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 * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
29 * NeXML parser fixes [fjossandon]
30 * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
31 * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
32 * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
33 * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
34 * Issue #81: small updates to make sure possible memory leaks are detected [cjfields]
35 * Issue #84: EMBL format wrapping problem [nyamned]
36 * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
42 * Bug/feature issue tracking has moved to GitHub Issues:
43 https://github.com/bioperl/bioperl-live/issues
44 * DB_File has been demoted from "required" to "recommended",
45 which should make easier for Windows users to install BioPerl
46 if they don't need that module.
50 * Bio::Search::HSP::GenericHSP
51 - Bug #3370, added a "posterior_string" method to retrieve the
52 posterior probability lines (PP) from HMMER3 reports [fjossandon]
53 - Added a "consensus_string" method to retrieve the consensus
54 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
55 * Bio::SearchIO::hmmer2
56 - The number of identical and conserved residues are now calculated
57 directly from the homology line [fjossandon]
58 - Now the Query Length and Hit Length are reported when the alignment
59 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
60 - Implemented the capture of the consensus structure lines [fjossandon]
61 * Bio::SearchIO::hmmer3
62 - The number of identical and conserved residues are now calculated
63 directly from the homology line [fjossandon]
64 - Now the Hit Length is reported when the alignment runs until the end
65 of the sequence/model ('.]' or '[]') [fjossandon]
66 - Implemented the capture of the consensus structure lines [fjossandon]
67 - Implemented the capture of the posterior probability lines [fjossandon]
68 - Completed the development of NHMMER parsing, including alignments [fjossandon]
69 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
70 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
71 "min_score", "min_bits, and "hit_filter" methods from
72 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
73 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
74 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
75 besides Blast, instead of being ignored. Added tests for all moved methods
76 using HMMER outputs and run the full test suite and everything pass [fjossandon]
77 * Bio::SeqIO::MultiFile
78 - Autodetection of file format [fangly]
79 * Bio::Tools::GuessSeqFormat:
80 - Format detection from non-seekable filehandles such as STDIN [fangly]
84 * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
85 * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
86 * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
87 * Abstract: Fixed ActivePerl incapability of removing temporary files
88 because of problems closing tied filehandles [fjossandon]
89 * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
90 because ActivePerl were producing a ".index.pag" and ".index.dir"
91 files instead of a single ".index" file (like Strawberry Perl).
92 Now those temporary files are correctly considered and deleted. [fjossandon]
93 * Test files: Added missing module requirements (DB_File and Data::Stag)
94 to several tests files that were failing because those modules were
95 not present. Now those test files are correctly skipped instead. [fjossandon]
96 * Blast: Added support to changes in bl2seq from BLAST+ output, which
97 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
98 * Phylip: Return undef in "next_aln" at file end to avoid
99 an infinite loop [yschensandiego]
100 * HMMER3: When a hit description is too long, it is truncated in
101 the Scores table. In those cases, the more complete description from
102 the Annotation line (>>) will be used [fjossandon]
103 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
104 since it is now used by HMMER3 format in alignments [fjossandon]
105 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
106 to return undef if the query/hit length is unknown (like in some
107 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
108 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
109 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
110 added support to multi-query reports, reduced code redundancy,
111 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
112 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
113 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
114 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
115 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
116 * Double-quotes on paths are needed in some places [fjossandon]
117 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
118 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
119 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
120 with the latest changes made in their own repositories [fjossandon]
121 * General synching of files with the master branch [fjossandon]
122 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
123 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
124 * Fixed broken MeSH parser [fjossandon]
125 * Fixed missing detection of format in SeqIO when given a -string [fangly]
129 * Major Windows support updates! [fjossandon]
130 * MAKER update to allow for stricter standard codon table [cjfields]
131 * Better support for circular sequences [fjossandon]
132 * Fixes for some complex location types [fjossandon]
133 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
134 * Fix bug #2978 related to BLAST report type [fjossandon]
135 * Deobfuscator fixes [DaveMessina]
139 * Address CPAN test failures [cjfields]
140 * Add BIOPROJECT support for Genbank files [hyphaltip]
141 * Better regex support for HMMER3 output [bosborne]
145 * Minor update to address CPAN test failures
149 * Remove Bio::Biblio and related files [carandraug]
150 - this cause version clashes with an independently-released
151 version of Bio::Biblio
157 * Hash randomization fixes for perl 5.18.x
158 - Note: at least one module (Bio::Map::Physical) still has a failing test;
159 this is documented in bug #3446 and has been TODO'd; we will be pulling
160 Bio::Map and similar modules out of core into separate distributions in the
161 1.7.x release series [cjfields]
165 * Bio::Seq::SimulatedRead
166 - New module to represent reads taken from other sequences [fangly]
168 - Support of Clone::Fast as a faster cloning alternative [fangly]
170 - Moved the format() and variant() methods from Bio::*IO modules to
171 Bio::Root::IO [fangly]
172 - Can now use format() to get the type of IO format in use [fangly]
174 - New regexp() method to create regular expressions from IUPAC sequences
176 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
177 - Code refresh [fangly]
179 - Added support for the Greengenes and Silva taxonomies [fangly]
180 * Bio::Tree::TreeFunctionsI
181 - get_lineage_string() represents a lineage as a string [fangly]
182 - add_trait() returns instead of reporting an error when the column
183 number is exceeded in add_trait() [fangly]
184 - Option to support tree leaves without trait [fangly]
185 - Allow ID of 0 in trait files [fangly]
186 * Bio::DB::Taxonomy::list
187 - Misc optimizations [fangly]
188 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
189 * Bio::DB::Taxonomy::*
190 - get_num_taxa() returns the number of taxa in the database [fangly]
191 * Bio::DB::Fasta and Bio::DB::Qual
192 - support indexing an arbitrary list of files [fangly]
193 - user can supply an arbitrary index file name [fangly]
194 - new option to remove index file at the end [fangly]
196 - now handles IUPAC degenerate residues [fangly]
197 * Bio::PrimarySeq and Bio::PrimarySeqI
198 - speed improvements for large sequences [Ben Woodcroft, fangly]
200 - tightened and optimized quality string validation [fangly]
202 - new method and option 'block', to create FASTA output with space
203 intervaled blocks (similar to genbank or EMBL) has been implemented.
204 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
205 in favour of the methods 'width' and 'preferred_id_type` respectively.
