3 Revision history for Bioperl core modules
9 The 1.6 series is derived from subversion HEAD and exists as a separate
10 release branch. This will represent the last of the alternating
11 developer/stable releases. Code in Subversion HEAD will be divided up into
12 several smaller packages, including a developer subdistribution for
13 code considered experimental, unstable, or untested.
15 Full detail of changes included since the 1.5.2 release are online at:
16 http://www.bioperl.org/wiki/Change_log. Bugs remaining to be addressed
17 are online at http://bugzilla.open-bio.org, with specific bugs intended
18 for this release series highlighted in BUGS.
20 1.6.0_1 Sept. 15, 2009
21 * Bio::Align::DNAStatistics
22 - fix divide by zero problem [jason]
24 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
25 * Bio::AlignIO::stockholm
26 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
27 * Bio::Assembly::Tools::ContigSpectrum
28 - function to score contig spectrum [fangly]
30 - small updates [cjfields]
32 - berkeleydb database now autoindexes wig files and locks correctly
35 - various small updates for stability; tracking changes to LANL
36 database interface [maj]
37 * Bio::DB::SeqFeature (lots of updates and changes)
38 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
39 - bug 2835 - patch [Dan Bolser]
40 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
42 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
43 * Bio::Factory::FTLocationFactory
44 - mailing list bug fix [cjfields]
46 - performance work on column_from_residue_number [hartzell]
47 * Bio::Matrix::IO::phylip
48 - bug 2800 - patch to fix phylip parsing [Wei Zou]
50 - Google Summer of Code project from Chase Miller - parsers for Nexml
51 file format [maj, chmille4]
53 - Make Individual, Population, Marker objects AnnotatableI [maj]
54 - simplify LD code [jason]
56 - deal with empty intersection [jason]
58 - significant overhaul of Bio::Restriction system: complete support for
59 external and non-palindromic cutters. [maj]
61 - CPANPLUS support, no automatic installation [sendu]
63 - allow IO::String (regression fix) [cjfields]
64 - catch unintentional undef values [cjfields]
65 - throw if non-fh is passed to -fh [maj]
66 * Bio::Root::Root/RootI
67 - small debugging and core fixes [cjfields]
69 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
70 * Bio::Root::Utilities
71 - bug 2737 - better warnings [cjfields]
73 - tiling completely refactored, HOWTO added [maj]
74 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
75 will deprecate usage of the older tiling code in the next BioPerl
77 - small fixes [cjfields]
79 - Infernal 1.0 output now parsed [cjfields]
80 - new parser for gmap -f9 output [hartzell]
81 - bug 2852 - fix infinite loop in some output [cjfields]
82 - blastxml output now passes all TODO tests [cjfields]
83 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
84 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
85 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
86 * Bio::Seq::LargePrimarySeq
87 - delete tempdirs [cjfields]
88 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
90 - extract regions based on quality threshold value [Dan Bolser, heikki]
91 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
92 * Bio::SeqFeature::Lite
93 - various Bio::DB::SeqFeature-related fixes [lstein]
94 * Bio::SeqFeature::Tools::TypeMapper
95 - additional terms for GenBank to SO map [scain]
96 * Bio::SeqIO::chadoxml
97 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
99 - support for CDS records [dave_messina, Sylvia]
101 - complete refactoring to handle all FASTQ variants, perform validation,
102 write output. API now conforms with other Bio* parsers and the rest of
103 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
105 * Bio::SeqIO::genbank
106 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
107 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
108 * Bio::SeqIO::largefasta
109 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
111 - add option for 'single' and 'multiple'
113 - bug 2881 - fix scf round-tripping [Adam Sj¿gren]
115 - bug 2766, 2810 - copy over tags from features, doc fixes [David
118 - bug 2793 - patch for add_seq index issue [jhannah, maj]
119 - bug 2801 - throw if args are required [cjfields]
120 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
121 [Tristan Lefebure, maj]
122 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
123 - fix POD and add get_SeqFeatures filter [maj]
124 * Bio::Tools::dpAlign
125 - add support for LocatableSeq [ymc]
126 - to be moved to a separate distribution [cjfields, rbuels]
127 * Bio::Tools::EUtilities
128 - fix for two bugs from mail list [Adam Whitney, cjfields]
129 - add generic ItemContainerI interface for containing same methods
132 - fix up code, add more warnings [cjfields]
133 - to be moved to a separate distribution [cjfields, rbuels]
134 * Bio::Tools::Primer3
135 - bug 2862 - fenceposting issue fixed [maj]
136 * Bio::Tools::Run::RemoteBlast
137 - tests for remote RPS-BLAST [mcook]
138 * Bio::Tools::SeqPattern
139 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
140 * Bio::Tools::tRNAscanSE
141 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
143 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
144 * Bio::Tree::Statistics
145 - several methods for calculating Fitch-based score, internal trait
146 values, statratio(), sum of leaf distances [heikki]
148 - bug 2869 - add docs indicating edge case where nodes can be
149 prematurely garbage-collected [cjfields]
150 - add as_text() function to create Tree as a string in specified format
152 * Bio::Tree::TreeFunctionsI
153 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
155 * Bio::TreeIO::newick
156 - fix small semicolon issue [cjfields]
158 - update to bp_seqfeature_load for SQLite [lstein]
159 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
160 - fastam9_to_table - fix for MPI output [jason]
161 - gccalc - total stats [jason]
163 - POD cleanup re: FEEDBACK section [maj]
164 - Use of no_* methods (indicating 'number of something') is deprecated
165 in favor of num_* [cjfields]
166 - lots of new tests for the above bugs and refactors [everyone!]
