mspire 0.8.6.2 → 0.8.7

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 (20) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +7 -0
  3. data/.travis.yml +6 -0
  4. data/Gemfile +6 -0
  5. data/README.md +16 -0
  6. data/Rakefile +2 -48
  7. data/bin/mspire +0 -0
  8. data/lib/mspire/ident/pepxml/modifications.rb +1 -1
  9. data/lib/mspire/ident/pepxml/search_hit/modification_info.rb +2 -1
  10. data/lib/mspire/ident/pepxml/search_hit.rb +1 -1
  11. data/lib/mspire/ident/pepxml/spectrum_query.rb +1 -1
  12. data/lib/mspire/ident/pepxml.rb +20 -5
  13. data/lib/mspire/version.rb +3 -0
  14. data/lib/mspire.rb +1 -3
  15. data/obo/mod.obo +37018 -0
  16. data/script/mascot_dat_to_peptide_hit_qvalues.rb +0 -2
  17. data/spec/spec_helper.rb +6 -47
  18. data/spec/spec_utilities.rb +45 -0
  19. metadata +163 -49
  20. data/VERSION +0 -1
data/script/mascot_dat_to_peptide_hit_qvalues.rb CHANGED
@@ -102,9 +102,7 @@ end
102
102
  to_run.each do |file_base, bundle|
103
103
  putsv "calculating qvalues for #{file_base}"
104
104
  hit_and_qvalue_pairs = Mspire::ErrorRate::Qvalue.target_decoy_qvalues(bundle.target, bundle.decoy, :z_together => opt[:z_together])
105
-
106
105
  outfile = Mspire::Ident::PeptideHit::Qvalue.to_phq(file_base, *hit_and_qvalue_pairs.transpose)
107
-
108
106
  putsv "created: #{outfile}"
109
107
  end
110
108
 
data/spec/spec_helper.rb CHANGED
@@ -1,8 +1,11 @@
1
- $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
2
- $LOAD_PATH.unshift(File.dirname(__FILE__))
1
+ #$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
2
+ #$LOAD_PATH.unshift(File.dirname(__FILE__))
3
+
4
+ require 'simplecov'
5
+ SimpleCov.start
3
6
 
4
- require 'rubygems'
5
7
  require 'rspec'
8
+ require 'spec_utilities'
6
9
 
7
10
  TESTFILES = File.dirname(__FILE__) + '/testfiles'
8
11
 
@@ -19,47 +22,3 @@ RSpec.configure do |config|
19
22
  end
20
23
 
21
24
 
22
- def benchmark(*args, &block)
23
- if ENV['BENCHMARK']
24
- Benchmark.bmbm(*args, &block)
25
- end
26
- end
27
-
28
- # given "filename.ext" returns "filename.CHECK.ext
29
- # block can be given to sanitize each string
30
- def file_check(filename, delete=true, &block)
31
- ext = File.extname(filename)
32
- base = filename.chomp(ext)
33
- checkfile = base + ".CHECK" + ext
34
- File.exist?(filename).should be_true
35
- fstring = IO.read(filename)
36
- cstring = IO.read(checkfile)
37
- if block
38
- (fstring, cstring) = [fstring, cstring].map do |string|
39
- block.call(string)
40
- end
41
- end
42
- fstring.should == cstring
43
- File.unlink(filename) if delete
44
- end
45
-
46
- def sanitize_mspire_version_xml(string)
47
- string.gsub(/"mspire(_[\d\.]+)?" version="([\.\d]+)"/, %Q{"mspire" version="X.X.X"})
48
- .gsub(/softwareRef="mspire_[\d\.]+/, 'softwareRef="mspire_X.X.X')
49
- end
50
-
51
- require 'stringio'
52
-
53
- module Kernel
54
-
55
- def capture_stdout
56
- out = StringIO.new
57
- $stdout = out
58
- yield
59
- out.string
60
- ensure
61
- $stdout = STDOUT
62
- end
63
-
64
- end
65
-
data/spec/spec_utilities.rb ADDED
@@ -0,0 +1,45 @@
1
+
2
+ def benchmark(*args, &block)
3
+ if ENV['BENCHMARK']
4
+ Benchmark.bmbm(*args, &block)
5
+ end
6
+ end
7
+
8
+ # given "filename.ext" returns "filename.CHECK.ext
9
+ # block can be given to sanitize each string
10
+ def file_check(filename, delete=true, &block)
11
+ ext = File.extname(filename)
12
+ base = filename.chomp(ext)
13
+ checkfile = base + ".CHECK" + ext
14
+ File.exist?(filename).should be_true
