1 ---------------------------------------------------------
2 Revision history for BioPerl core modules
3 ---------------------------------------------------------
5 The comprehensive history and ongoing development of BioPerl:
7 http://github.com/bioperl/bioperl-live
9 Some of that history is also highlighted on our wiki:
11 http://www.bioperl.org/wiki/Change_log
12 http://www.bioperl.org/wiki/History_of_BioPerl
16 http://bugzilla.open-bio.org
17 specific bugs intended for the next CPAN release series highlighted in BUGS
20 CPAN releases are branched off of 'master', verified stable, and pushed to PAUSE.
23 1.6.1_1 RELEASE_DATE_HERE (first 1.6.2 alpha)
26 - bug 2515 - new contribution [Ryan Golhar, jhannah]
28 - new ACE variant for 454 GS Assembler (Newbler) [fangly]
33 * bug 3077 - Bio::SimpleAlign slice() now correctly computes seq coordinates
34 for alignment slices [Ha X. Dang, cjfields]
38 * Repository moved from Subversion (SVN) to
39 http://github.com/bioperl/bioperl-live [cjfields]
41 1.6.1 Sept. 29, 2009 (point release)
42 * No change from last alpha except VERSION and doc updates [cjfields]
44 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
45 * Fix for silent OBDA bug related to FASTA validation [cjfields]
47 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
48 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
49 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
51 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
53 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
54 * WinXP test fixes [cjfields, maj]
55 * BioPerl.pod added for descriptive information, fixes CPAN indexing
57 * Minor doc fixes [cjfields]
59 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
60 * Fix tests failing due to merging issues [cjfields]
61 * More documentation updates for POD parsing [cjfields]
63 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
65 - fix YAML meta data generation [cjfields]
67 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
68 * Bio::Align::DNAStatistics
69 - fix divide by zero problem [jason]
71 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
72 * Bio::AlignIO::stockholm
73 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
74 * Bio::Assembly::Tools::ContigSpectrum
75 - function to score contig spectrum [fangly]
77 - small updates [cjfields]
79 - berkeleydb database now autoindexes wig files and locks correctly
82 - various small updates for stability; tracking changes to LANL
83 database interface [maj]
84 * Bio::DB::SeqFeature (lots of updates and changes)
85 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
86 - bug 2835 - patch [Dan Bolser]
87 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
89 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
90 * Bio::Factory::FTLocationFactory
91 - mailing list bug fix [cjfields]
93 - performance work on column_from_residue_number [hartzell]
94 * Bio::Matrix::IO::phylip
95 - bug 2800 - patch to fix phylip parsing [Wei Zou]
97 - Google Summer of Code project from Chase Miller - parsers for Nexml
98 file format [maj, chmille4]
100 - Make Individual, Population, Marker objects AnnotatableI [maj]
101 - simplify LD code [jason]
103 - deal with empty intersection [jason]
105 - significant overhaul of Bio::Restriction system: complete support for
106 external and non-palindromic cutters. [maj]
108 - CPANPLUS support, no automatic installation [sendu]
110 - allow IO::String (regression fix) [cjfields]
111 - catch unintentional undef values [cjfields]
112 - throw if non-fh is passed to -fh [maj]
113 * Bio::Root::Root/RootI
114 - small debugging and core fixes [cjfields]
116 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
117 * Bio::Root::Utilities
118 - bug 2737 - better warnings [cjfields]
120 - tiling completely refactored, HOWTO added [maj]
121 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
122 will deprecate usage of the older tiling code in the next BioPerl
124 - small fixes [cjfields]
126 - Infernal 1.0 output now parsed [cjfields]
127 - new parser for gmap -f9 output [hartzell]
128 - bug 2852 - fix infinite loop in some output [cjfields]
129 - blastxml output now passes all TODO tests [cjfields]
130 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
131 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
132 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
133 * Bio::Seq::LargePrimarySeq
134 - delete tempdirs [cjfields]
135 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
137 - extract regions based on quality threshold value [Dan Bolser, heikki]
138 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
139 * Bio::SeqFeature::Lite
140 - various Bio::DB::SeqFeature-related fixes [lstein]
141 * Bio::SeqFeature::Tools::TypeMapper
142 - additional terms for GenBank to SO map [scain]
143 * Bio::SeqIO::chadoxml
144 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
146 - support for CDS records [dave_messina, Sylvia]
148 - complete refactoring to handle all FASTQ variants, perform validation,
149 write output. API now conforms with other Bio* parsers and the rest of
150 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
152 * Bio::SeqIO::genbank
153 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
154 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
155 * Bio::SeqIO::largefasta
156 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
158 - add option for 'single' and 'multiple'
160 - bug 2881 - fix scf round-tripping [Adam Sj¿gren]
162 - bug 2766, 2810 - copy over tags from features, doc fixes [David
165 - bug 2793 - patch for add_seq index issue [jhannah, maj]
166 - bug 2801 - throw if args are required [cjfields]
167 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
168 [Tristan Lefebure, maj]
169 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
170 - fix POD and add get_SeqFeatures filter [maj]
171 * Bio::Tools::dpAlign
172 - add support for LocatableSeq [ymc]
173 - to be moved to a separate distribution [cjfields, rbuels]
174 * Bio::Tools::EUtilities
175 - fix for two bugs from mail list [Adam Whitney, cjfields]
176 - add generic ItemContainerI interface for containing same methods
179 - fix up code, add more warnings [cjfields]
180 - to be moved to a separate distribution [cjfields, rbuels]
181 * Bio::Tools::Primer3
182 - bug 2862 - fenceposting issue fixed [maj]
183 * Bio::Tools::Run::RemoteBlast
184 - tests for remote RPS-BLAST [mcook]
185 * Bio::Tools::SeqPattern
186 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
187 * Bio::Tools::tRNAscanSE
188 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
190 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
191 * Bio::Tree::Statistics
192 - several methods for calculating Fitch-based score, internal trait
193 values, statratio(), sum of leaf distances [heikki]
195 - bug 2869 - add docs indicating edge case where nodes can be
196 prematurely garbage-collected [cjfields]
197 - add as_text() function to create Tree as a string in specified format
199 * Bio::Tree::TreeFunctionsI
200 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
202 * Bio::TreeIO::newick
203 - fix small semicolon issue [cjfields]
205 - update to bp_seqfeature_load for SQLite [lstein]
206 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
207 - fastam9_to_table - fix for MPI output [jason]
208 - gccalc - total stats [jason]
210 - POD cleanup re: FEEDBACK section [maj, cjfields]
211 - cleanup or fix dead links [cjfields]
212 - Use of no_* methods (indicating 'number of something') is deprecated
213 in favor of num_* [cjfields]
214 - lots of new tests for the above bugs and refactors [everyone!]
