forked from bioruby/bioruby
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathbioruby.gemspec
670 lines (665 loc) · 26.4 KB
/
bioruby.gemspec
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
# This file is automatically generated from bioruby.gemspec.erb and
# should NOT be edited by hand.
#
Gem::Specification.new do |s|
s.name = 'bio'
s.version = "1.4.3.5000"
s.author = "BioRuby project"
s.email = "[email protected]"
s.homepage = "http://bioruby.org/"
s.rubyforge_project = "bioruby"
s.summary = "Bioinformatics library"
s.description = "BioRuby is a library for bioinformatics (biology + information science)."
s.platform = Gem::Platform::RUBY
s.files = [
".travis.yml",
"COPYING",
"COPYING.ja",
"ChangeLog",
"GPL",
"KNOWN_ISSUES.rdoc",
"LEGAL",
"LGPL",
"README.rdoc",
"README_DEV.rdoc",
"RELEASE_NOTES.rdoc",
"Rakefile",
"bin/bioruby",
"bin/br_biofetch.rb",
"bin/br_bioflat.rb",
"bin/br_biogetseq.rb",
"bin/br_pmfetch.rb",
"bioruby.gemspec",
"bioruby.gemspec.erb",
"doc/ChangeLog-1.4.3",
"doc/ChangeLog-before-1.3.1",
"doc/ChangeLog-before-1.4.2",
"doc/Changes-0.7.rd",
"doc/Changes-1.3.rdoc",
"doc/RELEASE_NOTES-1.4.0.rdoc",
"doc/RELEASE_NOTES-1.4.1.rdoc",
"doc/RELEASE_NOTES-1.4.2.rdoc",
"doc/RELEASE_NOTES-1.4.3.rdoc",
"doc/Tutorial.rd",
"doc/Tutorial.rd.html",
"doc/Tutorial.rd.ja",
"doc/Tutorial.rd.ja.html",
"doc/bioruby.css",
"etc/bioinformatics/seqdatabase.ini",
"extconf.rb",
"gemfiles/Gemfile.travis-jruby1.8",
"gemfiles/Gemfile.travis-jruby1.9",
"gemfiles/Gemfile.travis-ruby1.8",
"gemfiles/Gemfile.travis-ruby1.9",
"gemfiles/modify-Gemfile.rb",
"gemfiles/prepare-gemspec.rb",
"lib/bio.rb",
"lib/bio/alignment.rb",
"lib/bio/appl/bl2seq/report.rb",
"lib/bio/appl/blast.rb",
"lib/bio/appl/blast/ddbj.rb",
"lib/bio/appl/blast/format0.rb",
"lib/bio/appl/blast/format8.rb",
"lib/bio/appl/blast/genomenet.rb",
"lib/bio/appl/blast/ncbioptions.rb",
"lib/bio/appl/blast/remote.rb",
"lib/bio/appl/blast/report.rb",
"lib/bio/appl/blast/rexml.rb",
"lib/bio/appl/blast/rpsblast.rb",
"lib/bio/appl/blast/wublast.rb",
"lib/bio/appl/blast/xmlparser.rb",
"lib/bio/appl/blat/report.rb",
"lib/bio/appl/clustalw.rb",
"lib/bio/appl/clustalw/report.rb",
"lib/bio/appl/emboss.rb",
"lib/bio/appl/fasta.rb",
"lib/bio/appl/fasta/format10.rb",
"lib/bio/appl/gcg/msf.rb",
"lib/bio/appl/gcg/seq.rb",
"lib/bio/appl/genscan/report.rb",
"lib/bio/appl/hmmer.rb",
"lib/bio/appl/hmmer/report.rb",
"lib/bio/appl/iprscan/report.rb",
"lib/bio/appl/mafft.rb",
"lib/bio/appl/mafft/report.rb",
"lib/bio/appl/meme/mast.rb",
"lib/bio/appl/meme/mast/report.rb",
"lib/bio/appl/meme/motif.rb",
"lib/bio/appl/muscle.rb",
"lib/bio/appl/paml/baseml.rb",
"lib/bio/appl/paml/baseml/report.rb",
"lib/bio/appl/paml/codeml.rb",
"lib/bio/appl/paml/codeml/rates.rb",
"lib/bio/appl/paml/codeml/report.rb",
"lib/bio/appl/paml/common.rb",
"lib/bio/appl/paml/common_report.rb",
