mspire 0.7.2 → 0.7.3

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Files changed (8) hide show
  1. data/Rakefile +5 -3
  2. data/VERSION +1 -1
  3. data/lib/mspire/fasta.rb +4 -1
  4. data/mspire.gemspec +141 -139
  5. data/spec/mspire/fasta_spec.rb +0 -4
  6. data/spec/mspire/isotope/distribution_spec.rb +2 -2
  7. data/spec/mspire/quant/qspec_spec.rb +2 -0
  8. metadata +90 -29
data/Rakefile CHANGED
@@ -16,11 +16,13 @@ Jeweler::Tasks.new do |gem|
16
16
  gem.add_dependency "bsearch", ">= 1.5.0"
17
17
  gem.add_dependency "andand", ">= 1.3.1"
18
18
  gem.add_dependency "obo", ">= 0.1.0"
19
- gem.add_dependency "builder", ">= 3.0.0"
20
- gem.add_dependency "trollop", ">= 1.16.2"
19
+ gem.add_dependency "builder", "~> 3.0.0"
20
+ gem.add_dependency "bio", "~> 1.4.2"
21
+ gem.add_dependency "trollop", "~> 1.16.2"
22
+ gem.add_development_dependency "fftw3", "~> 0.3"
21
23
  gem.add_development_dependency "rspec", "~> 2.6"
22
24
  gem.add_development_dependency "jeweler", "~> 1.5.2"
23
- gem.add_development_dependency "rcov", ">= 0"
25
+ #gem.add_development_dependency "rcov", ">= 0"
24
26
  end
25
27
  Jeweler::RubygemsDotOrgTasks.new
26
28
 
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.7.2
1
+ 0.7.3
data/lib/mspire/fasta.rb CHANGED
@@ -1,4 +1,5 @@
1
- require 'bio'
1
+ require 'bio/io/flatfile'
2
+ require 'bio/db/fasta'
2
3
  require 'stringio'
3
4
 
4
5
  class Bio::FlatFile
@@ -57,6 +58,7 @@ module Mspire
57
58
  Bio::FlatFile.new(Bio::FastaFormat, io)
58
59
  end
59
60
 
61
+ =begin
60
62
  # returns two hashes [id_to_length, id_to_description]
61
63
  # faster (~4x) than official route.
62
64
  def self.protein_lengths_and_descriptions(file)
@@ -82,6 +84,7 @@ module Mspire
82
84
  lengths.shift # remove the first nil entry
83
85
  [Hash[ids.zip(lengths).to_a], protid_to_description]
84
86
  end
87
+ =end
85
88
 
86
89
  end
87
90
  end
data/mspire.gemspec CHANGED
@@ -5,11 +5,11 @@
5
5
 
6
6
  Gem::Specification.new do |s|
7
7
  s.name = "mspire"
8
- s.version = "0.6.26"
8
+ s.version = "0.7.3"
9
9
 
10
10
  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
11
11
  s.authors = ["John T. Prince", "Simon Chiang"]
12
- s.date = "2012-03-15"
12
+ s.date = "2012-03-20"
13
13
  s.description = "mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire, merging of ms-* gems"
14
14
  s.email = "jtprince@gmail.com"
15
15
  s.extra_rdoc_files = [
@@ -28,84 +28,83 @@ Gem::Specification.new do |s|
28
28
  "lib/cv/referenceable_param_group_ref.rb",
29
29
  "lib/io/bookmark.rb",
30
30
  "lib/merge.rb",
31
- "lib/ms.rb",
32
- "lib/ms/cv.rb",
33
- "lib/ms/cv/param.rb",
34
- "lib/ms/cv/paramable.rb",
35
- "lib/ms/digester.rb",
36
- "lib/ms/error_rate/decoy.rb",
37
- "lib/ms/error_rate/qvalue.rb",
38
- "lib/ms/fasta.rb",
39
- "lib/ms/ident.rb",
40
- "lib/ms/ident/peptide.rb",
41
- "lib/ms/ident/peptide/db.rb",
42
- "lib/ms/ident/peptide_hit.rb",
43
- "lib/ms/ident/peptide_hit/qvalue.rb",
44
- "lib/ms/ident/pepxml.rb",
45
- "lib/ms/ident/pepxml/modifications.rb",