215 - new template for Komodo text editor [cjfields]
218 * Feature/Annotation rollback
219 - Problematic changes introduced prior to the 1.5 release have been
220 rolled back. These changes led to subtle bugs involving operator
221 overloading and interface methods.
222 - Behavior is very similar to that for BioPerl 1.4, with tag values
223 being stored generically as simple scalars. Results in a modest
226 - Split into a separate distribution on CPAN, primarily so development
227 isn't reliant on a complete BioPerl release.
228 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
229 is only available via Subversion (via bioperl-live main trunk)
231 - Common test bed for all BioPerl modules
233 - Common Module::Build-based subclass for all BioPerl modules
234 * Bio::DB::EUtilities
235 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
236 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
237 and user agent request posting and retrieval
238 * Test implementation and reorganization
239 - Tests have been reorganized into groups based on classes or use
241 - Automated test coverage is now online:
242 http://www.bioperl.org/wiki/Test_Coverage
243 - After this release, untested modules will be moved into a
244 separate developer distribution until tests can be derived.
245 Also, new modules to be added are expected to have a test suite
246 and adequate test coverage.
248 1.5.2 Developer release
250 Full details of changes since 1.5.1 are available online at:
251 http://www.bioperl.org/wiki/Change_log
252 The following represents a brief overview of the most important changes.
255 - Overhaul. Brand new system fully allows markers to have multiple
256 positions on multiple maps, and to have relative positions. Should be
260 - This module and all the modules in the Taxonomy directory now
261 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
266 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
268 * New methods ancestor(), each_Descendent() and _handle_internal_id().
270 * Allows for different database modules to create Bio::Taxon objects
271 with the same internal id when the same taxon is requested from each.
274 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
276 * No longer includes the fake root node 'root'; there are multiple roots
277 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
280 * get_node() has new option -full
282 * Caches data retrieved from website
285 - Now a Bio::Taxon. Carries out the species name -> specific name munging
286 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
287 backward compatability in species() method.
289 o Bio::Search and Bio::SearchIO
290 - Overhaul. The existing system has been sped up via some minor changes
291 (mostly gain-of-function to the API). Bio::PullParserI is introduced
292 as a potential eventual replacment for the existing system, though as
293 yet only a Hmmpfam parser exists written using it.
296 1.5.1 Developer release
298 o Major problem with how Annotations were written out with
299 Bio::Seq is fixed by reverting to old behavior for
300 Bio::Annotation objects.
305 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
306 expect at l east 9 spaces at the beginning of a line to
307 indicate line wrapping.
309 * Treat multi-line SOURCE sections correctly, this defect broke
310 both common_name() and classification()
312 * parse swissprot fields in genpept file
314 * parse WGS genbank records
317 * Changed regexp for ID line. The capturing parentheses are
318 the same, the difference is an optional repeated-not-semi-
319 colon expression following the captured \S+. This means the
320 regexp works when the division looks like /PRO;/ or when the
321 division looks like /ANG ;/ - the latter is from EMBL
324 * fix ID line parsing: the molecule string can have spaces in
325 it. Like: "genomic DNA"
327 - swiss.pm: bugs #1727, #1734
330 * Added parser for entrezgene ASN1 (text format) files.
331 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
335 - maf.pm coordinate problem fixed
337 o Bio::Taxonomy and Bio::DB::Taxonomy
339 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
340 can be done via Web without downloading all the sequence.
342 o Bio::Tools::Run::RemoteBlast supports more options and complies
343 to changes to the NCBI interface. It is reccomended that you
344 retrieve the data in XML instead of plain-text BLAST report to
345 insure proper parsing and retrieval of all information as NCBI
346 fully expects to change things in the future.
