mspire 0.7.2 → 0.7.3

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.
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
176
  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
211
  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