code in the next BioPerl
272 - small fixes [cjfields]
274 - Infernal 1.0 output now parsed [cjfields]
275 - new parser for gmap -f9 output [hartzell]
276 - bug 2852 - fix infinite loop in some output [cjfields]
277 - blastxml output now passes all TODO tests [cjfields]
278 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
279 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
280 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
281 * Bio::Seq::LargePrimarySeq
282 - delete tempdirs [cjfields]
283 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
285 - extract regions based on quality threshold value [Dan Bolser, heikki]
286 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
287 * Bio::SeqFeature::Lite
288 - various Bio::DB::SeqFeature-related fixes [lstein]
289 * Bio::SeqFeature::Tools::TypeMapper
290 - additional terms for GenBank to SO map [scain]
291 * Bio::SeqIO::chadoxml
292 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
294 - support for CDS records [dave_messina, Sylvia]
296 - complete refactoring to handle all FASTQ variants, perform validation,
297 write output. API now conforms with other Bio* parsers and the rest of
298 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
300 * Bio::SeqIO::genbank
301 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
302 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
303 * Bio::SeqIO::largefasta
304 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
306 - add option for 'single' and 'multiple'
308 - bug 2881 - fix scf round-tripping [Adam Sj¿gren]
310 - bug 2766, 2810 - copy over tags from features, doc fixes [David
313 - bug 2793 - patch for add_seq index issue [jhannah, maj]
314 - bug 2801 - throw if args are required [cjfields]
315 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
316 [Tristan Lefebure, maj]
317 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
318 - fix POD and add get_SeqFeatures filter [maj]
319 * Bio::Tools::dpAlign
320 - add support for LocatableSeq [ymc]
321 - to be moved to a separate distribution [cjfields, rbuels]
322 * Bio::Tools::EUtilities
323 - fix for two bugs from mail list [Adam Whitney, cjfields]
324 - add generic ItemContainerI interface for containing same methods
327 - fix up code, add more warnings [cjfields]
328 - to be moved to a separate distribution [cjfields, rbuels]
329 * Bio::Tools::Primer3
330 - bug 2862 - fenceposting issue fixed [maj]
331 * Bio::Tools::Run::RemoteBlast
332 - tests for remote RPS-BLAST [mcook]
333 * Bio::Tools::SeqPattern
334 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
335 * Bio::Tools::tRNAscanSE
336 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
338 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
339 * Bio::Tree::Statistics
340 - several methods for calculating Fitch-based score, internal trait
341 values, statratio(), sum of leaf distances [heikki]
343 - bug 2869 - add docs indicating edge case where nodes can be
344 prematurely garbage-collected [cjfields]
345 - add as_text() function to create Tree as a string in specified format
347 * Bio::Tree::TreeFunctionsI
348 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
350 * Bio::TreeIO::newick
351 - fix small semicolon issue [cjfields]
353 - update to bp_seqfeature_load for SQLite [lstein]
354 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
355 - fastam9_to_table - fix for MPI output [jason]
356 - gccalc - total stats [jason]
358 - POD cleanup re: FEEDBACK section [maj, cjfields]
359 - cleanup or fix dead links [cjfields]
360 - Use of no_* methods (indicating 'number of something') is deprecated
361 in favor of num_* [cjfields]
362 - lots of new tests for the above bugs and refactors [everyone!]
363 - new template for Komodo text editor [cjfields]
366 * Feature/Annotation rollback
367 - Problematic changes introduced prior to the 1.5 release have been
368 rolled back. These changes led to subtle bugs involving operator
369 overloading and interface methods.
370 - Behavior is very similar to that for BioPerl 1.4, with tag values
371 being stored generically as simple scalars. Results in a modest
374 - Split into a separate distribution on CPAN, primarily so development
375 isn't reliant on a complete BioPerl release.
376 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
377 is only available via Subversion (via bioperl-live main trunk)
379 - Common test bed for all BioPerl modules
381 - Common Module::Build-based subclass for all BioPerl modules
382 * Bio::DB::EUtilities
383 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
384 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
385 and user agent request posting and retrieval
386 * Test implementation and reorganization
387 - Tests have been reorganized into groups based on classes or use
389 - Automated test coverage is now online:
390 http://www.bioperl.org/wiki/Test_Coverage
391 - After this release, untested modules will be moved into a
392 separate developer distribution until tests can be derived.
393 Also, new modules to be added are expected to have a test suite
394 and adequate test coverage.
396 1.5.2 Developer release
398 Full details of changes since 1.5.1 are available online at:
399 http://www.bioperl.org/wiki/Change_log
400 The following represents a brief overview of the most important changes.
403 - Overhaul. Brand new system fully allows markers to have multiple
404 positions on multiple maps, and to have relative positions. Should be
408 - This module and all the modules in the Taxonomy directory now
409 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
414 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
416 * New methods ancestor(), each_Descendent() and _handle_internal_id().