"lib/bio/appl/paml/yn00.rb",
"lib/bio/appl/paml/yn00/report.rb",
"lib/bio/appl/phylip/alignment.rb",
"lib/bio/appl/phylip/distance_matrix.rb",
"lib/bio/appl/probcons.rb",
"lib/bio/appl/psort.rb",
"lib/bio/appl/psort/report.rb",
"lib/bio/appl/pts1.rb",
"lib/bio/appl/sim4.rb",
"lib/bio/appl/sim4/report.rb",
"lib/bio/appl/sosui/report.rb",
"lib/bio/appl/spidey/report.rb",
"lib/bio/appl/targetp/report.rb",
"lib/bio/appl/tcoffee.rb",
"lib/bio/appl/tmhmm/report.rb",
"lib/bio/command.rb",
"lib/bio/compat/features.rb",
"lib/bio/compat/references.rb",
"lib/bio/data/aa.rb",
"lib/bio/data/codontable.rb",
"lib/bio/data/na.rb",
"lib/bio/db.rb",
"lib/bio/db/aaindex.rb",
"lib/bio/db/biosql/biosql_to_biosequence.rb",
"lib/bio/db/biosql/sequence.rb",
"lib/bio/db/embl/common.rb",
"lib/bio/db/embl/embl.rb",
"lib/bio/db/embl/embl_to_biosequence.rb",
"lib/bio/db/embl/format_embl.rb",
"lib/bio/db/embl/sptr.rb",
"lib/bio/db/embl/swissprot.rb",
"lib/bio/db/embl/trembl.rb",
"lib/bio/db/embl/uniprot.rb",
"lib/bio/db/fantom.rb",
"lib/bio/db/fasta.rb",
"lib/bio/db/fasta/defline.rb",
"lib/bio/db/fasta/fasta_to_biosequence.rb",
"lib/bio/db/fasta/format_fasta.rb",
"lib/bio/db/fasta/format_qual.rb",
"lib/bio/db/fasta/qual.rb",
"lib/bio/db/fasta/qual_to_biosequence.rb",
"lib/bio/db/fastq.rb",
"lib/bio/db/fastq/fastq_to_biosequence.rb",
"lib/bio/db/fastq/format_fastq.rb",
"lib/bio/db/genbank/common.rb",
"lib/bio/db/genbank/ddbj.rb",
"lib/bio/db/genbank/format_genbank.rb",
"lib/bio/db/genbank/genbank.rb",
"lib/bio/db/genbank/genbank_to_biosequence.rb",
"lib/bio/db/genbank/genpept.rb",
"lib/bio/db/genbank/refseq.rb",
"lib/bio/db/gff.rb",
"lib/bio/db/go.rb",
"lib/bio/db/kegg/brite.rb",
"lib/bio/db/kegg/common.rb",
"lib/bio/db/kegg/compound.rb",
"lib/bio/db/kegg/drug.rb",
"lib/bio/db/kegg/enzyme.rb",
"lib/bio/db/kegg/expression.rb",
"lib/bio/db/kegg/genes.rb",
"lib/bio/db/kegg/genome.rb",
"lib/bio/db/kegg/glycan.rb",
"lib/bio/db/kegg/keggtab.rb",
"lib/bio/db/kegg/kgml.rb",
"lib/bio/db/kegg/module.rb",
"lib/bio/db/kegg/orthology.rb",
"lib/bio/db/kegg/pathway.rb",
"lib/bio/db/kegg/reaction.rb",
"lib/bio/db/lasergene.rb",
"lib/bio/db/litdb.rb",
"lib/bio/db/medline.rb",
"lib/bio/db/nbrf.rb",
"lib/bio/db/newick.rb",
"lib/bio/db/nexus.rb",
"lib/bio/db/pdb.rb",
"lib/bio/db/pdb/atom.rb",
"lib/bio/db/pdb/chain.rb",
"lib/bio/db/pdb/chemicalcomponent.rb",
"lib/bio/db/pdb/model.rb",
"lib/bio/db/pdb/pdb.rb",
"lib/bio/db/pdb/residue.rb",
"lib/bio/db/pdb/utils.rb",
"lib/bio/db/phyloxml/phyloxml.xsd",
"lib/bio/db/phyloxml/phyloxml_elements.rb",
"lib/bio/db/phyloxml/phyloxml_parser.rb",
"lib/bio/db/phyloxml/phyloxml_writer.rb",
"lib/bio/db/prosite.rb",
"lib/bio/db/rebase.rb",
"lib/bio/db/sanger_chromatogram/abif.rb",
"lib/bio/db/sanger_chromatogram/chromatogram.rb",
"lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb",
"lib/bio/db/sanger_chromatogram/scf.rb",
