-
Notifications
You must be signed in to change notification settings - Fork 109
/
ChangeLog
1631 lines (1070 loc) · 48.8 KB
/
ChangeLog
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
2007-07-17 Toshiaki Katayama <k@bioruby.org>
* lib/bio/io/das.rb
Fixed that mapmaster method to return correct value (mapmaseter's
URL). This bug is reported and fixed by Dave Thorne.
2007-07-16 Naohisa Goto <ng@bioruby.org>
* lib/bio/mafft/report.rb
For generic multi-fasta formatted sequence alignment,
Bio::Alignment::MultiFastaFormat is newly added based on
Bio::MAFFT::Report class, and Bio::MAFFT::Report is
changed to inherit the new class.
Tests are added in test/unit/bio/appl/mafft/test_report.rb.
* lib/bio/alignment.rb
New modules and classes Bio::Alignment::FactoryTemplate::* are added.
They are used by following three new classes.
* lib/bio/appl/muscle.rb
* lib/bio/appl/probcons.rb
* lib/bio/appl/tcoffee.rb
New classess Bio::Muscle, Bio::Probcons, and Bio::Tcoffee are added
for MUSCLE, ProbCons, and T-Coffee multiple alignment programs.
Contributed by Jeffrey Blakeslee and colleagues.
* lib/bio/appl/clustalw.rb
* lib/bio/appl/mafft.rb
Interfaces of Bio::ClustalW and Bio::MAFFT are added/modified
to follow Bio::Alignment::FactoryTemplate (but not yet changed to
use it).
2007-07-09 Toshiaki Katayama <k@bioruby.org>
* BioRuby shell on Rails has new CSS theme
Completely new design for BioRuby shell on Rails translated from
the 'DibdoltRed' theme on www.openwebdesign.org which is created by
Darjan Panic and Brian Green as a public domain work!
2007-07-09 Toshiaki Katayama <k@bioruby.org>
* lib/bio/db/kegg/taxonomy.rb
Newly added KEGG taxonomy file parser which treats taxonomic tree
structure of the KEGG organisms. The file is available at
ftp://ftp.genome.jp/pub/kegg/genes/taxonomy
and is a replacement of the previously used keggtab file (obsoleted).
* lib/bio/db/kegg/keggtab.rb
Bio::KEGG::Keggtab is obsoleted as the file is no longer provided.
Use Bio::KEGG::Taxonomy (lib/bio/db/kegg/taxonomy.rb) instead.
* lib/bio/shell/plugin/soap.rb
Newly added web service plugins for BioRuby shell which supports
NCBI SOAP, EBI SOAP and DDBJ XML in addition to the KEGG API.
2007-07-09 Naohisa Goto <ng@bioruby.org>
* lib/bio/db/pdb/pdb.rb
Pdb_LString.new is changed not to raise error for nil.
Fixed a bug when below records does not exist in a PDB entry:
REMARK (remark), JRNL (jrnl), HELIX (helix),
TURN (turn), SHEET (sheet), SSBOND (ssbond), SEQRES (seqres),
DBREF (dbref), KEYWDS (keywords), AUTHOR (authors),
HEADER (entry_id, accession, classification),
TITLE (definition), and REVDAT (version) records (methods).
Incompatible change: Bio::PDB#record is changed to return
an empty array for nonexistent record.
(reported by Mikael Borg)
2007-07-09 Naohisa Goto <ng@bioruby.org>
* lib/bio/io/flatfile.rb
Bio::FlatFile.foreach is added (which is suggested by IO.foreach).
2007-06-28 Toshiaki Katayama <k@bioruby.org>
* lib/bio/shell/setup.rb, core.rb
Changed not to use Dir.chdir by caching full path of the save
directory at a start up time, so that user can freely change
the work directory without affecting object/history saving
functionality.
Bio::Shell.cache[:savedir] stores the session saving directory
(session means shell/session/{config,history,object} files),
Bio::Shell.cache[:workdir] stores the working directory at a start
up time (can be same directory with the :savedir) and both are
converted and stored as full path allowing user to use Dir.chdir
in the shell session).
If --rails (-r) option is applied, 'bioruby' command will run in
the Rails server mode, and the server will start in the :savedir.
