bio 0.7.0 → 0.7.1

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Files changed (17) hide show
  1. data/doc/Changes-0.7.rd +34 -13
  2. data/doc/Tutorial.rd.ja +16 -4
  3. data/lib/bio.rb +4 -17
  4. data/lib/bio/db.rb +8 -16
  5. data/lib/bio/db/pdb/atom.rb +40 -7
  6. data/lib/bio/db/pdb/chain.rb +152 -53
  7. data/lib/bio/db/pdb/model.rb +91 -39
  8. data/lib/bio/db/pdb/pdb.rb +431 -275
  9. data/lib/bio/db/pdb/residue.rb +114 -50
  10. data/lib/bio/db/pdb/utils.rb +245 -64
  11. data/lib/bio/sequence.rb +3 -3
  12. data/lib/bio/util/sirna.rb +3 -3
  13. data/test/functional/bio/io/test_soapwsdl.rb +64 -0
  14. data/test/runner.rb +5 -1
  15. data/test/unit/bio/db/test_rebase.rb +115 -0
  16. data/test/unit/bio/util/test_sirna.rb +10 -10
  17. metadata +274 -266
data/lib/bio/sequence.rb CHANGED
@@ -7,7 +7,7 @@
7
7
  # Naohisa Goto <ng@bioruby.org>
8
8
  # License:: LGPL
9
9
  #
10
- # $Id: sequence.rb,v 0.49 2005/11/27 15:46:01 k Exp $
10
+ # $Id: sequence.rb,v 0.50 2006/01/20 09:58:31 k Exp $
11
11
  #
12
12
  #--
13
13
  # *TODO* remove this functionality?
@@ -516,8 +516,8 @@ if __FILE__ == $0
516
516
  p rna.translate
517
517
 
518
518
  puts "\n== Test Bio::Sequence::NA#gc_percent"
519
- p na.gc
520
- p rna.gc
519
+ p na.gc_percent
520
+ p rna.gc_percent
521
521
 
522
522
  puts "\n== Test Bio::Sequence::NA#illegal_bases"
523
523
  p na.illegal_bases
data/lib/bio/util/sirna.rb CHANGED
@@ -5,7 +5,7 @@
5
5
  # Itoshi NIKAIDO <dritoshi@gmail.com>
6
6
  # License:: LGPL
7
7
  #
8
- # $Id: sirna.rb,v 1.6 2005/11/14 15:44:30 nakao Exp $
8
+ # $Id: sirna.rb,v 1.7 2005/12/27 17:27:38 k Exp $
9
9
  #
10
10
  # == Bio::SiRNA - Designing siRNA.
11
11
  #
@@ -201,10 +201,10 @@ module Bio
201
201
  # Designing shRNA.
202
202
  class ShRNA
203
203
 
204
- # aBio::Sequence::NA
204
+ # Bio::Sequence::NA
205
205
  attr_accessor :top_strand
206
206
 
207
- # aBio::Sequence::NA
207
+ # Bio::Sequence::NA
208
208
  attr_accessor :bottom_strand
209
209
 
210
210
  # Input is a Bio::SiRNA::Pair object (the target sequence).
data/test/functional/bio/io/test_soapwsdl.rb ADDED
@@ -0,0 +1,64 @@
1
+ #
2
+ # test/functional/bio/io/test_soapwsdl.rb - Unit test for SOAP/WSDL
3
+ #
4
+ # Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
5
+ #
6
+ # This library is free software; you can redistribute it and/or
7
+ # modify it under the terms of the GNU Lesser General Public
8
+ # License as published by the Free Software Foundation; either
9
+ # version 2 of the License, or (at your option) any later version.
10
+ #
11
+ # This library is distributed in the hope that it will be useful,
12
+ # but WITHOUT ANY WARRANTY; without even the implied warranty of
13
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
14
+ # Lesser General Public License for more details.
15
+ #
16
+ # You should have received a copy of the GNU Lesser General Public
17
+ # License along with this library; if not, write to the Free Software
18
+ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
19
+ #
20
+ # $Id: test_soapwsdl.rb,v 1.2 2006/01/20 12:04:03 k Exp $
21
+ #
22
+
23
+ require 'pathname'
24
+ libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
25
+ $:.unshift(libpath) unless $:.include?(libpath)
26
+
27
+
28
+ require 'test/unit'
29
+ require 'bio/io/soapwsdl'
30
+
31
+ module Bio
32
+
33
+ class FuncTestSOAPWSDL < Test::Unit::TestCase
34
+
35
+ def setup
36
+ @wsdl = 'http://www.ebi.ac.uk/xembl/XEMBL.wsdl'
37
+ @obj = Bio::SOAPWSDL.new(@wsdl)
38
+ end
39
+
40
+ def test_wsdl
41
+ assert_equal(@wsdl, @obj.wsdl)
42
+ end
43
+
44
+ def test_set_wsdl
45
+ @obj.wsdl = 'http://soap.genome.jp/KEGG.wsdl'
46
+ assert_equal('http://soap.genome.jp/KEGG.wsdl', @obj.wsdl)
47
+ end
48
+
49
+ def test_log
50
+ assert_equal(nil, @obj.log)
51
+ end
52
+
53
+ def test_set_log
54
+ require 'stringio'
55
+ io = StringIO.new
56
+ @obj.log = io
57
+
58
+ assert_equal(StringIO, @obj.log.class)
59
+ end
60
+
61
+ end
62
+
63
+ end
64
+
data/test/runner.rb CHANGED
@@ -6,5 +6,9 @@ require 'pathname'
6
6
  bioruby_libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'], 'lib')).cleanpath.to_s
7
7
  $:.unshift(bioruby_libpath) unless $:.include?(bioruby_libpath)
8
8
 
