mspire 0.3.9 → 0.4.2

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 (87) hide show
  1. data/INSTALL +24 -7
  2. data/README +15 -13
  3. data/README.rdoc +18 -0
  4. data/Rakefile +50 -14
  5. data/bin/aafreqs.rb +0 -0
  6. data/bin/bioworks2excel.rb +0 -0
  7. data/bin/bioworks_to_pepxml.rb +2 -1
  8. data/bin/bioworks_to_pepxml_gui.rb +0 -0
  9. data/bin/fasta_shaker.rb +0 -0
  10. data/bin/filter_and_validate.rb +0 -0
  11. data/bin/gi2annot.rb +0 -0
  12. data/bin/id_class_anal.rb +0 -0
  13. data/bin/id_precision.rb +0 -0
  14. data/bin/ms_to_lmat.rb +0 -0
  15. data/bin/pepproph_filter.rb +0 -0
  16. data/bin/protein_summary.rb +0 -0
  17. data/bin/protxml2prots_peps.rb +0 -0
  18. data/bin/raw_to_mzXML.rb +3 -3
  19. data/bin/run_percolator.rb +122 -0
  20. data/bin/sqt_group.rb +0 -0
  21. data/bin/srf_group.rb +0 -0
  22. data/changelog.txt +29 -0
  23. data/lib/ms/gradient_program.rb +0 -1
  24. data/lib/ms/msrun.rb +62 -29
  25. data/lib/ms/parser/mzdata/axml.rb +55 -0
  26. data/lib/ms/parser/mzdata/dom.rb +51 -36
  27. data/lib/ms/parser/mzdata.rb +8 -2
  28. data/lib/ms/parser/mzxml/axml.rb +59 -0
  29. data/lib/ms/parser/mzxml/dom.rb +80 -57
  30. data/lib/ms/parser/mzxml/hpricot.rb +1 -1
  31. data/lib/ms/parser/mzxml/libxml.rb +6 -2
  32. data/lib/ms/parser/mzxml.rb +110 -3
  33. data/lib/ms/parser.rb +4 -4
  34. data/lib/ms/precursor.rb +19 -4
  35. data/lib/ms/scan.rb +7 -7
  36. data/lib/ms/spectrum.rb +249 -58
  37. data/lib/mspire.rb +1 -1
  38. data/lib/spec_id/bioworks.rb +2 -2
  39. data/lib/spec_id/precision/filter/cmdline.rb +8 -1
  40. data/lib/spec_id/precision/prob/cmdline.rb +2 -2
  41. data/lib/spec_id/precision/prob.rb +1 -0
  42. data/lib/spec_id/proph/pep_summary.rb +3 -4
  43. data/lib/spec_id/proph/prot_summary.rb +3 -3
  44. data/lib/spec_id/protein_summary.rb +1 -1
  45. data/lib/spec_id/sequest/pepxml.rb +5 -5
  46. data/lib/spec_id/sqt.rb +4 -4
  47. data/lib/spec_id/srf.rb +49 -8
  48. data/lib/spec_id.rb +5 -0
  49. data/lib/xml_style_parser.rb +16 -2
  50. data/script/compile_and_plot_smriti_final.rb +0 -0
  51. data/script/create_little_pepxml.rb +0 -0
  52. data/script/degenerate_peptides.rb +0 -0
  53. data/script/estimate_fpr_by_cysteine.rb +0 -0
  54. data/script/extract_gradient_programs.rb +1 -1
  55. data/script/find_cysteine_background.rb +0 -0
  56. data/script/genuine_tps_and_probs.rb +0 -0
  57. data/script/get_apex_values_rexml.rb +0 -0
  58. data/script/mascot_fix_pepxml.rb +123 -0
  59. data/script/msvis.rb +0 -0
  60. data/script/mzXML2timeIndex.rb +0 -0
  61. data/script/peps_per_bin.rb +0 -0
  62. data/script/prep_dir.rb +0 -0
  63. data/script/simple_protein_digestion.rb +0 -0
  64. data/script/smriti_final_analysis.rb +0 -0
  65. data/script/sqt_to_meta.rb +0 -0
  66. data/script/top_hit_per_scan.rb +0 -0
  67. data/script/toppred_to_yaml.rb +0 -0
  68. data/script/tpp_installer.rb +0 -0
  69. data/specs/bin/prob_validate_spec.rb +5 -2
  70. data/specs/bin/protein_summary_spec.rb +5 -1
  71. data/specs/ms/msrun_spec.rb +176 -133
  72. data/specs/ms/parser_spec.rb +3 -3
  73. data/specs/ms/spectrum_spec.rb +0 -2
  74. data/specs/spec_id/precision/filter_spec.rb +4 -1
  75. data/specs/spec_id/precision/prob_spec.rb +2 -2