207 - moved from bioperl-live into the separate distribution Bio-FeatureIO
208 * Bio::SeqFeature::Annotated
209 - moved from bioperl-live into the separate distribution Bio-FeatureIO
210 * Bio::Cluster::SequenceFamily
211 - improved performance when using get_members with overlapping multiple
213 * Bio::SearchIO::hmmer3
214 - now supports nhmmer [bosborne]
218 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
219 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
220 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
221 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
222 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
223 information was lost in a multi-result blast file [Paul Cantalupo]
224 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
225 total gaps [Paul Cantalupo]
226 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
227 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
228 when end of domain indicator is split across lines [Paul Cantalupo]
229 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
231 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
232 instances where blank lines are within sequences [cjfields]
233 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
235 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
236 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
238 * Various fixes for Stockholm file indexing and processing [bosborne]
239 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
240 breaks parsing [cjfields]
241 * Fix case where Bio::Seq::Meta* objects with no meta information could not
242 be reverse-complemented [fangly]
243 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
244 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
245 when unsure that values will be numerical [fangly]
246 * Fix undef warnings in Bio::SeqIO::embl [fangly]
247 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
248 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
249 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
251 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
252 source_tag and display_name must return a string, not undef [fangly]
253 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
254 add_SeqFeature takes a single argument [fangly]
255 * Use cross-platform filenames and temporary directory in
256 Bio::DB::Taxonomy::flatfile [fangly]
257 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
258 properly identified as existing taxa in the database [fangly]
259 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
260 without also passing a lineage to store [fangly]
261 * Prevent passing a directory to the gi2taxid option (-g) of
262 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
264 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
265 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
266 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
267 object before trying to access, and no longer returns repeated sequences.
274 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
275 modules using Ace will also be deprecated [lds, cjfields]
276 * Minor bug fix release
277 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
278 * Address Build.PL issues when DBI is not present [hartzell]
279 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
280 * Remove deprecated code for perl 5.14.0 compat [cjfields]
281 * Due to schema changes and lack of support for older versions, support
282 for NeXML 0.9 is only (very) partially implemented.
283 See: https://redmine.open-bio.org/issues/3207
287 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
288 docs [genehack, cjfields]
289 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
290 module version from dist_version (probably not the best way to do this,
291 but it seems to work) [rbuels, cjfields]
294 1.6.900 April 14, 201
298 * This will probably be the last release to add significant features to
299 core modules; subsequent releases will be for bug fixes alone.
300 We are planning on a restructuring of core for summer 2011, potentially
301 as part of the Google Summer of Code. This may become BioPerl 2.0.
302 * Version bump represents 'just prior to v 1.7'. We may have point
303 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
304 This code essentially is what is on the github master branch.
308 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
310 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
311 - removal of Scalar::Util::weaken code, which was causing odd headaches
312 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
313 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
315 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
318 - bug 2515 - new contribution [Ryan Golhar, jhannah]
320 - support for reading Maq, Sam and Bowtie files [maj]
321 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
322 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
323 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
324 - bug 2726: reading/writing granularity: whole scaffold or one contig
325 at a time [Joshua Udall, fangly]
327 - Added parsing of xrefs to OBO files, which are stored as secondary
328 dbxrefs of the cvterm [Naama Menda]
329 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
330 * PAML code updated to work with PAML 4.4d [DaveMessina]
334 * [3198] - sort tabular BLAST hits by score [DaveMessina]
335 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
336 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
337 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
339 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
340 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
341 * [3164] - TreeFunctionsI syntax bug [gjuggler]
342 * [3163] - AssemblyIO speedup [fangly]
343 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
345 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
346 * [3158] - fix EMBL file mis-parsing [cjfields]
347 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
349 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
350 * [3148] - URL change for UniProt [cjfields]
351 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
352 * [3136] - HMMer3 parser fixes [kblin]
353 * [3126] - catch description [Toshihiko Akiba]
354 * [3122] - Catch instances where non-seekable filehandles were being
355 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
356 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
357 [dukeleto, rbuels, cjfields]
358 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
360 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
361 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
363 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
364 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
365 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
366 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
367 * [3086] - EMBL misparsing long tags [kblin, cjfields]
368 * [3085] - CommandExts and array of files [maj, hyphaltip]
369 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
370 for alignment slices [Ha X. Dang, cjfields]
371 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
372 * [3073] - fix parsing of GenBank files from RDP [cjfields]
373 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
374 * [3064] - All-gap midline BLAST report issues [cjfields]
375 * [3063] - BLASt report RID [Razi Khaja, cjfields]
376 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
377 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
378 * [3039] - correct Newick output root node branch length [gjuggler,
380 * [3038] - SELEX alignment error [Bernd, cjfields]
381 * [3033] - PrimarySeq ID setting [Bernd, maj]
382 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
383 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
384 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
385 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
386 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
387 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
388 PAML 4.4d [DaveMessina]
389 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
391 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
392 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
393 * [3017] - using threads with Bio::DB::GenBank [cjfields]
394 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
395 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
396 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
397 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
398 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
400 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
401 * [2977] - TreeIO issues [DaveMessina]
402 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
403 * [2944] - Bio::Tools::GFF score [cjfields]
404 * [2942] - correct MapTiling output [maj]
405 * [2939] - PDB residue insertion codes [John May, maj]
406 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
407 * [2928] - GuessSeqFormat raw [maj]
408 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
409 * [2922] - open() directive issue [cjfields]
410 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
411 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
412 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
413 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
415 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
416 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
417 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
418 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
419 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
420 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
421 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
422 * [2758] - Bio::AssemblyIO ace problems [fangly]
423 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
424 * [2726] - ace file IO [Josh, fangly]
425 * [2700] - Refactor Build.PL [cjfields]
426 * [2673] - addition of simple Root-based clone() method [cjfields]
427 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
428 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
429 * [2594] - Bio::Species memory leak [cjfields]
430 * [2515] - GenBank XML parser [jhannah]
431 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
432 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
433 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
435 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
439 * Bio::Expression modules - these were originally designed to go with the
440 bioperl-microarray suite of tools, however they have never been completed
441 and so have been removed from the distribution. The original code has
442 been moved into the inactive bioperl-microarray suite. [cjfields]
446 * Repository moved from Subversion (SVN) to
447 http://github.com/bioperl/bioperl-live [cjfields]
448 * Bug database has moved to Redmine (https://redmine.open-bio.org)
