bio-ucsc-api 0.6.3 → 0.6.4

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Files changed (70) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile +6 -9
  3. data/Gemfile.lock +27 -34
  4. data/README.md +4 -3
  5. data/VERSION +1 -1
  6. data/bio-ucsc-api.gemspec +49 -49
  7. data/lib/bio-ucsc.rb +2 -4
  8. data/lib/bio-ucsc/ailmel1.rb +4 -4
  9. data/lib/bio-ucsc/anocar2.rb +4 -4
  10. data/lib/bio-ucsc/anogam1.rb +4 -4
  11. data/lib/bio-ucsc/apimel2.rb +4 -4
  12. data/lib/bio-ucsc/aplcal1.rb +4 -4
  13. data/lib/bio-ucsc/bostau4.rb +4 -4
  14. data/lib/bio-ucsc/braflo1.rb +4 -4
  15. data/lib/bio-ucsc/caejap1.rb +4 -4
  16. data/lib/bio-ucsc/caepb2.rb +4 -4
  17. data/lib/bio-ucsc/caerem3.rb +4 -4
  18. data/lib/bio-ucsc/caljac3.rb +4 -4
  19. data/lib/bio-ucsc/canfam2.rb +4 -4
  20. data/lib/bio-ucsc/cavpor3.rb +4 -4
  21. data/lib/bio-ucsc/cb3.rb +4 -4
  22. data/lib/bio-ucsc/ce6.rb +4 -4
  23. data/lib/bio-ucsc/ci2.rb +4 -4
  24. data/lib/bio-ucsc/danrer7.rb +4 -4
  25. data/lib/bio-ucsc/dm3.rb +4 -4
  26. data/lib/bio-ucsc/dp3.rb +4 -4
  27. data/lib/bio-ucsc/droana2.rb +4 -4
  28. data/lib/bio-ucsc/droere1.rb +4 -4
  29. data/lib/bio-ucsc/drogri1.rb +4 -4
  30. data/lib/bio-ucsc/dromoj2.rb +4 -4
  31. data/lib/bio-ucsc/droper1.rb +4 -4
  32. data/lib/bio-ucsc/drosec1.rb +4 -4
  33. data/lib/bio-ucsc/drosim1.rb +4 -4
  34. data/lib/bio-ucsc/drovir2.rb +4 -4
  35. data/lib/bio-ucsc/droyak2.rb +4 -4
  36. data/lib/bio-ucsc/equcab2.rb +4 -4
  37. data/lib/bio-ucsc/felcat4.rb +4 -4
  38. data/lib/bio-ucsc/fr2.rb +4 -4
  39. data/lib/bio-ucsc/galgal4.rb +4 -4
  40. data/lib/bio-ucsc/gasacu1.rb +4 -4
  41. data/lib/bio-ucsc/go.rb +4 -4
  42. data/lib/bio-ucsc/hg18.rb +4 -4
  43. data/lib/bio-ucsc/hg19.rb +4 -4
  44. data/lib/bio-ucsc/hg38.rb +3 -3
  45. data/lib/bio-ucsc/hgfixed.rb +4 -4
  46. data/lib/bio-ucsc/loxafr3.rb +4 -4
  47. data/lib/bio-ucsc/mm10.rb +3 -3
  48. data/lib/bio-ucsc/mm9.rb +4 -4
  49. data/lib/bio-ucsc/mondom5.rb +4 -4
  50. data/lib/bio-ucsc/ornana1.rb +4 -4
  51. data/lib/bio-ucsc/orycun2.rb +4 -4
  52. data/lib/bio-ucsc/orylat2.rb +4 -4
  53. data/lib/bio-ucsc/oviari1.rb +4 -4
  54. data/lib/bio-ucsc/pantro3.rb +4 -4
  55. data/lib/bio-ucsc/petmar1.rb +4 -4
  56. data/lib/bio-ucsc/ponabe2.rb +4 -4
  57. data/lib/bio-ucsc/pripac1.rb +4 -4
  58. data/lib/bio-ucsc/proteome.rb +4 -4
  59. data/lib/bio-ucsc/rhemac2.rb +4 -4
  60. data/lib/bio-ucsc/rn4.rb +4 -4
  61. data/lib/bio-ucsc/rn5.rb +4 -4
  62. data/lib/bio-ucsc/saccer2.rb +4 -4
  63. data/lib/bio-ucsc/strpur2.rb +4 -4
  64. data/lib/bio-ucsc/susscr2.rb +4 -4
  65. data/lib/bio-ucsc/taegut1.rb +4 -4
  66. data/lib/bio-ucsc/tetnig2.rb +4 -4
  67. data/lib/bio-ucsc/uniprot.rb +4 -4
  68. data/lib/bio-ucsc/visigene.rb +4 -4
  69. data/lib/bio-ucsc/xentro2.rb +4 -4
  70. metadata +16 -16
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the Rat Nov. 2004 (Baylor 3.4/rn4) assembly
3
- # Copyright:: Copyright (C) 2011, 2012
3
+ # Copyright:: Copyright (C) 2011-2017
4
4
  # MISHIMA, Hiroyuki
5
5
  # <missy at be.to / hmishima at nagasaki-u.ac.jp>
6
- # License:: The Ruby licence (Ryby's / GPLv2 dual)
6
+ # License:: The MIT licence
7
7
  #
8
8
 