9
- exit Test::Unit::AutoRunner.run(false, File.dirname($0))
9
+ if RUBY_VERSION > "1.8.2"
10
+ exit Test::Unit::AutoRunner.run(true, File.dirname($0))
11
+ else
12
+ exit Test::Unit::AutoRunner.run(false, File.dirname($0))
13
+ end
10
14
 
data/test/unit/bio/db/test_rebase.rb ADDED
@@ -0,0 +1,115 @@
1
+ #
2
+ # test/unit/bio/db/test_rebase.rb - Unit test for Bio::REBASE
3
+ #
4
+ # Copyright:: Copyright (C) 2005 Trevor Wennblom <trevor@corevx.com>
5
+ # License:: LGPL
6
+ #
7
+ # $Id: test_rebase.rb,v 1.2 2006/01/20 09:53:24 k Exp $
8
+ #
9
+ #
10
+ #--
11
+ #
12
+ # This library is free software; you can redistribute it and/or
13
+ # modify it under the terms of the GNU Lesser General Public
14
+ # License as published by the Free Software Foundation; either
15
+ # version 2 of the License, or (at your option) any later version.
16
+ #
17
+ # This library is distributed in the hope that it will be useful,
18
+ # but WITHOUT ANY WARRANTY; without even the implied warranty of
19
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20
+ # Lesser General Public License for more details.
21
+ #
22
+ # You should have received a copy of the GNU Lesser General Public
23
+ # License along with this library; if not, write to the Free Software
24
+ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
25
+ #
26
+ #++
27
+ #
28
+ #
29
+
30
+ require 'pathname'
31
+ libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
32
+ $:.unshift(libpath) unless $:.include?(libpath)
33
+
34
+ require 'test/unit'
35
+ require 'bio/db/rebase'
36
+
37
+ module Bio
38
+ class TestREBASE < Test::Unit::TestCase
39
+
40
+ def setup
41
+ enzyme_data = <<END
42
+ #
43
+ # REBASE version 511 emboss_e.511
44
+ #
45
+ AarI CACCTGC 7 2 0 11 15 0 0
46
+ AasI GACNNNNNNGTC 12 2 0 7 5 0 0
47
+ AatI AGGCCT 6 2 1 3 3 0 0
48
+ END
49
+
50
+ reference_data = <<END
51
+ #
52
+ # REBASE version 511 emboss_r.511
53
+ #
54
+ #
55
+ AarI
56
+ Arthrobacter aurescens SS2-322
57
+
58
+
59
+ A. Janulaitis
60
+ F
61
+ 2
62
+ Grigaite, R., Maneliene, Z., Janulaitis, A., (2002) Nucleic Acids Res., vol. 30.
63
+ Maneliene, Z., Zakareviciene, L., Unpublished observations.
64
+ //
65
+ AasI
66
+ Arthrobacter aurescens RFL3
67
+
68
+
69
+ V. Butkus
70
+ F
71
+ 1
72
+ Kazlauskiene, R., Vaitkevicius, D., Maneliene, Z., Trinkunaite, L., Kiuduliene, L., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.
73
+ //
74
+ AatI
75
+ Acetobacter aceti
76
+
77
+
78
+ IFO 3281
79
+ O
80
+ 2
81
+ Sato, H., Yamada, Y., (1990) J. Gen. Appl. Microbiol., vol. 36, pp. 273-277.
82
+ Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Nucleic Acids Res., vol. 10, pp. 5747-5752.
83
+ //
84
+ END
85
+
86
+ supplier_data = <<END
87
+ #
88
+ # REBASE version 511 emboss_s.511
89
+ #
90
+ A GE Healthcare
91
+ B Invitrogen Corporation
92
+ C Minotech Biotechnology
93
+ E Stratagene
94
+ F Fermentas International Inc.
95
+ G Qbiogene
96
+ O Toyobo Biochemicals
97
+ END
98
+
99
+ @obj = Bio::REBASE.new(enzyme_data, reference_data, supplier_data)
100
+ end
101
+
102
+ def test_methods
103
+ a = @obj
104
+ assert_equal(a['AarI'].organism, 'Arthrobacter aurescens SS2-322')
105
+ assert_equal(a['AarI'].references.size, 2)
106
+ assert_equal(a['AarI'].supplier_names, ['Fermentas International Inc.'])
107
+ assert_equal(a['AarI'].pattern, 'CACCTGC')
108
+
109
+ assert_equal(a['AatI'].supplier_names, ['Toyobo Biochemicals'])
110
+ assert_equal(a['AatI'].suppliers, ['O'])
111
+ end
112
+
113
+ end
114
+
115
+ end
data/test/unit/bio/util/test_sirna.rb CHANGED
@@ -17,7 +17,7 @@
17
17
  # License along with this library; if not, write to the Free Software
18
18
  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
19
19
  #
20
- # $Id: test_sirna.rb,v 1.1 2005/11/14 14:46:06 nakao Exp $
20
+ # $Id: test_sirna.rb,v 1.2 2005/12/27 17:27:38 k Exp $
21
21
  #
22
22
 