"lib/bio/db/soft.rb",
"lib/bio/db/transfac.rb",
"lib/bio/feature.rb",
"lib/bio/io/biosql/ar-biosql.rb",
"lib/bio/io/biosql/biosql.rb",
"lib/bio/io/biosql/config/database.yml",
"lib/bio/io/das.rb",
"lib/bio/io/ddbjrest.rb",
"lib/bio/io/ddbjxml.rb",
"lib/bio/io/ebisoap.rb",
"lib/bio/io/fastacmd.rb",
"lib/bio/io/fetch.rb",
"lib/bio/io/flatfile.rb",
"lib/bio/io/flatfile/autodetection.rb",
"lib/bio/io/flatfile/bdb.rb",
"lib/bio/io/flatfile/buffer.rb",
"lib/bio/io/flatfile/index.rb",
"lib/bio/io/flatfile/indexer.rb",
"lib/bio/io/flatfile/splitter.rb",
"lib/bio/io/higet.rb",
"lib/bio/io/hinv.rb",
"lib/bio/io/ncbirest.rb",
"lib/bio/io/pubmed.rb",
"lib/bio/io/registry.rb",
"lib/bio/io/soapwsdl.rb",
"lib/bio/io/sql.rb",
"lib/bio/io/togows.rb",
"lib/bio/location.rb",
"lib/bio/map.rb",
"lib/bio/pathway.rb",
"lib/bio/reference.rb",
"lib/bio/sequence.rb",
"lib/bio/sequence/aa.rb",
"lib/bio/sequence/adapter.rb",
"lib/bio/sequence/common.rb",
"lib/bio/sequence/compat.rb",
"lib/bio/sequence/dblink.rb",
"lib/bio/sequence/format.rb",
"lib/bio/sequence/format_raw.rb",
"lib/bio/sequence/generic.rb",
"lib/bio/sequence/na.rb",
"lib/bio/sequence/quality_score.rb",
"lib/bio/sequence/sequence_masker.rb",
"lib/bio/shell.rb",
"lib/bio/shell/core.rb",
"lib/bio/shell/demo.rb",
"lib/bio/shell/interface.rb",
"lib/bio/shell/irb.rb",
"lib/bio/shell/object.rb",
"lib/bio/shell/plugin/blast.rb",
"lib/bio/shell/plugin/codon.rb",
"lib/bio/shell/plugin/das.rb",
"lib/bio/shell/plugin/emboss.rb",
"lib/bio/shell/plugin/entry.rb",
"lib/bio/shell/plugin/flatfile.rb",
"lib/bio/shell/plugin/midi.rb",
"lib/bio/shell/plugin/ncbirest.rb",
"lib/bio/shell/plugin/obda.rb",
"lib/bio/shell/plugin/psort.rb",
"lib/bio/shell/plugin/seq.rb",
"lib/bio/shell/plugin/soap.rb",
"lib/bio/shell/plugin/togows.rb",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif",
"lib/bio/shell/script.rb",
"lib/bio/shell/setup.rb",
"lib/bio/shell/web.rb",
"lib/bio/tree.rb",
"lib/bio/tree/output.rb",
"lib/bio/util/color_scheme.rb",
"lib/bio/util/color_scheme/buried.rb",
"lib/bio/util/color_scheme/helix.rb",
"lib/bio/util/color_scheme/hydropathy.rb",
"lib/bio/util/color_scheme/nucleotide.rb",
"lib/bio/util/color_scheme/strand.rb",
"lib/bio/util/color_scheme/taylor.rb",
"lib/bio/util/color_scheme/turn.rb",
"lib/bio/util/color_scheme/zappo.rb",
"lib/bio/util/contingency_table.rb",
"lib/bio/util/restriction_enzyme.rb",
"lib/bio/util/restriction_enzyme/analysis.rb",
"lib/bio/util/restriction_enzyme/analysis_basic.rb",
"lib/bio/util/restriction_enzyme/cut_symbol.rb",
"lib/bio/util/restriction_enzyme/dense_int_array.rb",
"lib/bio/util/restriction_enzyme/double_stranded.rb",
"lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb",
"lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb",
"lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb",
"lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb",
"lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb",
"lib/bio/util/restriction_enzyme/enzymes.yaml",
"lib/bio/util/restriction_enzyme/range/cut_range.rb",
"lib/bio/util/restriction_enzyme/range/cut_ranges.rb",
"lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb",
"lib/bio/util/restriction_enzyme/range/sequence_range.rb",
"lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb",
"lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb",
"lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb",
"lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb",
"lib/bio/util/restriction_enzyme/single_strand.rb",
"lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb",
"lib/bio/util/restriction_enzyme/single_strand_complement.rb",
"lib/bio/util/restriction_enzyme/sorted_num_array.rb",
"lib/bio/util/restriction_enzyme/string_formatting.rb",
"lib/bio/util/sirna.rb",
"lib/bio/version.rb",
"sample/any2fasta.rb",
"sample/biofetch.rb",
"sample/color_scheme_na.rb",
"sample/demo_aaindex.rb",
"sample/demo_aminoacid.rb",
"sample/demo_bl2seq_report.rb",
"sample/demo_blast_report.rb",
"sample/demo_codontable.rb",
"sample/demo_das.rb",
"sample/demo_ddbjxml.rb",
"sample/demo_fasta_remote.rb",
"sample/demo_fastaformat.rb",
"sample/demo_genbank.rb",
"sample/demo_genscan_report.rb",
"sample/demo_gff1.rb",
"sample/demo_go.rb",
"sample/demo_hmmer_report.rb",
"sample/demo_kegg_compound.rb",
"sample/demo_kegg_drug.rb",
"sample/demo_kegg_genome.rb",
"sample/demo_kegg_glycan.rb",
"sample/demo_kegg_orthology.rb",
"sample/demo_kegg_reaction.rb",
"sample/demo_litdb.rb",
"sample/demo_locations.rb",
"sample/demo_ncbi_rest.rb",
"sample/demo_nucleicacid.rb",
"sample/demo_pathway.rb",
"sample/demo_prosite.rb",
"sample/demo_psort.rb",
"sample/demo_psort_report.rb",
"sample/demo_pubmed.rb",
"sample/demo_sequence.rb",
"sample/demo_sirna.rb",
"sample/demo_sosui_report.rb",
"sample/demo_targetp_report.rb",
"sample/demo_tmhmm_report.rb",
"sample/enzymes.rb",
"sample/fasta2tab.rb",
"sample/fastagrep.rb",
"sample/fastasort.rb",
"sample/fsplit.rb",
"sample/gb2fasta.rb",
"sample/gb2tab.rb",
"sample/gbtab2mysql.rb",
"sample/genes2nuc.rb",
"sample/genes2pep.rb",
"sample/genes2tab.rb",
"sample/genome2rb.rb",
"sample/genome2tab.rb",
"sample/goslim.rb",
"sample/gt2fasta.rb",
"sample/na2aa.rb",
"sample/pmfetch.rb",
"sample/pmsearch.rb",
"sample/seqdatabase.ini",
"sample/ssearch2tab.rb",
"sample/tdiary.rb",
"sample/test_phyloxml_big.rb",
"sample/test_restriction_enzyme_long.rb",
"sample/tfastx2tab.rb",
"sample/vs-genes.rb",
"setup.rb",
"test/bioruby_test_helper.rb",
"test/data/HMMER/hmmpfam.out",
"test/data/HMMER/hmmsearch.out",
"test/data/KEGG/1.1.1.1.enzyme",
"test/data/KEGG/C00025.compound",
"test/data/KEGG/D00063.drug",
"test/data/KEGG/G00024.glycan",
"test/data/KEGG/G01366.glycan",
"test/data/KEGG/K02338.orthology",
