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Description: bioruby
Homepage: http://bioruby.open-bio.org
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bioruby / ChangeLog
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27a31e1f » Naohisa Goto 2009-02-19 BioRuby 1.3.0 is released. 1 2009-02-20 Naohisa Goto <ng@bioruby.org>
2
3 * BioRuby 1.3.0 is released.
4
5 2009-02-19 Naohisa Goto <ng@bioruby.org>
6
7 * lib/bio/version.rb
8
9 Preparation for bioruby-1.3.0 release.
10 (commit fd7fc9f78bc5f4d9a10b3c0d457d9781c9ec2e49)
11
12 * bioruby.gemspec.erb
13
14 Fixed a logic to determine whether in git repository, and file
15 lists are changed to be sorted.
16 (commit ede0c0d7aeab078b6183c4e0e7c74faec32739f7)
17
18 2009-02-18 Naohisa Goto <ng@bioruby.org>
19
20 * README.rdoc
21
22 Added list of document files bundled in the BioRuby distribution.
23 (commit 92748f848e4708766e44c22b2f02ac662491971f)
24
0d00b9a3 » Naohisa Goto 2009-02-10 ChangeLog is modified. 25 2009-02-10 Naohisa Goto <ng@bioruby.org>
26
27 * KNOWN_ISSUES.rdoc
28
29 Added details about the text mode issue on mswin32/mingw32/bccwin32
30 and about non-UNIX/Windows systems.
31 (commit 342a167a23d3b078bd77b3f16f0ceb1aa071df66)
32
33 2009-02-09 Naohisa Goto <ng@bioruby.org>
34
35 * test/unit/bio/db/test_gff.rb
36
37 Test bug fix: test_gff.rb failed in some environment (e.g. Windows)
38 because the default formatting rule of Float#to_s depends on the
39 libc implementation.
40 (commit f39bf88ed6a41bd328372ee7de7a23902235f833)
41
42
1eefaf11 » Naohisa Goto 2009-02-06 ChangeLog is modified. 43 2009-02-06 Naohisa Goto <ng@bioruby.org>
44
45 * lib/bio/db/gff.rb, test/unit/bio/db/test_gff.rb
46
47 * Bug fix: Bio::GFF::GFF3::Record#id and #id= should be changed
48 to follow the previous incompatible change of @attributes.
49 Thanks to Tomoaki NISHIYAMA who reports the bug ([BioRuby]
50 GFF3 status (possible bug?)).
51 * Unit tests are added.
52 (commit 5258d88ef98a12fd7829eb86aa8664a18a672a43)
0d00b9a3 » Naohisa Goto 2009-02-10 ChangeLog is modified. 53 (commit c0c7708b3e91b0d2f2d0d50a4a0ba36928057cc8)
1eefaf11 » Naohisa Goto 2009-02-06 ChangeLog is modified. 54
d08cbb93 » Naohisa Goto 2009-02-05 ChangeLog is modified. 55 2009-02-05 Naohisa Goto <ng@bioruby.org>
56
57 * Rakefile
58
59 New task "tutorial2html" to generate html from doc/Tutorial.rd
60 and doc/Tutorial.rd.ja.
61 (commit 8d66fae59477f01f12b2fa3509ea34c371102725)
62
63 * doc/Tutorial.rd.html, doc/Tutorial.rd.ja.html
64
65 Automatically generated tutorial html from RD formatted documents.
66 (commit 90c4a23eea08b06dd758aaa0a53bea789602d252)
67
68 * doc/bioruby.css
69
70 Newly added stylesheet for the tutorial html files. The bioruby.css
71 have been used in http://bioruby.org/ and have been maintained by
72 Toshiaki Katayama.
73 (commit b69dc243787525de065bdf2e6b7da68d6079ab91)
74
b5dc7e7b » Naohisa Goto 2009-02-05 ChangeLog is modified. 75 * test/runner.rb
76
77 Added workaroud for test-unit-2.0.x.
78 (commit 475ac6a6b38e8df30de3d9bf4c7e810759ab023d)
79
d08cbb93 » Naohisa Goto 2009-02-05 ChangeLog is modified. 80 2009-02-04 Naohisa Goto <ng@bioruby.org>
81
82 * lib/bio/appl/blast/format0.rb
83
84 Bug fix: a null line can be inserted after query name lines.
85 (commit bea9ce35b4177f407575ed0752c36bba8a50f502)
86
87 2009-02-03 Naohisa Goto <ng@bioruby.org>
88
89 * Tutorial.rd.ja
90
91 * Document bug: BioRuby shell commands seq, ent, obj were renamed to
92 getseq, getent, getobj, respectively. Thanks to Hiroyuki Mishima
93 who reports the issue ([BioRuby-ja]).
94 * Changes of returned value of getseq are also reflected to the
95 document.
96 * Recommended Ruby version and installation procedure are also
97 changed.
98 (commit 916e96ca549db71a550e7a5d3bd49a3149614313)
99
100 * doc/Changes-0.7.rd
101
102 Documentation forgotten in 1.1.0: rename of BioRuby shell commands.
103 (commit 64113314caac3453b4cc3b80ece9b5fb5841e069)
104
88042815 » Naohisa Goto 2009-01-30 ChangeLog modified 105 2009-01-30 Naohisa Goto <ng@bioruby.org>
106
96042d89 » Naohisa Goto 2009-01-30 ChangeLog is modified. 107 * lib/bio/appl/blast/format0.rb
108
109 Bug fix: incorrect parsing of hit sequence's whole length.
110 (commit 98e6f57630b2c3394a9403f58e76b102346c56ef)
111
112 Bug fix: Whole length of a hit sequence is mistakenly parsed when
113 it contains ",". WU-BLAST parser is also affected in addition to
114 NCBI BLAST parser.
115
88042815 » Naohisa Goto 2009-01-30 ChangeLog modified 116 * lib/bio/db/lasergene.rb, lib/bio/db/soft.rb,
117 lib/bio/util/color_scheme.rb, lib/bio/util/contingency_table.rb,
118 lib/bio/util/restriction_enzyme.rb
119
120 Removed ":nodoc:" in in "module Bio" which prevents RDoc of the
121 Bio module.
122 (commit 458db79b467d40ed02db0d085218f611e7dd5e04)
123
6c58c824 » Naohisa Goto 2009-01-29 Added documents about Bio::... 124 2009-01-29 Naohisa Goto <ng@bioruby.org>
125
126 * doc/Changes-1.3.rdoc
127
128 Added documents about Bio::TogoWS and Bio::BIORUBY_VERSION.
129
130 * lib/bio/shell/plugin/entry.rb
131
132 getent (BioRuby shell command) is changed to use EBI Dbfetch or
133 TogoWS in addition to NCBI or KEGG API.
134 (commit 0e172590f60dd5a5f27a24ecd230037a7909224c)
135
136 * lib/bio/shell/plugin/togows.rb, lib/bio/shell.rb
137
138 Added new shell plugin providing accesses to TogoWS REST services.
139 (commit 03f6720b90e90703c23536a11b3f12c8155550ff)
140
141 * lib/bio.rb
142
143 Added autoload of Bio::TogoWS.
144 (commit f8605e1234164a7aa7f236b4e96a4299229753d7)
145
146 * test/functional/bio/io/test_togows.rb,
147 test/unit/bio/io/test_togows.rb
148
149 Newly added functional and unit tests for Bio::TogoWS::REST.
150 (commit f04152b80d07f44f146fa3fa0729facede865aac)
151
152 * lib/bio/io/togows.rb
153
154 New class Bio::TogoWS::REST, a REST client for the TogoWS web
155 service (http://togows.dbcls.jp/site/en/rest.html).
156 (commit 652d2534163675182b9ce30cbb1dd5efff45cd60)
157
158 * bin/br_pmfetch.rb
159
160 Changed to use Bio::BIORUBY_VERSION_ID instead of CVS version ID.
161 (commit f69d538ffa9ded00eb68dd306e65505d03b6c656)
162
163 * lib/bio/shell/core.rb
164
165 Changed to use BIORUBY_VERSION_ID.
166 (commit 4ce11656a205e85cae64eca27cef7cd94eb80930)
167
168 * bioruby.gemspec.erb
169
170 Gem version is now determined from lib/bio/version.rb or
171 BIORUBY_GEM_VERSION environment variable.
172 (commit 1811e845e60bc2847ea5717ef936bad93f9f2c87)
173
174 * Rakefile
175
176 * Changed to use lib/bio/version.rb.
177 * Environment variable BIORUBY_EXTRAVERSION is renamed to
178 BIORUBY_EXTRA_VERSION.
179 * Added dependency on lib/bio/version.rb to bioruby.gemspec.
180 (commit fb27eaa584cda1bb4cb75e10085996503361c98a)
181
182 * lib/bio.rb, lib/bio/version.rb
183
184 Bio::BIORUBY_VERSION is split into lib/bio/version.rb.
185 (commit 9779398c3fa0e9405a875b754a5243e0d6922c32)
186
187 * New file lib/bio/version.rb contains BioRuby version information.
188 * New constants: Bio::BIORUBY_EXTRA_VERSION stores extra version
189 string (e.g. "-pre1") and Bio::BIORUBY_VERSION_ID stores BioRuby
190 version string (e.g. "1.3.0-pre1").
191 * Bio::BIORUBY_VERSION is changed to be frozen. Above two constants
192 also store frozen values.
193
20f1b148 » Naohisa Goto 2009-01-26 ChangeLog for today's changes 194 2009-01-26 Naohisa Goto <ng@bioruby.org>
195
196 * KNOWN_ISSUES.rdoc
197
198 Newly added KNOWN_ISSUES.rdoc that describes known issues and
199 bugs in current BioRuby.
200 (commit 06b10262be0bf797a3b133e4697e9b0955408944)
6c58c824 » Naohisa Goto 2009-01-29 Added documents about Bio::... 201 (commit a65ad8b42613e46b0b4bb0650d6301da0dcc88c9)
20f1b148 » Naohisa Goto 2009-01-26 ChangeLog for today's changes 202
203 * lib/bio/shell/plugin/ncbirest.rb, lib/bio/shell.rb
204
205 New shell plugin lib/bio/shell/plugin/ncbirest.rb, providing
206 "efetch", "einfo", "esearch", and "esearch_count" methods.
207 They act the same as those defined in Bio::NCBI::REST, except
34c46d33 » Naohisa Goto 2009-01-26 ChangeLog is modified for t... 208 that "efetch" fetches entries with pre-defined databases
209 depending on arguments.
20f1b148 » Naohisa Goto 2009-01-26 ChangeLog for today's changes 210 (commit c482e1864aa0dbca3727b1059d4fe3d0aefb3917)
34c46d33 » Naohisa Goto 2009-01-26 ChangeLog is modified for t... 211 (commit 3360b8905fdbcd4ca050470fdb2f02a7387e8bb9)
20f1b148 » Naohisa Goto 2009-01-26 ChangeLog for today's changes 212
213 * lib/bio/shell/plugin/entry.rb
214
34c46d33 » Naohisa Goto 2009-01-26 ChangeLog is modified for t... 215 Shell commands "getent" and "getseq" are changed to use
216 "efetch" method when "gb" or some variant is specified as
217 the database.
20f1b148 » Naohisa Goto 2009-01-26 ChangeLog for today's changes 218 (commit c482e1864aa0dbca3727b1059d4fe3d0aefb3917)
34c46d33 » Naohisa Goto 2009-01-26 ChangeLog is modified for t... 219 (commit 3360b8905fdbcd4ca050470fdb2f02a7387e8bb9)
20f1b148 » Naohisa Goto 2009-01-26 ChangeLog for today's changes 220
221 * bioruby.gemspec.erb, bioruby.gemspec
222
223 * Changed version to 1.2.9.9501.
224 * Changed to use "git ls-files" instead of "git-ls-files", and
225 changed not to redirect to /dev/null.
226 * Special treatment of bioruby.gemspec is removed.
227 * ChangeLog is included to RDoc.
228 * Set RDoc title to "BioRuby API documentation".
229 * Set "--line-numbers" and "--inline-source" to rdoc_options.
230 (commit f014685090c38eeb64219603f2c7e90574849431)
231 * added KNOWN_ISSUES.rdoc to files for no-git environment.
232 (commit 06b10262be0bf797a3b133e4697e9b0955408944)
233 * Ruby 1.9 support: command execution with shell can raise
234 an error.
235 (commit 3179de32f1dc746c8de975917b1718a523800d69)
236 * bioruby.gemspec is generated from bioruby.gemspec.erb.
237 (commit 4e1cd3bfb8207b357d5b71cc0fc8366f06491130)
238 (commit 06b10262be0bf797a3b133e4697e9b0955408944)
239
7a4b5e58 » Naohisa Goto 2009-01-21 Added recent changes and fi... 240 2009-01-21 Naohisa Goto <ng@bioruby.org>
241
242 * ChangeLog
243
244 Added recent changes and fixed typo for recent changes.
245
246 2009-01-20 Naohisa Goto <ng@bioruby.org>
247
248 * ChangeLog, doc/Changes-1.3.rdoc
249
250 Added ChangeLog and doc/Changes-1.3.rdoc for recent changes.
251 (commit be2254ddea152fddf51a2476eeb20d804b1e3123)
252
253 * bioruby.gemspec
254
255 Added bioruby.gemspec created from bioruby.gemspec.erb.
256 (commit 4c54597eaf09107c34ad06bc5f5f9cead77a0198)
257
258 * lib/bio/appl/blast/wublast.rb
259
260 Bug fix: parsing of exit code failed when ignoring fatal errors
261 (commit 44ed958acebe4324a9a48e7292c4f0ad5c0fb685)
262
263 * Bug fix: could not get exit code in WU-BLAST results executed
264 with a command line option "-nonnegok", "-novalidctxok", or
265 "-shortqueryok".
266 * New methods Bio::Blast::WU::Report#exit_code_message and #notes.
267
268 * Rakefile
269
270 Added package tasks and changed to use ERB instead of eruby.
271 (commit 7b081c173d3b1cbc46034297ea802a4e06f85b2f)
272
273 * bioruby.gemspec.erb
274
275 Use git-ls-files command to obtain list of files when available.
276 (commit 5d5cb24fdd56601bc43ee78facc255ca484245c0)
277
278 2009-01-17 Naohisa Goto <ng@bioruby.org>
279
280 * Rakefile
281
282 Simple Rakefile for dynamic generation of bioruby.gemspec
283 (commit d5161d164f3520db25bed9aececb962428b9d6bc)
284
285 * bioruby.gemspec.erb
286
287 bioruby.gemspec is renamed to bioruby.gemspec.erb with modification.
288 (commit bef311668e4a3be30965ce94d41e7bde4a4e17f9)
289
290 To prevent the error "Insecure operation - glob" in GitHub,
291 bioruby.gemspec is renamed to bioruby.gemspec.erb, and modified
292 to generate the file list by using eruby.
293
294 2009-01-15 Naohisa Goto <ng@bioruby.org>
295
296 * doc/Changes-1.3.rdoc
297
298 Changes-1.3.rd is renamed to Changes-1.3.rdoc with format
299 conversion, and fixed typo.
300 (commit 1aef599650d14362ed233dcc9a7db8d3c1db1777)
301
302 Added details about newly added classes etc.
303 (commit eda9fd0abbb8e430810468d777d0b585e33c25d8)
304
305 2009-01-13 Naohisa Goto <ng@bioruby.org>
306
307 * bioruby.gemspec
308
309 Changed version to 1.2.9001, set has_rdoc = true and rdoc options.
310 (commit 1f63d3d5389dd3b0316e9f312b56e62371caa253)
311
312 * Gem version number changed to 1.2.9.9001 for testing gem.
313 * Changed to has_rdoc = true.
314 * README.rdoc and README_DEV.rdoc are now included to gem's rdoc,
315 and README.rdoc is set to the main page.
316 * *.yaml is now excluded from rdoc.
317
318 2009-01-13 Jan Aerts <jan.aerts@gmail.com>
319
320 * bioruby.gemspec
321
322 Renamed gemspec.rb to bioruby.gemspec because so github builds
323 the gem automatically
324 (commit 561ae16d20f73dcd6fc3d47c41c97c32f9aadb1a)
325 (committer: Naohisa Goto)
326 (original commit date: Wed Jun 25 11:01:03 2008 +0100)
327
328 Edited gemspec because github returned an error while building gem.
329 (commit f0d91e07550872c2f0d5835e496af1add7759d42)
330 (committer: Naohisa Goto)
331 (original commit date: Wed Jun 25 11:03:04 2008 +0100)
332
333 2009-01-13 Naohisa Goto <ng@bioruby.org>
334
335 * README.rdoc
336
337 Changed format from RD to RDoc with some additional URLs
338 (commit cb8781d701f22cbaf16575bb237a9e0cbf8cd407)
339
340 Clarified copyright of README.rdoc and BioRuby
341 (commit acd9e6d6e6046281c6c9c03cff1021449b8e780f)
342
343 Updated descriptions about RubyGems, and added Ruby 1.9 partial
344 support
345 (commit ff63658b255988bf0e7a9f5a2d1523d5104fe588)
346
347 2009-01-09 Naohisa Goto <ng@bioruby.org>
348
349 * test/runner,rb
350
351 Ruby 1.9.1 support: using alternatives if no Test::Unit::AutoRunner
352 (commit 5df2a9dc0642d4f1e9a4398d6af908780d622a6e)
353
3ae1a16a » Naohisa Goto 2009-01-20 Added ChangeLog and doc/Cha... 354 2009-01-05 Naohisa Goto <ng@bioruby.org>
355
356 * lib/bio/db/fantom.rb
357
7a4b5e58 » Naohisa Goto 2009-01-21 Added recent changes and fi... 358 Bug fix: incomplete cgi parameter escaping, and suppressing warnings.
3ae1a16a » Naohisa Goto 2009-01-20 Added ChangeLog and doc/Cha... 359 (commit 754d8815255a0f0db20df9dd74f9f146605d430e)
360
361 * Bug fix: incomplete cgi parameter escaping for ID string in
362 Bio::FANTOM.get_by_id (and Bio::FANTOM.query which internally
363 calls the get_by_id method).
364 * Warning message "Net::HTTP v1.1 style assignment found" when
365 $VERBOSE=true is suppressed.
366 * Removed obsolete "rescue LoadError" when require 'rexml/document'.
367
368 * lib/bio/io/fetch.rb
369
370 Bug fix: possible incomplete form key/value escaping.
371 (commit ecaf2c66261e4ce19ab35f73e305468e1da412ed)
372
373 * Bug fix: possible incomplete form key/value escaping
374 * Refactoring: changed to use private methods _get and _get_single
375 to access remote site.
376
377 * lib/bio/io/pubmed.rb
378
379 Bug fix: possible incomplete escaping of parameters, and
380 suppressing warnings
381 (commit 93daccabb1a82bb20e92798c1810182dfb836ba7)
382
383 * Bug fix: possible incomplete string escaping of REST parameters
384 in Bio::PubMed#query and #pmfetch.
385 * Warning message "Net::HTTP v1.1 style assignment found" when
386 $VERBOSE=true is suppressed.
387 * Removed obsolete "unless defined?(CGI)".
388
389 * lib/bio/command.rb, test/unit/bio/test_command.rb
390
391 Bug fix: incomplete escaping in Bio::Command.make_cgi_params etc.
392 (commit 17c8f947e5d94012921f9252f71460e9d8f593e3)
393
394 * Buf fix: in Bio::Command.make_cgi_params and
395 make_cgi_params_key_value, string escaping of form keys and values
396 is incomplete.
397 * Warning message "useless use of :: in void context" is suppressed
398 when running test/unit/bio/test_command.rb with $VERBOSE=true.
399 * Unit tests are added.
400
401 * lib/bio/appl/, lib/bio/io/ (9 files)
402
7a4b5e58 » Naohisa Goto 2009-01-21 Added recent changes and fi... 403 Suppress warning message "Net::HTTP v1.1 style assignment found"
3ae1a16a » Naohisa Goto 2009-01-20 Added ChangeLog and doc/Cha... 404 when $VERBOSE = true.
405 (commit a2985eb1f3aed383f1b1b391f2184317c7fd21c7)
406
407 2009-01-02 Naohisa Goto <ng@bioruby.org>
408
409 * README.rdoc
410
411 Changing optional requirements, recommended Ruby version, and
412 setup.rb credit.
413 (commit a5462ab4bd403d2d833e5d6db26ae98ca763513c)
414
415 2008-12-30 Naohisa Goto <ng@bioruby.org>
416
417 * README.rdoc
418
419 Fixed grammar and spelling in README.rdoc, indicated by
420 Andrew Grimm at git://github.com/agrimm/bioruby.git
421 in Sun Sep 21 19:59:03 2008 +1000.