(A) IRB mode
1. run in the current directory and the session will be saved
in the ~/.bioruby directory
% bioruby
2. run in the current directory and the session will be saved
in the foo/bar directory
% bioruby foo/bar
3. run in the current directory and the session will be saved
in the /tmp/foo/bar directory
% bioruby /tmp/foo/bar
(B) Rails mode
4. run in the ~/.bioruby directory and the session will also be saved
in the ~/.bioruby directory
% bioruby -r
5. run in the foo/bar directory and the session will also be saved
in the foo/bar directory
% bioruby -r foo/bar
6. run in the /tmp/foo/bar directory and the session will also be
saved in the /tmp/foo/bar directory
% bioruby -r /tmp/foo/bar
(C) Script mode
7. run in the current directory using the session saved
in the ~/.bioruby directory
% bioruby ~/.bioruby/shell/script.rb
8. run in the current directory using the session saved
in the foo/bar directory
% bioruby foo/bar/shell/script.rb
9. run in the current directory using the session saved
in the /tmp/foo/bar directory
% bioruby /tmp/foo/bar/shell/script.rb
2007-06-21 Toshiaki Katayama <k@bioruby.org>
* lib/bio/shell/setup.rb
If no directory is specified to the bioruby command,
use ~/.bioruby directory as the default save directory
instead of the current directory, as suggested by Jun Sese.
User can use 'bioruby' command without botherd by directories
and files previously created by the 'bioruby' command
in the current directory even when not needed.
2007-05-19 Toshiaki Katayama <k@bioruby.org>
* lib/bio/appl/fasta.rb
Bug fixed that exec_local fails to exec when @ktup is nil.
This problem is reported and fixed by Fredrik Johansson.
* lib/bio/db/gff.rb
parser_attributes method in GFF3 class is modified to use
'=' char as a separator instead of ' ' (which is used in
GFF2 spec).
2007-04-06 Toshiaki Katayama <k@bioruby.org>
* COPYING, COPYING.LIB are removed
BioRuby is now distributed under the same terms as Ruby.
On behalf of the BioRuby developer, I have asked all authors of
the BioRuby code to change BioRuby's license from LGPL to Ruby's.
And we have finished to change license of all modules in the BioRuby
library. This means that Ruby user can freely use BioRuby library
without being annoyed by licensing issues.
* lib/bio/db/kegg/ko.rb is renamed to lib/bio/db/kegg/ortholog.rb
KEGG KO database is renamed to KEGG ORTHOLOG database, thus we
follow the change. Bio::KEGG::KO is renamed to Bio::KEGG::ORTHOLOG.
Bio::KEGG::ORTHOLOG#genes, dblinks methods are rewrited to use
lines_fetch method.
* lib/bio/data/aa.rb
to_re method is changed that the generated regexp to include
ambiguous amino acid itself - replacement of amino acid X should
include X itself.
2007-04-05 Trevor Wennblom <trevor@corevx.com>
* License headers are completely rewrited to Ruby's.
2007-04-02 Naohisa Goto <ng@bioruby.org>
* lib/bio/appl/mafft.rb
Incompatible change: Bio::MAFFT#output is changed to return
a string of multi-fasta formmatted text. To get an array of
Bio::FastaFormat objects (as of 1.0 or before), please use
report.data instead.
2007-03-29 Toshiaki Katayama <k@bioruby.org>
* lib/bio/db/kegg/cell.rb
Obsoleted as the KEGG CELL database is not publically available
any more.
2007-03-28 Toshiaki Katayama <k@bioruby.org>
* lib/bio/shell/rails/.../bioruby_controller.rb
BioRuby shell on Rails access is changed to be limited only from
the localhost for security reason (if local_request?).
* lib/bio/command.rb
The post_form method is modified to accept URL as a string and
extended to accept params as
array of string
array of hash
array of array
or
string
in addition to hash (also can be ommited if not needed - defaults
to nil).
Keys and parameters of params are forced to use to_s for sure.
* lib/bio/io/ensembl.rb
Re-designed to allows user to use Bio::Ensembl.new without
creating inherited sub class.