"test/data/KEGG/M00118.module",
"test/data/KEGG/R00006.reaction",
"test/data/KEGG/T00005.genome",
"test/data/KEGG/T00070.genome",
"test/data/KEGG/b0529.gene",
"test/data/KEGG/ec00072.pathway",
"test/data/KEGG/hsa00790.pathway",
"test/data/KEGG/ko00312.pathway",
"test/data/KEGG/map00030.pathway",
"test/data/KEGG/map00052.pathway",
"test/data/KEGG/rn00250.pathway",
"test/data/KEGG/test.kgml",
"test/data/SOSUI/sample.report",
"test/data/TMHMM/sample.report",
"test/data/aaindex/DAYM780301",
"test/data/aaindex/PRAM900102",
"test/data/bl2seq/cd8a_cd8b_blastp.bl2seq",
"test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq",
"test/data/blast/2.2.15.blastp.m7",
"test/data/blast/b0002.faa",
"test/data/blast/b0002.faa.m0",
"test/data/blast/b0002.faa.m7",
"test/data/blast/b0002.faa.m8",
"test/data/blast/blastp-multi.m7",
"test/data/clustalw/example1.aln",
"test/data/command/echoarg2.bat",
"test/data/command/echoarg2.sh",
"test/data/embl/AB090716.embl",
"test/data/embl/AB090716.embl.rel89",
"test/data/fasta/EFTU_BACSU.fasta",
"test/data/fasta/example1.txt",
"test/data/fasta/example2.txt",
"test/data/fastq/README.txt",
"test/data/fastq/error_diff_ids.fastq",
"test/data/fastq/error_double_qual.fastq",
"test/data/fastq/error_double_seq.fastq",
"test/data/fastq/error_long_qual.fastq",
"test/data/fastq/error_no_qual.fastq",
"test/data/fastq/error_qual_del.fastq",
"test/data/fastq/error_qual_escape.fastq",
"test/data/fastq/error_qual_null.fastq",
"test/data/fastq/error_qual_space.fastq",
"test/data/fastq/error_qual_tab.fastq",
"test/data/fastq/error_qual_unit_sep.fastq",
"test/data/fastq/error_qual_vtab.fastq",
"test/data/fastq/error_short_qual.fastq",
"test/data/fastq/error_spaces.fastq",
"test/data/fastq/error_tabs.fastq",
"test/data/fastq/error_trunc_at_plus.fastq",
"test/data/fastq/error_trunc_at_qual.fastq",
"test/data/fastq/error_trunc_at_seq.fastq",
"test/data/fastq/error_trunc_in_plus.fastq",
"test/data/fastq/error_trunc_in_qual.fastq",
"test/data/fastq/error_trunc_in_seq.fastq",
"test/data/fastq/error_trunc_in_title.fastq",
"test/data/fastq/illumina_full_range_as_illumina.fastq",
"test/data/fastq/illumina_full_range_as_sanger.fastq",
"test/data/fastq/illumina_full_range_as_solexa.fastq",
"test/data/fastq/illumina_full_range_original_illumina.fastq",
"test/data/fastq/longreads_as_illumina.fastq",
"test/data/fastq/longreads_as_sanger.fastq",
"test/data/fastq/longreads_as_solexa.fastq",
"test/data/fastq/longreads_original_sanger.fastq",
"test/data/fastq/misc_dna_as_illumina.fastq",
"test/data/fastq/misc_dna_as_sanger.fastq",
"test/data/fastq/misc_dna_as_solexa.fastq",
"test/data/fastq/misc_dna_original_sanger.fastq",
"test/data/fastq/misc_rna_as_illumina.fastq",
"test/data/fastq/misc_rna_as_sanger.fastq",
"test/data/fastq/misc_rna_as_solexa.fastq",
"test/data/fastq/misc_rna_original_sanger.fastq",