23
23
  require 'pathname'
@@ -28,10 +28,12 @@ require 'test/unit'
28
28
  require 'bio/util/sirna'
29
29
 
30
30
  module Bio
31
+
32
+ RANDOM_SEQ = "ctttcggtgcggacgtaaggagtattcctgtactaactaaatggagttaccaaggtaggaccacggtaaaatcgcgagcagcctcgatacaagcgttgtgctgaagcctatcgctgacctgaaggggggcgtaagcaaggcagcggttcaccttcatcagttctgctagaaatcacctagcaccccttatcatccgcgtcaggtccattacccttcccattatgtcggactcaattgaggtgcttgtgaacttatacttgaatccaaaacgtctactgtattggcgactaaaaagcacttgtggggagtcggcttgatcagcctccattagggccaggcactgaggatcatccagttaacgtcagattcaaggtctggctcttagcactcggagttgcac"
33
+
31
34
  class TestSiRNANew < Test::Unit::TestCase
32
35
  def test_new
33
- srand(1)
34
- naseq = Bio::Sequence::NA.new("ACGT" * 100).randomize
36
+ naseq = Bio::Sequence::NA.new(RANDOM_SEQ)
35
37
  assert(Bio::SiRNA.new(naseq))
36
38
  assert(Bio::SiRNA.new(naseq, 21))
37
39
  assert(Bio::SiRNA.new(naseq, 21, 60.0))
@@ -43,8 +45,7 @@ module Bio
43
45
 
44
46
  class TestSiRNA < Test::Unit::TestCase
45
47
  def setup
46
- srand(1)
47
- naseq = Bio::Sequence::NA.new("ACGT" * 100).randomize
48
+ naseq = Bio::Sequence::NA.new(RANDOM_SEQ)
48
49
  @obj = Bio::SiRNA.new(naseq)
49
50
  end
50
51
 
@@ -116,8 +117,7 @@ module Bio
116
117
 
117
118
  class TestSiRNAPair < Test::Unit::TestCase
118
119
  def setup
119
- srand(1)
120
- naseq = Bio::Sequence::NA.new("ACGT" * 100).randomize
120
+ naseq = Bio::Sequence::NA.new(RANDOM_SEQ)
121
121
  @obj = Bio::SiRNA.new(naseq).design.first
122
122
  end
123
123
 
@@ -175,8 +175,7 @@ END
175
175
 
176
176
  class TestShRNA < Test::Unit::TestCase
177
177
  def setup
178
- srand(1)
179
- naseq = Bio::Sequence::NA.new("ACGT" * 100).randomize
178
+ naseq = Bio::Sequence::NA.new(RANDOM_SEQ)
180
179
  sirna = Bio::SiRNA.new(naseq)
181
180
  pairs = sirna.design
182
181
  @obj = Bio::SiRNA::ShRNA.new(pairs.first)
@@ -246,7 +245,8 @@ Top strand shRNA (57 nt):
246
245
  Bottom strand shRNA (57 nt):
247
246
  3'-CCUGCAUUCCUCAUAAGGACACACACGACAGGUGUCCUUAUGAGGAAUGCAGGAAAA-5'
248
247
  END
249
- @obj.design
248
+ #@obj.design
249
+ @obj.block_it
250
250
  assert_equal(report, @obj.report)
251
251
  end
252
252
 
