bioroebe 0.10.80 → 0.12.12

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Files changed (242) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +3612 -2781
  3. data/bin/bioroebe +7 -1
  4. data/bin/bioroebe_hash +7 -0
  5. data/bin/codon_to_aminoacid +1 -0
  6. data/bioroebe.gemspec +3 -3
  7. data/doc/README.gen +3612 -2742
  8. data/doc/quality_control/commandline_applications.md +3 -3
  9. data/doc/todo/bioroebe_java_todo.md +22 -0
  10. data/doc/todo/bioroebe_todo.md +2059 -2615
  11. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -9
  12. data/lib/bioroebe/aminoacids/codon_percentage.rb +1 -9
  13. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +1 -9
  14. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -0
  15. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +1 -6
  16. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +18 -8
  17. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +15 -11
  18. data/lib/bioroebe/base/commandline_application/misc.rb +66 -49
  19. data/lib/bioroebe/base/commandline_application/opn.rb +8 -8
  20. data/lib/bioroebe/base/commandline_application/reset.rb +3 -2
  21. data/lib/bioroebe/base/misc.rb +35 -0
  22. data/lib/bioroebe/base/prototype/misc.rb +11 -1
  23. data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +2 -10
  24. data/lib/bioroebe/codons/codons.rb +1 -1
  25. data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +192 -58
  26. data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +1 -9
  27. data/lib/bioroebe/codons/show_codon_tables.rb +6 -2
  28. data/lib/bioroebe/codons/show_codon_usage.rb +15 -4
  29. data/lib/bioroebe/colours/rev.rb +4 -1
  30. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +1 -0
  31. data/lib/bioroebe/constants/database_constants.rb +1 -1
  32. data/lib/bioroebe/constants/files_and_directories.rb +31 -4
  33. data/lib/bioroebe/constants/misc.rb +20 -0
  34. data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +58 -24
  35. data/lib/bioroebe/count/count_amount_of_aminoacids.rb +3 -2
  36. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +3 -0
  37. data/lib/bioroebe/crystal/README.md +2 -0
  38. data/lib/bioroebe/crystal/to_rna.cr +19 -0
  39. data/lib/bioroebe/data/README.md +11 -8
  40. data/lib/bioroebe/data/electron_microscopy/pos_example.pos +396 -0
  41. data/lib/bioroebe/data/electron_microscopy/test_particles.star +36 -0
  42. data/lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_alpha_HBB_mRNA.fasta +9 -0
  43. data/lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_beta_HBB_mRNA.fasta +8 -0
  44. data/lib/bioroebe/data/fasta/human/README.md +2 -0
  45. data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +15 -18
  46. data/lib/bioroebe/{fasta_and_fastq/parse_fasta/run.rb → electron_microscopy/electron_microscopy_module.rb} +16 -8
  47. data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +1 -9
  48. data/lib/bioroebe/electron_microscopy/flipy.rb +83 -0
  49. data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +2 -10
  50. data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +1 -9
  51. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +4 -9
  52. data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +10 -3
  53. data/lib/bioroebe/enzymes/restriction_enzyme.rb +23 -1
  54. data/lib/bioroebe/enzymes/restriction_enzymes/statistics.rb +65 -0
  55. data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +1 -9
  56. data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +7 -9
  57. data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +1 -5
  58. data/lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb +81 -0
  59. data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +1465 -7
  60. data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +11 -2
  61. data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +27 -12
  62. data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +1 -5
  63. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb +0 -5