418 * Allows for different database modules to create Bio::Taxon objects
419 with the same internal id when the same taxon is requested from each.
422 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
424 * No longer includes the fake root node 'root'; there are multiple roots
425 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
428 * get_node() has new option -full
430 * Caches data retrieved from website
433 - Now a Bio::Taxon. Carries out the species name -> specific name munging
434 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
435 backward compatability in species() method.
437 o Bio::Search and Bio::SearchIO
438 - Overhaul. The existing system has been sped up via some minor changes
439 (mostly gain-of-function to the API). Bio::PullParserI is introduced
440 as a potential eventual replacment for the existing system, though as
441 yet only a Hmmpfam parser exists written using it.
444 1.5.1 Developer release
446 o Major problem with how Annotations were written out with
447 Bio::Seq is fixed by reverting to old behavior for
448 Bio::Annotation objects.
453 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
454 expect at l east 9 spaces at the beginning of a line to
455 indicate line wrapping.
457 * Treat multi-line SOURCE sections correctly, this defect broke
458 both common_name() and classification()
460 * parse swissprot fields in genpept file
462 * parse WGS genbank records
465 * Changed regexp for ID line. The capturing parentheses are
466 the same, the difference is an optional repeated-not-semi-
467 colon expression following the captured \S+. This means the
468 regexp works when the division looks like /PRO;/ or when the
469 division looks like /ANG ;/ - the latter is from EMBL
472 * fix ID line parsing: the molecule string can have spaces in
473 it. Like: "genomic DNA"
475 - swiss.pm: bugs #1727, #1734
478 * Added parser for entrezgene ASN1 (text format) files.
479 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
483 - maf.pm coordinate problem fixed
485 o Bio::Taxonomy and Bio::DB::Taxonomy
487 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
488 can be done via Web without downloading all the sequence.
490 o Bio::Tools::Run::RemoteBlast supports more options and complies
491 to changes to the NCBI interface. It is reccomended that you
492 retrieve the data in XML instead of plain-text BLAST report to
493 insure proper parsing and retrieval of all information as NCBI
494 fully expects to change things in the future.
496 o Bio::Tree and Bio::TreeIO
498 - Fixes so that re-rooting a tree works properly
500 - Writing out nhx format from a newick/nexus file will properly output
501 bootstrap information. The use must move the internal node labels over
503 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
504 $node->bootstrap($node->id);
507 - Nexus parsing is much more flexible now, does not care about
510 - Cladogram drawing module in Bio::Tree::Draw
512 - Node height and depth now properly calculated
514 - fix tree pruning algorithm so that node with 1 child gets merged
516 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
517 bugs and improvements were added, see Gbrowse mailing list for most of
520 o Bio::DB::GFF partially supports GFF3. See information about
521 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
523 o Better location parsing in Bio::Factory::FTLocationFactory -
524 this is part of the engine for parsing EMBL/GenBank feature table
525 locations. Nested join/order-by/complement are allowed now
527 o Bio::PrimarySeqI->translate now takes named parameters
529 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
530 reconstruction) is now supported. Parsing different models and
531 branch specific parametes are now supported.
533 o Bio::Factory::FTLocationFactory - parse hierarchical locations
536 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
537 for getter/setter functions
541 - blast bug #1739; match scientific notation in score
542 and possible e+ values
544 - blast.pm reads more WU-BLAST parameters and parameters, match
545 a full database pathname,
547 - Handle NCBI WEB and newer BLAST formats specifically
548 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
550 - psl off-by-one error fixed
552 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
553 and HSPs can be constructed from them.
555 - HSPs query/hit now have a seqdesc field filled out (this was
556 always available via $hit->description and
557 $result->query_description
559 - hmmer.pm can parse -A0 hmmpfam files
561 - Writer::GbrowseGFF more customizeable.
563 o Bio::Tools::Hmmpfam
564 make e-value default score displayed in gff, rather than raw score
565 allow parse of multiple records
568 1.5 Developer release
570 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
571 provide Jukes-Cantor and Kimura pairwise distance methods,
574 o Bio::AlignIO support for "po" format of POA, and "maf";
575 Bio::AlignIO::largemultifasta is a new alternative to
576 Bio::AlignIO::fasta for temporary file-based manipulation of
577 particularly large multiple sequence alignments.
579 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
580 be treated similarly as an assembled contig.
582 o Bio::CodonUsage provides new rare_codon() and probable_codons()
583 methods for identifying particular codons that encode a given
586 o Bio::Coordinate::Utils provides new from_align() method to build
587 a Bio::Coordinate pair directly from a
588 Bio::Align::AlignI-conforming object.
590 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
591 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
592 web service using standard Pubmed query syntax, and retrieve
595 o Bio::DB::GFF has various sundry bug fixes.
597 o Bio::FeatureIO is a new SeqIO-style subsystem for
598 writing/reading genomic features to/from files. I/O classes
599 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
600 classes only read/write Bio::SeqFeature::Annotated objects.
