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 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
26 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
27 instances where blank lines are within sequences [cjfields]
28 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
30 * Various fixes for Stockholm file indexing and processing [bosborne]
31 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
32 breaks parsing [cjfields]
38 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
39 modules using Ace will also be deprecated [lds, cjfields]
40 * Minor bug fix release
41 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
42 * Address Build.PL issues when DBI is not present [hartzell]
43 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
44 * Remove deprecated code for perl 5.14.0 compat [cjfields]
45 * Due to schema changes and lack of support for older versions, support
46 for NeXML 0.9 is only (very) partially implemented.
47 See: https://redmine.open-bio.org/issues/3207
51 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
52 docs [genehack, cjfields]
53 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
54 module version from dist_version (probably not the best way to do this,
55 but it seems to work) [rbuels, cjfields]
62 * This will probably be the last release to add significant features to
63 core modules; subsequent releases will be for bug fixes alone.
64 We are planning on a restructuring of core for summer 2011, potentially
65 as part of the Google Summer of Code. This may become BioPerl 2.0.
66 * Version bump represents 'just prior to v 1.7'. We may have point
67 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
68 This code essentially is what is on the github master branch.
72 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
74 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
75 - removal of Scalar::Util::weaken code, which was causing odd headaches
76 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
77 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
79 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
82 - bug 2515 - new contribution [Ryan Golhar, jhannah]
84 - support for reading Maq, Sam and Bowtie files [maj]
85 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
86 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
87 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
88 - bug 2726: reading/writing granularity: whole scaffold or one contig
89 at a time [Joshua Udall, fangly]
91 - Added parsing of xrefs to OBO files, which are stored as secondary
92 dbxrefs of the cvterm [Naama Menda]
93 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
94 * PAML code updated to work with PAML 4.4d [DaveMessina]
98 * [3198] - sort tabular BLAST hits by score [DaveMessina]
99 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
100 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
101 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
103 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
104 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
105 * [3164] - TreeFunctionsI syntax bug [gjuggler]
106 * [3163] - AssemblyIO speedup [fangly]
107 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
109 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
110 * [3158] - fix EMBL file mis-parsing [cjfields]
111 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
113 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
114 * [3148] - URL change for UniProt [cjfields]
115 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
116 * [3136] - HMMer3 parser fixes [kblin]
117 * [3126] - catch description [Toshihiko Akiba]
118 * [3122] - Catch instances where non-seekable filehandles were being
119 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
120 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
121 [dukeleto, rbuels, cjfields]
122 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
124 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
125 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
127 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
128 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
129 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
130 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
131 * [3086] - EMBL misparsing long tags [kblin, cjfields]
132 * [3085] - CommandExts and array of files [maj, hyphaltip]
133 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
134 for alignment slices [Ha X. Dang, cjfields]
135 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
136 * [3073] - fix parsing of GenBank files from RDP [cjfields]
137 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
138 * [3064] - All-gap midline BLAST report issues [cjfields]
139 * [3063] - BLASt report RID [Razi Khaja, cjfields]
140 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
141 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
142 * [3039] - correct Newick output root node branch length [gjuggler,
144 * [3038] - SELEX alignment error [Bernd, cjfields]
145 * [3033] - PrimarySeq ID setting [Bernd, maj]
146 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
147 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
148 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
149 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
150 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
151 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
152 PAML 4.4d [DaveMessina]
153 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
155 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
156 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
157 * [3017] - using threads with Bio::DB::GenBank [cjfields]
158 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
159 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
160 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
161 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
162 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
164 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
165 * [2977] - TreeIO issues [DaveMessina]
166 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
167 * [2944] - Bio::Tools::GFF score [cjfields]
168 * [2942] - correct MapTiling output [maj]
169 * [2939] - PDB residue insertion codes [John May, maj]
170 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
171 * [2928] - GuessSeqFormat raw [maj]
172 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
173 * [2922] - open() directive issue [cjfields]
174 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
175 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
176 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
177 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
179 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
180 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
181 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
182 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
183 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
184 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
185 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
186 * [2758] - Bio::AssemblyIO ace problems [fangly]
187 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
188 * [2726] - ace file IO [Josh, fangly]
189 * [2700] - Refactor Build.PL [cjfields]
190 * [2673] - addition of simple Root-based clone() method [cjfields]
191 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
192 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
193 * [2594] - Bio::Species memory leak [cjfields]
194 * [2515] - GenBank XML parser [jhannah]
195 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
196 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
197 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
199 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
203 * Bio::Expression modules - these were originally designed to go with the
204 bioperl-microarray suite of tools, however they have never been completed
205 and so have been removed from the distribution. The original code has
206 been moved into the inactive bioperl-microarray suite. [cjfields]
210 * Repository moved from Subversion (SVN) to
211 http://github.com/bioperl/bioperl-live [cjfields]
212 * Bug database has moved to Redmine (https://redmine.open-bio.org)