422 (commit 446918037bff392b9c6bc6828720c585733a8f4b)
423
424 2008-12-30 Naohisa Goto <ng@bioruby.org>
425
426 * lib/bio.rb
427
428 Changed BIORUBY_VERSION to 1.3.0, which will be the next BioRuby
429 release version number.
430 (commit b000b1c4a5a136ab287b517b8b8c66e54f99a8a8).
431
432 * doc/Changes-1.3.rd
433
434 Added documents about changed points for 1.3.0 release.
435 (commit 028e323e784eb60b18f941cce1e3752abff1433c)
436
437 * lib/bio/appl/blast/format8.rb
438
439 Ruby 1.9 support: String#each_line instead of String#each
440 (commit 1bc59708137fd46911d5892e4712cc49c71fa031)
441
442 * lib/bio/io/flatfile/splitter.rb
443
444 Checks for undefined constants are added for running without
445 "require 'bio'" in unit tests.
446 (commit 311176d4d390e5948348f623ff3632454136a03f)
447
448 * lib/bio/appl/blast.rb, lib/bio/appl/blast/report.rb,
449 test/unit/bio/appl/test_blast.rb
450
451 Support for default (-m 0) and tabular (-m 8) formats in
452 Bio::Blast.reports.
453
454 * Added support for default (-m 0) and tabular (-m 8) formats in
455 Bio::Blast.reports method. For the purpose, Bio::Blast::Report_tab
456 is added to read tabular format by using Bio::FlatFile.
457 * Unit tests are added.
458
459 2008-12-26 Naohisa Goto <ng@bioruby.org>
460
461 * lib/bio/appl/paml/codeml/rates.rb
462
463 Ruby 1.9 support: String#each_line instead of String#each
464 (commit 1789a3975c4c82d3b45f545893be8f2a7bf47a01)
465
466 2008-12-26 Naohisa Goto <ng@bioruby.org>
467
468 * lib/bio/command.rb, lib/bio/appl/fasta.rb,
469 lib/bio/appl/blast/genomenet.rb
470
471 Refactoring and following the change of the remote site
472 fasta.genome.jp.
473 (commit 671092dff67890fc48dd7ff2f606c4cedc2eb02c)
474
475 * New method Bio::Command.http_post_form.
476 * Bio::Blast::Remote::GenomeNet#exec_genomenet and
477 Bio::Fasta#exec_genomenet are changed to use the new method.
478 * Changed a regexp. in Bio::Fasta#exec_genomenet is changed
479 following the change of the remote GenomeNet (fasta.genome.jp).
480
481 2008-12-24 Naohisa Goto <ng@bioruby.org>
482
483 * lib/bio/location.rb, test/unit/bio/test_location.rb
484
485 New method Bio::Locations#to_s with bug fix, etc.
486 (commit 115b09456881e1d03730d0b9e7a61a65abf6a1fe)
487
488 * New method Bio::Locations#to_s is added.
489 * New attributes Bio::Locations#operator and Bio::Location#carat.
490 * Changed not to substitute from "order(...)" or "group(...)" to
491 "join(...)".
492 * Bug fix: Bio::Locations.new(str) changes the argument string
493 when the string contains whitespaces.
494 * Unit tests for Bio::Locations#to_s are added.
495
496 2008-12-20 Naohisa Goto <ng@bioruby.org>
497
498 * test/functional/bio/appl/test_pts1.rb,
499 test/unit/bio/appl/test_pts1.rb
500
501 Moved part of test_pts1.rb using network from test/unit to
502 test/functional.
503 (commit 933ff3e7d615fe6521934f137519ea84b3b517f2)
504
505 2008-12-18 Naohisa Goto <ng@bioruby.org>
506
507 * test/unit/bio/io/test_soapwsdl.rb
508
509 Ruby 1.9 support: following the change of Object#instance_methods
510 (commit 008cf5f43786f6143f74889e0ec53d1c8a452aa2)
511
512 Note that SOAP/WSDL library is no longer bundled with Ruby 1.9,
513 and tests in test_soapwsdl.rb may fail.
514
515 * test/unit/bio/io/test_ddbjxml.rb
516
517 Ruby 1.9 support: following the change of Module::constants
518 (commit ed1ad96e7ed9d6c7d67e5413a22ba935a3b36efa)
519
520 * lib/bio/util/restriction_enzyme/single_strand.rb
521
522 Ruby 1.9 support: changed Array#to_s to join, Symbol#to_i to __id__,
523 etc.
524 (commit a29debb8c03244c1ce61317d6df0a2c5d066de3d)
525
526 * Ruby 1.9 support: in pattern method, changed to use Array#join
527 instead of Array#to_s.
528 * Ruby 1.9 support: in self.once method, changed to use
529 Object#__id__ instead of Symbol#to_i.
530 * self.once is changed to be a private class method.
531
532 2008-12-18 Naohisa Goto <ng@bioruby.org>
533
534 * lib/bio/db/rebase.rb
535
536 Ruby 1.9 support: changed not to use String#each, etc.
537 (commit 47ba6e9fcf864f5881211e766f2e47b60dde178a)
538
539 * Ruby 1.9 support: In parse_enzymes, parse_references, and
540 parse_suppliers methods, String#each is changed to each_line.
541 * Changed to use require instead of autoload, to reduce support cost.
542
543 2008-12-16 Moses Hohman <moses@moseshohman.com>
544
545 * lib/bio/db/medline.rb, test/unit/bio/db/test_medline.rb
546
547 fix medline parsing of author last names that are all caps
548 (commit 5f37d566fc2efa4878efbd19e83f909a58c4cb00)
549
550 2008-12-15 Mitsuteru Nakao <n@bioruby.org>
551
552 * lib/bio/db/kegg/glycan.rb
553
554 Bug fix in Bio::KEGG::GLYCAN#mass.
555 Thanks to a reporter.
556 (commit cb8f1acc4caebf1f04d4a6c141dd4477fcb5394b)
557 (committer: Naohisa Goto)
558
559 2008-12-15 Naohisa Goto <ng@bioruby.org>
560
561 * lib/bio/pathway.rb, test/unit/bio/test_pathway.rb
562
563 Fixed pending bugs described in unit test, and Ruby 1.9 support
564 (commit 97b3cd4cf78eff8aede16369298aaacf1c319b68)
565
566 * Pending bugs described in test/unit/bio/test_pathway.rb are fixed.
567 Fixed a bug in subgraph: does not include nodes w/o edges.
568 A bug in cliquishness depending on the subgraph bug is also fixed.
569 * Bio::Pathway#cliquishness is changed to calculate cliquishness
570 (clustering coefficient) for not only undirected graphs but also
7a4b5e58 » Naohisa Goto 2009-01-21 Added recent changes and fi... 571 directed graphs. Note that pending proposed specification changes
572 previously written in test_pathway.rb (raises error for directed
3ae1a16a » Naohisa Goto 2009-01-20 Added ChangeLog and doc/Cha... 573 graphs, and return 1 for a node that has only one neighbor node)
574 are rejected.
575 * Ruby 1.9 support: To avoid dependency to the order of objects
576 in Hash#each (and each_keys, etc.), Bio::Pathway#index is used
577 to specify preferences of nodes in a graph. Affected methods
578 are: to_matrix, dump_matrix, dump_list, depth_first_search.
579 * Bug fix in the libpath magic in test/unit/bio/test_pathway.rb.
580
581 2008-12-09 Naohisa Goto <ng@bioruby.org>
582
583 * lib/bio/db/newick.rb, lib/bio/tree.rb
584
585 Ruby 1.9 support: suppressing "warning: shadowing outer local
586 variable".
587 (commit 6fe31f0a42a87631bdee3796cff65afb053b2add)
588
589 2008-12-05 Naohisa Goto <ng@bioruby.org>
590
591 * test/unit/bio/io/test_fastacmd.rb
592
593 Ruby 1.9 support: changed to use respond_to?, etc.
594 (commit 5d6c92c752c00f07ed856fd209c8078ef9fdf57a)
595
596 * Following the change of Module#methods in Ruby 1.9, changed
597 to use respond_to?().
598 * The test path '/tmp/test' is replaced with '/dev/null'
599
600 * lib/bio/db/gff.rb
601
602 Ruby 1.9 support: changes following the change of String#[]
603 (commit c25cc506bffcf1f2397ac2210153cfbfbbcb4942)
604
605 * lib/bio/reference.rb
606
607 Ruby 1.9 support: using enumerator instead of String#collect
608 (commit ea99242570fc8b2e2a869db84b7daaa7737f23e0)
609
610 * test/unit/bio/test_location.rb
611
612 Test bug fix: wrong number in libpath magic
613 (commit aa45101246bc42f78a21ee110bc58e59f532e24a)
614
615 * test/unit/bio/db/test_nexus.rb
616
617 Test bug fix: missing libpath magic
618 (commit d54eed426461f3a3148953fda1f7b428e74051c6)
619
620 Thanks to Anthony Underwood who reports the bug in his Github
621 repository.
622
623 * test/unit/bio/db/pdb/test_pdb.rb
624
625 Test bug fix: wrong number in libpath magic
626 (commit b53d703a8dd72608ab5ea03457c2828470069f2f)
627
628 2008-12-04 Naohisa Goto <ng@bioruby.org>
629
630 * test/unit/bio/db/embl/test_embl_to_bioseq.rb
631
632 Test bug fix: typing error (found by using Ruby 1.9)
633 (commit fa52f99406ddd42221be354346f67245b3572510)
634
635 * test/unit/bio/db/embl/test_common.rb
636
637 Ruby 1.9 support: following the change of Module#instance_methods
638 (commit d18fa7c1c3660cf04ec2a8a42d543a20a77cee2c)
639
640 In Ruby 1.9, Module#instance_methods returns Array containing
641 Symbol objects instead of String. To support both 1.8 and 1.9,
642 "to_s" is added to every affected test method.
643
644 * lib/bio/appl/tmhmm/report.rb
645
646 Ruby 1.9 support: using enumerator if the entry is a string
647 (commit 36968122b64b722e230e3e1b52d78221c0b60884)
648
649 * lib/bio/appl/pts1.rb
650
651 Ruby 1.9 support: String#each to each_line and Array#to_s to join('')
652 (commit c4c251d5e94167512a0b8a38073a09b72994c08f)
653
654 * test/unit/bio/appl/test_fasta.rb
655
656 Ruby 1.9 support: changed to use Array#join instead of Array#to_s
657 (commit bf8823014488166c6e1227dd26bdca344c9f07b7)
658
659 * lib/bio/appl/blast.rb
660
661 Ruby 1.9 support: String#each is changed to String#each_line
662 (commit 3e177b9aecf6b54a5112fd81fc02386d18fc14b9)
663
664 * lib/bio/appl/hmmer/report.rb
665
666 Ruby 1.9 support: String#each is changed to String#each_line
667 (commit 63bdb3a098bc447e7bd272b3be8f809b4b56d451)
668
669 * lib/bio/appl/genscan/report.rb
670
671 Ruby 1.9 support: String#each is changed to String#each_line
672 (commit 082250786756de2b4171b3a00e0c4faaa816fc8f)
673
674 * test/functional/bio/io/test_ensembl.rb
675
676 Using jul2008.archive.ensembl.org for workaround of test failure.
677 (commit 1d286f222cdc51cf1323d57c1c79e6943d574829)
678
679 Due to the renewal of Ensembl web site, lib/bio/io/ensembl.rb
680 does not work for the latest Ensembl. For a workaround of
681 the failure of tests in test/functional/bio/io/test_ensembl.rb,
682 tests for Ensembl#exportview are changed using Ensembl archive
683 (http://jul2008.archive.ensembl.org/).
684
685 2008-12-03 Naohisa Goto <ng@bioruby.org>
686
687 * sample/demo_sequence.rb
688
689 sample/demo_sequence.rb, example of sequence manipulation.
690 (commit b7f52b47dbcc7d32f4eb7377d2b1510eb1991fd5)
691
692 The content of this file is moved from previous version of
693 lib/bio/sequence.rb (inside the "if __FILE__ == $0").
694
695 2008-12-02 Naohisa Goto <ng@bioruby.org>
696
697 * lib/bio/appl/paml/baseml.rb, etc. (17 files)
698
699 Support for baseml and yn00 (still under construction), and
700 incompatible changes to Bio::PAML::Codeml.
701 (commit d2571013409661b4d7be8c5c9db14dbe9a9daaaf)
702
703 * Security fix: To prevent possible shell command injection,
704 changed to use Bio::Command.query_command instead of %x.
705 * Bug fix with incompatible changes: Using Tempfile.new.path
706 as default values are removed because this can cause
707 unexpected file loss during garbage collection.
708 * Change of method/file names: The term "config file" is changed
709 to "control file" because the term "config file" is never used
710 in PAML documents. The term "options" is changed to "parameters"
711 because the "options" have been used for command-line arguments
712 in other wrappers (e.g. Bio::Blast, Bio::ClustalW). The term
713 "parameters" is also used in BioPerl's
714 Bio::Tools::Run::Phylo::PAML.
715 * Bio::PAML::Codeml.create_config_file, create_control_file,
716 Bio::PAML::Codeml#options, and #options= are now deprecated.
717 They will be removed in the future.
718 * New class Bio::PAML::Common, basic wrapper common to PAML programs.
719 Bio::PAML::Codeml is changed to inherit the Common class.
720 * New classes Bio::PAML::Baseml and Bio::PAML::Yn00, wrappers for
721 baseml and yn00.
722 * New classes Bio::PAML::Common::Report, Bio::PAML::Baseml::Report
723 and Bio::PAML::Yn00::Report, but still under construction.
724 * New methods Bio::PAML::Codeml#query(alignment, tree), etc.
725 * test/data/paml/codeml/dummy_binary is removed because
726 the default of Bio::PAML::Codeml.new is changed to use
727 "codeml" command in PATH.
728 * test/data/paml/codeml/config.missing_tree.txt is removed
729 because treefile can be optional parameter depending on runmode.
730 test/data/paml/codeml/config.missing_align.txt is also removed
731 because test is changed to use normal control file parameters.
732
733 * lib/bio/command.rb, test/functional/bio/test_command.rb
734
735 Improvement of Bio::Command.query_command, call_command, etc.
736 (commit e68ee45589f8063e5a648ab235d6c8bbc2c6e5ff)
737
738 * Improvement of Bio::Command.query_command, call_command,
739 query_command_popen, query_command_fork, call_command_popen,
740 and call_command_fork: they can get an option :chdir => "path",
741 specifying working directory of the child process.
742 * New method Bio::Command.mktmpdir backported from Ruby 1.9.0.
743 * New method Bio::Command.remove_entry_secure that simply calls
744 FileUtils.remove_entry_secure or prints warning messages.
745 * Tests are added in test/functional/bio/test_command.rb.
746 * Ruby 1.9 followup: FuncTestCommandQuery#test_query_command_open3
747 failed in ruby 1.9 due to the change of Array#to_s.
748
749 2008-11-19 Naohisa Goto <ng@bioruby.org>
750
751 * test/data/paml/codeml/
752
753 Removed some files in test/data/paml/codeml/ because of potential
754 copyright problem, because they are completely identical with
755 those distributed in PAML 4.1.
756 (commit 086b83d3e54f69d2b9e71af3f9647518768353b0)
757
758 2008-10-21 Naohisa Goto <ng@bioruby.org>
759
760 * lib/bio/sequence/compat.rb
761
762 Bug fix: TypeError is raised in Bio::Sequence#to_s before
763 Sequence#seq is called.
764 (commit ea8e068a5b7f670ce62bc0d3d4b21639e3ca2714)
765
766 Thanks to Anthony Underwood who reported the bug and sent the patch.
767
768 2008-10-19 Naohisa Goto <ng@bioruby.org>
769
770 * setup.rb, README.rdoc
771
772 install.rb is replaced by new setup.rb.
773 (commit 9def7df5b81340c49534ff0bb932de62402a1c8d)
774
775 * install.rb is replaced by the latest version of setup.rb taken
776 from the original author's svn repository (svn r2637, newer than
777 version 3.4.1, latest release version.
778 $ svn co http://i.loveruby.net/svn/public/setup/trunk setup).
7a4b5e58 » Naohisa Goto 2009-01-21 Added recent changes and fi... 779 * README.rdoc is modified to follow the rename of install.rb to
3ae1a16a » Naohisa Goto 2009-01-20 Added ChangeLog and doc/Cha... 780 setup.rb.
781
782 2008-10-18 Toshiaki Katayama <k@bioruby.org>
783
784 * lib/bio/io/ncbirest.rb
785
786 * New methods: Bio::NCBI::REST#einfo, #esearch_count, etc.
787 * New classes: Bio::NCBI::REST::ESearch, Bio::NCBI::REST::EFetch.
788 (commit 637f97deefd6cc113ef18fe18ab628eb619f3dc1)
789 (committer: Naohisa Goto)
790
791 2008-10-14 Naohisa Goto <ng@bioruby.org>
792
793 * lib/bio/sequence/common.rb, test/unit/bio/sequence/test_common.rb,
794 test/unit/bio/sequence/test_compat.rb,
795 test/unit/bio/sequence/test_na.rb
796
797 Bug fix: Bio::Sequence::Common#randomize severely biased.
798 (commit 02de70cbf036b41a50d770954f3b16ba2beca880)
799
800 * Bug fix: Bio::Sequence::Common#randomize was severely biased.
801 To fix the bug, it is changed to used Fisher-Yates shuffle,
802 as suggested by Anders Jacobsen.
803 ([BioRuby] Biased Bio::Sequence randomize())
804 * The module method Bio::Sequence::Common.randomize is removed
805 because it is not used anymore.
806 * Unit tests for Bio::Sequence::Common#randomize are added.
807 * To avoid possible test class name conflicts, class/module
808 names are changed in test_na.rb, test_compat.rb, and
809 test_common.rb.
810
811 2008-10-14 Raoul Jean Pierre Bonnal <raoul.bonnal@itb.cnr.it>
812
813 * lib/bio/io/sql.rb
814
815 Changed the demonstration code in the "if __FILE__ == $0".
816 (commit 9942105920182c809564554bb0d1dba33fe4caab)
817
818 * lib/bio/db/biosql/sequence.rb
819
820 Fix: typing error
821 (commit 67fbbb93adaa8b4b91de3703a235bc75eaef842a)
822
823 2008-10-14 Naohisa Goto <ng@bioruby.org>
824
825 * lib/bio/db/biosql/sequence.rb, lib/bio/io/sql.rb
826
827 Merging patches by Raoul in commit
828 496561a70784d3a1a82bf3117b2d267c7625afac which are ignored
829 when rebasing, probably because of manually editing during merge.
830 (commit c699253d53510c0e76188a72004651a4635088b3)
831
832 2008-10-10 Raoul Jean Pierre Bonnal <raoul.bonnal@itb.cnr.it>
833
834 * lib/bio/db/biosql/sequence.rb
835
836 Fix: check on nil objects (to_biosql)
837 (commit f701e9a71f524ee4373c94ee1bd345e87f16f6ce)
838
839 BugFix: ex. /focus="true" in output was /focus="t",
7a4b5e58 » Naohisa Goto 2009-01-21 Added recent changes and fi... 840 qualifier.value.to_s fix the bug
3ae1a16a » Naohisa Goto 2009-01-20 Added ChangeLog and doc/Cha... 841 (commit f6e1530f3372c87031b551e5c76e24f264891e64)
842
843 * lib/bio/io/biosql/seqfeature.rb
844
845 BugFix: seqfeature_qualifier_value returned ordered only by rank
846 (commit fb74009393eeca6743f78b7b45cb66858c41d733)
847
848 * lib/bio/io/biosql/bioentry.rb
849
850 BugFix: seqfeatures returned ordered by rank
851 (commit 25a249d87d23bd9cb4e671053019675836fcd38c)
852
853 * lib/bio/db/biosql/sequence.rb
854
855 Fixed to suppress warnings: Bio::Features is obsoleted.
856 (commit 198a1e893dd4515d61276c9cce8905f02130e721)
857
858 * lib/bio/db/biosql/biosql_to_biosequence.rb
859
860 Removed alias comment.
861 (commit c037ec565987634b354ff6d77dbbe7c9d83a9e7c)
862
863 * lib/bio/db/biosql/sequence.rb
864
865 Implemented Entry's comments and reference's comments.
866 Fixed species common name.
867 (commit bd3b24ea53ebd9b0ec9dd9f15c27091fe6143e28)
868
869 * lib/bio/io/biosql/bioentry.rb
870
871 Cleaned, deleted pk and seq reference
872 (commit 14bcf90334ec3c3f1c1784977b329ae641e9e106)
873
874 * lib/bio/io/biosql/comment.rb
875
876 cleaned codes
877 (commit 54976693350ab0512cecf946999c2868b9e88007)
878
879 * lib/bio/db/biosql/biosql_to_biosequence.rb
880
881 Added comments, comment adapter.
882 (commit 5394ecea34778c9f571eb35cfc16e3b1a6cb6d1b)
883
884 2008-10-09 Raoul Jean Pierre Bonnal <raoul.bonnal@itb.cnr.it>
885
886 * lib/bio/io/sql.rb
887
888 Changed the demonstration code in the "if __FILE__ == $0".
889 (commit efb61d7c21d229e882c6706838c284404343fa9c)
890
891 * lib/bio/db/biosql/sequence.rb
892
893 Added support for reference. ToDo: handling comments.
894 (commit 29211059ee04214d7879f900ec563c0708d8c9d6)
895
896 * lib/bio/io/biosql/bioentry_reference.rb
897
898 Fix: compisite primary keys :bioentry_id, :reference_id, :rank
899 (commit eba61ba670c591f58866b37ababc4acac0cc7883)
900
901 * lib/bio/io/biosql/dbxref.rb
902
903 removed explicit pk and seq
904 (commit e149f94484469fb3dfd881b45b14be7093b67e0d)
905
906 2008-10-09 Naohisa Goto <ng@bioruby.org>
907
908 * test/functional/bio/test_command.rb,
909 test/data/command/echoarg2.bat
910
911 Bug fix: tests in FuncTestCommandCall are failed on mswin32,
912 and URL changed.