348 o Bio::Tree and Bio::TreeIO
350 - Fixes so that re-rooting a tree works properly
352 - Writing out nhx format from a newick/nexus file will properly output
353 bootstrap information. The use must move the internal node labels over
355 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
356 $node->bootstrap($node->id);
359 - Nexus parsing is much more flexible now, does not care about
362 - Cladogram drawing module in Bio::Tree::Draw
364 - Node height and depth now properly calculated
366 - fix tree pruning algorithm so that node with 1 child gets merged
368 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
369 bugs and improvements were added, see Gbrowse mailing list for most of
372 o Bio::DB::GFF partially supports GFF3. See information about
373 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
375 o Better location parsing in Bio::Factory::FTLocationFactory -
376 this is part of the engine for parsing EMBL/GenBank feature table
377 locations. Nested join/order-by/complement are allowed now
379 o Bio::PrimarySeqI->translate now takes named parameters
381 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
382 reconstruction) is now supported. Parsing different models and
383 branch specific parametes are now supported.
385 o Bio::Factory::FTLocationFactory - parse hierarchical locations
388 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
389 for getter/setter functions
393 - blast bug #1739; match scientific notation in score
394 and possible e+ values
396 - blast.pm reads more WU-BLAST parameters and parameters, match
397 a full database pathname,
399 - Handle NCBI WEB and newer BLAST formats specifically
400 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
402 - psl off-by-one error fixed
404 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
405 and HSPs can be constructed from them.
407 - HSPs query/hit now have a seqdesc field filled out (this was
408 always available via $hit->description and
409 $result->query_description
411 - hmmer.pm can parse -A0 hmmpfam files
413 - Writer::GbrowseGFF more customizeable.
415 o Bio::Tools::Hmmpfam
416 make e-value default score displayed in gff, rather than raw score
417 allow parse of multiple records
420 1.5 Developer release
422 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
423 provide Jukes-Cantor and Kimura pairwise distance methods,
426 o Bio::AlignIO support for "po" format of POA, and "maf";
427 Bio::AlignIO::largemultifasta is a new alternative to
428 Bio::AlignIO::fasta for temporary file-based manipulation of
429 particularly large multiple sequence alignments.
431 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
432 be treated similarly as an assembled contig.
434 o Bio::CodonUsage provides new rare_codon() and probable_codons()
435 methods for identifying particular codons that encode a given
438 o Bio::Coordinate::Utils provides new from_align() method to build
439 a Bio::Coordinate pair directly from a
440 Bio::Align::AlignI-conforming object.
442 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
443 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
444 web service using standard Pubmed query syntax, and retrieve
447 o Bio::DB::GFF has various sundry bug fixes.
449 o Bio::FeatureIO is a new SeqIO-style subsystem for
450 writing/reading genomic features to/from files. I/O classes
451 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
452 classes only read/write Bio::SeqFeature::Annotated objects.
453 Notably, the GFF v3 class requires features to be typed into the
456 o Bio::Graph namespace contains new modules for manipulation and
457 analysis of protein interaction graphs.
459 o Bio::Graphics has many bug fixes and shiny new glyphs.
461 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
462 indexing for HMMER reports and FASTA qual files, respectively.
464 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
465 new objects that can be placed within a Bio::Map::MapI-compliant
466 genetic/physical map; Bio::Map::Physical provides a new physical
467 map type; Bio::MapIO::fpc provides finger-printed clone mapping
470 o Bio::Matrix::PSM provide new support for postion-specific
471 (scoring) matrices (e.g. profiles, or "possums").
473 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
474 be instantiated without explicitly using Bio::OntologyIO. This
475 is possible through changes to Bio::Ontology::OntologyStore to
476 download ontology files from the web as necessary. Locations of
477 ontology files are hard-coded into
478 Bio::Ontology::DocumentRegistry.
480 o Bio::PopGen includes many new methods and data types for
481 population genetics analyses.
483 o New constructor to Bio::Range, unions(). Given a list of
484 ranges, returns another list of "flattened" ranges --
485 overlapping ranges are merged into a single range with the
486 mininum and maximum coordinates of the entire overlapping group.
488 o Bio::Root::IO now supports -url, in addition to -file and -fh.
489 The new -url argument allows one to specify the network address
490 of a file for input. -url currently only works for GET
491 requests, and thus is read-only.
493 o Bio::SearchIO::hmmer now returns individual Hit objects for each
494 domain alignment (thus containing only one HSP); previously
495 separate alignments would be merged into one hit if the domain
496 involved in the alignments was the same, but this only worked
497 when the repeated domain occured without interruption by any
498 other domain, leading to a confusing mixture of Hit and HSP
501 o Bio::Search::Result::ResultI-compliant report objects now
502 implement the "get_statistics" method to access
503 Bio::Search::StatisticsI objects that encapsulate any
504 statistical parameters associated with the search (e.g. Karlin's
505 lambda for BLAST/FASTA).
507 o Bio::Seq::LargeLocatableSeq combines the functionality already
508 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
510 o Bio::SeqFeature::Annotated is a replacement for
511 Bio::SeqFeature::Generic. It breaks compliance with the
512 Bio::SeqFeatureI interface because the author was sick of
513 dealing with untyped annotation tags. All
514 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
515 compliant, and accessible through Bio::Annotation::Collection.
517 o Bio::SeqFeature::Primer implements a Tm() method for primer
518 melting point predictions.
520 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
521 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
523 o Bio::Taxonomy::Node now implements the methods necessary for
524 Bio::Species interoperability.
526 o Bio::Tools::CodonTable has new reverse_translate_all() and
527 make_iupac_string() methods.