Changed to use Bio::Command.post_form
* lib/bio/das.rb
Changed to use Bio::Command
* lib/bio/shell/plugin/das.rb
Newly added BioDAS client plugin for BioRuby shell.
das.list_sequences
das.dna
das.features
2007-03-15 Toshiaki Katayama <k@bioruby.org>
* lib/bio/shell/irb.rb
Changed to load Rails environment when bioruby shell is invoked
in the Rails project directory. This means that user can use
'bioruby' command as a better './script/console' which has
persistent objects and shared history.
2007-03-08 Toshiaki Katayama <k@bioruby.org>
* lib/bio/db/kegg/drug.rb
Newly added KEGG DRUG database parser.
* lib/bio/db/kegg/glycan.rb
Bio::KEGG::GLYCAN#bindings method is removed.
Bio::KEGG::GLYCAN#comment, remarks methods are added.
Bio::KEGG::GLYCAN#orthologs and dblinks methods are changed to use
lines_fetch method.
* lib/bio/kegg/compound.rb
Bio::KEGG::COMPOUND#glycans method is added
Bio::KEGG::COMPOUND#names method is changed to return an array
of stripped strings.
* lib/bio/db/kegg/genes.rb
Bio::KEGG::GENES#orthologs method is added.
2007-03-27 Naohisa Goto <ng@bioruby.org>
* lib/bio/command.rb
Bio::Command.call_command_fork and query_command_fork methods
are changed to handle all Ruby exceptions in the child process.
* lib/bio/io/flatfile.rb
UniProt format autodetection was changed to follow the change of
UniProtKB release 9.0 of 31-Oct-2006.
2007-02-12 Naohisa Goto <ng@bioruby.org>
* lib/bio/io/flatfile.rb
Exception class UnknownDataFormatError is added.
It will be raised before reading data from IO when data format
hasn't been specified due to failure of file format autodetection.
2007-02-12 Toshiaki Katayama <k@bioruby.org>
* lib/bio/io/flatfile.rb
Added support for KEGG EGENES.
2007-02-02 Trevor Wennblom <trevor@corevx.com>
* lib/bio/util/restriction_enzyme*
Bio::RestrictionEnzyme stabilized.
2007-02-02 Trevor Wennblom <trevor@corevx.com>
* lib/bio/db/lasergene.rb
Bio::Lasergene Interface for DNAStar Lasergene sequence file format
2007-02-02 Trevor Wennblom <trevor@corevx.com>
* lib/bio/db/soft.rb
Bio::SOFT for reading SOFT formatted NCBI GEO files.
2007-01-16 Toshiaki Katayama <k@bioruby.org>
* BioRuby shell on Rails new features and fixes
New features:
* Input [#] is linked to action for filling textarea from history
* [methods] is separated into columns for readability
Fixes and improvements:
* HIDE_VARIABLES is moved from helper to controller to avoid warning
"already initialized constant - HIDE_VARIABLES" repeated on reload.
* <div id="evaluate"> is renamed to "log_#" with number for future
extention.
* <div id="log_#"> are inserted in the <div id="logs">
2007-01-15 Toshiaki Katayama <k@bioruby.org>
* lib/bio/db.rb
lines_fetch method (internally used various bio/db/*.rb modules)
is rewrited to concatenate indented sub field.
* lib/bio/db/kegg/compound.rb
Bio::KEGG::COMPOUND#comment method which returns contents of
the COMMENT line is added
* lib/bio/db/kegg/enzyme.rb
Bio::KEGG::ENZYME#entry_id is changed to return EC number only.
Previous version of entry_id method is renamed to entry method
which returns a "EC x.x.x.x Enzyme" style string.
Bio::KEGG::ENZYME#obsolete? method is added which returns boolean
value (true or false) according to the ENTRY line contains
a string 'Obsolete' or not.
Bio::KEGG::ENZYME#all_reac, iubmb_reactions, kegg_reactions methods
are added to support newly added ALL_REAC field.
Bio::KEGG::ENZYME#inhibitors and orthologs methods are added.
Bio::KEGG::ENZYME#substrates, products, inhibitors, cofactors,
pathways, orthologs, diseases, motifs methods are rewrited to
utilizes new lines_fetch method in db.rb to process continuous
sub field.
* lib/bio/db/kegg/genome.rb
Bio::KEGG::GENOME#scaffolds, gc, genomemap methods are obsoleted.
Bio::KEGG::GENOME#distance, data_source, original_db methods are
added.
