1 ---------------------------------------------------------
2 Revision history for BioPerl core modules
3 ---------------------------------------------------------
4 The comprehensive history and ongoing development of BioPerl:
6 http://github.com/bioperl/bioperl-live
8 Some of that history is also highlighted on our wiki:
10 http://www.bioperl.org/wiki/Change_log
11 http://www.bioperl.org/wiki/History_of_BioPerl
13 Bugs and requested features list:
15 https://github.com/bioperl/bioperl-live/issues
17 CPAN releases are branched from 'master'.
18 ---------------------------------------------------------
22 * WrapperBase quoted option values [majensen]
23 * Various documentation fixes and updates [bosborne]
27 * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
28 * NeXML parser fixes [fjossandon]
29 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
30 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
31 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
32 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
33 * Issue #81: small updates to make sure possible memory leaks are detected [cjfields]
34 * Issue #84: EMBL format wrapping problem [nyamned]
35 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
41 * Bug/feature issue tracking has moved to GitHub Issues:
42 https://github.com/bioperl/bioperl-live/issues
43 * DB_File has been demoted from "required" to "recommended",
44 which should make easier for Windows users to install BioPerl
45 if they don't need that module.
49 * Bio::Search::HSP::GenericHSP
50 - Bug #3370, added a "posterior_string" method to retrieve the
51 posterior probability lines (PP) from HMMER3 reports [fjossandon]
52 - Added a "consensus_string" method to retrieve the consensus
53 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
54 * Bio::SearchIO::hmmer2
55 - The number of identical and conserved residues are now calculated
56 directly from the homology line [fjossandon]
57 - Now the Query Length and Hit Length are reported when the alignment
58 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
59 - Implemented the capture of the consensus structure lines [fjossandon]
60 * Bio::SearchIO::hmmer3
61 - The number of identical and conserved residues are now calculated
62 directly from the homology line [fjossandon]
63 - Now the Hit Length is reported when the alignment runs until the end
64 of the sequence/model ('.]' or '[]') [fjossandon]
65 - Implemented the capture of the consensus structure lines [fjossandon]
66 - Implemented the capture of the posterior probability lines [fjossandon]
67 - Completed the development of NHMMER parsing, including alignments [fjossandon]
68 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
69 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
70 "min_score", "min_bits, and "hit_filter" methods from
71 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
72 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
73 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
74 besides Blast, instead of being ignored. Added tests for all moved methods
75 using HMMER outputs and run the full test suite and everything pass [fjossandon]
76 * Bio::SeqIO::MultiFile
77 - Autodetection of file format [fangly]
78 * Bio::Tools::GuessSeqFormat:
79 - Format detection from non-seekable filehandles such as STDIN [fangly]
83 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
84 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
85 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
86 * Abstract: Fixed ActivePerl incapability of removing temporary files
87 because of problems closing tied filehandles [fjossandon]
88 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
89 because ActivePerl were producing a ".index.pag" and ".index.dir"
90 files instead of a single ".index" file (like Strawberry Perl).
91 Now those temporary files are correctly considered and deleted. [fjossandon]
92 * Test files: Added missing module requirements (DB_File and Data::Stag)
93 to several tests files that were failing because those modules were
94 not present. Now those test files are correctly skipped instead. [fjossandon]
95 * Blast: Added support to changes in bl2seq from BLAST+ output, which
96 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
97 * Phylip: Return undef in "next_aln" at file end to avoid
98 an infinite loop [yschensandiego]
99 * HMMER3: When a hit description is too long, it is truncated in
100 the Scores table. In those cases, the more complete description from
101 the Annotation line (>>) will be used [fjossandon]
102 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
103 since it is now used by HMMER3 format in alignments [fjossandon]
104 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
105 to return undef if the query/hit length is unknown (like in some
106 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
107 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
108 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
109 added support to multi-query reports, reduced code redundancy,
110 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
111 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
112 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
113 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
114 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
115 * Double-quotes on paths are needed in some places [fjossandon]
116 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
117 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
118 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
119 with the latest changes made in their own repositories [fjossandon]
120 * General synching of files with the master branch [fjossandon]
121 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
122 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
123 * Fixed broken MeSH parser [fjossandon]
124 * Fixed missing detection of format in SeqIO when given a -string [fangly]
128 * Major Windows support updates! [fjossandon]
129 * MAKER update to allow for stricter standard codon table [cjfields]
130 * Better support for circular sequences [fjossandon]
131 * Fixes for some complex location types [fjossandon]
132 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
133 * Fix bug #2978 related to BLAST report type [fjossandon]
134 * Deobfuscator fixes [DaveMessina]
138 * Address CPAN test failures [cjfields]
139 * Add BIOPROJECT support for Genbank files [hyphaltip]
140 * Better regex support for HMMER3 output [bosborne]
144 * Minor update to address CPAN test failures
148 * Remove Bio::Biblio and related files [carandraug]
149 - this cause version clashes with an independently-released
150 version of Bio::Biblio
156 * Hash randomization fixes for perl 5.18.x
157 - Note: at least one module (Bio::Map::Physical) still has a failing test;
158 this is documented in bug #3446 and has been TODO'd; we will be pulling
159 Bio::Map and similar modules out of core into separate distributions in the
160 1.7.x release series [cjfields]
164 * Bio::Seq::SimulatedRead
165 - New module to represent reads taken from other sequences [fangly]
167 - Support of Clone::Fast as a faster cloning alternative [fangly]
169 - Moved the format() and variant() methods from Bio::*IO modules to
170 Bio::Root::IO [fangly]
171 - Can now use format() to get the type of IO format in use [fangly]
173 - New regexp() method to create regular expressions from IUPAC sequences
175 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
176 - Code refresh [fangly]
178 - Added support for the Greengenes and Silva taxonomies [fangly]
179 * Bio::Tree::TreeFunctionsI
180 - get_lineage_string() represents a lineage as a string [fangly]
181 - add_trait() returns instead of reporting an error when the column
182 number is exceeded in add_trait() [fangly]
183 - Option to support tree leaves without trait [fangly]
184 - Allow ID of 0 in trait files [fangly]
185 * Bio::DB::Taxonomy::list
186 - Misc optimizations [fangly]
187 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
188 * Bio::DB::Taxonomy::*
189 - get_num_taxa() returns the number of taxa in the database [fangly]
190 * Bio::DB::Fasta and Bio::DB::Qual
191 - support indexing an arbitrary list of files [fangly]
192 - user can supply an arbitrary index file name [fangly]
193 - new option to remove index file at the end [fangly]
195 - now handles IUPAC degenerate residues [fangly]
196 * Bio::PrimarySeq and Bio::PrimarySeqI
197 - speed improvements for large sequences [Ben Woodcroft, fangly]
199 - tightened and optimized quality string validation [fangly]
201 - new method and option 'block', to create FASTA output with space
202 intervaled blocks (similar to genbank or EMBL) has been implemented.