  76. data/specs/spec_id/sequest/pepxml_spec.rb +1 -1
  77. data/specs/spec_id/sqt_spec.rb +5 -5
  78. data/specs/spec_id/srf_spec.rb +56 -93
  79. data/specs/spec_id/srf_spec_helper.rb +121 -284
  80. data/specs/spec_id_spec.rb +3 -0
  81. data/specs/transmem/toppred_spec.rb +1 -0
  82. data/test_files/opd1_2runs_2mods/data/020.mzData.xml +683 -0
  83. data/test_files/opd1_2runs_2mods/data/020.readw.mzXML +382 -0
  84. data/test_files/opd1_2runs_2mods/data/040.mzData.xml +683 -0
  85. data/test_files/opd1_2runs_2mods/data/040.readw.mzXML +382 -0
  86. data/test_files/opd1_2runs_2mods/data/README.txt +6 -0
  87. metadata +247 -229
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: 0.3.9
4
+ version: 0.4.2
5
5
  platform: ruby
6
6
  authors:
7
7
  - John Prince
@@ -9,7 +9,7 @@ autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
11
 
12
- date: 2008-01-24 00:00:00 -06:00
12
+ date: 2008-08-06 00:00:00 -06:00
13
13
  default_executable:
14
14
  dependencies:
15
15
  - !ruby/object:Gem::Dependency
@@ -19,7 +19,7 @@ dependencies:
19
19
  requirements:
20
20
  - - ~>
21
21
  - !ruby/object:Gem::Version
22
- version: 0.2.13
22
+ version: 0.2.14
23
23
  version:
24
24
  - !ruby/object:Gem::Dependency
25
25
  name: axml
@@ -30,301 +30,319 @@ dependencies:
30
30
  - !ruby/object:Gem::Version
31
31
  version: 0.0.0
32
32
  version:
33
+ - !ruby/object:Gem::Dependency
34
+ name: arrayclass
35
+ version_requirement:
36
+ version_requirements: !ruby/object:Gem::Requirement
37
+ requirements:
38
+ - - ~>
39
+ - !ruby/object:Gem::Version
40
+ version: 0.1.0
41
+ version:
33
42
  description: mspire is for working with mass spectrometry proteomics data
34
43
  email: jprince@icmb.utexas.edu
35
44
  executables:
36
- - aafreqs.rb
37
- - prob_validate.rb
38
45
  - gi2annot.rb
39
- - bioworks_to_pepxml_gui.rb
46
+ - protxml2prots_peps.rb
40
47
  - filter_and_validate.rb
41
- - pepproph_filter.rb
42
- - bioworks2excel.rb
43
- - srf_group.rb
44
48
  - raw_to_mzXML.rb
45
- - fasta_shaker.rb
46
- - sqt_group.rb
49
+ - run_percolator.rb
47
50
  - srf_to_sqt.rb
48
- - bioworks_to_pepxml.rb
49
- - id_precision.rb
50
- - protein_summary.rb
51
- - protxml2prots_peps.rb
51
+ - prob_validate.rb
52
+ - srf_group.rb
52
53
  - ms_to_lmat.rb
54
+ - protein_summary.rb
55
+ - bioworks_to_pepxml_gui.rb
53
56
  - id_class_anal.rb
57
+ - id_precision.rb
58
+ - sqt_group.rb
59
+ - aafreqs.rb
60
+ - pepproph_filter.rb
61
+ - bioworks2excel.rb
62
+ - bioworks_to_pepxml.rb
63
+ - fasta_shaker.rb
54
64
  extensions: []
55
65
 
56
66
  extra_rdoc_files:
57
- - README
58
- - INSTALL
59
- - LICENSE
67
+ - README.rdoc
60
68
  files:
61
69
  - INSTALL
62
70
  - README
71
+ - README.rdoc
63
72
  - Rakefile
64
73
  - LICENSE
65
74
  - changelog.txt
66
75
  - release_notes.txt
76
+ - lib/ms
77
+ - lib/ms/parser
78
+ - lib/ms/parser/mzxml
79
+ - lib/ms/parser/mzxml/rexml.rb
80
+ - lib/ms/parser/mzxml/libxml.rb
81
+ - lib/ms/parser/mzxml/xmlparser.rb
82
+ - lib/ms/parser/mzxml/regexp.rb
83
+ - lib/ms/parser/mzxml/axml.rb
84
+ - lib/ms/parser/mzxml/hpricot.rb
85
+ - lib/ms/parser/mzxml/dom.rb
86
+ - lib/ms/parser/mzdata
87
+ - lib/ms/parser/mzdata/libxml.rb
88
+ - lib/ms/parser/mzdata/axml.rb
89
+ - lib/ms/parser/mzdata/dom.rb
90
+ - lib/ms/parser/mzdata.rb