2006-12-24 Toshiaki Katayama <k@bioruby.org>
* bin/bioruby, lib/bio/shell/, lib/bio/shell/rails/
(lib/bio/shell/rails/vendor/plugins/generators/)
Web functionallity of the BioRuby shell is completely rewrited
to utilize generator of the Ruby on Rails. This means we don't
need to have a copy of the rails installation in our code base
any more. The shell now run in threads so user does not need
to run 2 processes as before (drb and webrick). Most importantly,
the shell is extended to have textarea to input any code and
the evaluated result is returned with AJAX having various neat
visual effects.
* lib/bio/.rb
Extended to have Bio.command where command can be any BioRuby
shell methods.
ex. puts Bio.getseq("atgc" * 10).randomize.translate
* lib/bio/shell/plugin/entry.rb, seq.rb
seq, ent, obj commands are renamed to getseq, getent, getobj
respectively. This getseq is also changed to return Bio::Sequence
with @moltype = Bio::Sequence::NA object instead of Bio::Sequence::NA
object.
* lib/bio/db/kegg/kgml.rb
Some method names are changed to avoid confusion:
* entry_type is renamed to category (<entry type="">)
* map is renamed to pathway (<entry map="">)
2006-12-19 Christian Zmasek <czmasek@burnham.org>
* lib/bio/db/nexus.rb
Bio::Nexus is newly developed during the Phyloinformatics hackathon.
2006-12-16 Toshiaki Katayama <k@birouby.org>
* lib/bio/io/sql.rb
Updated to follow recent BioSQL schema contributed by
Raoul Jean Pierre Bonnal.
2006-12-15 Mitsuteru Nakao <n@bioruby.org>
* lib/bio/appl/iprscan/report.rb
Bio::Iprscan::Report for InterProScan output is newly added.
2006-12-15 Naohisa Goto <ng@bioruby.org>
* lib/bio/appl/mafft/report.rb
Bio::MAFFT::Report#initialize is changed to get a string of
multi-fasta formmatted text instead of Array.
2006-12-14 Naohisa Goto <ng@bioruby.org>
* lib/bio/appl/phylip/alignment.rb
Phylip format multiple sequence alignment parser class
Bio::Phylip::PhylipFormat is newly added.
* lib/bio/appl/phylip/distance_matrix.rb
Bio::Phylip::DistanceMatrix, a parser for phylip distance matrix
(generated by dnadist/protdist/restdist programs) is newly added.
* lib/bio/appl/gcg/msf.rb, lib/bio/appl/gcg/seq.rb
Bio::GCG::Msf in lib/bio/appl/gcg/msf.rb for GCG MSF multiple
sequence alignment format parser, and Bio::GCG::Seq in
lib/bio/appl/gcg/seq.rb for GCG sequence format parser are
newly added.
* lib/bio/alignment.rb
Output of Phylip interleaved/non-interleaved format (.phy),
Molphy alignment format (.mol), and GCG MSF format (.msf)
are supported. Bio::Alignment::ClustalWFormatter is removed
and methods in the module are renamed and moved to
Bio::Alignment::Output.
* lib/bio/appl/clustalw.rb, lib/bio/appl/mafft.rb, lib/bio/appl/sim4.rb
Changed to use Bio::Command instead of Open3.popen3.
2006-12-13 Naohisa Goto <ng@bioruby.org>
* lib/bio/tree.rb, lib/bio/db/newick.rb
Bio::PhylogeneticTree is renamed to Bio::Tree, and
lib/bio/phylogenetictree.rb is renamed to lib/bio/tree.rb.
NHX (New Hampshire eXtended) parser/writer support are added.
2006-12-13 Toshiaki Katayama <k@bioruby.org>
* doc/Desing.rd.ja, doc/TODO.rd.ja, doc/BioRuby.rd.ja are obsoletd.
2006-10-05 Naohisa Goto <ng@bioruby.org>
* lib/bio/db/newick.rb
Bio::Newick for Newick standard phylogenetic tree parser is
newly added (contributed by Daniel Amelang).
* lib/bio/phylogenetictree.rb
Bio::PhylogeneticTree for phylogenetic tree data structure
is newly added.