46
- "lib/ms/ident/pepxml/msms_pipeline_analysis.rb",
47
- "lib/ms/ident/pepxml/msms_run_summary.rb",
48
- "lib/ms/ident/pepxml/parameters.rb",
49
- "lib/ms/ident/pepxml/sample_enzyme.rb",
50
- "lib/ms/ident/pepxml/search_database.rb",
51
- "lib/ms/ident/pepxml/search_hit.rb",
52
- "lib/ms/ident/pepxml/search_hit/modification_info.rb",
53
- "lib/ms/ident/pepxml/search_result.rb",
54
- "lib/ms/ident/pepxml/search_summary.rb",
55
- "lib/ms/ident/pepxml/spectrum_query.rb",
56
- "lib/ms/ident/protein.rb",
57
- "lib/ms/ident/protein_group.rb",
58
- "lib/ms/ident/search.rb",
59
- "lib/ms/isotope.rb",
60
- "lib/ms/isotope/aa.rb",
61
- "lib/ms/isotope/distribution.rb",
62
- "lib/ms/isotope/nist_isotope_info.yml",
63
- "lib/ms/mascot.rb",
64
- "lib/ms/mass.rb",
65
- "lib/ms/mass/aa.rb",
66
- "lib/ms/molecular_formula.rb",
67
- "lib/ms/mzml.rb",
68
- "lib/ms/mzml/activation.rb",
69
- "lib/ms/mzml/chromatogram.rb",
70
- "lib/ms/mzml/chromatogram_list.rb",
71
- "lib/ms/mzml/component.rb",
72
- "lib/ms/mzml/contact.rb",
73
- "lib/ms/mzml/cv.rb",
74
- "lib/ms/mzml/data_array.rb",
75
- "lib/ms/mzml/data_array_container_like.rb",
76
- "lib/ms/mzml/data_processing.rb",
77
- "lib/ms/mzml/file_content.rb",
78
- "lib/ms/mzml/file_description.rb",
79
- "lib/ms/mzml/index_list.rb",
80
- "lib/ms/mzml/instrument_configuration.rb",
81
- "lib/ms/mzml/isolation_window.rb",
82
- "lib/ms/mzml/list.rb",
83
- "lib/ms/mzml/plms1.rb",
84
- "lib/ms/mzml/precursor.rb",
85
- "lib/ms/mzml/processing_method.rb",
86
- "lib/ms/mzml/product.rb",
87
- "lib/ms/mzml/referenceable_param_group.rb",
88
- "lib/ms/mzml/run.rb",
89
- "lib/ms/mzml/sample.rb",
90
- "lib/ms/mzml/scan.rb",
91
- "lib/ms/mzml/scan_list.rb",
92
- "lib/ms/mzml/scan_settings.rb",
93
- "lib/ms/mzml/selected_ion.rb",
94
- "lib/ms/mzml/software.rb",
95
- "lib/ms/mzml/source_file.rb",
96
- "lib/ms/mzml/spectrum.rb",
97
- "lib/ms/mzml/spectrum_list.rb",
98
- "lib/ms/obo.rb",
99
- "lib/ms/peak.rb",
100
- "lib/ms/peak/point.rb",
101
- "lib/ms/plms1.rb",
102
- "lib/ms/quant/qspec.rb",
103
- "lib/ms/quant/qspec/protein_group_comparison.rb",
104
- "lib/ms/spectrum.rb",
105
- "lib/ms/spectrum/centroid.rb",
106
- "lib/ms/spectrum_like.rb",
107
- "lib/ms/user_param.rb",
108
31
  "lib/mspire.rb",
32
+ "lib/mspire/cv.rb",
33
+ "lib/mspire/cv/param.rb",
34
+ "lib/mspire/cv/paramable.rb",
35
+ "lib/mspire/digester.rb",
36
+ "lib/mspire/error_rate/decoy.rb",
37
+ "lib/mspire/error_rate/qvalue.rb",
38
+ "lib/mspire/fasta.rb",
39
+ "lib/mspire/ident.rb",
40
+ "lib/mspire/ident/peptide.rb",
41
+ "lib/mspire/ident/peptide/db.rb",
42
+ "lib/mspire/ident/peptide_hit.rb",
43
+ "lib/mspire/ident/peptide_hit/qvalue.rb",
44
+ "lib/mspire/ident/pepxml.rb",
45
+ "lib/mspire/ident/pepxml/modifications.rb",
46
+ "lib/mspire/ident/pepxml/msms_pipeline_analysis.rb",
47
+ "lib/mspire/ident/pepxml/msms_run_summary.rb",
48
+ "lib/mspire/ident/pepxml/parameters.rb",
49
+ "lib/mspire/ident/pepxml/sample_enzyme.rb",
50
+ "lib/mspire/ident/pepxml/search_database.rb",
51
