bio 0.7.0 → 0.7.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
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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
+