91
+ - lib/ms/parser/mzxml.rb
92
+ - lib/ms/msrun.rb
93
+ - lib/ms/gradient_program.rb
94
+ - lib/ms/precursor.rb
95
+ - lib/ms/msrun_index.rb
96
+ - lib/ms/parser.rb
97
+ - lib/ms/spectrum.rb
98
+ - lib/ms/converter
99
+ - lib/ms/converter/mzxml.rb
100
+ - lib/ms/scan.rb
67
101
  - lib/scan_i.rb
68
- - lib/mspire.rb
102
+ - lib/fasta.rb
103
+ - lib/roc.rb
104
+ - lib/spec_id.rb
105
+ - lib/xml.rb
106
+ - lib/group_by.rb
107
+ - lib/index_by.rb
108
+ - lib/sample_enzyme.rb
69
109
  - lib/transmem
70
110
  - lib/transmem/phobius.rb
71
111
  - lib/transmem/toppred.rb
72
- - lib/group_by.rb
73
- - lib/align.rb
74
- - lib/sample_enzyme.rb
75
- - lib/xml.rb
76
- - lib/fasta.rb
77
- - lib/spec_id_xml.rb
112
+ - lib/ms.rb
78
113
  - lib/spec_id
114
+ - lib/spec_id/srf.rb
79
115
  - lib/spec_id/sequest.rb
80
- - lib/spec_id/digestor.rb
81
- - lib/spec_id/sqt.rb
82
- - lib/spec_id/proph
83
- - lib/spec_id/proph/pep_summary.rb
84
- - lib/spec_id/proph/prot_summary.rb
85
- - lib/spec_id/bioworks.rb
86
116
  - lib/spec_id/parser
87
117
  - lib/spec_id/parser/proph.rb
88
- - lib/spec_id/protein_summary.rb
89
- - lib/spec_id/aa_freqs.rb
118
+ - lib/spec_id/sequest
119
+ - lib/spec_id/sequest/params.rb
120
+ - lib/spec_id/sequest/pepxml.rb
90
121
  - lib/spec_id/precision
122
+ - lib/spec_id/precision/filter.rb
91
123
  - lib/spec_id/precision/prob.rb
92
124
  - lib/spec_id/precision/output.rb
93
125
  - lib/spec_id/precision/filter
94
- - lib/spec_id/precision/filter/output.rb
95
126
  - lib/spec_id/precision/filter/interactive.rb
96
127
  - lib/spec_id/precision/filter/cmdline.rb
97
- - lib/spec_id/precision/filter.rb
128
+ - lib/spec_id/precision/filter/output.rb
98
129
  - lib/spec_id/precision/prob
99
- - lib/spec_id/precision/prob/output.rb
100
130
  - lib/spec_id/precision/prob/cmdline.rb
101
- - lib/spec_id/sequest
102
- - lib/spec_id/sequest/params.rb
103
- - lib/spec_id/sequest/pepxml.rb
104
- - lib/spec_id/proph.rb
131
+ - lib/spec_id/precision/prob/output.rb
105
132
  - lib/spec_id/mass.rb
106
- - lib/spec_id/srf.rb
107
- - lib/ms.rb
133
+ - lib/spec_id/proph
134
+ - lib/spec_id/proph/pep_summary.rb
135
+ - lib/spec_id/proph/prot_summary.rb
136
+ - lib/spec_id/protein_summary.rb
137
+ - lib/spec_id/proph.rb
138
+ - lib/spec_id/aa_freqs.rb
139
+ - lib/spec_id/digestor.rb
140
+ - lib/spec_id/sqt.rb
141
+ - lib/spec_id/bioworks.rb
142
+ - lib/merge_deep.rb
143
+ - lib/align.rb
144
+ - lib/xmlparser_wrapper.rb
145
+ - lib/transmem.rb
146
+ - lib/align
147
+ - lib/align/chams.rb
148
+ - lib/validator.rb
108
149
  - lib/gi.rb
109
- - lib/roc.rb
110
- - lib/index_by.rb
111
150
  - lib/validator
112
- - lib/validator/background.rb
151
+ - lib/validator/prot_from_pep.rb
152
+ - lib/validator/aa.rb
153
+ - lib/validator/decoy.rb
154
+ - lib/validator/true_pos.rb
113
155
  - lib/validator/aa_est.rb
156
+ - lib/validator/probability.rb
114
157
  - lib/validator/cmdline.rb
115
- - lib/validator/aa.rb
116
158
  - lib/validator/digestion_based.rb
117
- - lib/validator/probability.rb
118
- - lib/validator/prot_from_pep.rb
119
- - lib/validator/q_value.rb
120
- - lib/validator/true_pos.rb
121
- - lib/validator/bias.rb
122
- - lib/validator/decoy.rb
123
159
  - lib/validator/transmem.rb
124
- - lib/spec_id.rb
160
