mspire 0.5.0 → 0.6.1

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 (107) hide show
  1. data/README.rdoc +24 -0
  2. data/Rakefile +51 -0
  3. data/VERSION +1 -0
  4. data/lib/cv/description.rb +18 -0
  5. data/lib/cv/param.rb +33 -0
  6. data/lib/cv.rb +3 -0
  7. data/lib/io/bookmark.rb +13 -0
  8. data/lib/merge.rb +7 -0
  9. data/lib/ms/cvlist.rb +76 -0
  10. data/lib/ms/digester.rb +245 -0
  11. data/lib/ms/fasta.rb +86 -0
  12. data/lib/ms/ident/peptide/db.rb +243 -0
  13. data/lib/ms/ident/peptide.rb +72 -0
  14. data/lib/ms/ident/peptide_hit/qvalue.rb +56 -0
  15. data/lib/ms/ident/peptide_hit.rb +26 -0
  16. data/lib/ms/ident/pepxml/modifications.rb +83 -0
  17. data/lib/ms/ident/pepxml/msms_pipeline_analysis.rb +70 -0
  18. data/lib/ms/ident/pepxml/msms_run_summary.rb +82 -0
  19. data/lib/ms/ident/pepxml/parameters.rb +14 -0
  20. data/lib/ms/ident/pepxml/sample_enzyme.rb +165 -0
  21. data/lib/ms/ident/pepxml/search_database.rb +49 -0
  22. data/lib/ms/ident/pepxml/search_hit/modification_info.rb +79 -0
  23. data/lib/ms/ident/pepxml/search_hit.rb +144 -0
  24. data/lib/ms/ident/pepxml/search_result.rb +35 -0
  25. data/lib/ms/ident/pepxml/search_summary.rb +92 -0
  26. data/lib/ms/ident/pepxml/spectrum_query.rb +85 -0
  27. data/lib/ms/ident/pepxml.rb +112 -0
  28. data/lib/ms/ident/protein.rb +33 -0
  29. data/lib/ms/ident/protein_group.rb +80 -0
  30. data/lib/ms/ident/search.rb +114 -0
  31. data/lib/ms/ident.rb +37 -0
  32. data/lib/ms/isotope/aa.rb +59 -0
  33. data/lib/ms/mascot.rb +6 -0
  34. data/lib/ms/mass/aa.rb +79 -0
  35. data/lib/ms/mass.rb +55 -0
  36. data/lib/ms/mzml/index_list.rb +98 -0
  37. data/lib/ms/mzml/plms1.rb +34 -0
  38. data/lib/ms/mzml.rb +197 -0
  39. data/lib/ms/obo.rb +38 -0
  40. data/lib/ms/plms1.rb +156 -0
  41. data/lib/ms/quant/qspec/protein_group_comparison.rb +22 -0
  42. data/lib/ms/quant/qspec.rb +112 -0
  43. data/lib/ms/spectrum.rb +154 -8
  44. data/lib/ms.rb +3 -10
  45. data/lib/msplat.rb +2 -0
  46. data/lib/obo/ims.rb +5 -0
  47. data/lib/obo/ms.rb +7 -0
  48. data/lib/obo/ontology.rb +41 -0
  49. data/lib/obo/unit.rb +5 -0
  50. data/lib/openany.rb +23 -0
  51. data/lib/write_file_or_string.rb +18 -0
  52. data/obo/ims.obo +562 -0
  53. data/obo/ms.obo +11677 -0
  54. data/obo/unit.obo +2563 -0
  55. data/spec/ms/cvlist_spec.rb +60 -0
  56. data/spec/ms/digester_spec.rb +351 -0
  57. data/spec/ms/fasta_spec.rb +100 -0
  58. data/spec/ms/ident/peptide/db_spec.rb +108 -0
  59. data/spec/ms/ident/pepxml/sample_enzyme_spec.rb +181 -0
  60. data/spec/ms/ident/pepxml/search_hit/modification_info_spec.rb +37 -0
  61. data/spec/ms/ident/pepxml_spec.rb +442 -0
  62. data/spec/ms/ident/protein_group_spec.rb +68 -0
  63. data/spec/ms/mass_spec.rb +8 -0
  64. data/spec/ms/mzml/index_list_spec.rb +122 -0
  65. data/spec/ms/mzml/plms1_spec.rb +62 -0
  66. data/spec/ms/mzml_spec.rb +50 -0
  67. data/spec/ms/plms1_spec.rb +38 -0
  68. data/spec/ms/quant/qspec_spec.rb +25 -0
  69. data/spec/msplat_spec.rb +24 -0
  70. data/spec/obo_spec.rb +25 -0
  71. data/spec/spec_helper.rb +25 -0
  72. data/spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.fasta +69 -0
  73. data/spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml +728 -0
  74. data/spec/testfiles/ms/mzml/j24z.idx_comp.3.mzML +271 -0
  75. data/spec/testfiles/ms/mzml/openms.noidx_nocomp.12.mzML +330 -0
  76. data/spec/testfiles/ms/quant/kill_extra_tabs.rb +13 -0
  77. data/spec/testfiles/ms/quant/max_quant_output.provenance.txt +15 -0
  78. data/spec/testfiles/ms/quant/max_quant_output.txt +199 -0
  79. data/spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv +199 -0
  80. data/spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp +199 -0
  81. data/spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp.csv +199 -0
  82. data/spec/testfiles/ms/quant/pdcd5_final.txt +199 -0
  83. data/spec/testfiles/ms/quant/pdcd5_final.txt_qspecgp +0 -0
  84. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.CSV.csv +199 -0