+ "lib/mspire/ident/pepxml/search_hit.rb",
52
+ "lib/mspire/ident/pepxml/search_hit/modification_info.rb",
53
+ "lib/mspire/ident/pepxml/search_result.rb",
54
+ "lib/mspire/ident/pepxml/search_summary.rb",
55
+ "lib/mspire/ident/pepxml/spectrum_query.rb",
56
+ "lib/mspire/ident/protein.rb",
57
+ "lib/mspire/ident/protein_group.rb",
58
+ "lib/mspire/ident/search.rb",
59
+ "lib/mspire/isotope.rb",
60
+ "lib/mspire/isotope/aa.rb",
61
+ "lib/mspire/isotope/distribution.rb",
62
+ "lib/mspire/isotope/nist_isotope_info.yml",
63
+ "lib/mspire/mascot.rb",
64
+ "lib/mspire/mass.rb",
65
+ "lib/mspire/mass/aa.rb",
66
+ "lib/mspire/molecular_formula.rb",
67
+ "lib/mspire/mzml.rb",
68
+ "lib/mspire/mzml/activation.rb",
69
+ "lib/mspire/mzml/chromatogram.rb",
70
+ "lib/mspire/mzml/chromatogram_list.rb",
71
+ "lib/mspire/mzml/component.rb",
72
+ "lib/mspire/mzml/contact.rb",
73
+ "lib/mspire/mzml/cv.rb",
74
+ "lib/mspire/mzml/data_array.rb",
75
+ "lib/mspire/mzml/data_array_container_like.rb",
76
+ "lib/mspire/mzml/data_processing.rb",
77
+ "lib/mspire/mzml/file_content.rb",
78
+ "lib/mspire/mzml/file_description.rb",
79
+ "lib/mspire/mzml/index_list.rb",
80
+ "lib/mspire/mzml/instrument_configuration.rb",
81
+ "lib/mspire/mzml/isolation_window.rb",
82
+ "lib/mspire/mzml/list.rb",
83
+ "lib/mspire/mzml/plms1.rb",
84
+ "lib/mspire/mzml/precursor.rb",
85
+ "lib/mspire/mzml/processing_method.rb",
86
+ "lib/mspire/mzml/product.rb",
87
+ "lib/mspire/mzml/referenceable_param_group.rb",
88
+ "lib/mspire/mzml/run.rb",
89
+ "lib/mspire/mzml/sample.rb",
90
+ "lib/mspire/mzml/scan.rb",
91
+ "lib/mspire/mzml/scan_list.rb",
92
+ "lib/mspire/mzml/scan_settings.rb",
93
+ "lib/mspire/mzml/selected_ion.rb",
94
+ "lib/mspire/mzml/software.rb",
95
+ "lib/mspire/mzml/source_file.rb",
96
+ "lib/mspire/mzml/spectrum.rb",
97
+ "lib/mspire/mzml/spectrum_list.rb",
98
+ "lib/mspire/obo.rb",
99
+ "lib/mspire/peak.rb",
100
+ "lib/mspire/peak/point.rb",
101
+ "lib/mspire/plms1.rb",
102
+ "lib/mspire/quant/qspec.rb",
103
+ "lib/mspire/quant/qspec/protein_group_comparison.rb",
104
+ "lib/mspire/spectrum.rb",
105
+ "lib/mspire/spectrum/centroid.rb",
106
+ "lib/mspire/spectrum_like.rb",
107
+ "lib/mspire/user_param.rb",
109
108
  "lib/obo/ims.rb",
110
109
  "lib/obo/ms.rb",
111
110
  "lib/obo/ontology.rb",
@@ -118,60 +117,60 @@ Gem::Specification.new do |s|
118
117
  "obo/unit.obo",
119
118
  "script/mzml_read_binary.rb",
120
119
  "spec/bin_spec.rb",
121
- "spec/ms/cv/param_spec.rb",
122
- "spec/ms/digester_spec.rb",
123
- "spec/ms/error_rate/qvalue_spec.rb",
124
- "spec/ms/fasta_spec.rb",
125
- "spec/ms/ident/peptide/db_spec.rb",
126
- "spec/ms/ident/pepxml/sample_enzyme_spec.rb",
127
- "spec/ms/ident/pepxml/search_hit/modification_info_spec.rb",
128
- "spec/ms/ident/pepxml_spec.rb",
129
- "spec/ms/ident/protein_group_spec.rb",
130
- "spec/ms/isotope/aa_spec.rb",
131
- "spec/ms/isotope/distribution_spec.rb",
132
- "spec/ms/isotope_spec.rb",
133
- "spec/ms/mass_spec.rb",
134
- "spec/ms/molecular_formula_spec.rb",
135