2006-09-19 Toshiaki Katayama <k@bioruby.org>
* lib/bio/io/soapwsdl.rb
* lib/bio/io/ebisoap.rb
* lib/bio/io/ncbisoap.rb
Newly added web service modules.
* lib/bio/db/kegg/kgml.rb
Accessor for the <component> attribute is added.
* lib/bio/shell/plugin/codon.rb
Support for Pyrrolysine and Selenocysteine are added in the
BioRuby shell.
* lib/bio/sshell/plugin/seq.rb
sixtrans, skip, step methods are added in the BioRuby shell.
bioruby> seqtrans(seq)
bioruby> seq.step(window_size) {|subseq|
# do something on subseq
}
bioruby> seq.skip(window_sizep, step_size) {|subseq|
# do something on subseq
}
2006-07-26 Toshiaki Katayama <k@bioruby.org>
* lib/bio/data/aa.rb
Amino acids J (Xle: I/L), O (Pyl: pyrrolysine) and X (unknown)
are added (now we have consumed 26 alphabets!).
* lib/bio/io/fastacmd.rb
Fixed that new version of fastacmd (in BLAST package) changed
the option from '-D T' to '-D 1', contributed by the author
of this module Shuji Shigenobu.
* lib/bio/shell/plugin/psort.rb
Newly added BioRuby shell plugin for PSORT
* lib/bio/shell/plugin/blast.rb
Newly added BioRuby shell plugin for BLAST search against KEGG GENES
* lib/bio/db/prosite.rb
PROSITE#re instance method is added to translate PATTERN of
the entry to Regexp using PROSITE.pa2re class method.
* lib/bio/db/kegg/genes.rb
Bio::KEGG::GENES#keggclass method is renamed to pathway
Bio::KEGG::GENES#splinks method is removed
Bio::KEGG::GENES#motifs method is added
these reflect changes made in the original KEGG GENES database.
Bio::KEGG::GENES#locations method is added to return Bio::Locations
Bio::KEGG::GENES#codon_usage is renamed cu_list (returns as Array)
Bio::KEGG::GENES#cu is renamed to codon_usage (returns as Hash)
Bio::KEGG::GENES#aalen, nalen methods are changed to return
the number written in the entry (use seq.length to obtain calculated
number as before).
* lib/bio/db/kegg/kgml.rb
Names of some accessors have been changed (including bug fixes)
and instance variable @dom is obsoleted. Here's a list of
incompatible attribute names with KGML tags by this change:
<entry>
:id -> :entry_id
:type -> :entry_type
names()
<graphics>
:name -> :label
:type -> :shape
<relation>
:entry1 -> :node1
:entry2 -> :node2
:type -> :rel
<subtype>
edge()
<reaction>
:name -> :entry_id
:type -> :direction
* lib/bio/io/das.rb
Bug fixed that the value of segment.stop was overwritten by
segment.orientation.
2006-07-14 Naohisa Goto <ng@bioruby.org>
* lib/bio/command.rb
Bio::Command::Tools and Bio::Command::NetTools are combined
and re-constructed into a new Bio::Command module.
lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb,
lib/bio/appl/emboss.rb, lib/bio/appl/psort.rb,
lib/bio/appl/hmmer.rb, lib/bio/db/fantom.rb,
lib/bio/io/fastacmd.rb, lib/bio/io/fetch.rb,
lib/bio/io/keggapi.rb, lib/bio/io/pubmed.rb, and
lib/bio/io/registry.rb are changed to use the new Bio::Command
instead of old Bio::Command or Net::HTTP.
2006-06-29 Naohisa Goto <ng@bioruby.org>
* lib/bio/appl/blat/report.rb
Bio::BLAT::Report::Hit#milli_bad, #percent_identity, #protein?,
#score, and #psl_version methods/attributes are newly added,
and psl files without headers are supported (discussed in
bioruby-ja ML).
2006-06-27 Naohisa Goto <ng@bioruby.org>
* lib/bio/sequence/na.rb
Bio::Sequence::NA#gc_content, #at_content, #gc_skew, #at_skew
are newly added. Bio::Sequence::NA#gc_percent are changed
not to raise ZeroDivisionError and returns 0 when given sequence
is empty.
* lib/bio/db/pdb/pdb.rb
Bio::PDB::ATOM#name, #resName, #iCode, #chaarge, #segID, and
#element are changed to strip whitespaces when initializing.