529 o Bio::Tools::dpAlign now provides sequence profile alignments.
531 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
533 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
536 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
537 for designing small inhibitory RNA.
539 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
540 methods based on a distance matrix.
542 o Bio::Tree::Statistics provides an assess_bootstrap() method to
543 calculate bootstrap support values on a guide tree topology,
544 based on provided bootstrap tree topologies.
546 o Bio::TreeIO now supports the Pagel (PAG) tree format.
552 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
554 o Bio::Graphics will work with gd1 or gd2
557 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
559 - blast.pm Parse multi-line query fields properly
560 - small speed improvements to blasttable.pm and others
562 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
563 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
564 supporting more complex queries
567 1.4. Stable major release
569 Since initial 1.2.0, 3000 separate changes have been made to make this release.
571 o installable scripts
573 o global module version from Bio::Root:Version
576 - major improvements; SVG support
579 - population genetics
580 - support several population genetics types of questions.
581 - Tests for statistical neutrality of mutations
582 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
583 Tests of population structure (Wright's F-statistic: Fst) is in
584 Bio::PopGen::PopStats. Calculating composite linkage
585 disequilibrium (LD) is available in Bio::PopGen::Statistics as
587 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
588 and csv (comma delimited formatted) data.
590 - a directory for implementing population simulations has
591 been added Bio::PopGen::Simulation and 2 simulations - a
592 Coalescent and a simple single-locus multi-allele genetic drift
593 simulation have been provided. This replaces the code in
594 Bio::Tree::RandomTree which has been deprecated until proper
595 methods for generating random phylogenetic trees are
599 - new restrion analysis modules
601 o Bio::Tools::Analysis
602 - web based DNA and Protein analysis framework and several
606 - per residue annotable sequences
609 - Bio::Matrix::PSM - Position Scoring Matrix
610 - Bio::Matrix::IO has been added for generalized parsing of
611 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
612 initial implementations for parsing BLOSUM/PAM and Phylip
613 Distance matricies respectively. A generic matrix
614 implementation for general use was added in
615 Bio::Matrix::Generic.
622 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
623 - small inhibitory RNA
625 o Bio::SeqFeature::Tools
626 - seqFeature mapping tools
627 - Bio::SeqFeature::Tools::Unflattener.pm
628 -- deal with mapping GenBank feature collections into
629 Chado/GFF3 processable feature sets (with SO term mappings)
631 o Bio::Tools::dpAlign
632 - pure perl dynamic programming sequence alignment
635 o new Bio::SearchIO formats
636 - axt and psl: UCSC formats.
637 - blasttable: NCBI -m 8 or -m 9 format from blastall
639 o new Bio::SeqIO formats
640 - chado, tab, kegg, tigr, game
641 - important fixes for old modules
645 o improved Bio::Tools::Genewise
647 o Bio::SeqIO now can recongnize sequence formats automatically from
650 o new parsers in Bio::Tools:
651 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
653 o Bio::DB::Registry bugs fixed
654 - BerkeleyDB-indexed flat files can be used by the OBDA system
655 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
656 used by the OBDA system
659 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
662 o hundreds of new and improved files
666 o Bio::Tree::AlleleNode has been updated to be a container of
667 an Bio::PopGen::Individual object for use in the Coalescent simulations.
672 1.2.3 Stable release update
673 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
675 o Bug #1477 - Sel --> Sec abbreviation fixed
676 o Fix bug #1487 where paring in-between locations when
677 end < start caused the FTLocationFactory logic to fail.
678 o Fix bug #1489 which was not dealing with keywords as an
679 arrayref properly (this is fixed on the main trunk because
680 keywords returns a string and the array is accessible via
682 o Bio::Tree::Tree memory leak (bug #1480) fixed
683 Added a new initialization option -nodelete which
684 won't try and cleanup the containing nodes if this
686 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
687 this was only present on the branch for the 1.2.1 and 1.2.2 series
688 - Also merged main trunk changes to the branch which make
689 newick -> nhx round tripping more effective (storing branch length
690 and bootstrap values in same locate for NodeNHX and Node
691 implementations.) Fixes to TreeIO parsing for labeled internal
692 also required small changes to TreeIO::nhx. Improved
693 tests for this module as well.
695 - Fixed bugs in BLAST parsing which couldn't parse NCBI
696 gapped blast properly (was losing hit significance values due to
697 the extra unexpeted column).
698 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
699 integer overflow (# of letters in nt seq dbs is > MAX_INT)
700 although doesn't try to correct it - will get the negative
701 number for you. Added a test for this as well.
702 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
703 has no top-level family classification scores but does have scores and
704 alignments for individual domains.
705 - Parsing FASTA reports where ungapped percent ID is < 10 and the
706 regular expression to match the line was missing the possibility of
707 an extra space. This is rare, which is why we probably did not
709 - BLAST parsing picks up more of the statistics/parameter fields
710 at the bottom of reports. Still not fully complete.
711 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
712 were fixed to include many improvements and added flexiblity
713 in outputting the files. Bug #1495 was also fixed in the process.
715 - Update for GFF3 compatibility.
716 - Added scripts for importing from UCSC and GenBank.
717 - Added a 1.2003 version number.
720 - Added a 1.2003 version number.
721 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
722 properly writing keywords out.