213 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
214 Thieme have been moved to their own distribution (Bio-Microarray).
217 1.6.1 Sept. 29, 2009 (point release)
218 * No change from last alpha except VERSION and doc updates [cjfields]
220 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
221 * Fix for silent OBDA bug related to FASTA validation [cjfields]
223 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
224 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
225 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
227 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
229 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
230 * WinXP test fixes [cjfields, maj]
231 * BioPerl.pod added for descriptive information, fixes CPAN indexing
233 * Minor doc fixes [cjfields]
235 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
236 * Fix tests failing due to merging issues [cjfields]
237 * More documentation updates for POD parsing [cjfields]
239 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
241 - fix YAML meta data generation [cjfields]
243 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
244 * Bio::Align::DNAStatistics
245 - fix divide by zero problem [jason]
247 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
248 * Bio::AlignIO::stockholm
249 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
250 * Bio::Assembly::Tools::ContigSpectrum
251 - function to score contig spectrum [fangly]
252 * Bio::DB::EUtilities
253 - small updates [cjfields]
255 - berkeleydb database now autoindexes wig files and locks correctly
258 - various small updates for stability; tracking changes to LANL
259 database interface [maj]
260 * Bio::DB::SeqFeature (lots of updates and changes)
261 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
262 - bug 2835 - patch [Dan Bolser]
263 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
265 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
266 * Bio::Factory::FTLocationFactory
267 - mailing list bug fix [cjfields]
269 - performance work on column_from_residue_number [hartzell]
270 * Bio::Matrix::IO::phylip
271 - bug 2800 - patch to fix phylip parsing [Wei Zou]
273 - Google Summer of Code project from Chase Miller - parsers for Nexml
274 file format [maj, chmille4]
276 - Make Individual, Population, Marker objects AnnotatableI [maj]
277 - simplify LD code [jason]
279 - deal with empty intersection [jason]
281 - significant overhaul of Bio::Restriction system: complete support for
282 external and non-palindromic cutters. [maj]
284 - CPANPLUS support, no automatic installation [sendu]
286 - allow IO::String (regression fix) [cjfields]
287 - catch unintentional undef values [cjfields]
288 - throw if non-fh is passed to -fh [maj]
289 * Bio::Root::Root/RootI
290 - small debugging and core fixes [cjfields]
292 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
293 * Bio::Root::Utilities
294 - bug 2737 - better warnings [cjfields]
296 - tiling completely refactored, HOWTO added [maj]
297 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
298 will deprecate usage of the older tiling code in the next BioPerl
300 - small fixes [cjfields]
302 - Infernal 1.0 output now parsed [cjfields]
303 - new parser for gmap -f9 output [hartzell]
304 - bug 2852 - fix infinite loop in some output [cjfields]
305 - blastxml output now passes all TODO tests [cjfields]
306 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
307 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
308 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
309 * Bio::Seq::LargePrimarySeq
310 - delete tempdirs [cjfields]
311 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
313 - extract regions based on quality threshold value [Dan Bolser, heikki]
314 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
315 * Bio::SeqFeature::Lite
316 - various Bio::DB::SeqFeature-related fixes [lstein]
317 * Bio::SeqFeature::Tools::TypeMapper
318 - additional terms for GenBank to SO map [scain]
319 * Bio::SeqIO::chadoxml
320 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
322 - support for CDS records [dave_messina, Sylvia]
324 - complete refactoring to handle all FASTQ variants, perform validation,
325 write output. API now conforms with other Bio* parsers and the rest of
326 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
328 * Bio::SeqIO::genbank
329 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
330 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
331 * Bio::SeqIO::largefasta
332 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
334 - add option for 'single' and 'multiple'
336 - bug 2881 - fix scf round-tripping [Adam Sj¿gren]
338 - bug 2766, 2810 - copy over tags from features, doc fixes [David
341 - bug 2793 - patch for add_seq index issue [jhannah, maj]
342 - bug 2801 - throw if args are required [cjfields]
343 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
344 [Tristan Lefebure, maj]
345 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
346 - fix POD and add get_SeqFeatures filter [maj]
347 * Bio::Tools::dpAlign
348 - add support for LocatableSeq [ymc]
349 - to be moved to a separate distribution [cjfields, rbuels]
350 * Bio::Tools::EUtilities
351 - fix for two bugs from mail list [Adam Whitney, cjfields]
352 - add generic ItemContainerI interface for containing same methods
355 - fix up code, add more warnings [cjfields]
356 - to be moved to a separate distribution [cjfields, rbuels]
357 * Bio::Tools::Primer3
358 - bug 2862 - fenceposting issue fixed [maj]
359 * Bio::Tools::Run::RemoteBlast
360 - tests for remote RPS-BLAST [mcook]
361 * Bio::Tools::SeqPattern
362 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
363 * Bio::Tools::tRNAscanSE
364 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
366 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
367 * Bio::Tree::Statistics
368 - several methods for calculating Fitch-based score, internal trait
369 values, statratio(), sum of leaf distances [heikki]
371 - bug 2869 - add docs indicating edge case where nodes can be
372 prematurely garbage-collected [cjfields]
373 - add as_text() function to create Tree as a string in specified format
375 * Bio::Tree::TreeFunctionsI
376 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
378 * Bio::TreeIO::newick
379 - fix small semicolon issue [cjfields]
381 - update to bp_seqfeature_load for SQLite [lstein]
382 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
383 - fastam9_to_table - fix for MPI output [jason]
384 - gccalc - total stats [jason]
386 - POD cleanup re: FEEDBACK section [maj, cjfields]
387 - cleanup or fix dead links [cjfields]
388 - Use of no_* methods (indicating 'number of something') is deprecated
389 in favor of num_* [cjfields]
390 - lots of new tests for the above bugs and refactors [everyone!]
391 - new template for Komodo text editor [cjfields]
394 * Feature/Annotation rollback
395 - Problematic changes introduced prior to the 1.5 release have been
396 rolled back. These changes led to subtle bugs involving operator
397 overloading and interface methods.
398 - Behavior is very similar to that for BioPerl 1.4, with tag values
399 being stored generically as simple scalars. Results in a modest
402 - Split into a separate distribution on CPAN, primarily so development
403 isn't reliant on a complete BioPerl release.
404 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
405 is only available via Subversion (via bioperl-live main trunk)
407 - Common test bed for all BioPerl modules
409 - Common Module::Build-based subclass for all BioPerl modules
410 * Bio::DB::EUtilities
411 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
412 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
413 and user agent request posting and retrieval
414 * Test implementation and reorganization
415 - Tests have been reorganized into groups based on classes or use
417 - Automated test coverage is now online:
418 http://www.bioperl.org/wiki/Test_Coverage
419 - After this release, untested modules will be moved into a
420 separate developer distribution until tests can be derived.