"test/data/fastq/sanger_full_range_as_illumina.fastq",
"test/data/fastq/sanger_full_range_as_sanger.fastq",
"test/data/fastq/sanger_full_range_as_solexa.fastq",
"test/data/fastq/sanger_full_range_original_sanger.fastq",
"test/data/fastq/solexa_full_range_as_illumina.fastq",
"test/data/fastq/solexa_full_range_as_sanger.fastq",
"test/data/fastq/solexa_full_range_as_solexa.fastq",
"test/data/fastq/solexa_full_range_original_solexa.fastq",
"test/data/fastq/wrapping_as_illumina.fastq",
"test/data/fastq/wrapping_as_sanger.fastq",
"test/data/fastq/wrapping_as_solexa.fastq",
"test/data/fastq/wrapping_original_sanger.fastq",
"test/data/gcg/pileup-aa.msf",
"test/data/genbank/CAA35997.gp",
"test/data/genbank/SCU49845.gb",
"test/data/genscan/sample.report",
"test/data/go/selected_component.ontology",
"test/data/go/selected_gene_association.sgd",
"test/data/go/selected_wikipedia2go",
"test/data/iprscan/merged.raw",
"test/data/iprscan/merged.txt",
"test/data/litdb/1717226.litdb",
"test/data/medline/20146148_modified.medline",
"test/data/meme/db",
"test/data/meme/mast",
"test/data/meme/mast.out",
"test/data/meme/meme.out",
"test/data/paml/codeml/control_file.txt",
"test/data/paml/codeml/models/aa.aln",
"test/data/paml/codeml/models/aa.dnd",
"test/data/paml/codeml/models/aa.ph",
"test/data/paml/codeml/models/alignment.phy",
"test/data/paml/codeml/models/results0-3.txt",
"test/data/paml/codeml/models/results7-8.txt",
"test/data/paml/codeml/output.txt",
"test/data/paml/codeml/rates",
"test/data/phyloxml/apaf.xml",
"test/data/phyloxml/bcl_2.xml",
"test/data/phyloxml/made_up.xml",
"test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml",
"test/data/phyloxml/phyloxml_examples.xml",
"test/data/pir/CRAB_ANAPL.pir",
"test/data/prosite/prosite.dat",
"test/data/refseq/nm_126355.entret",
"test/data/rpsblast/misc.rpsblast",
"test/data/sanger_chromatogram/test_chromatogram_abif.ab1",
"test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf",
"test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf",
"test/data/sim4/complement-A4.sim4",
"test/data/sim4/simple-A4.sim4",
"test/data/sim4/simple2-A4.sim4",
"test/data/soft/GDS100_partial.soft",
"test/data/soft/GSE3457_family_partial.soft",
"test/data/uniprot/p53_human.uniprot",
"test/functional/bio/sequence/test_output_embl.rb",
"test/functional/bio/test_command.rb",
"test/network/bio/appl/blast/test_remote.rb",
"test/network/bio/appl/test_blast.rb",
"test/network/bio/appl/test_pts1.rb",
"test/network/bio/io/test_ddbjrest.rb",
"test/network/bio/io/test_pubmed.rb",
"test/network/bio/io/test_soapwsdl.rb",
"test/network/bio/io/test_togows.rb",
"test/network/bio/test_command.rb",
"test/runner.rb",
"test/unit/bio/appl/bl2seq/test_report.rb",
"test/unit/bio/appl/blast/test_ncbioptions.rb",
"test/unit/bio/appl/blast/test_report.rb",
"test/unit/bio/appl/blast/test_rpsblast.rb",