203 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
204 in favour of the methods 'width' and 'preferred_id_type` respectively.
206 - moved from bioperl-live into the separate distribution Bio-FeatureIO
207 * Bio::SeqFeature::Annotated
208 - moved from bioperl-live into the separate distribution Bio-FeatureIO
209 * Bio::Cluster::SequenceFamily
210 - improved performance when using get_members with overlapping multiple
212 * Bio::SearchIO::hmmer3
213 - now supports nhmmer [bosborne]
217 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
218 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
219 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
220 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
221 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
222 information was lost in a multi-result blast file [Paul Cantalupo]
223 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
224 total gaps [Paul Cantalupo]
225 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
226 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
227 when end of domain indicator is split across lines [Paul Cantalupo]
228 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
230 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
231 instances where blank lines are within sequences [cjfields]
232 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
234 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
235 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
237 * Various fixes for Stockholm file indexing and processing [bosborne]
238 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
239 breaks parsing [cjfields]
240 * Fix case where Bio::Seq::Meta* objects with no meta information could not
241 be reverse-complemented [fangly]
242 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
243 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
244 when unsure that values will be numerical [fangly]
245 * Fix undef warnings in Bio::SeqIO::embl [fangly]
246 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
247 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
248 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
250 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
251 source_tag and display_name must return a string, not undef [fangly]
252 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
253 add_SeqFeature takes a single argument [fangly]
254 * Use cross-platform filenames and temporary directory in
255 Bio::DB::Taxonomy::flatfile [fangly]
256 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
257 properly identified as existing taxa in the database [fangly]
258 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
259 without also passing a lineage to store [fangly]
260 * Prevent passing a directory to the gi2taxid option (-g) of
261 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
263 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
264 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
265 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
266 object before trying to access, and no longer returns repeated sequences.
273 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
274 modules using Ace will also be deprecated [lds, cjfields]
275 * Minor bug fix release
276 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
277 * Address Build.PL issues when DBI is not present [hartzell]
278 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
279 * Remove deprecated code for perl 5.14.0 compat [cjfields]
280 * Due to schema changes and lack of support for older versions, support
281 for NeXML 0.9 is only (very) partially implemented.
282 See: https://redmine.open-bio.org/issues/3207
286 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
287 docs [genehack, cjfields]
288 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
289 module version from dist_version (probably not the best way to do this,
290 but it seems to work) [rbuels, cjfields]
293 1.6.900 April 14, 201
297 * This will probably be the last release to add significant features to
298 core modules; subsequent releases will be for bug fixes alone.
299 We are planning on a restructuring of core for summer 2011, potentially
300 as part of the Google Summer of Code. This may become BioPerl 2.0.
301 * Version bump represents 'just prior to v 1.7'. We may have point
302 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
303 This code essentially is what is on the github master branch.
307 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
309 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
310 - removal of Scalar::Util::weaken code, which was causing odd headaches
311 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
312 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
314 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
317 - bug 2515 - new contribution [Ryan Golhar, jhannah]
319 - support for reading Maq, Sam and Bowtie files [maj]
320 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
321 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
322 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
323 - bug 2726: reading/writing granularity: whole scaffold or one contig
324 at a time [Joshua Udall, fangly]
326 - Added parsing of xrefs to OBO files, which are stored as secondary
327 dbxrefs of the cvterm [Naama Menda]
328 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
329 * PAML code updated to work with PAML 4.4d [DaveMessina]
333 * [3198] - sort tabular BLAST hits by score [DaveMessina]
334 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
335 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
336 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
338 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
339 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
340 * [3164] - TreeFunctionsI syntax bug [gjuggler]
341 * [3163] - AssemblyIO speedup [fangly]
342 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
344 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
345 * [3158] - fix EMBL file mis-parsing [cjfields]
346 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
348 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
349 * [3148] - URL change for UniProt [cjfields]
350 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
351 * [3136] - HMMer3 parser fixes [kblin]
352 * [3126] - catch description [Toshihiko Akiba]
353 * [3122] - Catch instances where non-seekable filehandles were being
354 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
355 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
356 [dukeleto, rbuels, cjfields]
357 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
359 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
360 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
362 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
363 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
364 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
365 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
366 * [3086] - EMBL misparsing long tags [kblin, cjfields]
367 * [3085] - CommandExts and array of files [maj, hyphaltip]
368 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
369 for alignment slices [Ha X. Dang, cjfields]
370 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
371 * [3073] - fix parsing of GenBank files from RDP [cjfields]
372 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
373 * [3064] - All-gap midline BLAST report issues [cjfields]
374 * [3063] - BLASt report RID [Razi Khaja, cjfields]
375 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
376 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
377 * [3039] - correct Newick output root node branch length [gjuggler,
379 * [3038] - SELEX alignment error [Bernd, cjfields]
380 * [3033] - PrimarySeq ID setting [Bernd, maj]
381 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
382 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
383 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
384 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
385 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
386 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
387 PAML 4.4d [DaveMessina]
388 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
390 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
391 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
392 * [3017] - using threads with Bio::DB::GenBank [cjfields]
393 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
394 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
395 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
396 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
397 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
399 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
400 * [2977] - TreeIO issues [DaveMessina]
401 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
402 * [2944] - Bio::Tools::GFF score [cjfields]
403 * [2942] - correct MapTiling output [maj]
404 * [2939] - PDB residue insertion codes [John May, maj]
405 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
406 * [2928] - GuessSeqFormat raw [maj]
407 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
408 * [2922] - open() directive issue [cjfields]
409 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
410 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
411 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
412 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
414 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
415 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
416 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
417 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
418 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
419 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
420 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
421 * [2758] - Bio::AssemblyIO ace problems [fangly]
422 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
423 * [2726] - ace file IO [Josh, fangly]
424 * [2700] - Refactor Build.PL [cjfields]
425 * [2673] - addition of simple Root-based clone() method [cjfields]
426 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
427 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
428 * [2594] - Bio::Species memory leak [cjfields]
429 * [2515] - GenBank XML parser [jhannah]
430 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
431 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
432 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
434 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
438 * Bio::Expression modules - these were originally designed to go with the
439 bioperl-microarray suite of tools, however they have never been completed
440 and so have been removed from the distribution. The original code has
441 been moved into the inactive bioperl-microarray suite. [cjfields]
445 * Repository moved from Subversion (SVN) to
446 http://github.com/bioperl/bioperl-live [cjfields]
447 * Bug database has moved to Redmine (https://redmine.open-bio.org)