  85. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.csv +199 -0
  86. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.csv +199 -0
  87. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv +199 -0
  88. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp +199 -0
  89. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp.csv +199 -0
  90. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.txt +199 -0
  91. data/spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt +134 -0
  92. data/spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt_qspecgp +134 -0
  93. data/spec/testfiles/ms/quant/remove_rest_of_proteins.rb +13 -0
  94. data/spec/testfiles/ms/quant/unlog_transform.rb +13 -0
  95. data/spec/testfiles/plms1/output.key +0 -0
  96. metadata +157 -40
  97. data/README +0 -77
  98. data/changelog.txt +0 -196
  99. data/lib/ms/calc.rb +0 -32
  100. data/lib/ms/data/interleaved.rb +0 -60
  101. data/lib/ms/data/lazy_io.rb +0 -73
  102. data/lib/ms/data/lazy_string.rb +0 -15
  103. data/lib/ms/data/simple.rb +0 -59
  104. data/lib/ms/data/transposed.rb +0 -41
  105. data/lib/ms/data.rb +0 -57
  106. data/lib/ms/format/format_error.rb +0 -12
  107. data/lib/ms/support/binary_search.rb +0 -126
data/spec/testfiles/ms/mzml/openms.noidx_nocomp.12.mzML ADDED
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+ <?xml version="1.0" encoding="ISO-8859-1"?>
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+ <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" accession="" version="1.1.0">
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+ <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
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+ <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
221
+ <scanList count="1">
222
+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
223
+ <scan >
224
+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="6607.93" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
225
+ </scan>
226
+ </scanList>
227
+ </spectrum>
228
+ <spectrum id="scan=10936" index="7" defaultArrayLength="0">
229
+ <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
230
+ <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
231
+ <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
232
+ <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
233
+ <scanList count="1">
234
+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
235
+ <scan >
236
+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="6608.49" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
237
+ </scan>
238
+ </scanList>
239
+ <precursorList count="1">
240
+ <precursor>
241
+ <isolationWindow>
242
+ <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="640.64752197" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
243
+ <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
244
+ <cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
245
+ </isolationWindow>
246
+ <selectedIonList count="1">
247
+ <selectedIon>
248
+ <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="640.64752197" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
249
+ <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="3" />
250
+ <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="237991" unitAccession="MS:1000132" unitName="percent of base peak" unitCvRef="MS" />
251
+ </selectedIon>
252
+ </selectedIonList>
253
+ <activation>
254
+ <cvParam cvRef="MS" accession="MS:1000509" name="activation energy" value="0" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
255
+ <cvParam cvRef="MS" accession="MS:1000044" name="dissociation method" />
256
+ </activation>
257
+ </precursor>
258
+ </precursorList>
259
+ </spectrum>
260
+ <spectrum id="scan=10937" index="8" defaultArrayLength="0">
261
+ <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
262
+ <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
263
+ <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
264
+ <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
265
+ <scanList count="1">
266