metadata CHANGED
@@ -3,11 +3,11 @@ rubygems_version: 0.8.11
3
3
  specification_version: 1
4
4
  name: bio
5
5
  version: !ruby/object:Gem::Version
6
- version: 0.7.0
7
- date: 2005-12-19 00:00:00 +09:00
6
+ version: 0.7.1
7
+ date: 2006-01-20 00:00:00 +09:00
8
8
  summary: BioRuby is a library for bioinformatics (biology + information science).
9
9
  require_paths:
10
- - lib
10
+ - lib
11
11
  email: staff@bioruby.org
12
12
  homepage: http://bioruby.org/
13
13
  rubyforge_project:
@@ -18,278 +18,286 @@ bindir: bin
18
18
  has_rdoc: false
19
19
  required_ruby_version: !ruby/object:Gem::Version::Requirement
20
20
  requirements:
21
- -
22
- - ">"
23
- - !ruby/object:Gem::Version
24
- version: 0.0.0
21
+ - - ">"
22
+ - !ruby/object:Gem::Version
23
+ version: 0.0.0
25
24
  version:
26
25
  platform: ruby
27
26
  signing_key:
28
27
  cert_chain:
29
28
  authors:
30
- - BioRuby project
29
+ - BioRuby project
31
30
  files:
32
- - bin/bioruby
33
- - bin/br_biofetch.rb
34
- - bin/br_bioflat.rb
35
- - bin/br_biogetseq.rb
36
- - bin/br_pmfetch.rb
37
- - doc/BioRuby.rd.ja
38
- - doc/Changes-0.7.rd
39
- - doc/Design.rd.ja
40
- - doc/KEGG_API.rd
41
- - doc/KEGG_API.rd.ja
42
- - doc/TODO.rd.ja
43
- - doc/Tutorial.rd
44
- - doc/Tutorial.rd.ja
45
- - etc/bioinformatics
46
- - etc/bioinformatics/seqdatabase.ini
47
- - lib/bio
48
- - lib/bio.rb
49
- - lib/bioruby.rb
50
- - lib/bio/alignment.rb
51
- - lib/bio/appl
52
- - lib/bio/command.rb
53
- - lib/bio/data
54
- - lib/bio/db
55
- - lib/bio/db.rb
56
- - lib/bio/feature.rb
57
- - lib/bio/io
58
- - lib/bio/location.rb
59
- - lib/bio/pathway.rb
60
- - lib/bio/reference.rb
61
- - lib/bio/sequence.rb
62
- - lib/bio/shell
63
- - lib/bio/shell.rb
64
- - lib/bio/util
65
- - lib/bio/appl/bl2seq
66
- - lib/bio/appl/blast
67
- - lib/bio/appl/blast.rb
68
- - lib/bio/appl/blat
69
- - lib/bio/appl/clustalw
70
- - lib/bio/appl/clustalw.rb
71
- - lib/bio/appl/emboss.rb
72
- - lib/bio/appl/fasta
73
- - lib/bio/appl/fasta.rb
74
- - lib/bio/appl/genscan
75
- - lib/bio/appl/hmmer
76
- - lib/bio/appl/hmmer.rb
77
- - lib/bio/appl/mafft
78
- - lib/bio/appl/mafft.rb
79
- - lib/bio/appl/psort
80
- - lib/bio/appl/psort.rb
81
- - lib/bio/appl/sim4
82
- - lib/bio/appl/sim4.rb
83
- - lib/bio/appl/sosui
84
- - lib/bio/appl/spidey
85
- - lib/bio/appl/targetp
86
- - lib/bio/appl/tmhmm
87
- - lib/bio/appl/bl2seq/report.rb
88
- - lib/bio/appl/blast/format0.rb
89
- - lib/bio/appl/blast/format8.rb
90
- - lib/bio/appl/blast/report.rb
91
- - lib/bio/appl/blast/rexml.rb
92
- - lib/bio/appl/blast/wublast.rb
93
- - lib/bio/appl/blast/xmlparser.rb
94
- - lib/bio/appl/blat/report.rb
95
- - lib/bio/appl/clustalw/report.rb
96
- - lib/bio/appl/fasta/format10.rb
97
- - lib/bio/appl/fasta/format6.rb
98
- - lib/bio/appl/genscan/report.rb
99
- - lib/bio/appl/hmmer/report.rb
100
- - lib/bio/appl/mafft/report.rb
101
- - lib/bio/appl/psort/report.rb
102
- - lib/bio/appl/sim4/report.rb
103
- - lib/bio/appl/sosui/report.rb
104
- - lib/bio/appl/spidey/report.rb
105
- - lib/bio/appl/targetp/report.rb
106
- - lib/bio/appl/tmhmm/report.rb
107
- - lib/bio/data/aa.rb
108
- - lib/bio/data/codontable.rb
109
- - lib/bio/data/na.rb
110
- - lib/bio/db/aaindex.rb
111
- - lib/bio/db/embl
112
- - lib/bio/db/fantom.rb
113
- - lib/bio/db/fasta.rb
114
- - lib/bio/db/genbank
115
- - lib/bio/db/gff.rb
116
- - lib/bio/db/go.rb
117
- - lib/bio/db/kegg
118
- - lib/bio/db/litdb.rb
119
- - lib/bio/db/medline.rb
120
- - lib/bio/db/nbrf.rb
121
- - lib/bio/db/pdb
122
- - lib/bio/db/pdb.rb
123
- - lib/bio/db/prosite.rb
124
- - lib/bio/db/rebase.rb