+ - lib/validator/bias.rb
161
+ - lib/validator/background.rb
162
+ - lib/validator/q_value.rb
125
163
  - lib/xml_style_parser.rb
164
+ - lib/mspire.rb
165
+ - lib/spec_id_xml.rb
126
166
  - lib/bsearch.rb
127
- - lib/validator.rb
128
- - lib/merge_deep.rb
129
- - lib/align
130
- - lib/align/chams.rb
131
- - lib/ms
132
- - lib/ms/msrun.rb
133
- - lib/ms/scan.rb
134
- - lib/ms/converter
135
- - lib/ms/converter/mzxml.rb
136
- - lib/ms/msrun_index.rb
137
- - lib/ms/spectrum.rb
138
- - lib/ms/parser
139
- - lib/ms/parser/mzxml
140
- - lib/ms/parser/mzxml/rexml.rb
141
- - lib/ms/parser/mzxml/libxml.rb
142
- - lib/ms/parser/mzxml/xmlparser.rb
143
- - lib/ms/parser/mzxml/dom.rb
144
- - lib/ms/parser/mzxml/regexp.rb
145
- - lib/ms/parser/mzxml/hpricot.rb
146
- - lib/ms/parser/mzxml/axml.rb
147
- - lib/ms/parser/mzdata
148
- - lib/ms/parser/mzdata/libxml.rb
149
- - lib/ms/parser/mzdata/dom.rb
150
- - lib/ms/parser/mzdata/axml.rb
151
- - lib/ms/parser/mzdata.rb
152
- - lib/ms/parser/mzxml.rb
153
- - lib/ms/gradient_program.rb
154
- - lib/ms/parser.rb
155
- - lib/ms/precursor.rb
156
- - lib/xmlparser_wrapper.rb
157
- - lib/transmem.rb
158
- - bin/aafreqs.rb
159
- - bin/prob_validate.rb
160
167
  - bin/gi2annot.rb
161
- - bin/bioworks_to_pepxml_gui.rb
168
+ - bin/protxml2prots_peps.rb
162
169
  - bin/filter_and_validate.rb
163
- - bin/pepproph_filter.rb
164
- - bin/bioworks2excel.rb
165
- - bin/srf_group.rb
166
170
  - bin/raw_to_mzXML.rb
167
- - bin/fasta_shaker.rb
168
- - bin/sqt_group.rb
171
+ - bin/run_percolator.rb
169
172
  - bin/srf_to_sqt.rb
170
- - bin/bioworks_to_pepxml.rb
171
- - bin/id_precision.rb
172
- - bin/protein_summary.rb
173
- - bin/protxml2prots_peps.rb
173
+ - bin/prob_validate.rb
174
+ - bin/srf_group.rb
174
175
  - bin/ms_to_lmat.rb
176
+ - bin/protein_summary.rb
177
+ - bin/bioworks_to_pepxml_gui.rb
175
178
  - bin/id_class_anal.rb
176
- - script/histogram_probs.rb
177
- - script/extract_gradient_programs.rb
178
- - script/find_cysteine_background.rb
179
+ - bin/id_precision.rb
180
+ - bin/sqt_group.rb
181
+ - bin/aafreqs.rb
182
+ - bin/pepproph_filter.rb
183
+ - bin/bioworks2excel.rb
184
+ - bin/bioworks_to_pepxml.rb
185
+ - bin/fasta_shaker.rb
179
186
  - script/estimate_fpr_by_cysteine.rb
180
- - script/msvis.rb
181
187
  - script/toppred_to_yaml.rb
182
- - script/peps_per_bin.rb
183
- - script/create_little_pepxml.rb
184
- - script/sqt_to_meta.rb
185
- - script/compile_and_plot_smriti_final.rb
186
- - script/tpp_installer.rb
187
- - script/genuine_tps_and_probs.rb
188
- - script/get_apex_values_rexml.rb
188
+ - script/extract_gradient_programs.rb
189
189
  - script/mzXML2timeIndex.rb
190
+ - script/genuine_tps_and_probs.rb
191
+ - script/histogram_probs.rb
192
+ - script/find_cysteine_background.rb
190
193
  - script/degenerate_peptides.rb
191
- - script/top_hit_per_scan.rb
192
194
  - script/prep_dir.rb
195
+ - script/compile_and_plot_smriti_final.rb
196
+ - script/tpp_installer.rb
197
+ - script/mascot_fix_pepxml.rb
198
+ - script/top_hit_per_scan.rb
199
+ - script/create_little_pepxml.rb
193
200
  - script/smriti_final_analysis.rb
201
+ - script/get_apex_values_rexml.rb
202
+ - script/sqt_to_meta.rb
203
+ - script/msvis.rb
194
204
  - script/simple_protein_digestion.rb
195
