ms-ident 0.0.17 → 0.0.18
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- data/Rakefile +7 -12
- data/VERSION +1 -1
- data/lib/ms/ident/peptide/db.rb +224 -0
- data/lib/ms/ident/peptide.rb +0 -1
- data/lib/ms/ident/protein.rb +54 -1
- data/spec/ms/ident/peptide/db_spec.rb +95 -0
- data/spec/ms/ident/protein_spec.rb +69 -0
- data/spec/spec_helper.rb +1 -12
- data/spec/tfiles/ms/ident/peptide/db/uni_11_sp_tr.fasta +69 -0
- data/spec/tfiles/ms/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml +728 -0
- metadata +24 -39
- data/Gemfile +0 -31
- data/Gemfile.lock +0 -32
metadata
CHANGED
@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
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5
5
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segments:
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6
6
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- 0
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7
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- 0
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8
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-
-
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-
version: 0.0.
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8
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+
- 18
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9
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+
version: 0.0.18
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10
10
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platform: ruby
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11
11
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authors:
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12
12
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- John T. Prince
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@@ -14,11 +14,12 @@ autorequire:
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14
14
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bindir: bin
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15
15
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cert_chain: []
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16
16
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|
17
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-
date: 2011-03-
|
17
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+
date: 2011-03-28 00:00:00 -06:00
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18
18
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default_executable:
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19
19
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dependencies:
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20
20
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- !ruby/object:Gem::Dependency
|
21
21
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name: nokogiri
|
22
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+
prerelease: false
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22
23
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requirement: &id001 !ruby/object:Gem::Requirement
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23
24
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none: false
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24
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requirements:
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@@ -28,10 +29,10 @@ dependencies:
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28
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- 0
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29
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version: "0"
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30
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type: :runtime
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31
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-
prerelease: false
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32
32
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version_requirements: *id001
|
33
33
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- !ruby/object:Gem::Dependency
|
34
34
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name: ms-core
|
35
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+
prerelease: false
|
35
36
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requirement: &id002 !ruby/object:Gem::Requirement
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36
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none: false
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37
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requirements:
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@@ -43,10 +44,10 @@ dependencies:
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44
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- 12
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44
45
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version: 0.0.12
|
45
46
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type: :runtime
|
46
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-
prerelease: false
|
47
47
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version_requirements: *id002
|
48
48
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- !ruby/object:Gem::Dependency
|
49
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-
name:
|
49
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+
name: ms-in_silico
|
50
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+
prerelease: false
|
50
51
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requirement: &id003 !ruby/object:Gem::Requirement
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51
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none: false
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requirements:
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@@ -56,10 +57,10 @@ dependencies:
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- 0
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version: "0"
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58
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type: :runtime
|
59
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-
prerelease: false
|
60
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version_requirements: *id003
|
61
61
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- !ruby/object:Gem::Dependency
|
62
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-
name:
|
62
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+
name: andand
|
63
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+
prerelease: false
|
63
64
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requirement: &id004 !ruby/object:Gem::Requirement
|
64
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none: false
|
65
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requirements:
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@@ -67,45 +68,26 @@ dependencies:
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- !ruby/object:Gem::Version
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segments:
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- 0
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-
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-
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-
version: 0.0.4
|
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-
type: :development
|
74
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-
prerelease: false
|
71
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+
version: "0"
|
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+
type: :runtime
|
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version_requirements: *id004
|
76
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- !ruby/object:Gem::Dependency
|
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-
name:
|
75
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+
name: spec-more
|
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+
prerelease: false
|
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requirement: &id005 !ruby/object:Gem::Requirement
|
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none: false
|
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requirements:
|
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-
- -
|
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+
- - ">="
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- !ruby/object:Gem::Version
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segments:
|
84
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-
- 1
|
85
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- 0
|
86
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-
|
87
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-
version: 1.0.0
|
84
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+
version: "0"
|
88
85
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type: :development
|
89
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-
prerelease: false
|
90
86
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version_requirements: *id005
|
91
87
|
- !ruby/object:Gem::Dependency
|
92
88
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name: jeweler
|
93
|
-
requirement: &id006 !ruby/object:Gem::Requirement
|
94
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-
none: false
|
95
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-
requirements:
|
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-
- - ~>
|
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- !ruby/object:Gem::Version
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segments:
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- 1
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- 5
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- 2
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version: 1.5.2
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-