913 (commit 921292f1188d85994742ce4aa156b39d6e720aad)
914
915 * Bug fix: tests in FuncTestCommandCall were failed on mswin32.
916 To fix the test bug, a batch file test/data/command/echoarg2.bat
917 is newly added. This file is only used on mswin32 or bccwin32.
918 * URL for test to fetch a web page is changed to
919 http://bioruby.open-bio.org/.
920
921 2008-10-07 Naohisa Goto <ng@bioruby.org>
922
923 * test/unit/bio/appl/paml/test_codeml.rb
924
925 Bug fix: error on mswin32 in
926 test_expected_options_set_in_config_file.
927 (commit 16b8f321c653502ef801d801383a019bc45f67de)
928
929 Bug fix: On mswin32, test_expected_options_set_in_config_file
930 in Bio::TestCodemlConfigGeneration failed with the error
931 "Errno::EACCESS: Permission denied" because it attempts to remove
932 the temporary file that is previously opened but not explicitly
933 closed, and, in Windows, the opend file is automatically locked
7a4b5e58 » Naohisa Goto 2009-01-21 Added recent changes and fi... 934 and protected from being removed.
3ae1a16a » Naohisa Goto 2009-01-20 Added ChangeLog and doc/Cha... 935
936 * lib/bio/command.rb, test/functional/bio/test_command.rb,
937 test/unit/bio/test_command.rb
938
939 Bio::Command improved, and added functional tests.
940 (commit bb618cdfbfb56c40249aff81b6ef84742465851c)
941
942 * In Bio::Command.call_command_* and Bio::Command.query_command_*,
943 when giving command-line array with size 1, the command might
944 passed to shell. To prevent this, changed to call a new method
945 Bio::Command#safe_command_line_array internally.
946 * Added test/functional/bio/test_command.rb, contains unit tests
947 to call external commands and to access external web sites.
948
949 2008-10-06 Naohisa Goto <ng@bioruby.org>
950
951 * lib/bio/db/biosql/sequence.rb
952
953 Bio::Sequence::SQL::Sequence#seq is changed to return a
954 Bio::Sequence::Generic object, because of avoiding to create
955 nested Bio::Sequence object in #to_biosequence and because
956 Bio::FastaFormat#seq also returns a Bio::Sequence::Generic object.
957 (commit 8fb944c964ab5e1ca8905e6c4ce8e68479952935)
958
959 2008-10-03 Raoul Jean Pierre Bonnal <raoul.bonnal@itb.cnr.it>
960
961 * lib/bio/io/biosql/taxon.rb
962
963 Added has_one :taxon_genbank_common_name,
964 :class_name => "TaxonName",
965 :conditions => "name_class = 'genbank common name'"
966 (commit dc7a18b17cad8e603e0d3c20a5a80bc2a6f0899c)
967
968 * lib/bio/db/biosql/sequence.rb
969
970 Fix taxon identification by splitting scientific name and genbank
971 common name. Fix organism/source's name composed by scientific
972 name and genbank common name.
973 (commit 5d6abcc0dcd05d7083622360489a5f4c361e0cc7)
974
975 * lib/bio/io/sql.rb
976
977 Working on tests about format import/export.
978 (commit d28a343e4bab3cc0c04ac65dce677cfee0f81a46)
979
980 * lib/bio/io/biosql/term.rb
981
982 Fix foreign keys
983 (commit c19c8766c7c0bec7561727abf2ef1bdf47d4e032)
984
985 * lib/bio/io/biosql/seqfeature_qualifier_value.rb
986
987 added composite primary keys :seqfeature_id, :term_id, :rank
988 (commit cdd6a3bfc1ab748acb0c0d9161ebeb3dc7a76544)
989
990 * lib/bio/io/biosql/ontology.rb
991
992 class cleaned.
993 (commit 81eb2c246d01790db72f0b08929bec5d862c959e)
994
995 * lib/bio/io/biosql/biodatabase.rb
996
997 class cleaned.
998 (commit 4aede5c5fee92c2f8cdf151a3e038025b6c7fd74)
999
1000 * lib/bio/db/biosql/sequence.rb
1001
1002 to_biosequence: removed not adapter comments.
1003 (commit 591fda23464c7b7031db09a8ca85deca320a5c87)
1004
1005 Removed main garbage comments.
1006 (commit c46d7a2b4e188a0592d5b49def17b9e6fd598268)
1007
1008 feature= Fix creation of Ontology and Term.
1009 (commit 95fe6d1a65e94da502529e597b137d12c3fe2fc2)
1010
1011 * lib/bio/db/biosql/biosql_to_biosequence.rb
1012
1013 :seq cleaned.
1014 (commit d6f719693286b74c1a0ea8a42c09a12f775b74dc)
1015
1016 2008-10-01 Naohisa Goto <ng@bioruby.org>
1017
1018 * test/functional/bio/io/test_ensembl.rb
1019
1020 Bug fix: 3 failures occurred in test_ensembl.rb because of recent
1021 changes in Ensembl database (the gene ENSG00000206158 used as
1022 an example in this file was removed from the Ensembl database).
1023 To fix this, the example gene is changed to ENSG00000172146
1024 (OR1A1, olfactory receptor 1A1).
1025 (commit e20c86d2cd7d4fd1723762e8a5acc3bc311a5c1b)
1026
1027 * lib/bio/db/embl/sptr.rb, test/unit/bio/db/embl/test_sptr.rb
1028
1029 Ruby 1.9 support: in Bio::SPTR, avoid using String#each and
1030 Array#to_s.
1031 (commit 5ff56653cd7cc2520c2c04acbc9ce2bf2a0fae9a)
1032
1033 * In Bio::SPTR#gn_uniprot_parser, String#each (which is removed
1034 in Ruby 1.9) is changed to each_line.
1035 * In Bio::SPTR#cc and cc_* (private) methods, Array#to_s (whose
1036 behavior is changed in Ruby 1.9) is changed to join('').
1037 * Unit test for Bio::STPR#dr method is added and changed.
1038
1039 2008-09-30 Naohisa Goto <ng@bioruby.org>
1040
1041 * lib/bio/db/embl/sptr.rb, test/unit/bio/db/embl/test_sptr.rb
1042
1043 Bug fix in Bio::SPTR#dr: raised error when asked it to return
1044 a DR key that didn't exist in the uniprot entry. Thanks to
1045 Ben Woodcroft who reports the bug and send a patch.
1046 ([BioRuby] Bio::SPTR bug and fix).
1047 (commit 3147683c0b41e3f9418e26b481bf8b3e9ce63b8c)
1048
1049 * lib/bio.rb
1050
1051 Added autoload of Bio::NCBI::REST, and BIORUBY_VERSION incremented.
7a4b5e58 » Naohisa Goto 2009-01-21 Added recent changes and fi... 1052 (commit d6a37b0fcf1fb2f6e134dcdb8e29e79ec2a8fea7)
3ae1a16a » Naohisa Goto 2009-01-20 Added ChangeLog and doc/Cha... 1053
1054 * Added autoload of Bio::NCBI::REST.
1055 * Added comments for autoloading Bio::Sequence and Bio::Blast.
1056 * BIORUBY_VERSION is temporary incremented to 1.2.2, though
1057 the version number will not be used in upcoming release.
1058 Upcoming release will probably be using larger version number.
1059
1060 2008-09-25 Raoul Jean Pierre Bonnal <raoul.bonnal@itb.cnr.it>
1061
1062 * lib/bio/db/biosql/sequence.rb
1063
1064 Updated with adapter. Problem saving big sequences.
1065 (commit 82d87fbaf70f9a46c40dded0b2db510a40964e62)
1066
1067 * lib/bio/io/biosql/* (25 files)
1068
1069 AR: explicit class and foreign_key reference.
1070 (commit 70327998186c2f943addb5d46b4bda8007ed5444)
1071
1072 2008-09-24 Naohisa Goto <ng@bioruby.org>
1073
1074 * lib/bio/db/gff.rb, test/unit/bio/db/test_gff.rb
1075
1076 Bug fix and incompatible changes in GFF2 and GFF3 attributes.
1077 (commit 7b174bb842d9dcf9fd7f4b59e8f3b13ebc0ff3d4)
1078
1079 * Bug fix: GFF2 attributes parser misunderstand semicolons.
1080 * Incompatible change in Bio::GFF::GFF2::Record#attributes
1081 and Bio::GFF::GFF3::Record#attributes. Now, instead of Hash,
1082 the method is changed to return a nested Array, containing
1083 [ tag, value ] pairs, because of supporting multiple tags
1084 in same name. If you want to get a Hash, use
1085 Record#attributes_to_hash method, though some tag-value pairs
1086 in same tag name may not be included.
1087 * Bio::GFF::Record#attribute still returns a Hash for compatibility.
7a4b5e58 » Naohisa Goto 2009-01-21 Added recent changes and fi... 1088 * New methods for getting, setting and manipulating attributes:
3ae1a16a » Naohisa Goto 2009-01-20 Added ChangeLog and doc/Cha... 1089 Bio::GFF::GFF2::Record#attribute, #get_attribute, #get_attributes,
1090 #set_attribute, #replace_attributes, #add_attribute,
7a4b5e58 » Naohisa Goto 2009-01-21 Added recent changes and fi... 1091 #delete_attribute, #delete_attributes, and #sort_attributes_by_tag!
3ae1a16a » Naohisa Goto 2009-01-20 Added ChangeLog and doc/Cha... 1092 (These are also added to Bio::GFF::GFF3::Record).
1093 It is recommended to use these methods instead of directly
7a4b5e58 » Naohisa Goto 2009-01-21 Added recent changes and fi... 1094 manipulating the array returned by Record#attributes.
3ae1a16a » Naohisa Goto 2009-01-20 Added ChangeLog and doc/Cha... 1095 * Incompatible change in GFF2 attributes parser: the priority
1096 of '"' (double quote) is greater than ';' (semicolon).
1097 Special treatment of '\;' in GFF2 is now removed.
1098 Unlike GFF2, in Bio::GFF, the '\;' can still be used for
1099 backward compatibility.
1100 * Incompatible changes in attribute values in Bio::GFF::GFF2.
1101 Now, GFF2 attribute values are automatically unescaped.
1102 In addition, if a value of an attribute is consisted of two
1103 or more tokens delimited by spaces, an object of the new class
1104 Bio::GFF::GFF2::Record::Value is returned instead of String.
1105 The new class Bio::GFF::GFF2::Record::Value aims to store
1106 a parsed value of an attribute. If you really want to get
1107 unparsed string, Value#to_s can be used.
1108 * Incompatible changes about data type in GFF2 columns:
1109 Bio::GFF::GFF2::Record#start, #end, and #frame return
1110 Integer or nil, and #score returns Float or nil.
1111 * Incompatible changes about the metadata in GFF2.
1112 The "##gff-version" line is parsed and the version string
1113 is stored to Bio::GFF::GFF2#gff_version. Other metadata
1114 lines are stored in an array obtained with a new method
1115 Bio::GFF::GFF2#metadata. Each metadata is parsed to
1116 Bio::GFF::GFF2::MetaData object.
1117 * Bio::GFF::Record#comments is renamed to #comment, and
1118 #comments= is renamed to #comment=, because they only allow
1119 a single String (or nil) and the plural form "comments"
1120 may be confusable. The "comments" and "comments=" methods
1121 can still be used, but warning messages will be shown
1122 when using in GFF2::Record and GFF3::Record objects.
1123 * New methods Bio::GFF::GFF2#to_s, Bio::GFF::GFF2::Record#to_s.
1124 * New methods Bio::GFF::GFF2::Record#comment_only?
1125 (also added in Bio::GFF::GFF3::Record).
1126 * Unit tests are added and modified.
1127
1128 2008-09-18 Naohisa Goto <ng@bioruby.org>
1129
1130 * lib/bio/appl/blast/rpsblast.rb, lib/bio/appl/blast/format0.rb,
1131 lib/bio/io/flatfile/autodetection.rb,
1132 test/unit/bio/appl/blast/test_rpsblast.rb,
1133 test/data/rpsblast/misc.rpsblast
1134
1135 Improved support for RPS-BLAST results from multi-fasta query
1136 sequences.
1137 (commit 11f1787cf93c046c06d4a33a554210d56866274e)
1138
1139 * By using Bio::FlatFile (e.g. Bio::FlatFile.open), a rpsblast
1140 result generated from multiple query sequences is automatically
7a4b5e58 » Naohisa Goto 2009-01-21 Added recent changes and fi... 1141 split into multiple Bio::Blast::RPSBlast::Report objects
3ae1a16a » Naohisa Goto 2009-01-20 Added ChangeLog and doc/Cha... 1142 corresponding to query sequences. For the purpose, new
1143 flatfile splitter class Bio::Blast::RPSBlast::RPSBlastSplitter
1144 is added.
1145 * File format autodetection for RPS-BLAST default report is added.
1146 * Bug fix: Bio::Blast::RPSBlast::Report#program returns incorrect
1147 value. To fix the bug, regular expression in
1148 Bio::Blast::Default::Report#format0_parse_header (private method)
1149 is changed.
1150 * Unit tests are added for Bio::Blast::RPSBlast.
1151
1152 2008-09-17 Naohisa Goto <ng@bioruby.org>
1153
1154 * lib/bio/io/flatfile/buffer.rb,
1155 test/unit/bio/io/flatfile/test_buffer.rb
1156
1157 Bug fix in Bio::FlatFile::BufferedInputStream#gets.
1158 (commit e15012e2a94d05308d139cb010749a1829d5c57f)
1159
1160 * Bug fix: Bio::FlatFile::BufferedInputStream#gets('') might not
1161 work correctly. Now, BufferedInputStream#gets is refactored.
1162 Note that when rs = '' (paragraph mode), the behavior may still
1163 differ from that of IO#gets('').
1164 * Test methods are added to test_buffer.rb.
1165
1166 2008-09-16 Naohisa Goto <ng@bioruby.org>
1167
1168 * lib/bio/appl/blast/wublast.rb
1169
1170 Bug fix: parse error or infinite loop for WU-BLAST reports.
1171 (commit 07d1554c945400f9202d7b856055743e11860752)
1172
1173 * Bug fix in Bio::Blast::WU::Report: fixed parse errors
1174 (errors, infinite loop, and wrong results could be generated)
1175 when parsing WU-BLAST reports generated by recent version of
1176 WU-BLAST.
1177 * New methods Bio::Blast::WU::Report#query_record_number,
1178 #exit_code, and #fatal_errors.
1179
1180 2008-09-03 Naohisa Goto <ng@bioruby.org>
1181
1182 * lib/bio/appl/blat/report.rb
1183
1184 Bug fix: headers were parsed incorrectly with warning.
1185 (commit 3ff940988b76bdff75679cdf0af4c836f76fa3a1)
1186
1187 * lib/bio/io/flatfile/splitter.rb
1188
1189 To suppress warning messages "warning: private attribute?",
1190 private attributes are explicitly specified by using "private".
1191 (commit 1440b766202a2b66ac7386b9b46928834a9c9873)
1192
1193 2008-09-01 Michael Barton <mail@michaelbarton.me.uk>
1194
1195 * lib/bio/appl/paml/codeml/report.rb
1196
1197 Added code to pull estimated tree from codeml report.
1198 (commit 64cc5ef6f2d949cc9193b08dfc3fde6b221950d7)
1199
1200 2008-09-01 Naohisa Goto <ng@bioruby.org>
1201
1202 * test/unit/bio/db/embl/test_embl_rel89.rb
1203
1204 Changed test class name because of name conflict of Bio::TestEMBL.
1205 (commit 536cdf903a3c3908c117efd554d33117d91452f4)
1206
1207 * test/unit/bio/util/restriction_enzyme/
1208
1209 To prevent possible test class name conflicts about restriction
1210 enzyme.
1211 (commit 0fe1e7d3ed02185632f4a34d8efe1f21f755b289)
1212
1213 * Tests about restriction enzyme are moved under a new module
1214 Bio::TestRestrictionEnzyme to prevent possible name conflict.
1215 * Conflicted test class names are changed.
1216
1217 2008-08-31 Naohisa Goto <ng@bioruby.org>
1218
1219 * test/unit/bio/db/test_prosite.rb
1220
1221 Fixed failed test due to the change of hash algorithm in Ruby 1.8.7.
1222 (Probably also affected in Ruby 1.9.0).
1223 (commit e86f8d757c45805389e154f06ccde5a3d9e8a557)
1224
1225 2008-08-29 Naohisa Goto <ng@bioruby.org>
1226
1227 * lib/bio/appl/blast.rb
1228
1229 Bio::Blast.reports is changed to support new BLAST XML format.
1230 (commit 02cc0695b85f18e8254aefed78a912812fc896d6)
1231
1232 * Bio::Blast.reports is changed to support new BLAST XML format.
1233 * Removed unused require.
1234
1235 2008-08-28 Naohisa Goto <ng@bioruby.org>
1236
1237 * lib/bio/appl/blast/report.rb, lib/bio/appl/blast/rexml.rb,
1238 lib/bio/appl/blast/xmlparser.rb,
1239 test/unit/bio/appl/blast/test_report.rb
1240
1241 Support for BLAST XML format with multiple queries after blastall
1242 2.2.14.
1243 (commit de7897b5690279aae14d9bded5e682458bc61f9c)
1244
1245 * BLAST XML format with multiple query sequences generated by
1246 blastall 2.2.14 or later is now supported.
1247 * New methods Bio::Blast::Report#reports, stores Bio::Blast::Report
1248 objects corresponding to the multiple query sequences.
1249 * New methods Bio::Blast::Report::Iteration#query_id, query_def,
1250 and query_len, which are available only for the new format.
1251 * New class Bio::Blast::Report::BlastXmlSplitter, flatfile splitter
1252 for Bio::FlatFile system.
1253 * Bug fix: Bio::Blast::Report#expect returned incorrect value.
1254 * Fixed typo and added tests in
1255 test/unit/bio/appl/blast/test_report.rb.
1256 * Some RDoc documents are added/modified.
1257
1258 2008-08-19 Michael Barton <mail@michaelbarton.me.uk>
1259
1260 * lib/bio/appl/paml/codeml/rates.rb
1261
1262 Updated regex for rates parser to include columns that have a '*'
1263 character.
1264
1265 * test/unit/bio/appl/paml/codeml/test_rates.rb
1266
1267 Updated testing for new rates file with * characters.
1268
1269 * test/data/paml/codeml/rates
1270
1271 Added rates file that includes positions with * characters.
1272
1273 2008-08-18 Naohisa Goto <ng@bioruby.org>
1274
1275 * test/unit/bio/io/test_ddbjxml.rb
1276
1277 Changed a failed test, and added a test for
1278 Bio::DDBJ::XML::RequestManager.
1279
1280 2008-08-16 Michael Barton <mail@michaelbarton.me.uk>
1281
1282 * lib/bio/appl/paml/, test/unit/bio/appl/paml/, test/data/paml/
1283
1284 Wrapper and parser for PAML Codeml program is added
1285 (merged from git://github.com/michaelbarton/bioruby).
1286 After merging, some changes were made by Naohisa Goto.
1287 See git log for details.
1288
1289 2008-08-15 Naohisa Goto <ng@bioruby.org>
1290
1291 * lib/bio/appl/blast.rb, lib/bio/appl/blast/genomenet.rb
1292
1293 "-m 0" (BLAST's default) format support is improved, and fixed
1294 wrong example in the RDoc of Bio::Blast#query.