- - specs/gi_spec.rb
205
+ - script/peps_per_bin.rb
206
+ - specs/ms
207
+ - specs/ms/parser
208
+ - specs/ms/gradient_program_spec.rb
209
+ - specs/ms/parser_spec.rb
210
+ - specs/ms/spectrum_spec.rb
211
+ - specs/ms/msrun_spec.rb
212
+ - specs/merge_deep_spec.rb
213
+ - specs/spec_helper.rb
214
+ - specs/fasta_spec.rb
196
215
  - specs/transmem
197
216
  - specs/transmem/phobius_spec.rb
198
217
  - specs/transmem/toppred_spec.rb
199
218
  - specs/align_spec.rb
200
- - specs/fasta_spec.rb
219
+ - specs/spec_id_helper.rb
201
220
  - specs/transmem_spec.rb
202
221
  - specs/spec_id
203
- - specs/spec_id/sequest_spec.rb
204
- - specs/spec_id/proph
205
- - specs/spec_id/proph/prot_summary_spec.rb
206
- - specs/spec_id/proph/pep_summary_spec.rb
207
222
  - specs/spec_id/protein_summary_spec.rb
208
- - specs/spec_id/srf_spec_helper.rb
209
- - specs/spec_id/digestor_spec.rb
223
+ - specs/spec_id/bioworks_spec.rb
210
224
  - specs/spec_id/sqt_spec.rb
211
- - specs/spec_id/aa_freqs_spec.rb
212
- - specs/spec_id/srf_spec.rb
225
+ - specs/spec_id/sequest
226
+ - specs/spec_id/sequest/pepxml_spec.rb
227
+ - specs/spec_id/sequest/params_spec.rb
213
228
  - specs/spec_id/precision
229
+ - specs/spec_id/precision/filter_spec.rb
230
+ - specs/spec_id/precision/prob_spec_helper.rb
231
+ - specs/spec_id/precision/prob_spec.rb
214
232
  - specs/spec_id/precision/filter
215
233
  - specs/spec_id/precision/filter/cmdline_spec.rb
216
234
  - specs/spec_id/precision/filter/output_spec.rb
217
- - specs/spec_id/precision/prob_spec.rb
218
- - specs/spec_id/precision/filter_spec.rb
219
- - specs/spec_id/precision/prob_spec_helper.rb
220
- - specs/spec_id/sequest
221
- - specs/spec_id/sequest/pepxml_spec.rb
222
- - specs/spec_id/sequest/params_spec.rb
223
- - specs/spec_id/bioworks_spec.rb
235
+ - specs/spec_id/proph
236
+ - specs/spec_id/proph/prot_summary_spec.rb
237
+ - specs/spec_id/proph/pep_summary_spec.rb
238
+ - specs/spec_id/srf_spec.rb
239
+ - specs/spec_id/srf_spec_helper.rb
240
+ - specs/spec_id/sequest_spec.rb
241
+ - specs/spec_id/digestor_spec.rb
242
+ - specs/spec_id/aa_freqs_spec.rb
243
+ - specs/rspec_autotest.rb
244
+ - specs/xml_spec.rb
245
+ - specs/sample_enzyme_spec.rb
246
+ - specs/transmem_spec_shared.rb
247
+ - specs/gi_spec.rb
248
+ - specs/load_bin_path.rb
224
249
  - specs/spec_id_spec.rb
225
- - specs/roc_spec.rb
226
- - specs/spec_id_helper.rb
227
- - specs/merge_deep_spec.rb
228
250
  - specs/validator
229
- - specs/validator/aa_spec.rb
230
- - specs/validator/transmem_spec.rb
231
- - specs/validator/decoy_spec.rb
232
- - specs/validator/bias_spec.rb
233
251
  - specs/validator/true_pos_spec.rb
252
+ - specs/validator/aa_est_spec.rb
253
+ - specs/validator/background_spec.rb
254
+ - specs/validator/bias_spec.rb
255
+ - specs/validator/transmem_spec.rb
234
256
  - specs/validator/prot_from_pep_spec.rb
257
+ - specs/validator/decoy_spec.rb
258
+ - specs/validator/aa_spec.rb
235
259
  - specs/validator/fasta_helper.rb
236
- - specs/validator/background_spec.rb
237
- - specs/validator/aa_est_spec.rb
238
- - specs/transmem_spec_shared.rb
239
260
  - specs/bin
261
+ - specs/bin/filter_and_validate__multiple_vals_helper.yaml
262
+ - specs/bin/protein_summary_spec.rb
263
+ - specs/bin/filter_and_validate_spec.rb