125
- - lib/bio/db/transfac.rb
126
- - lib/bio/db/embl/common.rb
127
- - lib/bio/db/embl/embl.rb
128
- - lib/bio/db/embl/sptr.rb
129
- - lib/bio/db/embl/swissprot.rb
130
- - lib/bio/db/embl/trembl.rb
131
- - lib/bio/db/embl/uniprot.rb
132
- - lib/bio/db/genbank/common.rb
133
- - lib/bio/db/genbank/ddbj.rb
134
- - lib/bio/db/genbank/genbank.rb
135
- - lib/bio/db/genbank/genpept.rb
136
- - lib/bio/db/genbank/refseq.rb
137
- - lib/bio/db/kegg/brite.rb
138
- - lib/bio/db/kegg/cell.rb
139
- - lib/bio/db/kegg/compound.rb
140
- - lib/bio/db/kegg/enzyme.rb
141
- - lib/bio/db/kegg/expression.rb
142
- - lib/bio/db/kegg/genes.rb
143
- - lib/bio/db/kegg/genome.rb
144
- - lib/bio/db/kegg/glycan.rb
145
- - lib/bio/db/kegg/keggtab.rb
146
- - lib/bio/db/kegg/kgml.rb
147
- - lib/bio/db/kegg/ko.rb
148
- - lib/bio/db/kegg/reaction.rb
149
- - lib/bio/db/pdb/atom.rb
150
- - lib/bio/db/pdb/chain.rb
151
- - lib/bio/db/pdb/model.rb
152
- - lib/bio/db/pdb/pdb.rb
153
- - lib/bio/db/pdb/residue.rb
154
- - lib/bio/db/pdb/utils.rb
155
- - lib/bio/io/brdb.rb
156
- - lib/bio/io/das.rb
157
- - lib/bio/io/dbget.rb
158
- - lib/bio/io/ddbjxml.rb
159
- - lib/bio/io/fastacmd.rb
160
- - lib/bio/io/fetch.rb
161
- - lib/bio/io/flatfile
162
- - lib/bio/io/flatfile.rb
163
- - lib/bio/io/higet.rb
164
- - lib/bio/io/keggapi.rb
165
- - lib/bio/io/pubmed.rb
166
- - lib/bio/io/registry.rb
167
- - lib/bio/io/soapwsdl.rb
168
- - lib/bio/io/sql.rb
169
- - lib/bio/io/flatfile/bdb.rb
170
- - lib/bio/io/flatfile/index.rb
171
- - lib/bio/io/flatfile/indexer.rb
172
- - lib/bio/shell/core.rb
173
- - lib/bio/shell/plugin
174
- - lib/bio/shell/session.rb
175
- - lib/bio/shell/plugin/codon.rb
176
- - lib/bio/shell/plugin/entry.rb
177
- - lib/bio/shell/plugin/flatfile.rb
178
- - lib/bio/shell/plugin/keggapi.rb
179
- - lib/bio/shell/plugin/midi.rb
180
- - lib/bio/shell/plugin/obda.rb
181
- - lib/bio/shell/plugin/seq.rb
182
- - lib/bio/util/color_scheme
183
- - lib/bio/util/color_scheme.rb
184
- - lib/bio/util/contingency_table.rb
185
- - lib/bio/util/sirna.rb
186
- - lib/bio/util/color_scheme/buried.rb
187
- - lib/bio/util/color_scheme/helix.rb
188
- - lib/bio/util/color_scheme/hydropathy.rb
189
- - lib/bio/util/color_scheme/nucleotide.rb
190
- - lib/bio/util/color_scheme/strand.rb
191
- - lib/bio/util/color_scheme/taylor.rb
192
- - lib/bio/util/color_scheme/turn.rb
193
- - lib/bio/util/color_scheme/zappo.rb
194
- - sample/biofetch.rb
195
- - sample/color_scheme_na.rb
196
- - sample/dbget
197
- - sample/fasta2tab.rb
198
- - sample/fsplit.rb
199
- - sample/gb2fasta.rb
200
- - sample/gb2tab.rb
201
- - sample/gbtab2mysql.rb
202
- - sample/genes2nuc.rb
203
- - sample/genes2pep.rb
204
- - sample/genes2tab.rb
205
- - sample/genome2rb.rb
206
- - sample/genome2tab.rb
207
- - sample/goslim.rb
208
- - sample/gt2fasta.rb
209
- - sample/pmfetch.rb
210
- - sample/pmsearch.rb
211
- - sample/psortplot_html.rb
212
- - sample/ssearch2tab.rb
213
- - sample/tdiary.rb
214
- - sample/tfastx2tab.rb
215
- - sample/vs-genes.rb
216
- - test/data
217
- - test/functional
218
- - test/runner.rb
219
- - test/unit
220
- - test/data/blast
221
- - test/data/embl
222
- - test/data/genscan
223
- - test/data/prosite
224
- - test/data/refseq
225
- - test/data/SOSUI
226
- - test/data/TMHMM
227
- - test/data/uniprot
228
- - test/data/blast/eco:b0002.faa
229
- - test/data/blast/eco:b0002.faa.m0
230
- - test/data/blast/eco:b0002.faa.m7
231
- - test/data/blast/eco:b0002.faa.m8
232
- - test/data/embl/AB090716.embl
233
- - test/data/genscan/sample.report
234
- - test/data/prosite/prosite.dat