601 Notably, the GFF v3 class requires features to be typed into the
604 o Bio::Graph namespace contains new modules for manipulation and
605 analysis of protein interaction graphs.
607 o Bio::Graphics has many bug fixes and shiny new glyphs.
609 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
610 indexing for HMMER reports and FASTA qual files, respectively.
612 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
613 new objects that can be placed within a Bio::Map::MapI-compliant
614 genetic/physical map; Bio::Map::Physical provides a new physical
615 map type; Bio::MapIO::fpc provides finger-printed clone mapping
618 o Bio::Matrix::PSM provide new support for postion-specific
619 (scoring) matrices (e.g. profiles, or "possums").
621 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
622 be instantiated without explicitly using Bio::OntologyIO. This
623 is possible through changes to Bio::Ontology::OntologyStore to
624 download ontology files from the web as necessary. Locations of
625 ontology files are hard-coded into
626 Bio::Ontology::DocumentRegistry.
628 o Bio::PopGen includes many new methods and data types for
629 population genetics analyses.
631 o New constructor to Bio::Range, unions(). Given a list of
632 ranges, returns another list of "flattened" ranges --
633 overlapping ranges are merged into a single range with the
634 mininum and maximum coordinates of the entire overlapping group.
636 o Bio::Root::IO now supports -url, in addition to -file and -fh.
637 The new -url argument allows one to specify the network address
638 of a file for input. -url currently only works for GET
639 requests, and thus is read-only.
641 o Bio::SearchIO::hmmer now returns individual Hit objects for each
642 domain alignment (thus containing only one HSP); previously
643 separate alignments would be merged into one hit if the domain
644 involved in the alignments was the same, but this only worked
645 when the repeated domain occured without interruption by any
646 other domain, leading to a confusing mixture of Hit and HSP
649 o Bio::Search::Result::ResultI-compliant report objects now
650 implement the "get_statistics" method to access
651 Bio::Search::StatisticsI objects that encapsulate any
652 statistical parameters associated with the search (e.g. Karlin's
653 lambda for BLAST/FASTA).
655 o Bio::Seq::LargeLocatableSeq combines the functionality already
656 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
658 o Bio::SeqFeature::Annotated is a replacement for
659 Bio::SeqFeature::Generic. It breaks compliance with the
660 Bio::SeqFeatureI interface because the author was sick of
661 dealing with untyped annotation tags. All
662 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
663 compliant, and accessible through Bio::Annotation::Collection.
665 o Bio::SeqFeature::Primer implements a Tm() method for primer
666 melting point predictions.
668 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
669 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
671 o Bio::Taxonomy::Node now implements the methods necessary for
672 Bio::Species interoperability.
674 o Bio::Tools::CodonTable has new reverse_translate_all() and
675 make_iupac_string() methods.
677 o Bio::Tools::dpAlign now provides sequence profile alignments.
679 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
681 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
684 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
685 for designing small inhibitory RNA.
687 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
688 methods based on a distance matrix.
690 o Bio::Tree::Statistics provides an assess_bootstrap() method to
691 calculate bootstrap support values on a guide tree topology,
692 based on provided bootstrap tree topologies.
694 o Bio::TreeIO now supports the Pagel (PAG) tree format.
700 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
702 o Bio::Graphics will work with gd1 or gd2
705 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
707 - blast.pm Parse multi-line query fields properly
708 - small speed improvements to blasttable.pm and others
710 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
711 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
712 supporting more complex queries
715 1.4. Stable major release
717 Since initial 1.2.0, 3000 separate changes have been made to make this release.
719 o installable scripts
721 o global module version from Bio::Root:Version
724 - major improvements; SVG support
727 - population genetics
728 - support several population genetics types of questions.
729 - Tests for statistical neutrality of mutations
730 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
731 Tests of population structure (Wright's F-statistic: Fst) is in
732 Bio::PopGen::PopStats. Calculating composite linkage
733 disequilibrium (LD) is available in Bio::PopGen::Statistics as
735 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
736 and csv (comma delimited formatted) data.
738 - a directory for implementing population simulations has
739 been added Bio::PopGen::Simulation and 2 simulations - a
740 Coalescent and a simple single-locus multi-allele genetic drift
741 simulation have been provided. This replaces the code in
742 Bio::Tree::RandomTree which has been deprecated until proper
743 methods for generating random phylogenetic trees are
747 - new restrion analysis modules
749 o Bio::Tools::Analysis
750 - web based DNA and Protein analysis framework and several
754 - per residue annotable sequences
757 - Bio::Matrix::PSM - Position Scoring Matrix
758 - Bio::Matrix::IO has been added for generalized parsing of
759 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
760 initial implementations for parsing BLOSUM/PAM and Phylip
761 Distance matricies respectively. A generic matrix
762 implementation for general use was added in
763 Bio::Matrix::Generic.
770 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
771 - small inhibitory RNA
773 o Bio::SeqFeature::Tools
774 - seqFeature mapping tools
775 - Bio::SeqFeature::Tools::Unflattener.pm
776 -- deal with mapping GenBank feature collections into
777 Chado/GFF3 processable feature sets (with SO term mappings)
779 o Bio::Tools::dpAlign
780 - pure perl dynamic programming sequence alignment
783 o new Bio::SearchIO formats
784 - axt and psl: UCSC formats.