15
+ fstring = IO.read(filename)
16
+ cstring = IO.read(checkfile)
17
+ if block
18
+ (fstring, cstring) = [fstring, cstring].map do |string|
19
+ block.call(string)
20
+ end
21
+ end
22
+ fstring.should == cstring
23
+ File.unlink(filename) if delete
24
+ end
25
+
26
+ def sanitize_mspire_version_xml(string)
27
+ string.gsub(/"mspire(_[\d\.]+)?" version="([\.\d]+)"/, %Q{"mspire" version="X.X.X"})
28
+ .gsub(/softwareRef="mspire_[\d\.]+/, 'softwareRef="mspire_X.X.X')
29
+ end
30
+
31
+ require 'stringio'
32
+
33
+ module Kernel
34
+
35
+ def capture_stdout
36
+ out = StringIO.new
37
+ $stdout = out
38
+ yield
39
+ out.string
40
+ ensure
41
+ $stdout = STDOUT
42
+ end
43
+
44
+ end
45
+
metadata CHANGED
@@ -1,8 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: mspire
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.8.6.2
5
- prerelease:
4
+ version: 0.8.7
6
5
  platform: ruby
7
6
  authors:
8
7
  - John T. Prince
@@ -10,12 +9,11 @@ authors:
10
9
  autorequire:
11
10
  bindir: bin
12
11
  cert_chain: []
13
- date: 2013-05-29 00:00:00.000000000 Z
12
+ date: 2013-07-31 00:00:00.000000000 Z
14
13
  dependencies:
15
14
  - !ruby/object:Gem::Dependency
16
15
  name: nokogiri
17
16
  requirement: !ruby/object:Gem::Requirement
18
- none: false
19
17
  requirements:
20
18
  - - ~>
21
19
  - !ruby/object:Gem::Version
@@ -23,7 +21,6 @@ dependencies:
23
21
  type: :runtime
24
22
  prerelease: false
25
23
  version_requirements: !ruby/object:Gem::Requirement
26
- none: false
27
24
  requirements:
28
25
  - - ~>
29
26
  - !ruby/object:Gem::Version
@@ -31,55 +28,48 @@ dependencies:
31
28
  - !ruby/object:Gem::Dependency
32
29
  name: bsearch
33
30
  requirement: !ruby/object:Gem::Requirement
34
- none: false
35
31
  requirements:
36
- - - ! '>='
32
+ - - '>='
37
33
  - !ruby/object:Gem::Version
38
34
  version: 1.5.0
39
35
  type: :runtime
40
36
  prerelease: false
41
37
  version_requirements: !ruby/object:Gem::Requirement
42
- none: false
43
38
  requirements:
44
- - - ! '>='
39
+ - - '>='
45
40
  - !ruby/object:Gem::Version
46
41
  version: 1.5.0
47
42
  - !ruby/object:Gem::Dependency
48
43
  name: andand
49
44
  requirement: !ruby/object:Gem::Requirement
50
- none: false
51
45
  requirements:
52
- - - ! '>='
46
+ - - '>='
53
47
  - !ruby/object:Gem::Version
54
48
  version: 1.3.3
55
49
  type: :runtime
56
50
  prerelease: false
57
51
  version_requirements: !ruby/object:Gem::Requirement
58
- none: false
59
52
  requirements:
60
- - - ! '>='
53
+ - - '>='
61
54
  - !ruby/object:Gem::Version
62
55
  version: 1.3.3
63
56
  - !ruby/object:Gem::Dependency
64
57
  name: obo
65
58
  requirement: !ruby/object:Gem::Requirement
66
- none: false
67
59
  requirements:
68
- - - ! '>='
60
+ - - '>='
69
61
  - !ruby/object:Gem::Version
70
62
  version: 0.1.3
71
63
  type: :runtime
72
64
  prerelease: false
73
65
  version_requirements: !ruby/object:Gem::Requirement
74
- none: false
75
66
  requirements:
76
- - - ! '>='
67
+ - - '>='
77
68
  - !ruby/object:Gem::Version
78
69
  version: 0.1.3
79
70
  - !ruby/object:Gem::Dependency
80
71
  name: builder
81
72
  requirement: !ruby/object:Gem::Requirement
82
- none: false
83
73
  requirements:
84
74
  - - ~>
85
75
  - !ruby/object:Gem::Version
@@ -87,7 +77,6 @@ dependencies:
87
77
  type: :runtime
88
78
  prerelease: false
89
79
  version_requirements: !ruby/object:Gem::Requirement
90
- none: false
91
80
  requirements:
92
81
  - - ~>
93
82
  - !ruby/object:Gem::Version