449 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
450 Thieme have been moved to their own distribution (Bio-Microarray).
453 1.6.1 Sept. 29, 2009 (point release)
454 * No change from last alpha except VERSION and doc updates [cjfields]
456 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
457 * Fix for silent OBDA bug related to FASTA validation [cjfields]
459 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
460 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
461 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
463 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
465 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
466 * WinXP test fixes [cjfields, maj]
467 * BioPerl.pod added for descriptive information, fixes CPAN indexing
469 * Minor doc fixes [cjfields]
471 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
472 * Fix tests failing due to merging issues [cjfields]
473 * More documentation updates for POD parsing [cjfields]
475 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
477 - fix YAML meta data generation [cjfields]
479 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
480 * Bio::Align::DNAStatistics
481 - fix divide by zero problem [jason]
483 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
484 * Bio::AlignIO::stockholm
485 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
486 * Bio::Assembly::Tools::ContigSpectrum
487 - function to score contig spectrum [fangly]
488 * Bio::DB::EUtilities
489 - small updates [cjfields]
491 - berkeleydb database now autoindexes wig files and locks correctly
494 - various small updates for stability; tracking changes to LANL
495 database interface [maj]
496 * Bio::DB::SeqFeature (lots of updates and changes)
497 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
498 - bug 2835 - patch [Dan Bolser]
499 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
501 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
502 * Bio::Factory::FTLocationFactory
503 - mailing list bug fix [cjfields]
505 - performance work on column_from_residue_number [hartzell]
506 * Bio::Matrix::IO::phylip
507 - bug 2800 - patch to fix phylip parsing [Wei Zou]
509 - Google Summer of Code project from Chase Miller - parsers for Nexml
510 file format [maj, chmille4]
512 - Make Individual, Population, Marker objects AnnotatableI [maj]
513 - simplify LD code [jason]
515 - deal with empty intersection [jason]
517 - significant overhaul of Bio::Restriction system: complete support for
518 external and non-palindromic cutters. [maj]
520 - CPANPLUS support, no automatic installation [sendu]
522 - allow IO::String (regression fix) [cjfields]
523 - catch unintentional undef values [cjfields]
524 - throw if non-fh is passed to -fh [maj]
525 * Bio::Root::Root/RootI
526 - small debugging and core fixes [cjfields]
528 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
529 * Bio::Root::Utilities
530 - bug 2737 - better warnings [cjfields]
532 - tiling completely refactored, HOWTO added [maj]
533 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
534 will deprecate usage of the older tiling code in the next BioPerl
536 - small fixes [cjfields]
538 - Infernal 1.0 output now parsed [cjfields]
539 - new parser for gmap -f9 output [hartzell]
540 - bug 2852 - fix infinite loop in some output [cjfields]
541 - blastxml output now passes all TODO tests [cjfields]
542 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
543 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
544 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
545 * Bio::Seq::LargePrimarySeq
546 - delete tempdirs [cjfields]
547 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
549 - extract regions based on quality threshold value [Dan Bolser, heikki]
550 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
551 * Bio::SeqFeature::Lite
552 - various Bio::DB::SeqFeature-related fixes [lstein]
553 * Bio::SeqFeature::Tools::TypeMapper
554 - additional terms for GenBank to SO map [scain]
555 * Bio::SeqIO::chadoxml
556 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
558 - support for CDS records [dave_messina, Sylvia]
560 - complete refactoring to handle all FASTQ variants, perform validation,
561 write output. API now conforms with other Bio* parsers and the rest of
562 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
564 * Bio::SeqIO::genbank
565 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
566 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
567 * Bio::SeqIO::largefasta
568 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
570 - add option for 'single' and 'multiple'
572 - bug 2881 - fix scf round-tripping [Adam Søgren]
574 - bug 2766, 2810 - copy over tags from features, doc fixes [David
577 - bug 2793 - patch for add_seq index issue [jhannah, maj]
578 - bug 2801 - throw if args are required [cjfields]
579 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
580 [Tristan Lefebure, maj]
581 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
582 - fix POD and add get_SeqFeatures filter [maj]
583 * Bio::Tools::dpAlign
584 - add support for LocatableSeq [ymc]
585 - to be moved to a separate distribution [cjfields, rbuels]
586 * Bio::Tools::EUtilities
587 - fix for two bugs from mail list [Adam Whitney, cjfields]
588 - add generic ItemContainerI interface for containing same methods
591 - fix up code, add more warnings [cjfields]
592 - to be moved to a separate distribution [cjfields, rbuels]
593 * Bio::Tools::Primer3
594 - bug 2862 - fenceposting issue fixed [maj]
595 * Bio::Tools::Run::RemoteBlast
596 - tests for remote RPS-BLAST [mcook]
597 * Bio::Tools::SeqPattern
598 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
599 * Bio::Tools::tRNAscanSE
600 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
602 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
603 * Bio::Tree::Statistics
604 - several methods for calculating Fitch-based score, internal trait
605 values, statratio(), sum of leaf distances [heikki]
607 - bug 2869 - add docs indicating edge case where nodes can be
608 prematurely garbage-collected [cjfields]
609 - add as_text() function to create Tree as a string in specified format
611 * Bio::Tree::TreeFunctionsI
612 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
614 * Bio::TreeIO::newick
615 - fix small semicolon issue [cjfields]
617 - update to bp_seqfeature_load for SQLite [lstein]
618 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
619 - fastam9_to_table - fix for MPI output [jason]
620 - gccalc - total stats [jason]
622 - POD cleanup re: FEEDBACK section [maj, cjfields]
623 - cleanup or fix dead links [cjfields]
624 - Use of no_* methods (indicating 'number of something') is deprecated
625 in favor of num_* [cjfields]
626 - lots of new tests for the above bugs and refactors [everyone!]
627 - new template for Komodo text editor [cjfields]
630 * Feature/Annotation rollback
631 - Problematic changes introduced prior to the 1.5 release have been
632 rolled back. These changes led to subtle bugs involving operator
633 overloading and interface methods.
634 - Behavior is very similar to that for BioPerl 1.4, with tag values
635 being stored generically as simple scalars. Results in a modest
638 - Split into a separate distribution on CPAN, primarily so development
639 isn't reliant on a complete BioPerl release.
640 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
641 is only available via Subversion (via bioperl-live main trunk)
643 - Common test bed for all BioPerl modules
645 - Common Module::Build-based subclass for all BioPerl modules
646 * Bio::DB::EUtilities
647 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
648 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
649 and user agent request posting and retrieval
650 * Test implementation and reorganization
651 - Tests have been reorganized into groups based on classes or use
653 - Automated test coverage is now online:
654 http://www.bioperl.org/wiki/Test_Coverage
655 - After this release, untested modules will be moved into a
656 separate developer distribution until tests can be derived.
657 Also, new modules to be added are expected to have a test suite
658 and adequate test coverage.
660 1.5.2 Developer release
662 Full details of changes since 1.5.1 are available online at:
663 http://www.bioperl.org/wiki/Change_log
664 The following represents a brief overview of the most important changes.
667 - Overhaul. Brand new system fully allows markers to have multiple
668 positions on multiple maps, and to have relative positions. Should be
672 - This module and all the modules in the Taxonomy directory now
673 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
678 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
680 * New methods ancestor(), each_Descendent() and _handle_internal_id().
682 * Allows for different database modules to create Bio::Taxon objects
683 with the same internal id when the same taxon is requested from each.
686 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
688 * No longer includes the fake root node 'root'; there are multiple roots
689 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
692 * get_node() has new option -full
694 * Caches data retrieved from website
697 - Now a Bio::Taxon. Carries out the species name -> specific name munging
698 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
699 backward compatability in species() method.