448 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
449 Thieme have been moved to their own distribution (Bio-Microarray).
452 1.6.1 Sept. 29, 2009 (point release)
453 * No change from last alpha except VERSION and doc updates [cjfields]
455 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
456 * Fix for silent OBDA bug related to FASTA validation [cjfields]
458 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
459 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
460 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
462 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
464 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
465 * WinXP test fixes [cjfields, maj]
466 * BioPerl.pod added for descriptive information, fixes CPAN indexing
468 * Minor doc fixes [cjfields]
470 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
471 * Fix tests failing due to merging issues [cjfields]
472 * More documentation updates for POD parsing [cjfields]
474 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
476 - fix YAML meta data generation [cjfields]
478 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
479 * Bio::Align::DNAStatistics
480 - fix divide by zero problem [jason]
482 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
483 * Bio::AlignIO::stockholm
484 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
485 * Bio::Assembly::Tools::ContigSpectrum
486 - function to score contig spectrum [fangly]
487 * Bio::DB::EUtilities
488 - small updates [cjfields]
490 - berkeleydb database now autoindexes wig files and locks correctly
493 - various small updates for stability; tracking changes to LANL
494 database interface [maj]
495 * Bio::DB::SeqFeature (lots of updates and changes)
496 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
497 - bug 2835 - patch [Dan Bolser]
498 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
500 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
501 * Bio::Factory::FTLocationFactory
502 - mailing list bug fix [cjfields]
504 - performance work on column_from_residue_number [hartzell]
505 * Bio::Matrix::IO::phylip
506 - bug 2800 - patch to fix phylip parsing [Wei Zou]
508 - Google Summer of Code project from Chase Miller - parsers for Nexml
509 file format [maj, chmille4]
511 - Make Individual, Population, Marker objects AnnotatableI [maj]
512 - simplify LD code [jason]
514 - deal with empty intersection [jason]
516 - significant overhaul of Bio::Restriction system: complete support for
517 external and non-palindromic cutters. [maj]
519 - CPANPLUS support, no automatic installation [sendu]
521 - allow IO::String (regression fix) [cjfields]
522 - catch unintentional undef values [cjfields]
523 - throw if non-fh is passed to -fh [maj]
524 * Bio::Root::Root/RootI
525 - small debugging and core fixes [cjfields]
527 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
528 * Bio::Root::Utilities
529 - bug 2737 - better warnings [cjfields]
531 - tiling completely refactored, HOWTO added [maj]
532 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
533 will deprecate usage of the older tiling code in the next BioPerl
535 - small fixes [cjfields]
537 - Infernal 1.0 output now parsed [cjfields]
538 - new parser for gmap -f9 output [hartzell]
539 - bug 2852 - fix infinite loop in some output [cjfields]
540 - blastxml output now passes all TODO tests [cjfields]
541 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
542 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
543 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
544 * Bio::Seq::LargePrimarySeq
545 - delete tempdirs [cjfields]
546 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
548 - extract regions based on quality threshold value [Dan Bolser, heikki]
549 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
550 * Bio::SeqFeature::Lite
551 - various Bio::DB::SeqFeature-related fixes [lstein]
552 * Bio::SeqFeature::Tools::TypeMapper
553 - additional terms for GenBank to SO map [scain]
554 * Bio::SeqIO::chadoxml
555 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
557 - support for CDS records [dave_messina, Sylvia]
559 - complete refactoring to handle all FASTQ variants, perform validation,
560 write output. API now conforms with other Bio* parsers and the rest of
561 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
563 * Bio::SeqIO::genbank
564 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
565 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
566 * Bio::SeqIO::largefasta
567 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
569 - add option for 'single' and 'multiple'
571 - bug 2881 - fix scf round-tripping [Adam Søgren]
573 - bug 2766, 2810 - copy over tags from features, doc fixes [David
576 - bug 2793 - patch for add_seq index issue [jhannah, maj]
577 - bug 2801 - throw if args are required [cjfields]
578 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
579 [Tristan Lefebure, maj]
580 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
581 - fix POD and add get_SeqFeatures filter [maj]
582 * Bio::Tools::dpAlign
583 - add support for LocatableSeq [ymc]
584 - to be moved to a separate distribution [cjfields, rbuels]
585 * Bio::Tools::EUtilities
586 - fix for two bugs from mail list [Adam Whitney, cjfields]
587 - add generic ItemContainerI interface for containing same methods
590 - fix up code, add more warnings [cjfields]
591 - to be moved to a separate distribution [cjfields, rbuels]
592 * Bio::Tools::Primer3
593 - bug 2862 - fenceposting issue fixed [maj]
594 * Bio::Tools::Run::RemoteBlast
595 - tests for remote RPS-BLAST [mcook]
596 * Bio::Tools::SeqPattern
597 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
598 * Bio::Tools::tRNAscanSE
599 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
601 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
602 * Bio::Tree::Statistics
603 - several methods for calculating Fitch-based score, internal trait
604 values, statratio(), sum of leaf distances [heikki]
606 - bug 2869 - add docs indicating edge case where nodes can be
607 prematurely garbage-collected [cjfields]
608 - add as_text() function to create Tree as a string in specified format
610 * Bio::Tree::TreeFunctionsI
611 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
613 * Bio::TreeIO::newick
614 - fix small semicolon issue [cjfields]
616 - update to bp_seqfeature_load for SQLite [lstein]
617 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
618 - fastam9_to_table - fix for MPI output [jason]
619 - gccalc - total stats [jason]
621 - POD cleanup re: FEEDBACK section [maj, cjfields]
622 - cleanup or fix dead links [cjfields]
623 - Use of no_* methods (indicating 'number of something') is deprecated
624 in favor of num_* [cjfields]
625 - lots of new tests for the above bugs and refactors [everyone!]
626 - new template for Komodo text editor [cjfields]
629 * Feature/Annotation rollback
630 - Problematic changes introduced prior to the 1.5 release have been
631 rolled back. These changes led to subtle bugs involving operator
632 overloading and interface methods.
633 - Behavior is very similar to that for BioPerl 1.4, with tag values
634 being stored generically as simple scalars. Results in a modest
637 - Split into a separate distribution on CPAN, primarily so development
638 isn't reliant on a complete BioPerl release.
639 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
640 is only available via Subversion (via bioperl-live main trunk)
642 - Common test bed for all BioPerl modules
644 - Common Module::Build-based subclass for all BioPerl modules
645 * Bio::DB::EUtilities
646 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
647 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
648 and user agent request posting and retrieval
649 * Test implementation and reorganization
650 - Tests have been reorganized into groups based on classes or use
652 - Automated test coverage is now online:
653 http://www.bioperl.org/wiki/Test_Coverage
654 - After this release, untested modules will be moved into a
655 separate developer distribution until tests can be derived.
656 Also, new modules to be added are expected to have a test suite
657 and adequate test coverage.
659 1.5.2 Developer release
661 Full details of changes since 1.5.1 are available online at:
662 http://www.bioperl.org/wiki/Change_log
663 The following represents a brief overview of the most important changes.
666 - Overhaul. Brand new system fully allows markers to have multiple
667 positions on multiple maps, and to have relative positions. Should be
671 - This module and all the modules in the Taxonomy directory now
672 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
677 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
679 * New methods ancestor(), each_Descendent() and _handle_internal_id().