- "spec/ms/mzml/cv_spec.rb",
136
- "spec/ms/mzml/data_array_spec.rb",
137
- "spec/ms/mzml/file_content_spec.rb",
138
- "spec/ms/mzml/file_description_spec.rb",
139
- "spec/ms/mzml/index_list_spec.rb",
140
- "spec/ms/mzml/plms1_spec.rb",
141
- "spec/ms/mzml/referenceable_param_group_spec.rb",
142
- "spec/ms/mzml_spec.rb",
143
- "spec/ms/peak_spec.rb",
144
- "spec/ms/plms1_spec.rb",
145
- "spec/ms/quant/qspec_spec.rb",
146
- "spec/ms/spectrum_spec.rb",
147
- "spec/ms/user_param_spec.rb",
120
+ "spec/mspire/cv/param_spec.rb",
121
+ "spec/mspire/digester_spec.rb",
122
+ "spec/mspire/error_rate/qvalue_spec.rb",
123
+ "spec/mspire/fasta_spec.rb",
124
+ "spec/mspire/ident/peptide/db_spec.rb",
125
+ "spec/mspire/ident/pepxml/sample_enzyme_spec.rb",
126
+ "spec/mspire/ident/pepxml/search_hit/modification_info_spec.rb",
127
+ "spec/mspire/ident/pepxml_spec.rb",
128
+ "spec/mspire/ident/protein_group_spec.rb",
129
+ "spec/mspire/isotope/aa_spec.rb",
130
+ "spec/mspire/isotope/distribution_spec.rb",
131
+ "spec/mspire/isotope_spec.rb",
132
+ "spec/mspire/mass_spec.rb",
133
+ "spec/mspire/molecular_formula_spec.rb",
134
+ "spec/mspire/mzml/cv_spec.rb",
135
+ "spec/mspire/mzml/data_array_spec.rb",
136
+ "spec/mspire/mzml/file_content_spec.rb",
137
+ "spec/mspire/mzml/file_description_spec.rb",
138
+ "spec/mspire/mzml/index_list_spec.rb",
139
+ "spec/mspire/mzml/plms1_spec.rb",
140
+ "spec/mspire/mzml/referenceable_param_group_spec.rb",
141
+ "spec/mspire/mzml_spec.rb",
142
+ "spec/mspire/peak_spec.rb",
143
+ "spec/mspire/plms1_spec.rb",
144
+ "spec/mspire/quant/qspec_spec.rb",
145
+ "spec/mspire/spectrum_spec.rb",
146
+ "spec/mspire/user_param_spec.rb",
148
147
  "spec/mspire_spec.rb",
149
148
  "spec/obo_spec.rb",
150
149
  "spec/spec_helper.rb",
151
- "spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.fasta",
152
- "spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml",
153
- "spec/testfiles/ms/mzml/j24z.idx_comp.3.mzML",
154
- "spec/testfiles/ms/mzml/mspire_simulated.MSn.check.mzML",
155
- "spec/testfiles/ms/mzml/openms.noidx_nocomp.12.mzML",
156
- "spec/testfiles/ms/quant/kill_extra_tabs.rb",
157
- "spec/testfiles/ms/quant/max_quant_output.provenance.txt",
158
- "spec/testfiles/ms/quant/max_quant_output.txt",
159
- "spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv",
160
- "spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp",
161
- "spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp.csv",
162
- "spec/testfiles/ms/quant/pdcd5_final.txt",
163
- "spec/testfiles/ms/quant/pdcd5_final.txt_qspecgp",
164
- "spec/testfiles/ms/quant/pdcd5_lfq_qspec.CSV.csv",
165
- "spec/testfiles/ms/quant/pdcd5_lfq_qspec.csv",
166
- "spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.csv",
167
- "spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv",
168
- "spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp",
169
- "spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp.csv",
170
- "spec/testfiles/ms/quant/pdcd5_lfq_qspec.txt",
171