421 Also, new modules to be added are expected to have a test suite
422 and adequate test coverage.
424 1.5.2 Developer release
426 Full details of changes since 1.5.1 are available online at:
427 http://www.bioperl.org/wiki/Change_log
428 The following represents a brief overview of the most important changes.
431 - Overhaul. Brand new system fully allows markers to have multiple
432 positions on multiple maps, and to have relative positions. Should be
436 - This module and all the modules in the Taxonomy directory now
437 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
442 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
444 * New methods ancestor(), each_Descendent() and _handle_internal_id().
446 * Allows for different database modules to create Bio::Taxon objects
447 with the same internal id when the same taxon is requested from each.
450 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
452 * No longer includes the fake root node 'root'; there are multiple roots
453 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
456 * get_node() has new option -full
458 * Caches data retrieved from website
461 - Now a Bio::Taxon. Carries out the species name -> specific name munging
462 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
463 backward compatability in species() method.
465 o Bio::Search and Bio::SearchIO
466 - Overhaul. The existing system has been sped up via some minor changes
467 (mostly gain-of-function to the API). Bio::PullParserI is introduced
468 as a potential eventual replacment for the existing system, though as
469 yet only a Hmmpfam parser exists written using it.
472 1.5.1 Developer release
474 o Major problem with how Annotations were written out with
475 Bio::Seq is fixed by reverting to old behavior for
476 Bio::Annotation objects.
481 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
482 expect at l east 9 spaces at the beginning of a line to
483 indicate line wrapping.
485 * Treat multi-line SOURCE sections correctly, this defect broke
486 both common_name() and classification()
488 * parse swissprot fields in genpept file
490 * parse WGS genbank records
493 * Changed regexp for ID line. The capturing parentheses are
494 the same, the difference is an optional repeated-not-semi-
495 colon expression following the captured \S+. This means the
496 regexp works when the division looks like /PRO;/ or when the
497 division looks like /ANG ;/ - the latter is from EMBL
500 * fix ID line parsing: the molecule string can have spaces in
501 it. Like: "genomic DNA"
503 - swiss.pm: bugs #1727, #1734
506 * Added parser for entrezgene ASN1 (text format) files.
507 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
511 - maf.pm coordinate problem fixed
513 o Bio::Taxonomy and Bio::DB::Taxonomy
515 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
516 can be done via Web without downloading all the sequence.
518 o Bio::Tools::Run::RemoteBlast supports more options and complies
519 to changes to the NCBI interface. It is reccomended that you
520 retrieve the data in XML instead of plain-text BLAST report to
521 insure proper parsing and retrieval of all information as NCBI
522 fully expects to change things in the future.
524 o Bio::Tree and Bio::TreeIO
526 - Fixes so that re-rooting a tree works properly
528 - Writing out nhx format from a newick/nexus file will properly output
529 bootstrap information. The use must move the internal node labels over
531 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
532 $node->bootstrap($node->id);
535 - Nexus parsing is much more flexible now, does not care about
538 - Cladogram drawing module in Bio::Tree::Draw
540 - Node height and depth now properly calculated
542 - fix tree pruning algorithm so that node with 1 child gets merged
544 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
545 bugs and improvements were added, see Gbrowse mailing list for most of
548 o Bio::DB::GFF partially supports GFF3. See information about
549 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
551 o Better location parsing in Bio::Factory::FTLocationFactory -
552 this is part of the engine for parsing EMBL/GenBank feature table
553 locations. Nested join/order-by/complement are allowed now
555 o Bio::PrimarySeqI->translate now takes named parameters
557 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
558 reconstruction) is now supported. Parsing different models and
559 branch specific parametes are now supported.
561 o Bio::Factory::FTLocationFactory - parse hierarchical locations
564 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
565 for getter/setter functions
569 - blast bug #1739; match scientific notation in score
570 and possible e+ values
572 - blast.pm reads more WU-BLAST parameters and parameters, match
573 a full database pathname,
575 - Handle NCBI WEB and newer BLAST formats specifically
576 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
578 - psl off-by-one error fixed
580 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
581 and HSPs can be constructed from them.
583 - HSPs query/hit now have a seqdesc field filled out (this was
584 always available via $hit->description and
585 $result->query_description
587 - hmmer.pm can parse -A0 hmmpfam files
589 - Writer::GbrowseGFF more customizeable.
591 o Bio::Tools::Hmmpfam
592 make e-value default score displayed in gff, rather than raw score
593 allow parse of multiple records
596 1.5 Developer release
598 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
599 provide Jukes-Cantor and Kimura pairwise distance methods,
602 o Bio::AlignIO support for "po" format of POA, and "maf";
603 Bio::AlignIO::largemultifasta is a new alternative to
604 Bio::AlignIO::fasta for temporary file-based manipulation of
605 particularly large multiple sequence alignments.
607 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
608 be treated similarly as an assembled contig.
610 o Bio::CodonUsage provides new rare_codon() and probable_codons()
611 methods for identifying particular codons that encode a given
614 o Bio::Coordinate::Utils provides new from_align() method to build
615 a Bio::Coordinate pair directly from a
616 Bio::Align::AlignI-conforming object.
618 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
619 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
620 web service using standard Pubmed query syntax, and retrieve
623 o Bio::DB::GFF has various sundry bug fixes.
625 o Bio::FeatureIO is a new SeqIO-style subsystem for
626 writing/reading genomic features to/from files. I/O classes
627 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
628 classes only read/write Bio::SeqFeature::Annotated objects.
629 Notably, the GFF v3 class requires features to be typed into the
632 o Bio::Graph namespace contains new modules for manipulation and
633 analysis of protein interaction graphs.
635 o Bio::Graphics has many bug fixes and shiny new glyphs.
637 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
638 indexing for HMMER reports and FASTA qual files, respectively.
