mspire 0.10.2 → 0.10.3

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Files changed (6) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +1 -0
  3. data/lib/mspire/isotope/distribution.rb +34 -24
  4. data/lib/mspire/version.rb +1 -1
  5. data/spec/mspire/isotope/distribution_spec.rb +28 -12
  6. metadata +35 -35
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data/.gitignore CHANGED
@@ -4,3 +4,4 @@ doc/output/*
4
4
  .*.swp
5
5
  playing_around_with
6
6
  coverage
7
+ /.bundle
data/lib/mspire/isotope/distribution.rb CHANGED
@@ -17,11 +17,19 @@ end
17
17
  module Mspire
18
18
  class MolecularFormula < Hash
19
19
 
20
- # takes any element composition (see any_to_num_elements).
20
+ # Returns isotopic distribution beginning with the lightest possible peak.
21
+ # (for most molecules this will also be the monoisotopic peak)
21
22
  #
22
- # returns isotopic distribution beginning with monoisotopic peak. It cuts
23
- # off when no more peaks contribute more than percent_cutoff to the total
24
- # distribution. After that, normalization is performed.
23
+ # Two cutoff protocols may be specified, percent_cutoff or
24
+ # peak_cutoff. Normalization is performed *after* cutoff.
25
+ #
26
+ # percent_cutoff: cuts off when no more peaks contribute more than percent_cutoff
27
+ # to the total distribution.
28
+ # peak_cutoff: cuts off after that many peaks.
29
+ #
30
+ # prefer_lowest_index controls the behavior if both percent_cutoff and
31
+ # peak_cutoff are specified. If true, then the lowest index found between
32
+ # the two methods will be used, otherwise the highest index.
25
33
  #
26
34
  # all values will be fractional. normalize may be one of:
27
35
  #
@@ -29,22 +37,24 @@ module Mspire
29
37
  # :max normalize to the highest peak intensity
30
38
  # :first normalize to the intensity of the first peak
31
39
  # (this is typically the monoisotopic peak)
32
- def isotope_distribution(normalize=Mspire::Isotope::Distribution::NORMALIZE, percent_cutoff=nil, isotope_table=Mspire::Isotope::BY_ELEMENT)
33
- mono_dist = raw_isotope_distribution(isotope_table)
40
+ def isotope_distribution(normalize: Mspire::Isotope::Distribution::NORMALIZE, peak_cutoff: nil, percent_cutoff: nil, prefer_lowest_index: true, isotope_table: Mspire::Isotope::BY_ELEMENT)
41
+ mono_dist = raw_isotope_distribution(isotope_table: isotope_table)
34
42
 
35
- if percent_cutoff
36
- total_signal = mono_dist.reduce(:+)
37
- cutoff_index = (mono_dist.size-1).downto(0).find do |i|
38
- (mono_dist[i] / total_signal) >= (percent_cutoff/100.0)
39
- end
40
- # deletes these elements
41
- if cutoff_index
42
- mono_dist.slice!((cutoff_index+1)..-1)
43
- else
44
- # no peaks pass that percent cutoff threshold!
45
- mono_dist = []
46
- end
47
- end
43
+ cutoff_index = [
44
+ if percent_cutoff
45
+ total_signal = mono_dist.reduce(:+)
46
+ cutoff_index_less1 = (mono_dist.size-1).downto(0).find do |i|
47
+ # finds the index
48
+ (mono_dist[i] / total_signal) >= (percent_cutoff/100.0)
49
+ end
50
+ cutoff_index = cutoff_index_less1 ? (cutoff_index_less1 + 1) : 0
51
+ end,
52
+ peak_cutoff
53
+ ].compact.send( prefer_lowest_index ? :min : :max ) || mono_dist.size
54
+
55
+ # mono_dist.size will result in nothing sliced off (i.e., for no cutoff)
56
+
57
+ mono_dist.slice!(cutoff_index..-1)
48
58
 