240
264
  - specs/bin/ms_to_lmat_spec.rb
265
+ - specs/bin/fasta_shaker_spec.rb
241
266
  - specs/bin/bioworks_to_pepxml_spec.rb
242
267
  - specs/bin/prob_validate_spec.rb
243
- - specs/bin/protein_summary_spec.rb
244
- - specs/bin/fasta_shaker_spec.rb
245
- - specs/bin/filter_and_validate__multiple_vals_helper.yaml
246
- - specs/bin/filter_and_validate_spec.rb
247
- - specs/rspec_autotest.rb
248
- - specs/xml_spec.rb
268
+ - specs/roc_spec.rb
249
269
  - specs/spec_id_xml_spec.rb
250
- - specs/load_bin_path.rb
251
- - specs/sample_enzyme_spec.rb
252
- - specs/spec_helper.rb
253
270
  - specs/validator_helper.rb
254
- - specs/ms
255
- - specs/ms/msrun_spec.rb
256
- - specs/ms/spectrum_spec.rb
257
- - specs/ms/gradient_program_spec.rb
258
- - specs/ms/parser_spec.rb
259
- - test_files/toppred.small.out
260
- - test_files/bioworks_with_INV_small.xml
261
- - test_files/tf_bioworks2excel.bioXML
262
- - test_files/messups.fasta
271
+ - test_files/020a.mzXML.timeIndex
272
+ - test_files/yeast_gly_small2.parentTimes
263
273
  - test_files/bioworks_single_run_small.xml
264
- - test_files/000_pepxml18_small.xml
265
- - test_files/toppred.xml.out
274
+ - test_files/bioworks_with_INV_small.xml
275
+ - test_files/validator_hits_separate
276
+ - test_files/validator_hits_separate/bioworks_small_HS.xml
277
+ - test_files/validator_hits_separate/bias_bioworks_small_HS.fasta
278
+ - test_files/opd1
279
+ - test_files/opd1/twenty_scans_answ.lmata
280
+ - test_files/opd1/000.tpp_2.9.2.first10.xml
281
+ - test_files/opd1/000.v2.1.mzXML.timeIndex
282
+ - test_files/opd1/opd1_cat_inv_small-prot.xml
283
+ - test_files/opd1/000_020_3prots-prot.mod_initprob.xml
284
+ - test_files/opd1/sequest.3.1.params
285
+ - test_files/opd1/000_020-prot.png
286
+ - test_files/opd1/twenty_scans.mzXML
287
+ - test_files/opd1/twenty_scans.v2.1.mzXML
288
+ - test_files/opd1/000.tpp_1.2.3.first10.xml
289
+ - test_files/opd1/000_020_3prots-prot.xml
290
+ - test_files/opd1/000.my_answer.100lines.xml
291
+ - test_files/opd1/twenty_scans_answ.lmat
292
+ - test_files/opd1/sequest.3.2.params
293
+ - test_files/bioworks_small.xml
294
+ - test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes
295
+ - test_files/bioworks_with_SHUFF_small.xml
296
+ - test_files/yeast_gly_small.xml
297
+ - test_files/bioworks_small.toppred.out
298
+ - test_files/4-03-03_small-prot.xml
299
+ - test_files/bioworks32.params
300
+ - test_files/bioworks_small.fasta
301
+ - test_files/pepproph_small.xml
266
302
  - test_files/4-03-03_mzXML
267
- - test_files/4-03-03_mzXML/000.mzXML.timeIndex
268
303
  - test_files/4-03-03_mzXML/020.mzXML.timeIndex
269
- - test_files/bioworks_small.fasta
270
- - test_files/bioworks_small.toppred.out
271
- - test_files/opd1_020_beginning.RAW
304
+ - test_files/4-03-03_mzXML/000.mzXML.timeIndex
305
+ - test_files/smallraw.RAW
306
+ - test_files/toppred.small.out
307
+ - test_files/head_of_7MIX.srf
308
+ - test_files/bioworks-3.3_10prots.xml
309
+ - test_files/interact-opd1_mods_small-prot.xml
310
+ - test_files/s01_anC1_ld020mM.meth
272
311
  - test_files/phobius.small.noheader.txt
312
+ - test_files/opd1_020_beginning.RAW
313
+ - test_files/toppred.xml.out
314
+ - test_files/4-03-03_small.xml
273
315
  - test_files/bioworks_small.phobius