167 - new template for Komodo text editor [cjfields]
170 * Feature/Annotation rollback
171 - Problematic changes introduced prior to the 1.5 release have been
172 rolled back. These changes led to subtle bugs involving operator
173 overloading and interface methods.
174 - Behavior is very similar to that for BioPerl 1.4, with tag values
175 being stored generically as simple scalars. Results in a modest
178 - Split into a separate distribution on CPAN, primarily so development
179 isn't reliant on a complete BioPerl release.
180 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
181 is only available via Subversion (via bioperl-live main trunk)
183 - Common test bed for all BioPerl modules
185 - Common Module::Build-based subclass for all BioPerl modules
186 * Bio::DB::EUtilities
187 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
188 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
189 and user agent request posting and retrieval
190 * Test implementation and reorganization
191 - Tests have been reorganized into groups based on classes or use
193 - Automated test coverage is now online:
194 http://www.bioperl.org/wiki/Test_Coverage
195 - After this release, untested modules will be moved into a
196 separate developer distribution until tests can be derived.
197 Also, new modules to be added are expected to have a test suite
198 and adequate test coverage.
200 1.5.2 Developer release
202 Full details of changes since 1.5.1 are available online at:
203 http://www.bioperl.org/wiki/Change_log
204 The following represents a brief overview of the most important changes.
207 - Overhaul. Brand new system fully allows markers to have multiple
208 positions on multiple maps, and to have relative positions. Should be
212 - This module and all the modules in the Taxonomy directory now
213 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
218 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
220 * New methods ancestor(), each_Descendent() and _handle_internal_id().
222 * Allows for different database modules to create Bio::Taxon objects
223 with the same internal id when the same taxon is requested from each.
226 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
228 * No longer includes the fake root node 'root'; there are multiple roots
229 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
232 * get_node() has new option -full
234 * Caches data retrieved from website
237 - Now a Bio::Taxon. Carries out the species name -> specific name munging
238 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
239 backward compatability in species() method.
241 o Bio::Search and Bio::SearchIO
242 - Overhaul. The existing system has been sped up via some minor changes
243 (mostly gain-of-function to the API). Bio::PullParserI is introduced
244 as a potential eventual replacment for the existing system, though as
245 yet only a Hmmpfam parser exists written using it.
248 1.5.1 Developer release
250 o Major problem with how Annotations were written out with
251 Bio::Seq is fixed by reverting to old behavior for
252 Bio::Annotation objects.
257 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
258 expect at l east 9 spaces at the beginning of a line to
259 indicate line wrapping.
261 * Treat multi-line SOURCE sections correctly, this defect broke
262 both common_name() and classification()
264 * parse swissprot fields in genpept file
266 * parse WGS genbank records
269 * Changed regexp for ID line. The capturing parentheses are
270 the same, the difference is an optional repeated-not-semi-
271 colon expression following the captured \S+. This means the
272 regexp works when the division looks like /PRO;/ or when the
273 division looks like /ANG ;/ - the latter is from EMBL
276 * fix ID line parsing: the molecule string can have spaces in
277 it. Like: "genomic DNA"
279 - swiss.pm: bugs #1727, #1734
282 * Added parser for entrezgene ASN1 (text format) files.
283 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
287 - maf.pm coordinate problem fixed
289 o Bio::Taxonomy and Bio::DB::Taxonomy
291 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
292 can be done via Web without downloading all the sequence.
294 o Bio::Tools::Run::RemoteBlast supports more options and complies
295 to changes to the NCBI interface. It is reccomended that you
296 retrieve the data in XML instead of plain-text BLAST report to
297 insure proper parsing and retrieval of all information as NCBI
298 fully expects to change things in the future.
300 o Bio::Tree and Bio::TreeIO
302 - Fixes so that re-rooting a tree works properly
304 - Writing out nhx format from a newick/nexus file will properly output
305 bootstrap information. The use must move the internal node labels over
307 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
308 $node->bootstrap($node->id);
311 - Nexus parsing is much more flexible now, does not care about
314 - Cladogram drawing module in Bio::Tree::Draw
316 - Node height and depth now properly calculated
318 - fix tree pruning algorithm so that node with 1 child gets merged
320 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
321 bugs and improvements were added, see Gbrowse mailing list for most of
324 o Bio::DB::GFF partially supports GFF3. See information about
325 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
327 o Better location parsing in Bio::Factory::FTLocationFactory -
328 this is part of the engine for parsing EMBL/GenBank feature table
329 locations. Nested join/order-by/complement are allowed now
331 o Bio::PrimarySeqI->translate now takes named parameters
333 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
334 reconstruction) is now supported. Parsing different models and
335 branch specific parametes are now supported.