9
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  require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -33,7 +33,7 @@ chrX)
33
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  include SafeAttributes
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  self.inheritance_column = 'dummy_not_to_use'
35
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36
- @@db_adapter ||= 'mysql'
36
+ @@db_adapter ||= 'mysql2'
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  @@db_host ||= 'genome-mysql.cse.ucsc.edu'
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  @@db_username ||= 'genome'
39
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  @@db_password ||= ''
@@ -44,7 +44,7 @@ chrX)
44
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  self.abstract_class = true
45
45
 
46
46
  def self.default
47
- @@db_adapter = 'mysql'
47
+ @@db_adapter = 'mysql2'
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  @@db_host = 'genome-mysql.cse.ucsc.edu'
49
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  @@db_username = 'genome'
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  @@db_password = ''
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the Rat Rn5 assembly
3
- # Copyright:: Copyright (C) 2011, 2012, 2013
3
+ # Copyright:: Copyright (C) 2011-2017
4
4
  # MISHIMA, Hiroyuki
5
5
  # <missy at be.to / hmishima at nagasaki-u.ac.jp>
6
- # License:: The Ruby licence (Ryby's / GPLv2 dual)
6
+ # License:: The MIT licence
7
7
  #
8
8
 
9
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  require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -33,7 +33,7 @@ chrX)
33
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  include SafeAttributes
34
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  self.inheritance_column = 'dummy_not_to_use'
35
35
 
36
- @@db_adapter ||= 'mysql'
36
+ @@db_adapter ||= 'mysql2'
37
37
  @@db_host ||= 'genome-mysql.cse.ucsc.edu'
38
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  @@db_username ||= 'genome'
39
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  @@db_password ||= ''
@@ -44,7 +44,7 @@ chrX)
44
44
  self.abstract_class = true
45
45
 
46
46
  def self.default
47
- @@db_adapter = 'mysql'
47
+ @@db_adapter = 'mysql2'
48
48
  @@db_host = 'genome-mysql.cse.ucsc.edu'
49
49
  @@db_username = 'genome'
50
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  @@db_password = ''
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the S. cerevisiae June 2008 (SGD/sacCer2) assembly
3
- # Copyright:: Copyright (C) 2011, 2012
3
+ # Copyright:: Copyright (C) 2011-2017
4
4
  # MISHIMA, Hiroyuki
5
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  # <missy at be.to / hmishima at nagasaki-u.ac.jp>
6
- # License:: The Ruby licence (Ryby's / GPLv2 dual)
6
+ # License:: The MIT licence
7
7
  #
8
8
 
9
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  require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -32,7 +32,7 @@ chrXI chrXII chrXIII chrXIV chrXV chrXVI chrM 2micron)
32
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  include SafeAttributes
33
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  self.inheritance_column = 'dummy_not_to_use'
34
34
 
35
- @@db_adapter ||= 'mysql'
35
+ @@db_adapter ||= 'mysql2'
36
36
  @@db_host ||= 'genome-mysql.cse.ucsc.edu'
37
37
  @@db_username ||= 'genome'
38
38
  @@db_password ||= ''
@@ -43,7 +43,7 @@ chrXI chrXII chrXIII chrXIV chrXV chrXVI chrM 2micron)
43
43
  self.abstract_class = true
44
44
 
45
45
  def self.default
46
- @@db_adapter = 'mysql'
46
+ @@db_adapter = 'mysql2'
47
47
  @@db_host = 'genome-mysql.cse.ucsc.edu'
48
48
  @@db_username = 'genome'
49
49
  @@db_password = ''
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the S. purpuratus Sep. 2006 (Baylor 2.1/strPur2) assembly
3
- # Copyright:: Copyright (C) 2011
3
+ # Copyright:: Copyright (C) 2011-2017
4
4
  # MISHIMA, Hiroyuki
5
5
  # <missy at be.to / hmishima at nagasaki-u.ac.jp>
6
- # License:: The Ruby licence (Ryby's / GPLv2 dual)
6
+ # License:: The MIT licence
7
7
  #
8
8
 