- "spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt",
172
- "spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt_qspecgp",
173
- "spec/testfiles/ms/quant/remove_rest_of_proteins.rb",
174
- "spec/testfiles/ms/quant/unlog_transform.rb",
150
+ "spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.fasta",
151
+ "spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml",
152
+ "spec/testfiles/mspire/mzml/j24z.idx_comp.3.mzML",
153
+ "spec/testfiles/mspire/mzml/mspire_simulated.MSn.check.mzML",
154
+ "spec/testfiles/mspire/mzml/openms.noidx_nocomp.12.mzML",
155
+ "spec/testfiles/mspire/quant/kill_extra_tabs.rb",
156
+ "spec/testfiles/mspire/quant/max_quant_output.provenance.txt",
157
+ "spec/testfiles/mspire/quant/max_quant_output.txt",
158
+ "spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv",
159
+ "spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv_qspecgp",
160
+ "spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv_qspecgp.csv",
161
+ "spec/testfiles/mspire/quant/pdcd5_final.txt",
162
+ "spec/testfiles/mspire/quant/pdcd5_final.txt_qspecgp",
163
+ "spec/testfiles/mspire/quant/pdcd5_lfq_qspec.CSV.csv",
164
+ "spec/testfiles/mspire/quant/pdcd5_lfq_qspec.csv",
165
+ "spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.csv",
166
+ "spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv",
167
+ "spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp",
168
+ "spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp.csv",
169
+ "spec/testfiles/mspire/quant/pdcd5_lfq_qspec.txt",
170
+ "spec/testfiles/mspire/quant/pdcd5_lfq_tabdel.txt",
171
+ "spec/testfiles/mspire/quant/pdcd5_lfq_tabdel.txt_qspecgp",
172
+ "spec/testfiles/mspire/quant/remove_rest_of_proteins.rb",
173
+ "spec/testfiles/mspire/quant/unlog_transform.rb",
175
174
  "spec/testfiles/plms1/output.key"
176
175
  ]
177
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  s.homepage = "http://github.com/princelab/mspire"
@@ -188,32 +187,35 @@ Gem::Specification.new do |s|
188
187
  s.add_runtime_dependency(%q<bsearch>, [">= 1.5.0"])
189
188
  s.add_runtime_dependency(%q<andand>, [">= 1.3.1"])
190
189
  s.add_runtime_dependency(%q<obo>, [">= 0.1.0"])
191
- s.add_runtime_dependency(%q<builder>, [">= 3.0.0"])
192
- s.add_runtime_dependency(%q<trollop>, [">= 1.16.2"])
190
+ s.add_runtime_dependency(%q<builder>, ["~> 3.0.0"])
191
+ s.add_runtime_dependency(%q<bio>, ["~> 1.4.2"])
192
+ s.add_runtime_dependency(%q<trollop>, ["~> 1.16.2"])
193
+ s.add_development_dependency(%q<fftw3>, ["~> 0.3"])
193
194
  s.add_development_dependency(%q<rspec>, ["~> 2.6"])
194
195
  s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
195
- s.add_development_dependency(%q<rcov>, [">= 0"])
196
196
  else
197
197
  s.add_dependency(%q<nokogiri>, ["~> 1.5"])
198
198
  s.add_dependency(%q<bsearch>, [">= 1.5.0"])
199
199
  s.add_dependency(%q<andand>, [">= 1.3.1"])
200
200
  s.add_dependency(%q<obo>, [">= 0.1.0"])
201
- s.add_dependency(%q<builder>, [">= 3.0.0"])
202
- s.add_dependency(%q<trollop>, [">= 1.16.2"])
201