681 * Allows for different database modules to create Bio::Taxon objects
682 with the same internal id when the same taxon is requested from each.
685 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
687 * No longer includes the fake root node 'root'; there are multiple roots
688 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
691 * get_node() has new option -full
693 * Caches data retrieved from website
696 - Now a Bio::Taxon. Carries out the species name -> specific name munging
697 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
698 backward compatability in species() method.
700 o Bio::Search and Bio::SearchIO
701 - Overhaul. The existing system has been sped up via some minor changes
702 (mostly gain-of-function to the API). Bio::PullParserI is introduced
703 as a potential eventual replacment for the existing system, though as
704 yet only a Hmmpfam parser exists written using it.
707 1.5.1 Developer release
709 o Major problem with how Annotations were written out with
710 Bio::Seq is fixed by reverting to old behavior for
711 Bio::Annotation objects.
716 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
717 expect at l east 9 spaces at the beginning of a line to
718 indicate line wrapping.
720 * Treat multi-line SOURCE sections correctly, this defect broke
721 both common_name() and classification()
723 * parse swissprot fields in genpept file
725 * parse WGS genbank records
728 * Changed regexp for ID line. The capturing parentheses are
729 the same, the difference is an optional repeated-not-semi-
730 colon expression following the captured \S+. This means the
731 regexp works when the division looks like /PRO;/ or when the
732 division looks like /ANG ;/ - the latter is from EMBL
735 * fix ID line parsing: the molecule string can have spaces in
736 it. Like: "genomic DNA"
738 - swiss.pm: bugs #1727, #1734
741 * Added parser for entrezgene ASN1 (text format) files.
742 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
746 - maf.pm coordinate problem fixed
748 o Bio::Taxonomy and Bio::DB::Taxonomy
750 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
751 can be done via Web without downloading all the sequence.
753 o Bio::Tools::Run::RemoteBlast supports more options and complies
754 to changes to the NCBI interface. It is reccomended that you
755 retrieve the data in XML instead of plain-text BLAST report to
756 insure proper parsing and retrieval of all information as NCBI
757 fully expects to change things in the future.
759 o Bio::Tree and Bio::TreeIO
761 - Fixes so that re-rooting a tree works properly
763 - Writing out nhx format from a newick/nexus file will properly output
764 bootstrap information. The use must move the internal node labels over
766 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
767 $node->bootstrap($node->id);
770 - Nexus parsing is much more flexible now, does not care about
773 - Cladogram drawing module in Bio::Tree::Draw
775 - Node height and depth now properly calculated
777 - fix tree pruning algorithm so that node with 1 child gets merged
779 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
780 bugs and improvements were added, see Gbrowse mailing list for most of
783 o Bio::DB::GFF partially supports GFF3. See information about
784 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
786 o Better location parsing in Bio::Factory::FTLocationFactory -
787 this is part of the engine for parsing EMBL/GenBank feature table
788 locations. Nested join/order-by/complement are allowed now
790 o Bio::PrimarySeqI->translate now takes named parameters
792 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
793 reconstruction) is now supported. Parsing different models and
794 branch specific parametes are now supported.
796 o Bio::Factory::FTLocationFactory - parse hierarchical locations
799 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
800 for getter/setter functions
804 - blast bug #1739; match scientific notation in score
805 and possible e+ values
807 - blast.pm reads more WU-BLAST parameters and parameters, match
808 a full database pathname,
810 - Handle NCBI WEB and newer BLAST formats specifically
811 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
813 - psl off-by-one error fixed
815 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
816 and HSPs can be constructed from them.
818 - HSPs query/hit now have a seqdesc field filled out (this was
819 always available via $hit->description and
820 $result->query_description
822 - hmmer.pm can parse -A0 hmmpfam files
824 - Writer::GbrowseGFF more customizeable.
826 o Bio::Tools::Hmmpfam
827 make e-value default score displayed in gff, rather than raw score
828 allow parse of multiple records
831 1.5 Developer release
833 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
834 provide Jukes-Cantor and Kimura pairwise distance methods,
837 o Bio::AlignIO support for "po" format of POA, and "maf";
838 Bio::AlignIO::largemultifasta is a new alternative to
839 Bio::AlignIO::fasta for temporary file-based manipulation of
840 particularly large multiple sequence alignments.
842 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
843 be treated similarly as an assembled contig.
845 o Bio::CodonUsage provides new rare_codon() and probable_codons()
846 methods for identifying particular codons that encode a given
849 o Bio::Coordinate::Utils provides new from_align() method to build
850 a Bio::Coordinate pair directly from a
851 Bio::Align::AlignI-conforming object.
853 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
854 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
855 web service using standard Pubmed query syntax, and retrieve
858 o Bio::DB::GFF has various sundry bug fixes.
860 o Bio::FeatureIO is a new SeqIO-style subsystem for
861 writing/reading genomic features to/from files. I/O classes
862 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
863 classes only read/write Bio::SeqFeature::Annotated objects.
864 Notably, the GFF v3 class requires features to be typed into the
867 o Bio::Graph namespace contains new modules for manipulation and
868 analysis of protein interaction graphs.
870 o Bio::Graphics has many bug fixes and shiny new glyphs.
872 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
873 indexing for HMMER reports and FASTA qual files, respectively.
875 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
876 new objects that can be placed within a Bio::Map::MapI-compliant
877 genetic/physical map; Bio::Map::Physical provides a new physical
878 map type; Bio::MapIO::fpc provides finger-printed clone mapping
881 o Bio::Matrix::PSM provide new support for postion-specific
882 (scoring) matrices (e.g. profiles, or "possums").
884 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
885 be instantiated without explicitly using Bio::OntologyIO. This
886 is possible through changes to Bio::Ontology::OntologyStore to
887 download ontology files from the web as necessary. Locations of
888 ontology files are hard-coded into
889 Bio::Ontology::DocumentRegistry.
891 o Bio::PopGen includes many new methods and data types for
892 population genetics analyses.
894 o New constructor to Bio::Range, unions(). Given a list of
895 ranges, returns another list of "flattened" ranges --
896 overlapping ranges are merged into a single range with the
897 mininum and maximum coordinates of the entire overlapping group.
899 o Bio::Root::IO now supports -url, in addition to -file and -fh.
900 The new -url argument allows one to specify the network address
901 of a file for input. -url currently only works for GET
902 requests, and thus is read-only.
904 o Bio::SearchIO::hmmer now returns individual Hit objects for each
905 domain alignment (thus containing only one HSP); previously
906 separate alignments would be merged into one hit if the domain
907 involved in the alignments was the same, but this only worked
908 when the repeated domain occured without interruption by any
909 other domain, leading to a confusing mixture of Hit and HSP
912 o Bio::Search::Result::ResultI-compliant report objects now
913 implement the "get_statistics" method to access
914 Bio::Search::StatisticsI objects that encapsulate any
915 statistical parameters associated with the search (e.g. Karlin's
916 lambda for BLAST/FASTA).
