protk 1.1.0.pre

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Files changed (63) hide show
  1. data/README.md +85 -0
  2. data/bin/annotate_ids.rb +59 -0
  3. data/bin/big_search.rb +41 -0
  4. data/bin/correct_omssa_retention_times.rb +27 -0
  5. data/bin/feature_finder.rb +76 -0
  6. data/bin/file_convert.rb +157 -0
  7. data/bin/generate_omssa_loc.rb +42 -0
  8. data/bin/interprophet.rb +91 -0
  9. data/bin/make_decoy.rb +64 -0
  10. data/bin/manage_db.rb +123 -0
  11. data/bin/mascot_search.rb +187 -0
  12. data/bin/mascot_to_pepxml.rb +44 -0
  13. data/bin/msgfplus_search.rb +191 -0
  14. data/bin/omssa_search.rb +205 -0
  15. data/bin/peptide_prophet.rb +245 -0
  16. data/bin/pepxml_to_table.rb +78 -0
  17. data/bin/protein_prophet.rb +140 -0
  18. data/bin/protk_setup.rb +31 -0
  19. data/bin/repair_run_summary.rb +113 -0
  20. data/bin/tandem_search.rb +292 -0
  21. data/bin/template_search.rb +144 -0
  22. data/bin/unimod_to_loc.rb +118 -0
  23. data/bin/xls_to_table.rb +46 -0
  24. data/ext/protk/extconf.rb +3 -0
  25. data/ext/protk/protk.c +235 -0
  26. data/lib/protk/big_search_rakefile.rake +16 -0
  27. data/lib/protk/big_search_tool.rb +23 -0
  28. data/lib/protk/bio_sptr_extensions.rb +210 -0
  29. data/lib/protk/biotools_excel_converter.rb +60 -0
  30. data/lib/protk/command_runner.rb +84 -0
  31. data/lib/protk/constants.rb +296 -0
  32. data/lib/protk/data/FeatureFinderCentroided.ini +63 -0
  33. data/lib/protk/data/apt-get_packages.yaml +47 -0
  34. data/lib/protk/data/brew_packages.yaml +10 -0
  35. data/lib/protk/data/default_config.yml +20 -0
  36. data/lib/protk/data/predefined_db.crap.yaml +19 -0
  37. data/lib/protk/data/predefined_db.sphuman.yaml +25 -0
  38. data/lib/protk/data/predefined_db.swissprot_annotation.yaml +20 -0
  39. data/lib/protk/data/predefined_db.swissprot_fasta_annotation.yaml +20 -0
  40. data/lib/protk/data/tandem_params.xml +56 -0
  41. data/lib/protk/data/taxonomy_template.xml +9 -0
  42. data/lib/protk/data/unimod.xml +16780 -0
  43. data/lib/protk/eupathdb_gene_information_table.rb +158 -0
  44. data/lib/protk/galaxy_stager.rb +24 -0
  45. data/lib/protk/galaxy_util.rb +9 -0
  46. data/lib/protk/manage_db_rakefile.rake +484 -0
  47. data/lib/protk/manage_db_tool.rb +181 -0
  48. data/lib/protk/mascot_util.rb +63 -0
  49. data/lib/protk/omssa_util.rb +57 -0
  50. data/lib/protk/plasmodb.rb +50 -0
  51. data/lib/protk/prophet_tool.rb +85 -0
  52. data/lib/protk/protein_annotator.rb +646 -0
  53. data/lib/protk/protxml.rb +137 -0
  54. data/lib/protk/randomize.rb +7 -0
  55. data/lib/protk/search_tool.rb +182 -0
  56. data/lib/protk/setup_rakefile.rake +245 -0
  57. data/lib/protk/setup_tool.rb +19 -0
  58. data/lib/protk/spreadsheet_extensions.rb +78 -0
  59. data/lib/protk/swissprot_database.rb +38 -0
  60. data/lib/protk/tool.rb +182 -0
  61. data/lib/protk/xtandem_defaults.rb +11 -0
  62. data/lib/protk.rb +18 -0
  63. metadata +256 -0

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