+ s.add_dependency(%q<builder>, ["~> 3.0.0"])
202
+ s.add_dependency(%q<bio>, ["~> 1.4.2"])
203
+ s.add_dependency(%q<trollop>, ["~> 1.16.2"])
204
+ s.add_dependency(%q<fftw3>, ["~> 0.3"])
203
205
  s.add_dependency(%q<rspec>, ["~> 2.6"])
204
206
  s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
205
- s.add_dependency(%q<rcov>, [">= 0"])
206
207
  end
207
208
  else
208
209
  s.add_dependency(%q<nokogiri>, ["~> 1.5"])
209
210
  s.add_dependency(%q<bsearch>, [">= 1.5.0"])
210
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  s.add_dependency(%q<andand>, [">= 1.3.1"])
211
212
  s.add_dependency(%q<obo>, [">= 0.1.0"])
212
- s.add_dependency(%q<builder>, [">= 3.0.0"])
213
- s.add_dependency(%q<trollop>, [">= 1.16.2"])
213
+ s.add_dependency(%q<builder>, ["~> 3.0.0"])
214
+ s.add_dependency(%q<bio>, ["~> 1.4.2"])
215
+ s.add_dependency(%q<trollop>, ["~> 1.16.2"])
216
+ s.add_dependency(%q<fftw3>, ["~> 0.3"])
214
217
  s.add_dependency(%q<rspec>, ["~> 2.6"])
215
218
  s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
216
- s.add_dependency(%q<rcov>, [">= 0"])
217
219
  end
218
220
  end
219
221
 
data/spec/mspire/fasta_spec.rb CHANGED
@@ -41,10 +41,6 @@ describe 'basic fasta operations' do
41
41
  end
42
42
  end
43
43
 
44
- xit 'can deliver length and description hashes' do
45
- # need to test
46
- end
47
-
48
44
  it 'can read a file' do
49
45
  %w(newlines_file carriage_returns_and_newlines_file).each do |file|
50
46
  Mspire::Fasta.open(@data[file]) do |fasta|
data/spec/mspire/isotope/distribution_spec.rb CHANGED
@@ -4,7 +4,7 @@ require 'mspire/isotope/distribution'
4
4
 
5
5
  describe 'Mspire::Isotope::Distribution class methods' do
6
6
  before do
7
- @data = [1.0, 0.08919230588715289, 0.017894161377222082, 0.0013573997600723623, 0.0001398330738144092]
7
+ @data = [1.0, 0.08919230588715311, 0.017894161377222138, 0.0013573997600723345, 0.0001398330738144181]
8
8
  end
9
9
 
10
10
  it 'can calculate isotope distributions' do
@@ -15,6 +15,6 @@ describe 'Mspire::Isotope::Distribution class methods' do
15
15
  it 'can calculate isotope distribution spectrum' do
16
16
  spec = Mspire::Isotope::Distribution.spectrum('C8O7', :max)
17
17
  spec.mzs.should == [207.96440233692, 208.97306725252, 209.98173216812, 210.99039708372, 211.99906199932002]
18
- spec.intensities.should == [1.0, 0.08919230588715289, 0.017894161377222082, 0.0013573997600723623, 0.0001398330738144092]
18
+ spec.intensities.should == [1.0, 0.08919230588715311, 0.017894161377222138, 0.0013573997600723345, 0.0001398330738144181]
19
19
  end
20
20
  end
data/spec/mspire/quant/qspec_spec.rb CHANGED
@@ -3,6 +3,7 @@ require 'spec_helper'
3
3
  require 'mspire/quant/qspec'
4
4
  require 'csv'
5
5
 
6
+ =begin
6
7
  describe 'running qspec' do
7
8
  before do
8
9
  #@file = TESTFILES + '/mspire/quant/max_quant_output.txt'
@@ -23,3 +24,4 @@ describe 'running qspec' do
23
24
  describe 'on MaxQuant LFQ data' do
24
25
  end
25
26
  end
27
+ =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: 0.7.2
4