+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
267
+ <scan >
268
+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="6608.92" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
269
+ </scan>
270
+ </scanList>
271
+ </spectrum>
272
+ <spectrum id="scan=10938" index="9" defaultArrayLength="0">
273
+ <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
274
+ <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
275
+ <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
276
+ <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
277
+ <scanList count="1">
278
+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
279
+ <scan >
280
+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="6609.49" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
281
+ </scan>
282
+ </scanList>
283
+ <precursorList count="1">
284
+ <precursor>
285
+ <isolationWindow>
286
+ <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="460.55426025" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
287
+ <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
288
+ <cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
289
+ </isolationWindow>
290
+ <selectedIonList count="1">
291
+ <selectedIon>
292
+ <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="460.55426025" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
293
+ <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="3" />
294
+ <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="182959" unitAccession="MS:1000132" unitName="percent of base peak" unitCvRef="MS" />
295
+ </selectedIon>
296
+ </selectedIonList>
297
+ <activation>
298
+ <cvParam cvRef="MS" accession="MS:1000509" name="activation energy" value="0" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
299
+ <cvParam cvRef="MS" accession="MS:1000044" name="dissociation method" />
300
+ </activation>
301
+ </precursor>
302
+ </precursorList>
303
+ </spectrum>
304
+ <spectrum id="scan=10939" index="10" defaultArrayLength="0">
305
+ <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
306
+ <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
307
+ <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
308
+ <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
309
+ <scanList count="1">
310
+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
311
+ <scan >
312
+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="6609.94" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
313
+ </scan>
314
+ </scanList>
315
+ </spectrum>
316
+ <spectrum id="scan=10940" index="11" defaultArrayLength="0">
317
+ <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
318
+ <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
319
+ <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
320
+ <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
321
+ <scanList count="1">
322
+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
323
+ <scan >
324
+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="6610.53" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
325
+ </scan>
326
+ </scanList>
327
+ </spectrum>
328
+ </spectrumList>
329
+ </run>
330
+ </mzML>
data/spec/testfiles/ms/quant/kill_extra_tabs.rb ADDED
@@ -0,0 +1,13 @@
1
+ #!/usr/bin/env ruby
2
+
3
+ file = ARGV.shift
4
+
5
+ base = file.chomp(File.extname(file))
6
+
7
+ File.open(base + '.killedextratabs.tsv','w') do |out|
8
+ IO.foreach(file) do |line|
9
+ data = line.chomp.split("\t")
10
+ data = data[0,data.rindex {|v| !v.nil? }+1]
11
+ out.puts data.join("\t")
12
+ end
13
+ end
data/spec/testfiles/ms/quant/max_quant_output.provenance.txt ADDED
@@ -0,0 +1,15 @@
1
+ To get this file, used MaxQuant 1.2.2.5
2
+
3
+ Used Perseus 1.2.0.17 to transform the data:
4
+
5
+ First removed contaminants
6
+ Then removed those that showed up in reverse search
7
+ Ln of LFQ intensities
8
+ Imputation of LFQ int (normal distr) so that there are no zeros [ Width 0.3 and Downshift 1.8 ]
9
+
10
+ Columns selected (included):
11
+ LFQ Intensities
12
+ MS/MS
13
+ Protein ID's
14
+
15
+ note, the file is really tab delimited