49
59
  # normalization
50
60
  norm_by =
@@ -83,7 +93,7 @@ module Mspire
83
93
 
84
94
  # returns relative ratios from low nominal mass to high nominal mass.
85
95
  # These are *not* normalized at all.
86
- def raw_isotope_distribution(isotope_table=Mspire::Isotope::BY_ELEMENT)
96
+ def raw_isotope_distribution(isotope_table: Mspire::Isotope::BY_ELEMENT)
87
97
  low_nominal = 0
88
98
  high_nominal = 0
89
99
  self.each do |el,cnt|
@@ -112,14 +122,14 @@ module Mspire
112
122
  obj.is_a?(Mspire::MolecularFormula) ? obj : Mspire::MolecularFormula.from_any(obj)
113
123
  end
114
124
 
115
- def calculate(molecular_formula_like, normalize=NORMALIZE, percent_cutoff=nil, isotope_table=Mspire::Isotope::BY_ELEMENT)
125
+ def calculate(molecular_formula_like, *args)
116
126
  mf = to_mf(molecular_formula_like)
117
- mf.isotope_distribution(normalize, percent_cutoff, isotope_table)
127
+ mf.isotope_distribution(*args)
118
128
  end
119
129
 
120
- def spectrum(molecular_formula_like, normalize=NORMALIZE, percent_cutoff=nil, isotope_table=Mspire::Isotope::BY_ELEMENT)
130
+ def spectrum(molecular_formula_like, *args)
121
131
  mf = to_mf(molecular_formula_like)
122
- mf.isotope_distribution_spectrum(normalize, percent_cutoff, isotope_table)
132
+ mf.isotope_distribution_spectrum(*args)
123
133
  end
124
134
  end
125
135
  end
data/lib/mspire/version.rb CHANGED
@@ -1,3 +1,3 @@
1
1
  module Mspire
2
- VERSION = "0.10.2"
2
+ VERSION = "0.10.3"
3
3
  end
data/spec/mspire/isotope/distribution_spec.rb CHANGED
@@ -4,6 +4,12 @@ require 'mspire/isotope/distribution'
4
4
 
5
5
  describe 'Mspire::Isotope::Distribution class methods' do
6
6
 
7
+ def similar_distributions(a_dist, b_dist)
8
+ b_dist.zip(a_dist) do |b,a|
9
+ expect(a).to be_within(1e-9).of b
10
+ end
11
+ end
12
+
7
13
  before(:all) do
8
14
  @nist = Mspire::Isotope::NIST::BY_ELEMENT
9
15
  @norm = Mspire::Isotope::Distribution::NORMALIZE
@@ -19,47 +25,57 @@ describe 'Mspire::Isotope::Distribution class methods' do
19
25
 
20
26
  describe 'normalizing isotope distributions' do
21
27
 
28
+
22
29
  it 'defaults to normalizing by total signal with no cutoff' do
23
- dist = Mspire::Isotope::Distribution.calculate( subject, @norm, @pcut, @nist )
24
- dist.size.should == 253
25
- dist[0,5].should == [0.31740518639058685, 0.35635707398291416, 0.20793431846543858, 0.08373257192958428, 0.026084566135229446]
30
+ dist = Mspire::Isotope::Distribution.calculate( subject, normalize: @norm, percent_cutoff: @pcut, isotope_table: @nist )
31
+ expect(dist.size).to eq(253)
32
+ similar_distributions dist[0,5], [0.31740518639058685, 0.35635707398291416, 0.20793431846543858, 0.08373257192958428, 0.026084566135229446]
26
33
  end
27
34
 
28
35
  it 'can normalize by first peak' do
29
- dist = Mspire::Isotope::Distribution.calculate( subject, :first, @pcut, @nist )
36
+ dist = Mspire::Isotope::Distribution.calculate( subject, normalize: :first, percent_cutoff: @pcut, isotope_table: @nist )
30
37
  dist.size.should == 253
31
38
  dist[0].should == 1.0
32
39
  dist[1].should_not == 1.0
33
40
  end
34
41
 
35
42
  it 'can normalize by the max peak' do
36
- dist = Mspire::Isotope::Distribution.calculate( subject, :max, @pcut, @nist )
43
+ dist = Mspire::Isotope::Distribution.calculate( subject, normalize: :max, percent_cutoff: @pcut, isotope_table: @nist )
37
44
  dist.size.should == 253
38
45
  dist[0].should_not == 1.0
39
46
  dist[1].should == 1.0
40
47
  end
41
48
 