785 - blasttable: NCBI -m 8 or -m 9 format from blastall
787 o new Bio::SeqIO formats
788 - chado, tab, kegg, tigr, game
789 - important fixes for old modules
793 o improved Bio::Tools::Genewise
795 o Bio::SeqIO now can recongnize sequence formats automatically from
798 o new parsers in Bio::Tools:
799 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
801 o Bio::DB::Registry bugs fixed
802 - BerkeleyDB-indexed flat files can be used by the OBDA system
803 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
804 used by the OBDA system
807 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
810 o hundreds of new and improved files
814 o Bio::Tree::AlleleNode has been updated to be a container of
815 an Bio::PopGen::Individual object for use in the Coalescent simulations.
820 1.2.3 Stable release update
821 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
823 o Bug #1477 - Sel --> Sec abbreviation fixed
824 o Fix bug #1487 where paring in-between locations when
825 end < start caused the FTLocationFactory logic to fail.
826 o Fix bug #1489 which was not dealing with keywords as an
827 arrayref properly (this is fixed on the main trunk because
828 keywords returns a string and the array is accessible via
830 o Bio::Tree::Tree memory leak (bug #1480) fixed
831 Added a new initialization option -nodelete which
832 won't try and cleanup the containing nodes if this
834 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
835 this was only present on the branch for the 1.2.1 and 1.2.2 series
836 - Also merged main trunk changes to the branch which make
837 newick -> nhx round tripping more effective (storing branch length
838 and bootstrap values in same locate for NodeNHX and Node
839 implementations.) Fixes to TreeIO parsing for labeled internal
840 also required small changes to TreeIO::nhx. Improved
841 tests for this module as well.
843 - Fixed bugs in BLAST parsing which couldn't parse NCBI
844 gapped blast properly (was losing hit significance values due to
845 the extra unexpeted column).
846 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
847 integer overflow (# of letters in nt seq dbs is > MAX_INT)
848 although doesn't try to correct it - will get the negative
849 number for you. Added a test for this as well.
850 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
851 has no top-level family classification scores but does have scores and
852 alignments for individual domains.
853 - Parsing FASTA reports where ungapped percent ID is < 10 and the
854 regular expression to match the line was missing the possibility of
855 an extra space. This is rare, which is why we probably did not
857 - BLAST parsing picks up more of the statistics/parameter fields
858 at the bottom of reports. Still not fully complete.
859 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
860 were fixed to include many improvements and added flexiblity
861 in outputting the files. Bug #1495 was also fixed in the process.
863 - Update for GFF3 compatibility.
864 - Added scripts for importing from UCSC and GenBank.
865 - Added a 1.2003 version number.
868 - Added a 1.2003 version number.
869 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
870 properly writing keywords out.
871 o Bio::SeqIO::genbank
872 - Fixed bug/enhancement #1513 where dates of
873 the form D-MMM-YYYY were not parsed. Even though this is
874 invalid format we can handle it - and also cleanup the date
875 string so it is properly formatted.
876 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
877 and written with Genbank format. Similarly bug #1515 is fixed to
878 parse in the ORIGIN text.
879 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
880 to specify the ID type, one of (accession accession.version
881 display primary). See Bio::SeqIO::preferred_id_type method
882 documentation for more information.
883 o Unigene parsing updated to handle file format changes by NCBI
885 1.2.2 Stable release update
887 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
888 - auto-discover ontology name
889 - bug in parsing relationships when certain characters are in the term
890 - fixed hard-coded prefix for term identifiers
891 - various smaller issues
893 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
894 of Bio::Ontology::TermI
896 o brought the OBDA Registry code up to latest specs
900 - accession number retrieval fixed
902 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
904 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
905 #1459 which now properly report alignment start/end info
906 for translated BLAST/FASTA searches.
908 o Bio::TreeIO::newick can parse labeled internal nodes
910 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
911 for BLASTX if if you provide -report_type => 'BLASTX' when
912 initializing a BPbl2seq object. Bioperl 1.3 will have better
913 support for bl2seq in the SearchIO system.
915 o Bio::Root::IO support a -noclose boolean flag which will not
916 close a filehandle upon object cleanup - useful when sharing
917 a filehandle among objects. Additionally code added s.t.
