rbbt-entities 1.1.1 → 2.0.0

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Files changed (18) hide show
  1. data/bin/icgc2rbbt.rb +23 -0
  2. data/bin/vcf2rbbt.rb +15 -0
  3. data/lib/rbbt/entity/chromosome_range.rb +73 -0
  4. data/lib/rbbt/entity/cnv.rb +20 -2
  5. data/lib/rbbt/entity/gene.rb +147 -74
  6. data/lib/rbbt/entity/genomic_mutation.rb +380 -50
  7. data/lib/rbbt/entity/genotype.rb +10 -4
  8. data/lib/rbbt/entity/interactor.rb +6 -0
  9. data/lib/rbbt/entity/mutated_isoform.rb +171 -83
  10. data/lib/rbbt/entity/pmid.rb +33 -6
  11. data/lib/rbbt/entity/protein.rb +36 -7
  12. data/lib/rbbt/entity/transcript.rb +20 -4
  13. data/lib/rbbt/entity.rb +123 -68
  14. data/test/rbbt/entity/test_gene.rb +16 -2
  15. data/test/rbbt/entity/test_genomic_mutation.rb +53 -1
  16. data/test/rbbt/entity/test_pmid.rb +19 -0
  17. data/test/rbbt/test_entity.rb +100 -5
  18. metadata +51 -72
metadata CHANGED
@@ -1,79 +1,65 @@
1
- --- !ruby/object:Gem::Specification
1
+ --- !ruby/object:Gem::Specification
2
2
  name: rbbt-entities
3
- version: !ruby/object:Gem::Version
4
- hash: 17
3
+ version: !ruby/object:Gem::Version
4
+ version: 2.0.0
5
5
  prerelease:
6
- segments:
7
- - 1
8
- - 1
9
- - 1
10
- version: 1.1.1
11
6
  platform: ruby
12
- authors:
7
+ authors:
13
8
  - Miguel Vazquez
14
9
  autorequire:
15
10
  bindir: bin
16
11
  cert_chain: []
17
-
18
- date: 2012-01-31 00:00:00 Z
19
- dependencies:
20
- - !ruby/object:Gem::Dependency
12
+ date: 2012-12-21 00:00:00.000000000 Z
13
+ dependencies:
14
+ - !ruby/object:Gem::Dependency
21
15
  name: rbbt-util
22
- prerelease: false
23
- requirement: &id001 !ruby/object:Gem::Requirement
16
+ requirement: !ruby/object:Gem::Requirement
24
17
  none: false
25
- requirements:
26
- - - ">="
27
- - !ruby/object:Gem::Version
28
- hash: 3
29
- segments:
30
- - 0
31
- version: "0"
18
+ requirements:
19
+ - - ! '>='
20
+ - !ruby/object:Gem::Version
21
+ version: '0'
32
22
  type: :runtime
33
- version_requirements: *id001
34
- - !ruby/object:Gem::Dependency
35
- name: rbbt-sources
36
23
  prerelease: false
37
- requirement: &id002 !ruby/object:Gem::Requirement
24
+ version_requirements: !ruby/object:Gem::Requirement
38
25
  none: false
39
- requirements:
40
- - - ">="
41
- - !ruby/object:Gem::Version
42
- hash: 3
43
- segments:
44
- - 0
45
- version: "0"
46
- type: :runtime
47
- version_requirements: *id002
48
- - !ruby/object:Gem::Dependency
26
+ requirements:
27
+ - - ! '>='
28
+ - !ruby/object:Gem::Version
29
+ version: '0'
30
+ - !ruby/object:Gem::Dependency
49
31
  name: rbbt-dm
50
- prerelease: false
51
- requirement: &id003 !ruby/object:Gem::Requirement
32
+ requirement: !ruby/object:Gem::Requirement
52
33
  none: false
53
- requirements:
54
- - - ">="
55
- - !ruby/object:Gem::Version
56