235
- - test/data/refseq/nm_126355.entret
236
- - test/data/SOSUI/sample.report
237
- - test/data/TMHMM/sample.report
238
- - test/data/uniprot/p53_human.uniprot
239
- - test/functional/bio
240
- - test/functional/bio/io
241
- - test/unit/bio
242
- - test/unit/bio/appl
243
- - test/unit/bio/data
244
- - test/unit/bio/db
245
- - test/unit/bio/io
246
- - test/unit/bio/shell
247
- - test/unit/bio/test_alignment.rb
248
- - test/unit/bio/test_command.rb
249
- - test/unit/bio/test_db.rb
250
- - test/unit/bio/test_feature.rb
251
- - test/unit/bio/test_location.rb
252
- - test/unit/bio/test_pathway.rb
253
- - test/unit/bio/test_sequence.rb
254
- - test/unit/bio/test_shell.rb
255
- - test/unit/bio/util
256
- - test/unit/bio/appl/blast
257
- - test/unit/bio/appl/genscan
258
- - test/unit/bio/appl/sosui
259
- - test/unit/bio/appl/targetp
260
- - test/unit/bio/appl/test_blast.rb
261
- - test/unit/bio/appl/test_fasta.rb
262
- - test/unit/bio/appl/tmhmm
263
- - test/unit/bio/appl/blast/test_report.rb
264
- - test/unit/bio/appl/blast/test_xmlparser.rb
265
- - test/unit/bio/appl/genscan/test_report.rb
266
- - test/unit/bio/appl/sosui/test_report.rb
267
- - test/unit/bio/appl/targetp/test_report.rb
268
- - test/unit/bio/appl/tmhmm/test_report.rb
269
- - test/unit/bio/data/test_aa.rb
270
- - test/unit/bio/data/test_codontable.rb
271
- - test/unit/bio/data/test_na.rb
272
- - test/unit/bio/db/embl
273
- - test/unit/bio/db/kegg
274
- - test/unit/bio/db/test_fasta.rb
275
- - test/unit/bio/db/test_gff.rb
276
- - test/unit/bio/db/test_prosite.rb
277
- - test/unit/bio/db/embl/test_common.rb
278
- - test/unit/bio/db/embl/test_embl.rb
279
- - test/unit/bio/db/embl/test_sptr.rb
280
- - test/unit/bio/db/embl/test_uniprot.rb
281
- - test/unit/bio/db/kegg/test_genes.rb
282
- - test/unit/bio/io/test_ddbjxml.rb
283
- - test/unit/bio/io/test_soapwsdl.rb
284
- - test/unit/bio/shell/plugin
285
- - test/unit/bio/shell/plugin/test_seq.rb
286
- - test/unit/bio/util/test_color_scheme.rb
287
- - test/unit/bio/util/test_contingency_table.rb
288
- - test/unit/bio/util/test_sirna.rb
31
+ - bin/bioruby
32
+ - bin/br_biofetch.rb
33
+ - bin/br_bioflat.rb
34
+ - bin/br_biogetseq.rb
35
+ - bin/br_pmfetch.rb
36
+ - doc/BioRuby.rd.ja
37
+ - doc/Changes-0.7.rd
38
+ - doc/Design.rd.ja
39
+ - doc/KEGG_API.rd
40
+ - doc/KEGG_API.rd.ja
41
+ - doc/TODO.rd.ja
42
+ - doc/Tutorial.rd
43
+ - doc/Tutorial.rd.ja
44
+ - etc/bioinformatics
45
+ - etc/bioinformatics/seqdatabase.ini
46
+ - lib/bio
47
+ - lib/bio.rb
48
+ - lib/bioruby.rb
49
+ - lib/bio/alignment.rb
50
+ - lib/bio/appl
51
+ - lib/bio/command.rb
52
+ - lib/bio/data
53
+ - lib/bio/db
54
+ - lib/bio/db.rb
55
+ - lib/bio/feature.rb
56
+ - lib/bio/io
57
+ - lib/bio/location.rb
58
+ - lib/bio/pathway.rb
59
+ - lib/bio/reference.rb
60
+ - lib/bio/sequence.rb
61
+ - lib/bio/shell
62
+ - lib/bio/shell.rb
63
+ - lib/bio/util
64
+ - lib/bio/appl/bl2seq
65
+ - lib/bio/appl/blast
66
+ - lib/bio/appl/blast.rb
67
+ - lib/bio/appl/blat
68
+ - lib/bio/appl/clustalw
69
+ - lib/bio/appl/clustalw.rb
70
+ - lib/bio/appl/emboss.rb
71
+ - lib/bio/appl/fasta
72
+ - lib/bio/appl/fasta.rb
73
+ - lib/bio/appl/genscan
74
+ - lib/bio/appl/hmmer
75
+ - lib/bio/appl/hmmer.rb
76
+ - lib/bio/appl/mafft
77
+ - lib/bio/appl/mafft.rb
78
+ - lib/bio/appl/psort
79
+ - lib/bio/appl/psort.rb
80
+ - lib/bio/appl/sim4
81
+ - lib/bio/appl/sim4.rb
82
+ - lib/bio/appl/sosui
83
+ - lib/bio/appl/spidey
84
+ - lib/bio/appl/targetp
85
+ - lib/bio/appl/tmhmm
86
+ - lib/bio/appl/bl2seq/report.rb
87
+ - lib/bio/appl/blast/format0.rb
88