918 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
920 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
922 o Bio::SeqIO::genbank
923 - bug #1456 fixed which generated extra sequence lines
924 - write moltype correctly for genpept
926 1.2.1 Stable release update
928 o Inclusion of WrapperBase, a needed component for StandAloneBlast
930 o Addition from main trunk of Ontology objects, principly to allow
931 BioSQL releases against 1.2.1
933 o Fixes and cleanup of Bio::Coordinate modules
935 o A fix to Bio::Index::EMBL allowing retrieval of entries using
936 the primary accession number
938 o Other bug fixes, including bpindex GenBank fix
940 o Bio::SeqIO::genbank bug #1389 fixed
942 1.2 Stable major release
944 o More functionality added to Bio::Perl, the newbie module
946 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
947 Support for New Hampshire Extended (NHX) format parsing.
949 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
950 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
953 o New ontology parsing Bio::Ontology
955 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
956 multi-report (mlib) fasta reports, support for waba and exonerate.
958 o Bio::ClusterIO for parsing Unigene clusters
960 o Bio::Assembly added for representing phrap and ace assembly clusters.
962 o Rudimentary support for writing Chado XML (see
963 GMOD project: www.gmod.org for more information)
965 o Bio::Coordinate for mapping between different coordinate systems such
966 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
967 features into different coordinate systems.
969 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
970 with the get_Stream_by_query method and supports the latest
971 NCBI eutils interface.
973 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
974 object for extracting subsets of features : currently only
975 supports extraction by location.
977 1.1.1 Developer release
979 o Deprecated modules are now listed in the DEPRECATED file
981 o New HowTo documents located in doc/howto describing
984 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
985 and all old bugs are searchable through the bugzilla interface.
987 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
990 o Support for Genewise parsing in Bio::Tools::Genewise
992 o Start of Ontology framework with Bio::Ontology
994 o Speedup to the Bio::Root::Root object method _rearrange.
995 A global _load_module method was implemented to simplify the
996 dynamic loading of modules ala Bio::SeqIO::genbank. This
997 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1000 o Several performance improvements to sequence parsing in Bio::SeqIO.
1001 Attempt to speedup by reducing object creation overhead.
1003 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1004 method for sequence retrieval with their E-utils CGI scripts.
1005 More work to support Entrez queries to their fullest is planned
1008 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1010 1.1 Developer release
1012 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1013 this separation removes some of the complexity in our test suite
1014 and separates the core modules in bioperl from those that need
1015 external programs to run.
1017 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1018 not run into trouble running the makefile
1020 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1021 read,create,and write locations for grouped/split locations
1022 (like mRNA features on genomic sequence).
1024 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1025 and PAML (codeml,aaml, etc) parsing.
1027 o Bio::Tree:: objects expanded to handle testing monophyly,
1028 paraphyly, least common ancestor, etc.
1030 o Bio::Coordinate for mapping locations from different coordinate spaces
1032 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1033 added for parsing hmmpfam and hmmsearch output.
1035 o Bio::SearchIO::Writer::TextResultWriter for outputting
1036 a pseudo-blast textfile format
1039 1.0.2 Bug fix release
1041 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1042 in this release will not work after December 2002 when NCBI
1043 shuts off the old Entrez cgi scripts. We have already fixed
1044 on our main development branch and the functionality will be
1045 available in the next stable bioperl release (1.2) slated for
1048 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1049 testset by Robin Emig. These were fixed as was the get_aln
1050 method in Bio::Search::HSP::GenericHSP to handle the extra
1051 context sequence that is provided with a FastA alignment.
1053 o Migrating differences between Bio::Search::XX::BlastXX to
1054 Bio::Search::XX::GenericXX objects. This included mechanism
1055 to retrieve whole list of HSPs from Hits and whole list of Hits from
1056 Results in addition to the current next_XX iterator methods that
1057 are available. Added seq_inds() method to GenericHSP which identifies
1058 indexes in the query or hit sequences where conserved,identical,gaps,
1059 or mismatch residues are located (adapted from Steve Chervitz's
1060 implementation in BlastHSP).
1062 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1063 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1065 o Bio::Graphics glyph set improved and extended for GBrowse release
1067 o Bio::Tree::Tree get_nodes implementation improvement thanks
1068 to Howard Ross notice performance problem when writing out
1071 o Bio::Location::Fuzzy::new named parameter -loc_type became
1072 -location_type, Bio::Location::Simple::new named parameter
1073 -seqid becamse -seq_id.
1075 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1076 was mis-detecting that gaps should be placed at the beginning of
1077 the alignment when the best alignment starts internally in the
1080 1.0.1 Bug fix release
1082 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1084 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1085 and mixed (3.3 - 3.4) versions of FASTA.
1087 o Small API change to add methods for completeness across
1088 implementations of Bio::Search objects. These new methods
1089 in the interface are implemented by the GenericXX object as well
1090 as the BlastXX objects.