723 o Bio::SeqIO::genbank
724 - Fixed bug/enhancement #1513 where dates of
725 the form D-MMM-YYYY were not parsed. Even though this is
726 invalid format we can handle it - and also cleanup the date
727 string so it is properly formatted.
728 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
729 and written with Genbank format. Similarly bug #1515 is fixed to
730 parse in the ORIGIN text.
731 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
732 to specify the ID type, one of (accession accession.version
733 display primary). See Bio::SeqIO::preferred_id_type method
734 documentation for more information.
735 o Unigene parsing updated to handle file format changes by NCBI
737 1.2.2 Stable release update
739 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
740 - auto-discover ontology name
741 - bug in parsing relationships when certain characters are in the term
742 - fixed hard-coded prefix for term identifiers
743 - various smaller issues
745 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
746 of Bio::Ontology::TermI
748 o brought the OBDA Registry code up to latest specs
752 - accession number retrieval fixed
754 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
756 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
757 #1459 which now properly report alignment start/end info
758 for translated BLAST/FASTA searches.
760 o Bio::TreeIO::newick can parse labeled internal nodes
762 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
763 for BLASTX if if you provide -report_type => 'BLASTX' when
764 initializing a BPbl2seq object. Bioperl 1.3 will have better
765 support for bl2seq in the SearchIO system.
767 o Bio::Root::IO support a -noclose boolean flag which will not
768 close a filehandle upon object cleanup - useful when sharing
769 a filehandle among objects. Additionally code added s.t.
770 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
772 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
774 o Bio::SeqIO::genbank
775 - bug #1456 fixed which generated extra sequence lines
776 - write moltype correctly for genpept
778 1.2.1 Stable release update
780 o Inclusion of WrapperBase, a needed component for StandAloneBlast
782 o Addition from main trunk of Ontology objects, principly to allow
783 BioSQL releases against 1.2.1
785 o Fixes and cleanup of Bio::Coordinate modules
787 o A fix to Bio::Index::EMBL allowing retrieval of entries using
788 the primary accession number
790 o Other bug fixes, including bpindex GenBank fix
792 o Bio::SeqIO::genbank bug #1389 fixed
794 1.2 Stable major release
796 o More functionality added to Bio::Perl, the newbie module
798 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
799 Support for New Hampshire Extended (NHX) format parsing.
801 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
802 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
805 o New ontology parsing Bio::Ontology
807 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
808 multi-report (mlib) fasta reports, support for waba and exonerate.
810 o Bio::ClusterIO for parsing Unigene clusters
812 o Bio::Assembly added for representing phrap and ace assembly clusters.
814 o Rudimentary support for writing Chado XML (see
815 GMOD project: www.gmod.org for more information)
817 o Bio::Coordinate for mapping between different coordinate systems such
818 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
819 features into different coordinate systems.
821 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
822 with the get_Stream_by_query method and supports the latest
823 NCBI eutils interface.
825 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
826 object for extracting subsets of features : currently only
827 supports extraction by location.
829 1.1.1 Developer release
831 o Deprecated modules are now listed in the DEPRECATED file
833 o New HowTo documents located in doc/howto describing
836 o Note that bugs are now stored at bugzilla.bioperl.org
837 and all old bugs are searchable through the bugzilla interface.
839 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
842 o Support for Genewise parsing in Bio::Tools::Genewise
844 o Start of Ontology framework with Bio::Ontology
846 o Speedup to the Bio::Root::Root object method _rearrange.
847 A global _load_module method was implemented to simplify the
848 dynamic loading of modules ala Bio::SeqIO::genbank. This
849 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
852 o Several performance improvements to sequence parsing in Bio::SeqIO.
853 Attempt to speedup by reducing object creation overhead.
855 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
856 method for sequence retrieval with their E-utils CGI scripts.
857 More work to support Entrez queries to their fullest is planned
860 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
862 1.1 Developer release
864 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
865 this separation removes some of the complexity in our test suite
866 and separates the core modules in bioperl from those that need
867 external programs to run.
869 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
870 not run into trouble running the makefile
872 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
873 read,create,and write locations for grouped/split locations
874 (like mRNA features on genomic sequence).
876 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
877 and PAML (codeml,aaml, etc) parsing.
879 o Bio::Tree:: objects expanded to handle testing monophyly,
880 paraphyly, least common ancestor, etc.
882 o Bio::Coordinate for mapping locations from different coordinate spaces
884 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
885 added for parsing hmmpfam and hmmsearch output.
887 o Bio::SearchIO::Writer::TextResultWriter for outputting
888 a pseudo-blast textfile format
891 1.0.2 Bug fix release
893 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
894 in this release will not work after December 2002 when NCBI
895 shuts off the old Entrez cgi scripts. We have already fixed
896 on our main development branch and the functionality will be
897 available in the next stable bioperl release (1.2) slated for
900 o Numerous parsing bugs in Bio::SearchIO::fasta found through
901 testset by Robin Emig. These were fixed as was the get_aln
902 method in Bio::Search::HSP::GenericHSP to handle the extra
903 context sequence that is provided with a FastA alignment.
905 o Migrating differences between Bio::Search::XX::BlastXX to
906 Bio::Search::XX::GenericXX objects. This included mechanism
907 to retrieve whole list of HSPs from Hits and whole list of Hits from
908 Results in addition to the current next_XX iterator methods that
909 are available. Added seq_inds() method to GenericHSP which identifies
910 indexes in the query or hit sequences where conserved,identical,gaps,
911 or mismatch residues are located (adapted from Steve Chervitz's
912 implementation in BlastHSP).