@@ -95,7 +84,6 @@ dependencies:
95
84
  - !ruby/object:Gem::Dependency
96
85
  name: bio
97
86
  requirement: !ruby/object:Gem::Requirement
98
- none: false
99
87
  requirements:
100
88
  - - ~>
101
89
  - !ruby/object:Gem::Version
@@ -103,7 +91,6 @@ dependencies:
103
91
  type: :runtime
104
92
  prerelease: false
105
93
  version_requirements: !ruby/object:Gem::Requirement
106
- none: false
107
94
  requirements:
108
95
  - - ~>
109
96
  - !ruby/object:Gem::Version
@@ -111,7 +98,6 @@ dependencies:
111
98
  - !ruby/object:Gem::Dependency
112
99
  name: trollop
113
100
  requirement: !ruby/object:Gem::Requirement
114
- none: false
115
101
  requirements:
116
102
  - - ~>
117
103
  - !ruby/object:Gem::Version
@@ -119,73 +105,123 @@ dependencies:
119
105
  type: :runtime
120
106
  prerelease: false
121
107
  version_requirements: !ruby/object:Gem::Requirement
122
- none: false
123
108
  requirements:
124
109
  - - ~>
125
110
  - !ruby/object:Gem::Version
126
111
  version: 2.0.0
127
112
  - !ruby/object:Gem::Dependency
128
- name: fftw3
113
+ name: bundler
129
114
  requirement: !ruby/object:Gem::Requirement
130
- none: false
131
115
  requirements:
132
116
  - - ~>
133
117
  - !ruby/object:Gem::Version
134
- version: '0.3'
118
+ version: '1.3'
135
119
  type: :development
136
120
  prerelease: false
137
121
  version_requirements: !ruby/object:Gem::Requirement
138
- none: false
139
122
  requirements:
140
123
  - - ~>
141
124
  - !ruby/object:Gem::Version
142
- version: '0.3'
125
+ version: '1.3'
126
+ - !ruby/object:Gem::Dependency
127
+ name: rake
128
+ requirement: !ruby/object:Gem::Requirement
129
+ requirements:
130
+ - - '>='
131
+ - !ruby/object:Gem::Version
132
+ version: '0'
133
+ type: :development
134
+ prerelease: false
135
+ version_requirements: !ruby/object:Gem::Requirement
136
+ requirements:
137
+ - - '>='
138
+ - !ruby/object:Gem::Version
139
+ version: '0'
143
140
  - !ruby/object:Gem::Dependency
144
141
  name: rspec
145
142
  requirement: !ruby/object:Gem::Requirement
146
- none: false
147
143
  requirements:
148
144
  - - ~>
149
145
  - !ruby/object:Gem::Version
150
- version: '2.13'
146
+ version: 2.13.0
151
147
  type: :development
152
148
  prerelease: false
153
149
  version_requirements: !ruby/object:Gem::Requirement
154
- none: false
155
150
  requirements:
156
151
  - - ~>
157
152
  - !ruby/object:Gem::Version
158
- version: '2.13'
153
+ version: 2.13.0
159
154
  - !ruby/object:Gem::Dependency
160
- name: jeweler
155
+ name: rdoc
161
156
  requirement: !ruby/object:Gem::Requirement
162
- none: false
163
157
  requirements:
164
158
  - - ~>
165
159
  - !ruby/object:Gem::Version
166
- version: 1.8.4
160
+ version: '3.12'
167
161
  type: :development
168
162
  prerelease: false
169
163
  version_requirements: !ruby/object:Gem::Requirement
170
- none: false
171
164
  requirements:
172
165
  - - ~>
173
166
  - !ruby/object:Gem::Version
174
- version: 1.8.4
167
+ version: '3.12'
168
+ - !ruby/object:Gem::Dependency
169
+ name: simplecov
170
+ requirement: !ruby/object:Gem::Requirement
171
+ requirements:
172
+ - - '>='
173
+ - !ruby/object:Gem::Version
174
+ version: '0'
175
+ type: :development
176
+ prerelease: false
177
+ version_requirements: !ruby/object:Gem::Requirement
178
+ requirements:
179
+ - - '>='
180
+ - !ruby/object:Gem::Version
181
+ version: '0'
182
+ - !ruby/object:Gem::Dependency
183
+ name: coveralls
184
+ requirement: !ruby/object:Gem::Requirement
185
+ requirements:
186
+ - - '>='
187
+ - !ruby/object:Gem::Version
188
+ version: '0'
189
+ type: :development
190
+ prerelease: false
191
+ version_requirements: !ruby/object:Gem::Requirement
192
+ requirements:
193
+ - - '>='
194
+ - !ruby/object:Gem::Version
195
+ version: '0'
196
+ - !ruby/object:Gem::Dependency
197
+ name: fftw3
198
+ requirement: !ruby/object:Gem::Requirement
199
+ requirements:
200
+ - - ~>
201
+ - !ruby/object:Gem::Version
202
+ version: '0.3'
203
+ type: :development
204
+ prerelease: false
205
+ version_requirements: !ruby/object:Gem::Requirement
206
+ requirements:
207
+ - - ~>
208
+ - !ruby/object:Gem::Version
209
+ version: '0.3'
175
210
  description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
176
211
  merging of ms-* gems
177
- email: jtprince@gmail.com
212
+ email:
213
+ - jtprince@gmail.com
178
214
  executables:
179
215
  - mspire
180
216
  extensions: []
181
- extra_rdoc_files:
182
- - LICENSE
183
- - README.md
217
+ extra_rdoc_files: []
184
218
  files:
219
+ - .gitignore
220
+ - .travis.yml
221
+ - Gemfile
185
222
  - LICENSE
186
223
  - README.md
187
224
  - Rakefile
188
- - VERSION
189
225
  - bin/mspire
190
226
  - lib/core_ext/array/in_groups.rb
191
227
  - lib/core_ext/enumerable.rb
@@ -288,6 +324,7 @@ files:
288
324
  - lib/mspire/spectrum_like.rb
289
325
  - lib/mspire/tagged_peak.rb
290
326
  - lib/mspire/user_param.rb
327
+ - lib/mspire/version.rb
291
328
  - lib/obo/ims.rb
292
329
  - lib/obo/ms.rb
293
330
  - lib/obo/ontology.rb
@@ -295,6 +332,7 @@ files:
295
332
  - lib/openany.rb
296
333
  - lib/write_file_or_string.rb
297
334
  - obo/ims.obo
335
+ - obo/mod.obo
298
336
  - obo/ms.obo
299
337
  - obo/unit.obo
300
338
  - schema/peptide_hit_qvalues.pqh.tsv
@@ -348,6 +386,7 @@ files:
348
386
  - spec/mspire_spec.rb
349
387
  - spec/obo_spec.rb
350
388
  - spec/spec_helper.rb
389
+ - spec/spec_utilities.rb
351
390
  - spec/testfiles/continuous_binary.tmp.ibd
352
391
  - spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.PEPTIDE_CENTRIC.yml
353
392
  - spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.fasta
@@ -386,26 +425,101 @@ files:
386
425
  homepage: http://github.com/princelab/mspire
387
426
  licenses:
388
427
  - MIT
428
+ metadata: {}
389
429
  post_install_message:
390
430
  rdoc_options: []
391
431
  require_paths:
392
432
  - lib
393
433
  required_ruby_version: !ruby/object:Gem::Requirement
394
- none: false
395
434
  requirements:
396
- - - ! '>='
435
+ - - '>='
397
436
  - !ruby/object:Gem::Version
398
437
  version: '0'
399
438
  required_rubygems_version: !ruby/object:Gem::Requirement
400
- none: false
401
439
  requirements:
402
- - - ! '>='
440
+ - - '>='
403
441
  - !ruby/object:Gem::Version
404
442
  version: '0'
405
443
  requirements: []
406
444
  rubyforge_project:
407
- rubygems_version: 1.8.23
445
+ rubygems_version: 2.0.3
408
446
  signing_key:
409
- specification_version: 3
447
+ specification_version: 4
410
448
  summary: mass spectrometry proteomics, lipidomics, and tools
411
- test_files: []
449
+ test_files:
450
+ - spec/cv/param_spec.rb
451
+ - spec/mspire/bin_spec.rb
452
+ - spec/mspire/cv/obo_spec.rb
453
+ - spec/mspire/cv/param_spec.rb
454
+ - spec/mspire/cv/paramable_spec.rb
455
+ - spec/mspire/digester_spec.rb
456
+ - spec/mspire/error_rate/qvalue_spec.rb
457
+ - spec/mspire/fasta_spec.rb
458
+ - spec/mspire/ident/peptide/db/creator_spec.rb
459
+ - spec/mspire/ident/peptide/db/io_spec.rb
460
+ - spec/mspire/ident/peptide/db_spec.rb