+ version: 0.7.3
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: 2012-03-16 00:00:00.000000000 Z
13
+ date: 2012-03-20 00:00:00.000000000 Z
14
14
  dependencies:
15
15
  - !ruby/object:Gem::Dependency
16
16
  name: nokogiri
17
- requirement: &19248100 !ruby/object:Gem::Requirement
17
+ requirement: !ruby/object:Gem::Requirement
18
18
  none: false
19
19
  requirements:
20
20
  - - ~>
@@ -22,10 +22,15 @@ dependencies:
22
22
  version: '1.5'
23
23
  type: :runtime
24
24
  prerelease: false
25
- version_requirements: *19248100
25
+ version_requirements: !ruby/object:Gem::Requirement
26
+ none: false
27
+ requirements:
28
+ - - ~>
29
+ - !ruby/object:Gem::Version
30
+ version: '1.5'
26
31
  - !ruby/object:Gem::Dependency
27
32
  name: bsearch
28
- requirement: &19245800 !ruby/object:Gem::Requirement
33
+ requirement: !ruby/object:Gem::Requirement
29
34
  none: false
30
35
  requirements:
31
36
  - - ! '>='
@@ -33,10 +38,15 @@ dependencies:
33
38
  version: 1.5.0
34
39
  type: :runtime
35
40
  prerelease: false
36
- version_requirements: *19245800
41
+ version_requirements: !ruby/object:Gem::Requirement
42
+ none: false
43
+ requirements:
44
+ - - ! '>='
45
+ - !ruby/object:Gem::Version
46
+ version: 1.5.0
37
47
  - !ruby/object:Gem::Dependency
38
48
  name: andand
39
- requirement: &19243220 !ruby/object:Gem::Requirement
49
+ requirement: !ruby/object:Gem::Requirement
40
50
  none: false
41
51
  requirements:
42
52
  - - ! '>='
@@ -44,10 +54,15 @@ dependencies:
44
54
  version: 1.3.1
45
55
  type: :runtime
46
56
  prerelease: false
47
- version_requirements: *19243220
57
+ version_requirements: !ruby/object:Gem::Requirement
58
+ none: false
59
+ requirements:
60
+ - - ! '>='
61
+ - !ruby/object:Gem::Version
62
+ version: 1.3.1
48
63
  - !ruby/object:Gem::Dependency
49
64
  name: obo
50
- requirement: &19629860 !ruby/object:Gem::Requirement
65
+ requirement: !ruby/object:Gem::Requirement
51
66
  none: false
52
67
  requirements:
53
68
  - - ! '>='
@@ -55,32 +70,79 @@ dependencies:
55
70
  version: 0.1.0
56
71
  type: :runtime
57
72
  prerelease: false
58
- version_requirements: *19629860
73
+ version_requirements: !ruby/object:Gem::Requirement
74
+ none: false
75
+ requirements:
76
+ - - ! '>='
77
+ - !ruby/object:Gem::Version
78
+ version: 0.1.0
59
79
  - !ruby/object:Gem::Dependency
60
80
  name: builder
61
- requirement: &19626740 !ruby/object:Gem::Requirement
81
+ requirement: !ruby/object:Gem::Requirement
62
82
  none: false
63
83
  requirements:
64
- - - ! '>='
84
+ - - ~>
65
85
  - !ruby/object:Gem::Version
66
86
  version: 3.0.0
67
87
  type: :runtime
68
88
  prerelease: false
69
- version_requirements: *19626740
89
+ version_requirements: !ruby/object:Gem::Requirement
90
+ none: false
91
+ requirements:
92
+ - - ~>
93
+ - !ruby/object:Gem::Version
94
+ version: 3.0.0
95
+ - !ruby/object:Gem::Dependency
96
+ name: bio
97
+ requirement: !ruby/object:Gem::Requirement
98
+ none: false
99
+ requirements:
100
+ - - ~>
101
+ - !ruby/object:Gem::Version
102
