mspire-sequest 0.2.5

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Files changed (40) hide show
  1. data/.autotest +30 -0
  2. data/.gitmodules +9 -0
  3. data/History +79 -0
  4. data/LICENSE +22 -0
  5. data/README.rdoc +85 -0
  6. data/Rakefile +52 -0
  7. data/VERSION +1 -0
  8. data/bin/srf_to_pepxml.rb +7 -0
  9. data/bin/srf_to_search.rb +7 -0
  10. data/bin/srf_to_sqt.rb +8 -0
  11. data/lib/mspire/sequest/params.rb +331 -0
  12. data/lib/mspire/sequest/pepxml/modifications.rb +247 -0
  13. data/lib/mspire/sequest/pepxml/params.rb +32 -0
  14. data/lib/mspire/sequest/sqt.rb +393 -0
  15. data/lib/mspire/sequest/srf/pepxml/sequest.rb +21 -0
  16. data/lib/mspire/sequest/srf/pepxml.rb +333 -0
  17. data/lib/mspire/sequest/srf/search.rb +158 -0
  18. data/lib/mspire/sequest/srf/sqt.rb +218 -0
  19. data/lib/mspire/sequest/srf.rb +715 -0
  20. data/lib/mspire/sequest.rb +6 -0
  21. data/script/fasta_ipi_to_ncbi-ish.rb +29 -0
  22. data/spec/mspire/sequest/params_spec.rb +135 -0
  23. data/spec/mspire/sequest/pepxml/modifications_spec.rb +50 -0
  24. data/spec/mspire/sequest/pepxml_spec.rb +311 -0
  25. data/spec/mspire/sequest/sqt_spec.rb +51 -0
  26. data/spec/mspire/sequest/sqt_spec_helper.rb +34 -0
  27. data/spec/mspire/sequest/srf/pepxml_spec.rb +89 -0
  28. data/spec/mspire/sequest/srf/search_spec.rb +131 -0
  29. data/spec/mspire/sequest/srf/sqt_spec.rb +228 -0
  30. data/spec/mspire/sequest/srf_spec.rb +113 -0
  31. data/spec/mspire/sequest/srf_spec_helper.rb +172 -0
  32. data/spec/spec_helper.rb +22 -0
  33. data/spec/testfiles/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
  34. data/spec/testfiles/bioworks31.params +77 -0
  35. data/spec/testfiles/bioworks32.params +62 -0
  36. data/spec/testfiles/bioworks33.params +63 -0
  37. data/spec/testfiles/corrupted_900.srf +0 -0
  38. data/spec/testfiles/small.sqt +87 -0
  39. data/spec/testfiles/small2.sqt +176 -0
  40. metadata +185 -0
metadata ADDED
@@ -0,0 +1,185 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: mspire-sequest
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.2.5
5
+ prerelease:
6
+ platform: ruby
7
+ authors:
8
+ - John T. Prince
9
+ autorequire:
10
+ bindir: bin
11
+ cert_chain: []
12
+ date: 2012-03-20 00:00:00.000000000 Z
13
+ dependencies:
14
+ - !ruby/object:Gem::Dependency
15
+ name: mspire
16
+ requirement: !ruby/object:Gem::Requirement
17
+ none: false
18
+ requirements:
19
+ - - ~>
20
+ - !ruby/object:Gem::Version
21
+ version: 0.7.3
22
+ type: :runtime
23
+ prerelease: false
24
+ version_requirements: !ruby/object:Gem::Requirement
25
+ none: false
26
+ requirements:
27
+ - - ~>
28
+ - !ruby/object:Gem::Version
29
+ version: 0.7.3
30
+ - !ruby/object:Gem::Dependency
31
+ name: trollop
32
+ requirement: !ruby/object:Gem::Requirement
33
+ none: false
34
+ requirements:
35
+ - - ~>
36
+ - !ruby/object:Gem::Version
37
+ version: '1.16'
38
+ type: :runtime
39
+ prerelease: false
40
+ version_requirements: !ruby/object:Gem::Requirement
41
+ none: false
42
+ requirements:
43
+ - - ~>
44
+ - !ruby/object:Gem::Version
45
+ version: '1.16'
46
+ - !ruby/object:Gem::Dependency
47
+ name: jeweler
48
+ requirement: !ruby/object:Gem::Requirement
49
+ none: false
50
+ requirements:
51
+ - - ~>
52
+ - !ruby/object:Gem::Version
53
+ version: 1.5.2
54
+ type: :development
55
+ prerelease: false
56
+ version_requirements: !ruby/object:Gem::Requirement
57
+ none: false
58
+ requirements:
59
+ - - ~>
60
+ - !ruby/object:Gem::Version
61
+ version: 1.5.2
62
+ - !ruby/object:Gem::Dependency
63
+ name: bio
64
+ requirement: !ruby/object:Gem::Requirement