1295
1296 * Added support for "-m 0" (BLAST's default) format to the Bio::Blast
1297 factory. For the purpose, Bio::Blast#parse_result (private method)
1298 is changed.
1299 * Added support for "-m 0" (default) format to the GenomeNet BLAST
1300 factory (in Bio::Blast::Remote::GenomeNet).
7a4b5e58 » Naohisa Goto 2009-01-21 Added recent changes and fi... 1301 * Bug fix: wrong example in the RDoc in Bio::Blast#query is changed.
3ae1a16a » Naohisa Goto 2009-01-20 Added ChangeLog and doc/Cha... 1302 * Bio::Blast#set_option (private method) is changed to determine
1303 format correctly.
1304
1305 * lib/bio/appl/blast/ddbj.rb, lib/bio/io/ddbjxml.rb
1306
1307 Changed always using REST version of RequestManager, and changed
1308 to raise error when busy.
1309
1310 * In Bio::Blast::Remote::DDBJ, changed always to use REST version
1311 for RequestManager, because of suppressing warning messages.
1312 * In Bio::DDBJ::XML::RequestManager, module REST_RequestManager is
1313 changed to class REST.
1314 * In Bio::Blast::Remote::DDBJ#exec_ddbj, changed to raise
1315 RuntimeError when "The search and analysis service by WWW is very
1316 busy now" message is returned from the server (which implies
1317 invalid options or queries may be given).
1318
1319 2008-08-14 Naohisa Goto <ng@bioruby.org>
1320
1321 * lib/bio/appl/blast.rb, lib/bio/appl/blast/genomenet.rb,
1322 lib/bio/appl/blast/remote.rb
1323
1324 Bio::Blast#exec_genomenet is moved to genomenet.rb, with bug fix.
1325
1326 * Bio::Blast#exec_genomenet is moved to
1327 lib/bio/appl/blast/genomenet.rb.
1328 * Incompatible change: Bio::Blast#exec_* is changed to return
1329 String. Parsing the string is now processed in query method.
1330 * New module Bio::Blast::Remote, to store remote BLAST factories.
1331 * New module Bio::Blast::Remote::GenomeNet (and Genomenet for
1332 lazy including), to store exec_genomenet and other methods.
1333 In the future, it might be a standalone class (or something else).
1334 * New module methods Bio::Blast::Remote::GenomeNet.databases,
1335 nucleotide_databases, protein_databases, and database_description,
1336 to provide information of available databases.
1337 * Bug fix: remote BLAST on GenomeNet with long query sequences
1338 fails because of the change of the behavior of the remote site.
1339 * Incompatible change: Bio::Blast#options= can change program,
1340 db, format, matrix, and filter instance variables.
1341 * Bio::Blast#format= is added.
1342 * Bio::Blast.local changed to accept 4th argument: full path to
1343 the blastall command.
1344
1345 * lib/bio/appl/blast/ddbj.rb, lib/bio/io/ddbjxml.rb,
1346 lib/bio/appl/blast/genomenet.rb, lib/bio/appl/blast/remote.rb,
1347 lib/bio/appl/blast.rb
1348
1349 New module Bio::Blast::Remote::DDBJ, remote BLAST on DDBJ.
1350
1351 * New module Bio::Blast::Remote::DDBJ, remote BLAST routine using
1352 DDBJ Web API for Biology (WABI). Now, Bio::Blast.new(program,
1353 db, options, 'ddbj') works.
1354 * New class Bio::DDBJ::XML::RequestManager. In this class,
1355 workaround for Ruby 1.8.5's bundled SOAP4R is made.
1356 * Some common codes are moved from
1357 Bio::Blast::Remote::GenomeNet::Information to
1358 Bio::Blast::Remote::Information.
1359
1360 * lib/bio/io/ddbjxml.rb
1361
1362 Changed to use DDBJ REST interface for a workaround instead of
1363 editing WSDL. (commit a64c8da5df5076c5f55b54b7f134d22a2e8d281c)
1364
1365 2008-08-09 Naohisa Goto <ng@bioruby.org>
1366
1367 * lib/bio/appl/blast.rb
1368
1369 * Bug fix: Bio::Blast raises TypeError without "-m" option,
1370 reported by Natapol Pornputapong.
1371 * New class Bio::Blast::NCBIOptions to treat command-line options
1372 for blastall (and for other NCBI tools, e.g. formatdb).
1373 * Changed not to overwrite @filter, @matrix or @format unless
1374 '-F', '-M', or '-m' option is given, respectively.
1375
fbf3d241 » ngoto 2008-07-30 ChangeLog about merge of bi... 1376 2008-07-30 BioHackathon2008 participants from BioRuby project
1377
1378 * Branch 'biohackathon2008' is merged.
1379 See doc/Changes-1.3.rd for incompatible changes.
1380
1381 * lib/bio/sequence.rb, lib/bio/sequence/
1382 * lib/bio/db/embl/
1383 * lib/bio/db/genbank/
1384 * lib/bio/db/fasta.rb, lib/bio/db/fasta/
1385
1386 A new method #to_biosequence is added to Bio::EMBL, Bio::GenBank
1387 and Bio::FastaFormat. Bio::FastaFormat#to_seq is now an alias of
1388 the #to_biosequence method.
1389
1390 Bio::Sequence#output is added to output formatted text.
1391 Supported formats are: EMBL, GenBank, Fasta, or raw.
1392
1393 Written by Naohisa Goto and Jan Aerts.
1394
1395 * lib/bio/db/biosql/
1396 * lib/bio/io/sql.rb, lib/bio/io/biosql/
1397
1398 New BioSQL implementation by Raoul Jean Pierre Bonnal.
1399
1400 * lib/bio/reference.rb
1401 * lib/bio/feature.rb
1402
1403 Bio::References and Bio::Features are obsoleted.
1404 For more information, see doc/Changes-1.3.rd.
1405
1406 * (Many changes are not listed here. See git log for details.)
1407
1408 2008-07-30 Naohisa Goto <ng@bioruby.org>
1409
1410 * lib/bio/db/gff.rb, test/unit/bio/db/test_gff.rb
1411
1412 Branch 'test-gff3' in git://github.com/ngoto/bioruby is merged.
1413 Fixed gff3 attribute bug, and many improvements are added.
1414 See doc/Changes-1.3.rd for incompatible changes.
1415 Thanks to Ben Woodcroft who reported the bug and contributed codes.
1416
46713aed » ngoto 2008-07-30 Merge changes to ChangeLog ... 1417 2008-07-29 Naohisa Goto <ng@bioruby.org>
1418
1419 * lib/bio/appl/blast/format0.rb
1420
1421 Bug fix: fixed ScanError when bit score is in exponential notation
1422 such as 1.234e+5. Regular expressions for numerics including
1423 exponential notations are changed to get correct values.
1424
1425 2008-07-18 Naohisa Goto <ng@bioruby.org>
1426
1427 * lib/bio/appl/hmmer.rb
1428
1429 Bug fix: ArgumentError caused by misspelling of a variable name.
1430
1431 2008-06-23 Jan Aerts <jan.aerts@gmail.com>
1432
1433 * README.rdoc
1434 * README_DEV.rdoc
1435 * gemspec.rb
1436
1437 Renamed README files to RDoc gets parsed on github website.
1438 (commit 34b7693f74de2358759e955d8ce36cfe15e64b54)
1439 Edited README.rdoc and README_DEV.rdoc to reflect move from CVS
1440 to git.
1441 (commit a61b16163d3ca74f3f7c8d8e8f03f5f8c68dee60)
1442
1443 2008-06-13 Naohisa Goto <ng@bioruby.org>
1444
1445 * lib/bio/reference.rb
1446 * test/unit/bio/test_reference.rb
1447
1448 * New method Bio::Reference#pubmed_url added (renamed the url method
1449 in CVS revision 1.25).
1450 * Bio::Reference#endnote is changed not to overwrite url if url is
1451 already given by user.
1452 * Improvement of Bio::Reference#bibtex method. (Idea to improve
1453 bibtex method is originally made by Pjotr Prins.)
1454
1455 * test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb
1456 "require 'bio/sequence'" is needed to run the tests in this file.
1457 (commit 735e3563b723645afa65f0e4213a7c92152f68ec)
1458
1459 2008-05-19 Pjotr Prins <pjotr.prins@wur.nl>
1460
1461 * sample/fastasort.rb
1462
1463 Simple example for sorting a flatfile
1464 (commit 677ac7c0707860f0478e75f72f23faa05b29dc6d)
1465
1466 * doc/Tutorial.rd
1467 * sample/fastagrep.rb
1468 * sample/fastasort.rb
1469
1470 Piping FASTA files (examples and doc)
1471 (commit ecd5e04477246dcf6cac84a6fbd21fb59efa3cf0)
1472
e8453b9a » Naohisa Goto 2008-05-14 ChangeLog for lib/bio/appl/... 1473 2008-05-14 Naohisa Goto <ng@bioruby.org>
1474
1475 * lib/bio/appl/blast/format0.rb
1476
1477 Bug fix: Possibly because of the output format changes of PHI-BLAST,
1478 Bio::Blast::Default::Report::Iteration#eff_space (and the shortcut
1479 method in the Report class) failed for PHI-BLAST (blastpgp) results,
1480 and Iteration#pattern and #pattern_positions (and the
1481 shortcut methods in the Report class) returned incorrect values.
1482
cb74035a » Naohisa Goto 2008-05-12 * lib/bio/appl/blast/xmlpa... 1483 2008-05-12 Naohisa Goto <ng@bioruby.org>
1484
1485 * lib/bio/appl/blast/xmlparser.rb, lib/bio/appl/blast/rexml.rb
1486
1487 Bug fix: unit test sometime fails due to improper treatment of some
1488 Blast parameters and difference between rexml and xmlparser.
1489 To fix the bug, types of some parameters may be changed, e.g.
1490 Bio::Blast::Report#expect is changed to return Float or nil.
1491
1492 * lib/bio/appl/blast/format0.rb
1493
1494 Bug fix: Bio::Blast::Default::Report#eff_space returns wrong value
1495 ("Effective length of database"). It should return the value of
1496 "Effective search space".
1497
1498 * test/unit/bio/appl/blast/test_xmlparser.rb
1499
1500 Bug fix: tests in test/unit/bio/appl/blast/test_report.rb were
1501 ignored because of conflicts of the names of test classes.
1502 Class name in test_xmlparser.rb is changed to fix the bug.
1503
46713aed » ngoto 2008-07-30 Merge changes to ChangeLog ... 1504 2008-04-23 Naohisa Goto <ng@bioruby.org>
1505
1506 * lib/bio/db/embl/common.rb
1507
1508 Bug fix: Bio::EMBL#references failed to parse journal name,
1509 volume, issue, pages, and year. In addition, it might failed
1510 to parse PubMed ID.
1511 (commit c715f51729b115309a78cf29fdce7fef992da875)
1512
1513 2008-04-18 Naohisa Goto <ng@bioruby.org>
1514
1515 * lib/bio/db/embl/sptr.rb
1516
1517 Bug fix: Bio::SPTR#references raises NoMethodError since
1518 lib/bio/db/embl/sptr.rb CVS version 1.34.
1519 (commit 1b3e484e19c9c547cecfe53858a646b525685e0d)
1520
eb71e54a » Naohisa Goto 2008-04-15 Newly added RPS-Blast defau... 1521 2008-04-15 Naohisa Goto <ng@bioruby.org>
1522
1523 * lib/bio/appl/blast/rpsblast.rb
1524
1525 Newly added RPS-Blast default (-m 0) output parser.
1526
96d97605 » Naohisa Goto 2008-04-01 ChangeLog added for lib/bio... 1527 2008-04-01 Naohisa Goto <ng@bioruby.org>
1528
1529 * lib/bio/appl/blast/format0.rb
1530
1531 Fixed a bug: Failed to parse database name in some cases.
1532 Thanks to Tomoaki Nishiyama who reported the bug and sent patches
1533 ([BioRuby-ja] BLAST format0 parser fails header parsing output
1534 of specific databases).
1535
1536 * lib/bio/db/pdb/chain.rb, lib/bio/db/pdb/pdb.rb
1537
1538 Fixed bugs: Bio::PDB::Chain#aaseq failed for nucleotide chain;
1539 Failed to parse chains for some entries (e.g. 1B2M).
1540 Thanks to Semin Lee who reported the bugs and sent patches
1541 ([BioRuby] Bio::PDB parsing problem (1B2M)).
1542
46713aed » ngoto 2008-07-30 Merge changes to ChangeLog ... 1543 2008-02-19 Toshiaki Katayama <k@bioruby.org>
1544
1545 * lib/bio/io/ncbirest.rb
1546 * lib/bio/io/pubmed.rb
1547
1548 NCBI E-Utilities (REST) functionality is separated to ncbirest.rb
1549 and pubmed.rb is changed to utilize the Bio::NCBI::REST class for
1550 esearch and efetch. You can now search and retrieve any database
1551 in any format that NCBI supports by E-Utilities through the
1552 Bio::NCBI::REST interface (currently, only esearch and efetch methods
1553 are implemented).
1554 (commit 0677bb69044cf6cfba453420bc1bbeb422f691c1)
1555 (commit f60e9f8153efacff0c97d12fb5c0830ebeb02edd)
1556 (commit 6e4670ab5e67ca596788f4c26a95a9687d36ce84)
1557
1558 2008-02-13 Pjotr Prins <pjotr.prins@wur.nl>
1559
1560 * doc/Tutorial.rd
1561 (commit d7ee01d86d6982f6b8aa19eba9adac95bebb08e8)
1562
cac57400 » Naohisa Goto 2008-02-11 ChangeLog for lib/bio/appl/... 1563 2008-02-12 Naohisa Goto <ng@bioruby.org>
1564
1565 * lib/bio/appl/blast/format0.rb
1566
1567 Fixed bugs: Failed to parse query length for long query
1568 (>= 10000 letters) as comma is inserted for digit separator
1569 by blastall; Failed to parse e-value for some BLASTX results.
1570 Thanks to Shuji Shigenobu who reported the bugs and sent patches.
1571
46713aed » ngoto 2008-07-30 Merge changes to ChangeLog ... 1572 2008-02-11 Pjotr Prins <pjotr.prins@wur.nl>
1573
1574 * doc/Tutorial.rd
1575
1576 Expanding on the Tutorial
1577 (bdc1d14f497909041fa761f659a74d98702a335a)
1578 Minor adjustments to Tutorial
1579 (72b5f4f0667a3a0c44ca31b0ab8228381e37919c)
1580
1581 2008-02-06 Pjotr Prins <pjotr.prins@wur.nl>
1582
1583 * sample/na2aa.rb
1584
1585 Simple example to translate any NA to AA fasta
1586 (commit 433f974219cf04342935c1760464af24a5696c49)
1587
1588 2008-02-05 Pjotr Prins <pjotr.prins@wur.nl>
1589
1590 * sample/gb2fasta.rb
1591
1592 Fixed broken require in gb2fasta example
1593 (commit b55daed0d6cff2e45155be01ef2a946925c972cf)
1594
1595 2008-02-05 Pjotr Prins <pjotr.prins@wur.nl>
1596
1597 * doc/Tutorial.rd
1598
1599 Minor tweak to Tutorial.rd
1600 (commit 75416d780f99de24498a47fd22703d74f9a22329)
1601
1602 2008-02-03 Pjotr Prins <pjotr.prins@wur.nl>
1603
1604 * doc/Tutorial.rd
1605
1606 More doctests in Tutorial.rd
1607 (commit 39d182bb67977956c0f22631ac596d65ccce74ff)
1608
1609 2008-02-02 Pjotr Prins <pjotr.prins@wur.nl>
1610
1611 * doc/Tutorial.rd
1612
1613 Tabs in the Tutorial broke the rd parser - the Wiki will be fixed
1614 now.
1615 (commit 49078a5dea4f16f44add1882c60bf75df67ea19b)
1616 Updating tutorial.
1617 (commit f2f2005c3964f37e2d65afef0d52e63950d6bcb7)
1618 (commit d2b05581953712d0ac67ba0de1aa43853ed4e27f)
1619
1aa241b1 » ktym 2008-02-01 fix typo 1620 2008-02-02 Toshiaki Katayama <k@bioruby.org>
153b7883 » ktym 2008-01-09 * Bio::Hinv is added 1621
20f02080 » ktym 2008-02-01 * lib/bio/shell/rails/vendo... 1622 * lib/bio/shell/rails/vendor/plugins/
1623
1624 The 'generators' directory is moved under the 'bioruby' subdirectory
1625 so that 'bioruby --rails' command can work with Rails 2.x series
1626 in addition to the Rails 1.2.x series.
1627
46713aed » ngoto 2008-07-30 Merge changes to ChangeLog ... 1628 2008-01-30 Mitsuteru Nakao <n@bioruby.org>
1629
1630 * lib/bio/appl/blast.rb
1631
1632 Fixed the bug at building the blastall command line options ('-m 0').
1633 (commit 61443d177847825505103488573186dfc4e7568e)
1634
1635 2008-01-10 Naohisa Goto <ng@bioruby.org>
1636
1637 * lib/bio/appl/emboss.rb
1638
1639 Added a method Bio::EMBOSS.run(program, arguments...)
1640 and Bio::EMBOSS.new is obsoleted.
1641 (commit fa04d97b073aefe05edc34a84498ba0a57ff98d2)
1642
20f02080 » ktym 2008-02-01 * lib/bio/shell/rails/vendo... 1643 2008-01-10 Toshiaki Katayama <k@bioruby.org>
1644
153b7883 » ktym 2008-01-09 * Bio::Hinv is added 1645 * lib/bio/io/hinv.rb
1646
1647 Bio::Hinv to access the H-invitational DB (http://h-invitational.jp/)
1648 web service in REST mode is added.
1649
23cf32c7 » ktym 2007-12-29 * preparation for BioRuby 1... 1650 2007-12-30 Toshiaki Katayama <k@bioruby.org>
1651
1652 * BioRuby 1.2.1 released
1653
1654 This version is not Ruby 1.9 (released few days ago) compliant yet.
1655
3cf0b1b4 » Naohisa Goto 2007-12-27 Fixed parse error for NCBI ... 1656 2007-12-28 Naohisa Goto <ng@bioruby.org>
1657
1658 * lib/bio/appl/blast/report/format0.rb
1659
23cf32c7 » ktym 2007-12-29 * preparation for BioRuby 1... 1660 Fixed parse error when compisition-based statistics were enabled.
1661 In addition, Bio::Blast::Default::Report#references and
1662 Bio::Blast::Default::Report::HSP#stat_method methods are added.
1663 In NCBI BLAST 2.2.17, default option of composition-based
1664 statistics for blastp or tblastn are changed to be enabled
1665 by default.
3cf0b1b4 » Naohisa Goto 2007-12-27 Fixed parse error for NCBI ... 1666
1667 * lib/bio/appl/blast/report/wublast.rb
1668
23cf32c7 » ktym 2007-12-29 * preparation for BioRuby 1... 1669 Changed to follow the above changes in format0.rb.
3cf0b1b4 » Naohisa Goto 2007-12-27 Fixed parse error for NCBI ... 1670
8a0a73c1 » Naohisa Goto 2007-12-28 changes of lib/bio/sequence... 1671 * lib/bio/sequence/common.rb
1672
23cf32c7 » ktym 2007-12-29 * preparation for BioRuby 1... 1673 Ruby 1.9 compliant: in window_search method, a local variable name
1674 outside the iterator loop is changed not to be shadowed by the
1675 iterator variable.
8a0a73c1 » Naohisa Goto 2007-12-28 changes of lib/bio/sequence... 1676
1677 * lib/bio/db/pdb/pdb.rb
1678
23cf32c7 » ktym 2007-12-29 * preparation for BioRuby 1... 1679 Ruby 1.9 compliant: changed to avoid "RuntimeError: implicit
1680 argument passing of super from method defined by define_method()
1681 is not supported. Specify all arguments explicitly." error.
8a0a73c1 » Naohisa Goto 2007-12-28 changes of lib/bio/sequence... 1682
23cf32c7 » ktym 2007-12-29 * preparation for BioRuby 1... 1683 Ruby 1.9 compliant: Bio::PDB::Record.get_record_class and
1684 Bio::PDB::Record.create_definition_hash (Note: they should only
1685 be internally used by PDB parser and users should not call them)
1686 are changed to follow the change of Module#constants which
1687 returns an array of Symbol instead of String.
d405ed08 » Naohisa Goto 2007-12-28 Ruby 1.9 compliant: Bio::PD... 1688
8880267f » Naohisa Goto 2007-12-26 changelog for changes of li... 1689 2007-12-26 Naohisa Goto <ng@bioruby.org>
1690
1691 * lib/bio/alignment.rb
1692
1693 Ruby 1.9 compliant: in EnumerableExtension#each_window and
1694 OriginalAlignment#index methods, local variable names outside the
1695 iterator loops are changed not to be shadowed by iterator
1696 variables.