9
9
  require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -31,7 +31,7 @@ module Bio
31
31
  include SafeAttributes
32
32
  self.inheritance_column = 'dummy_not_to_use'
33
33
 
34
- @@db_adapter ||= 'mysql'
34
+ @@db_adapter ||= 'mysql2'
35
35
  @@db_host ||= 'genome-mysql.cse.ucsc.edu'
36
36
  @@db_username ||= 'genome'
37
37
  @@db_password ||= ''
@@ -42,7 +42,7 @@ module Bio
42
42
  self.abstract_class = true
43
43
 
44
44
  def self.default
45
- @@db_adapter = 'mysql'
45
+ @@db_adapter = 'mysql2'
46
46
  @@db_host = 'genome-mysql.cse.ucsc.edu'
47
47
  @@db_username = 'genome'
48
48
  @@db_password = ''
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the Dog May 2005 (Broad/canFam2) assembly
3
- # Copyright:: Copyright (C) 2011, 2012
3
+ # Copyright:: Copyright (C) 2011-2017
4
4
  # MISHIMA, Hiroyuki
5
5
  # <missy at be.to / hmishima at nagasaki-u.ac.jp>
6
- # License:: The Ruby licence (Ryby's / GPLv2 dual)
6
+ # License:: The MIT licence
7
7
  #
8
8
 
9
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  require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -32,7 +32,7 @@ Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 ChrX)
32
32
  include SafeAttributes
33
33
  self.inheritance_column = 'dummy_not_to_use'
34
34
 
35
- @@db_adapter ||= 'mysql'
35
+ @@db_adapter ||= 'mysql2'
36
36
  @@db_host ||= 'genome-mysql.cse.ucsc.edu'
37
37
  @@db_username ||= 'genome'
38
38
  @@db_password ||= ''
@@ -43,7 +43,7 @@ Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 ChrX)
43
43
  self.abstract_class = true
44
44
 
45
45
  def self.default
46
- @@db_adapter = 'mysql'
46
+ @@db_adapter = 'mysql2'
47
47
  @@db_host = 'genome-mysql.cse.ucsc.edu'
48
48
  @@db_username = 'genome'
49
49
  @@db_password = ''
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) assembly
3
- # Copyright:: Copyright (C) 2011m 2012
3
+ # Copyright:: Copyright (C) 2011-2017
4
4
  # MISHIMA, Hiroyuki
5
5
  # <missy at be.to / hmishima at nagasaki-u.ac.jp>
6
- # License:: The Ruby licence (Ryby's / GPLv2 dual)
6
+ # License:: The MIT licence
7
7
  #
8
8
 
9
9
  require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -34,7 +34,7 @@ chr21 chr22 chr23 chr24 chr25 chr26 chr27 chr28 chrZ chrM)
34
34
  include SafeAttributes
35
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  self.inheritance_column = 'dummy_not_to_use'
36
36
 
37
- @@db_adapter ||= 'mysql'
37
+ @@db_adapter ||= 'mysql2'
38
38
  @@db_host ||= 'genome-mysql.cse.ucsc.edu'
39
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  @@db_username ||= 'genome'
40
40
  @@db_password ||= ''
@@ -45,7 +45,7 @@ chr21 chr22 chr23 chr24 chr25 chr26 chr27 chr28 chrZ chrM)
45
45
  self.abstract_class = true
46
46
 
47
47
  def self.default
48
- @@db_adapter = 'mysql'
48
+ @@db_adapter = 'mysql2'
49
49
  @@db_host = 'genome-mysql.cse.ucsc.edu'
50
50
  @@db_username = 'genome'
51
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  @@db_password = ''
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the Tetraodon Mar. 2007 (Genoscope 8.0/tetNig2) assembly
3
- # Copyright:: Copyright (C) 2011, 2012
3
+ # Copyright:: Copyright (C) 2011-2017
4
4
  # MISHIMA, Hiroyuki
5
5
  # <missy at be.to / hmishima at nagasaki-u.ac.jp>
6
- # License:: The Ruby licence (Ryby's / GPLv2 dual)
6
+ # License:: The MIT licence
7
7
  #
8
8
 
9
9
  require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -33,7 +33,7 @@ Chr20 Chr21 ChrM ChrUn_random)
33
33
  include SafeAttributes
34
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  self.inheritance_column = 'dummy_not_to_use'
35
35
 