640 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
641 new objects that can be placed within a Bio::Map::MapI-compliant
642 genetic/physical map; Bio::Map::Physical provides a new physical
643 map type; Bio::MapIO::fpc provides finger-printed clone mapping
646 o Bio::Matrix::PSM provide new support for postion-specific
647 (scoring) matrices (e.g. profiles, or "possums").
649 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
650 be instantiated without explicitly using Bio::OntologyIO. This
651 is possible through changes to Bio::Ontology::OntologyStore to
652 download ontology files from the web as necessary. Locations of
653 ontology files are hard-coded into
654 Bio::Ontology::DocumentRegistry.
656 o Bio::PopGen includes many new methods and data types for
657 population genetics analyses.
659 o New constructor to Bio::Range, unions(). Given a list of
660 ranges, returns another list of "flattened" ranges --
661 overlapping ranges are merged into a single range with the
662 mininum and maximum coordinates of the entire overlapping group.
664 o Bio::Root::IO now supports -url, in addition to -file and -fh.
665 The new -url argument allows one to specify the network address
666 of a file for input. -url currently only works for GET
667 requests, and thus is read-only.
669 o Bio::SearchIO::hmmer now returns individual Hit objects for each
670 domain alignment (thus containing only one HSP); previously
671 separate alignments would be merged into one hit if the domain
672 involved in the alignments was the same, but this only worked
673 when the repeated domain occured without interruption by any
674 other domain, leading to a confusing mixture of Hit and HSP
677 o Bio::Search::Result::ResultI-compliant report objects now
678 implement the "get_statistics" method to access
679 Bio::Search::StatisticsI objects that encapsulate any
680 statistical parameters associated with the search (e.g. Karlin's
681 lambda for BLAST/FASTA).
683 o Bio::Seq::LargeLocatableSeq combines the functionality already
684 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
686 o Bio::SeqFeature::Annotated is a replacement for
687 Bio::SeqFeature::Generic. It breaks compliance with the
688 Bio::SeqFeatureI interface because the author was sick of
689 dealing with untyped annotation tags. All
690 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
691 compliant, and accessible through Bio::Annotation::Collection.
693 o Bio::SeqFeature::Primer implements a Tm() method for primer
694 melting point predictions.
696 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
697 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
699 o Bio::Taxonomy::Node now implements the methods necessary for
700 Bio::Species interoperability.
702 o Bio::Tools::CodonTable has new reverse_translate_all() and
703 make_iupac_string() methods.
705 o Bio::Tools::dpAlign now provides sequence profile alignments.
707 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
709 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
712 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
713 for designing small inhibitory RNA.
715 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
716 methods based on a distance matrix.
718 o Bio::Tree::Statistics provides an assess_bootstrap() method to
719 calculate bootstrap support values on a guide tree topology,
720 based on provided bootstrap tree topologies.
722 o Bio::TreeIO now supports the Pagel (PAG) tree format.
728 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
730 o Bio::Graphics will work with gd1 or gd2
733 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
735 - blast.pm Parse multi-line query fields properly
736 - small speed improvements to blasttable.pm and others
738 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
739 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
740 supporting more complex queries
743 1.4. Stable major release
745 Since initial 1.2.0, 3000 separate changes have been made to make this release.
747 o installable scripts
749 o global module version from Bio::Root:Version
752 - major improvements; SVG support
755 - population genetics
756 - support several population genetics types of questions.
757 - Tests for statistical neutrality of mutations
758 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
759 Tests of population structure (Wright's F-statistic: Fst) is in
760 Bio::PopGen::PopStats. Calculating composite linkage
761 disequilibrium (LD) is available in Bio::PopGen::Statistics as
763 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
764 and csv (comma delimited formatted) data.
766 - a directory for implementing population simulations has
767 been added Bio::PopGen::Simulation and 2 simulations - a
768 Coalescent and a simple single-locus multi-allele genetic drift
769 simulation have been provided. This replaces the code in
770 Bio::Tree::RandomTree which has been deprecated until proper
771 methods for generating random phylogenetic trees are
775 - new restrion analysis modules
777 o Bio::Tools::Analysis
778 - web based DNA and Protein analysis framework and several
782 - per residue annotable sequences
785 - Bio::Matrix::PSM - Position Scoring Matrix
786 - Bio::Matrix::IO has been added for generalized parsing of
787 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
788 initial implementations for parsing BLOSUM/PAM and Phylip
789 Distance matricies respectively. A generic matrix
790 implementation for general use was added in
791 Bio::Matrix::Generic.
798 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
799 - small inhibitory RNA
801 o Bio::SeqFeature::Tools
802 - seqFeature mapping tools
803 - Bio::SeqFeature::Tools::Unflattener.pm
804 -- deal with mapping GenBank feature collections into
805 Chado/GFF3 processable feature sets (with SO term mappings)
807 o Bio::Tools::dpAlign
808 - pure perl dynamic programming sequence alignment
811 o new Bio::SearchIO formats
812 - axt and psl: UCSC formats.
813 - blasttable: NCBI -m 8 or -m 9 format from blastall
815 o new Bio::SeqIO formats
816 - chado, tab, kegg, tigr, game
817 - important fixes for old modules
821 o improved Bio::Tools::Genewise
823 o Bio::SeqIO now can recongnize sequence formats automatically from
826 o new parsers in Bio::Tools:
827 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
829 o Bio::DB::Registry bugs fixed
830 - BerkeleyDB-indexed flat files can be used by the OBDA system
831 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
832 used by the OBDA system
835 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
838 o hundreds of new and improved files
842 o Bio::Tree::AlleleNode has been updated to be a container of
843 an Bio::PopGen::Individual object for use in the Coalescent simulations.
848 1.2.3 Stable release update
849 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
851 o Bug #1477 - Sel --> Sec abbreviation fixed
852 o Fix bug #1487 where paring in-between locations when
853 end < start caused the FTLocationFactory logic to fail.