337 o Bio::Factory::FTLocationFactory - parse hierarchical locations
340 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
341 for getter/setter functions
345 - blast bug #1739; match scientific notation in score
346 and possible e+ values
348 - blast.pm reads more WU-BLAST parameters and parameters, match
349 a full database pathname,
351 - Handle NCBI WEB and newer BLAST formats specifically
352 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
354 - psl off-by-one error fixed
356 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
357 and HSPs can be constructed from them.
359 - HSPs query/hit now have a seqdesc field filled out (this was
360 always available via $hit->description and
361 $result->query_description
363 - hmmer.pm can parse -A0 hmmpfam files
365 - Writer::GbrowseGFF more customizeable.
367 o Bio::Tools::Hmmpfam
368 make e-value default score displayed in gff, rather than raw score
369 allow parse of multiple records
372 1.5 Developer release
374 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
375 provide Jukes-Cantor and Kimura pairwise distance methods,
378 o Bio::AlignIO support for "po" format of POA, and "maf";
379 Bio::AlignIO::largemultifasta is a new alternative to
380 Bio::AlignIO::fasta for temporary file-based manipulation of
381 particularly large multiple sequence alignments.
383 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
384 be treated similarly as an assembled contig.
386 o Bio::CodonUsage provides new rare_codon() and probable_codons()
387 methods for identifying particular codons that encode a given
390 o Bio::Coordinate::Utils provides new from_align() method to build
391 a Bio::Coordinate pair directly from a
392 Bio::Align::AlignI-conforming object.
394 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
395 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
396 web service using standard Pubmed query syntax, and retrieve
399 o Bio::DB::GFF has various sundry bug fixes.
401 o Bio::FeatureIO is a new SeqIO-style subsystem for
402 writing/reading genomic features to/from files. I/O classes
403 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
404 classes only read/write Bio::SeqFeature::Annotated objects.
405 Notably, the GFF v3 class requires features to be typed into the
408 o Bio::Graph namespace contains new modules for manipulation and
409 analysis of protein interaction graphs.
411 o Bio::Graphics has many bug fixes and shiny new glyphs.
413 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
414 indexing for HMMER reports and FASTA qual files, respectively.
416 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
417 new objects that can be placed within a Bio::Map::MapI-compliant
418 genetic/physical map; Bio::Map::Physical provides a new physical
419 map type; Bio::MapIO::fpc provides finger-printed clone mapping
422 o Bio::Matrix::PSM provide new support for postion-specific
423 (scoring) matrices (e.g. profiles, or "possums").
425 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
426 be instantiated without explicitly using Bio::OntologyIO. This
427 is possible through changes to Bio::Ontology::OntologyStore to
428 download ontology files from the web as necessary. Locations of
429 ontology files are hard-coded into
430 Bio::Ontology::DocumentRegistry.
432 o Bio::PopGen includes many new methods and data types for
433 population genetics analyses.
435 o New constructor to Bio::Range, unions(). Given a list of
436 ranges, returns another list of "flattened" ranges --
437 overlapping ranges are merged into a single range with the
438 mininum and maximum coordinates of the entire overlapping group.
440 o Bio::Root::IO now supports -url, in addition to -file and -fh.
441 The new -url argument allows one to specify the network address
442 of a file for input. -url currently only works for GET
443 requests, and thus is read-only.
445 o Bio::SearchIO::hmmer now returns individual Hit objects for each
446 domain alignment (thus containing only one HSP); previously
447 separate alignments would be merged into one hit if the domain
448 involved in the alignments was the same, but this only worked
449 when the repeated domain occured without interruption by any
450 other domain, leading to a confusing mixture of Hit and HSP
453 o Bio::Search::Result::ResultI-compliant report objects now
454 implement the "get_statistics" method to access
455 Bio::Search::StatisticsI objects that encapsulate any
456 statistical parameters associated with the search (e.g. Karlin's
457 lambda for BLAST/FASTA).
459 o Bio::Seq::LargeLocatableSeq combines the functionality already
460 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
462 o Bio::SeqFeature::Annotated is a replacement for
463 Bio::SeqFeature::Generic. It breaks compliance with the
464 Bio::SeqFeatureI interface because the author was sick of
465 dealing with untyped annotation tags. All
466 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
467 compliant, and accessible through Bio::Annotation::Collection.
469 o Bio::SeqFeature::Primer implements a Tm() method for primer
470 melting point predictions.
472 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
473 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
475 o Bio::Taxonomy::Node now implements the methods necessary for
476 Bio::Species interoperability.
478 o Bio::Tools::CodonTable has new reverse_translate_all() and
479 make_iupac_string() methods.
481 o Bio::Tools::dpAlign now provides sequence profile alignments.
483 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
485 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
488 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
489 for designing small inhibitory RNA.
491 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
492 methods based on a distance matrix.
494 o Bio::Tree::Statistics provides an assess_bootstrap() method to
495 calculate bootstrap support values on a guide tree topology,
496 based on provided bootstrap tree topologies.
498 o Bio::TreeIO now supports the Pagel (PAG) tree format.
504 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
506 o Bio::Graphics will work with gd1 or gd2
509 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
511 - blast.pm Parse multi-line query fields properly
512 - small speed improvements to blasttable.pm and others
514 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
515 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
516 supporting more complex queries
519 1.4. Stable major release
521 Since initial 1.2.0, 3000 separate changes have been made to make this release.
523 o installable scripts
525 o global module version from Bio::Root:Version
528 - major improvements; SVG support
531 - population genetics
532 - support several population genetics types of questions.