  64. data/lib/bioroebe/genome/README.md +4 -0
  65. data/lib/bioroebe/genome/genome.rb +67 -0
  66. data/lib/bioroebe/genomes/genome_pattern.rb +3 -9
  67. data/lib/bioroebe/gui/gtk +1 -0
  68. data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +73 -128
  69. data/lib/bioroebe/gui/gtk3/controller/controller.rb +45 -27
  70. data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +76 -50
  71. data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +99 -21
  72. data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +42 -28
  73. data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +119 -71
  74. data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +18 -18
  75. data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +19 -11
  76. data/lib/bioroebe/gui/jruby/alignment/alignment.rb +165 -0
  77. data/lib/bioroebe/gui/libui/alignment/alignment.rb +3 -1
  78. data/lib/bioroebe/gui/libui/controller/controller.rb +116 -0
  79. data/lib/bioroebe/gui/libui/random_sequence/random_sequence.rb +18 -2
  80. data/lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb +2 -0
  81. data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +8 -6
  82. data/lib/bioroebe/gui/shared_code/alignment/alignment_module.rb +102 -0
  83. data/lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb +18 -16
  84. data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +14 -14
  85. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$1.class +0 -0
  86. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$CloseListener.class +0 -0
  87. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.class +0 -0
  88. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.java +141 -0
  89. data/lib/bioroebe/images/FORWARD_PRIMER.png +0 -0
  90. data/lib/bioroebe/images/REVERSE_PRIMER.png +0 -0
  91. data/lib/bioroebe/java/README.md +4 -0
  92. data/lib/bioroebe/java/bioroebe/Sequence.java +25 -1
  93. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Base.class +0 -0
  94. data/lib/bioroebe/java/bioroebe/{Base.java → src/main/java/bioroebe/Base.java} +15 -2
  95. data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.class → src/main/java/bioroebe/BisulfiteTreatment.class} +0 -0
  96. data/lib/bioroebe/java/bioroebe/{Codons.class → src/main/java/bioroebe/Codons.class} +0 -0
  97. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Codons.java +34 -0
  98. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Commandline.class +0 -0
  99. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Commandline.java +101 -0
  100. data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.class → src/main/java/bioroebe/GenerateRandomDnaSequence.class} +0 -0
  101. data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.java → src/main/java/bioroebe/GenerateRandomDnaSequence.java} +8 -2
  102. data/lib/bioroebe/java/bioroebe/{IsPalindrome.class → src/main/java/bioroebe/IsPalindrome.class} +0 -0
  103. data/lib/bioroebe/java/bioroebe/{IsPalindrome.java → src/main/java/bioroebe/IsPalindrome.java} +5 -1
  104. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/PartnerNucleotide.class +0 -0
  105. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/PartnerNucleotide.java +56 -0
  106. data/lib/bioroebe/java/bioroebe/{RemoveFile.java → src/main/java/bioroebe/RemoveFile.java} +10 -4
  107. data/lib/bioroebe/java/bioroebe/{RemoveNumbers.class → src/main/java/bioroebe/RemoveNumbers.class} +0 -0
  108. data/lib/bioroebe/java/bioroebe/{RemoveNumbers.java → src/main/java/bioroebe/RemoveNumbers.java} +1 -0
  109. data/lib/bioroebe/java/bioroebe/{ToCamelcase.class → src/main/java/bioroebe/ToCamelcase.class} +0 -0
  110. data/lib/bioroebe/java/bioroebe/{ToCamelcase.java → src/main/java/bioroebe/ToCamelcase.java} +3 -3
  111. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToRNA.class +0 -0
  112. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToRNA.java +42 -0
  113. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/toplevel_methods/BaseComposition.class +0 -0