+ version: 1.4.2
103
+ type: :runtime
104
+ prerelease: false
105
+ version_requirements: !ruby/object:Gem::Requirement
106
+ none: false
107
+ requirements:
108
+ - - ~>
109
+ - !ruby/object:Gem::Version
110
+ version: 1.4.2
70
111
  - !ruby/object:Gem::Dependency
71
112
  name: trollop
72
- requirement: &19624700 !ruby/object:Gem::Requirement
113
+ requirement: !ruby/object:Gem::Requirement
73
114
  none: false
74
115
  requirements:
75
- - - ! '>='
116
+ - - ~>
76
117
  - !ruby/object:Gem::Version
77
118
  version: 1.16.2
78
119
  type: :runtime
79
120
  prerelease: false
80
- version_requirements: *19624700
121
+ version_requirements: !ruby/object:Gem::Requirement
122
+ none: false
123
+ requirements:
124
+ - - ~>
125
+ - !ruby/object:Gem::Version
126
+ version: 1.16.2
127
+ - !ruby/object:Gem::Dependency
128
+ name: fftw3
129
+ requirement: !ruby/object:Gem::Requirement
130
+ none: false
131
+ requirements:
132
+ - - ~>
133
+ - !ruby/object:Gem::Version
134
+ version: '0.3'
135
+ type: :development
136
+ prerelease: false
137
+ version_requirements: !ruby/object:Gem::Requirement
138
+ none: false
139
+ requirements:
140
+ - - ~>
141
+ - !ruby/object:Gem::Version
142
+ version: '0.3'
81
143
  - !ruby/object:Gem::Dependency
82
144
  name: rspec
83
- requirement: &19713620 !ruby/object:Gem::Requirement
145
+ requirement: !ruby/object:Gem::Requirement
84
146
  none: false
85
147
  requirements:
86
148
  - - ~>
@@ -88,10 +150,15 @@ dependencies:
88
150
  version: '2.6'
89
151
  type: :development
90
152
  prerelease: false
91
- version_requirements: *19713620
153
+ version_requirements: !ruby/object:Gem::Requirement
154
+ none: false
155
+ requirements:
156
+ - - ~>
157
+ - !ruby/object:Gem::Version
158
+ version: '2.6'
92
159
  - !ruby/object:Gem::Dependency
93
160
  name: jeweler
94
- requirement: &19712460 !ruby/object:Gem::Requirement
161
+ requirement: !ruby/object:Gem::Requirement
95
162
  none: false
96
163
  requirements:
97
164
  - - ~>
@@ -99,18 +166,12 @@ dependencies:
99
166
  version: 1.5.2
100
167
  type: :development
101
168
  prerelease: false
102
- version_requirements: *19712460
103
- - !ruby/object:Gem::Dependency
104
- name: rcov
105
- requirement: &19709160 !ruby/object:Gem::Requirement
169
+ version_requirements: !ruby/object:Gem::Requirement
106
170
  none: false
107
171
  requirements:
108
- - - ! '>='
172
+ - - ~>
109
173
  - !ruby/object:Gem::Version
110
- version: '0'
111
- type: :development
112
- prerelease: false
113
- version_requirements: *19709160
174
+ version: 1.5.2
114
175
  description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
115
176
  merging of ms-* gems
116
177
  email: jtprince@gmail.com
@@ -296,7 +357,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
296
357
  version: '0'
297
358
  requirements: []
298
359
  rubyforge_project:
299
- rubygems_version: 1.8.15
360
+ rubygems_version: 1.8.18
300
361
  signing_key:
301
362
  specification_version: 3
302
363
  summary: mass spectrometry proteomics, lipidomics, and tools