918 o Bio::Seq::LargeLocatableSeq combines the functionality already
919 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
921 o Bio::SeqFeature::Annotated is a replacement for
922 Bio::SeqFeature::Generic. It breaks compliance with the
923 Bio::SeqFeatureI interface because the author was sick of
924 dealing with untyped annotation tags. All
925 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
926 compliant, and accessible through Bio::Annotation::Collection.
928 o Bio::SeqFeature::Primer implements a Tm() method for primer
929 melting point predictions.
931 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
932 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
934 o Bio::Taxonomy::Node now implements the methods necessary for
935 Bio::Species interoperability.
937 o Bio::Tools::CodonTable has new reverse_translate_all() and
938 make_iupac_string() methods.
940 o Bio::Tools::dpAlign now provides sequence profile alignments.
942 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
944 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
947 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
948 for designing small inhibitory RNA.
950 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
951 methods based on a distance matrix.
953 o Bio::Tree::Statistics provides an assess_bootstrap() method to
954 calculate bootstrap support values on a guide tree topology,
955 based on provided bootstrap tree topologies.
957 o Bio::TreeIO now supports the Pagel (PAG) tree format.
963 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
965 o Bio::Graphics will work with gd1 or gd2
968 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
970 - blast.pm Parse multi-line query fields properly
971 - small speed improvements to blasttable.pm and others
973 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
974 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
975 supporting more complex queries
978 1.4. Stable major release
980 Since initial 1.2.0, 3000 separate changes have been made to make this release.
982 o installable scripts
984 o global module version from Bio::Root:Version
987 - major improvements; SVG support
990 - population genetics
991 - support several population genetics types of questions.
992 - Tests for statistical neutrality of mutations
993 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
994 Tests of population structure (Wright's F-statistic: Fst) is in
995 Bio::PopGen::PopStats. Calculating composite linkage
996 disequilibrium (LD) is available in Bio::PopGen::Statistics as
998 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
999 and csv (comma delimited formatted) data.
1001 - a directory for implementing population simulations has
1002 been added Bio::PopGen::Simulation and 2 simulations - a
1003 Coalescent and a simple single-locus multi-allele genetic drift
1004 simulation have been provided. This replaces the code in
1005 Bio::Tree::RandomTree which has been deprecated until proper
1006 methods for generating random phylogenetic trees are
1010 - new restrion analysis modules
1012 o Bio::Tools::Analysis
1013 - web based DNA and Protein analysis framework and several
1017 - per residue annotable sequences
1020 - Bio::Matrix::PSM - Position Scoring Matrix
1021 - Bio::Matrix::IO has been added for generalized parsing of
1022 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1023 initial implementations for parsing BLOSUM/PAM and Phylip
1024 Distance matricies respectively. A generic matrix
1025 implementation for general use was added in
1026 Bio::Matrix::Generic.
1033 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1034 - small inhibitory RNA
1036 o Bio::SeqFeature::Tools
1037 - seqFeature mapping tools
1038 - Bio::SeqFeature::Tools::Unflattener.pm
1039 -- deal with mapping GenBank feature collections into
1040 Chado/GFF3 processable feature sets (with SO term mappings)
1042 o Bio::Tools::dpAlign
1043 - pure perl dynamic programming sequence alignment
1046 o new Bio::SearchIO formats
1047 - axt and psl: UCSC formats.
1048 - blasttable: NCBI -m 8 or -m 9 format from blastall
1050 o new Bio::SeqIO formats
1051 - chado, tab, kegg, tigr, game
1052 - important fixes for old modules
1056 o improved Bio::Tools::Genewise
1058 o Bio::SeqIO now can recongnize sequence formats automatically from
1061 o new parsers in Bio::Tools:
1062 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1064 o Bio::DB::Registry bugs fixed
1065 - BerkeleyDB-indexed flat files can be used by the OBDA system
1066 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1067 used by the OBDA system
1069 o several new HOWTOs
1070 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1073 o hundreds of new and improved files
1077 o Bio::Tree::AlleleNode has been updated to be a container of
1078 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1083 1.2.3 Stable release update
1084 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1086 o Bug #1477 - Sel --> Sec abbreviation fixed
1087 o Fix bug #1487 where paring in-between locations when
1088 end < start caused the FTLocationFactory logic to fail.
1089 o Fix bug #1489 which was not dealing with keywords as an
1090 arrayref properly (this is fixed on the main trunk because
1091 keywords returns a string and the array is accessible via
1093 o Bio::Tree::Tree memory leak (bug #1480) fixed
1094 Added a new initialization option -nodelete which
1095 won't try and cleanup the containing nodes if this
1097 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1098 this was only present on the branch for the 1.2.1 and 1.2.2 series
1099 - Also merged main trunk changes to the branch which make
1100 newick -> nhx round tripping more effective (storing branch length
1101 and bootstrap values in same locate for NodeNHX and Node
1102 implementations.) Fixes to TreeIO parsing for labeled internal
1103 also required small changes to TreeIO::nhx. Improved
1104 tests for this module as well.
1106 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1107 gapped blast properly (was losing hit significance values due to
1108 the extra unexpeted column).
1109 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1110 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1111 although doesn't try to correct it - will get the negative
1112 number for you. Added a test for this as well.
1113 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1114 has no top-level family classification scores but does have scores and
1115 alignments for individual domains.
1116 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1117 regular expression to match the line was missing the possibility of
1118 an extra space. This is rare, which is why we probably did not
1120 - BLAST parsing picks up more of the statistics/parameter fields
1121 at the bottom of reports. Still not fully complete.
1122 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1123 were fixed to include many improvements and added flexiblity
1124 in outputting the files. Bug #1495 was also fixed in the process.
1126 - Update for GFF3 compatibility.
1127 - Added scripts for importing from UCSC and GenBank.
1128 - Added a 1.2003 version number.
1131 - Added a 1.2003 version number.
1132 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1133 properly writing keywords out.
1134 o Bio::SeqIO::genbank
1135 - Fixed bug/enhancement #1513 where dates of
1136 the form D-MMM-YYYY were not parsed. Even though this is
1137 invalid format we can handle it - and also cleanup the date
1138 string so it is properly formatted.
1139 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1140 and written with Genbank format. Similarly bug #1515 is fixed to
1141 parse in the ORIGIN text.
1142 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1143 to specify the ID type, one of (accession accession.version
1144 display primary). See Bio::SeqIO::preferred_id_type method
1145 documentation for more information.
1146 o Unigene parsing updated to handle file format changes by NCBI
1148 1.2.2 Stable release update
1150 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1151 - auto-discover ontology name
1152 - bug in parsing relationships when certain characters are in the term
1153 - fixed hard-coded prefix for term identifiers
1154 - various smaller issues
1156 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1157 of Bio::Ontology::TermI
1159 o brought the OBDA Registry code up to latest specs
1163 - accession number retrieval fixed
1165 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1167 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1168 #1459 which now properly report alignment start/end info
1169 for translated BLAST/FASTA searches.