Bio::PDB::HETATM is also subject to the above changes.
(suggested by Mikael Borg)
2006-06-12 Naohisa Goto <ng@bioruby.org>
* lib/bio/io/flatfile.rb
Bug fix: Bio::FlatFile.open(klass, filename) didn't work.
2006-05-30 Toshiaki Katayama <k@bioruby.org>
* lib/bio/io/soapwsdl.rb
Generic list_methods method which extracts web service methods
defined in the WSDL file is added.
2006-05-02 Mitsuteru Nakao <n@bioruby.org>
* lib/bio/appl/pts1.rb
Bio::PTS1 first commit.
2006-04-30 Naohisa Goto <ng@bioruby.org>
* lib/bio/appl/blast/format0.rb
Bug fix: parse error for hits whose database sequence names
contain 'Score', and subsequent hits after them would lost
(reported by Tomoaki NISHIYAMA).
2006-04-14 Mitsuteru Nakao <n@bioruby.org>
* lib/bio/io/ensembl.rb
Bio::Ensembl first commit. It is a client class for Ensembl Genome
Browser.
2006-03-22 Naohisa Goto <ng@bioruby.org>
* lib/bio/io/flatfile.rb
Bug fix: Bio::FlatFile raises error for pipes, ARGF, etc.
The bug also affects bio/appl/mafft.rb, bio/appl/clustalw.rb,
bio/appl/blast.rb, bio/io/fastacmd.rb, and so on.
Bio::FlatFile#entry_start_pos and #entry_ended_pos are
changed to be enabled only when Bio::FlatFile#entry_pos_flag
is true.
2006-02-27 Toshiaki Katayama <k@bioruby.org>
* BioRuby 1.0.0 released
2006-02-10 Toshiaki Katayama <k@bioruby.org>
* BioRuby shell is changed to use session/ directory under the current
or specified directory to store the session information instead of
./.bioruby directory.
2006-02-05 Toshiaki Katayama <k@bioruby.org>
* License to be changed to Ruby's (not yet completed).
2006-02-01 Trevor Wennblom <trevor@corevx.com>
* Bio::RestrictionEnzyme first commit for comments.
* See lib/bio/util/restriction_enzyme.rb and
test/unit/bio/util/restriction_enzyme
2006-01-28 Toshiaki Katayama <k@bioruby.org>
* lib/bio/appl/emboss.rb
EMBOSS USA format is now accepted via seqret/entret commands
and also utilized in the BioRuby shell (lib/bio/shell.rb,
plugin/entry.rb, plugin/emboss.rb).
* lib/bio/io/brdb.rb is removed - unused Bio::BRDB (BioRuby DB)
2006-01-23 Toshiaki Katayama <k@bioruby.org>
* lib/bio/sequence.rb
Bio::Sequence is refactored to be a container class for
any sequence annotations. Functionality is separared into
several files under the lib/bio/sequence/ direcotry as
common.rb, compat.rb, aa.rb, na.rb, format.rb
2006-01-20 Toshiaki Katayama <k@bioruby.org>
* BioRuby 0.7.1 is released.
2006-01-12 Toshiaki Katayama <k@bioruby.org>
* lib/bio/db.ra: fixed a bug of the tag_cut method introduced in 0.7.0
(reported by Alex Gutteridge)
2006-01-04 Naohisa Goto <ng@bioruby.org>
* Bio::PDB is refactored. See doc/Changes-0.7 for more details.
2005-12-19 Toshiaki Katayama <k@bioruby.org>
* BioRuby 0.7.0 is released.
See doc/Changes-0.7.rd file for major and incompatible changes.
2005-12-19 Naohisa Goto <ng@bioruby.org>
* lib/bio/db/pdb.rb, lib/bio/db/pdb/pdb.rb, lib/bio/db/pdb/*.rb
* Many changes have been made.
* Bio::PDB::FieldDef is removed and Bio::PDB::Record is completely
changed. Now, Record is changed from hash to Struct, and
method_missing is no longer used.
* In the "MODEL" record, model_serial is changed to serial.
* In any records, record_type is changed to record_name.
* In most records contains real numbers, changed to return
float values instead of strings.