701 o Bio::Search and Bio::SearchIO
702 - Overhaul. The existing system has been sped up via some minor changes
703 (mostly gain-of-function to the API). Bio::PullParserI is introduced
704 as a potential eventual replacment for the existing system, though as
705 yet only a Hmmpfam parser exists written using it.
708 1.5.1 Developer release
710 o Major problem with how Annotations were written out with
711 Bio::Seq is fixed by reverting to old behavior for
712 Bio::Annotation objects.
717 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
718 expect at l east 9 spaces at the beginning of a line to
719 indicate line wrapping.
721 * Treat multi-line SOURCE sections correctly, this defect broke
722 both common_name() and classification()
724 * parse swissprot fields in genpept file
726 * parse WGS genbank records
729 * Changed regexp for ID line. The capturing parentheses are
730 the same, the difference is an optional repeated-not-semi-
731 colon expression following the captured \S+. This means the
732 regexp works when the division looks like /PRO;/ or when the
733 division looks like /ANG ;/ - the latter is from EMBL
736 * fix ID line parsing: the molecule string can have spaces in
737 it. Like: "genomic DNA"
739 - swiss.pm: bugs #1727, #1734
742 * Added parser for entrezgene ASN1 (text format) files.
743 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
747 - maf.pm coordinate problem fixed
749 o Bio::Taxonomy and Bio::DB::Taxonomy
751 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
752 can be done via Web without downloading all the sequence.
754 o Bio::Tools::Run::RemoteBlast supports more options and complies
755 to changes to the NCBI interface. It is reccomended that you
756 retrieve the data in XML instead of plain-text BLAST report to
757 insure proper parsing and retrieval of all information as NCBI
758 fully expects to change things in the future.
760 o Bio::Tree and Bio::TreeIO
762 - Fixes so that re-rooting a tree works properly
764 - Writing out nhx format from a newick/nexus file will properly output
765 bootstrap information. The use must move the internal node labels over
767 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
768 $node->bootstrap($node->id);
771 - Nexus parsing is much more flexible now, does not care about
774 - Cladogram drawing module in Bio::Tree::Draw
776 - Node height and depth now properly calculated
778 - fix tree pruning algorithm so that node with 1 child gets merged
780 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
781 bugs and improvements were added, see Gbrowse mailing list for most of
784 o Bio::DB::GFF partially supports GFF3. See information about
785 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
787 o Better location parsing in Bio::Factory::FTLocationFactory -
788 this is part of the engine for parsing EMBL/GenBank feature table
789 locations. Nested join/order-by/complement are allowed now
791 o Bio::PrimarySeqI->translate now takes named parameters
793 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
794 reconstruction) is now supported. Parsing different models and
795 branch specific parametes are now supported.
797 o Bio::Factory::FTLocationFactory - parse hierarchical locations
800 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
801 for getter/setter functions
805 - blast bug #1739; match scientific notation in score
806 and possible e+ values
808 - blast.pm reads more WU-BLAST parameters and parameters, match
809 a full database pathname,
811 - Handle NCBI WEB and newer BLAST formats specifically
812 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
814 - psl off-by-one error fixed
816 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
817 and HSPs can be constructed from them.
819 - HSPs query/hit now have a seqdesc field filled out (this was
820 always available via $hit->description and
821 $result->query_description
823 - hmmer.pm can parse -A0 hmmpfam files
825 - Writer::GbrowseGFF more customizeable.
827 o Bio::Tools::Hmmpfam
828 make e-value default score displayed in gff, rather than raw score
829 allow parse of multiple records
832 1.5 Developer release
834 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
835 provide Jukes-Cantor and Kimura pairwise distance methods,
838 o Bio::AlignIO support for "po" format of POA, and "maf";
839 Bio::AlignIO::largemultifasta is a new alternative to
840 Bio::AlignIO::fasta for temporary file-based manipulation of
841 particularly large multiple sequence alignments.
843 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
844 be treated similarly as an assembled contig.
846 o Bio::CodonUsage provides new rare_codon() and probable_codons()
847 methods for identifying particular codons that encode a given
850 o Bio::Coordinate::Utils provides new from_align() method to build
851 a Bio::Coordinate pair directly from a
852 Bio::Align::AlignI-conforming object.
854 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
855 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
856 web service using standard Pubmed query syntax, and retrieve
859 o Bio::DB::GFF has various sundry bug fixes.
861 o Bio::FeatureIO is a new SeqIO-style subsystem for
862 writing/reading genomic features to/from files. I/O classes
863 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
864 classes only read/write Bio::SeqFeature::Annotated objects.
865 Notably, the GFF v3 class requires features to be typed into the
868 o Bio::Graph namespace contains new modules for manipulation and
869 analysis of protein interaction graphs.
871 o Bio::Graphics has many bug fixes and shiny new glyphs.
873 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
874 indexing for HMMER reports and FASTA qual files, respectively.
876 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
877 new objects that can be placed within a Bio::Map::MapI-compliant
878 genetic/physical map; Bio::Map::Physical provides a new physical
879 map type; Bio::MapIO::fpc provides finger-printed clone mapping
882 o Bio::Matrix::PSM provide new support for postion-specific
883 (scoring) matrices (e.g. profiles, or "possums").
885 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
886 be instantiated without explicitly using Bio::OntologyIO. This
887 is possible through changes to Bio::Ontology::OntologyStore to
888 download ontology files from the web as necessary. Locations of
889 ontology files are hard-coded into
890 Bio::Ontology::DocumentRegistry.
892 o Bio::PopGen includes many new methods and data types for
893 population genetics analyses.
895 o New constructor to Bio::Range, unions(). Given a list of
896 ranges, returns another list of "flattened" ranges --
897 overlapping ranges are merged into a single range with the
898 mininum and maximum coordinates of the entire overlapping group.
900 o Bio::Root::IO now supports -url, in addition to -file and -fh.
901 The new -url argument allows one to specify the network address
902 of a file for input. -url currently only works for GET
903 requests, and thus is read-only.
905 o Bio::SearchIO::hmmer now returns individual Hit objects for each
906 domain alignment (thus containing only one HSP); previously
907 separate alignments would be merged into one hit if the domain
908 involved in the alignments was the same, but this only worked
909 when the repeated domain occured without interruption by any
910 other domain, leading to a confusing mixture of Hit and HSP
913 o Bio::Search::Result::ResultI-compliant report objects now
914 implement the "get_statistics" method to access
915 Bio::Search::StatisticsI objects that encapsulate any
916 statistical parameters associated with the search (e.g. Karlin's
917 lambda for BLAST/FASTA).