1171 o Bio::TreeIO::newick can parse labeled internal nodes
1173 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1174 for BLASTX if if you provide -report_type => 'BLASTX' when
1175 initializing a BPbl2seq object. Bioperl 1.3 will have better
1176 support for bl2seq in the SearchIO system.
1178 o Bio::Root::IO support a -noclose boolean flag which will not
1179 close a filehandle upon object cleanup - useful when sharing
1180 a filehandle among objects. Additionally code added s.t.
1181 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1183 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1185 o Bio::SeqIO::genbank
1186 - bug #1456 fixed which generated extra sequence lines
1187 - write moltype correctly for genpept
1189 1.2.1 Stable release update
1191 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1193 o Addition from main trunk of Ontology objects, principly to allow
1194 BioSQL releases against 1.2.1
1196 o Fixes and cleanup of Bio::Coordinate modules
1198 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1199 the primary accession number
1201 o Other bug fixes, including bpindex GenBank fix
1203 o Bio::SeqIO::genbank bug #1389 fixed
1205 1.2 Stable major release
1207 o More functionality added to Bio::Perl, the newbie module
1209 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1210 Support for New Hampshire Extended (NHX) format parsing.
1212 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1213 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1216 o New ontology parsing Bio::Ontology
1218 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1219 multi-report (mlib) fasta reports, support for waba and exonerate.
1221 o Bio::ClusterIO for parsing Unigene clusters
1223 o Bio::Assembly added for representing phrap and ace assembly clusters.
1225 o Rudimentary support for writing Chado XML (see
1226 GMOD project: www.gmod.org for more information)
1228 o Bio::Coordinate for mapping between different coordinate systems such
1229 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1230 features into different coordinate systems.
1232 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1233 with the get_Stream_by_query method and supports the latest
1234 NCBI eutils interface.
1236 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1237 object for extracting subsets of features : currently only
1238 supports extraction by location.
1240 1.1.1 Developer release
1242 o Deprecated modules are now listed in the DEPRECATED file
1244 o New HowTo documents located in doc/howto describing
1245 a domain of Bioperl.
1247 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1248 and all old bugs are searchable through the bugzilla interface.
1250 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1251 have been addressed.
1253 o Support for Genewise parsing in Bio::Tools::Genewise
1255 o Start of Ontology framework with Bio::Ontology
1257 o Speedup to the Bio::Root::Root object method _rearrange.
1258 A global _load_module method was implemented to simplify the
1259 dynamic loading of modules ala Bio::SeqIO::genbank. This
1260 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1263 o Several performance improvements to sequence parsing in Bio::SeqIO.
1264 Attempt to speedup by reducing object creation overhead.
1266 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1267 method for sequence retrieval with their E-utils CGI scripts.
1268 More work to support Entrez queries to their fullest is planned
1271 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1273 1.1 Developer release
1275 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1276 this separation removes some of the complexity in our test suite
1277 and separates the core modules in bioperl from those that need
1278 external programs to run.
1280 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1281 not run into trouble running the makefile
1283 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1284 read,create,and write locations for grouped/split locations
1285 (like mRNA features on genomic sequence).
1287 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1288 and PAML (codeml,aaml, etc) parsing.
1290 o Bio::Tree:: objects expanded to handle testing monophyly,
1291 paraphyly, least common ancestor, etc.
1293 o Bio::Coordinate for mapping locations from different coordinate spaces
1295 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1296 added for parsing hmmpfam and hmmsearch output.
1298 o Bio::SearchIO::Writer::TextResultWriter for outputting
1299 a pseudo-blast textfile format
1302 1.0.2 Bug fix release
1304 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1305 in this release will not work after December 2002 when NCBI
1306 shuts off the old Entrez cgi scripts. We have already fixed
1307 on our main development branch and the functionality will be
1308 available in the next stable bioperl release (1.2) slated for
1311 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1312 testset by Robin Emig. These were fixed as was the get_aln
1313 method in Bio::Search::HSP::GenericHSP to handle the extra
1314 context sequence that is provided with a FastA alignment.
1316 o Migrating differences between Bio::Search::XX::BlastXX to
1317 Bio::Search::XX::GenericXX objects. This included mechanism
1318 to retrieve whole list of HSPs from Hits and whole list of Hits from
1319 Results in addition to the current next_XX iterator methods that
1320 are available. Added seq_inds() method to GenericHSP which identifies
1321 indexes in the query or hit sequences where conserved,identical,gaps,
1322 or mismatch residues are located (adapted from Steve Chervitz's
1323 implementation in BlastHSP).
1325 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1326 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1328 o Bio::Graphics glyph set improved and extended for GBrowse release
1330 o Bio::Tree::Tree get_nodes implementation improvement thanks
1331 to Howard Ross notice performance problem when writing out
1334 o Bio::Location::Fuzzy::new named parameter -loc_type became
1335 -location_type, Bio::Location::Simple::new named parameter
1336 -seqid becamse -seq_id.
1338 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1339 was mis-detecting that gaps should be placed at the beginning of
1340 the alignment when the best alignment starts internally in the
1343 1.0.1 Bug fix release
1345 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1347 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1348 and mixed (3.3 - 3.4) versions of FASTA.
1350 o Small API change to add methods for completeness across
1351 implementations of Bio::Search objects. These new methods
1352 in the interface are implemented by the GenericXX object as well
1353 as the BlastXX objects.
1354 * Bio::Search::Result::ResultI
1355 - hits() method returns list of all Hits (next_hit is an
1358 * Bio::Search::Hit::HitI
1359 - hsps() method returns list of all HSPs (next_hsp is an
1362 o The Bio::SearchIO::Writer classes have been fixed to handle results
1363 created from either psiblast (Search::BlastXX objects) or
1364 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1365 has to be done here to make it work properly and will nee major
1368 o Bugs in Bio::Tools::HMMER fixed, including
1369 * #1178 - Root::IO destructor wasn't being called
1370 * #1034 - filter_on_cutoff now behaves properly
1372 o Bio::SeqFeature::Computation initialization args fixed and
1375 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1377 o Updated FAQ with more example based answers to typical questions
1379 o Bug #1202 was fixed which would improperly join together qual values
1380 parsed by Bio::SeqIO::qual when a trailing space was not present before
1383 1.0.0 Major Stable Release
1385 This represents a major release of bioperl with significant
1386 improvements over the 0.7.x series of releases.
1388 o Bio::Tools::Blast is officially deprecated. Please see
1389 Bio::SearchIO for BLAST and FastA parsing.
1391 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1392 Bio::LocationI objects as well as start/end.
1394 o Bio::Biblio contains modules for Bibliographic data.