42
49
  it 'can cutoff based on percent of total signal' do
43
- Mspire::Isotope::Distribution.calculate(subject, :max, 100, @nist).should == []
44
- Mspire::Isotope::Distribution.calculate(subject, :max, 20, @nist).should == [0.8906942209481861, 1.0, 0.5834999040187656]
45
- Mspire::Isotope::Distribution.calculate(subject, :max, 5, @nist).should == [0.8906942209481861, 1.0, 0.5834999040187656, 0.23496817670469172]
46
- Mspire::Isotope::Distribution.calculate(subject, :max, 0.0001, @nist).size.should == 11
50
+ Mspire::Isotope::Distribution.calculate(subject, normalize: :max, percent_cutoff: 100, isotope_table: @nist).should == []
51
+ similar_distributions Mspire::Isotope::Distribution.calculate(subject, normalize: :max, percent_cutoff: 20, isotope_table: @nist), [0.8906942209481861, 1.0, 0.5834999040187656]
52
+ similar_distributions Mspire::Isotope::Distribution.calculate(subject, normalize: :max, percent_cutoff: 5, isotope_table: @nist), [0.8906942209481861, 1.0, 0.5834999040187656, 0.23496817670469172]
53
+ Mspire::Isotope::Distribution.calculate(subject, normalize: :max, percent_cutoff: 0.0001, isotope_table: @nist).size.should == 11
47
54
  end
55
+
56
+ it 'can cutoff based on a given number of peaks' do
57
+ Mspire::Isotope::Distribution.calculate(subject, normalize: :max, peak_cutoff: 0, isotope_table: @nist).should == []
58
+ similar_distributions Mspire::Isotope::Distribution.calculate(subject, normalize: :total, peak_cutoff: 4, isotope_table: @nist), [0.3287710818944283, 0.3691177894299527, 0.2153801947039964, 0.08673093397162249]
59
+ expect(Mspire::Isotope::Distribution.calculate(subject, normalize: :max, peak_cutoff: 1, isotope_table: @nist)).to eql([1.0])
60
+ end
61
+
62
+ xspecify 'prefers the lowest of cutoffs' ## need to test
63
+
48
64
  end
49
65
 
50
66
  describe 'calculating an isotope distribution spectrum' do
51
67
 
52
68
  it 'gives neutral masses if no charge' do
53
- spec = Mspire::Isotope::Distribution.spectrum( subject, @norm, @pcut, @nist )
69
+ spec = Mspire::Isotope::Distribution.spectrum( subject, normalize: @norm, percent_cutoff: @pcut, isotope_table: @nist )
54
70
  [:mzs, :intensities].each {|att| spec.send(att).size.should == 253 }
55
71
  spec.mzs[0,5].should == [1584.8627231418, 1585.8713880574, 1586.8800529730001, 1587.8887178886002, 1588.8973828042003]
56
- spec.intensities[0,5].should == [0.31740518639058685, 0.35635707398291416, 0.20793431846543858, 0.08373257192958428, 0.026084566135229446]
72
+ similar_distributions spec.intensities[0,5], [0.31740518639058685, 0.35635707398291416, 0.20793431846543858, 0.08373257192958428, 0.026084566135229446]
57
73
  end
58
74
 