36
- @@db_adapter ||= 'mysql'
36
+ @@db_adapter ||= 'mysql2'
37
37
  @@db_host ||= 'genome-mysql.cse.ucsc.edu'
38
38
  @@db_username ||= 'genome'
39
39
  @@db_password ||= ''
@@ -44,7 +44,7 @@ Chr20 Chr21 ChrM ChrUn_random)
44
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  self.abstract_class = true
45
45
 
46
46
  def self.default
47
- @@db_adapter = 'mysql'
47
+ @@db_adapter = 'mysql2'
48
48
  @@db_host = 'genome-mysql.cse.ucsc.edu'
49
49
  @@db_username = 'genome'
50
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  @@db_password = ''
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of Uniprot
3
- # Copyright:: Copyright (C) 2011, 2012
3
+ # Copyright:: Copyright (C) 2011-2017
4
4
  # MISHIMA, Hiroyuki
5
5
  # <missy at be.to / hmishima at nagasaki-u.ac.jp>
6
- # License:: The Ruby licence (Ryby's / GPLv2 dual)
6
+ # License:: The MIT licence
7
7
  #
8
8
 
9
9
  require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -29,7 +29,7 @@ module Bio
29
29
  include SafeAttributes
30
30
  self.inheritance_column = 'dummy_not_to_use'
31
31
 
32
- @@db_adapter ||= 'mysql'
32
+ @@db_adapter ||= 'mysql2'
33
33
  @@db_host ||= 'genome-mysql.cse.ucsc.edu'
34
34
  @@db_username ||= 'genome'
35
35
  @@db_password ||= ''
@@ -40,7 +40,7 @@ module Bio
40
40
  self.abstract_class = true
41
41
 
42
42
  def self.default
43
- @@db_adapter = 'mysql'
43
+ @@db_adapter = 'mysql2'
44
44
  @@db_host = 'genome-mysql.cse.ucsc.edu'
45
45
  @@db_username = 'genome'
46
46
  @@db_password = ''
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of VisiGene
3
- # Copyright:: Copyright (C) 2011
3
+ # Copyright:: Copyright (C) 2011-2017
4
4
  # MISHIMA, Hiroyuki
5
5
  # <missy at be.to / hmishima at nagasaki-u.ac.jp>
6
- # License:: The Ruby licence (Ryby's / GPLv2 dual)
6
+ # License:: The MIT licence
7
7
  #
8
8
 
9
9
  require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -29,7 +29,7 @@ module Bio
29
29
  include SafeAttributes
30
30
  self.inheritance_column = 'dummy_not_to_use'
31
31
 
32
- @@db_adapter ||= 'mysql'
32
+ @@db_adapter ||= 'mysql2'
33
33
  @@db_host ||= 'genome-mysql.cse.ucsc.edu'
34
34
  @@db_username ||= 'genome'
35
35
  @@db_password ||= ''
@@ -40,7 +40,7 @@ module Bio
40
40
  self.abstract_class = true
41
41
 
42
42
  def self.default
43
- @@db_adapter = 'mysql'
43
+ @@db_adapter = 'mysql2'
44
44
  @@db_host = 'genome-mysql.cse.ucsc.edu'
45
45
  @@db_username = 'genome'
46
46
  @@db_password = ''
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the X. tropicalis Aug. 2005 (JGI 4.1/xenTro2) assembly
3
- # Copyright:: Copyright (C) 2011, 2012
3
+ # Copyright:: Copyright (C) 2011-2017
4
4
  # MISHIMA, Hiroyuki
5
5
  # <missy at be.to / hmishima at nagasaki-u.ac.jp>
6
- # License:: The Ruby licence (Ryby's / GPLv2 dual)
6
+ # License:: The MIT licence
7
7
  #
8
8
 
9
9
  require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -31,7 +31,7 @@ module Bio
31
31
  include SafeAttributes
32
32
  self.inheritance_column = 'dummy_not_to_use'
33
33
 
34
- @@db_adapter ||= 'mysql'
34
+ @@db_adapter ||= 'mysql2'
35
35
  @@db_host ||= 'genome-mysql.cse.ucsc.edu'
36
36
  @@db_username ||= 'genome'
37
37
  @@db_password ||= ''
@@ -42,7 +42,7 @@ module Bio
42
42
  self.abstract_class = true
43
43
 