914 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
915 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
917 o Bio::Graphics glyph set improved and extended for GBrowse release
919 o Bio::Tree::Tree get_nodes implementation improvement thanks
920 to Howard Ross notice performance problem when writing out
923 o Bio::Location::Fuzzy::new named parameter -loc_type became
924 -location_type, Bio::Location::Simple::new named parameter
925 -seqid becamse -seq_id.
927 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
928 was mis-detecting that gaps should be placed at the beginning of
929 the alignment when the best alignment starts internally in the
932 1.0.1 Bug fix release
934 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
936 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
937 and mixed (3.3 - 3.4) versions of FASTA.
939 o Small API change to add methods for completeness across
940 implementations of Bio::Search objects. These new methods
941 in the interface are implemented by the GenericXX object as well
942 as the BlastXX objects.
943 * Bio::Search::Result::ResultI
944 - hits() method returns list of all Hits (next_hit is an
947 * Bio::Search::Hit::HitI
948 - hsps() method returns list of all HSPs (next_hsp is an
951 o The Bio::SearchIO::Writer classes have been fixed to handle results
952 created from either psiblast (Search::BlastXX objects) or
953 blast|fasta|blastxml objects (Search::GenericXX objects). More work
954 has to be done here to make it work properly and will nee major
957 o Bugs in Bio::Tools::HMMER fixed, including
958 * #1178 - Root::IO destructor wasn't being called
959 * #1034 - filter_on_cutoff now behaves properly
961 o Bio::SeqFeature::Computation initialization args fixed and
964 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
966 o Updated FAQ with more example based answers to typical questions
968 o Bug #1202 was fixed which would improperly join together qual values
969 parsed by Bio::SeqIO::qual when a trailing space was not present before
972 1.0.0 Major Stable Release
974 This represents a major release of bioperl with significant
975 improvements over the 0.7.x series of releases.
977 o Bio::Tools::Blast is officially deprecated. Please see
978 Bio::SearchIO for BLAST and FastA parsing.
980 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
981 Bio::LocationI objects as well as start/end.
983 o Bio::Biblio contains modules for Bibliographic data.
984 Bio::DB::Biblio contains the query modules. Additionally one can
985 parse medlinexml from the ebi bibliographic query service (BQS)
986 system and Pubmed xml from NCBI. See Martin Senger's
987 documentation in Bio::Biblio for more information.
989 o Bio::DB::Registry is a sequence database registry part of
990 Open Bioinformatics Database Access. See
991 http://obda.open-bio.org for more information.
993 o File-based and In-Memory Sequence caching is provided by
994 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
997 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
998 been added by Lincoln Stein.
1000 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1002 o A FAQ has been started and is included in the release to provide
1003 a starting point for frequent questions and issues.
1005 0.9.3 Developer's release
1007 o Event based parsing system improved (SearchIO). With parsers for
1008 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1009 Additionally a lazy parsing system for text and html blast reports was
1010 added and is called psiblast (name subject to change in future releases).
1012 o Bio::Search objects improved and standardized with associated Interfaces
1013 written. The concept of a search "Hit" was standardized to be called
1014 "hit" consistently and the use of "subject" was deprecated in all active
1017 o Bio::Structure added (since 0.9.1) for Protein structure objects
1018 and PDB parser to retrieve and write these structures from data files.
1020 o Several important Bio::DB::GFF bug fixes for handling features that
1021 are mapped to multiple reference points. Updated mysql adaptor
1022 so as to be able to store large (>100 megabase) chunks of DNA into
1023 Bio::DB::GFF databases.
1025 0.9.2 Developer's release
1027 o Bio::Search and Bio::SearchIO system introduced for event based
1028 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1029 in text and XML and FASTA reports in standard output format.
1031 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1032 generator is included in Bio::TreeIO::RandomTrees and a
1033 statistics module for evaluating.
1035 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1036 server for DAS servers.
1038 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1039 files. The entire BPlite system migrated to using Bio::Root::IO
1040 for the data stream.
1042 o Bio::Tools::Alignment for Consed and sequence Trimming
1045 o Bio::Structure for Protein structure information and parsing
1047 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1048 cgi-bin entry point which should be more reliable.
1050 o Bio::Map and Bio::MapIO for biological map navigation and a
1051 framework afor parsing them in. Only preliminary work here.
1053 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1054 Future work will integrate Pise and allow submission of analysis on
1057 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1058 introduced as new objects for handling Sequence Annotation
1059 information (dblinks, references, etc) and is more robust that
1062 o Bio::Tools::FASTAParser introduced.
1064 o Scripts from the bioperl script submission project and new
1065 scripts from bioperl authors are included in "scripts" directory.
1067 o Factory objects and interfaces are being introduced and are more
1070 o Bio::Root::Root introduced as the base object while
1071 Bio::Root::RootI is now simply an interface.
1073 o Bio::DB::RefSeq provides database access to copy of the NCBI
1074 RefSeq database using the EBI dbfetch script.
1076 0.9.0 Developer's release
1078 o perl version at least 5.005 is now required instead of perl 5.004
1080 o Bio::Tools::Run::RemoteBlast is available for running remote
1083 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1085 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1086 Also added are related modules UTR3, UTR5, Exon, Intron,
1087 Promotor, PolyA and Transcript.
1089 o Speedup of translate method in PrimarySeq
1091 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1092 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1094 o Various fixes to Variation toolkit
1096 o Bio::DB::EMBL provides database access to EMBL sequence data.