59
75
  it 'gives proper m/z values if the molecule is charged' do
60
76
  charged_molecule = Mspire::MolecularFormula.from_any( subject )
61
77
  charged_molecule.charge = -3
62
- spec = Mspire::Isotope::Distribution.spectrum( charged_molecule, @norm, @pcut, @nist )
78
+ spec = Mspire::Isotope::Distribution.spectrum( charged_molecule, normalize: @norm, percent_cutoff: @pcut, isotope_table: @nist )
63
79
  [:mzs, :intensities].each {|att| spec.send(att).size.should == 253 }
64
80
  spec.mzs[0,5].should == [-528.2881229806, -528.6243446191334, -528.9605662576668, -529.2967878962, -529.6330095347334]
65
81
  end
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: 0.10.2
4
+ version: 0.10.3
5
5
  platform: ruby
6
6
  authors:
7
7
  - John T. Prince
@@ -9,202 +9,202 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2013-10-02 00:00:00.000000000 Z
12
+ date: 2014-01-01 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: nokogiri
16
16
  requirement: !ruby/object:Gem::Requirement
17
17
  requirements:
18
- - - ~>
18
+ - - "~>"
19
19
  - !ruby/object:Gem::Version
20
20
  version: 1.5.9
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
27
  version: 1.5.9
28
28
  - !ruby/object:Gem::Dependency
29
29
  name: bsearch
30
30
  requirement: !ruby/object:Gem::Requirement
31
31
  requirements:
32
- - - '>='
32
+ - - ">="
33
33
  - !ruby/object:Gem::Version
34
34
  version: 1.5.0
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
41
  version: 1.5.0
42
42
  - !ruby/object:Gem::Dependency
43
43
  name: andand
44
44
  requirement: !ruby/object:Gem::Requirement
45
45
  requirements:
46
- - - '>='
46
+ - - ">="
47
47
  - !ruby/object:Gem::Version
48
48
  version: 1.3.3
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
55
  version: 1.3.3
56
56
  - !ruby/object:Gem::Dependency
57
57
  name: obo
58
58
  requirement: !ruby/object:Gem::Requirement
59
59
  requirements:
60
- - - '>='
60
+ - - ">="
61
61
  - !ruby/object:Gem::Version
62
62
  version: 0.1.3
63
63
  type: :runtime
64
64
  prerelease: false
65
65
  version_requirements: !ruby/object:Gem::Requirement
66
66
  requirements:
67
- - - '>='
67
+ - - ">="
68
68
  - !ruby/object:Gem::Version
69
69
  version: 0.1.3
70
70
  - !ruby/object:Gem::Dependency
71
71
  name: builder
72
72
  requirement: !ruby/object:Gem::Requirement
73
73
  requirements:
74
- - - ~>
74
+ - - "~>"
75
75
  - !ruby/object:Gem::Version
76
76
  version: 3.2.0
77
77
  type: :runtime
78
78
  prerelease: false
79
79
  version_requirements: !ruby/object:Gem::Requirement
80
80
  requirements:
81
- - - ~>
81
+ - - "~>"
82
82
  - !ruby/object:Gem::Version
83
83
  version: 3.2.0
84
84
  - !ruby/object:Gem::Dependency
85
85
  name: bio
86
86
  requirement: !ruby/object:Gem::Requirement
87
87
  requirements:
88
- - - ~>
88
+ - - "~>"
89
89
  - !ruby/object:Gem::Version
90
90
  version: 1.4.3
91
91
  type: :runtime
92
92
  prerelease: false
93
93
  version_requirements: !ruby/object:Gem::Requirement
94
94
  requirements:
95
- - - ~>
95
+ - - "~>"
96
96
  - !ruby/object:Gem::Version
97
97
  version: 1.4.3
98
98
  - !ruby/object:Gem::Dependency
99
99
  name: trollop
100
100
  requirement: !ruby/object:Gem::Requirement
101
101
  requirements:
102
- - - ~>
102
+ - - "~>"
103
103
  - !ruby/object:Gem::Version
104
104
  version: 2.0.0
105
105
  type: :runtime
106
106
  prerelease: false
107
107
  version_requirements: !ruby/object:Gem::Requirement
108
108
  requirements:
109
- - - ~>
109
+ - - "~>"
110
110
  - !ruby/object:Gem::Version
111
111
  version: 2.0.0
112
112
  - !ruby/object:Gem::Dependency
113
113
  name: bundler
114
114
  requirement: !ruby/object:Gem::Requirement
115
115
  requirements:
116
- - - ~>
116
+ - - "~>"
117
117
  - !ruby/object:Gem::Version
118
118
  version: '1.3'
119
119
  type: :development
120
120