854 o Fix bug #1489 which was not dealing with keywords as an
855 arrayref properly (this is fixed on the main trunk because
856 keywords returns a string and the array is accessible via
858 o Bio::Tree::Tree memory leak (bug #1480) fixed
859 Added a new initialization option -nodelete which
860 won't try and cleanup the containing nodes if this
862 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
863 this was only present on the branch for the 1.2.1 and 1.2.2 series
864 - Also merged main trunk changes to the branch which make
865 newick -> nhx round tripping more effective (storing branch length
866 and bootstrap values in same locate for NodeNHX and Node
867 implementations.) Fixes to TreeIO parsing for labeled internal
868 also required small changes to TreeIO::nhx. Improved
869 tests for this module as well.
871 - Fixed bugs in BLAST parsing which couldn't parse NCBI
872 gapped blast properly (was losing hit significance values due to
873 the extra unexpeted column).
874 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
875 integer overflow (# of letters in nt seq dbs is > MAX_INT)
876 although doesn't try to correct it - will get the negative
877 number for you. Added a test for this as well.
878 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
879 has no top-level family classification scores but does have scores and
880 alignments for individual domains.
881 - Parsing FASTA reports where ungapped percent ID is < 10 and the
882 regular expression to match the line was missing the possibility of
883 an extra space. This is rare, which is why we probably did not
885 - BLAST parsing picks up more of the statistics/parameter fields
886 at the bottom of reports. Still not fully complete.
887 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
888 were fixed to include many improvements and added flexiblity
889 in outputting the files. Bug #1495 was also fixed in the process.
891 - Update for GFF3 compatibility.
892 - Added scripts for importing from UCSC and GenBank.
893 - Added a 1.2003 version number.
896 - Added a 1.2003 version number.
897 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
898 properly writing keywords out.
899 o Bio::SeqIO::genbank
900 - Fixed bug/enhancement #1513 where dates of
901 the form D-MMM-YYYY were not parsed. Even though this is
902 invalid format we can handle it - and also cleanup the date
903 string so it is properly formatted.
904 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
905 and written with Genbank format. Similarly bug #1515 is fixed to
906 parse in the ORIGIN text.
907 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
908 to specify the ID type, one of (accession accession.version
909 display primary). See Bio::SeqIO::preferred_id_type method
910 documentation for more information.
911 o Unigene parsing updated to handle file format changes by NCBI
913 1.2.2 Stable release update
915 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
916 - auto-discover ontology name
917 - bug in parsing relationships when certain characters are in the term
918 - fixed hard-coded prefix for term identifiers
919 - various smaller issues
921 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
922 of Bio::Ontology::TermI
924 o brought the OBDA Registry code up to latest specs
928 - accession number retrieval fixed
930 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
932 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
933 #1459 which now properly report alignment start/end info
934 for translated BLAST/FASTA searches.
936 o Bio::TreeIO::newick can parse labeled internal nodes
938 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
939 for BLASTX if if you provide -report_type => 'BLASTX' when
940 initializing a BPbl2seq object. Bioperl 1.3 will have better
941 support for bl2seq in the SearchIO system.
943 o Bio::Root::IO support a -noclose boolean flag which will not
944 close a filehandle upon object cleanup - useful when sharing
945 a filehandle among objects. Additionally code added s.t.
946 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
948 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
950 o Bio::SeqIO::genbank
951 - bug #1456 fixed which generated extra sequence lines
952 - write moltype correctly for genpept
954 1.2.1 Stable release update
956 o Inclusion of WrapperBase, a needed component for StandAloneBlast
958 o Addition from main trunk of Ontology objects, principly to allow
959 BioSQL releases against 1.2.1
961 o Fixes and cleanup of Bio::Coordinate modules
963 o A fix to Bio::Index::EMBL allowing retrieval of entries using
964 the primary accession number
966 o Other bug fixes, including bpindex GenBank fix
968 o Bio::SeqIO::genbank bug #1389 fixed
970 1.2 Stable major release
972 o More functionality added to Bio::Perl, the newbie module
974 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
975 Support for New Hampshire Extended (NHX) format parsing.
977 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
978 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
981 o New ontology parsing Bio::Ontology
983 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
984 multi-report (mlib) fasta reports, support for waba and exonerate.
986 o Bio::ClusterIO for parsing Unigene clusters
988 o Bio::Assembly added for representing phrap and ace assembly clusters.
990 o Rudimentary support for writing Chado XML (see
991 GMOD project: www.gmod.org for more information)
993 o Bio::Coordinate for mapping between different coordinate systems such
994 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
995 features into different coordinate systems.
997 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
998 with the get_Stream_by_query method and supports the latest
999 NCBI eutils interface.
1001 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1002 object for extracting subsets of features : currently only
1003 supports extraction by location.
1005 1.1.1 Developer release
1007 o Deprecated modules are now listed in the DEPRECATED file
1009 o New HowTo documents located in doc/howto describing
1010 a domain of Bioperl.
1012 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1013 and all old bugs are searchable through the bugzilla interface.
1015 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1016 have been addressed.
1018 o Support for Genewise parsing in Bio::Tools::Genewise
1020 o Start of Ontology framework with Bio::Ontology
1022 o Speedup to the Bio::Root::Root object method _rearrange.
1023 A global _load_module method was implemented to simplify the
1024 dynamic loading of modules ala Bio::SeqIO::genbank. This
1025 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1028 o Several performance improvements to sequence parsing in Bio::SeqIO.
1029 Attempt to speedup by reducing object creation overhead.
1031 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1032 method for sequence retrieval with their E-utils CGI scripts.
1033 More work to support Entrez queries to their fullest is planned
1036 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1038 1.1 Developer release
1040 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1041 this separation removes some of the complexity in our test suite
1042 and separates the core modules in bioperl from those that need
1043 external programs to run.