"test/unit/bio/appl/clustalw/test_report.rb",
"test/unit/bio/appl/gcg/test_msf.rb",
"test/unit/bio/appl/genscan/test_report.rb",
"test/unit/bio/appl/hmmer/test_report.rb",
"test/unit/bio/appl/iprscan/test_report.rb",
"test/unit/bio/appl/mafft/test_report.rb",
"test/unit/bio/appl/meme/mast/test_report.rb",
"test/unit/bio/appl/meme/test_mast.rb",
"test/unit/bio/appl/meme/test_motif.rb",
"test/unit/bio/appl/paml/codeml/test_rates.rb",
"test/unit/bio/appl/paml/codeml/test_report.rb",
"test/unit/bio/appl/paml/codeml/test_report_single.rb",
"test/unit/bio/appl/paml/test_codeml.rb",
"test/unit/bio/appl/sim4/test_report.rb",
"test/unit/bio/appl/sosui/test_report.rb",
"test/unit/bio/appl/targetp/test_report.rb",
"test/unit/bio/appl/test_blast.rb",
"test/unit/bio/appl/test_fasta.rb",
"test/unit/bio/appl/test_pts1.rb",
"test/unit/bio/appl/tmhmm/test_report.rb",
"test/unit/bio/data/test_aa.rb",
"test/unit/bio/data/test_codontable.rb",
"test/unit/bio/data/test_na.rb",
"test/unit/bio/db/biosql/tc_biosql.rb",
"test/unit/bio/db/biosql/ts_suite_biosql.rb",
"test/unit/bio/db/embl/test_common.rb",
"test/unit/bio/db/embl/test_embl.rb",
"test/unit/bio/db/embl/test_embl_rel89.rb",
"test/unit/bio/db/embl/test_embl_to_bioseq.rb",
"test/unit/bio/db/embl/test_sptr.rb",
"test/unit/bio/db/embl/test_uniprot.rb",
"test/unit/bio/db/embl/test_uniprot_new_part.rb",
"test/unit/bio/db/fasta/test_defline.rb",
"test/unit/bio/db/fasta/test_defline_misc.rb",
"test/unit/bio/db/fasta/test_format_qual.rb",
"test/unit/bio/db/genbank/test_common.rb",
"test/unit/bio/db/genbank/test_genbank.rb",
"test/unit/bio/db/genbank/test_genpept.rb",
"test/unit/bio/db/kegg/test_compound.rb",
"test/unit/bio/db/kegg/test_drug.rb",
"test/unit/bio/db/kegg/test_enzyme.rb",
"test/unit/bio/db/kegg/test_genes.rb",
"test/unit/bio/db/kegg/test_genome.rb",
"test/unit/bio/db/kegg/test_glycan.rb",
"test/unit/bio/db/kegg/test_kgml.rb",
"test/unit/bio/db/kegg/test_module.rb",
"test/unit/bio/db/kegg/test_orthology.rb",
"test/unit/bio/db/kegg/test_pathway.rb",
"test/unit/bio/db/kegg/test_reaction.rb",
"test/unit/bio/db/pdb/test_pdb.rb",
"test/unit/bio/db/sanger_chromatogram/test_abif.rb",
"test/unit/bio/db/sanger_chromatogram/test_scf.rb",
"test/unit/bio/db/test_aaindex.rb",
"test/unit/bio/db/test_fasta.rb",
"test/unit/bio/db/test_fastq.rb",
"test/unit/bio/db/test_gff.rb",
"test/unit/bio/db/test_go.rb",
"test/unit/bio/db/test_lasergene.rb",
"test/unit/bio/db/test_litdb.rb",
"test/unit/bio/db/test_medline.rb",
"test/unit/bio/db/test_nbrf.rb",
"test/unit/bio/db/test_newick.rb",
"test/unit/bio/db/test_nexus.rb",
"test/unit/bio/db/test_phyloxml.rb",
"test/unit/bio/db/test_phyloxml_writer.rb",
"test/unit/bio/db/test_prosite.rb",
"test/unit/bio/db/test_qual.rb",
"test/unit/bio/db/test_rebase.rb",
"test/unit/bio/db/test_soft.rb",
"test/unit/bio/io/flatfile/test_autodetection.rb",