919 o Bio::Seq::LargeLocatableSeq combines the functionality already
920 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
922 o Bio::SeqFeature::Annotated is a replacement for
923 Bio::SeqFeature::Generic. It breaks compliance with the
924 Bio::SeqFeatureI interface because the author was sick of
925 dealing with untyped annotation tags. All
926 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
927 compliant, and accessible through Bio::Annotation::Collection.
929 o Bio::SeqFeature::Primer implements a Tm() method for primer
930 melting point predictions.
932 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
933 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
935 o Bio::Taxonomy::Node now implements the methods necessary for
936 Bio::Species interoperability.
938 o Bio::Tools::CodonTable has new reverse_translate_all() and
939 make_iupac_string() methods.
941 o Bio::Tools::dpAlign now provides sequence profile alignments.
943 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
945 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
948 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
949 for designing small inhibitory RNA.
951 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
952 methods based on a distance matrix.
954 o Bio::Tree::Statistics provides an assess_bootstrap() method to
955 calculate bootstrap support values on a guide tree topology,
956 based on provided bootstrap tree topologies.
958 o Bio::TreeIO now supports the Pagel (PAG) tree format.
964 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
966 o Bio::Graphics will work with gd1 or gd2
969 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
971 - blast.pm Parse multi-line query fields properly
972 - small speed improvements to blasttable.pm and others
974 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
975 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
976 supporting more complex queries
979 1.4. Stable major release
981 Since initial 1.2.0, 3000 separate changes have been made to make this release.
983 o installable scripts
985 o global module version from Bio::Root:Version
988 - major improvements; SVG support
991 - population genetics
992 - support several population genetics types of questions.
993 - Tests for statistical neutrality of mutations
994 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
995 Tests of population structure (Wright's F-statistic: Fst) is in
996 Bio::PopGen::PopStats. Calculating composite linkage
997 disequilibrium (LD) is available in Bio::PopGen::Statistics as
999 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
1000 and csv (comma delimited formatted) data.
1002 - a directory for implementing population simulations has
1003 been added Bio::PopGen::Simulation and 2 simulations - a
1004 Coalescent and a simple single-locus multi-allele genetic drift
1005 simulation have been provided. This replaces the code in
1006 Bio::Tree::RandomTree which has been deprecated until proper
1007 methods for generating random phylogenetic trees are
1011 - new restrion analysis modules
1013 o Bio::Tools::Analysis
1014 - web based DNA and Protein analysis framework and several
1018 - per residue annotable sequences
1021 - Bio::Matrix::PSM - Position Scoring Matrix
1022 - Bio::Matrix::IO has been added for generalized parsing of
1023 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
1024 initial implementations for parsing BLOSUM/PAM and Phylip
1025 Distance matricies respectively. A generic matrix
1026 implementation for general use was added in
1027 Bio::Matrix::Generic.
1034 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1035 - small inhibitory RNA
1037 o Bio::SeqFeature::Tools
1038 - seqFeature mapping tools
1039 - Bio::SeqFeature::Tools::Unflattener.pm
1040 -- deal with mapping GenBank feature collections into
1041 Chado/GFF3 processable feature sets (with SO term mappings)
1043 o Bio::Tools::dpAlign
1044 - pure perl dynamic programming sequence alignment
1047 o new Bio::SearchIO formats
1048 - axt and psl: UCSC formats.
1049 - blasttable: NCBI -m 8 or -m 9 format from blastall
1051 o new Bio::SeqIO formats
1052 - chado, tab, kegg, tigr, game
1053 - important fixes for old modules
1057 o improved Bio::Tools::Genewise
1059 o Bio::SeqIO now can recongnize sequence formats automatically from
1062 o new parsers in Bio::Tools:
1063 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1065 o Bio::DB::Registry bugs fixed
1066 - BerkeleyDB-indexed flat files can be used by the OBDA system
1067 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1068 used by the OBDA system
1070 o several new HOWTOs
1071 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1074 o hundreds of new and improved files
1078 o Bio::Tree::AlleleNode has been updated to be a container of
1079 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1084 1.2.3 Stable release update
1085 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1087 o Bug #1477 - Sel --> Sec abbreviation fixed
1088 o Fix bug #1487 where paring in-between locations when
1089 end < start caused the FTLocationFactory logic to fail.
1090 o Fix bug #1489 which was not dealing with keywords as an
1091 arrayref properly (this is fixed on the main trunk because
1092 keywords returns a string and the array is accessible via
1094 o Bio::Tree::Tree memory leak (bug #1480) fixed
1095 Added a new initialization option -nodelete which
1096 won't try and cleanup the containing nodes if this
1098 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1099 this was only present on the branch for the 1.2.1 and 1.2.2 series
1100 - Also merged main trunk changes to the branch which make
1101 newick -> nhx round tripping more effective (storing branch length
1102 and bootstrap values in same locate for NodeNHX and Node
1103 implementations.) Fixes to TreeIO parsing for labeled internal
1104 also required small changes to TreeIO::nhx. Improved
1105 tests for this module as well.
1107 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1108 gapped blast properly (was losing hit significance values due to
1109 the extra unexpeted column).
1110 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1111 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1112 although doesn't try to correct it - will get the negative
1113 number for you. Added a test for this as well.
1114 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1115 has no top-level family classification scores but does have scores and
1116 alignments for individual domains.
1117 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1118 regular expression to match the line was missing the possibility of
1119 an extra space. This is rare, which is why we probably did not
1121 - BLAST parsing picks up more of the statistics/parameter fields
1122 at the bottom of reports. Still not fully complete.
1123 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1124 were fixed to include many improvements and added flexiblity
1125 in outputting the files. Bug #1495 was also fixed in the process.
1127 - Update for GFF3 compatibility.
1128 - Added scripts for importing from UCSC and GenBank.
1129 - Added a 1.2003 version number.
1132 - Added a 1.2003 version number.
1133 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1134 properly writing keywords out.
1135 o Bio::SeqIO::genbank
1136 - Fixed bug/enhancement #1513 where dates of
1137 the form D-MMM-YYYY were not parsed. Even though this is
1138 invalid format we can handle it - and also cleanup the date
1139 string so it is properly formatted.
1140 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1141 and written with Genbank format. Similarly bug #1515 is fixed to
1142 parse in the ORIGIN text.
1143 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1144 to specify the ID type, one of (accession accession.version
1145 display primary). See Bio::SeqIO::preferred_id_type method
1146 documentation for more information.
1147 o Unigene parsing updated to handle file format changes by NCBI
1149 1.2.2 Stable release update
1151 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1152 - auto-discover ontology name
1153 - bug in parsing relationships when certain characters are in the term
1154 - fixed hard-coded prefix for term identifiers
1155 - various smaller issues
1157 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1158 of Bio::Ontology::TermI
1160 o brought the OBDA Registry code up to latest specs
1164 - accession number retrieval fixed
1166 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1168 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1169 #1459 which now properly report alignment start/end info
1170 for translated BLAST/FASTA searches.