1091 * Bio::Search::Result::ResultI
1092 - hits() method returns list of all Hits (next_hit is an
1095 * Bio::Search::Hit::HitI
1096 - hsps() method returns list of all HSPs (next_hsp is an
1099 o The Bio::SearchIO::Writer classes have been fixed to handle results
1100 created from either psiblast (Search::BlastXX objects) or
1101 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1102 has to be done here to make it work properly and will nee major
1105 o Bugs in Bio::Tools::HMMER fixed, including
1106 * #1178 - Root::IO destructor wasn't being called
1107 * #1034 - filter_on_cutoff now behaves properly
1109 o Bio::SeqFeature::Computation initialization args fixed and
1112 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1114 o Updated FAQ with more example based answers to typical questions
1116 o Bug #1202 was fixed which would improperly join together qual values
1117 parsed by Bio::SeqIO::qual when a trailing space was not present before
1120 1.0.0 Major Stable Release
1122 This represents a major release of bioperl with significant
1123 improvements over the 0.7.x series of releases.
1125 o Bio::Tools::Blast is officially deprecated. Please see
1126 Bio::SearchIO for BLAST and FastA parsing.
1128 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1129 Bio::LocationI objects as well as start/end.
1131 o Bio::Biblio contains modules for Bibliographic data.
1132 Bio::DB::Biblio contains the query modules. Additionally one can
1133 parse medlinexml from the ebi bibliographic query service (BQS)
1134 system and Pubmed xml from NCBI. See Martin Senger's
1135 documentation in Bio::Biblio for more information.
1137 o Bio::DB::Registry is a sequence database registry part of
1138 Open Bioinformatics Database Access. See
1139 http://obda.open-bio.org for more information.
1141 o File-based and In-Memory Sequence caching is provided by
1142 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1145 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1146 been added by Lincoln Stein.
1148 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1150 o A FAQ has been started and is included in the release to provide
1151 a starting point for frequent questions and issues.
1153 0.9.3 Developer's release
1155 o Event based parsing system improved (SearchIO). With parsers for
1156 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1157 Additionally a lazy parsing system for text and html blast reports was
1158 added and is called psiblast (name subject to change in future releases).
1160 o Bio::Search objects improved and standardized with associated Interfaces
1161 written. The concept of a search "Hit" was standardized to be called
1162 "hit" consistently and the use of "subject" was deprecated in all active
1165 o Bio::Structure added (since 0.9.1) for Protein structure objects
1166 and PDB parser to retrieve and write these structures from data files.
1168 o Several important Bio::DB::GFF bug fixes for handling features that
1169 are mapped to multiple reference points. Updated mysql adaptor
1170 so as to be able to store large (>100 megabase) chunks of DNA into
1171 Bio::DB::GFF databases.
1173 0.9.2 Developer's release
1175 o Bio::Search and Bio::SearchIO system introduced for event based
1176 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1177 in text and XML and FASTA reports in standard output format.
1179 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1180 generator is included in Bio::TreeIO::RandomTrees and a
1181 statistics module for evaluating.
1183 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1184 server for DAS servers.
1186 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1187 files. The entire BPlite system migrated to using Bio::Root::IO
1188 for the data stream.
1190 o Bio::Tools::Alignment for Consed and sequence Trimming
1193 o Bio::Structure for Protein structure information and parsing
1195 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1196 cgi-bin entry point which should be more reliable.
1198 o Bio::Map and Bio::MapIO for biological map navigation and a
1199 framework afor parsing them in. Only preliminary work here.
1201 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1202 Future work will integrate Pise and allow submission of analysis on
1205 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1206 introduced as new objects for handling Sequence Annotation
1207 information (dblinks, references, etc) and is more robust that
1210 o Bio::Tools::FASTAParser introduced.
1212 o Scripts from the bioperl script submission project and new
1213 scripts from bioperl authors are included in "scripts" directory.
1215 o Factory objects and interfaces are being introduced and are more
1218 o Bio::Root::Root introduced as the base object while
1219 Bio::Root::RootI is now simply an interface.
1221 o Bio::DB::RefSeq provides database access to copy of the NCBI
1222 RefSeq database using the EBI dbfetch script.
1224 0.9.0 Developer's release
1226 o perl version at least 5.005 is now required instead of perl 5.004
1228 o Bio::Tools::Run::RemoteBlast is available for running remote
1231 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1233 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1234 Also added are related modules UTR3, UTR5, Exon, Intron,
1235 Promotor, PolyA and Transcript.
1237 o Speedup of translate method in PrimarySeq
1239 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1240 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1242 o Various fixes to Variation toolkit
1244 o Bio::DB::EMBL provides database access to EMBL sequence data.
1245 Bio::DB::Universal provides a central way to point to indexes
1246 and dbs in a single interface.
1248 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1250 o Bio::Factory::EMBOSS is still in design phase as is
1251 Bio::Factory::ApplicationFactoryI
1253 o Dia models for bioperl design are provided in the models/ directory
1255 0.7.2 Bug fix release
1257 o documentation fixes in many modules - SYNOPSIS code verified
1258 to be runnable in many (but not all modules)
1260 o corrected MANIFEST file from 0.7.1 release
1262 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1265 o Bio::SeqIO::genbank
1266 * Correct parsing and writing of genbank format with protein data
1267 * moltype and molecule separation
1269 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1271 o Bio::SimpleAlign fixed to correctly handle consensus
1272 sequence calculation
1274 o Bio::Tools::HMMER supports hmmer 2.2g
1276 o Bio::Tools::BPlite to support report type specific parsing. Most
1277 major changes are not on the 0.7 branch.
