bioroebe 0.10.80 → 0.11.25

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Files changed (134) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +3117 -2645
  3. data/bioroebe.gemspec +3 -3
  4. data/doc/README.gen +3116 -2644
  5. data/doc/todo/bioroebe_todo.md +418 -387
  6. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -9
  7. data/lib/bioroebe/aminoacids/codon_percentage.rb +1 -9
  8. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +1 -9
  9. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -0
  10. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +1 -6
  11. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +18 -8
  12. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +13 -11
  13. data/lib/bioroebe/base/commandline_application/misc.rb +18 -8
  14. data/lib/bioroebe/base/misc.rb +16 -0
  15. data/lib/bioroebe/base/prototype/misc.rb +1 -1
  16. data/lib/bioroebe/codons/show_codon_tables.rb +6 -2
  17. data/lib/bioroebe/codons/show_codon_usage.rb +2 -1
  18. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +1 -0
  19. data/lib/bioroebe/constants/database_constants.rb +1 -1
  20. data/lib/bioroebe/constants/files_and_directories.rb +24 -4
  21. data/lib/bioroebe/constants/misc.rb +20 -0
  22. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +3 -0
  23. data/lib/bioroebe/crystal/README.md +2 -0
  24. data/lib/bioroebe/crystal/to_rna.cr +19 -0
  25. data/lib/bioroebe/data/README.md +11 -8
  26. data/lib/bioroebe/data/electron_microscopy/pos_example.pos +396 -0
  27. data/lib/bioroebe/data/electron_microscopy/test_particles.star +36 -0
  28. data/lib/bioroebe/{shell/tk.rb → electron_microscopy/electron_microscopy_module.rb} +15 -10
  29. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +4 -9
  30. data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +27 -12
  31. data/lib/bioroebe/genome/README.md +4 -0
  32. data/lib/bioroebe/genome/genome.rb +67 -0
  33. data/lib/bioroebe/gui/gtk +1 -0
  34. data/lib/bioroebe/gui/gtk3/controller/controller.rb +45 -27
  35. data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +76 -50
  36. data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +42 -28
  37. data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +119 -71
  38. data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +18 -18
  39. data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +19 -11
  40. data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +14 -14
  41. data/lib/bioroebe/misc/ruler.rb +1 -0
  42. data/lib/bioroebe/parsers/genbank_parser.rb +353 -24
  43. data/lib/bioroebe/parsers/gff.rb +1 -9
  44. data/lib/bioroebe/pdb/parse_pdb_file.rb +1 -9
  45. data/lib/bioroebe/project/project.rb +1 -1
  46. data/lib/bioroebe/python/README.md +1 -0
  47. data/lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc +0 -0
  48. data/lib/bioroebe/python/gui/gtk3/all_in_one.css +4 -0
  49. data/lib/bioroebe/python/gui/gtk3/all_in_one.py +59 -0
  50. data/lib/bioroebe/python/gui/gtk3/widget1.py +20 -0
  51. data/lib/bioroebe/python/gui/tkinter/all_in_one.py +91 -0
  52. data/lib/bioroebe/python/mymodule.py +8 -0
  53. data/lib/bioroebe/python/protein_to_dna.py +33 -0
  54. data/lib/bioroebe/python/shell/shell.py +19 -0
  55. data/lib/bioroebe/python/to_rna.py +14 -0
  56. data/lib/bioroebe/python/toplevel_methods/open_in_browser.py +20 -0
  57. data/lib/bioroebe/python/toplevel_methods/palindromes.py +42 -0
  58. data/lib/bioroebe/python/toplevel_methods/rds.py +13 -0
  59. data/lib/bioroebe/python/toplevel_methods/three_delimiter.py +34 -0
  60. data/lib/bioroebe/python/toplevel_methods/time_and_date.py +43 -0
  61. data/lib/bioroebe/python/toplevel_methods/to_camelcase.py +11 -0
  62. data/lib/bioroebe/requires/require_the_bioroebe_project.rb +3 -1
  63. data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +28 -25
  64. data/lib/bioroebe/sequence/protein.rb +105 -3