1097 Bio::DB::Universal provides a central way to point to indexes
1098 and dbs in a single interface.
1100 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1102 o Bio::Factory::EMBOSS is still in design phase as is
1103 Bio::Factory::ApplicationFactoryI
1105 o Dia models for bioperl design are provided in the models/ directory
1107 0.7.2 Bug fix release
1109 o documentation fixes in many modules - SYNOPSIS code verified
1110 to be runnable in many (but not all modules)
1112 o corrected MANIFEST file from 0.7.1 release
1114 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1117 o Bio::SeqIO::genbank
1118 * Correct parsing and writing of genbank format with protein data
1119 * moltype and molecule separation
1121 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1123 o Bio::SimpleAlign fixed to correctly handle consensus
1124 sequence calculation
1126 o Bio::Tools::HMMER supports hmmer 2.2g
1128 o Bio::Tools::BPlite to support report type specific parsing. Most
1129 major changes are not on the 0.7 branch.
1131 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1134 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1135 in several types of mutations:
1136 1.) AA level: deletion, complex
1137 2.) AA level: complex, inframe
1138 3.) RNA level: silent
1140 o BPbl2seq parsing of empty reports will not die, but will return
1141 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1142 $report->query() and $report->subject() methods. So an easy
1143 way to test if report was empty is to see if
1144 $report->query->seqname is undefined.
1146 0.7.1 Bug fix release
1148 o Better parsing of genbank/EMBL files especially fixing bugs
1149 related to Feature table parsing and locations on remote
1150 sequences. Additionally, species name parsing was better.
1152 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1153 which include a number of header lines.
1155 o More strict genbank and EMBL format writing (corrected number of
1156 spaces where appropriate).
1158 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1159 for related BPlite BUGS that are unresolved in this release.
1161 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1162 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1163 use expasy mirrors or EBI dbfetch cgi-script.
1165 o A moderate number of documentation improvements were made as
1166 well to provide a better code synopsis in each module.
1169 0.7 Large number of changes, including refactoring of the
1170 Object system, new parsers, new functionality and
1171 all round better system. Highlights are:
1174 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1175 Bio::Root::IO for I/O and file/handle capabilities.
1177 o Imported BPlite modules from Ian Korf for BLAST
1178 parsing. This is considered the supported BLAST parser;
1179 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1181 o Improved Sequence Feature model. Added complete location
1182 modelling (with fuzzy and compound locations). See
1183 Bio::LocationI and the modules under Bio/Location. Added
1184 support in Genbank/EMBL format parsing to completely parse
1185 feature tables for complex locations.
1187 o Moved special support for databanks etc to specialized modules under
1188 Bio/Seq/. One of these supports very large sequences through
1189 a temporary file as a backend.
1191 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1192 CDS retrieval and exon shuffling.
1194 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1196 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1197 DB/GDB (the latter has platform-specific limitations).
1199 o New analysis parser framework for HT sequence annotation (see
1200 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1202 o New Alignment IO framework
1204 o New Index modules (Swissprot)
1206 o New modules for running Blast within perl
1207 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1208 Multiple Sequence Alignment tools ClustalW and TCoffee
1209 (Bio::Tools::Run::Alignment).
1211 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1212 documentation across the package.
1214 o Much improved cross platform support. Many known incompatibilities
1215 have been fixed; however, NT and Mac do not work across the entire
1216 setup (see PLATFORMS).
1218 o Many bug fixes, code restructuring, etc. Overall stability and
1219 maintainability benefit a lot.
1221 o A total of 957 automatic tests
1226 There are very few functionality changes but a large
1227 number of software improvements/bug fixes across the package.
1229 o The EMBL/GenBank parsing are improved.
1231 o The Swissprot reading is improved. Swissprot writing
1232 is disabled as it doesn't work at all. This needs to
1233 wait for 0.7 release
1235 o BLAST reports with no hits are correctly parsed.
1237 o Several other bugs of the BLAST parser (regular expressions, ...)
1240 o Old syntax calls have been replaced with more modern syntax
1242 o Modules that did not work at all, in particular the Sim4
1243 set have been removed
1245 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1246 have improved compliance with interface specs and documentation
1248 o Mailing list documentation updated throughout the distribution
1250 o Most minor bug fixes have happened.
1252 o The scripts in /examples now work and have the modern syntax
1253 rather than the deprecated syntax
1256 0.6.1 Sun April 2 2000
1258 o Sequences can have Sequence Features attached to them
1259 - The sequence features can be read from or written to
1260 EMBL and GenBank style flat files
1262 o Objects for Annotation, including References (but not
1263 full medline abstracts), Database links and Comments are
1266 o A Species object to represent nodes on a taxonomy tree
1269 o The ability to parse HMMER and Sim4 output has been added
1271 o The Blast parsing has been improved, with better PSI-BLAST
1272 support and better overall behaviour.
1274 o Flat file indexed databases provide both random access
1275 and sequential access to their component sequences.
1277 o A CodonTable object has been written with all known
1278 CodonTables accessible.
1280 o A number of new lightweight analysis tools have been
1281 added, such as molecular weight determination.
