mspire 0.6.22 → 0.6.24
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.
- data/Rakefile +2 -0
- data/VERSION +1 -1
- data/lib/ms/isotope.rb +93 -0
- data/lib/ms/isotope/aa.rb +2 -1
- data/lib/ms/isotope/nist_isotope_info.yml +2017 -0
- data/lib/ms/mzml.rb +0 -18
- data/lib/ms/mzml/data_array.rb +79 -11
- data/lib/ms/mzml/spectrum.rb +2 -3
- data/mspire.gemspec +14 -3
- data/script/mzml_read_binary.rb +34 -0
- data/spec/ms/isotope_spec.rb +31 -0
- data/spec/ms/mzml/data_array_spec.rb +38 -0
- data/spec/ms/mzml_spec.rb +5 -62
- data/spec/testfiles/ms/mzml/{mspire_simulated.noidx.check.mzML → mspire_simulated.MSn.check.mzML} +14 -4
- metadata +44 -17
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: mspire
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.6.
|
|
4
|
+
version: 0.6.24
|
|
5
5
|
prerelease:
|
|
6
6
|
platform: ruby
|
|
7
7
|
authors:
|
|
@@ -10,11 +10,11 @@ authors:
|
|
|
10
10
|
autorequire:
|
|
11
11
|
bindir: bin
|
|
12
12
|
cert_chain: []
|
|
13
|
-
date: 2012-
|
|
13
|
+
date: 2012-03-13 00:00:00.000000000 Z
|
|
14
14
|
dependencies:
|
|
15
15
|
- !ruby/object:Gem::Dependency
|
|
16
16
|
name: nokogiri
|
|
17
|
-
requirement: &
|
|
17
|
+
requirement: &13307340 !ruby/object:Gem::Requirement
|
|
18
18
|
none: false
|
|
19
19
|
requirements:
|
|
20
20
|
- - ~>
|
|
@@ -22,10 +22,10 @@ dependencies:
|
|
|
22
22
|
version: '1.5'
|
|
23
23
|
type: :runtime
|
|
24
24
|
prerelease: false
|
|
25
|
-
version_requirements: *
|
|
25
|
+
version_requirements: *13307340
|
|
26
26
|
- !ruby/object:Gem::Dependency
|
|
27
27
|
name: bsearch
|
|
28
|
-
requirement: &
|
|
28
|
+
requirement: &13323080 !ruby/object:Gem::Requirement
|
|
29
29
|
none: false
|
|
30
30
|
requirements:
|
|
31
31
|
- - ! '>='
|
|
@@ -33,10 +33,10 @@ dependencies:
|
|
|
33
33
|
version: 1.5.0
|
|
34
34
|
type: :runtime
|
|
35
35
|
prerelease: false
|
|
36
|
-
version_requirements: *
|
|
36
|
+
version_requirements: *13323080
|
|
37
37
|
- !ruby/object:Gem::Dependency
|
|
38
38
|
name: andand
|
|
39
|
-
requirement: &
|
|
39
|
+
requirement: &13322420 !ruby/object:Gem::Requirement
|
|
40
40
|
none: false
|
|
41
41
|
requirements:
|
|
42
42
|
- - ! '>='
|
|
@@ -44,10 +44,10 @@ dependencies:
|
|
|
44
44
|
version: 1.3.1
|
|
45
45
|
type: :runtime
|
|
46
46
|
prerelease: false
|
|
47
|
-
version_requirements: *
|
|
47
|
+
version_requirements: *13322420
|
|
48
48
|
- !ruby/object:Gem::Dependency
|
|
49
49
|
name: obo
|
|
50
|
-
requirement: &
|
|
50
|
+
requirement: &13321500 !ruby/object:Gem::Requirement
|
|
51
51
|
none: false
|
|
52
52
|
requirements:
|
|
53
53
|
- - ! '>='
|
|
@@ -55,10 +55,32 @@ dependencies:
|
|
|
55
55
|
version: 0.1.0
|
|
56
56
|
type: :runtime
|
|
57
57
|
prerelease: false
|
|
58
|
-
version_requirements: *
|
|
58
|
+
version_requirements: *13321500
|
|
59
|
+
- !ruby/object:Gem::Dependency
|
|
60
|
+
name: builder
|
|
61
|
+
requirement: &13320060 !ruby/object:Gem::Requirement
|
|
62
|
+
none: false
|
|
63
|
+
requirements:
|
|
64
|
+
- - ! '>='
|
|
65
|
+
- !ruby/object:Gem::Version
|
|
66
|
+
version: 3.0.0
|
|
67
|
+
type: :runtime
|
|
68
|
+
prerelease: false
|
|
69
|
+
version_requirements: *13320060
|
|
70
|
+
- !ruby/object:Gem::Dependency
|
|
71
|
+
name: trollop
|
|
72
|
+
requirement: &13319460 !ruby/object:Gem::Requirement
|
|
73
|
+
none: false
|
|
74
|
+
requirements:
|
|
75
|
+
- - ! '>='
|
|
76
|
+
- !ruby/object:Gem::Version
|
|
77
|
+
version: 1.16.2
|
|
78
|
+
type: :runtime
|
|
79
|
+
prerelease: false
|
|
80
|
+
version_requirements: *13319460
|
|
59
81
|
- !ruby/object:Gem::Dependency
|
|
60
82
|
name: rspec
|
|
61
|
-
requirement: &
|
|
83
|
+
requirement: &13318520 !ruby/object:Gem::Requirement
|
|
62
84
|
none: false
|
|
63
85
|
requirements:
|
|
64
86
|
- - ~>
|
|
@@ -66,10 +88,10 @@ dependencies:
|
|
|
66
88
|
version: '2.6'
|
|
67
89
|
type: :development
|
|
68
90
|
prerelease: false
|
|
69
|
-
version_requirements: *
|
|
91
|
+
version_requirements: *13318520
|
|
70
92
|
- !ruby/object:Gem::Dependency
|
|
71
93
|
name: jeweler
|
|
72
|
-
requirement: &
|
|
94
|
+
requirement: &13317560 !ruby/object:Gem::Requirement
|
|
73
95
|
none: false
|
|
74
96
|
requirements:
|
|
75
97
|
- - ~>
|
|
@@ -77,10 +99,10 @@ dependencies:
|
|
|
77
99
|
version: 1.5.2
|
|
78
100
|
type: :development
|
|
79
101
|
prerelease: false
|
|
80
|
-
version_requirements: *
|
|
102
|
+
version_requirements: *13317560
|
|
81
103
|
- !ruby/object:Gem::Dependency
|
|
82
104
|
name: rcov
|
|
83
|
-
requirement: &
|
|
105
|
+
requirement: &13316940 !ruby/object:Gem::Requirement
|
|
84
106
|
none: false
|
|
85
107
|
requirements:
|
|
86
108
|
- - ! '>='
|
|
@@ -88,7 +110,7 @@ dependencies:
|
|
|
88
110
|
version: '0'
|
|
89
111
|
type: :development
|
|
90
112
|
prerelease: false
|
|
91
|
-
version_requirements: *
|
|
113
|
+
version_requirements: *13316940
|
|
92
114
|
description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
|
|
93
115
|
merging of ms-* gems
|
|
94
116
|
email: jtprince@gmail.com
|
|
@@ -137,7 +159,9 @@ files:
|
|
|
137
159
|
- lib/ms/ident/protein.rb
|
|
138
160
|
- lib/ms/ident/protein_group.rb
|
|
139
161
|
- lib/ms/ident/search.rb
|
|
162
|
+
- lib/ms/isotope.rb
|
|
140
163
|
- lib/ms/isotope/aa.rb
|
|
164
|
+
- lib/ms/isotope/nist_isotope_info.yml
|
|
141
165
|
- lib/ms/mascot.rb
|
|
142
166
|
- lib/ms/mass.rb
|
|
143
167
|
- lib/ms/mass/aa.rb
|
|
@@ -193,6 +217,7 @@ files:
|
|
|
193
217
|
- obo/ims.obo
|
|
194
218
|
- obo/ms.obo
|
|
195
219
|
- obo/unit.obo
|
|
220
|
+
- script/mzml_read_binary.rb
|
|
196
221
|
- spec/bin_spec.rb
|
|
197
222
|
- spec/ms/cv/param_spec.rb
|
|
198
223
|
- spec/ms/digester_spec.rb
|
|
@@ -204,8 +229,10 @@ files:
|
|
|
204
229
|
- spec/ms/ident/pepxml_spec.rb
|
|
205
230
|
- spec/ms/ident/protein_group_spec.rb
|
|
206
231
|
- spec/ms/isotope/aa_spec.rb
|
|
232
|
+
- spec/ms/isotope_spec.rb
|
|
207
233
|
- spec/ms/mass_spec.rb
|
|
208
234
|
- spec/ms/mzml/cv_spec.rb
|
|
235
|
+
- spec/ms/mzml/data_array_spec.rb
|
|
209
236
|
- spec/ms/mzml/file_content_spec.rb
|
|
210
237
|
- spec/ms/mzml/file_description_spec.rb
|
|
211
238
|
- spec/ms/mzml/index_list_spec.rb
|
|
@@ -223,7 +250,7 @@ files:
|
|
|
223
250
|
- spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.fasta
|
|
224
251
|
- spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml
|
|
225
252
|
- spec/testfiles/ms/mzml/j24z.idx_comp.3.mzML
|
|
226
|
-
- spec/testfiles/ms/mzml/mspire_simulated.
|
|
253
|
+
- spec/testfiles/ms/mzml/mspire_simulated.MSn.check.mzML
|
|
227
254
|
- spec/testfiles/ms/mzml/openms.noidx_nocomp.12.mzML
|
|
228
255
|
- spec/testfiles/ms/quant/kill_extra_tabs.rb
|
|
229
256
|
- spec/testfiles/ms/quant/max_quant_output.provenance.txt
|