* Pdb_AChar, Pdb_Atom, Pdb_Character, Pdb_Continuation,
Pdb_Date, Pdb_IDcode, Pdb_Integer, Pdb_LString, Pdb_List,
Pdb_Real, Pdb_Residue_name, Pdb_SList, Pdb_Specification_list,
Pdb_String, Pdb_StringRJ and Pdb_SymOP are moved under
Bio::PDB::DataType.
* There are more and more changes to be written...
* lib/bio/db/pdb/atom.rb
* Bio::PDB::Atom is removed.
Instead, please use Bio::PDB::Record::ATOM and
Bio::PDB::Record::HETATM.
2005-12-02 Naohisa Goto <ng:bioruby.org>
* lib/bio/alignment.rb
* Old Bio::Alignment class is renamed to
Bio::Alignment::OriginalAlignment.
Now, new Bio::Alignment is a module. However,
you don't mind so much because most of the class methods
previously existed are defined to delegate to the new
Bio::Alignment::OriginalAlignment class,
for keeping backward compatibility.
* New classes and modules are introduced. Please refer RDoc.
* each_site and some methods changed to return Bio::Alignment::Site,
which inherits Array (previously returned Array).
* consensus_iupac now returns only standard bases
'a', 'c', 'g', 't', 'm', 'r', 'w', 's', 'y', 'k', 'v',
'h', 'd', 'b', 'n', or nil (in SiteMethods#consensus_iupac) or
'?' (or missing_char, in EnumerableExtension#consensus_iupac).
Note that consensus_iupac now does not return u and invalid
letters not defined in IUPAC standard even if all bases
are equal.
* There are more and more changes to be written...
2005-11-05 Toshiaki Katayama <k@bioruby.org>
* lib/bio/sequence.rb
Bio::Sequence.auto(str) method is added which auto detect the
molecular type of the string and then returns the
Bio::Sequence::NA or Bio::Sequence::AA object.
Bio::Sequence#blast and Bio::Sequence#fasta methods are removed.
* lib/bio/shell/plugin/codon.rb
Newly added plugin to treat codon table.
ColoredCodonTable is ported from the codontable.rb
2005-11-01 Toshiaki Katayama <k@bioruby.org>
* bin/bioruby, lib/bio/shell/
All methods are changed to private methods to avoid adding them
in top level binding, which caused many unexpected behaviors,
as adviced by Koichi Sasada.
The MIDI plugin is now able to select musical scales.
2005-10-23 Toshiaki Katayama <k@bioruby.org>
* lib/bio/util/color_scheme
Newly contributed Bio::ColorScheme
* lib/bio/db/kegg/kgml.rb
Newly added KEGG KGML parser.
2005-10-05 Toshiaki Katayama <k@bioruby.org>
* lib/bio/shell/plugin/midi.rb
Sequcne to MIDI plugin is contributed by Natsuhiro Ichinose
2005-09-25 Toshiaki Katayama <k@bioruby.org>
* README.DEV
Newly added guideline document for the contributors.
* README
Updated and added instructions on RubyGems.
2005-09-23 Toshiaki Katayama <k@bioruby.org>
* bin/bioruby, lib/bio/shell.rb, lib/bio/shell/core.rb,
lib/bio/shell/session.rb, lib/bio/shell/plugin/seq.rb,
lib/bio/shell/flatfile.rb, lib/bio/shell/obda.rb
Newly added BioRuby shell, the command line user interface.
Try 'bioruby' command in your terminal.
* doc/Changes-0.7.rd
Newly added document describing incompatible and important
changes between the BioRuby 0.6 and 0.7 versions.
* lib/bio/sequence.rb
Bio::Sequence.guess, Bio::Sequence#guess methods are added
which guess the sequence type by following fomula (default
value for the threshold is 0.9).