1283 The 0.6 release also has improved software engineering
1285 o The sequence objects have been rewritten, providing more
1286 maintainable and easier to implement objects. These
1287 objects are backwardly compatible with the 0.05.1 objects
1289 o Many objects are defined in terms of interfaces and then
1290 a Perl implementation has been provided. The interfaces
1291 are found in the 'I' files (module names ending in 'I').
1293 This means that it is possible to wrap C/CORBA/SQL access
1294 as true "bioperl" objects, compatible with the rest of
1297 o The SeqIO system has been overhauled to provide better
1298 processing and perl-like automatic interpretation of <>
1301 o Many more tests have been added (a total of 172 automatic
1302 tests are now run before release).
1306 0.05.1 Tue Jun 29 05:30:44 1999
1307 - Central distribution now requires Perl 5.004. This was
1308 done to get around 5.003-based problems in Bio/Index/*
1310 - Various bug fixes in the Bio::Tools::Blast modules
1311 including better exception handling and PSI-Blast
1312 support. See Bio/Tools/Blast/CHANGES for more.
1313 - Fixed the Parse mechanism in Seq.pm to use readseq.
1314 Follow the instructions in README for how to install
1315 it (basically, you have to edit Parse.pm).
1316 - Improved documentation of Seq.pm, indicating where
1317 objects are returned and where strings are returned.
1318 - Fixed uninitialized warnings in Bio::Root::Object.pm
1319 and Bio::Tools::SeqPattern.pm.
1320 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1322 0.05 Sun Apr 25 01:14:11 1999
1323 - Bio::Tools::Blast modules have less memory problems
1324 and faster parsing. Webblast uses LWP and supports
1325 more functionality. See Bio/Tools/Blast/CHANGES for more.
1326 - The Bio::SeqIO system has been started, moving the
1327 sequence reformatting code out of the sequence object
1328 - The Bio::Index:: system has been started, providing
1329 generic index capabilities and specifically works for
1330 Fasta formatted databases and EMBL .dat formatted
1332 - The Bio::DB:: system started, providing access to
1333 databases, both via flat file + index (see above) and
1335 - The scripts/ directory, where industrial strength scripts
1336 are put has been started.
1337 - Many changes - a better distribution all round.
1339 0.04.4 Wed Feb 17 02:20:13 1999
1340 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1341 (see Bio::Tools::Blast::CHANGES).
1342 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1343 - Beefed up the t/Fasta.t test script.
1344 - Small fix in Bio::Seq::type() (now always returns a string).
1345 - Changed Bio::Root::Utilities::get_newline_char() to
1346 get_newline() since it could return more than one char.
1347 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1348 - Changed default timeout to 20 seconds (was 3).
1349 - Moved lengthy modification notes to the bottom of some files.
1350 - Fixed SimpleAlign write_fasta bug.
1351 - Beefed up SimpleAlign.t test
1353 0.04.3 Thu Feb 4 07:48:53 1999
1354 - Bio::Root::Object.pm and Global.pm now detect when
1355 script is run as a CGI and suppress output that is only
1356 appropriate when running interactively.
1357 - Bio::Root::Err::_set_context() adds name of script ($0).
1358 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1359 regarding the use of the static objects via the qw(:obj) tag.
1360 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1361 CORE::reverse, avoiding Perl warnings.
1362 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1363 example scripts (see Bio::Tools::Blast::CHANGES).
1364 - examples/seq/seqtools.pl no longer always warns about using
1365 -prot or -nucl command-line arguments; only when using the
1367 - Methods added to Bio::Root::Utilities: create_filehandle(),
1368 get_newline_char(), and taste_file() to generalize filehandle
1369 creation and autodetect newline characters in files/streams
1370 (see bug report #19).
1371 - Bio::Root::IOManager::read() now handles timeouts and uses
1372 Utilities::create_filehandle().
1373 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1374 of hardwiring in "\n".
1375 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1377 0.04.2 Wed Dec 30 02:27:36 1998
1378 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1379 (see Bio::Tools::Blast::CHANGES).
1380 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1381 to CORE::reverse (prevents ambiguous warnings with 5.005).
1382 - Appending '.tmp.bioperl' to temporary files created by
1383 Bio::Root::Utilities::compress() or uncompress() to
1384 make it easy to identify & cleanup these files as needed.
1385 - Developers: Created CVS branch release-0-04-bug from
1386 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1387 be sure to cvs checkout this branch into a clean area.
1389 0.04.1 Wed Dec 16 05:39:15 1998
1390 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1391 (see Bio::Tools::Blast::CHANGES).
1392 - Compile/SW/Makefile.PL now removes *.o and *.a files
1395 0.04 Tue Dec 8 07:49:19 1998
1396 - Lots of new modules added including:
1397 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1398 and Bio/Compile directory containing XS-linked C code for
1399 creating Smith-Waterman sequence alignments from within Perl.
1400 * Steve Chervitz's Blast distribution has been incorporated.
1401 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1402 - Bio/examples directory for demo scripts for all included modules.
1403 - Bio/t directory containing test suit for all included modules.
1404 - For changes specific to the Blast-related modules prior to
1405 incorporation in this central distribution, see the CHANGES
1406 file in the Bio/Tools/Blast directory.
1408 0.01 Tue Sep 8 14:23:22 1998
1409 - original version from central CVS tree; created by h2xs 1.18