  114. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/toplevel_methods/BaseComposition.java +75 -0
  115. data/lib/bioroebe/misc/ruler.rb +11 -2
  116. data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +1 -9
  117. data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +7 -7
  118. data/lib/bioroebe/parsers/genbank_parser.rb +347 -26
  119. data/lib/bioroebe/parsers/gff.rb +1 -9
  120. data/lib/bioroebe/patterns/scan_for_repeat.rb +1 -5
  121. data/lib/bioroebe/pdb/fetch_fasta_sequence_from_pdb.rb +1 -9
  122. data/lib/bioroebe/pdb/parse_mmCIF_file.rb +1 -9
  123. data/lib/bioroebe/pdb/parse_pdb_file.rb +4 -10
  124. data/lib/bioroebe/project/project.rb +1 -1
  125. data/lib/bioroebe/python/README.md +1 -0
  126. data/lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc +0 -0
  127. data/lib/bioroebe/python/gui/gtk3/all_in_one.css +4 -0
  128. data/lib/bioroebe/python/gui/gtk3/all_in_one.py +59 -0
  129. data/lib/bioroebe/python/gui/gtk3/widget1.py +20 -0
  130. data/lib/bioroebe/python/gui/tkinter/all_in_one.py +91 -0
  131. data/lib/bioroebe/python/mymodule.py +8 -0
  132. data/lib/bioroebe/python/protein_to_dna.py +33 -0
  133. data/lib/bioroebe/python/shell/shell.py +19 -0
  134. data/lib/bioroebe/python/to_rna.py +14 -0
  135. data/lib/bioroebe/python/toplevel_methods/esystem.py +12 -0
  136. data/lib/bioroebe/python/toplevel_methods/open_in_browser.py +20 -0
  137. data/lib/bioroebe/python/toplevel_methods/palindromes.py +42 -0
  138. data/lib/bioroebe/python/toplevel_methods/rds.py +13 -0
  139. data/lib/bioroebe/python/toplevel_methods/shuffleseq.py +23 -0
  140. data/lib/bioroebe/python/toplevel_methods/three_delimiter.py +37 -0
  141. data/lib/bioroebe/python/toplevel_methods/time_and_date.py +43 -0
  142. data/lib/bioroebe/python/toplevel_methods/to_camelcase.py +21 -0
  143. data/lib/bioroebe/requires/require_the_bioroebe_project.rb +3 -1
  144. data/lib/bioroebe/sequence/alignment.rb +14 -4
  145. data/lib/bioroebe/sequence/dna.rb +1 -0
  146. data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +28 -25
  147. data/lib/bioroebe/sequence/protein.rb +105 -3
  148. data/lib/bioroebe/sequence/sequence.rb +87 -21
  149. data/lib/bioroebe/shell/menu.rb +3829 -3714
  150. data/lib/bioroebe/shell/misc.rb +59 -4307
  151. data/lib/bioroebe/shell/readline/readline.rb +1 -1
  152. data/lib/bioroebe/shell/shell.rb +11255 -28
  153. data/lib/bioroebe/siRNA/siRNA.rb +81 -1
  154. data/lib/bioroebe/string_matching/find_longest_substring.rb +3 -2
  155. data/lib/bioroebe/string_matching/hamming_distance.rb +1 -9
  156. data/lib/bioroebe/taxonomy/class_methods.rb +3 -8
  157. data/lib/bioroebe/taxonomy/constants.rb +4 -3
  158. data/lib/bioroebe/taxonomy/edit.rb +2 -1
  159. data/lib/bioroebe/taxonomy/help/help.rb +10 -10
  160. data/lib/bioroebe/taxonomy/help/helpline.rb +2 -2
  161. data/lib/bioroebe/taxonomy/info/check_available.rb +15 -9
  162. data/lib/bioroebe/taxonomy/info/info.rb +18 -11
  163. data/lib/bioroebe/taxonomy/info/is_dna.rb +46 -36
  164. data/lib/bioroebe/taxonomy/interactive.rb +140 -104
  165. data/lib/bioroebe/taxonomy/menu.rb +27 -18
  166. data/lib/bioroebe/taxonomy/parse_fasta.rb +3 -1
  167. data/lib/bioroebe/taxonomy/shared.rb +1 -0
  168. data/lib/bioroebe/taxonomy/taxonomy.rb +1 -0
  169. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +31 -24
  170. data/lib/bioroebe/toplevel_methods/colourize_related_methods.rb +164 -0
  171. data/lib/bioroebe/toplevel_methods/databases.rb +1 -1
  172. data/lib/bioroebe/toplevel_methods/digest.rb +18 -8
  173. data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +107 -63
  174. data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +14 -2
  175. data/lib/bioroebe/toplevel_methods/frequencies.rb +8 -1
  176. data/lib/bioroebe/toplevel_methods/misc.rb +142 -12
  177. data/lib/bioroebe/toplevel_methods/nucleotides.rb +118 -46
  178. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +2 -0