+ - lib/bio/appl/blast/format8.rb
89
+ - lib/bio/appl/blast/report.rb
90
+ - lib/bio/appl/blast/rexml.rb
91
+ - lib/bio/appl/blast/wublast.rb
92
+ - lib/bio/appl/blast/xmlparser.rb
93
+ - lib/bio/appl/blat/report.rb
94
+ - lib/bio/appl/clustalw/report.rb
95
+ - lib/bio/appl/fasta/format10.rb
96
+ - lib/bio/appl/fasta/format6.rb
97
+ - lib/bio/appl/genscan/report.rb
98
+ - lib/bio/appl/hmmer/report.rb
99
+ - lib/bio/appl/mafft/report.rb
100
+ - lib/bio/appl/psort/report.rb
101
+ - lib/bio/appl/sim4/report.rb
102
+ - lib/bio/appl/sosui/report.rb
103
+ - lib/bio/appl/spidey/report.rb
104
+ - lib/bio/appl/targetp/report.rb
105
+ - lib/bio/appl/tmhmm/report.rb
106
+ - lib/bio/data/aa.rb
107
+ - lib/bio/data/codontable.rb
108
+ - lib/bio/data/na.rb
109
+ - lib/bio/db/aaindex.rb
110
+ - lib/bio/db/embl
111
+ - lib/bio/db/fantom.rb
112
+ - lib/bio/db/fasta.rb
113
+ - lib/bio/db/genbank
114
+ - lib/bio/db/gff.rb
115
+ - lib/bio/db/go.rb
116
+ - lib/bio/db/kegg
117
+ - lib/bio/db/litdb.rb
118
+ - lib/bio/db/medline.rb
119
+ - lib/bio/db/nbrf.rb
120
+ - lib/bio/db/pdb
121
+ - lib/bio/db/pdb.rb
122
+ - lib/bio/db/prosite.rb
123
+ - lib/bio/db/rebase.rb
124
+ - lib/bio/db/transfac.rb
125
+ - lib/bio/db/embl/common.rb
126
+ - lib/bio/db/embl/embl.rb
127
+ - lib/bio/db/embl/sptr.rb
128
+ - lib/bio/db/embl/swissprot.rb
129
+ - lib/bio/db/embl/trembl.rb
130
+ - lib/bio/db/embl/uniprot.rb
131
+ - lib/bio/db/genbank/common.rb
132
+ - lib/bio/db/genbank/ddbj.rb
133
+ - lib/bio/db/genbank/genbank.rb
134
+ - lib/bio/db/genbank/genpept.rb
135
+ - lib/bio/db/genbank/refseq.rb
136
+ - lib/bio/db/kegg/brite.rb
137
+ - lib/bio/db/kegg/cell.rb
138
+ - lib/bio/db/kegg/compound.rb
139
+ - lib/bio/db/kegg/enzyme.rb
140
+ - lib/bio/db/kegg/expression.rb
141
+ - lib/bio/db/kegg/genes.rb
142
+ - lib/bio/db/kegg/genome.rb
143
+ - lib/bio/db/kegg/glycan.rb
144
+ - lib/bio/db/kegg/keggtab.rb
145
+ - lib/bio/db/kegg/kgml.rb
146
+ - lib/bio/db/kegg/ko.rb
147
+ - lib/bio/db/kegg/reaction.rb
148
+ - lib/bio/db/pdb/atom.rb
149
+ - lib/bio/db/pdb/chain.rb
150
+ - lib/bio/db/pdb/model.rb
151
+ - lib/bio/db/pdb/pdb.rb
152
+ - lib/bio/db/pdb/residue.rb
153
+ - lib/bio/db/pdb/utils.rb
154
+ - lib/bio/io/brdb.rb
155
+ - lib/bio/io/das.rb
156
+ - lib/bio/io/dbget.rb
157
+ - lib/bio/io/ddbjxml.rb
158
+ - lib/bio/io/fastacmd.rb
159
+ - lib/bio/io/fetch.rb
160
+ - lib/bio/io/flatfile
161
+ - lib/bio/io/flatfile.rb
162
+ - lib/bio/io/higet.rb
163
+ - lib/bio/io/keggapi.rb
164
+ - lib/bio/io/pubmed.rb
165
+ - lib/bio/io/registry.rb
166
+ - lib/bio/io/soapwsdl.rb
167
+ - lib/bio/io/sql.rb
168
+ - lib/bio/io/flatfile/bdb.rb
169
+ - lib/bio/io/flatfile/index.rb
170
+ - lib/bio/io/flatfile/indexer.rb
171
+ - lib/bio/shell/core.rb
172
+ - lib/bio/shell/plugin
173
+ - lib/bio/shell/session.rb
174
+ - lib/bio/shell/plugin/codon.rb
175
+ - lib/bio/shell/plugin/entry.rb
176
+ - lib/bio/shell/plugin/flatfile.rb
177
+ - lib/bio/shell/plugin/keggapi.rb
178
+ - lib/bio/shell/plugin/midi.rb
179
+ - lib/bio/shell/plugin/obda.rb
180
+ - lib/bio/shell/plugin/seq.rb
181
+ - lib/bio/util/color_scheme
182
+ - lib/bio/util/color_scheme.rb
183
+ - lib/bio/util/contingency_table.rb
184
+ - lib/bio/util/sirna.rb
185
+ - lib/bio/util/color_scheme/buried.rb
186
+ - lib/bio/util/color_scheme/helix.rb
187
+ - lib/bio/util/color_scheme/hydropathy.rb
188
+ - lib/bio/util/color_scheme/nucleotide.rb
189
+ - lib/bio/util/color_scheme/strand.rb
190
+ - lib/bio/util/color_scheme/taylor.rb
191
+ - lib/bio/util/color_scheme/turn.rb
192
+ - lib/bio/util/color_scheme/zappo.rb
193
+ - sample/biofetch.rb