1172 o Bio::TreeIO::newick can parse labeled internal nodes
1174 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1175 for BLASTX if if you provide -report_type => 'BLASTX' when
1176 initializing a BPbl2seq object. Bioperl 1.3 will have better
1177 support for bl2seq in the SearchIO system.
1179 o Bio::Root::IO support a -noclose boolean flag which will not
1180 close a filehandle upon object cleanup - useful when sharing
1181 a filehandle among objects. Additionally code added s.t.
1182 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1184 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1186 o Bio::SeqIO::genbank
1187 - bug #1456 fixed which generated extra sequence lines
1188 - write moltype correctly for genpept
1190 1.2.1 Stable release update
1192 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1194 o Addition from main trunk of Ontology objects, principly to allow
1195 BioSQL releases against 1.2.1
1197 o Fixes and cleanup of Bio::Coordinate modules
1199 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1200 the primary accession number
1202 o Other bug fixes, including bpindex GenBank fix
1204 o Bio::SeqIO::genbank bug #1389 fixed
1206 1.2 Stable major release
1208 o More functionality added to Bio::Perl, the newbie module
1210 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1211 Support for New Hampshire Extended (NHX) format parsing.
1213 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1214 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1217 o New ontology parsing Bio::Ontology
1219 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1220 multi-report (mlib) fasta reports, support for waba and exonerate.
1222 o Bio::ClusterIO for parsing Unigene clusters
1224 o Bio::Assembly added for representing phrap and ace assembly clusters.
1226 o Rudimentary support for writing Chado XML (see
1227 GMOD project: www.gmod.org for more information)
1229 o Bio::Coordinate for mapping between different coordinate systems such
1230 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1231 features into different coordinate systems.
1233 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1234 with the get_Stream_by_query method and supports the latest
1235 NCBI eutils interface.
1237 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1238 object for extracting subsets of features : currently only
1239 supports extraction by location.
1241 1.1.1 Developer release
1243 o Deprecated modules are now listed in the DEPRECATED file
1245 o New HowTo documents located in doc/howto describing
1246 a domain of Bioperl.
1248 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1249 and all old bugs are searchable through the bugzilla interface.
1251 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1252 have been addressed.
1254 o Support for Genewise parsing in Bio::Tools::Genewise
1256 o Start of Ontology framework with Bio::Ontology
1258 o Speedup to the Bio::Root::Root object method _rearrange.
1259 A global _load_module method was implemented to simplify the
1260 dynamic loading of modules ala Bio::SeqIO::genbank. This
1261 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1264 o Several performance improvements to sequence parsing in Bio::SeqIO.
1265 Attempt to speedup by reducing object creation overhead.
1267 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1268 method for sequence retrieval with their E-utils CGI scripts.
1269 More work to support Entrez queries to their fullest is planned
1272 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1274 1.1 Developer release
1276 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1277 this separation removes some of the complexity in our test suite
1278 and separates the core modules in bioperl from those that need
1279 external programs to run.
1281 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1282 not run into trouble running the makefile
1284 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1285 read,create,and write locations for grouped/split locations
1286 (like mRNA features on genomic sequence).
1288 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1289 and PAML (codeml,aaml, etc) parsing.
1291 o Bio::Tree:: objects expanded to handle testing monophyly,
1292 paraphyly, least common ancestor, etc.
1294 o Bio::Coordinate for mapping locations from different coordinate spaces
1296 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1297 added for parsing hmmpfam and hmmsearch output.
1299 o Bio::SearchIO::Writer::TextResultWriter for outputting
1300 a pseudo-blast textfile format
1303 1.0.2 Bug fix release
1305 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1306 in this release will not work after December 2002 when NCBI
1307 shuts off the old Entrez cgi scripts. We have already fixed
1308 on our main development branch and the functionality will be
1309 available in the next stable bioperl release (1.2) slated for
1312 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1313 testset by Robin Emig. These were fixed as was the get_aln
1314 method in Bio::Search::HSP::GenericHSP to handle the extra
1315 context sequence that is provided with a FastA alignment.
1317 o Migrating differences between Bio::Search::XX::BlastXX to
1318 Bio::Search::XX::GenericXX objects. This included mechanism
1319 to retrieve whole list of HSPs from Hits and whole list of Hits from
1320 Results in addition to the current next_XX iterator methods that
1321 are available. Added seq_inds() method to GenericHSP which identifies
1322 indexes in the query or hit sequences where conserved,identical,gaps,
1323 or mismatch residues are located (adapted from Steve Chervitz's
1324 implementation in BlastHSP).
1326 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1327 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1329 o Bio::Graphics glyph set improved and extended for GBrowse release
1331 o Bio::Tree::Tree get_nodes implementation improvement thanks
1332 to Howard Ross notice performance problem when writing out
1335 o Bio::Location::Fuzzy::new named parameter -loc_type became
1336 -location_type, Bio::Location::Simple::new named parameter
1337 -seqid becamse -seq_id.
1339 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1340 was mis-detecting that gaps should be placed at the beginning of
1341 the alignment when the best alignment starts internally in the
1344 1.0.1 Bug fix release
1346 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1348 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1349 and mixed (3.3 - 3.4) versions of FASTA.
1351 o Small API change to add methods for completeness across
1352 implementations of Bio::Search objects. These new methods
1353 in the interface are implemented by the GenericXX object as well
1354 as the BlastXX objects.
1355 * Bio::Search::Result::ResultI
1356 - hits() method returns list of all Hits (next_hit is an
1359 * Bio::Search::Hit::HitI
1360 - hsps() method returns list of all HSPs (next_hsp is an
1363 o The Bio::SearchIO::Writer classes have been fixed to handle results
1364 created from either psiblast (Search::BlastXX objects) or
1365 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1366 has to be done here to make it work properly and will nee major
1369 o Bugs in Bio::Tools::HMMER fixed, including
1370 * #1178 - Root::IO destructor wasn't being called
1371 * #1034 - filter_on_cutoff now behaves properly
1373 o Bio::SeqFeature::Computation initialization args fixed and
1376 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1378 o Updated FAQ with more example based answers to typical questions
1380 o Bug #1202 was fixed which would improperly join together qual values
1381 parsed by Bio::SeqIO::qual when a trailing space was not present before
1384 1.0.0 Major Stable Release
1386 This represents a major release of bioperl with significant
1387 improvements over the 0.7.x series of releases.
1389 o Bio::Tools::Blast is officially deprecated. Please see
1390 Bio::SearchIO for BLAST and FastA parsing.
1392 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1393 Bio::LocationI objects as well as start/end.
1395 o Bio::Biblio contains modules for Bibliographic data.
1396 Bio::DB::Biblio contains the query modules. Additionally one can
1397 parse medlinexml from the ebi bibliographic query service (BQS)
1398 system and Pubmed xml from NCBI. See Martin Senger's
1399 documentation in Bio::Biblio for more information.