  179. data/lib/bioroebe/toplevel_methods/palindromes.rb +1 -2
  180. data/lib/bioroebe/toplevel_methods/taxonomy.rb +2 -2
  181. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +5 -0
  182. data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +1 -9
  183. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +1 -9
  184. data/lib/bioroebe/utility_scripts/compacter.rb +1 -9
  185. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +1 -9
  186. data/lib/bioroebe/utility_scripts/consensus_sequence.rb +6 -6
  187. data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +1 -9
  188. data/lib/bioroebe/utility_scripts/dot_alignment.rb +1 -9
  189. data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +1 -4
  190. data/lib/bioroebe/utility_scripts/parse_taxonomy.rb +2 -2
  191. data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -5
  192. data/lib/bioroebe/utility_scripts/showorf/reset.rb +1 -4
  193. data/lib/bioroebe/version/version.rb +2 -2
  194. data/lib/bioroebe/www/embeddable_interface.rb +103 -54
  195. data/lib/bioroebe/www/sinatra/sinatra.rb +186 -70
  196. data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +2 -2
  197. data/lib/bioroebe/yaml/configuration/browser.yml +1 -1
  198. data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -1
  199. data/lib/bioroebe/yaml/genomes/README.md +3 -4
  200. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +27 -27
  201. metadata +81 -64
  202. data/doc/setup.rb +0 -1655
  203. data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +0 -50
  204. data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +0 -86
  205. data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +0 -117
  206. data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +0 -981
  207. data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +0 -156
  208. data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +0 -128
  209. data/lib/bioroebe/genbank/genbank_parser.rb +0 -291
  210. data/lib/bioroebe/java/bioroebe/Base.class +0 -0
  211. data/lib/bioroebe/java/bioroebe/Codons.java +0 -22
  212. data/lib/bioroebe/java/bioroebe/PartnerNucleotide.class +0 -0
  213. data/lib/bioroebe/java/bioroebe/PartnerNucleotide.java +0 -19
  214. data/lib/bioroebe/java/bioroebe.jar +0 -0
  215. data/lib/bioroebe/shell/add.rb +0 -108
  216. data/lib/bioroebe/shell/assign.rb +0 -360
  217. data/lib/bioroebe/shell/chop_and_cut.rb +0 -281
  218. data/lib/bioroebe/shell/constants.rb +0 -166
  219. data/lib/bioroebe/shell/download.rb +0 -335
  220. data/lib/bioroebe/shell/enable_and_disable.rb +0 -158
  221. data/lib/bioroebe/shell/enzymes.rb +0 -310
  222. data/lib/bioroebe/shell/fasta.rb +0 -345
  223. data/lib/bioroebe/shell/gtk.rb +0 -76
  224. data/lib/bioroebe/shell/history.rb +0 -132
  225. data/lib/bioroebe/shell/initialize.rb +0 -217
  226. data/lib/bioroebe/shell/loop.rb +0 -74
  227. data/lib/bioroebe/shell/prompt.rb +0 -107
  228. data/lib/bioroebe/shell/random.rb +0 -289
  229. data/lib/bioroebe/shell/reset.rb +0 -335
  230. data/lib/bioroebe/shell/scan_and_parse.rb +0 -135
  231. data/lib/bioroebe/shell/search.rb +0 -337
  232. data/lib/bioroebe/shell/sequences.rb +0 -200
  233. data/lib/bioroebe/shell/show_report_and_display.rb +0 -2901
  234. data/lib/bioroebe/shell/startup.rb +0 -127
  235. data/lib/bioroebe/shell/taxonomy.rb +0 -14
  236. data/lib/bioroebe/shell/tk.rb +0 -23
  237. data/lib/bioroebe/shell/user_input.rb +0 -88
  238. data/lib/bioroebe/shell/xorg.rb +0 -45
  239. /data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.java → src/main/java/bioroebe/BisulfiteTreatment.java} +0 -0
  240. /data/lib/bioroebe/java/bioroebe/{Esystem.class → src/main/java/bioroebe/Esystem.class} +0 -0
  241. /data/lib/bioroebe/java/bioroebe/{Esystem.java → src/main/java/bioroebe/Esystem.java} +0 -0
  242. /data/lib/bioroebe/java/bioroebe/{RemoveFile.class → src/main/java/bioroebe/RemoveFile.class} +0 -0
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