  prerelease: false
121
121
  version_requirements: !ruby/object:Gem::Requirement
122
122
  requirements:
123
- - - ~>
123
+ - - "~>"
124
124
  - !ruby/object:Gem::Version
125
125
  version: '1.3'
126
126
  - !ruby/object:Gem::Dependency
127
127
  name: rake
128
128
  requirement: !ruby/object:Gem::Requirement
129
129
  requirements:
130
- - - '>='
130
+ - - ">="
131
131
  - !ruby/object:Gem::Version
132
132
  version: '0'
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
139
  version: '0'
140
140
  - !ruby/object:Gem::Dependency
141
141
  name: rspec
142
142
  requirement: !ruby/object:Gem::Requirement
143
143
  requirements:
144
- - - ~>
144
+ - - "~>"
145
145
  - !ruby/object:Gem::Version
146
146
  version: 2.13.0
147
147
  type: :development
148
148
  prerelease: false
149
149
  version_requirements: !ruby/object:Gem::Requirement
150
150
  requirements:
151
- - - ~>
151
+ - - "~>"
152
152
  - !ruby/object:Gem::Version
153
153
  version: 2.13.0
154
154
  - !ruby/object:Gem::Dependency
155
155
  name: rdoc
156
156
  requirement: !ruby/object:Gem::Requirement
157
157
  requirements:
158
- - - ~>
158
+ - - "~>"
159
159
  - !ruby/object:Gem::Version
160
160
  version: '3.12'
161
161
  type: :development
162
162
  prerelease: false
163
163
  version_requirements: !ruby/object:Gem::Requirement
164
164
  requirements:
165
- - - ~>
165
+ - - "~>"
166
166
  - !ruby/object:Gem::Version
167
167
  version: '3.12'
168
168
  - !ruby/object:Gem::Dependency
169
169
  name: simplecov
170
170
  requirement: !ruby/object:Gem::Requirement
171
171
  requirements:
172
- - - '>='
172
+ - - ">="
173
173
  - !ruby/object:Gem::Version
174
174
  version: '0'
175
175
  type: :development
176
176
  prerelease: false
177
177
  version_requirements: !ruby/object:Gem::Requirement
178
178
  requirements:
179
- - - '>='
179
+ - - ">="
180
180
  - !ruby/object:Gem::Version
181
181
  version: '0'
182
182
  - !ruby/object:Gem::Dependency
183
183
  name: coveralls
184
184
  requirement: !ruby/object:Gem::Requirement
185
185
  requirements:
186
- - - '>='
186
+ - - ">="
187
187
  - !ruby/object:Gem::Version
188
188
  version: '0'
189
189
  type: :development
190
190
  prerelease: false
191
191
  version_requirements: !ruby/object:Gem::Requirement
192
192
  requirements:
193
- - - '>='
193
+ - - ">="
194
194
  - !ruby/object:Gem::Version
195
195
  version: '0'
196
196
  - !ruby/object:Gem::Dependency
197
197
  name: fftw3
198
198
  requirement: !ruby/object:Gem::Requirement
199
199
  requirements:
200
- - - ~>
200
+ - - "~>"
201
201
  - !ruby/object:Gem::Version
202
202
  version: '0.3'
203
203
  type: :development
204
204
  prerelease: false
205
205
  version_requirements: !ruby/object:Gem::Requirement
206
206
  requirements:
207
- - - ~>
207
+ - - "~>"
208
208
  - !ruby/object:Gem::Version
209
209
  version: '0.3'
210
210
  description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
@@ -216,8 +216,8 @@ executables:
216
216
  extensions: []
217
217
  extra_rdoc_files: []
218
218
  files:
219
- - .gitignore
220
- - .travis.yml
219
+ - ".gitignore"
220
+ - ".travis.yml"
221
221
  - Gemfile
222
222
  - LICENSE
223
223
  - README.md
@@ -450,17 +450,17 @@ require_paths:
450
450
  - lib
451
451
  required_ruby_version: !ruby/object:Gem::Requirement
452
452
  requirements:
453
- - - '>='
453
+ - - ">="
454
454
  - !ruby/object:Gem::Version
455
455
  version: '0'
456
456
  required_rubygems_version: !ruby/object:Gem::Requirement
457
457
  requirements:
458
- - - '>='
458
+ - - ">="
459
459
  - !ruby/object:Gem::Version
460
460
  version: '0'
461
461
  requirements: []
462
462
  rubyforge_project:
463
- rubygems_version: 2.0.3
463
+ rubygems_version: 2.2.0
464
464
  signing_key:
465
465
  specification_version: 4
466
466
  summary: mass spectrometry proteomics, lipidomics, and tools