1697
1698 Warning messages for uninitialized instance variables of
1699 @gap_regexp, @gap_char, @missing_char, and @seqclass
1700 are suppressed.
1701
1702 * test/unit/bio/test_alignment.rb
1703
1704 Ruby 1.9 compliant: Ruby 1.9 compliant: The last comma in Array.[]
1705 is no longer allowed. (For example,
1706 class A < Array; end; A[ 1, 2, 3, ]
1707 raises syntax error in Ruby 1.9.)
1708
3476cb49 » ktym 2007-12-20 * In Bio::MEDLINE, doi and ... 1709 2007-12-21 Toshiaki Katayama <k@bioruby.org>
1710
1711 * lib/bio/db/medline.rb
1712
1713 Added doi and pii methods to extract DOI and PII number from AID field
1714
3a4d5e99 » Naohisa Goto 2007-12-18 ChangeLog added for changes... 1715 2007-12-18 Naohisa Goto <ng@bioruby.org>
1716
1717 * lib/bio/db/pdb/pdb.rb
1718
23cf32c7 » ktym 2007-12-29 * preparation for BioRuby 1... 1719 Bio::PDB#inspect is added to prevent memory exhaust problem.
1720 ([BioRuby] Parse big PDB use up all memory)
3a4d5e99 » Naohisa Goto 2007-12-18 ChangeLog added for changes... 1721
1722 * lib/bio/db/pdb/model.rb
1723
23cf32c7 » ktym 2007-12-29 * preparation for BioRuby 1... 1724 Bio::PDB::Model#inspect is added.
3a4d5e99 » Naohisa Goto 2007-12-18 ChangeLog added for changes... 1725
1726 * lib/bio/db/pdb/chain.rb
1727
23cf32c7 » ktym 2007-12-29 * preparation for BioRuby 1... 1728 Bio::PDB::Chain#inspect is added.
3a4d5e99 » Naohisa Goto 2007-12-18 ChangeLog added for changes... 1729
1730 * lib/bio/db/pdb/residue.rb
1731
23cf32c7 » ktym 2007-12-29 * preparation for BioRuby 1... 1732 Bio::PDB::Residue#inspect is added.
1733 This also affects Bio::PDB::Heterogen#inspect.
3a4d5e99 » Naohisa Goto 2007-12-18 ChangeLog added for changes... 1734
52f2c174 » ktym 2007-12-14 * preparation for BioRuby 1... 1735 2007-12-15 Toshiaki Katayama <k@bioruby.org>
1736
1737 * BioRuby 1.2.0 released
1738
1739 * BioRuby shell is improved
1740 * file save functionality is fixed
1741 * deprecated require_gem is changed to gem to suppress warnings
1742 * deprecated end_form_tag is rewrited to suppress warnings
1743 * images for Rails shell are separated to the bioruby directory
1744 * spinner is shown during the evaluation
1745 * background image in the textarea is removed for the visibility
1746 * Bio::Blast is fixed to parse -m 8 formatted result correctly
1747 * Bio::PubMed is rewrited to enhance its functionality
1748 * e.g. 'rettype' => 'count' and 'retmode' => 'xml' are available
1749 * Bio::FlatFile is improved to accept recent MEDLINE format
1750 * Bio::KEGG::COMPOUND is enhanced to utilize REMARK field
1751 * Bio::KEGG::API is fixed to skip filter when the value is Fixnum
1752 * A number of minor bug fixes
1753
8d16bd50 » Naohisa Goto 2007-12-12 * lib/bio/db/newick.rb: 1754 2007-12-12 Naohisa Goto <ng@bioruby.org>
1755
1756 * lib/bio/db/newick.rb:
1757
1758 Changed to be compliant with the Gary Olsen's Interpretation of
1759 the "Newick's 8:45" Tree Format Standard.
1760
1761 * test/unit/bio/db/test_newick.rb
1762
1763 More tests are added.
1764
1765 * lib/bio/io/flatfile/indexer.rb
1766
1767 Fixed a misspelling in Bio::FlatFileIndex.formatstring2class.
1768
52f2c174 » ktym 2007-12-14 * preparation for BioRuby 1... 1769 2007-11-28 Toshiaki Katayama <k@bioruby.org>
81c49e77 » ktym 2007-11-10 * updated 1770
1771 * lib/bio/io/pubmed.rb:
1772
1773 Fixed search, query methods (but use of esearch and efetch is
1774 strongly recommended).
1775
52f2c174 » ktym 2007-12-14 * preparation for BioRuby 1... 1776 efetch method is enhanced to accept any PubMed search options
1777 as a hash (to retrieve in XML format etc.)
1778
1779 Changed to wait 3 seconds among each access by default to be
1780 compliant with the NCBI terms (Make no more than one request
1781 every 3 seconds).
1782
1783 All Bio::PubMed.* class methods are changed to instance methods
1784 (interface as the class methods are remained for the backward
1785 compatibility).
1786
6eae2bb5 » ktym 2007-07-18 * BioRuby 1.1.0 is released 1787 2007-07-19 Toshiaki Katayama <k@bioruby.org>
1788
1789 * BioRuby 1.1.0 released
1790
54457543 » ktym 2007-07-18 * Added changes made by Kat... 1791 2007-07-17 Toshiaki Katayama <k@bioruby.org>
1792
1793 * lib/bio/io/das.rb
1794
1795 Fixed that mapmaster method to return correct value (mapmaseter's
1796 URL). This bug is reported and fixed by Dave Thorne.
1797
31eab903 » Naohisa Goto 2007-07-16 documents are added 1798 2007-07-16 Naohisa Goto <ng@bioruby.org>
1799
1800 * lib/bio/mafft/report.rb
1801
54457543 » ktym 2007-07-18 * Added changes made by Kat... 1802 For generic multi-fasta formatted sequence alignment,
1803 Bio::Alignment::MultiFastaFormat is newly added based on
1804 Bio::MAFFT::Report class, and Bio::MAFFT::Report is
1805 changed to inherit the new class.
1806 Tests are added in test/unit/bio/appl/mafft/test_report.rb.
31eab903 » Naohisa Goto 2007-07-16 documents are added 1807
1808 * lib/bio/alignment.rb
1809
54457543 » ktym 2007-07-18 * Added changes made by Kat... 1810 New modules and classes Bio::Alignment::FactoryTemplate::* are added.
1811 They are used by following three new classes.
31eab903 » Naohisa Goto 2007-07-16 documents are added 1812
1813 * lib/bio/appl/muscle.rb
1814 * lib/bio/appl/probcons.rb
1815 * lib/bio/appl/tcoffee.rb
1816
54457543 » ktym 2007-07-18 * Added changes made by Kat... 1817 New classess Bio::Muscle, Bio::Probcons, and Bio::Tcoffee are added
1818 for MUSCLE, ProbCons, and T-Coffee multiple alignment programs.
1819 Contributed by Jeffrey Blakeslee and colleagues.
31eab903 » Naohisa Goto 2007-07-16 documents are added 1820
1821 * lib/bio/appl/clustalw.rb
1822 * lib/bio/appl/mafft.rb
1823
54457543 » ktym 2007-07-18 * Added changes made by Kat... 1824 Interfaces of Bio::ClustalW and Bio::MAFFT are added/modified
1825 to follow Bio::Alignment::FactoryTemplate (but not yet changed to
1826 use it).
1827
1828 2007-07-09 Toshiaki Katayama <k@bioruby.org>
1829
1830 * BioRuby shell on Rails has new CSS theme
1831
1832 Completely new design for BioRuby shell on Rails translated from
1833 the 'DibdoltRed' theme on www.openwebdesign.org which is created by
1834 Darjan Panic and Brian Green as a public domain work!
1835
1836 2007-07-09 Toshiaki Katayama <k@bioruby.org>
1837
1838 * lib/bio/db/kegg/taxonomy.rb
1839
1840 Newly added KEGG taxonomy file parser which treats taxonomic tree
1841 structure of the KEGG organisms. The file is available at
1842 ftp://ftp.genome.jp/pub/kegg/genes/taxonomy
1843 and is a replacement of the previously used keggtab file (obsoleted).
1844
1845 * lib/bio/db/kegg/keggtab.rb
1846
1847 Bio::KEGG::Keggtab is obsoleted as the file is no longer provided.
1848 Use Bio::KEGG::Taxonomy (lib/bio/db/kegg/taxonomy.rb) instead.
1849
1850 * lib/bio/shell/plugin/soap.rb
1851
1852 Newly added web service plugins for BioRuby shell which supports
1853 NCBI SOAP, EBI SOAP and DDBJ XML in addition to the KEGG API.
31eab903 » Naohisa Goto 2007-07-16 documents are added 1854
bb099902 » Naohisa Goto 2007-07-09 Bio::FlatFile.foreach is ad... 1855 2007-07-09 Naohisa Goto <ng@bioruby.org>
ee36db73 » Naohisa Goto 2007-07-10 Pdb_LString.new is changed ... 1856
1857 * lib/bio/db/pdb/pdb.rb
1858
54457543 » ktym 2007-07-18 * Added changes made by Kat... 1859 Pdb_LString.new is changed not to raise error for nil.
ee36db73 » Naohisa Goto 2007-07-10 Pdb_LString.new is changed ... 1860
54457543 » ktym 2007-07-18 * Added changes made by Kat... 1861 Fixed a bug when below records does not exist in a PDB entry:
1862 REMARK (remark), JRNL (jrnl), HELIX (helix),
1863 TURN (turn), SHEET (sheet), SSBOND (ssbond), SEQRES (seqres),
1864 DBREF (dbref), KEYWDS (keywords), AUTHOR (authors),
1865 HEADER (entry_id, accession, classification),
1866 TITLE (definition), and REVDAT (version) records (methods).
ee36db73 » Naohisa Goto 2007-07-10 Pdb_LString.new is changed ... 1867
54457543 » ktym 2007-07-18 * Added changes made by Kat... 1868 Incompatible change: Bio::PDB#record is changed to return
1869 an empty array for nonexistent record.
ee36db73 » Naohisa Goto 2007-07-10 Pdb_LString.new is changed ... 1870
54457543 » ktym 2007-07-18 * Added changes made by Kat... 1871 (reported by Mikael Borg)
ee36db73 » Naohisa Goto 2007-07-10 Pdb_LString.new is changed ... 1872
1873 2007-07-09 Naohisa Goto <ng@bioruby.org>
bb099902 » Naohisa Goto 2007-07-09 Bio::FlatFile.foreach is ad... 1874
1875 * lib/bio/io/flatfile.rb
1876
54457543 » ktym 2007-07-18 * Added changes made by Kat... 1877 Bio::FlatFile.foreach is added (which is suggested by IO.foreach).
1878
1879 2007-06-28 Toshiaki Katayama <k@bioruby.org>
1880
1881 * lib/bio/shell/setup.rb, core.rb
1882
1883 Changed not to use Dir.chdir by caching full path of the save
1884 directory at a start up time, so that user can freely change
1885 the work directory without affecting object/history saving
1886 functionality.
1887
1888 Bio::Shell.cache[:savedir] stores the session saving directory
1889 (session means shell/session/{config,history,object} files),
1890 Bio::Shell.cache[:workdir] stores the working directory at a start
1891 up time (can be same directory with the :savedir) and both are
1892 converted and stored as full path allowing user to use Dir.chdir
1893 in the shell session).
1894
1895 If --rails (-r) option is applied, 'bioruby' command will run in
1896 the Rails server mode, and the server will start in the :savedir.
1897
1898 (A) IRB mode
1899
1900 1. run in the current directory and the session will be saved
1901 in the ~/.bioruby directory
1902
1903 % bioruby
1904
1905 2. run in the current directory and the session will be saved
1906 in the foo/bar directory
1907
1908 % bioruby foo/bar
1909
1910 3. run in the current directory and the session will be saved
1911 in the /tmp/foo/bar directory
1912
1913 % bioruby /tmp/foo/bar
1914
1915 (B) Rails mode
1916
1917 4. run in the ~/.bioruby directory and the session will also be saved
1918 in the ~/.bioruby directory
1919
1920 % bioruby -r
1921
1922 5. run in the foo/bar directory and the session will also be saved
1923 in the foo/bar directory
1924
1925 % bioruby -r foo/bar
1926
1927 6. run in the /tmp/foo/bar directory and the session will also be
1928 saved in the /tmp/foo/bar directory
1929
1930 % bioruby -r /tmp/foo/bar
1931
1932 (C) Script mode
1933
1934 7. run in the current directory using the session saved
1935 in the ~/.bioruby directory
1936
1937 % bioruby ~/.bioruby/shell/script.rb
1938
1939 8. run in the current directory using the session saved
1940 in the foo/bar directory
1941
1942 % bioruby foo/bar/shell/script.rb
1943
1944 9. run in the current directory using the session saved
1945 in the /tmp/foo/bar directory
1946
1947 % bioruby /tmp/foo/bar/shell/script.rb
1948
1949 2007-06-21 Toshiaki Katayama <k@bioruby.org>
1950
1951 * lib/bio/shell/setup.rb
1952
1953 If no directory is specified to the bioruby command,
1954 use ~/.bioruby directory as the default save directory
1955 instead of the current directory, as suggested by Jun Sese.
1956
1957 User can use 'bioruby' command without botherd by directories
1958 and files previously created by the 'bioruby' command
1959 in the current directory even when not needed.
1960
1961 2007-05-19 Toshiaki Katayama <k@bioruby.org>
1962
1963 * lib/bio/appl/fasta.rb
1964
1965 Bug fixed that exec_local fails to exec when @ktup is nil.
1966 This problem is reported and fixed by Fredrik Johansson.
1967
1968 * lib/bio/db/gff.rb
1969
1970 parser_attributes method in GFF3 class is modified to use
1971 '=' char as a separator instead of ' ' (which is used in
1972 GFF2 spec).
1973
1974 2007-04-06 Toshiaki Katayama <k@bioruby.org>
1975
1976 * COPYING, COPYING.LIB are removed
1977
1978 BioRuby is now distributed under the same terms as Ruby.
1979
1980 On behalf of the BioRuby developer, I have asked all authors of
1981 the BioRuby code to change BioRuby's license from LGPL to Ruby's.
1982 And we have finished to change license of all modules in the BioRuby
1983 library. This means that Ruby user can freely use BioRuby library
1984 without being annoyed by licensing issues.
1985
1986 * lib/bio/db/kegg/ko.rb is renamed to lib/bio/db/kegg/ortholog.rb
1987
1988 KEGG KO database is renamed to KEGG ORTHOLOG database, thus we
1989 follow the change. Bio::KEGG::KO is renamed to Bio::KEGG::ORTHOLOG.
1990
1991 Bio::KEGG::ORTHOLOG#genes, dblinks methods are rewrited to use
1992 lines_fetch method.
1993
1994 * lib/bio/data/aa.rb
1995
1996 to_re method is changed that the generated regexp to include
1997 ambiguous amino acid itself - replacement of amino acid X should
1998 include X itself.
1999
2000 2007-04-05 Trevor Wennblom <trevor@corevx.com>
2001
2002 * License headers are completely rewrited to Ruby's.
bb099902 » Naohisa Goto 2007-07-09 Bio::FlatFile.foreach is ad... 2003
d6f4b42b » Naohisa Goto 2007-04-02 Incompatible change: Bio::M... 2004 2007-04-02 Naohisa Goto <ng@bioruby.org>
2005
2006 * lib/bio/appl/mafft.rb
2007
54457543 » ktym 2007-07-18 * Added changes made by Kat... 2008 Incompatible change: Bio::MAFFT#output is changed to return
2009 a string of multi-fasta formmatted text. To get an array of
2010 Bio::FastaFormat objects (as of 1.0 or before), please use
2011 report.data instead.
2012
2013 2007-03-29 Toshiaki Katayama <k@bioruby.org>
2014
2015 * lib/bio/db/kegg/cell.rb
2016
2017 Obsoleted as the KEGG CELL database is not publically available
2018 any more.
2019
2020 2007-03-28 Toshiaki Katayama <k@bioruby.org>
2021
2022 * lib/bio/shell/rails/.../bioruby_controller.rb
2023
2024 BioRuby shell on Rails access is changed to be limited only from
2025 the localhost for security reason (if local_request?).
2026
2027 * lib/bio/command.rb
2028
2029 The post_form method is modified to accept URL as a string and
2030 extended to accept params as
2031 array of string
2032 array of hash
2033 array of array
2034 or
2035 string
2036 in addition to hash (also can be ommited if not needed - defaults
2037 to nil).
2038
2039 Keys and parameters of params are forced to use to_s for sure.
2040
2041 * lib/bio/io/ensembl.rb
2042
2043 Re-designed to allows user to use Bio::Ensembl.new without
2044 creating inherited sub class.
2045
2046 Changed to use Bio::Command.post_form
2047
2048 * lib/bio/das.rb
2049
2050 Changed to use Bio::Command
2051
2052 * lib/bio/shell/plugin/das.rb
2053
2054 Newly added BioDAS client plugin for BioRuby shell.
2055
2056 das.list_sequences
2057 das.dna
2058 das.features
2059
2060 2007-03-15 Toshiaki Katayama <k@bioruby.org>
2061
2062 * lib/bio/shell/irb.rb
2063
2064 Changed to load Rails environment when bioruby shell is invoked
2065 in the Rails project directory. This means that user can use
2066 'bioruby' command as a better './script/console' which has
2067 persistent objects and shared history.
2068
2069 2007-03-08 Toshiaki Katayama <k@bioruby.org>
2070
2071 * lib/bio/db/kegg/drug.rb
2072
2073 Newly added KEGG DRUG database parser.
2074
2075 * lib/bio/db/kegg/glycan.rb
2076
2077 Bio::KEGG::GLYCAN#bindings method is removed.
2078 Bio::KEGG::GLYCAN#comment, remarks methods are added.
2079 Bio::KEGG::GLYCAN#orthologs and dblinks methods are changed to use
2080 lines_fetch method.
2081
2082 * lib/bio/kegg/compound.rb
2083
2084 Bio::KEGG::COMPOUND#glycans method is added
2085 Bio::KEGG::COMPOUND#names method is changed to return an array
2086 of stripped strings.
2087
2088 * lib/bio/db/kegg/genes.rb
2089
2090 Bio::KEGG::GENES#orthologs method is added.
d6f4b42b » Naohisa Goto 2007-04-02 Incompatible change: Bio::M... 2091
8f355c11 » Naohisa Goto 2007-03-27 UniProt format autodetectio... 2092 2007-03-27 Naohisa Goto <ng@bioruby.org>
2093
2094 * lib/bio/command.rb
2095
54457543 » ktym 2007-07-18 * Added changes made by Kat... 2096 Bio::Command.call_command_fork and query_command_fork methods
2097 are changed to handle all Ruby exceptions in the child process.
8f355c11 » Naohisa Goto 2007-03-27 UniProt format autodetectio... 2098
2099 * lib/bio/io/flatfile.rb
2100
54457543 » ktym 2007-07-18 * Added changes made by Kat... 2101 UniProt format autodetection was changed to follow the change of
2102 UniProtKB release 9.0 of 31-Oct-2006.
8f355c11 » Naohisa Goto 2007-03-27 UniProt format autodetectio... 2103
aa0dfd38 » Naohisa Goto 2007-02-12 Changelog for bioruby/lib/b... 2104 2007-02-12 Naohisa Goto <ng@bioruby.org>
2105
2106 * lib/bio/io/flatfile.rb
2107
54457543 » ktym 2007-07-18 * Added changes made by Kat... 2108 Exception class UnknownDataFormatError is added.
2109 It will be raised before reading data from IO when data format
2110 hasn't been specified due to failure of file format autodetection.
2111
2112 2007-02-12 Toshiaki Katayama <k@bioruby.org>
2113
2114 * lib/bio/io/flatfile.rb
2115
2116 Added support for KEGG EGENES.
aa0dfd38 » Naohisa Goto 2007-02-12 Changelog for bioruby/lib/b... 2117
090c0c20 » Trevor Wennblom 2007-02-01 Updated ChangeLog 2118 2007-02-02 Trevor Wennblom <trevor@corevx.com>
2119
a1c1a54d » Trevor Wennblom 2007-02-01 Updated ChangeLog 2120 * lib/bio/util/restriction_enzyme*
2121
2122 Bio::RestrictionEnzyme stabilized.
2123
2124 2007-02-02 Trevor Wennblom <trevor@corevx.com>
2125
ca237700 » Trevor Wennblom 2007-02-01 Updated ChangeLog 2126 * lib/bio/db/lasergene.rb
2127
2128 Bio::Lasergene Interface for DNAStar Lasergene sequence file format
2129
2130 2007-02-02 Trevor Wennblom <trevor@corevx.com>
2131
090c0c20 » Trevor Wennblom 2007-02-01 Updated ChangeLog 2132 * lib/bio/db/soft.rb
2133
2134 Bio::SOFT for reading SOFT formatted NCBI GEO files.
2135
54457543 » ktym 2007-07-18 * Added changes made by Kat... 2136 2007-01-16 Toshiaki Katayama <k@bioruby.org>
2137
2138 * BioRuby shell on Rails new features and fixes
2139
2140 New features:
2141 * Input [#] is linked to action for filling textarea from history
2142 * [methods] is separated into columns for readability
2143
2144 Fixes and improvements:
2145 * HIDE_VARIABLES is moved from helper to controller to avoid warning
2146 "already initialized constant - HIDE_VARIABLES" repeated on reload.