1045 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1046 not run into trouble running the makefile
1048 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1049 read,create,and write locations for grouped/split locations
1050 (like mRNA features on genomic sequence).
1052 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1053 and PAML (codeml,aaml, etc) parsing.
1055 o Bio::Tree:: objects expanded to handle testing monophyly,
1056 paraphyly, least common ancestor, etc.
1058 o Bio::Coordinate for mapping locations from different coordinate spaces
1060 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1061 added for parsing hmmpfam and hmmsearch output.
1063 o Bio::SearchIO::Writer::TextResultWriter for outputting
1064 a pseudo-blast textfile format
1067 1.0.2 Bug fix release
1069 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1070 in this release will not work after December 2002 when NCBI
1071 shuts off the old Entrez cgi scripts. We have already fixed
1072 on our main development branch and the functionality will be
1073 available in the next stable bioperl release (1.2) slated for
1076 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1077 testset by Robin Emig. These were fixed as was the get_aln
1078 method in Bio::Search::HSP::GenericHSP to handle the extra
1079 context sequence that is provided with a FastA alignment.
1081 o Migrating differences between Bio::Search::XX::BlastXX to
1082 Bio::Search::XX::GenericXX objects. This included mechanism
1083 to retrieve whole list of HSPs from Hits and whole list of Hits from
1084 Results in addition to the current next_XX iterator methods that
1085 are available. Added seq_inds() method to GenericHSP which identifies
1086 indexes in the query or hit sequences where conserved,identical,gaps,
1087 or mismatch residues are located (adapted from Steve Chervitz's
1088 implementation in BlastHSP).
1090 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1091 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1093 o Bio::Graphics glyph set improved and extended for GBrowse release
1095 o Bio::Tree::Tree get_nodes implementation improvement thanks
1096 to Howard Ross notice performance problem when writing out
1099 o Bio::Location::Fuzzy::new named parameter -loc_type became
1100 -location_type, Bio::Location::Simple::new named parameter
1101 -seqid becamse -seq_id.
1103 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1104 was mis-detecting that gaps should be placed at the beginning of
1105 the alignment when the best alignment starts internally in the
1108 1.0.1 Bug fix release
1110 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1112 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1113 and mixed (3.3 - 3.4) versions of FASTA.
1115 o Small API change to add methods for completeness across
1116 implementations of Bio::Search objects. These new methods
1117 in the interface are implemented by the GenericXX object as well
1118 as the BlastXX objects.
1119 * Bio::Search::Result::ResultI
1120 - hits() method returns list of all Hits (next_hit is an
1123 * Bio::Search::Hit::HitI
1124 - hsps() method returns list of all HSPs (next_hsp is an
1127 o The Bio::SearchIO::Writer classes have been fixed to handle results
1128 created from either psiblast (Search::BlastXX objects) or
1129 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1130 has to be done here to make it work properly and will nee major
1133 o Bugs in Bio::Tools::HMMER fixed, including
1134 * #1178 - Root::IO destructor wasn't being called
1135 * #1034 - filter_on_cutoff now behaves properly
1137 o Bio::SeqFeature::Computation initialization args fixed and
1140 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1142 o Updated FAQ with more example based answers to typical questions
1144 o Bug #1202 was fixed which would improperly join together qual values
1145 parsed by Bio::SeqIO::qual when a trailing space was not present before
1148 1.0.0 Major Stable Release
1150 This represents a major release of bioperl with significant
1151 improvements over the 0.7.x series of releases.
1153 o Bio::Tools::Blast is officially deprecated. Please see
1154 Bio::SearchIO for BLAST and FastA parsing.
1156 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1157 Bio::LocationI objects as well as start/end.
1159 o Bio::Biblio contains modules for Bibliographic data.
1160 Bio::DB::Biblio contains the query modules. Additionally one can
1161 parse medlinexml from the ebi bibliographic query service (BQS)
1162 system and Pubmed xml from NCBI. See Martin Senger's
1163 documentation in Bio::Biblio for more information.
1165 o Bio::DB::Registry is a sequence database registry part of
1166 Open Bioinformatics Database Access. See
1167 http://obda.open-bio.org for more information.
1169 o File-based and In-Memory Sequence caching is provided by
1170 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1173 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1174 been added by Lincoln Stein.
1176 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1178 o A FAQ has been started and is included in the release to provide
1179 a starting point for frequent questions and issues.
1181 0.9.3 Developer's release
1183 o Event based parsing system improved (SearchIO). With parsers for
1184 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1185 Additionally a lazy parsing system for text and html blast reports was
1186 added and is called psiblast (name subject to change in future releases).
1188 o Bio::Search objects improved and standardized with associated Interfaces
1189 written. The concept of a search "Hit" was standardized to be called
1190 "hit" consistently and the use of "subject" was deprecated in all active
1193 o Bio::Structure added (since 0.9.1) for Protein structure objects
1194 and PDB parser to retrieve and write these structures from data files.
1196 o Several important Bio::DB::GFF bug fixes for handling features that
1197 are mapped to multiple reference points. Updated mysql adaptor
1198 so as to be able to store large (>100 megabase) chunks of DNA into
1199 Bio::DB::GFF databases.
1201 0.9.2 Developer's release
1203 o Bio::Search and Bio::SearchIO system introduced for event based
1204 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1205 in text and XML and FASTA reports in standard output format.
1207 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1208 generator is included in Bio::TreeIO::RandomTrees and a
1209 statistics module for evaluating.
1211 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1212 server for DAS servers.
1214 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1215 files. The entire BPlite system migrated to using Bio::Root::IO
1216 for the data stream.
1218 o Bio::Tools::Alignment for Consed and sequence Trimming
1221 o Bio::Structure for Protein structure information and parsing
1223 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1224 cgi-bin entry point which should be more reliable.