461
+ - spec/mspire/ident/pepxml/sample_enzyme_spec.rb
462
+ - spec/mspire/ident/pepxml/search_hit/modification_info_spec.rb
463
+ - spec/mspire/ident/pepxml_spec.rb
464
+ - spec/mspire/ident/protein_group_spec.rb
465
+ - spec/mspire/imzml/writer_spec.rb
466
+ - spec/mspire/isotope/aa_spec.rb
467
+ - spec/mspire/isotope/distribution_spec.rb
468
+ - spec/mspire/isotope_spec.rb
469
+ - spec/mspire/mass_spec.rb
470
+ - spec/mspire/molecular_formula_spec.rb
471
+ - spec/mspire/mzml/cv_spec.rb
472
+ - spec/mspire/mzml/data_array_spec.rb
473
+ - spec/mspire/mzml/file_content_spec.rb
474
+ - spec/mspire/mzml/index_list_spec.rb
475
+ - spec/mspire/mzml/plms1_spec.rb
476
+ - spec/mspire/mzml/referenceable_param_group_spec.rb
477
+ - spec/mspire/mzml/source_file_spec.rb
478
+ - spec/mspire/mzml/spectrum_list_spec.rb
479
+ - spec/mspire/mzml/spectrum_spec.rb
480
+ - spec/mspire/mzml_spec.rb
481
+ - spec/mspire/peaklist_spec.rb
482
+ - spec/mspire/plms1_spec.rb
483
+ - spec/mspire/quant/qspec_spec.rb
484
+ - spec/mspire/readme_spec.rb
485
+ - spec/mspire/spectrum_spec.rb
486
+ - spec/mspire/user_param_spec.rb
487
+ - spec/mspire_spec.rb
488
+ - spec/obo_spec.rb
489
+ - spec/spec_helper.rb
490
+ - spec/spec_utilities.rb
491
+ - spec/testfiles/continuous_binary.tmp.ibd
492
+ - spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.PEPTIDE_CENTRIC.yml
493
+ - spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.fasta
494
+ - spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml
495
+ - spec/testfiles/mspire/imzml/1_BB7_SIM_478.5.CHECK.ibd
496
+ - spec/testfiles/mspire/imzml/1_BB7_SIM_478.5.CHECK.imzML
497
+ - spec/testfiles/mspire/imzml/continuous_binary.CHECK.ibd
498
+ - spec/testfiles/mspire/imzml/processed_binary.CHECK.ibd
499
+ - spec/testfiles/mspire/mzml/1_BB7_SIM_478.5.mzML
500
+ - spec/testfiles/mspire/mzml/j24z.idx_comp.3.NORMALIZED.CHECK.mzML
501
+ - spec/testfiles/mspire/mzml/j24z.idx_comp.3.ROUNDTRIP.CHECK.mzML
502
+ - spec/testfiles/mspire/mzml/j24z.idx_comp.3.mzML
503
+ - spec/testfiles/mspire/mzml/mspire_simulated.MSn.CHECK.mzML
504
+ - spec/testfiles/mspire/mzml/openms.noidx_nocomp.12.mzML
505
+ - spec/testfiles/mspire/quant/kill_extra_tabs.rb
506
+ - spec/testfiles/mspire/quant/max_quant_output.provenance.txt
507
+ - spec/testfiles/mspire/quant/max_quant_output.txt
508
+ - spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv
509
+ - spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv_qspecgp
510
+ - spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv_qspecgp.csv
511
+ - spec/testfiles/mspire/quant/pdcd5_final.txt
512
+ - spec/testfiles/mspire/quant/pdcd5_final.txt_qspecgp
513
+ - spec/testfiles/mspire/quant/pdcd5_lfq_qspec.CSV.csv
514
+ - spec/testfiles/mspire/quant/pdcd5_lfq_qspec.csv
515
+ - spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.csv
516
+ - spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv
517
+ - spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp
518
+ - spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp.csv
519
+ - spec/testfiles/mspire/quant/pdcd5_lfq_qspec.txt
520
+ - spec/testfiles/mspire/quant/pdcd5_lfq_tabdel.txt
521
+ - spec/testfiles/mspire/quant/pdcd5_lfq_tabdel.txt_qspecgp
522
+ - spec/testfiles/mspire/quant/remove_rest_of_proteins.rb
523
+ - spec/testfiles/mspire/quant/unlog_transform.rb
524
+ - spec/testfiles/plms1/output.key
525
+ - spec/testfiles/processed_binary.tmp.ibd
data/VERSION DELETED
@@ -1 +0,0 @@
1
- 0.8.6.2