1279 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1282 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1283 in several types of mutations:
1284 1.) AA level: deletion, complex
1285 2.) AA level: complex, inframe
1286 3.) RNA level: silent
1288 o BPbl2seq parsing of empty reports will not die, but will return
1289 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1290 $report->query() and $report->subject() methods. So an easy
1291 way to test if report was empty is to see if
1292 $report->query->seqname is undefined.
1294 0.7.1 Bug fix release
1296 o Better parsing of genbank/EMBL files especially fixing bugs
1297 related to Feature table parsing and locations on remote
1298 sequences. Additionally, species name parsing was better.
1300 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1301 which include a number of header lines.
1303 o More strict genbank and EMBL format writing (corrected number of
1304 spaces where appropriate).
1306 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1307 for related BPlite BUGS that are unresolved in this release.
1309 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1310 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1311 use expasy mirrors or EBI dbfetch cgi-script.
1313 o A moderate number of documentation improvements were made as
1314 well to provide a better code synopsis in each module.
1317 0.7 Large number of changes, including refactoring of the
1318 Object system, new parsers, new functionality and
1319 all round better system. Highlights are:
1322 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1323 Bio::Root::IO for I/O and file/handle capabilities.
1325 o Imported BPlite modules from Ian Korf for BLAST
1326 parsing. This is considered the supported BLAST parser;
1327 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1329 o Improved Sequence Feature model. Added complete location
1330 modelling (with fuzzy and compound locations). See
1331 Bio::LocationI and the modules under Bio/Location. Added
1332 support in Genbank/EMBL format parsing to completely parse
1333 feature tables for complex locations.
1335 o Moved special support for databanks etc to specialized modules under
1336 Bio/Seq/. One of these supports very large sequences through
1337 a temporary file as a backend.
1339 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1340 CDS retrieval and exon shuffling.
1342 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1344 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1345 DB/GDB (the latter has platform-specific limitations).
1347 o New analysis parser framework for HT sequence annotation (see
1348 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1350 o New Alignment IO framework
1352 o New Index modules (Swissprot)
1354 o New modules for running Blast within perl
1355 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1356 Multiple Sequence Alignment tools ClustalW and TCoffee
1357 (Bio::Tools::Run::Alignment).
1359 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1360 documentation across the package.
1362 o Much improved cross platform support. Many known incompatibilities
1363 have been fixed; however, NT and Mac do not work across the entire
1364 setup (see PLATFORMS).
1366 o Many bug fixes, code restructuring, etc. Overall stability and
1367 maintainability benefit a lot.
1369 o A total of 957 automatic tests
1374 There are very few functionality changes but a large
1375 number of software improvements/bug fixes across the package.
1377 o The EMBL/GenBank parsing are improved.
1379 o The Swissprot reading is improved. Swissprot writing
1380 is disabled as it doesn't work at all. This needs to
1381 wait for 0.7 release
1383 o BLAST reports with no hits are correctly parsed.
1385 o Several other bugs of the BLAST parser (regular expressions, ...)
1388 o Old syntax calls have been replaced with more modern syntax
1390 o Modules that did not work at all, in particular the Sim4
1391 set have been removed
1393 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1394 have improved compliance with interface specs and documentation
1396 o Mailing list documentation updated throughout the distribution
1398 o Most minor bug fixes have happened.
1400 o The scripts in /examples now work and have the modern syntax
1401 rather than the deprecated syntax
1404 0.6.1 Sun April 2 2000
1406 o Sequences can have Sequence Features attached to them
1407 - The sequence features can be read from or written to
1408 EMBL and GenBank style flat files
1410 o Objects for Annotation, including References (but not
1411 full medline abstracts), Database links and Comments are
1414 o A Species object to represent nodes on a taxonomy tree
1417 o The ability to parse HMMER and Sim4 output has been added
1419 o The Blast parsing has been improved, with better PSI-BLAST
1420 support and better overall behaviour.
1422 o Flat file indexed databases provide both random access
1423 and sequential access to their component sequences.
1425 o A CodonTable object has been written with all known
1426 CodonTables accessible.
1428 o A number of new lightweight analysis tools have been
1429 added, such as molecular weight determination.
1431 The 0.6 release also has improved software engineering
1433 o The sequence objects have been rewritten, providing more
1434 maintainable and easier to implement objects. These
1435 objects are backwardly compatible with the 0.05.1 objects
1437 o Many objects are defined in terms of interfaces and then
1438 a Perl implementation has been provided. The interfaces
1439 are found in the 'I' files (module names ending in 'I').