65
+ none: false
66
+ requirements:
67
+ - - ~>
68
+ - !ruby/object:Gem::Version
69
+ version: 1.4.2
70
+ type: :development
71
+ prerelease: false
72
+ version_requirements: !ruby/object:Gem::Requirement
73
+ none: false
74
+ requirements:
75
+ - - ~>
76
+ - !ruby/object:Gem::Version
77
+ version: 1.4.2
78
+ - !ruby/object:Gem::Dependency
79
+ name: ms-testdata
80
+ requirement: !ruby/object:Gem::Requirement
81
+ none: false
82
+ requirements:
83
+ - - '='
84
+ - !ruby/object:Gem::Version
85
+ version: 0.2.1
86
+ type: :development
87
+ prerelease: false
88
+ version_requirements: !ruby/object:Gem::Requirement
89
+ none: false
90
+ requirements:
91
+ - - '='
92
+ - !ruby/object:Gem::Version
93
+ version: 0.2.1
94
+ - !ruby/object:Gem::Dependency
95
+ name: rspec
96
+ requirement: !ruby/object:Gem::Requirement
97
+ none: false
98
+ requirements:
99
+ - - ~>
100
+ - !ruby/object:Gem::Version
101
+ version: 2.8.0
102
+ type: :development
103
+ prerelease: false
104
+ version_requirements: !ruby/object:Gem::Requirement
105
+ none: false
106
+ requirements:
107
+ - - ~>
108
+ - !ruby/object:Gem::Version
109
+ version: 2.8.0
110
+ description: reads .SRF, .SQT and supports conversions
111
+ email: jtprince@gmail.com
112
+ executables:
113
+ - srf_to_pepxml.rb
114
+ - srf_to_search.rb
115
+ - srf_to_sqt.rb
116
+ extensions: []
117
+ extra_rdoc_files:
118
+ - LICENSE
119
+ - README.rdoc
120
+ files:
121
+ - .autotest
122
+ - .gitmodules
123
+ - History
124
+ - LICENSE
125
+ - README.rdoc
126
+ - Rakefile
127
+ - VERSION
128
+ - bin/srf_to_pepxml.rb
129
+ - bin/srf_to_search.rb
130
+ - bin/srf_to_sqt.rb
131
+ - lib/mspire/sequest.rb
132
+ - lib/mspire/sequest/params.rb
133
+ - lib/mspire/sequest/pepxml/modifications.rb
134
+ - lib/mspire/sequest/pepxml/params.rb
135
+ - lib/mspire/sequest/sqt.rb
136
+ - lib/mspire/sequest/srf.rb
137
+ - lib/mspire/sequest/srf/pepxml.rb
138
+ - lib/mspire/sequest/srf/pepxml/sequest.rb
139
+ - lib/mspire/sequest/srf/search.rb
140
+ - lib/mspire/sequest/srf/sqt.rb
141
+ - script/fasta_ipi_to_ncbi-ish.rb
142
+ - spec/mspire/sequest/params_spec.rb
143
+ - spec/mspire/sequest/pepxml/modifications_spec.rb
144
+ - spec/mspire/sequest/pepxml_spec.rb
145
+ - spec/mspire/sequest/sqt_spec.rb
146
+ - spec/mspire/sequest/sqt_spec_helper.rb
147
+ - spec/mspire/sequest/srf/pepxml_spec.rb
148
+ - spec/mspire/sequest/srf/search_spec.rb
149
+ - spec/mspire/sequest/srf/sqt_spec.rb
150
+ - spec/mspire/sequest/srf_spec.rb
151
+ - spec/mspire/sequest/srf_spec_helper.rb
152
+ - spec/spec_helper.rb
153
+ - spec/testfiles/7MIX_STD_110802_1.sequest_params_fragment.srf
154
+ - spec/testfiles/bioworks31.params
155
+ - spec/testfiles/bioworks32.params
156
+ - spec/testfiles/bioworks33.params
157
+ - spec/testfiles/corrupted_900.srf
158
+ - spec/testfiles/small.sqt
159
+ - spec/testfiles/small2.sqt
160
+ homepage: http://github.com/princelab/mspire-sequest
161
+ licenses:
162
+ - MIT
163
+ post_install_message:
164
+ rdoc_options: []
165
+ require_paths:
166
+ - lib
167
+ required_ruby_version: !ruby/object:Gem::Requirement
168
+ none: false
169
+ requirements:
170
+ - - ! '>='
171
+ - !ruby/object:Gem::Version
172
+ version: '0'
173
+ required_rubygems_version: !ruby/object:Gem::Requirement
174
+ none: false
175
+ requirements:
176
+ - - ! '>='
177
+ - !ruby/object:Gem::Version
178
+ version: '0'
179
+ requirements: []
180
+ rubyforge_project: mspire
181
+ rubygems_version: 1.8.18
182
+ signing_key:
183
+ specification_version: 3
184
+ summary: An mspire library supporting SEQUEST, Bioworks, SQT, etc
185
+ test_files: []