1401 o Bio::DB::Registry is a sequence database registry part of
1402 Open Bioinformatics Database Access. See
1403 http://obda.open-bio.org for more information.
1405 o File-based and In-Memory Sequence caching is provided by
1406 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1409 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1410 been added by Lincoln Stein.
1412 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1414 o A FAQ has been started and is included in the release to provide
1415 a starting point for frequent questions and issues.
1417 0.9.3 Developer's release
1419 o Event based parsing system improved (SearchIO). With parsers for
1420 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1421 Additionally a lazy parsing system for text and html blast reports was
1422 added and is called psiblast (name subject to change in future releases).
1424 o Bio::Search objects improved and standardized with associated Interfaces
1425 written. The concept of a search "Hit" was standardized to be called
1426 "hit" consistently and the use of "subject" was deprecated in all active
1429 o Bio::Structure added (since 0.9.1) for Protein structure objects
1430 and PDB parser to retrieve and write these structures from data files.
1432 o Several important Bio::DB::GFF bug fixes for handling features that
1433 are mapped to multiple reference points. Updated mysql adaptor
1434 so as to be able to store large (>100 megabase) chunks of DNA into
1435 Bio::DB::GFF databases.
1437 0.9.2 Developer's release
1439 o Bio::Search and Bio::SearchIO system introduced for event based
1440 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1441 in text and XML and FASTA reports in standard output format.
1443 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1444 generator is included in Bio::TreeIO::RandomTrees and a
1445 statistics module for evaluating.
1447 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1448 server for DAS servers.
1450 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1451 files. The entire BPlite system migrated to using Bio::Root::IO
1452 for the data stream.
1454 o Bio::Tools::Alignment for Consed and sequence Trimming
1457 o Bio::Structure for Protein structure information and parsing
1459 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1460 cgi-bin entry point which should be more reliable.
1462 o Bio::Map and Bio::MapIO for biological map navigation and a
1463 framework afor parsing them in. Only preliminary work here.
1465 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1466 Future work will integrate Pise and allow submission of analysis on
1469 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1470 introduced as new objects for handling Sequence Annotation
1471 information (dblinks, references, etc) and is more robust that
1474 o Bio::Tools::FASTAParser introduced.
1476 o Scripts from the bioperl script submission project and new
1477 scripts from bioperl authors are included in "scripts" directory.
1479 o Factory objects and interfaces are being introduced and are more
1482 o Bio::Root::Root introduced as the base object while
1483 Bio::Root::RootI is now simply an interface.
1485 o Bio::DB::RefSeq provides database access to copy of the NCBI
1486 RefSeq database using the EBI dbfetch script.
1488 0.9.0 Developer's release
1490 o perl version at least 5.005 is now required instead of perl 5.004
1492 o Bio::Tools::Run::RemoteBlast is available for running remote
1495 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1497 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1498 Also added are related modules UTR3, UTR5, Exon, Intron,
1499 Promotor, PolyA and Transcript.
1501 o Speedup of translate method in PrimarySeq
1503 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1504 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1506 o Various fixes to Variation toolkit
1508 o Bio::DB::EMBL provides database access to EMBL sequence data.
1509 Bio::DB::Universal provides a central way to point to indexes
1510 and dbs in a single interface.
1512 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1514 o Bio::Factory::EMBOSS is still in design phase as is
1515 Bio::Factory::ApplicationFactoryI
1517 o Dia models for bioperl design are provided in the models/ directory
1519 0.7.2 Bug fix release
1521 o documentation fixes in many modules - SYNOPSIS code verified
1522 to be runnable in many (but not all modules)
1524 o corrected MANIFEST file from 0.7.1 release
1526 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1529 o Bio::SeqIO::genbank
1530 * Correct parsing and writing of genbank format with protein data
1531 * moltype and molecule separation
1533 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1535 o Bio::SimpleAlign fixed to correctly handle consensus
1536 sequence calculation
1538 o Bio::Tools::HMMER supports hmmer 2.2g
1540 o Bio::Tools::BPlite to support report type specific parsing. Most
1541 major changes are not on the 0.7 branch.
1543 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1546 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1547 in several types of mutations:
1548 1.) AA level: deletion, complex
1549 2.) AA level: complex, inframe
1550 3.) RNA level: silent
1552 o BPbl2seq parsing of empty reports will not die, but will return
1553 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1554 $report->query() and $report->subject() methods. So an easy
1555 way to test if report was empty is to see if
1556 $report->query->seqname is undefined.
1558 0.7.1 Bug fix release
1560 o Better parsing of genbank/EMBL files especially fixing bugs
1561 related to Feature table parsing and locations on remote
1562 sequences. Additionally, species name parsing was better.
1564 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1565 which include a number of header lines.
1567 o More strict genbank and EMBL format writing (corrected number of
1568 spaces where appropriate).
1570 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1571 for related BPlite BUGS that are unresolved in this release.
1573 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1574 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1575 use expasy mirrors or EBI dbfetch cgi-script.
1577 o A moderate number of documentation improvements were made as
1578 well to provide a better code synopsis in each module.
1581 0.7 Large number of changes, including refactoring of the
1582 Object system, new parsers, new functionality and
1583 all round better system. Highlights are:
1586 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1587 Bio::Root::IO for I/O and file/handle capabilities.
1589 o Imported BPlite modules from Ian Korf for BLAST
1590 parsing. This is considered the supported BLAST parser;
1591 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1593 o Improved Sequence Feature model. Added complete location
1594 modelling (with fuzzy and compound locations). See
1595 Bio::LocationI and the modules under Bio/Location. Added
1596 support in Genbank/EMBL format parsing to completely parse
1597 feature tables for complex locations.
1599 o Moved special support for databanks etc to specialized modules under
1600 Bio/Seq/. One of these supports very large sequences through
1601 a temporary file as a backend.
1603 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1604 CDS retrieval and exon shuffling.
1606 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1608 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1609 DB/GDB (the latter has platform-specific limitations).
1611 o New analysis parser framework for HT sequence annotation (see
1612 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1614 o New Alignment IO framework
1616 o New Index modules (Swissprot)
1618 o New modules for running Blast within perl
1619 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1620 Multiple Sequence Alignment tools ClustalW and TCoffee
1621 (Bio::Tools::Run::Alignment).
1623 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1624 documentation across the package.
1626 o Much improved cross platform support. Many known incompatibilities
1627 have been fixed; however, NT and Mac do not work across the entire
1628 setup (see PLATFORMS).
1630 o Many bug fixes, code restructuring, etc. Overall stability and
1631 maintainability benefit a lot.
1633 o A total of 957 automatic tests
1638 There are very few functionality changes but a large
1639 number of software improvements/bug fixes across the package.