533 - Tests for statistical neutrality of mutations
534 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
535 Tests of population structure (Wright's F-statistic: Fst) is in
536 Bio::PopGen::PopStats. Calculating composite linkage
537 disequilibrium (LD) is available in Bio::PopGen::Statistics as
539 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
540 and csv (comma delimited formatted) data.
542 - a directory for implementing population simulations has
543 been added Bio::PopGen::Simulation and 2 simulations - a
544 Coalescent and a simple single-locus multi-allele genetic drift
545 simulation have been provided. This replaces the code in
546 Bio::Tree::RandomTree which has been deprecated until proper
547 methods for generating random phylogenetic trees are
551 - new restrion analysis modules
553 o Bio::Tools::Analysis
554 - web based DNA and Protein analysis framework and several
558 - per residue annotable sequences
561 - Bio::Matrix::PSM - Position Scoring Matrix
562 - Bio::Matrix::IO has been added for generalized parsing of
563 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
564 initial implementations for parsing BLOSUM/PAM and Phylip
565 Distance matricies respectively. A generic matrix
566 implementation for general use was added in
567 Bio::Matrix::Generic.
574 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
575 - small inhibitory RNA
577 o Bio::SeqFeature::Tools
578 - seqFeature mapping tools
579 - Bio::SeqFeature::Tools::Unflattener.pm
580 -- deal with mapping GenBank feature collections into
581 Chado/GFF3 processable feature sets (with SO term mappings)
583 o Bio::Tools::dpAlign
584 - pure perl dynamic programming sequence alignment
587 o new Bio::SearchIO formats
588 - axt and psl: UCSC formats.
589 - blasttable: NCBI -m 8 or -m 9 format from blastall
591 o new Bio::SeqIO formats
592 - chado, tab, kegg, tigr, game
593 - important fixes for old modules
597 o improved Bio::Tools::Genewise
599 o Bio::SeqIO now can recongnize sequence formats automatically from
602 o new parsers in Bio::Tools:
603 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
605 o Bio::DB::Registry bugs fixed
606 - BerkeleyDB-indexed flat files can be used by the OBDA system
607 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
608 used by the OBDA system
611 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
614 o hundreds of new and improved files
618 o Bio::Tree::AlleleNode has been updated to be a container of
619 an Bio::PopGen::Individual object for use in the Coalescent simulations.
624 1.2.3 Stable release update
625 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
627 o Bug #1477 - Sel --> Sec abbreviation fixed
628 o Fix bug #1487 where paring in-between locations when
629 end < start caused the FTLocationFactory logic to fail.
630 o Fix bug #1489 which was not dealing with keywords as an
631 arrayref properly (this is fixed on the main trunk because
632 keywords returns a string and the array is accessible via
634 o Bio::Tree::Tree memory leak (bug #1480) fixed
635 Added a new initialization option -nodelete which
636 won't try and cleanup the containing nodes if this
638 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
639 this was only present on the branch for the 1.2.1 and 1.2.2 series
640 - Also merged main trunk changes to the branch which make
641 newick -> nhx round tripping more effective (storing branch length
642 and bootstrap values in same locate for NodeNHX and Node
643 implementations.) Fixes to TreeIO parsing for labeled internal
644 also required small changes to TreeIO::nhx. Improved
645 tests for this module as well.
647 - Fixed bugs in BLAST parsing which couldn't parse NCBI
648 gapped blast properly (was losing hit significance values due to
649 the extra unexpeted column).
650 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
651 integer overflow (# of letters in nt seq dbs is > MAX_INT)
652 although doesn't try to correct it - will get the negative
653 number for you. Added a test for this as well.
654 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
655 has no top-level family classification scores but does have scores and
656 alignments for individual domains.
657 - Parsing FASTA reports where ungapped percent ID is < 10 and the
658 regular expression to match the line was missing the possibility of
659 an extra space. This is rare, which is why we probably did not
661 - BLAST parsing picks up more of the statistics/parameter fields
662 at the bottom of reports. Still not fully complete.
663 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
664 were fixed to include many improvements and added flexiblity
665 in outputting the files. Bug #1495 was also fixed in the process.
667 - Update for GFF3 compatibility.
668 - Added scripts for importing from UCSC and GenBank.
669 - Added a 1.2003 version number.
672 - Added a 1.2003 version number.
673 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
674 properly writing keywords out.
675 o Bio::SeqIO::genbank
676 - Fixed bug/enhancement #1513 where dates of
677 the form D-MMM-YYYY were not parsed. Even though this is
678 invalid format we can handle it - and also cleanup the date
679 string so it is properly formatted.
680 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
681 and written with Genbank format. Similarly bug #1515 is fixed to
682 parse in the ORIGIN text.
683 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
684 to specify the ID type, one of (accession accession.version
685 display primary). See Bio::SeqIO::preferred_id_type method
686 documentation for more information.