number of ATGC
--------------------------------------- > threshold
number of other chars - number of N
2005-09-10 Naohisa Goto <ng@bioruby.org>
* lib/bio.rb, lib/bio/appl/blast.rb, lib/bio/appl/blast/format0.rb,
lib/bio/appl/blast/report.rb, lib/bio/appl/clustalw.rb,
lib/bio/appl/fasta.rb, lib/bio/appl/fasta/format10.rb,
lib/bio/appl/hmmer.rb, lib/bio/appl/hmmer/report.rb,
lib/bio/appl/mafft.rb, lib/bio/appl/psort.rb,
lib/bio/appl/psort/report.rb, lib/bio/appl/sim4.rb,
lib/bio/db/genbank/ddbj.rb, lib/bio/io/flatfile/bdb.rb,
lib/bio/io/flatfile/index.rb, lib/bio/io/flatfile/indexer.rb
fixed autoload problem
* lib/bio/appl/blast.rb, lib/bio/appl/blast/report.rb
Bio::Blast.reports method was moved from lib/bio/appl/blast/report.rb
to lib/bio/appl/blast.rb for autoload.
2005-08-31 Toshiaki Katayama <k@bioryby.org>
* BioRuby 0.6.4 is released.
* doc/KEGG_API.rd
Newly added English version of the KEGG API manual.
* lib/bio/aa.rb
the 'one2name' method introduced in 0.6.3 is fixed and added 'one'
and 'three' methods as aliases for 'to_1' and 'to_3' methods.
2005-08-31 Naohisa Goto <ng@bioruby.org>
* removed unused file lib/bio/appl/factory.rb
(the functionality had been integrated into lib/bio/command.rb)
* doc/Tutorial.rd
Newly added an English translation of the Japanese tutorial.
2005-08-16 Naohisa Goto <ng@bioruby.org>
* lib/bio/command.rb
Newly added Bio::Command::Tools module.
Bio::Command::Tools is a collection of useful methods
for execution of external commands.
* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb,
lib/bio/appl/hmmer.rb, lib/bio/io/fastacmd.rb
For security reason, shell special characters are escaped.
* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb, lib/bio/appl/hmmer.rb
Options are stored with an array (@options).
#options and #opions= methods are added.
* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb
Bio::Blast.remote and Bio::Fasta.remote is fixed to work
with the recent change of the GenomeNet.
2005-08-11 Toshiaki Katayama <k@bioruby.org>
* Sequence#to_re method to have compatibility with 0.6.2 for RNA
* Fixed Bio::Fastacmd#fetch to work
* Bio::Fastacmd and Bio::Bl2seq classes (introduced in 0.6.3) are
renamed to Bio::Blast::Fastacmd, Bio::Blast::Bl2seq respectively.
2005-08-09 Toshiaki Katayama <k@bioruby.org>
* BioRuby 0.6.3 is released.
This version would be the final release to support Ruby 1.6 series
(as long as no serious bug is found:).
* lib/bio/util/sirna.rb:
Newly added method for desing of siRNA, contributed by
Itoshi Nikaido. The lib/bio/util/ directory if reserved
for bioinfomatics algorithms implemented by pure Ruby.
* lib/bio/io/fastacmd.rb:
Newly added wrapper for NCBI fastacmd program, contributed by
Shinji Shigenobu.
* lib/bio/appl/hmmer/report.rb:
Bug fixed by Masashi Fujita when the position of sequence
rarely becomes '-' instead of digits.
2005-08-08 Mitsuteru Nakao <n@bioruby.org>
* lib/bio/db/embl/sptr.rb:
Added Bio::SPTR#protein_name and Bio::SPTR#synoyms methods.
contributed by Luca Pireddu.
Changed Bio::SPTR#gn, Bio::SPTR#gene_name and
Bio::SPTR#gene_names methods. contributed by Luca Pireddu.
2005-08-08 Naohisa Goto <ng@bioruby.org>
* lib/bio/appl/bl2seq/report.rb:
Newly added bl2seq (BLAST 2 sequences) output parser.
* lib/bio/appl/blast/format0.rb:
Added `self.class::` before F0dbstat.new for bl2seq/report.rb
2005-08-07 Toshiaki Katayama <k@bioruby.org>
* lib/bio/sequence.rb, lib/bio/data/na.rb, lib/bio/data/aa.rb:
Bio::NucleicAcid, Bio::AminoAcid classes are refactored to have
Data module, and this module is included and extended to make
all methods as both of instance methods and class methods.
Bio::Sequence::NA and AA classes are rewrited (molecular_weight,
to_re methods) to use Bio::NucleicAcid.
Bio::Sequence::NA#molecular_weight method is fixed to subtract
two hydrogens per each base.