1441 This means that it is possible to wrap C/CORBA/SQL access
1442 as true "bioperl" objects, compatible with the rest of
1445 o The SeqIO system has been overhauled to provide better
1446 processing and perl-like automatic interpretation of <>
1449 o Many more tests have been added (a total of 172 automatic
1450 tests are now run before release).
1454 0.05.1 Tue Jun 29 05:30:44 1999
1455 - Central distribution now requires Perl 5.004. This was
1456 done to get around 5.003-based problems in Bio/Index/*
1458 - Various bug fixes in the Bio::Tools::Blast modules
1459 including better exception handling and PSI-Blast
1460 support. See Bio/Tools/Blast/CHANGES for more.
1461 - Fixed the Parse mechanism in Seq.pm to use readseq.
1462 Follow the instructions in README for how to install
1463 it (basically, you have to edit Parse.pm).
1464 - Improved documentation of Seq.pm, indicating where
1465 objects are returned and where strings are returned.
1466 - Fixed uninitialized warnings in Bio::Root::Object.pm
1467 and Bio::Tools::SeqPattern.pm.
1468 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1470 0.05 Sun Apr 25 01:14:11 1999
1471 - Bio::Tools::Blast modules have less memory problems
1472 and faster parsing. Webblast uses LWP and supports
1473 more functionality. See Bio/Tools/Blast/CHANGES for more.
1474 - The Bio::SeqIO system has been started, moving the
1475 sequence reformatting code out of the sequence object
1476 - The Bio::Index:: system has been started, providing
1477 generic index capabilities and specifically works for
1478 Fasta formatted databases and EMBL .dat formatted
1480 - The Bio::DB:: system started, providing access to
1481 databases, both via flat file + index (see above) and
1483 - The scripts/ directory, where industrial strength scripts
1484 are put has been started.
1485 - Many changes - a better distribution all round.
1487 0.04.4 Wed Feb 17 02:20:13 1999
1488 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1489 (see Bio::Tools::Blast::CHANGES).
1490 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1491 - Beefed up the t/Fasta.t test script.
1492 - Small fix in Bio::Seq::type() (now always returns a string).
1493 - Changed Bio::Root::Utilities::get_newline_char() to
1494 get_newline() since it could return more than one char.
1495 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1496 - Changed default timeout to 20 seconds (was 3).
1497 - Moved lengthy modification notes to the bottom of some files.
1498 - Fixed SimpleAlign write_fasta bug.
1499 - Beefed up SimpleAlign.t test
1501 0.04.3 Thu Feb 4 07:48:53 1999
1502 - Bio::Root::Object.pm and Global.pm now detect when
1503 script is run as a CGI and suppress output that is only
1504 appropriate when running interactively.
1505 - Bio::Root::Err::_set_context() adds name of script ($0).
1506 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1507 regarding the use of the static objects via the qw(:obj) tag.
1508 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1509 CORE::reverse, avoiding Perl warnings.
1510 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1511 example scripts (see Bio::Tools::Blast::CHANGES).
1512 - examples/seq/seqtools.pl no longer always warns about using
1513 -prot or -nucl command-line arguments; only when using the
1515 - Methods added to Bio::Root::Utilities: create_filehandle(),
1516 get_newline_char(), and taste_file() to generalize filehandle
1517 creation and autodetect newline characters in files/streams
1518 (see bug report #19).
1519 - Bio::Root::IOManager::read() now handles timeouts and uses
1520 Utilities::create_filehandle().
1521 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1522 of hardwiring in "\n".
1523 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1525 0.04.2 Wed Dec 30 02:27:36 1998
1526 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1527 (see Bio::Tools::Blast::CHANGES).
1528 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1529 to CORE::reverse (prevents ambiguous warnings with 5.005).
1530 - Appending '.tmp.bioperl' to temporary files created by
1531 Bio::Root::Utilities::compress() or uncompress() to
1532 make it easy to identify & cleanup these files as needed.
1533 - Developers: Created CVS branch release-0-04-bug from
1534 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1535 be sure to cvs checkout this branch into a clean area.
1537 0.04.1 Wed Dec 16 05:39:15 1998
1538 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1539 (see Bio::Tools::Blast::CHANGES).
1540 - Compile/SW/Makefile.PL now removes *.o and *.a files
1543 0.04 Tue Dec 8 07:49:19 1998
1544 - Lots of new modules added including:
1545 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1546 and Bio/Compile directory containing XS-linked C code for
1547 creating Smith-Waterman sequence alignments from within Perl.
1548 * Steve Chervitz's Blast distribution has been incorporated.
1549 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1550 - Bio/examples directory for demo scripts for all included modules.
1551 - Bio/t directory containing test suit for all included modules.
1552 - For changes specific to the Blast-related modules prior to
1553 incorporation in this central distribution, see the CHANGES
1554 file in the Bio/Tools/Blast directory.
1556 0.01 Tue Sep 8 14:23:22 1998
1557 - original version from central CVS tree; created by h2xs 1.18