687 o Unigene parsing updated to handle file format changes by NCBI
689 1.2.2 Stable release update
691 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
692 - auto-discover ontology name
693 - bug in parsing relationships when certain characters are in the term
694 - fixed hard-coded prefix for term identifiers
695 - various smaller issues
697 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
698 of Bio::Ontology::TermI
700 o brought the OBDA Registry code up to latest specs
704 - accession number retrieval fixed
706 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
708 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
709 #1459 which now properly report alignment start/end info
710 for translated BLAST/FASTA searches.
712 o Bio::TreeIO::newick can parse labeled internal nodes
714 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
715 for BLASTX if if you provide -report_type => 'BLASTX' when
716 initializing a BPbl2seq object. Bioperl 1.3 will have better
717 support for bl2seq in the SearchIO system.
719 o Bio::Root::IO support a -noclose boolean flag which will not
720 close a filehandle upon object cleanup - useful when sharing
721 a filehandle among objects. Additionally code added s.t.
722 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
724 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
726 o Bio::SeqIO::genbank
727 - bug #1456 fixed which generated extra sequence lines
728 - write moltype correctly for genpept
730 1.2.1 Stable release update
732 o Inclusion of WrapperBase, a needed component for StandAloneBlast
734 o Addition from main trunk of Ontology objects, principly to allow
735 BioSQL releases against 1.2.1
737 o Fixes and cleanup of Bio::Coordinate modules
739 o A fix to Bio::Index::EMBL allowing retrieval of entries using
740 the primary accession number
742 o Other bug fixes, including bpindex GenBank fix
744 o Bio::SeqIO::genbank bug #1389 fixed
746 1.2 Stable major release
748 o More functionality added to Bio::Perl, the newbie module
750 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
751 Support for New Hampshire Extended (NHX) format parsing.
753 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
754 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
757 o New ontology parsing Bio::Ontology
759 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
760 multi-report (mlib) fasta reports, support for waba and exonerate.
762 o Bio::ClusterIO for parsing Unigene clusters
764 o Bio::Assembly added for representing phrap and ace assembly clusters.
766 o Rudimentary support for writing Chado XML (see
767 GMOD project: www.gmod.org for more information)
769 o Bio::Coordinate for mapping between different coordinate systems such
770 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
771 features into different coordinate systems.
773 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
774 with the get_Stream_by_query method and supports the latest
775 NCBI eutils interface.
777 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
778 object for extracting subsets of features : currently only
779 supports extraction by location.
781 1.1.1 Developer release
783 o Deprecated modules are now listed in the DEPRECATED file
785 o New HowTo documents located in doc/howto describing
788 o Note that bugs are now stored at bugzilla.bioperl.org
789 and all old bugs are searchable through the bugzilla interface.
791 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
794 o Support for Genewise parsing in Bio::Tools::Genewise
796 o Start of Ontology framework with Bio::Ontology
798 o Speedup to the Bio::Root::Root object method _rearrange.
799 A global _load_module method was implemented to simplify the
800 dynamic loading of modules ala Bio::SeqIO::genbank. This
801 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
804 o Several performance improvements to sequence parsing in Bio::SeqIO.
805 Attempt to speedup by reducing object creation overhead.
807 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
808 method for sequence retrieval with their E-utils CGI scripts.
809 More work to support Entrez queries to their fullest is planned
812 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
814 1.1 Developer release
816 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
817 this separation removes some of the complexity in our test suite
818 and separates the core modules in bioperl from those that need
819 external programs to run.
821 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
822 not run into trouble running the makefile
824 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
825 read,create,and write locations for grouped/split locations
826 (like mRNA features on genomic sequence).
828 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
829 and PAML (codeml,aaml, etc) parsing.
831 o Bio::Tree:: objects expanded to handle testing monophyly,
832 paraphyly, least common ancestor, etc.
834 o Bio::Coordinate for mapping locations from different coordinate spaces
836 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
837 added for parsing hmmpfam and hmmsearch output.
839 o Bio::SearchIO::Writer::TextResultWriter for outputting
840 a pseudo-blast textfile format
843 1.0.2 Bug fix release
845 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
846 in this release will not work after December 2002 when NCBI
847 shuts off the old Entrez cgi scripts. We have already fixed
848 on our main development branch and the functionality will be
849 available in the next stable bioperl release (1.2) slated for
852 o Numerous parsing bugs in Bio::SearchIO::fasta found through
853 testset by Robin Emig. These were fixed as was the get_aln
854 method in Bio::Search::HSP::GenericHSP to handle the extra
855 context sequence that is provided with a FastA alignment.
857 o Migrating differences between Bio::Search::XX::BlastXX to
858 Bio::Search::XX::GenericXX objects. This included mechanism
859 to retrieve whole list of HSPs from Hits and whole list of Hits from
860 Results in addition to the current next_XX iterator methods that
861 are available. Added seq_inds() method to GenericHSP which identifies
862 indexes in the query or hit sequences where conserved,identical,gaps,
863 or mismatch residues are located (adapted from Steve Chervitz's
864 implementation in BlastHSP).
866 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
867 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
869 o Bio::Graphics glyph set improved and extended for GBrowse release
871 o Bio::Tree::Tree get_nodes implementation improvement thanks
872 to Howard Ross notice performance problem when writing out
875 o Bio::Location::Fuzzy::new named parameter -loc_type became
876 -location_type, Bio::Location::Simple::new named parameter
877 -seqid becamse -seq_id.