1395 Bio::DB::Biblio contains the query modules. Additionally one can
1396 parse medlinexml from the ebi bibliographic query service (BQS)
1397 system and Pubmed xml from NCBI. See Martin Senger's
1398 documentation in Bio::Biblio for more information.
1400 o Bio::DB::Registry is a sequence database registry part of
1401 Open Bioinformatics Database Access. See
1402 http://obda.open-bio.org for more information.
1404 o File-based and In-Memory Sequence caching is provided by
1405 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1408 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1409 been added by Lincoln Stein.
1411 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1413 o A FAQ has been started and is included in the release to provide
1414 a starting point for frequent questions and issues.
1416 0.9.3 Developer's release
1418 o Event based parsing system improved (SearchIO). With parsers for
1419 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1420 Additionally a lazy parsing system for text and html blast reports was
1421 added and is called psiblast (name subject to change in future releases).
1423 o Bio::Search objects improved and standardized with associated Interfaces
1424 written. The concept of a search "Hit" was standardized to be called
1425 "hit" consistently and the use of "subject" was deprecated in all active
1428 o Bio::Structure added (since 0.9.1) for Protein structure objects
1429 and PDB parser to retrieve and write these structures from data files.
1431 o Several important Bio::DB::GFF bug fixes for handling features that
1432 are mapped to multiple reference points. Updated mysql adaptor
1433 so as to be able to store large (>100 megabase) chunks of DNA into
1434 Bio::DB::GFF databases.
1436 0.9.2 Developer's release
1438 o Bio::Search and Bio::SearchIO system introduced for event based
1439 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1440 in text and XML and FASTA reports in standard output format.
1442 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1443 generator is included in Bio::TreeIO::RandomTrees and a
1444 statistics module for evaluating.
1446 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1447 server for DAS servers.
1449 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1450 files. The entire BPlite system migrated to using Bio::Root::IO
1451 for the data stream.
1453 o Bio::Tools::Alignment for Consed and sequence Trimming
1456 o Bio::Structure for Protein structure information and parsing
1458 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1459 cgi-bin entry point which should be more reliable.
1461 o Bio::Map and Bio::MapIO for biological map navigation and a
1462 framework afor parsing them in. Only preliminary work here.
1464 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1465 Future work will integrate Pise and allow submission of analysis on
1468 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1469 introduced as new objects for handling Sequence Annotation
1470 information (dblinks, references, etc) and is more robust that
1473 o Bio::Tools::FASTAParser introduced.
1475 o Scripts from the bioperl script submission project and new
1476 scripts from bioperl authors are included in "scripts" directory.
1478 o Factory objects and interfaces are being introduced and are more
1481 o Bio::Root::Root introduced as the base object while
1482 Bio::Root::RootI is now simply an interface.
1484 o Bio::DB::RefSeq provides database access to copy of the NCBI
1485 RefSeq database using the EBI dbfetch script.
1487 0.9.0 Developer's release
1489 o perl version at least 5.005 is now required instead of perl 5.004
1491 o Bio::Tools::Run::RemoteBlast is available for running remote
1494 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1496 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1497 Also added are related modules UTR3, UTR5, Exon, Intron,
1498 Promotor, PolyA and Transcript.
1500 o Speedup of translate method in PrimarySeq
1502 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1503 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1505 o Various fixes to Variation toolkit
1507 o Bio::DB::EMBL provides database access to EMBL sequence data.
1508 Bio::DB::Universal provides a central way to point to indexes
1509 and dbs in a single interface.
1511 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1513 o Bio::Factory::EMBOSS is still in design phase as is
1514 Bio::Factory::ApplicationFactoryI
1516 o Dia models for bioperl design are provided in the models/ directory
1518 0.7.2 Bug fix release
1520 o documentation fixes in many modules - SYNOPSIS code verified
1521 to be runnable in many (but not all modules)
1523 o corrected MANIFEST file from 0.7.1 release
1525 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1528 o Bio::SeqIO::genbank
1529 * Correct parsing and writing of genbank format with protein data
1530 * moltype and molecule separation
1532 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1534 o Bio::SimpleAlign fixed to correctly handle consensus
1535 sequence calculation
1537 o Bio::Tools::HMMER supports hmmer 2.2g
1539 o Bio::Tools::BPlite to support report type specific parsing. Most
1540 major changes are not on the 0.7 branch.
1542 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1545 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1546 in several types of mutations:
1547 1.) AA level: deletion, complex
1548 2.) AA level: complex, inframe
1549 3.) RNA level: silent
1551 o BPbl2seq parsing of empty reports will not die, but will return
1552 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1553 $report->query() and $report->subject() methods. So an easy
1554 way to test if report was empty is to see if
1555 $report->query->seqname is undefined.
1557 0.7.1 Bug fix release
1559 o Better parsing of genbank/EMBL files especially fixing bugs
1560 related to Feature table parsing and locations on remote
1561 sequences. Additionally, species name parsing was better.
1563 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1564 which include a number of header lines.
1566 o More strict genbank and EMBL format writing (corrected number of
1567 spaces where appropriate).
1569 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1570 for related BPlite BUGS that are unresolved in this release.
1572 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1573 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1574 use expasy mirrors or EBI dbfetch cgi-script.
1576 o A moderate number of documentation improvements were made as
1577 well to provide a better code synopsis in each module.
1580 0.7 Large number of changes, including refactoring of the
1581 Object system, new parsers, new functionality and
1582 all round better system. Highlights are:
1585 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1586 Bio::Root::IO for I/O and file/handle capabilities.
1588 o Imported BPlite modules from Ian Korf for BLAST
1589 parsing. This is considered the supported BLAST parser;
1590 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1592 o Improved Sequence Feature model. Added complete location
1593 modelling (with fuzzy and compound locations). See
1594 Bio::LocationI and the modules under Bio/Location. Added
1595 support in Genbank/EMBL format parsing to completely parse
1596 feature tables for complex locations.
1598 o Moved special support for databanks etc to specialized modules under
1599 Bio/Seq/. One of these supports very large sequences through
1600 a temporary file as a backend.
1602 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1603 CDS retrieval and exon shuffling.
1605 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1607 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1608 DB/GDB (the latter has platform-specific limitations).
1610 o New analysis parser framework for HT sequence annotation (see
1611 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1613 o New Alignment IO framework
1615 o New Index modules (Swissprot)
1617 o New modules for running Blast within perl
1618 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1619 Multiple Sequence Alignment tools ClustalW and TCoffee
1620 (Bio::Tools::Run::Alignment).
1622 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1623 documentation across the package.
1625 o Much improved cross platform support. Many known incompatibilities
1626 have been fixed; however, NT and Mac do not work across the entire
1627 setup (see PLATFORMS).
1629 o Many bug fixes, code restructuring, etc. Overall stability and
1630 maintainability benefit a lot.
