mspire 0.5.0 → 0.6.1

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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

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