1226 o Bio::Map and Bio::MapIO for biological map navigation and a
1227 framework afor parsing them in. Only preliminary work here.
1229 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1230 Future work will integrate Pise and allow submission of analysis on
1233 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1234 introduced as new objects for handling Sequence Annotation
1235 information (dblinks, references, etc) and is more robust that
1238 o Bio::Tools::FASTAParser introduced.
1240 o Scripts from the bioperl script submission project and new
1241 scripts from bioperl authors are included in "scripts" directory.
1243 o Factory objects and interfaces are being introduced and are more
1246 o Bio::Root::Root introduced as the base object while
1247 Bio::Root::RootI is now simply an interface.
1249 o Bio::DB::RefSeq provides database access to copy of the NCBI
1250 RefSeq database using the EBI dbfetch script.
1252 0.9.0 Developer's release
1254 o perl version at least 5.005 is now required instead of perl 5.004
1256 o Bio::Tools::Run::RemoteBlast is available for running remote
1259 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1261 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1262 Also added are related modules UTR3, UTR5, Exon, Intron,
1263 Promotor, PolyA and Transcript.
1265 o Speedup of translate method in PrimarySeq
1267 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1268 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1270 o Various fixes to Variation toolkit
1272 o Bio::DB::EMBL provides database access to EMBL sequence data.
1273 Bio::DB::Universal provides a central way to point to indexes
1274 and dbs in a single interface.
1276 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1278 o Bio::Factory::EMBOSS is still in design phase as is
1279 Bio::Factory::ApplicationFactoryI
1281 o Dia models for bioperl design are provided in the models/ directory
1283 0.7.2 Bug fix release
1285 o documentation fixes in many modules - SYNOPSIS code verified
1286 to be runnable in many (but not all modules)
1288 o corrected MANIFEST file from 0.7.1 release
1290 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1293 o Bio::SeqIO::genbank
1294 * Correct parsing and writing of genbank format with protein data
1295 * moltype and molecule separation
1297 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1299 o Bio::SimpleAlign fixed to correctly handle consensus
1300 sequence calculation
1302 o Bio::Tools::HMMER supports hmmer 2.2g
1304 o Bio::Tools::BPlite to support report type specific parsing. Most
1305 major changes are not on the 0.7 branch.
1307 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1310 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1311 in several types of mutations:
1312 1.) AA level: deletion, complex
1313 2.) AA level: complex, inframe
1314 3.) RNA level: silent
1316 o BPbl2seq parsing of empty reports will not die, but will return
1317 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1318 $report->query() and $report->subject() methods. So an easy
1319 way to test if report was empty is to see if
1320 $report->query->seqname is undefined.
1322 0.7.1 Bug fix release
1324 o Better parsing of genbank/EMBL files especially fixing bugs
1325 related to Feature table parsing and locations on remote
1326 sequences. Additionally, species name parsing was better.
1328 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1329 which include a number of header lines.
1331 o More strict genbank and EMBL format writing (corrected number of
1332 spaces where appropriate).
1334 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1335 for related BPlite BUGS that are unresolved in this release.
1337 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1338 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1339 use expasy mirrors or EBI dbfetch cgi-script.
1341 o A moderate number of documentation improvements were made as
1342 well to provide a better code synopsis in each module.
1345 0.7 Large number of changes, including refactoring of the
1346 Object system, new parsers, new functionality and
1347 all round better system. Highlights are:
1350 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1351 Bio::Root::IO for I/O and file/handle capabilities.
1353 o Imported BPlite modules from Ian Korf for BLAST
1354 parsing. This is considered the supported BLAST parser;
1355 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1357 o Improved Sequence Feature model. Added complete location
1358 modelling (with fuzzy and compound locations). See
1359 Bio::LocationI and the modules under Bio/Location. Added
1360 support in Genbank/EMBL format parsing to completely parse
1361 feature tables for complex locations.
1363 o Moved special support for databanks etc to specialized modules under
1364 Bio/Seq/. One of these supports very large sequences through
1365 a temporary file as a backend.
1367 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1368 CDS retrieval and exon shuffling.
1370 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1372 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1373 DB/GDB (the latter has platform-specific limitations).
1375 o New analysis parser framework for HT sequence annotation (see
1376 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1378 o New Alignment IO framework
1380 o New Index modules (Swissprot)
1382 o New modules for running Blast within perl
1383 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1384 Multiple Sequence Alignment tools ClustalW and TCoffee
1385 (Bio::Tools::Run::Alignment).
1387 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1388 documentation across the package.
1390 o Much improved cross platform support. Many known incompatibilities
1391 have been fixed; however, NT and Mac do not work across the entire
1392 setup (see PLATFORMS).
1394 o Many bug fixes, code restructuring, etc. Overall stability and
1395 maintainability benefit a lot.
1397 o A total of 957 automatic tests
1402 There are very few functionality changes but a large
1403 number of software improvements/bug fixes across the package.
1405 o The EMBL/GenBank parsing are improved.
1407 o The Swissprot reading is improved. Swissprot writing
1408 is disabled as it doesn't work at all. This needs to
1409 wait for 0.7 release
1411 o BLAST reports with no hits are correctly parsed.
1413 o Several other bugs of the BLAST parser (regular expressions, ...)
1416 o Old syntax calls have been replaced with more modern syntax
1418 o Modules that did not work at all, in particular the Sim4
1419 set have been removed
1421 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1422 have improved compliance with interface specs and documentation
1424 o Mailing list documentation updated throughout the distribution
1426 o Most minor bug fixes have happened.
1428 o The scripts in /examples now work and have the modern syntax
1429 rather than the deprecated syntax
1432 0.6.1 Sun April 2 2000
1434 o Sequences can have Sequence Features attached to them
1435 - The sequence features can be read from or written to
1436 EMBL and GenBank style flat files
1438 o Objects for Annotation, including References (but not
1439 full medline abstracts), Database links and Comments are
1442 o A Species object to represent nodes on a taxonomy tree
1445 o The ability to parse HMMER and Sim4 output has been added
1447 o The Blast parsing has been improved, with better PSI-BLAST
1448 support and better overall behaviour.