1641 o The EMBL/GenBank parsing are improved.
1643 o The Swissprot reading is improved. Swissprot writing
1644 is disabled as it doesn't work at all. This needs to
1645 wait for 0.7 release
1647 o BLAST reports with no hits are correctly parsed.
1649 o Several other bugs of the BLAST parser (regular expressions, ...)
1652 o Old syntax calls have been replaced with more modern syntax
1654 o Modules that did not work at all, in particular the Sim4
1655 set have been removed
1657 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1658 have improved compliance with interface specs and documentation
1660 o Mailing list documentation updated throughout the distribution
1662 o Most minor bug fixes have happened.
1664 o The scripts in /examples now work and have the modern syntax
1665 rather than the deprecated syntax
1668 0.6.1 Sun April 2 2000
1670 o Sequences can have Sequence Features attached to them
1671 - The sequence features can be read from or written to
1672 EMBL and GenBank style flat files
1674 o Objects for Annotation, including References (but not
1675 full medline abstracts), Database links and Comments are
1678 o A Species object to represent nodes on a taxonomy tree
1681 o The ability to parse HMMER and Sim4 output has been added
1683 o The Blast parsing has been improved, with better PSI-BLAST
1684 support and better overall behaviour.
1686 o Flat file indexed databases provide both random access
1687 and sequential access to their component sequences.
1689 o A CodonTable object has been written with all known
1690 CodonTables accessible.
1692 o A number of new lightweight analysis tools have been
1693 added, such as molecular weight determination.
1695 The 0.6 release also has improved software engineering
1697 o The sequence objects have been rewritten, providing more
1698 maintainable and easier to implement objects. These
1699 objects are backwardly compatible with the 0.05.1 objects
1701 o Many objects are defined in terms of interfaces and then
1702 a Perl implementation has been provided. The interfaces
1703 are found in the 'I' files (module names ending in 'I').
1705 This means that it is possible to wrap C/CORBA/SQL access
1706 as true "bioperl" objects, compatible with the rest of
1709 o The SeqIO system has been overhauled to provide better
1710 processing and perl-like automatic interpretation of <>
1713 o Many more tests have been added (a total of 172 automatic
1714 tests are now run before release).
1718 0.05.1 Tue Jun 29 05:30:44 1999
1719 - Central distribution now requires Perl 5.004. This was
1720 done to get around 5.003-based problems in Bio/Index/*
1722 - Various bug fixes in the Bio::Tools::Blast modules
1723 including better exception handling and PSI-Blast
1724 support. See Bio/Tools/Blast/CHANGES for more.
1725 - Fixed the Parse mechanism in Seq.pm to use readseq.
1726 Follow the instructions in README for how to install
1727 it (basically, you have to edit Parse.pm).
1728 - Improved documentation of Seq.pm, indicating where
1729 objects are returned and where strings are returned.
1730 - Fixed uninitialized warnings in Bio::Root::Object.pm
1731 and Bio::Tools::SeqPattern.pm.
1732 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1734 0.05 Sun Apr 25 01:14:11 1999
1735 - Bio::Tools::Blast modules have less memory problems
1736 and faster parsing. Webblast uses LWP and supports
1737 more functionality. See Bio/Tools/Blast/CHANGES for more.
1738 - The Bio::SeqIO system has been started, moving the
1739 sequence reformatting code out of the sequence object
1740 - The Bio::Index:: system has been started, providing
1741 generic index capabilities and specifically works for
1742 Fasta formatted databases and EMBL .dat formatted
1744 - The Bio::DB:: system started, providing access to
1745 databases, both via flat file + index (see above) and
1747 - The scripts/ directory, where industrial strength scripts
1748 are put has been started.
1749 - Many changes - a better distribution all round.
1751 0.04.4 Wed Feb 17 02:20:13 1999
1752 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1753 (see Bio::Tools::Blast::CHANGES).
1754 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1755 - Beefed up the t/Fasta.t test script.
1756 - Small fix in Bio::Seq::type() (now always returns a string).
1757 - Changed Bio::Root::Utilities::get_newline_char() to
1758 get_newline() since it could return more than one char.
1759 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1760 - Changed default timeout to 20 seconds (was 3).
1761 - Moved lengthy modification notes to the bottom of some files.
1762 - Fixed SimpleAlign write_fasta bug.
1763 - Beefed up SimpleAlign.t test
1765 0.04.3 Thu Feb 4 07:48:53 1999
1766 - Bio::Root::Object.pm and Global.pm now detect when
1767 script is run as a CGI and suppress output that is only
1768 appropriate when running interactively.
1769 - Bio::Root::Err::_set_context() adds name of script ($0).
1770 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1771 regarding the use of the static objects via the qw(:obj) tag.
1772 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1773 CORE::reverse, avoiding Perl warnings.
1774 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1775 example scripts (see Bio::Tools::Blast::CHANGES).
1776 - examples/seq/seqtools.pl no longer always warns about using
1777 -prot or -nucl command-line arguments; only when using the
1779 - Methods added to Bio::Root::Utilities: create_filehandle(),
1780 get_newline_char(), and taste_file() to generalize filehandle
1781 creation and autodetect newline characters in files/streams
1782 (see bug report #19).
1783 - Bio::Root::IOManager::read() now handles timeouts and uses
1784 Utilities::create_filehandle().
1785 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1786 of hardwiring in "\n".
1787 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1789 0.04.2 Wed Dec 30 02:27:36 1998
1790 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1791 (see Bio::Tools::Blast::CHANGES).
1792 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1793 to CORE::reverse (prevents ambiguous warnings with 5.005).
1794 - Appending '.tmp.bioperl' to temporary files created by
1795 Bio::Root::Utilities::compress() or uncompress() to
1796 make it easy to identify & cleanup these files as needed.
1797 - Developers: Created CVS branch release-0-04-bug from
1798 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1799 be sure to cvs checkout this branch into a clean area.
1801 0.04.1 Wed Dec 16 05:39:15 1998
1802 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1803 (see Bio::Tools::Blast::CHANGES).
1804 - Compile/SW/Makefile.PL now removes *.o and *.a files
1807 0.04 Tue Dec 8 07:49:19 1998
1808 - Lots of new modules added including:
1809 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1810 and Bio/Compile directory containing XS-linked C code for
1811 creating Smith-Waterman sequence alignments from within Perl.
1812 * Steve Chervitz's Blast distribution has been incorporated.
1813 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1814 - Bio/examples directory for demo scripts for all included modules.
1815 - Bio/t directory containing test suit for all included modules.
1816 - For changes specific to the Blast-related modules prior to
1817 incorporation in this central distribution, see the CHANGES
1818 file in the Bio/Tools/Blast directory.
1820 0.01 Tue Sep 8 14:23:22 1998
1821 - original version from central CVS tree; created by h2xs 1.18