1632 o A total of 957 automatic tests
1637 There are very few functionality changes but a large
1638 number of software improvements/bug fixes across the package.
1640 o The EMBL/GenBank parsing are improved.
1642 o The Swissprot reading is improved. Swissprot writing
1643 is disabled as it doesn't work at all. This needs to
1644 wait for 0.7 release
1646 o BLAST reports with no hits are correctly parsed.
1648 o Several other bugs of the BLAST parser (regular expressions, ...)
1651 o Old syntax calls have been replaced with more modern syntax
1653 o Modules that did not work at all, in particular the Sim4
1654 set have been removed
1656 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1657 have improved compliance with interface specs and documentation
1659 o Mailing list documentation updated throughout the distribution
1661 o Most minor bug fixes have happened.
1663 o The scripts in /examples now work and have the modern syntax
1664 rather than the deprecated syntax
1667 0.6.1 Sun April 2 2000
1669 o Sequences can have Sequence Features attached to them
1670 - The sequence features can be read from or written to
1671 EMBL and GenBank style flat files
1673 o Objects for Annotation, including References (but not
1674 full medline abstracts), Database links and Comments are
1677 o A Species object to represent nodes on a taxonomy tree
1680 o The ability to parse HMMER and Sim4 output has been added
1682 o The Blast parsing has been improved, with better PSI-BLAST
1683 support and better overall behaviour.
1685 o Flat file indexed databases provide both random access
1686 and sequential access to their component sequences.
1688 o A CodonTable object has been written with all known
1689 CodonTables accessible.
1691 o A number of new lightweight analysis tools have been
1692 added, such as molecular weight determination.
1694 The 0.6 release also has improved software engineering
1696 o The sequence objects have been rewritten, providing more
1697 maintainable and easier to implement objects. These
1698 objects are backwardly compatible with the 0.05.1 objects
1700 o Many objects are defined in terms of interfaces and then
1701 a Perl implementation has been provided. The interfaces
1702 are found in the 'I' files (module names ending in 'I').
1704 This means that it is possible to wrap C/CORBA/SQL access
1705 as true "bioperl" objects, compatible with the rest of
1708 o The SeqIO system has been overhauled to provide better
1709 processing and perl-like automatic interpretation of <>
1712 o Many more tests have been added (a total of 172 automatic
1713 tests are now run before release).
1717 0.05.1 Tue Jun 29 05:30:44 1999
1718 - Central distribution now requires Perl 5.004. This was
1719 done to get around 5.003-based problems in Bio/Index/*
1721 - Various bug fixes in the Bio::Tools::Blast modules
1722 including better exception handling and PSI-Blast
1723 support. See Bio/Tools/Blast/CHANGES for more.
1724 - Fixed the Parse mechanism in Seq.pm to use readseq.
1725 Follow the instructions in README for how to install
1726 it (basically, you have to edit Parse.pm).
1727 - Improved documentation of Seq.pm, indicating where
1728 objects are returned and where strings are returned.
1729 - Fixed uninitialized warnings in Bio::Root::Object.pm
1730 and Bio::Tools::SeqPattern.pm.
1731 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1733 0.05 Sun Apr 25 01:14:11 1999
1734 - Bio::Tools::Blast modules have less memory problems
1735 and faster parsing. Webblast uses LWP and supports
1736 more functionality. See Bio/Tools/Blast/CHANGES for more.
1737 - The Bio::SeqIO system has been started, moving the
1738 sequence reformatting code out of the sequence object
1739 - The Bio::Index:: system has been started, providing
1740 generic index capabilities and specifically works for
1741 Fasta formatted databases and EMBL .dat formatted
1743 - The Bio::DB:: system started, providing access to
1744 databases, both via flat file + index (see above) and
1746 - The scripts/ directory, where industrial strength scripts
1747 are put has been started.
1748 - Many changes - a better distribution all round.
1750 0.04.4 Wed Feb 17 02:20:13 1999
1751 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1752 (see Bio::Tools::Blast::CHANGES).
1753 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1754 - Beefed up the t/Fasta.t test script.
1755 - Small fix in Bio::Seq::type() (now always returns a string).
1756 - Changed Bio::Root::Utilities::get_newline_char() to
1757 get_newline() since it could return more than one char.
1758 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1759 - Changed default timeout to 20 seconds (was 3).
1760 - Moved lengthy modification notes to the bottom of some files.
1761 - Fixed SimpleAlign write_fasta bug.
1762 - Beefed up SimpleAlign.t test
1764 0.04.3 Thu Feb 4 07:48:53 1999
1765 - Bio::Root::Object.pm and Global.pm now detect when
1766 script is run as a CGI and suppress output that is only
1767 appropriate when running interactively.
1768 - Bio::Root::Err::_set_context() adds name of script ($0).
1769 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1770 regarding the use of the static objects via the qw(:obj) tag.
1771 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1772 CORE::reverse, avoiding Perl warnings.
1773 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1774 example scripts (see Bio::Tools::Blast::CHANGES).
1775 - examples/seq/seqtools.pl no longer always warns about using
1776 -prot or -nucl command-line arguments; only when using the
1778 - Methods added to Bio::Root::Utilities: create_filehandle(),
1779 get_newline_char(), and taste_file() to generalize filehandle
1780 creation and autodetect newline characters in files/streams
1781 (see bug report #19).
1782 - Bio::Root::IOManager::read() now handles timeouts and uses
1783 Utilities::create_filehandle().
1784 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1785 of hardwiring in "\n".
1786 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1788 0.04.2 Wed Dec 30 02:27:36 1998
1789 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1790 (see Bio::Tools::Blast::CHANGES).
1791 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1792 to CORE::reverse (prevents ambiguous warnings with 5.005).
1793 - Appending '.tmp.bioperl' to temporary files created by
1794 Bio::Root::Utilities::compress() or uncompress() to
1795 make it easy to identify & cleanup these files as needed.
1796 - Developers: Created CVS branch release-0-04-bug from
1797 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1798 be sure to cvs checkout this branch into a clean area.
1800 0.04.1 Wed Dec 16 05:39:15 1998
1801 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1802 (see Bio::Tools::Blast::CHANGES).
1803 - Compile/SW/Makefile.PL now removes *.o and *.a files
1806 0.04 Tue Dec 8 07:49:19 1998
1807 - Lots of new modules added including:
1808 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1809 and Bio/Compile directory containing XS-linked C code for
1810 creating Smith-Waterman sequence alignments from within Perl.
1811 * Steve Chervitz's Blast distribution has been incorporated.
1812 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1813 - Bio/examples directory for demo scripts for all included modules.
1814 - Bio/t directory containing test suit for all included modules.
1815 - For changes specific to the Blast-related modules prior to
1816 incorporation in this central distribution, see the CHANGES
1817 file in the Bio/Tools/Blast directory.
1819 0.01 Tue Sep 8 14:23:22 1998
1820 - original version from central CVS tree; created by h2xs 1.18