1450 o Flat file indexed databases provide both random access
1451 and sequential access to their component sequences.
1453 o A CodonTable object has been written with all known
1454 CodonTables accessible.
1456 o A number of new lightweight analysis tools have been
1457 added, such as molecular weight determination.
1459 The 0.6 release also has improved software engineering
1461 o The sequence objects have been rewritten, providing more
1462 maintainable and easier to implement objects. These
1463 objects are backwardly compatible with the 0.05.1 objects
1465 o Many objects are defined in terms of interfaces and then
1466 a Perl implementation has been provided. The interfaces
1467 are found in the 'I' files (module names ending in 'I').
1469 This means that it is possible to wrap C/CORBA/SQL access
1470 as true "bioperl" objects, compatible with the rest of
1473 o The SeqIO system has been overhauled to provide better
1474 processing and perl-like automatic interpretation of <>
1477 o Many more tests have been added (a total of 172 automatic
1478 tests are now run before release).
1482 0.05.1 Tue Jun 29 05:30:44 1999
1483 - Central distribution now requires Perl 5.004. This was
1484 done to get around 5.003-based problems in Bio/Index/*
1486 - Various bug fixes in the Bio::Tools::Blast modules
1487 including better exception handling and PSI-Blast
1488 support. See Bio/Tools/Blast/CHANGES for more.
1489 - Fixed the Parse mechanism in Seq.pm to use readseq.
1490 Follow the instructions in README for how to install
1491 it (basically, you have to edit Parse.pm).
1492 - Improved documentation of Seq.pm, indicating where
1493 objects are returned and where strings are returned.
1494 - Fixed uninitialized warnings in Bio::Root::Object.pm
1495 and Bio::Tools::SeqPattern.pm.
1496 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1498 0.05 Sun Apr 25 01:14:11 1999
1499 - Bio::Tools::Blast modules have less memory problems
1500 and faster parsing. Webblast uses LWP and supports
1501 more functionality. See Bio/Tools/Blast/CHANGES for more.
1502 - The Bio::SeqIO system has been started, moving the
1503 sequence reformatting code out of the sequence object
1504 - The Bio::Index:: system has been started, providing
1505 generic index capabilities and specifically works for
1506 Fasta formatted databases and EMBL .dat formatted
1508 - The Bio::DB:: system started, providing access to
1509 databases, both via flat file + index (see above) and
1511 - The scripts/ directory, where industrial strength scripts
1512 are put has been started.
1513 - Many changes - a better distribution all round.
1515 0.04.4 Wed Feb 17 02:20:13 1999
1516 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1517 (see Bio::Tools::Blast::CHANGES).
1518 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1519 - Beefed up the t/Fasta.t test script.
1520 - Small fix in Bio::Seq::type() (now always returns a string).
1521 - Changed Bio::Root::Utilities::get_newline_char() to
1522 get_newline() since it could return more than one char.
1523 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1524 - Changed default timeout to 20 seconds (was 3).
1525 - Moved lengthy modification notes to the bottom of some files.
1526 - Fixed SimpleAlign write_fasta bug.
1527 - Beefed up SimpleAlign.t test
1529 0.04.3 Thu Feb 4 07:48:53 1999
1530 - Bio::Root::Object.pm and Global.pm now detect when
1531 script is run as a CGI and suppress output that is only
1532 appropriate when running interactively.
1533 - Bio::Root::Err::_set_context() adds name of script ($0).
1534 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1535 regarding the use of the static objects via the qw(:obj) tag.
1536 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1537 CORE::reverse, avoiding Perl warnings.
1538 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1539 example scripts (see Bio::Tools::Blast::CHANGES).
1540 - examples/seq/seqtools.pl no longer always warns about using
1541 -prot or -nucl command-line arguments; only when using the
1543 - Methods added to Bio::Root::Utilities: create_filehandle(),
1544 get_newline_char(), and taste_file() to generalize filehandle
1545 creation and autodetect newline characters in files/streams
1546 (see bug report #19).
1547 - Bio::Root::IOManager::read() now handles timeouts and uses
1548 Utilities::create_filehandle().
1549 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1550 of hardwiring in "\n".
1551 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1553 0.04.2 Wed Dec 30 02:27:36 1998
1554 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1555 (see Bio::Tools::Blast::CHANGES).
1556 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1557 to CORE::reverse (prevents ambiguous warnings with 5.005).
1558 - Appending '.tmp.bioperl' to temporary files created by
1559 Bio::Root::Utilities::compress() or uncompress() to
1560 make it easy to identify & cleanup these files as needed.
1561 - Developers: Created CVS branch release-0-04-bug from
1562 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1563 be sure to cvs checkout this branch into a clean area.
1565 0.04.1 Wed Dec 16 05:39:15 1998
1566 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1567 (see Bio::Tools::Blast::CHANGES).
1568 - Compile/SW/Makefile.PL now removes *.o and *.a files
1571 0.04 Tue Dec 8 07:49:19 1998
1572 - Lots of new modules added including:
1573 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1574 and Bio/Compile directory containing XS-linked C code for
1575 creating Smith-Waterman sequence alignments from within Perl.
1576 * Steve Chervitz's Blast distribution has been incorporated.
1577 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1578 - Bio/examples directory for demo scripts for all included modules.
1579 - Bio/t directory containing test suit for all included modules.
1580 - For changes specific to the Blast-related modules prior to
1581 incorporation in this central distribution, see the CHANGES
1582 file in the Bio/Tools/Blast directory.
1584 0.01 Tue Sep 8 14:23:22 1998
1585 - original version from central CVS tree; created by h2xs 1.18