879 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
880 was mis-detecting that gaps should be placed at the beginning of
881 the alignment when the best alignment starts internally in the
884 1.0.1 Bug fix release
886 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
888 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
889 and mixed (3.3 - 3.4) versions of FASTA.
891 o Small API change to add methods for completeness across
892 implementations of Bio::Search objects. These new methods
893 in the interface are implemented by the GenericXX object as well
894 as the BlastXX objects.
895 * Bio::Search::Result::ResultI
896 - hits() method returns list of all Hits (next_hit is an
899 * Bio::Search::Hit::HitI
900 - hsps() method returns list of all HSPs (next_hsp is an
903 o The Bio::SearchIO::Writer classes have been fixed to handle results
904 created from either psiblast (Search::BlastXX objects) or
905 blast|fasta|blastxml objects (Search::GenericXX objects). More work
906 has to be done here to make it work properly and will nee major
909 o Bugs in Bio::Tools::HMMER fixed, including
910 * #1178 - Root::IO destructor wasn't being called
911 * #1034 - filter_on_cutoff now behaves properly
913 o Bio::SeqFeature::Computation initialization args fixed and
916 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
918 o Updated FAQ with more example based answers to typical questions
920 o Bug #1202 was fixed which would improperly join together qual values
921 parsed by Bio::SeqIO::qual when a trailing space was not present before
924 1.0.0 Major Stable Release
926 This represents a major release of bioperl with significant
927 improvements over the 0.7.x series of releases.
929 o Bio::Tools::Blast is officially deprecated. Please see
930 Bio::SearchIO for BLAST and FastA parsing.
932 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
933 Bio::LocationI objects as well as start/end.
935 o Bio::Biblio contains modules for Bibliographic data.
936 Bio::DB::Biblio contains the query modules. Additionally one can
937 parse medlinexml from the ebi bibliographic query service (BQS)
938 system and Pubmed xml from NCBI. See Martin Senger's
939 documentation in Bio::Biblio for more information.
941 o Bio::DB::Registry is a sequence database registry part of
942 Open Bioinformatics Database Access. See
943 http://obda.open-bio.org for more information.
945 o File-based and In-Memory Sequence caching is provided by
946 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
949 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
950 been added by Lincoln Stein.
952 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
954 o A FAQ has been started and is included in the release to provide
955 a starting point for frequent questions and issues.
957 0.9.3 Developer's release
959 o Event based parsing system improved (SearchIO). With parsers for
960 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
961 Additionally a lazy parsing system for text and html blast reports was
962 added and is called psiblast (name subject to change in future releases).
964 o Bio::Search objects improved and standardized with associated Interfaces
965 written. The concept of a search "Hit" was standardized to be called
966 "hit" consistently and the use of "subject" was deprecated in all active
969 o Bio::Structure added (since 0.9.1) for Protein structure objects
970 and PDB parser to retrieve and write these structures from data files.
972 o Several important Bio::DB::GFF bug fixes for handling features that
973 are mapped to multiple reference points. Updated mysql adaptor
974 so as to be able to store large (>100 megabase) chunks of DNA into
975 Bio::DB::GFF databases.
977 0.9.2 Developer's release
979 o Bio::Search and Bio::SearchIO system introduced for event based
980 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
981 in text and XML and FASTA reports in standard output format.
983 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
984 generator is included in Bio::TreeIO::RandomTrees and a
985 statistics module for evaluating.
987 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
988 server for DAS servers.
990 o Bio::Tools::BPlite is provides more robust parsing of BLAST
991 files. The entire BPlite system migrated to using Bio::Root::IO
994 o Bio::Tools::Alignment for Consed and sequence Trimming
997 o Bio::Structure for Protein structure information and parsing
999 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1000 cgi-bin entry point which should be more reliable.
1002 o Bio::Map and Bio::MapIO for biological map navigation and a
1003 framework afor parsing them in. Only preliminary work here.
1005 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1006 Future work will integrate Pise and allow submission of analysis on
1009 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1010 introduced as new objects for handling Sequence Annotation
1011 information (dblinks, references, etc) and is more robust that
1014 o Bio::Tools::FASTAParser introduced.
1016 o Scripts from the bioperl script submission project and new
1017 scripts from bioperl authors are included in "scripts" directory.
1019 o Factory objects and interfaces are being introduced and are more
1022 o Bio::Root::Root introduced as the base object while
1023 Bio::Root::RootI is now simply an interface.
1025 o Bio::DB::RefSeq provides database access to copy of the NCBI
1026 RefSeq database using the EBI dbfetch script.
1028 0.9.0 Developer's release
1030 o perl version at least 5.005 is now required instead of perl 5.004
1032 o Bio::Tools::Run::RemoteBlast is available for running remote
1035 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1037 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1038 Also added are related modules UTR3, UTR5, Exon, Intron,
1039 Promotor, PolyA and Transcript.
1041 o Speedup of translate method in PrimarySeq
1043 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1044 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1046 o Various fixes to Variation toolkit
1048 o Bio::DB::EMBL provides database access to EMBL sequence data.