2147 * <div id="evaluate"> is renamed to "log_#" with number for future
2148 extention.
2149 * <div id="log_#"> are inserted in the <div id="logs">
2150
2151 2007-01-15 Toshiaki Katayama <k@bioruby.org>
2152
2153 * lib/bio/db.rb
2154
2155 lines_fetch method (internally used various bio/db/*.rb modules)
2156 is rewrited to concatenate indented sub field.
2157
2158 * lib/bio/db/kegg/compound.rb
2159
2160 Bio::KEGG::COMPOUND#comment method which returns contents of
2161 the COMMENT line is added
2162
2163 * lib/bio/db/kegg/enzyme.rb
2164
2165 Bio::KEGG::ENZYME#entry_id is changed to return EC number only.
2166 Previous version of entry_id method is renamed to entry method
2167 which returns a "EC x.x.x.x Enzyme" style string.
2168
2169 Bio::KEGG::ENZYME#obsolete? method is added which returns boolean
2170 value (true or false) according to the ENTRY line contains
2171 a string 'Obsolete' or not.
2172
2173 Bio::KEGG::ENZYME#all_reac, iubmb_reactions, kegg_reactions methods
2174 are added to support newly added ALL_REAC field.
2175
2176 Bio::KEGG::ENZYME#inhibitors and orthologs methods are added.
2177
2178 Bio::KEGG::ENZYME#substrates, products, inhibitors, cofactors,
2179 pathways, orthologs, diseases, motifs methods are rewrited to
2180 utilizes new lines_fetch method in db.rb to process continuous
2181 sub field.
2182
2183 * lib/bio/db/kegg/genome.rb
2184
2185 Bio::KEGG::GENOME#scaffolds, gc, genomemap methods are obsoleted.
2186 Bio::KEGG::GENOME#distance, data_source, original_db methods are
2187 added.
2188
e6c861b0 » ktym 2006-12-24 * some additional notes bef... 2189 2006-12-24 Toshiaki Katayama <k@bioruby.org>
2190
2191 * bin/bioruby, lib/bio/shell/, lib/bio/shell/rails/
54457543 » ktym 2007-07-18 * Added changes made by Kat... 2192 (lib/bio/shell/rails/vendor/plugins/generators/)
e6c861b0 » ktym 2006-12-24 * some additional notes bef... 2193
2194 Web functionallity of the BioRuby shell is completely rewrited
2195 to utilize generator of the Ruby on Rails. This means we don't
2196 need to have a copy of the rails installation in our code base
2197 any more. The shell now run in threads so user does not need
2198 to run 2 processes as before (drb and webrick). Most importantly,
2199 the shell is extended to have textarea to input any code and
2200 the evaluated result is returned with AJAX having various neat
2201 visual effects.
2202
81c49e77 » ktym 2007-11-10 * updated 2203 * lib/bio.rb
54457543 » ktym 2007-07-18 * Added changes made by Kat... 2204
2205 Extended to have Bio.command where command can be any BioRuby
2206 shell methods.
2207 ex. puts Bio.getseq("atgc" * 10).randomize.translate
2208
2209 * lib/bio/shell/plugin/entry.rb, seq.rb
2210
2211 seq, ent, obj commands are renamed to getseq, getent, getobj
2212 respectively. This getseq is also changed to return Bio::Sequence
2213 with @moltype = Bio::Sequence::NA object instead of Bio::Sequence::NA
2214 object.
2215
2216 * lib/bio/db/kegg/kgml.rb
2217
2218 Some method names are changed to avoid confusion:
2219 * entry_type is renamed to category (<entry type="">)
2220 * map is renamed to pathway (<entry map="">)
2221
e6c861b0 » ktym 2006-12-24 * some additional notes bef... 2222 2006-12-19 Christian Zmasek <czmasek@burnham.org>
2223
2224 * lib/bio/db/nexus.rb
2225
2226 Bio::Nexus is newly developed during the Phyloinformatics hackathon.
2227
2228 2006-12-16 Toshiaki Katayama <k@birouby.org>
2229
2230 * lib/bio/io/sql.rb
2231
2232 Updated to follow recent BioSQL schema contributed by
2233 Raoul Jean Pierre Bonnal.
2234
ec95710d » Mitsuteru Nakao 2006-12-14 * lib/bio/appl/iprscan/repo... 2235 2006-12-15 Mitsuteru Nakao <n@bioruby.org>
2236
2237 * lib/bio/appl/iprscan/report.rb
2238
2239 Bio::Iprscan::Report for InterProScan output is newly added.
12dc637b » Naohisa Goto 2006-12-28 Changes by ngoto during Phy... 2240 2006-12-15 Naohisa Goto <ng@bioruby.org>
2241
2242 * lib/bio/appl/mafft/report.rb
2243
2244 Bio::MAFFT::Report#initialize is changed to get a string of
2245 multi-fasta formmatted text instead of Array.
2246
2247 2006-12-14 Naohisa Goto <ng@bioruby.org>
2248
2249 * lib/bio/appl/phylip/alignment.rb
2250
2251 Phylip format multiple sequence alignment parser class
2252 Bio::Phylip::PhylipFormat is newly added.
2253
2254 * lib/bio/appl/phylip/distance_matrix.rb
2255
2256 Bio::Phylip::DistanceMatrix, a parser for phylip distance matrix
2257 (generated by dnadist/protdist/restdist programs) is newly added.
2258
2259 * lib/bio/appl/gcg/msf.rb, lib/bio/appl/gcg/seq.rb
2260
2261 Bio::GCG::Msf in lib/bio/appl/gcg/msf.rb for GCG MSF multiple
2262 sequence alignment format parser, and Bio::GCG::Seq in
2263 lib/bio/appl/gcg/seq.rb for GCG sequence format parser are
2264 newly added.
2265
2266 * lib/bio/alignment.rb
2267
2268 Output of Phylip interleaved/non-interleaved format (.phy),
2269 Molphy alignment format (.mol), and GCG MSF format (.msf)
2270 are supported. Bio::Alignment::ClustalWFormatter is removed
2271 and methods in the module are renamed and moved to
2272 Bio::Alignment::Output.
2273
2274 * lib/bio/appl/clustalw.rb, lib/bio/appl/mafft.rb, lib/bio/appl/sim4.rb
2275
2276 Changed to use Bio::Command instead of Open3.popen3.
2277
2278 2006-12-13 Naohisa Goto <ng@bioruby.org>
2279
2280 * lib/bio/tree.rb, lib/bio/db/newick.rb
2281
2282 Bio::PhylogeneticTree is renamed to Bio::Tree, and
2283 lib/bio/phylogenetictree.rb is renamed to lib/bio/tree.rb.
2284 NHX (New Hampshire eXtended) parser/writer support are added.
ec95710d » Mitsuteru Nakao 2006-12-14 * lib/bio/appl/iprscan/repo... 2285
54457543 » ktym 2007-07-18 * Added changes made by Kat... 2286 2006-12-13 Toshiaki Katayama <k@bioruby.org>
2287
2288 * doc/Desing.rd.ja, doc/TODO.rd.ja, doc/BioRuby.rd.ja are obsoletd.
2289
95dcd207 » Naohisa Goto 2006-10-06 Added Changelog (made by N.... 2290 2006-10-05 Naohisa Goto <ng@bioruby.org>
2291
2292 * lib/bio/db/newick.rb
2293
2294 Bio::Newick for Newick standard phylogenetic tree parser is
2295 newly added (contributed by Daniel Amelang).
2296
2297 * lib/bio/phylogenetictree.rb
2298
2299 Bio::PhylogeneticTree for phylogenetic tree data structure
2300 is newly added.
2301
54457543 » ktym 2007-07-18 * Added changes made by Kat... 2302 2006-09-19 Toshiaki Katayama <k@bioruby.org>
2303
2304 * lib/bio/io/soapwsdl.rb
2305 * lib/bio/io/ebisoap.rb
2306 * lib/bio/io/ncbisoap.rb
2307
2308 Newly added web service modules.
2309
2310 * lib/bio/db/kegg/kgml.rb
2311
2312 Accessor for the <component> attribute is added.
2313
2314 * lib/bio/shell/plugin/codon.rb
2315
2316 Support for Pyrrolysine and Selenocysteine are added in the
2317 BioRuby shell.
2318
2319 * lib/bio/sshell/plugin/seq.rb
2320
2321 sixtrans, skip, step methods are added in the BioRuby shell.
2322 bioruby> seqtrans(seq)
2323
2324 bioruby> seq.step(window_size) {|subseq|
2325 # do something on subseq
2326 }
2327
2328 bioruby> seq.skip(window_sizep, step_size) {|subseq|
2329 # do something on subseq
2330 }
2331
2332 2006-07-26 Toshiaki Katayama <k@bioruby.org>
2333
2334 * lib/bio/data/aa.rb
2335
2336 Amino acids J (Xle: I/L), O (Pyl: pyrrolysine) and X (unknown)
2337 are added (now we have consumed 26 alphabets!).
2338
2339 * lib/bio/io/fastacmd.rb
2340
2341 Fixed that new version of fastacmd (in BLAST package) changed
2342 the option from '-D T' to '-D 1', contributed by the author
2343 of this module Shuji Shigenobu.
2344
2345 * lib/bio/shell/plugin/psort.rb
2346
2347 Newly added BioRuby shell plugin for PSORT
2348
2349 * lib/bio/shell/plugin/blast.rb
2350
2351 Newly added BioRuby shell plugin for BLAST search against KEGG GENES
2352
2353 * lib/bio/db/prosite.rb
2354
2355 PROSITE#re instance method is added to translate PATTERN of
2356 the entry to Regexp using PROSITE.pa2re class method.
2357
2358 * lib/bio/db/kegg/genes.rb
2359
2360 Bio::KEGG::GENES#keggclass method is renamed to pathway
2361 Bio::KEGG::GENES#splinks method is removed
2362 Bio::KEGG::GENES#motifs method is added
2363 these reflect changes made in the original KEGG GENES database.
2364
2365 Bio::KEGG::GENES#locations method is added to return Bio::Locations
2366 Bio::KEGG::GENES#codon_usage is renamed cu_list (returns as Array)
2367 Bio::KEGG::GENES#cu is renamed to codon_usage (returns as Hash)
2368 Bio::KEGG::GENES#aalen, nalen methods are changed to return
2369 the number written in the entry (use seq.length to obtain calculated
2370 number as before).
2371
2372 * lib/bio/db/kegg/kgml.rb
2373
2374 Names of some accessors have been changed (including bug fixes)
2375 and instance variable @dom is obsoleted. Here's a list of
2376 incompatible attribute names with KGML tags by this change:
2377 <entry>
2378 :id -> :entry_id
2379 :type -> :entry_type
2380 names()
2381 <graphics>
2382 :name -> :label
2383 :type -> :shape
2384 <relation>
2385 :entry1 -> :node1
2386 :entry2 -> :node2
2387 :type -> :rel
2388 <subtype>
2389 edge()
2390 <reaction>
2391 :name -> :entry_id
2392 :type -> :direction
2393
2394 * lib/bio/io/das.rb
2395
2396 Bug fixed that the value of segment.stop was overwritten by
2397 segment.orientation.
2398
95dcd207 » Naohisa Goto 2006-10-06 Added Changelog (made by N.... 2399 2006-07-14 Naohisa Goto <ng@bioruby.org>
2400
2401 * lib/bio/command.rb
2402
2403 Bio::Command::Tools and Bio::Command::NetTools are combined
2404 and re-constructed into a new Bio::Command module.
2405
2406 lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb,
2407 lib/bio/appl/emboss.rb, lib/bio/appl/psort.rb,
2408 lib/bio/appl/hmmer.rb, lib/bio/db/fantom.rb,
2409 lib/bio/io/fastacmd.rb, lib/bio/io/fetch.rb,
2410 lib/bio/io/keggapi.rb, lib/bio/io/pubmed.rb, and
2411 lib/bio/io/registry.rb are changed to use the new Bio::Command
2412 instead of old Bio::Command or Net::HTTP.
2413
2414 2006-06-29 Naohisa Goto <ng@bioruby.org>
2415
2416 * lib/bio/appl/blat/report.rb
2417
2418 Bio::BLAT::Report::Hit#milli_bad, #percent_identity, #protein?,
2419 #score, and #psl_version methods/attributes are newly added,
2420 and psl files without headers are supported (discussed in
2421 bioruby-ja ML).
2422
edfe6b22 » Naohisa Goto 2006-06-26 Bio::Sequence::NA#gc_conten... 2423 2006-06-27 Naohisa Goto <ng@bioruby.org>
2424
2425 * lib/bio/sequence/na.rb
2426
2427 Bio::Sequence::NA#gc_content, #at_content, #gc_skew, #at_skew
2428 are newly added. Bio::Sequence::NA#gc_percent are changed
2429 not to raise ZeroDivisionError and returns 0 when given sequence
2430 is empty.
2431
95dcd207 » Naohisa Goto 2006-10-06 Added Changelog (made by N.... 2432 * lib/bio/db/pdb/pdb.rb
2433
2434 Bio::PDB::ATOM#name, #resName, #iCode, #chaarge, #segID, and
2435 #element are changed to strip whitespaces when initializing.
2436 Bio::PDB::HETATM is also subject to the above changes.
2437 (suggested by Mikael Borg)
2438
2439 2006-06-12 Naohisa Goto <ng@bioruby.org>
2440
2441 * lib/bio/io/flatfile.rb
2442
2443 Bug fix: Bio::FlatFile.open(klass, filename) didn't work.
2444
54457543 » ktym 2007-07-18 * Added changes made by Kat... 2445 2006-05-30 Toshiaki Katayama <k@bioruby.org>
2446
2447 * lib/bio/io/soapwsdl.rb
2448
2449 Generic list_methods method which extracts web service methods
2450 defined in the WSDL file is added.
2451
4dc20716 » Mitsuteru Nakao 2006-05-02 * Added comment for lib/bio... 2452 2006-05-02 Mitsuteru Nakao <n@bioruby.org>
2453
2454 * lib/bio/appl/pts1.rb
2455
2456 Bio::PTS1 first commit.
2457
95dcd207 » Naohisa Goto 2006-10-06 Added Changelog (made by N.... 2458 2006-04-30 Naohisa Goto <ng@bioruby.org>
2459
2460 * lib/bio/appl/blast/format0.rb
2461
2462 Bug fix: parse error for hits whose database sequence names
2463 contain 'Score', and subsequent hits after them would lost
2464 (reported by Tomoaki NISHIYAMA).
2465
582dd825 » Mitsuteru Nakao 2006-04-13 * Bio::Ensembl first commit. 2466 2006-04-14 Mitsuteru Nakao <n@bioruby.org>
2467
2468 * lib/bio/io/ensembl.rb
2469
2470 Bio::Ensembl first commit. It is a client class for Ensembl Genome
2471 Browser.
2472
95dcd207 » Naohisa Goto 2006-10-06 Added Changelog (made by N.... 2473 2006-03-22 Naohisa Goto <ng@bioruby.org>
2474
2475 * lib/bio/io/flatfile.rb
2476
2477 Bug fix: Bio::FlatFile raises error for pipes, ARGF, etc.
2478 The bug also affects bio/appl/mafft.rb, bio/appl/clustalw.rb,
2479 bio/appl/blast.rb, bio/io/fastacmd.rb, and so on.
2480
2481 Bio::FlatFile#entry_start_pos and #entry_ended_pos are
2482 changed to be enabled only when Bio::FlatFile#entry_pos_flag
2483 is true.
582dd825 » Mitsuteru Nakao 2006-04-13 * Bio::Ensembl first commit. 2484
a13decb0 » ktym 2006-02-27 * prepared for 1.0.0 release 2485 2006-02-27 Toshiaki Katayama <k@bioruby.org>
9f9faa39 » Trevor Wennblom 2006-01-31 Bio::RestrictionEnzyme init... 2486
a13decb0 » ktym 2006-02-27 * prepared for 1.0.0 release 2487 * BioRuby 1.0.0 released
2488
2489 2006-02-10 Toshiaki Katayama <k@bioruby.org>
2490
2491 * BioRuby shell is changed to use session/ directory under the current
2492 or specified directory to store the session information instead of
2493 ./.bioruby directory.
2494
2495 2006-02-05 Toshiaki Katayama <k@bioruby.org>
2496
2497 * License to be changed to Ruby's (not yet completed).
2498
2499 2006-02-01 Trevor Wennblom <trevor@corevx.com>
2500
2501 * Bio::RestrictionEnzyme first commit for comments.
9f9faa39 » Trevor Wennblom 2006-01-31 Bio::RestrictionEnzyme init... 2502 * See lib/bio/util/restriction_enzyme.rb and
a13decb0 » ktym 2006-02-27 * prepared for 1.0.0 release 2503 test/unit/bio/util/restriction_enzyme
2504
2505 2006-01-28 Toshiaki Katayama <k@bioruby.org>
2506
2507 * lib/bio/appl/emboss.rb
2508
2509 EMBOSS USA format is now accepted via seqret/entret commands
2510 and also utilized in the BioRuby shell (lib/bio/shell.rb,
2511 plugin/entry.rb, plugin/emboss.rb).
2512
2513 * lib/bio/io/brdb.rb is removed - unused Bio::BRDB (BioRuby DB)
2514
2515 2006-01-23 Toshiaki Katayama <k@bioruby.org>
2516
2517 * lib/bio/sequence.rb
2518
2519 Bio::Sequence is refactored to be a container class for
2520 any sequence annotations. Functionality is separared into
2521 several files under the lib/bio/sequence/ direcotry as
2522 common.rb, compat.rb, aa.rb, na.rb, format.rb
9f9faa39 » Trevor Wennblom 2006-01-31 Bio::RestrictionEnzyme init... 2523
a13decb0 » ktym 2006-02-27 * prepared for 1.0.0 release 2524 2006-01-20 Toshiaki Katayama <k@bioruby.org>
fe715cc6 » ktym 2006-01-20 * updated for 0.7.1 2525
2526 * BioRuby 0.7.1 is released.
2527
a13decb0 » ktym 2006-02-27 * prepared for 1.0.0 release 2528 2006-01-12 Toshiaki Katayama <k@bioruby.org>
fe715cc6 » ktym 2006-01-20 * updated for 0.7.1 2529
2530 * lib/bio/db.ra: fixed a bug of the tag_cut method introduced in 0.7.0
2531 (reported by Alex Gutteridge)
2532
a13decb0 » ktym 2006-02-27 * prepared for 1.0.0 release 2533 2006-01-04 Naohisa Goto <ng@bioruby.org>
fe715cc6 » ktym 2006-01-20 * updated for 0.7.1 2534
2535 * Bio::PDB is refactored. See doc/Changes-0.7 for more details.
2536
eead664c » ktym 2006-01-16 * 0.7.0 release is recorded 2537 2005-12-19 Toshiaki Katayama <k@bioruby.org>
2538
2539 * BioRuby 0.7.0 is released.
2540
3d80025e » ktym 2006-01-20 * removed trivial changes (... 2541 See doc/Changes-0.7.rd file for major and incompatible changes.
2542
52b40e2b » Naohisa Goto 2005-12-18 added changelog for PDB cla... 2543 2005-12-19 Naohisa Goto <ng@bioruby.org>
2544
2545 * lib/bio/db/pdb.rb, lib/bio/db/pdb/pdb.rb, lib/bio/db/pdb/*.rb
2546 * Many changes have been made.
2547 * Bio::PDB::FieldDef is removed and Bio::PDB::Record is completely
2548 changed. Now, Record is changed from hash to Struct, and
2549 method_missing is no longer used.
2550 * In the "MODEL" record, model_serial is changed to serial.
2551 * In any records, record_type is changed to record_name.
2552 * In most records contains real numbers, changed to return
2553 float values instead of strings.