44
44
  def self.default
45
- @@db_adapter = 'mysql'
45
+ @@db_adapter = 'mysql2'
46
46
  @@db_host = 'genome-mysql.cse.ucsc.edu'
47
47
  @@db_username = 'genome'
48
48
  @@db_password = ''
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bio-ucsc-api
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.6.3
4
+ version: 0.6.4
5
5
  platform: ruby
6
6
  authors:
7
7
  - Hiroyuki Mishima
@@ -9,7 +9,7 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2017-08-17 00:00:00.000000000 Z
12
+ date: 2017-09-12 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: activerecord
@@ -17,42 +17,42 @@ dependencies:
17
17
  requirements:
18
18
  - - "~>"
19
19
  - !ruby/object:Gem::Version
20
- version: 4.0.2
20
+ version: 4.2.9
21
21
  type: :runtime
22
22
  prerelease: false
23
23
  version_requirements: !ruby/object:Gem::Requirement
24
24
  requirements:
25
25
  - - "~>"
26
26
  - !ruby/object:Gem::Version
27
- version: 4.0.2
27
+ version: 4.2.9
28
28
  - !ruby/object:Gem::Dependency
29
29
  name: activesupport
30
30
  requirement: !ruby/object:Gem::Requirement
31
31
  requirements:
32
32
  - - "~>"
33
33
  - !ruby/object:Gem::Version
34
- version: 4.0.2
34
+ version: 4.2.9
35
35
  type: :runtime
36
36
  prerelease: false
37
37
  version_requirements: !ruby/object:Gem::Requirement
38
38
  requirements:
39
39
  - - "~>"
40
40
  - !ruby/object:Gem::Version
41
- version: 4.0.2
41
+ version: 4.2.9
42
42
  - !ruby/object:Gem::Dependency
43
- name: mysql
43
+ name: mysql2
44
44
  requirement: !ruby/object:Gem::Requirement
45
45
  requirements:
46
46
  - - "~>"
47
47
  - !ruby/object:Gem::Version
48
- version: 2.9.1
48
+ version: 0.4.9
49
49
  type: :runtime
50
50
  prerelease: false
51
51
  version_requirements: !ruby/object:Gem::Requirement
52
52
  requirements:
53
53
  - - "~>"
54
54
  - !ruby/object:Gem::Version
55
- version: 2.9.1
55
+ version: 0.4.9
56
56
  - !ruby/object:Gem::Dependency
57
57
  name: safe_attributes
58
58
  requirement: !ruby/object:Gem::Requirement
@@ -73,14 +73,14 @@ dependencies:
73
73
  requirements:
74
74
  - - "~>"
75
75
  - !ruby/object:Gem::Version
76
- version: 1.0.3
76
+ version: 1.0.4
77
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  type: :runtime
78
78
  prerelease: false
79
79
  version_requirements: !ruby/object:Gem::Requirement
80
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  requirements:
81
81
  - - "~>"
82
82
  - !ruby/object:Gem::Version
83
- version: 1.0.3
83
+ version: 1.0.4
84
84
  - !ruby/object:Gem::Dependency
85
85
  name: bio-genomic-interval
86
86
  requirement: !ruby/object:Gem::Requirement
@@ -101,14 +101,14 @@ dependencies:
101
101
  requirements:
102
102
  - - ">="
103
103
  - !ruby/object:Gem::Version
104
- version: 10.1.0
104
+ version: 12.1.0
105
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  type: :development
106
106
  prerelease: false
107
107
  version_requirements: !ruby/object:Gem::Requirement
108
108
  requirements:
109
109
  - - ">="
110
110
  - !ruby/object:Gem::Version
111
- version: 10.1.0
111
+ version: 12.1.0
112
112
  - !ruby/object:Gem::Dependency
113
113
  name: rspec
114
114
  requirement: !ruby/object:Gem::Requirement
@@ -129,14 +129,14 @@ dependencies:
129
129
  requirements:
130
130
  - - ">="
131
131
  - !ruby/object:Gem::Version
132
- version: 1.3.5
132
+ version: 1.15.4
133
133
  type: :development
134
134
  prerelease: false
135
135
  version_requirements: !ruby/object:Gem::Requirement
136
136
  requirements:
137
137
  - - ">="
138
138
  - !ruby/object:Gem::Version
139
- version: 1.3.5
139
+ version: 1.15.4
140
140
  - !ruby/object:Gem::Dependency
141
141
  name: jeweler
142
142
  requirement: !ruby/object:Gem::Requirement
@@ -624,7 +624,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
624
624
  version: '0'
625
625
  requirements: []
626
626
  rubyforge_project:
627
- rubygems_version: 2.5.1
627
+ rubygems_version: 2.6.11
628
628
  signing_key:
629
629
  specification_version: 4
630
630
  summary: 'The Ruby UCSC API: accessing the UCSC Genome Database using Ruby'