1049 Bio::DB::Universal provides a central way to point to indexes
1050 and dbs in a single interface.
1052 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1054 o Bio::Factory::EMBOSS is still in design phase as is
1055 Bio::Factory::ApplicationFactoryI
1057 o Dia models for bioperl design are provided in the models/ directory
1059 0.7.2 Bug fix release
1061 o documentation fixes in many modules - SYNOPSIS code verified
1062 to be runnable in many (but not all modules)
1064 o corrected MANIFEST file from 0.7.1 release
1066 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1069 o Bio::SeqIO::genbank
1070 * Correct parsing and writing of genbank format with protein data
1071 * moltype and molecule separation
1073 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1075 o Bio::SimpleAlign fixed to correctly handle consensus
1076 sequence calculation
1078 o Bio::Tools::HMMER supports hmmer 2.2g
1080 o Bio::Tools::BPlite to support report type specific parsing. Most
1081 major changes are not on the 0.7 branch.
1083 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1086 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1087 in several types of mutations:
1088 1.) AA level: deletion, complex
1089 2.) AA level: complex, inframe
1090 3.) RNA level: silent
1092 o BPbl2seq parsing of empty reports will not die, but will return
1093 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1094 $report->query() and $report->subject() methods. So an easy
1095 way to test if report was empty is to see if
1096 $report->query->seqname is undefined.
1098 0.7.1 Bug fix release
1100 o Better parsing of genbank/EMBL files especially fixing bugs
1101 related to Feature table parsing and locations on remote
1102 sequences. Additionally, species name parsing was better.
1104 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1105 which include a number of header lines.
1107 o More strict genbank and EMBL format writing (corrected number of
1108 spaces where appropriate).
1110 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1111 for related BPlite BUGS that are unresolved in this release.
1113 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1114 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1115 use expasy mirrors or EBI dbfetch cgi-script.
1117 o A moderate number of documentation improvements were made as
1118 well to provide a better code synopsis in each module.
1121 0.7 Large number of changes, including refactoring of the
1122 Object system, new parsers, new functionality and
1123 all round better system. Highlights are:
1126 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1127 Bio::Root::IO for I/O and file/handle capabilities.
1129 o Imported BPlite modules from Ian Korf for BLAST
1130 parsing. This is considered the supported BLAST parser;
1131 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1133 o Improved Sequence Feature model. Added complete location
1134 modelling (with fuzzy and compound locations). See
1135 Bio::LocationI and the modules under Bio/Location. Added
1136 support in Genbank/EMBL format parsing to completely parse
1137 feature tables for complex locations.
1139 o Moved special support for databanks etc to specialized modules under
1140 Bio/Seq/. One of these supports very large sequences through
1141 a temporary file as a backend.
1143 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1144 CDS retrieval and exon shuffling.
1146 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1148 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1149 DB/GDB (the latter has platform-specific limitations).
1151 o New analysis parser framework for HT sequence annotation (see
1152 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1154 o New Alignment IO framework
1156 o New Index modules (Swissprot)
1158 o New modules for running Blast within perl
1159 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1160 Multiple Sequence Alignment tools ClustalW and TCoffee
1161 (Bio::Tools::Run::Alignment).
1163 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1164 documentation across the package.
1166 o Much improved cross platform support. Many known incompatibilities
1167 have been fixed; however, NT and Mac do not work across the entire
1168 setup (see PLATFORMS).
1170 o Many bug fixes, code restructuring, etc. Overall stability and
1171 maintainability benefit a lot.
1173 o A total of 957 automatic tests
1178 There are very few functionality changes but a large
1179 number of software improvements/bug fixes across the package.
1181 o The EMBL/GenBank parsing are improved.
1183 o The Swissprot reading is improved. Swissprot writing
1184 is disabled as it doesn't work at all. This needs to
1185 wait for 0.7 release
1187 o BLAST reports with no hits are correctly parsed.
1189 o Several other bugs of the BLAST parser (regular expressions, ...)
1192 o Old syntax calls have been replaced with more modern syntax
1194 o Modules that did not work at all, in particular the Sim4
1195 set have been removed
1197 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1198 have improved compliance with interface specs and documentation
1200 o Mailing list documentation updated throughout the distribution
1202 o Most minor bug fixes have happened.
1204 o The scripts in /examples now work and have the modern syntax
1205 rather than the deprecated syntax
1208 0.6.1 Sun April 2 2000
1210 o Sequences can have Sequence Features attached to them
1211 - The sequence features can be read from or written to
1212 EMBL and GenBank style flat files
1214 o Objects for Annotation, including References (but not
1215 full medline abstracts), Database links and Comments are
1218 o A Species object to represent nodes on a taxonomy tree
1221 o The ability to parse HMMER and Sim4 output has been added
1223 o The Blast parsing has been improved, with better PSI-BLAST
1224 support and better overall behaviour.
1226 o Flat file indexed databases provide both random access
1227 and sequential access to their component sequences.
1229 o A CodonTable object has been written with all known
1230 CodonTables accessible.
1232 o A number of new lightweight analysis tools have been
1233 added, such as molecular weight determination.