274
- - test_files/corrupted_900.srf
275
316
  - test_files/phobius.small.small.txt
317
+ - test_files/tf_bioworks2excel.bioXML
318
+ - test_files/000_pepxml18_small.xml
319
+ - test_files/bioworks33.params
320
+ - test_files/tf_bioworks2excel.txt.actual
321
+ - test_files/s01_anC1_ld020mM.key.txt
276
322
  - test_files/bioworks_small.params
277
- - test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes
278
- - test_files/pepproph_small.xml
279
323
  - test_files/yeast_gly_small-prot.xml
324
+ - test_files/messups.fasta
280
325
  - test_files/orbitrap_mzData
281
326
  - test_files/orbitrap_mzData/000_cut.xml
282
- - test_files/yeast_gly_small.xml
283
- - test_files/yeast_gly_small2.parentTimes
284
- - test_files/4-03-03_small.xml
285
- - test_files/tf_bioworks2excel.txt.actual
286
- - test_files/s01_anC1_ld020mM.meth
287
- - test_files/head_of_7MIX.srf
327
+ - test_files/7MIX_STD_110802_1.sequest_params_fragment.srf
288
328
  - test_files/bioworks31.params
289
- - test_files/bioworks32.params
290
- - test_files/validator_hits_separate
291
- - test_files/validator_hits_separate/bias_bioworks_small_HS.fasta
292
- - test_files/validator_hits_separate/bioworks_small_HS.xml
293
- - test_files/bioworks-3.3_10prots.xml
294
- - test_files/smallraw.RAW
295
- - test_files/bioworks_small.xml
296
- - test_files/bioworks_with_SHUFF_small.xml
297
329
  - test_files/small.sqt
298
- - test_files/4-03-03_small-prot.xml
299
- - test_files/020a.mzXML.timeIndex
300
- - test_files/s01_anC1_ld020mM.key.txt
301
330
  - test_files/small.fasta
302
- - test_files/bioworks33.params
303
- - test_files/7MIX_STD_110802_1.sequest_params_fragment.srf
304
331
  - test_files/opd1_2runs_2mods
305
332
  - test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml
306
- - test_files/interact-opd1_mods_small-prot.xml
307
- - test_files/opd1
308
- - test_files/opd1/000.tpp_2.9.2.first10.xml
309
- - test_files/opd1/000_020-prot.png
310
- - test_files/opd1/sequest.3.2.params
311
- - test_files/opd1/sequest.3.1.params
312
- - test_files/opd1/twenty_scans.v2.1.mzXML
313
- - test_files/opd1/000.tpp_1.2.3.first10.xml
314
- - test_files/opd1/twenty_scans_answ.lmata
315
- - test_files/opd1/000.my_answer.100lines.xml
316
- - test_files/opd1/twenty_scans.mzXML
317
- - test_files/opd1/twenty_scans_answ.lmat
318
- - test_files/opd1/000.v2.1.mzXML.timeIndex
319
- - test_files/opd1/opd1_cat_inv_small-prot.xml
320
- - test_files/opd1/000_020_3prots-prot.mod_initprob.xml
321
- - test_files/opd1/000_020_3prots-prot.xml
333
+ - test_files/opd1_2runs_2mods/data
334
+ - test_files/opd1_2runs_2mods/data/README.txt
335
+ - test_files/opd1_2runs_2mods/data/040.mzData.xml
336
+ - test_files/opd1_2runs_2mods/data/020.readw.mzXML
337
+ - test_files/opd1_2runs_2mods/data/040.readw.mzXML
338
+ - test_files/opd1_2runs_2mods/data/020.mzData.xml
339
+ - test_files/corrupted_900.srf
322
340
  has_rdoc: true
323
341
  homepage: http://mspire.rubyforge.org
324
342
  post_install_message:
325
343
  rdoc_options:
326
344
  - --main
327
- - README
345
+ - README.rdoc
328
346
  - --title
329
347
  - mspire
330
348
  require_paths:
@@ -348,53 +366,53 @@ requirements:
348
366
  - "\"rake\" is useful for development"
349
367
  - "\"webgen (with gems redcloth and bluecloth) is necessary to build web pages"