type: :development
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prerelease: false
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-
|
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-
- !ruby/object:Gem::Dependency
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-
name: rcov
|
108
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-
requirement: &id007 !ruby/object:Gem::Requirement
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+
requirement: &id006 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ">="
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@@ -114,8 +96,7 @@ dependencies:
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- 0
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version: "0"
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type: :development
|
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-
|
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-
version_requirements: *id007
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99
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+
version_requirements: *id006
|
119
100
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description: mspire library for working with mzIdentML and pepxml
|
120
101
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email: jtprince@gmail.com
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121
102
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executables: []
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@@ -127,8 +108,6 @@ extra_rdoc_files:
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127
108
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- README.rdoc
|
128
109
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files:
|
129
110
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- .document
|
130
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-
- Gemfile
|
131
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-
- Gemfile.lock
|
132
111
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- LICENSE
|
133
112
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- README.rdoc
|
134
113
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- Rakefile
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@@ -136,6 +115,7 @@ files:
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136
115
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- lib/merge.rb
|
137
116
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- lib/ms/ident.rb
|
138
117
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- lib/ms/ident/peptide.rb
|
118
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+
- lib/ms/ident/peptide/db.rb
|
139
119
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- lib/ms/ident/pepxml.rb
|
140
120
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- lib/ms/ident/pepxml/modifications.rb
|
141
121
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- lib/ms/ident/pepxml/msms_pipeline_analysis.rb
|
@@ -154,10 +134,14 @@ files:
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|
154
134
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- lib/ms/ident/search.rb
|
155
135
|
- schema/pepXML_v115.xsd
|
156
136
|
- schema/pepXML_v19.xsd
|
137
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+
- spec/ms/ident/peptide/db_spec.rb
|
157
138
|
- spec/ms/ident/pepxml/sample_enzyme_spec.rb
|
158
139
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- spec/ms/ident/pepxml/search_hit/modification_info_spec.rb
|
159
140
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- spec/ms/ident/pepxml_spec.rb
|
141
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+
- spec/ms/ident/protein_spec.rb
|
160
142
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- spec/spec_helper.rb
|
143
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+
- spec/tfiles/ms/ident/peptide/db/uni_11_sp_tr.fasta
|
144
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+
- spec/tfiles/ms/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml
|
161
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has_rdoc: true
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162
146
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homepage: http://github.com/jtprince/ms-ident
|
163
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licenses:
|
@@ -172,7 +156,6 @@ required_ruby_version: !ruby/object:Gem::Requirement
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requirements:
|
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157
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- - ">="
|
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158
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- !ruby/object:Gem::Version
|
175
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-
hash: -1969914373934932629
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176
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segments:
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- 0
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version: "0"
|
@@ -192,7 +175,9 @@ signing_key:
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175
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specification_version: 3
|
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176
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summary: mspire library for working with mzIdentML and pepxml
|
194
177
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test_files:
|
178
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+
- spec/ms/ident/peptide/db_spec.rb
|
195
179
|
- spec/ms/ident/pepxml/sample_enzyme_spec.rb
|
196
180
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- spec/ms/ident/pepxml/search_hit/modification_info_spec.rb
|
197
181
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- spec/ms/ident/pepxml_spec.rb
|
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+
- spec/ms/ident/protein_spec.rb
|
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- spec/spec_helper.rb
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data/Gemfile
DELETED
@@ -1,31 +0,0 @@
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1
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-
source "http://rubygems.org"
|
2
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-
# Add dependencies required to use your gem here.
|
3
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-
# Example:
|
4
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-
# gem "activesupport", ">= 2.3.5"
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5
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gem 'nokogiri'
|
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gem 'ms-core', ">= 0.0.12"
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-
gem 'andand'
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-
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9
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-
dev_gems = {
|
10
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-
"spec-more" => ">= 0.0.4",
|
11
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-
"bundler" => "~> 1.0.0",
|
12
|
-
"jeweler" => "~> 1.5.2",
|
13
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-
"rcov" => ">= 0",
|
14
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-
}
|
15
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-
|
16
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-
# Add dependencies to develop your gem here.
|
17
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-
# Include everything needed to run rake, tests, features, etc.
|
18
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-
group :development do
|
19
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-
dev_gems.each do |name,version_string|
|
20
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gem name, version_string
|
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-
end
|
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-
end
|
23
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-
|
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# Add dependencies to develop your gem here.
|
25
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-
# Include everything needed to run rake, tests, features, etc.
|
26
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-
group :development_large do
|
27
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-
dev_gems.each do |name,version_string|
|
28
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-
gem name, version_string
|
29
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-
end
|
30
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-
gem "ms-testdata", ">= 0.1.1"
|
31
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-
end
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data/Gemfile.lock
DELETED
@@ -1,32 +0,0 @@
|
|
1
|
-
GEM
|
2
|
-
remote: http://rubygems.org/
|
3
|
-
specs:
|
4
|
-
andand (1.3.1)
|
5
|
-
bacon (1.1.0)
|
6
|
-
bio (1.4.1)
|
7
|
-
git (1.2.5)
|
8
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-
jeweler (1.5.2)
|
9
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-
bundler (~> 1.0.0)
|
10
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-
git (>= 1.2.5)
|
11
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-
rake
|
12
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-
ms-core (0.0.12)
|
13
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-
bio (>= 1.4.1)
|
14
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-
ms-testdata (0.1.1)
|
15
|
-
nokogiri (1.4.4)
|
16
|
-
rake (0.8.7)
|
17
|
-
rcov (0.9.9)
|
18
|
-
spec-more (0.0.4)
|
19
|
-
bacon
|
20
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-
|
21
|
-
PLATFORMS
|
22
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-
ruby
|
23
|
-
|
24
|
-
DEPENDENCIES
|
25
|
-
andand
|
26
|
-
bundler (~> 1.0.0)
|
27
|
-
jeweler (~> 1.5.2)
|
28
|
-
ms-core (>= 0.0.12)
|
29
|
-
ms-testdata (>= 0.1.1)
|
30
|
-
nokogiri
|
31
|
-
rcov
|
32
|
-
spec-more (>= 0.0.4)
|