- hash: 3
57
- segments:
58
- - 0
59
- version: "0"
34
+ requirements:
35
+ - - ! '>='
36
+ - !ruby/object:Gem::Version
37
+ version: '0'
60
38
  type: :runtime
61
- version_requirements: *id003
39
+ prerelease: false
40
+ version_requirements: !ruby/object:Gem::Requirement
41
+ none: false
42
+ requirements:
43
+ - - ! '>='
44
+ - !ruby/object:Gem::Version
45
+ version: '0'
62
46
  description: Entities for handling tsv files, caches, etc
63
47
  email: miguel.vazquez@cnio.es
64
48
  executables: []
65
-
66
49
  extensions: []
67
-
68
- extra_rdoc_files:
50
+ extra_rdoc_files:
69
51
  - LICENSE
70
- files:
52
+ files:
71
53
  - LICENSE
54
+ - bin/icgc2rbbt.rb
55
+ - bin/vcf2rbbt.rb
72
56
  - lib/rbbt/entity.rb
57
+ - lib/rbbt/entity/chromosome_range.rb
73
58
  - lib/rbbt/entity/cnv.rb
74
59
  - lib/rbbt/entity/gene.rb
75
60
  - lib/rbbt/entity/genomic_mutation.rb
76
61
  - lib/rbbt/entity/genotype.rb
62
+ - lib/rbbt/entity/interactor.rb
77
63
  - lib/rbbt/entity/misc.rb
78
64
  - lib/rbbt/entity/mutated_isoform.rb
79
65
  - lib/rbbt/entity/pmid.rb
@@ -84,44 +70,37 @@ files:
84
70
  - test/rbbt/entity/test_genomic_mutation.rb
85
71
  - test/rbbt/entity/test_mutated_isoform.rb
86
72
  - test/rbbt/entity/test_protein.rb
73
+ - test/rbbt/entity/test_pmid.rb
87
74
  - test/rbbt/test_entity.rb
88
75
  homepage: http://github.com/mikisvaz/rbbt-util
89
76
  licenses: []
90
-
91
77
  post_install_message:
92
78
  rdoc_options: []
93
-
94
- require_paths:
79
+ require_paths:
95
80
  - lib
96
- required_ruby_version: !ruby/object:Gem::Requirement
81
+ required_ruby_version: !ruby/object:Gem::Requirement
97
82
  none: false
98
- requirements:
99
- - - ">="
100
- - !ruby/object:Gem::Version
101
- hash: 3
102
- segments:
103
- - 0
104
- version: "0"
105
- required_rubygems_version: !ruby/object:Gem::Requirement
83
+ requirements:
84
+ - - ! '>='
85
+ - !ruby/object:Gem::Version
86
+ version: '0'
87
+ required_rubygems_version: !ruby/object:Gem::Requirement
106
88
  none: false
107
- requirements:
108
- - - ">="
109
- - !ruby/object:Gem::Version
110
- hash: 3
111
- segments:
112
- - 0
113
- version: "0"
89
+ requirements:
90
+ - - ! '>='
91
+ - !ruby/object:Gem::Version
92
+ version: '0'
114
93
  requirements: []
115
-
116
94
  rubyforge_project:
117
- rubygems_version: 1.8.12
95
+ rubygems_version: 1.8.24
118
96
  signing_key:
119
97
  specification_version: 3
120
98
  summary: Entities for the Ruby Bioinformatics Toolkit (rbbt)
121
- test_files:
99
+ test_files:
122
100
  - test/test_helper.rb
123
101
  - test/rbbt/entity/test_gene.rb
124
102
  - test/rbbt/entity/test_genomic_mutation.rb
125
103
  - test/rbbt/entity/test_mutated_isoform.rb
126
104
  - test/rbbt/entity/test_protein.rb
105
+ - test/rbbt/entity/test_pmid.rb
127
106
  - test/rbbt/test_entity.rb