"test/unit/bio/io/flatfile/test_buffer.rb",
"test/unit/bio/io/flatfile/test_splitter.rb",
"test/unit/bio/io/test_ddbjxml.rb",
"test/unit/bio/io/test_fastacmd.rb",
"test/unit/bio/io/test_flatfile.rb",
"test/unit/bio/io/test_soapwsdl.rb",
"test/unit/bio/io/test_togows.rb",
"test/unit/bio/sequence/test_aa.rb",
"test/unit/bio/sequence/test_common.rb",
"test/unit/bio/sequence/test_compat.rb",
"test/unit/bio/sequence/test_dblink.rb",
"test/unit/bio/sequence/test_na.rb",
"test/unit/bio/sequence/test_quality_score.rb",
"test/unit/bio/sequence/test_sequence_masker.rb",
"test/unit/bio/shell/plugin/test_seq.rb",
"test/unit/bio/test_alignment.rb",
"test/unit/bio/test_command.rb",
"test/unit/bio/test_db.rb",
"test/unit/bio/test_feature.rb",
"test/unit/bio/test_location.rb",
"test/unit/bio/test_map.rb",
"test/unit/bio/test_pathway.rb",
"test/unit/bio/test_reference.rb",
"test/unit/bio/test_sequence.rb",
"test/unit/bio/test_shell.rb",
"test/unit/bio/test_tree.rb",
"test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb",
"test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb",
"test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb",
"test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb",
"test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb",
"test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb",
"test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb",
"test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb",
"test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb",
"test/unit/bio/util/restriction_enzyme/test_analysis.rb",
"test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb",
"test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb",
"test/unit/bio/util/restriction_enzyme/test_double_stranded.rb",
"test/unit/bio/util/restriction_enzyme/test_single_strand.rb",
"test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb",
"test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb",
"test/unit/bio/util/restriction_enzyme/test_string_formatting.rb",
"test/unit/bio/util/test_color_scheme.rb",
"test/unit/bio/util/test_contingency_table.rb",
"test/unit/bio/util/test_restriction_enzyme.rb",
"test/unit/bio/util/test_sirna.rb"
]
s.has_rdoc = true
s.extra_rdoc_files = [
"KNOWN_ISSUES.rdoc",
"README.rdoc",
"README_DEV.rdoc",
"RELEASE_NOTES.rdoc",
"doc/Changes-1.3.rdoc",
"doc/RELEASE_NOTES-1.4.0.rdoc",
"doc/RELEASE_NOTES-1.4.1.rdoc",
"doc/RELEASE_NOTES-1.4.2.rdoc",
"doc/RELEASE_NOTES-1.4.3.rdoc"
]
s.rdoc_options << '--main' << 'README.rdoc'
s.rdoc_options << '--title' << 'BioRuby API documentation'
s.rdoc_options << '--exclude' << '\.yaml\z'
s.rdoc_options << '--line-numbers' << '--inline-source'
s.require_path = 'lib'
s.bindir = "bin"
s.executables = [
"bioruby",
"br_biofetch.rb",
"br_bioflat.rb",
"br_biogetseq.rb",
"br_pmfetch.rb"
]
s.default_executable = "bioruby"
end