350
368
  rubyforge_project: mspire
351
- rubygems_version: 1.0.1
369
+ rubygems_version: 1.1.1
352
370
  signing_key:
353
371
  specification_version: 2
354
372
  summary: Mass Spectrometry Proteomics Objects, Scripts, and Executables
355
373
  test_files:
356
- - specs/gi_spec.rb
374
+ - specs/ms/gradient_program_spec.rb
375
+ - specs/ms/parser_spec.rb
376
+ - specs/ms/spectrum_spec.rb
377
+ - specs/ms/msrun_spec.rb
378
+ - specs/merge_deep_spec.rb
379
+ - specs/fasta_spec.rb
357
380
  - specs/transmem/phobius_spec.rb
358
381
  - specs/transmem/toppred_spec.rb
359
382
  - specs/align_spec.rb
360
- - specs/fasta_spec.rb
361
383
  - specs/transmem_spec.rb
362
- - specs/spec_id/sequest_spec.rb
363
- - specs/spec_id/proph/prot_summary_spec.rb
364
- - specs/spec_id/proph/pep_summary_spec.rb
365
384
  - specs/spec_id/protein_summary_spec.rb
366
- - specs/spec_id/digestor_spec.rb
385
+ - specs/spec_id/bioworks_spec.rb
367
386
  - specs/spec_id/sqt_spec.rb
368
- - specs/spec_id/aa_freqs_spec.rb
369
- - specs/spec_id/srf_spec.rb
370
- - specs/spec_id/precision/filter/cmdline_spec.rb
371
- - specs/spec_id/precision/filter/output_spec.rb
372
- - specs/spec_id/precision/prob_spec.rb
373
- - specs/spec_id/precision/filter_spec.rb
374
387
  - specs/spec_id/sequest/pepxml_spec.rb
375
388
  - specs/spec_id/sequest/params_spec.rb
376
- - specs/spec_id/bioworks_spec.rb
389
+ - specs/spec_id/precision/filter_spec.rb
390
+ - specs/spec_id/precision/prob_spec.rb
391
+ - specs/spec_id/precision/filter/cmdline_spec.rb
392
+ - specs/spec_id/precision/filter/output_spec.rb
393
+ - specs/spec_id/proph/prot_summary_spec.rb
394
+ - specs/spec_id/proph/pep_summary_spec.rb
395
+ - specs/spec_id/srf_spec.rb
396
+ - specs/spec_id/sequest_spec.rb
397
+ - specs/spec_id/digestor_spec.rb
398
+ - specs/spec_id/aa_freqs_spec.rb
399
+ - specs/xml_spec.rb
400
+ - specs/sample_enzyme_spec.rb
401
+ - specs/gi_spec.rb
377
402
  - specs/spec_id_spec.rb
378
- - specs/roc_spec.rb
379
- - specs/merge_deep_spec.rb
380
- - specs/validator/aa_spec.rb
381
- - specs/validator/transmem_spec.rb
382
- - specs/validator/decoy_spec.rb
383
- - specs/validator/bias_spec.rb
384
403
  - specs/validator/true_pos_spec.rb
385
- - specs/validator/prot_from_pep_spec.rb
386
- - specs/validator/background_spec.rb
387
404
  - specs/validator/aa_est_spec.rb
405
+ - specs/validator/background_spec.rb
406
+ - specs/validator/bias_spec.rb
407
+ - specs/validator/transmem_spec.rb
408
+ - specs/validator/prot_from_pep_spec.rb
409
+ - specs/validator/decoy_spec.rb
410
+ - specs/validator/aa_spec.rb
411
+ - specs/bin/protein_summary_spec.rb
412
+ - specs/bin/filter_and_validate_spec.rb
388
413
  - specs/bin/ms_to_lmat_spec.rb
414
+ - specs/bin/fasta_shaker_spec.rb
389
415
  - specs/bin/bioworks_to_pepxml_spec.rb
390
416
  - specs/bin/prob_validate_spec.rb
391
- - specs/bin/protein_summary_spec.rb
392
- - specs/bin/fasta_shaker_spec.rb
393
- - specs/bin/filter_and_validate_spec.rb
394
- - specs/xml_spec.rb
417
+ - specs/roc_spec.rb
395
418
  - specs/spec_id_xml_spec.rb
396
- - specs/sample_enzyme_spec.rb
397
- - specs/ms/msrun_spec.rb
398
- - specs/ms/spectrum_spec.rb
399
- - specs/ms/gradient_program_spec.rb
400
- - specs/ms/parser_spec.rb