2554 * Pdb_AChar, Pdb_Atom, Pdb_Character, Pdb_Continuation,
2555 Pdb_Date, Pdb_IDcode, Pdb_Integer, Pdb_LString, Pdb_List,
2556 Pdb_Real, Pdb_Residue_name, Pdb_SList, Pdb_Specification_list,
2557 Pdb_String, Pdb_StringRJ and Pdb_SymOP are moved under
2558 Bio::PDB::DataType.
2af1fab7 » Naohisa Goto 2005-12-18 * added changelogs for Bio:... 2559 * There are more and more changes to be written...
52b40e2b » Naohisa Goto 2005-12-18 added changelog for PDB cla... 2560
2561 * lib/bio/db/pdb/atom.rb
2562 * Bio::PDB::Atom is removed.
2563 Instead, please use Bio::PDB::Record::ATOM and
2564 Bio::PDB::Record::HETATM.
2565
2af1fab7 » Naohisa Goto 2005-12-18 * added changelogs for Bio:... 2566 2005-12-02 Naohisa Goto <ng:bioruby.org>
2567
2568 * lib/bio/alignment.rb
2569 * Old Bio::Alignment class is renamed to
2570 Bio::Alignment::OriginalAlignment.
2571 Now, new Bio::Alignment is a module. However,
2572 you don't mind so much because most of the class methods
2573 previously existed are defined to delegate to the new
2574 Bio::Alignment::OriginalAlignment class,
2575 for keeping backward compatibility.
2576 * New classes and modules are introduced. Please refer RDoc.
2577 * each_site and some methods changed to return Bio::Alignment::Site,
2578 which inherits Array (previously returned Array).
2579 * consensus_iupac now returns only standard bases
2580 'a', 'c', 'g', 't', 'm', 'r', 'w', 's', 'y', 'k', 'v',
2581 'h', 'd', 'b', 'n', or nil (in SiteMethods#consensus_iupac) or
2582 '?' (or missing_char, in EnumerableExtension#consensus_iupac).
2583 Note that consensus_iupac now does not return u and invalid
2584 letters not defined in IUPAC standard even if all bases
2585 are equal.
2586 * There are more and more changes to be written...
2587
7528cad1 » ktym 2005-11-05 * added changes on Bio::Seq... 2588 2005-11-05 Toshiaki Katayama <k@bioruby.org>
2589
2590 * lib/bio/sequence.rb
2591
2592 Bio::Sequence.auto(str) method is added which auto detect the
2593 molecular type of the string and then returns the
2594 Bio::Sequence::NA or Bio::Sequence::AA object.
2595
2596 Bio::Sequence#blast and Bio::Sequence#fasta methods are removed.
2597
2598 * lib/bio/shell/plugin/codon.rb
2599
2600 Newly added plugin to treat codon table.
2601 ColoredCodonTable is ported from the codontable.rb
2602
2603 2005-11-01 Toshiaki Katayama <k@bioruby.org>
2604
2605 * bin/bioruby, lib/bio/shell/
2606
2607 All methods are changed to private methods to avoid adding them
2608 in top level binding, which caused many unexpected behaviors,
2609 as adviced by Koichi Sasada.
2610
2611 The MIDI plugin is now able to select musical scales.
2612
be56343a » ktym 2005-11-04 * midi, colorscheme 2613 2005-10-23 Toshiaki Katayama <k@bioruby.org>
2614
2615 * lib/bio/util/color_scheme
2616
2617 Newly contributed Bio::ColorScheme
2618
2619 * lib/bio/db/kegg/kgml.rb
2620
2621 Newly added KEGG KGML parser.
2622
2623 2005-10-05 Toshiaki Katayama <k@bioruby.org>
2624
2625 * lib/bio/shell/plugin/midi.rb
2626
2627 Sequcne to MIDI plugin is contributed by Natsuhiro Ichinose
2628
ad981a41 » ktym 2005-09-25 * updated on changes by Kat... 2629 2005-09-25 Toshiaki Katayama <k@bioruby.org>
2630
2631 * README.DEV
2632
2633 Newly added guideline document for the contributors.
2634
2635 * README
2636
2637 Updated and added instructions on RubyGems.
2638
2639 2005-09-23 Toshiaki Katayama <k@bioruby.org>
2640
2641 * bin/bioruby, lib/bio/shell.rb, lib/bio/shell/core.rb,
2642 lib/bio/shell/session.rb, lib/bio/shell/plugin/seq.rb,
2643 lib/bio/shell/flatfile.rb, lib/bio/shell/obda.rb
2644
2645 Newly added BioRuby shell, the command line user interface.
2646 Try 'bioruby' command in your terminal.
2647
2648 * doc/Changes-0.7.rd
2649
2650 Newly added document describing incompatible and important
2651 changes between the BioRuby 0.6 and 0.7 versions.
2652
2653 * lib/bio/sequence.rb
2654
2655 Bio::Sequence.guess, Bio::Sequence#guess methods are added
2656 which guess the sequence type by following fomula (default
2657 value for the threshold is 0.9).
2658
2659 number of ATGC
2660 --------------------------------------- > threshold
2661 number of other chars - number of N
2662
ca435ea2 » Naohisa Goto 2005-09-09 added changelog for fixing ... 2663 2005-09-10 Naohisa Goto <ng@bioruby.org>
2664
2665 * lib/bio.rb, lib/bio/appl/blast.rb, lib/bio/appl/blast/format0.rb,
2666 lib/bio/appl/blast/report.rb, lib/bio/appl/clustalw.rb,
2667 lib/bio/appl/fasta.rb, lib/bio/appl/fasta/format10.rb,
2668 lib/bio/appl/hmmer.rb, lib/bio/appl/hmmer/report.rb,
2669 lib/bio/appl/mafft.rb, lib/bio/appl/psort.rb,
2670 lib/bio/appl/psort/report.rb, lib/bio/appl/sim4.rb,
2671 lib/bio/db/genbank/ddbj.rb, lib/bio/io/flatfile/bdb.rb,
2672 lib/bio/io/flatfile/index.rb, lib/bio/io/flatfile/indexer.rb
2673
2674 fixed autoload problem
2675
2676 * lib/bio/appl/blast.rb, lib/bio/appl/blast/report.rb
2677
2678 Bio::Blast.reports method was moved from lib/bio/appl/blast/report.rb
2679 to lib/bio/appl/blast.rb for autoload.
2680
3306af08 » ktym 2005-08-31 * prepared for 0.6.4 2681 2005-08-31 Toshiaki Katayama <k@bioryby.org>
2682
2683 * BioRuby 0.6.4 is released.
2684
c08193bf » ktym 2005-08-31 * prepared for 0.6.4 again 2685 * doc/KEGG_API.rd
2686
2687 Newly added English version of the KEGG API manual.
2688
2689 * lib/bio/aa.rb
2690
2691 the 'one2name' method introduced in 0.6.3 is fixed and added 'one'
2692 and 'three' methods as aliases for 'to_1' and 'to_3' methods.
2693
c005cc2d » Naohisa Goto 2005-08-30 removed unused file lib/bio... 2694 2005-08-31 Naohisa Goto <ng@bioruby.org>
2695
2696 * removed unused file lib/bio/appl/factory.rb
3306af08 » ktym 2005-08-31 * prepared for 0.6.4 2697 (the functionality had been integrated into lib/bio/command.rb)
2698
2699 * doc/Tutorial.rd
2700
2701 Newly added an English translation of the Japanese tutorial.
c005cc2d » Naohisa Goto 2005-08-30 removed unused file lib/bio... 2702
b942ff90 » Naohisa Goto 2005-08-16 * lib/bio/command.rb 2703 2005-08-16 Naohisa Goto <ng@bioruby.org>
2704
2705 * lib/bio/command.rb
2706
2707 Newly added Bio::Command::Tools module.
2708 Bio::Command::Tools is a collection of useful methods
2709 for execution of external commands.
2710
2711 * lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb,
2712 lib/bio/appl/hmmer.rb, lib/bio/io/fastacmd.rb
2713
2714 For security reason, shell special characters are escaped.
2715
2716 * lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb, lib/bio/appl/hmmer.rb
2717
2718 Options are stored with an array (@options).
2719 #options and #opions= methods are added.
2720
2721 * lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb
2722
3306af08 » ktym 2005-08-31 * prepared for 0.6.4 2723 Bio::Blast.remote and Bio::Fasta.remote is fixed to work
2724 with the recent change of the GenomeNet.
b942ff90 » Naohisa Goto 2005-08-16 * lib/bio/command.rb 2725
05725dc6 » ktym 2005-08-10 * prepared for 0.6.4 release 2726 2005-08-11 Toshiaki Katayama <k@bioruby.org>
0307af86 » ktym 2005-08-10 * prepared for 0.6.4 release 2727
3306af08 » ktym 2005-08-31 * prepared for 0.6.4 2728 * Sequence#to_re method to have compatibility with 0.6.2 for RNA
2729
2730 * Fixed Bio::Fastacmd#fetch to work
0307af86 » ktym 2005-08-10 * prepared for 0.6.4 release 2731
3306af08 » ktym 2005-08-31 * prepared for 0.6.4 2732 * Bio::Fastacmd and Bio::Bl2seq classes (introduced in 0.6.3) are
2733 renamed to Bio::Blast::Fastacmd, Bio::Blast::Bl2seq respectively.
0307af86 » ktym 2005-08-10 * prepared for 0.6.4 release 2734
f7d032ba » ktym 2005-08-09 * added sirna, fastacmd 2735 2005-08-09 Toshiaki Katayama <k@bioruby.org>
2736
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2737 * BioRuby 0.6.3 is released.
2738
2739 This version would be the final release to support Ruby 1.6 series
2740 (as long as no serious bug is found:).
2741
f7d032ba » ktym 2005-08-09 * added sirna, fastacmd 2742 * lib/bio/util/sirna.rb:
2743
2744 Newly added method for desing of siRNA, contributed by
2745 Itoshi Nikaido. The lib/bio/util/ directory if reserved
2746 for bioinfomatics algorithms implemented by pure Ruby.
2747
2748 * lib/bio/io/fastacmd.rb:
2749
2750 Newly added wrapper for NCBI fastacmd program, contributed by
2751 Shinji Shigenobu.
2752
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2753 * lib/bio/appl/hmmer/report.rb:
2754
2755 Bug fixed by Masashi Fujita when the position of sequence
2756 rarely becomes '-' instead of digits.
2757
0bdf8096 » Mitsuteru Nakao 2005-08-09 * added log for lib/bio/db/... 2758 2005-08-08 Mitsuteru Nakao <n@bioruby.org>
2759
2760 * lib/bio/db/embl/sptr.rb:
2761
2762 Added Bio::SPTR#protein_name and Bio::SPTR#synoyms methods.
2763 contributed by Luca Pireddu.
2764
2765 Changed Bio::SPTR#gn, Bio::SPTR#gene_name and
2766 Bio::SPTR#gene_names methods. contributed by Luca Pireddu.
2767
35b8a4e1 » Naohisa Goto 2005-08-07 added Changelog for lib/bio... 2768 2005-08-08 Naohisa Goto <ng@bioruby.org>
2769
2770 * lib/bio/appl/bl2seq/report.rb:
f7d032ba » ktym 2005-08-09 * added sirna, fastacmd 2771
35b8a4e1 » Naohisa Goto 2005-08-07 added Changelog for lib/bio... 2772 Newly added bl2seq (BLAST 2 sequences) output parser.
f7d032ba » ktym 2005-08-09 * added sirna, fastacmd 2773
35b8a4e1 » Naohisa Goto 2005-08-07 added Changelog for lib/bio... 2774 * lib/bio/appl/blast/format0.rb:
f7d032ba » ktym 2005-08-09 * added sirna, fastacmd 2775
35b8a4e1 » Naohisa Goto 2005-08-07 added Changelog for lib/bio... 2776 Added `self.class::` before F0dbstat.new for bl2seq/report.rb
2777
f7d032ba » ktym 2005-08-09 * added sirna, fastacmd 2778 2005-08-07 Toshiaki Katayama <k@bioruby.org>
2779
2780 * lib/bio/sequence.rb, lib/bio/data/na.rb, lib/bio/data/aa.rb:
2781
2782 Bio::NucleicAcid, Bio::AminoAcid classes are refactored to have
2783 Data module, and this module is included and extended to make
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2784 all methods as both of instance methods and class methods.
f7d032ba » ktym 2005-08-09 * added sirna, fastacmd 2785
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2786 Bio::Sequence::NA and AA classes are rewrited (molecular_weight,
2787 to_re methods) to use Bio::NucleicAcid.
f7d032ba » ktym 2005-08-09 * added sirna, fastacmd 2788
2789 Bio::Sequence::NA#molecular_weight method is fixed to subtract
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2790 two hydrogens per each base.
f7d032ba » ktym 2005-08-09 * added sirna, fastacmd 2791
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2792 * lib/bio/db/medline.rb: publication_type (pt) method is added.
f7d032ba » ktym 2005-08-09 * added sirna, fastacmd 2793
4b5cd72f » Naohisa Goto 2005-08-06 added log for lib/bio/db/ge... 2794 2005-08-07 Naohisa Goto <ng@bioruby.org>
2795
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2796 * lib/bio/db/genbank/common.rb:
f7d032ba » ktym 2005-08-09 * added sirna, fastacmd 2797
2798 Avoid NoMethodError (private method `chomp` called for nil:NilClass)
2799 when parsing features of
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2800
4b5cd72f » Naohisa Goto 2005-08-06 added log for lib/bio/db/ge... 2801 ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2802 Salmonella_typhimurium_LT2/AE006468.gbk
4b5cd72f » Naohisa Goto 2005-08-06 added log for lib/bio/db/ge... 2803
1fde02d2 » ktym 2005-07-11 * added higet 2804 2005-07-11 Toshiaki Katayama <k@bioruby.org>
2805
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2806 * bin/br_pmfetch.rb:
2807
2808 Added sort by page option (--sort page)
1fde02d2 » ktym 2005-07-11 * added higet 2809
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2810 * lib/io/higet.rb:
1fde02d2 » ktym 2005-07-11 * added higet 2811
2812 Newly added Bio::HGC::HiGet class for HiGet SOAP service.
2813
31cb1b80 » ktym 2005-06-29 * commit test for loginfo 2814 2005-06-28 Toshiaki Katayama <k@bioruby.org>
2815
2816 * gemspec.rb: newly added RubyGems spec file.
2817
51715139 » Naohisa Goto 2005-08-06 added old Changelog modifie... 2818 2005-06-21 Naohisa Goto <ng@bioruby.org>
2819
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2820 * lib/bio/appl/blast/report.rb:
51715139 » Naohisa Goto 2005-08-06 added old Changelog modifie... 2821
2822 Newly added support for reading BLAST -m 7 result files
2823 through Bio::FlatFile by adding
2824 DELIMITER = "</BlastOutput>\n" to Bio::Blast::Report class.
2825 (Note that tab-delimited format (-m 8 and -m 9) are not yet
2826 supported by Bio::FlatFile)
2827
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2828 * lib/bio/io/flatfile.rb:
51715139 » Naohisa Goto 2005-08-06 added old Changelog modifie... 2829
2830 Added file format autodetection of BLAST XML format.
2831
2832 2005-06-20 Naohisa Goto <ng@bioruby.org>
2833
2834 * lib/bio/appl/blast/format0.rb: added 'to_s' to store original entry
2835
bf74106e » Mitsuteru Nakao 2005-04-04 * Added changelog for lib/b... 2836 2005-04-04 Mitsuteru Nakao <n@bioruby.org>
2837
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2838 * lib/bio/db/go.rb:
bf74106e » Mitsuteru Nakao 2005-04-04 * Added changelog for lib/b... 2839
f7d032ba » ktym 2005-08-09 * added sirna, fastacmd 2840 Newly added Bio::GO::External2go class for parsing external2go file.
bf74106e » Mitsuteru Nakao 2005-04-04 * Added changelog for lib/b... 2841
51715139 » Naohisa Goto 2005-08-06 added old Changelog modifie... 2842 2005-03-10 Naohisa Goto <ng@bioruby.org>
2843
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2844 * lib/bio/io/flatfile.rb:
51715139 » Naohisa Goto 2005-08-06 added old Changelog modifie... 2845
2846 Added file format autodetection of Spidey (Bio::Spidey::Report).
2847
2848 2005-03-10 Naohisa Goto <ng@bioruby.org>
2849
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2850 * lib/bio/io/flatfile.rb:
f7d032ba » ktym 2005-08-09 * added sirna, fastacmd 2851
2852 Added file format autodetection for Bio::KEGG::KO,
2853 Bio::KEGG::GLYCAN, Bio::KEGG::REACTION, Bio::Blat::Report
2854 and Bio::Sim4::Report.
2855
2856 In order to distinguish Bio::KEGG::REACTION and
2857 Bio::KEGG::COMPOUND, autodetection regexp. of
2858 Bio::KEGG::COMPOUND were modified.
51715139 » Naohisa Goto 2005-08-06 added old Changelog modifie... 2859
1fde02d2 » ktym 2005-07-11 * added higet 2860 2005-02-09 KATAYAMA Toshiaki <k@bioruby.org>
2861
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2862 * lib/bio/db/kegg/genes.rb:
1fde02d2 » ktym 2005-07-11 * added higet 2863
2864 Added cu method which returns codon usage in Hash for the
2865 convenience (codon_usage method returns in Array or Fixnum).
2866
9c82f756 » ktym 2004-12-12 * prepared for 0.6.2 release 2867 2004-12-13 KATAYAMA Toshiaki <k@bioruby.org>
2868
2869 * BioRuby 0.6.2 released.
2870
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2871 * test/all_tests.rb:
9c82f756 » ktym 2004-12-12 * prepared for 0.6.2 release 2872
2873 Unit tests for some classes are newly incorporated by
2874 Moses Hohman. You can try it by 'ruby install.rb test'
2875
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2876 * lib/bio/appl/spidey/report.rb:
9c82f756 » ktym 2004-12-12 * prepared for 0.6.2 release 2877
2878 Newly added Spidey result parser class.
2879
5f211f68 » ktym 2005-08-09 * prepared for 0.6.3 release 2880 * lib/bio/appl/blat/report.rb:
9c82f756 » ktym 2004-12-12 * prepared for 0.6.2 release 2881
2882 Newly added BLAT result parser class.
2883
2884 * fixes and improvements:
2885 * lib/bio/appl/blast/blast/format0.rb
2886 * minor fix for the Blast default format parser
2887 * lib/bio/alignment.rb
2888 * Alignment class
2889 * lib/bio/db/prosite.rb
2890 * bug reported by Rolv Seehuus is fixed
2891 * some methods are added
2892
2893 2004-10-25 KATAYAMA Toshiaki <k@bioruby.org>
2894
2895 * lib/bio/db/{compound.rb,reaction.rb,glycan.rb}:
2896
2897 Newly added parser for KEGG REACTION and KEGG GLYCAN database
2898 entries, fix for KEGG COMPOUND parser to support the new format.
2899
0c6f4e29 » Naohisa Goto 2004-10-08 Added changelog for lib/bio... 2900 2004-10-09 GOTO Naohisa <ng@bioruby.org>
2901
2902 * lib/bio/appl/sim4.rb
2903
2904 Newly added sim4 wrapper class.
2905 This is test version, specs would be changed frequently.
2906
2907 * lib/bio/appl/sim4/report.rb
2908
2909 Newly added sim4 result parser class.
2910
17034c1a » ktym 2004-08-25 * prepared for BioRuby 0.6.... 2911 2004-08-25 KATAYAMA Toshiaki <k@bioruby.org>
2912
2913 * BioRuby 0.6.1 released.
2914 * fix for the packaging miss of 0.6.0
2915 * bin/*.rb are renamed to bin/br_*.rb (similar to the BioPerl's
2916 convention: bp_*.pl)
2917
d568d6ce » ktym 2004-08-23 * updated for BioRuby 0.6.0... 2918 2004-08-24 KATAYAMA Toshiaki <k@bioruby.org>
2919
2920 * BioRuby 0.6.0 released.
2921 * many fixes for Ruby 1.8
2922 * updated for genome.ad.jp -> genome.jp transition
2923
2924 * lib/bio/db/pdb.rb
2925
2926 Newly added parser for PDB contributed by Alex Gutteridge (EBI).
2927
2928 * lib/bio/data/codontable.rb
2929
2930 Bio::CodonTable is rewrited to be a class instead of static variable.
2931 Now it can hold table definition, start codons, stop codons and
2932 added methods to detect start/stop codons and reverse translation.
2933
2934 Also includes sample code to show codon table in ANSI colored
2935 ascii art, have fun.
2936
2937 * lib/bio/sequence.rb
2938
2939 Bio::Sequence::NA#translate is rewrited to accept an user defined
2940 codon table as a Bio::CodonTable object and any character can be
2941 specified for the unknown codon. This method runs about 30% faster
2942 than ever before.