  65. data/lib/bioroebe/sequence/sequence.rb +61 -2
  66. data/lib/bioroebe/shell/menu.rb +3752 -3667
  67. data/lib/bioroebe/shell/misc.rb +51 -4311
  68. data/lib/bioroebe/shell/readline/readline.rb +1 -1
  69. data/lib/bioroebe/shell/shell.rb +11199 -28
  70. data/lib/bioroebe/siRNA/siRNA.rb +81 -1
  71. data/lib/bioroebe/string_matching/find_longest_substring.rb +3 -2
  72. data/lib/bioroebe/taxonomy/class_methods.rb +3 -8
  73. data/lib/bioroebe/taxonomy/constants.rb +4 -3
  74. data/lib/bioroebe/taxonomy/edit.rb +2 -1
  75. data/lib/bioroebe/taxonomy/help/help.rb +10 -10
  76. data/lib/bioroebe/taxonomy/info/check_available.rb +15 -9
  77. data/lib/bioroebe/taxonomy/info/info.rb +17 -2
  78. data/lib/bioroebe/taxonomy/info/is_dna.rb +46 -36
  79. data/lib/bioroebe/taxonomy/interactive.rb +139 -95
  80. data/lib/bioroebe/taxonomy/menu.rb +27 -18
  81. data/lib/bioroebe/taxonomy/parse_fasta.rb +3 -1
  82. data/lib/bioroebe/taxonomy/shared.rb +1 -0
  83. data/lib/bioroebe/taxonomy/taxonomy.rb +1 -0
  84. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +31 -24
  85. data/lib/bioroebe/toplevel_methods/databases.rb +1 -1
  86. data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +101 -63
  87. data/lib/bioroebe/toplevel_methods/misc.rb +17 -16
  88. data/lib/bioroebe/toplevel_methods/nucleotides.rb +22 -5
  89. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +2 -0
  90. data/lib/bioroebe/toplevel_methods/palindromes.rb +1 -2
  91. data/lib/bioroebe/toplevel_methods/taxonomy.rb +2 -2
  92. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +5 -0
  93. data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +1 -9
  94. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +1 -9
  95. data/lib/bioroebe/utility_scripts/compacter.rb +1 -9
  96. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +1 -9
  97. data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +1 -9
  98. data/lib/bioroebe/utility_scripts/dot_alignment.rb +1 -9
  99. data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +1 -4
  100. data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -5
  101. data/lib/bioroebe/utility_scripts/showorf/reset.rb +1 -4
  102. data/lib/bioroebe/version/version.rb +2 -2
  103. data/lib/bioroebe/www/embeddable_interface.rb +101 -52
  104. data/lib/bioroebe/www/sinatra/sinatra.rb +186 -70
  105. data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +2 -2
  106. data/lib/bioroebe/yaml/configuration/browser.yml +1 -1
  107. data/lib/bioroebe/yaml/genomes/README.md +3 -4
  108. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +3 -3
  109. metadata +33 -35
  110. data/doc/setup.rb +0 -1655
  111. data/lib/bioroebe/genbank/genbank_parser.rb +0 -291
  112. data/lib/bioroebe/shell/add.rb +0 -108
  113. data/lib/bioroebe/shell/assign.rb +0 -360
  114. data/lib/bioroebe/shell/chop_and_cut.rb +0 -281
  115. data/lib/bioroebe/shell/constants.rb +0 -166
  116. data/lib/bioroebe/shell/download.rb +0 -335
  117. data/lib/bioroebe/shell/enable_and_disable.rb +0 -158
  118. data/lib/bioroebe/shell/enzymes.rb +0 -310
  119. data/lib/bioroebe/shell/fasta.rb +0 -345
  120. data/lib/bioroebe/shell/gtk.rb +0 -76
  121. data/lib/bioroebe/shell/history.rb +0 -132
  122. data/lib/bioroebe/shell/initialize.rb +0 -217
  123. data/lib/bioroebe/shell/loop.rb +0 -74
  124. data/lib/bioroebe/shell/prompt.rb +0 -107
  125. data/lib/bioroebe/shell/random.rb +0 -289
  126. data/lib/bioroebe/shell/reset.rb +0 -335
  127. data/lib/bioroebe/shell/scan_and_parse.rb +0 -135
  128. data/lib/bioroebe/shell/search.rb +0 -337
  129. data/lib/bioroebe/shell/sequences.rb +0 -200
  130. data/lib/bioroebe/shell/show_report_and_display.rb +0 -2901
  131. data/lib/bioroebe/shell/startup.rb +0 -127
  132. data/lib/bioroebe/shell/taxonomy.rb +0 -14
  133. data/lib/bioroebe/shell/user_input.rb +0 -88
  134. data/lib/bioroebe/shell/xorg.rb +0 -45
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