1235 The 0.6 release also has improved software engineering
1237 o The sequence objects have been rewritten, providing more
1238 maintainable and easier to implement objects. These
1239 objects are backwardly compatible with the 0.05.1 objects
1241 o Many objects are defined in terms of interfaces and then
1242 a Perl implementation has been provided. The interfaces
1243 are found in the 'I' files (module names ending in 'I').
1245 This means that it is possible to wrap C/CORBA/SQL access
1246 as true "bioperl" objects, compatible with the rest of
1249 o The SeqIO system has been overhauled to provide better
1250 processing and perl-like automatic interpretation of <>
1253 o Many more tests have been added (a total of 172 automatic
1254 tests are now run before release).
1258 0.05.1 Tue Jun 29 05:30:44 1999
1259 - Central distribution now requires Perl 5.004. This was
1260 done to get around 5.003-based problems in Bio/Index/*
1262 - Various bug fixes in the Bio::Tools::Blast modules
1263 including better exception handling and PSI-Blast
1264 support. See Bio/Tools/Blast/CHANGES for more.
1265 - Fixed the Parse mechanism in Seq.pm to use readseq.
1266 Follow the instructions in README for how to install
1267 it (basically, you have to edit Parse.pm).
1268 - Improved documentation of Seq.pm, indicating where
1269 objects are returned and where strings are returned.
1270 - Fixed uninitialized warnings in Bio::Root::Object.pm
1271 and Bio::Tools::SeqPattern.pm.
1272 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1274 0.05 Sun Apr 25 01:14:11 1999
1275 - Bio::Tools::Blast modules have less memory problems
1276 and faster parsing. Webblast uses LWP and supports
1277 more functionality. See Bio/Tools/Blast/CHANGES for more.
1278 - The Bio::SeqIO system has been started, moving the
1279 sequence reformatting code out of the sequence object
1280 - The Bio::Index:: system has been started, providing
1281 generic index capabilities and specifically works for
1282 Fasta formatted databases and EMBL .dat formatted
1284 - The Bio::DB:: system started, providing access to
1285 databases, both via flat file + index (see above) and
1287 - The scripts/ directory, where industrial strength scripts
1288 are put has been started.
1289 - Many changes - a better distribution all round.
1291 0.04.4 Wed Feb 17 02:20:13 1999
1292 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1293 (see Bio::Tools::Blast::CHANGES).
1294 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1295 - Beefed up the t/Fasta.t test script.
1296 - Small fix in Bio::Seq::type() (now always returns a string).
1297 - Changed Bio::Root::Utilities::get_newline_char() to
1298 get_newline() since it could return more than one char.
1299 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1300 - Changed default timeout to 20 seconds (was 3).
1301 - Moved lengthy modification notes to the bottom of some files.
1302 - Fixed SimpleAlign write_fasta bug.
1303 - Beefed up SimpleAlign.t test
1305 0.04.3 Thu Feb 4 07:48:53 1999
1306 - Bio::Root::Object.pm and Global.pm now detect when
1307 script is run as a CGI and suppress output that is only
1308 appropriate when running interactively.
1309 - Bio::Root::Err::_set_context() adds name of script ($0).
1310 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1311 regarding the use of the static objects via the qw(:obj) tag.
1312 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1313 CORE::reverse, avoiding Perl warnings.
1314 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1315 example scripts (see Bio::Tools::Blast::CHANGES).
1316 - examples/seq/seqtools.pl no longer always warns about using
1317 -prot or -nucl command-line arguments; only when using the
1319 - Methods added to Bio::Root::Utilities: create_filehandle(),
1320 get_newline_char(), and taste_file() to generalize filehandle
1321 creation and autodetect newline characters in files/streams
1322 (see bug report #19).
1323 - Bio::Root::IOManager::read() now handles timeouts and uses
1324 Utilities::create_filehandle().
1325 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1326 of hardwiring in "\n".
1327 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1329 0.04.2 Wed Dec 30 02:27:36 1998
1330 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1331 (see Bio::Tools::Blast::CHANGES).
1332 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1333 to CORE::reverse (prevents ambiguous warnings with 5.005).
1334 - Appending '.tmp.bioperl' to temporary files created by
1335 Bio::Root::Utilities::compress() or uncompress() to
1336 make it easy to identify & cleanup these files as needed.
1337 - Developers: Created CVS branch release-0-04-bug from
1338 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1339 be sure to cvs checkout this branch into a clean area.
1341 0.04.1 Wed Dec 16 05:39:15 1998
1342 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1343 (see Bio::Tools::Blast::CHANGES).
1344 - Compile/SW/Makefile.PL now removes *.o and *.a files
1347 0.04 Tue Dec 8 07:49:19 1998
1348 - Lots of new modules added including:
1349 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1350 and Bio/Compile directory containing XS-linked C code for
1351 creating Smith-Waterman sequence alignments from within Perl.
1352 * Steve Chervitz's Blast distribution has been incorporated.
1353 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1354 - Bio/examples directory for demo scripts for all included modules.
1355 - Bio/t directory containing test suit for all included modules.
1356 - For changes specific to the Blast-related modules prior to
1357 incorporation in this central distribution, see the CHANGES
1358 file in the Bio/Tools/Blast directory.
1360 0.01 Tue Sep 8 14:23:22 1998
1361 - original version from central CVS tree; created by h2xs 1.18