2943
2944 Bio::Sequence::AA#to_re method is added for the symmetry.
2945
2946 Bio::Seq will be changed to hold generic rich sequence features.
2947 This means Bio::Seq is no longer an alias of Bio::Sequence but
2948 is a sequence object model, something like contents of a GenBank
2949 entry, common in BioPerl, BioJava etc.
2950
2951 * lib/bio/io/soapwsdl.rb
2952
2953 Newly added common interface for SOAP/WSDL in BioRuby
2954 used by keggapi.rb, ddbjxml.rb.
2955
2956 * lib/bio/io/keggapi.rb
2957
2958 Completely rewrited to support KEGG API v3.0
2959
2960 * lib/bio/io/esoap.rb
2961
2962 Newly added client library for Entrez Utilities SOAP interface.
2963
2964 * lib/bio/db/genbank, lib/bio/db/embl
2965
2966 Refactored to use common.rb as a common module.
2967
2968 * bin/pmfetch.rb
2969
2970 Newly added command to search PubMed.
2971
2972 * bin/biofetch.rb, flatfile.rb, biogetseq.rb
2973
2974 Renamed to have .rb suffix.
2975
2976 * sample/biofetch.rb
2977
2978 Rewrited to use KEGG API instead of DBGET
2979
2980
6f295d24 » ktym 2003-10-13 * prepared for 0.5.3 2981 2003-10-13 KATAYAMA Toshiaki <k@bioruby.org>
2982
2983 * BioRuby 0.5.3 released.
2984
2985 Fixed bugs in Blast XML parsers: xmlparser.rb is fixed not to
2986 omit the string after ' and " in sequence definitions,
2987 rexml.rb is fixed not to raise NoMethodError as "undefined
2988 method `each_element_with_text' for nil:NilClass".
2989
b92805d2 » Naohisa Goto 2003-10-10 modifled changelog 2990 2003-10-07 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
2991
2992 * lib/bio/db/nbrf.rb
2993
2994 Newly added NBRF/PIR flatfile sequence format class.
2995
2996 2003-09-30 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
2997
2998 * lib/bio/db/pdb.rb
2999
3000 Newly added PDB database flatfile format class.
3001 This is pre-alpha version, specs shall be changed frequently.
3002
23de54b0 » ktym 2003-08-21 * for bioruby 0.5.2 3003 2003-08-22 KATAYAMA Toshiaki <k@bioruby.org>
3004
3005 * BioRuby 0.5.2 released.
3006
3007 Fixed to be loaded in Ruby 1.8.0 without warnings.
3008
d568d6ce » ktym 2004-08-23 * updated for BioRuby 0.6.0... 3009 * doc/KEGG_API.rd.ja
23de54b0 » ktym 2003-08-21 * for bioruby 0.5.2 3010
3011 Newly added a Japanese document on the KEGG API.
3012
2d177e62 » Naohisa Goto 2003-08-21 changed ChangeLog 3013 2003-08-12 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
3014
3015 * lib/bio/appl/blast/format0.rb
3016
3017 Newly added NCBI BLAST default (-m 0) output parser,
3018 which may be 5-10x faster than BioPerl's parser.
3019 This is alpha version, specs may be frequently changed.
3020 PHI-BLAST support is still incomplete.
3021 Ruby 1.8 recommended. In ruby 1.6, you need strscan.
3022
3023 * lib/bio/appl/blast/wublast.rb
3024
3025 Newly added WU-BLAST default output parser.
3026 This is alpha version, specs may be frequently changed.
3027 Support for parameters and statistics are still incomplete.
3028 Ruby 1.8 recommended. In ruby 1.6, you need strscan.
3029
4d69aa75 » Naohisa Goto 2003-07-25 added changelog about bio/a... 3030 2003-07-25 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
3031
3032 * lib/bio/alignment.rb:
3033
3034 Newly added multiple sequence alignment class.
3035
3036 * lib/bio/appl/alignfactory.rb:
3037
3038 Newly added template class for multiple alignment software.
3039
3040 * lib/bio/appl/clustalw.rb:
3041
3042 Newly added CLUSTAL W wrapper.
3043 <http://www.ebk.ac.uk/clustalw/>
3044 <ftp://ftp.ebk.ac.uk/pub/software/unix/clustalw/>
3045
3046 * lib/bio/appl/clustalw/report.rb:
3047
3048 Newly added CLUSTAL W result data (*.aln file) parser.
3049
3050 * lib/bio/appl/mafft.rb, lib/bio/appl/mafft/report.rb:
3051
3052 Newly added MAFFT wrapper and report parser.
3053 (MAFFT is a multiple sequence alignment program based on FFT.)
3054 <http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/>
3055
a3fae771 » ktym 2003-07-16 * added recent bug fixes 3056 2003-07-16 KATAYAMA Toshiaki <k@bioruby.org>
3057
7a3b2b5c » ktym 2003-07-16 * updated for 0.5.1 3058 * BioRuby version 0.5.1 released.
3059
a3fae771 » ktym 2003-07-16 * added recent bug fixes 3060 * lib/bio/sequence.rb: some methods (using 'rna?' internally) were
3061 temporally unusable by the changes in 0.5.0 is fixed.
3062
3063 * lib/bio/io/flatfile.rb: autodetection failure of the fasta entry
3064 without sequence is fixed. FlatFile.auto method is added.
3065
3066 * lib/bio/db.rb: sugtag2array fixed. DB.open now accepts IO/ARGF.
3067
3068 * lib/bio/db/embl.rb: references method is added.
3069
3070
bbf098fa » ktym 2003-06-24 * update for 0.5.0 3071 2003-06-25 KATAYAMA Toshiaki <k@bioruby.org>
3072
3073 * BioRuby version 0.5.0 released.
3074
3075 * lib/bio/appl/blast/report.rb:
3076
3077 Refactored from xmlparser.rb, rexml.rb, and format8.rb files.
3078 Formats are auto detected and parsers are automatically
3079 selected by checking whether XMLParser or REXML are installed.
3080 You can call simply as
3081 Bio::Blast::Report.new(blastoutput)
3082 or you can choose parsers/format explicitly by
3083 Bio::Blast::Report.xmlparser(format7blastoutput)
3084 Bio::Blast::Report.rexml(fomat7blastoutput)
3085 Bio::Blast::Report.tab(format8blastoutput)
3086 You can also use newly added class method reports for multiple
3087 xml blast output.
3088 Bio::Blast.reports(output) # output can be IO or String
3089
3090 * lib/bio/appl/fasta/report.rb:
3091
3092 Refactored from format10.rb, format6.rb and sample/* files.
3093
3094 * lib/bio/appl/hmmer/report.rb:
3095
3096 Bug fix and clean up.
3097
3098 * bin/biogetseq:
3099
3100 Newly added OBDA (BioRegistry) entry retrieval command.
3101
3102 * etc/bioinformatics/seqdatabase.ini, lib/bio/io/registry.rb:
3103 Updated for new OBDA spec (Singapore version).
3104 Including config file versioning and changes in tag names,
3105 support for OBDA_SEARCH_PATH environmental variable.
3106
3107 * lib/bio/io/keggapi.rb:
3108
3109 Newly added KEGG API client library.
3110 <http://www.genome.ad.jp/kegg/soap/>
3111
3112 * lib/bio/io/ddbjxml.rb:
3113
3114 Newly added DDBJ XML client library (test needed).
3115 <http://xml.nig.ac.jp/>
3116
3117 * lib/bio/io/das.rb:
3118
3119 Newly added BioDAS client library.
3120
3121 * lib/bio/db/gff.rb:
3122
3123 Newly added GFF format parser/store library.
3124
3125 * lib/bio/appl/tmhmm/report.rb:
3126
3127 Newly added TMHMM report parser.
3128 <http://www.cbs.dtu.dk/services/TMHMM/>
3129
3130 * lib/bio/appl/targetp/report.rb:
3131
3132 Newly added TargetP report parser.
3133 <http://www.cbs.dtu.dk/services/TargetP/>
3134
3135 * lib/bio/appl/sosui/report.rb:
3136
3137 Newly added SOSUI report parser.
3138 <http://sosui.proteome.bio.tuat.ac.jp/cgi-bin/sosui.cgi>
3139
3140 * lib/bio/appl/psort/report.rb:
3141
3142 Newly added PSORT report parser.
3143 <http://www.psort.org/>, <http://psort.ims.u-tokyo.ac.jp/>
3144
3145 * lib/bio/appl/genscan/report.rb:
3146
3147 Newly added GENSCAN report parser.
3148 <http://genes.mit.edu/GENSCAN.html>
3149
3150 * lib/bio/db/prosite.rb: bug fix in ps2re method.
3151
3152 * lib/bio/db/fantom.rb:
3153
3154 Newly added FANTOM database parser (XML).
3155 <http://fantom2.gsc.riken.go.jp/>
3156
3157 * lib/bio/db/go.rb:
3158
3159 Newly added GO parser.
3160 <http://www.geneontology.org/>
3161
3162 * lib/bio/feature.rb:
3163
3164 'each' method now accepts an argument to select specific feature.
3165
3166 * lib/bio/db/fasta.rb: definition=, data= to change comment line.
3167
3168 * lib/bio/db/genbank.rb:
3169
3170 References and features now accept a block. 'acc_version' method
3171 is added to return the Accsession.Version string.
3172 'accession' method now returns Accession part of the acc_version.
3173 'version' method now returns Version part of the acc_version as
3174 an integer.
3175
3176 * lib/bio/db/keggtab.rb:
3177
3178 Rewrited for bug fix and clean up (note: some methods renamed!)
3179 * gsub('abrev', 'abbrev') in method names
3180 * db_path_by_keggorg is changed to db_path_by_abbrev
3181 * @bio_root is changed to @bioroot (ENV['BIOROOT'] overrides)
3182 * Bio::KEGG::DBname is changed to Bio::KEGG::Keggtab::DB
3183 * @database is added (a hash with its key db_abbreb)
3184 * database, name, path methods added with its argument db_abbreb
3185
3186 * lib/bio/io/flatfile.rb:
3187
3188 Enumerable mix-in is included.
3189
3190 * lib/bio/io/flatfile/indexer.rb:
3191
3192 Indexing of the FASTA format file is now supported with various
3193 type of definition line.
3194
3195 * bin/dbget:
3196
3197 Removed (moved under sample directory because the port of the
3198 dbget server is now closed).
3199
3200 * install.rb:
3201
3202 Changed to use setup 3.1.4 to avoid installing CVS/ directory.
3203
3204 * sample/goslim.rb:
3205
3206 Added a sample to generate histogram from GO slim.
3207
3208 * sample/tdiary.rb:
3209
3210 Added for tDiary <http://www.tdiary.org/> users. have fun. :)
3211
afd5084d » ktym 2003-01-27 * release for 0.4.0 3212 2003-01-28 KATAYAMA Toshiaki <k@bioruby.org>
3213
3214 * BioRuby version 0.4.0 released.
3215 * bin/bioflat:
3216 * newly added for the BioFlat indexing
3217 * lib/bio/io/flatfile.rb, flatfile/{indexer.rb,index.rb,bdb.rb}:
3218 * flatfile indexing is supported by N. Goto
3219 * lib/bio/db/genbank.rb: changed to contain common methods only
3220 * lib/bio/db/genbank/genbank.rb
3221 * lib/bio/db/genbank/genpept.rb
3222 * lib/bio/db/genbank/refseq.rb
3223 * lib/bio/db/genbank/ddbj.rb
3224 * lib/bio/db/embl.rb: changed to contain common methods only
3225 * lib/bio/db/embl/embl.rb
3226 * lib/bio/db/embl/sptr.rb
3227 * lib/bio/db/embl/swissprot.rb
3228 * lib/bio/db/embl/trembl.rb
3229 * lib/bio/appl/emboss.rb:
3230 * added - just a generic wrapper, no specific parsers yet.
3231 * lib/bio/appl/hmmer.rb:
3232 * added - execution wrapper
3233 * lib/bio/appl/hmmer/report.rb:
3234 * added - parsers for hmmsearch, hmmpfam contributed by H. Suga
3235 * lib/bio/db.rb: open method added for easy use of flatfile.
3236 * lib/bio/db/kegg/genes.rb:
3237 * fixed bug in codon_usage method in the case of long sequence >999
3238 * eclinks, splinks, pathways, gbposition, chromosome methods added
3239 * lib/bio/db/aaindex.rb:
3240 * adapted for the new AAindex2 format (release >= 6.0).
3241 * lib/bio/db/fasta.rb: entry_id is changed to return first word only
3242 * lib/bio/data/na.rb, aa.rb, keggorg.rb:
3243 * moved under class NucleicAcid, AminoAcid, KEGG (!)
3244 * in the test codes, DBGET is replaced by BioFetch
3245
4968505e » Yoshinori Okuji 2002-08-29 Remove Bio::Matrix. 3246 2002-08-30 Yoshinori K. Okuji <okuji@enbug.org>
3247
3248 * lib/bio/matrix.rb: Removed.
3249 * lib/bio/db/aaindex.rb: Require matrix instead of bio/matrix.
3250 * lib/bio/db/transfac.rb: Likewise.
3251 * lib/bio/pathway.rb: Likewise.
afd5084d » ktym 2003-01-27 * release for 0.4.0 3252 (Pathway#dump_matrix): Don't use Matrix#dump.
4968505e » Yoshinori Okuji 2002-08-29 Remove Bio::Matrix. 3253
9811bb5e » ktym 2002-07-30 * update for 0.3.9 3254 2002-07-30 KATAYAMA Toshiaki <k@bioruby.org>
3255
3256 * BioRuby version 0.3.9 released.
3257 * lib/bio/location.rb:
3258 * Locations#length (size) methods added (contributed by N. Goto)
3259 * Locations#relative method added (contributed by N. Goto)
3260 * Locations#absolute method is renamed from offset
3261 * Locations#offset, offset_aa methods removed
3262 * use absolute/relative(n, :aa) for _aa
3263 * Locations#[], range methods added
3264 * Location#range method added
3265 * lib/bio/db/embl.rb:
3266 * fix accession method.
3267 * lib/bio/db/genpept.rb:
3268 * temporally added - in the next release, we will make refactoring.
3269 * lib/bio/reference.rb:
3270 * in bibtex and bibitem format, "PMIDnum" is changed to "PMID:num".
3271 * lib/bio/io/pubmed.rb:
3272 * esearch, efetch methods are added.
3273 * lib/bio/db/aaindex.rb:
3274 * fix serious bug in the index method to support negative values.
3275 * lib/bio/db.rb:
3276 * fix fetch method to cut tag without fail.
3277 * lib/bio/extend.rb:
3278 * added first_line_only option for the prefix in fill method.
3279 * doc/Tutorial.rd.ja:
3280 * added docs on BibTeX etc.
3281
15d1e6a7 » ktym 2002-06-25 * updated for release 0.3.8 3282 2002-06-26 KATAYAMA Toshiaki <k@bioruby.org>
3283
3284 * BioRuby version 0.3.8 released.
3285 * lib/bio/sequence.rb:
3286 * normalize! method added for clean up the object itself.
3287 * 'to_seq' method was renamed to 'seq' (!)
3288 * to_xxxx should be used when the class of the object changes.
3289 * lib/bio/appl/blast/xmparser.rb:
3290 * each_iteration, each_hit, each, hits, statistics, message methods
3291 are added in Report class.
3292 * statistics, message methods are added in Iteration class.
3293 * methods compatible with Fasta::Report::Hit are added in Hit class.
3294 * lib/bio/appl/blast/rexml.rb:
3295 * many APIs were changed to follow the xmlparser.rb's. (!)
3296 * lib/bio/appl/{blast.rb,fasta.rb]:
3297 * class method parser() is added for loading specified Report class.
3298 * etc/bioinformatics/seqdatabase.ini: added for OBDA (!)
3299 * sample setup for BioRegistry - Open Bio Sequence Database Access.
3300 * lib/bio/extend.rb: added (!)
3301 * This module adds some functionarity to the existing classes and
3302 not loaded by default. User should require specifically if needed.
3303 * lib/bio/util/*: removed and merged into lib/bio/extend.rb (!)
3304 * lib/bio/id.rb: removed (!)
3305 * lib/bio/db/{embl.rb,sptr.rb,transfac.rb}: added entry_id
3306 * lib/bio/data/keggorg.rb: updated
3307 * sample/genes2* sample/genome2*: updated
3308 * doc/Tutrial.rd.ja: updated
3309
7be18c53 » ktym 2002-06-18 * updated for release 0.3.7 3310 2002-06-19 KATAYAMA Toshiaki <k@bioruby.org>
3311
3312 * BioRuby version 0.3.7 released.
15d1e6a7 » ktym 2002-06-25 * updated for release 0.3.8 3313 * lib/bio/sequence.rb: Sequence inherits String again (!)
7be18c53 » ktym 2002-06-18 * updated for release 0.3.7 3314 * lib/bio/db.rb, db/embl.rb, db/sptr.rb: moved EMBL specific methods
3315
3316 2002-06-18 KATAYAMA Toshiaki <k@bioruby.org>
3317
3318 * lib/bio/feature.rb: Bio::Feature#[] method added
3319 * doc/Tutrial.rd.ja: changed to use Feature class
3320
3321 2002-05-28 KATAYAMA Toshiaki <k@bioruby.org>
3322
15d1e6a7 » ktym 2002-06-25 * updated for release 0.3.8 3323 * lib/bio/appl/fasta.rb: parser separated, API renewal (!)
7be18c53 » ktym 2002-06-18 * updated for release 0.3.7 3324 * lib/bio/appl/fasta/format10.rb: moved from fasta.rb
3325
15d1e6a7 » ktym 2002-06-25 * updated for release 0.3.8 3326 * lib/bio/appl/blast.rb: parser separated, API renewal (!)
7be18c53 » ktym 2002-06-18 * updated for release 0.3.7 3327 * lib/bio/appl/blast/format8.rb: newly added
3328 * lib/bio/appl/blast/rexml.rb: newly added
3329 * lib/bio/appl/blast/xmlparser.rb: moved from blast.rb
3330
3331 2002-05-16 KATAYAMA Toshiaki <k@bioruby.org>
3332
3333 * lib/bio/sequence.rb: added alias 'Seq' for class Sequence
3334 * lib/bio/db/fasta.rb: entry method added
3335
3336 2002-05-15 KATAYAMA Toshiaki <k@bioruby.org>
3337
3338 * lib/bio/io/dbget.rb: bug fixed for pfam (was wrongly skip # lines)
3339 * lib/bio/location.rb: offset method added, eased range check
3340
3341 2002-04-26 KATAYAMA Toshiaki <k@bioruby.org>
3342
3343 * sample/biofetch.rb: new 'info=' option added
3344
3345 2002-04-22 KATAYAMA Toshiaki <k@bioruby.org>
3346
3347 * lib/bio/appl/fasta.rb: follow changes made at fasta.genome.ad.jp
3348 * sample/gb2tab.rb: fixed to use authors.inspect for reference
3349
3350 2002-04-15 KATAYAMA Toshiaki <k@bioruby.org>
3351
3352 * sample/gb2fasta.rb: changed to follow new genbank.rb spec.
3353 * sample/gt2fasta.rb: changed to follow new genbank.rb spec.
3354 * sample/gbtab2mysql.rb: added for loading tab delimited data.
3355
78e1ede3 » ktym 2002-04-08 updated for bioruby 0.3.6 3356 2002/04/08
3357 * version 0.3.6 released -k
7be18c53 » ktym 2002-06-18 * updated for release 0.3.7 3358 * fixed inconsistency among db.rb, genbank.rb, genome.rb -k
3359 * lib/bio/db/genbank.rb : serious bug fixed in locus method -k
3360 * lib/bio/feature.rb : method name 'type' has changed -k
3361
3362 2002/03/27
3363 * sample/gb2tab.rb changed to follow new genbank.rb w/ new schema -k
78e1ede3 » ktym 2002-04-08 updated for bioruby 0.3.6 3364
e254cc66 » Yoshinori Okuji 2002-03-25 * sample/gb2tab.rb use ruby... 3365 2002/03/26
3366 * sample/gb2tab.rb use ruby instead of perl in the example -o
274ab74c » Yoshinori Okuji 2002-03-25 * sample/gb2fasta.rb update... 3367 * sample/gb2fasta.rb updated -o
78e1ede3 » ktym 2002-04-08 updated for bioruby 0.3.6 3368
834f907e » ktym 2002-03-11 * changes between 0.3.4 to ... 3369 2002/03/11
3370 * version 0.3.5 released -k
3371
3372 2002/03/04
3373 * lib/bio/sequence.rb to_a, to_ary methods renamed to names, codes -k
3374 * sample/biofetch.rb added for BioFetch server -k
3375 * bin/biofetch ad