194
+ - sample/color_scheme_na.rb
195
+ - sample/dbget
196
+ - sample/fasta2tab.rb
197
+ - sample/fsplit.rb
198
+ - sample/gb2fasta.rb
199
+ - sample/gb2tab.rb
200
+ - sample/gbtab2mysql.rb
201
+ - sample/genes2nuc.rb
202
+ - sample/genes2pep.rb
203
+ - sample/genes2tab.rb
204
+ - sample/genome2rb.rb
205
+ - sample/genome2tab.rb
206
+ - sample/goslim.rb
207
+ - sample/gt2fasta.rb
208
+ - sample/pmfetch.rb
209
+ - sample/pmsearch.rb
210
+ - sample/psortplot_html.rb
211
+ - sample/ssearch2tab.rb
212
+ - sample/tdiary.rb
213
+ - sample/tfastx2tab.rb
214
+ - sample/vs-genes.rb
215
+ - test/data
216
+ - test/functional
217
+ - test/runner.rb
218
+ - test/unit
219
+ - test/data/blast
220
+ - test/data/embl
221
+ - test/data/genscan
222
+ - test/data/prosite
223
+ - test/data/refseq
224
+ - test/data/SOSUI
225
+ - test/data/TMHMM
226
+ - test/data/uniprot
227
+ - test/data/blast/eco:b0002.faa
228
+ - test/data/blast/eco:b0002.faa.m0
229
+ - test/data/blast/eco:b0002.faa.m7
230
+ - test/data/blast/eco:b0002.faa.m8
231
+ - test/data/embl/AB090716.embl
232
+ - test/data/genscan/sample.report
233
+ - test/data/prosite/prosite.dat
234
+ - test/data/refseq/nm_126355.entret
235
+ - test/data/SOSUI/sample.report
236
+ - test/data/TMHMM/sample.report
237
+ - test/data/uniprot/p53_human.uniprot
238
+ - test/functional/bio
239
+ - test/functional/bio/io
240
+ - test/functional/bio/io/test_soapwsdl.rb
241
+ - test/unit/bio
242
+ - test/unit/bio/appl
243
+ - test/unit/bio/data
244
+ - test/unit/bio/db
245
+ - test/unit/bio/io
246
+ - test/unit/bio/shell
247
+ - test/unit/bio/test_alignment.rb
248
+ - test/unit/bio/test_command.rb
249
+ - test/unit/bio/test_db.rb
250
+ - test/unit/bio/test_feature.rb
251
+ - test/unit/bio/test_location.rb
252
+ - test/unit/bio/test_pathway.rb
253
+ - test/unit/bio/test_sequence.rb
254
+ - test/unit/bio/test_shell.rb
255
+ - test/unit/bio/util
256
+ - test/unit/bio/appl/blast
257
+ - test/unit/bio/appl/genscan
258
+ - test/unit/bio/appl/sosui
259
+ - test/unit/bio/appl/targetp
260
+ - test/unit/bio/appl/test_blast.rb
261
+ - test/unit/bio/appl/test_fasta.rb
262
+ - test/unit/bio/appl/tmhmm
263
+ - test/unit/bio/appl/blast/test_report.rb
264
+ - test/unit/bio/appl/blast/test_xmlparser.rb
265
+ - test/unit/bio/appl/genscan/test_report.rb
266
+ - test/unit/bio/appl/sosui/test_report.rb
267
+ - test/unit/bio/appl/targetp/test_report.rb
268
+ - test/unit/bio/appl/tmhmm/test_report.rb
269
+ - test/unit/bio/data/test_aa.rb
270
+ - test/unit/bio/data/test_codontable.rb
271
+ - test/unit/bio/data/test_na.rb
272
+ - test/unit/bio/db/embl
273
+ - test/unit/bio/db/kegg
274
+ - test/unit/bio/db/test_fasta.rb
275
+ - test/unit/bio/db/test_gff.rb
276
+ - test/unit/bio/db/test_prosite.rb
277
+ - test/unit/bio/db/test_rebase.rb
278
+ - test/unit/bio/db/embl/test_common.rb
279
+ - test/unit/bio/db/embl/test_embl.rb
280
+ - test/unit/bio/db/embl/test_sptr.rb
281
+ - test/unit/bio/db/embl/test_uniprot.rb
282
+ - test/unit/bio/db/kegg/test_genes.rb
283
+ - test/unit/bio/io/test_ddbjxml.rb
284
+ - test/unit/bio/io/test_soapwsdl.rb
285
+ - test/unit/bio/shell/plugin
286
+ - test/unit/bio/shell/plugin/test_seq.rb
287
+ - test/unit/bio/util/test_color_scheme.rb
288
+ - test/unit/bio/util/test_contingency_table.rb
289
+ - test/unit/bio/util/test_sirna.rb
289
290
  test_files: []
291
+
290
292
  rdoc_options: []
293
+
291
294
  extra_rdoc_files: []
295
+
292
296
  executables: []
297
+
293
298
  extensions: []
299
+
294
300
  requirements: []
295
- dependencies: []
301
+
302
+ dependencies: []
303
+