bioroebe 0.10.80 → 0.11.12

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Files changed (67) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +507 -310
  3. data/bioroebe.gemspec +3 -3
  4. data/doc/README.gen +506 -309
  5. data/doc/todo/bioroebe_todo.md +29 -40
  6. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -0
  7. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +18 -8
  8. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +13 -11
  9. data/lib/bioroebe/base/commandline_application/misc.rb +18 -8
  10. data/lib/bioroebe/base/prototype/misc.rb +1 -1
  11. data/lib/bioroebe/codons/show_codon_tables.rb +6 -2
  12. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +1 -0
  13. data/lib/bioroebe/constants/files_and_directories.rb +8 -1
  14. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +3 -0
  15. data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +18 -18
  16. data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +14 -14
  17. data/lib/bioroebe/parsers/genbank_parser.rb +353 -24
  18. data/lib/bioroebe/python/README.md +1 -0
  19. data/lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc +0 -0
  20. data/lib/bioroebe/python/gui/gtk3/widget1.py +22 -0
  21. data/lib/bioroebe/python/mymodule.py +8 -0
  22. data/lib/bioroebe/python/protein_to_dna.py +30 -0
  23. data/lib/bioroebe/python/shell/shell.py +19 -0
  24. data/lib/bioroebe/python/to_rna.py +14 -0
  25. data/lib/bioroebe/python/toplevel_methods/to_camelcase.py +11 -0
  26. data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +28 -25
  27. data/lib/bioroebe/sequence/sequence.rb +54 -2
  28. data/lib/bioroebe/shell/menu.rb +3336 -3304
  29. data/lib/bioroebe/shell/readline/readline.rb +1 -1
  30. data/lib/bioroebe/shell/shell.rb +11233 -28
  31. data/lib/bioroebe/siRNA/siRNA.rb +81 -1
  32. data/lib/bioroebe/string_matching/find_longest_substring.rb +3 -2
  33. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +31 -24
  34. data/lib/bioroebe/toplevel_methods/nucleotides.rb +22 -5
  35. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +2 -0
  36. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +5 -0
  37. data/lib/bioroebe/version/version.rb +2 -2
  38. data/lib/bioroebe/yaml/configuration/browser.yml +1 -1
  39. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +3 -3
  40. metadata +17 -36
  41. data/doc/setup.rb +0 -1655
  42. data/lib/bioroebe/genbank/genbank_parser.rb +0 -291
  43. data/lib/bioroebe/shell/add.rb +0 -108
  44. data/lib/bioroebe/shell/assign.rb +0 -360
  45. data/lib/bioroebe/shell/chop_and_cut.rb +0 -281
  46. data/lib/bioroebe/shell/constants.rb +0 -166
  47. data/lib/bioroebe/shell/download.rb +0 -335
  48. data/lib/bioroebe/shell/enable_and_disable.rb +0 -158
  49. data/lib/bioroebe/shell/enzymes.rb +0 -310
  50. data/lib/bioroebe/shell/fasta.rb +0 -345
  51. data/lib/bioroebe/shell/gtk.rb +0 -76
  52. data/lib/bioroebe/shell/history.rb +0 -132
  53. data/lib/bioroebe/shell/initialize.rb +0 -217
  54. data/lib/bioroebe/shell/loop.rb +0 -74
  55. data/lib/bioroebe/shell/misc.rb +0 -4341
  56. data/lib/bioroebe/shell/prompt.rb +0 -107
  57. data/lib/bioroebe/shell/random.rb +0 -289
  58. data/lib/bioroebe/shell/reset.rb +0 -335
  59. data/lib/bioroebe/shell/scan_and_parse.rb +0 -135
  60. data/lib/bioroebe/shell/search.rb +0 -337
  61. data/lib/bioroebe/shell/sequences.rb +0 -200
  62. data/lib/bioroebe/shell/show_report_and_display.rb +0 -2901
  63. data/lib/bioroebe/shell/startup.rb +0 -127
  64. data/lib/bioroebe/shell/taxonomy.rb +0 -14
  65. data/lib/bioroebe/shell/tk.rb +0 -23
  66. data/lib/bioroebe/shell/user_input.rb +0 -88
  67. data/lib/bioroebe/shell/xorg.rb +0 -45

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