mspire 0.8.6.2 → 0.8.7

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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
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  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