bioroebe 0.10.80 → 0.12.24

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (301) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +3946 -2817
  3. data/bin/bioroebe +13 -2
  4. data/bin/bioroebe_hash +7 -0
  5. data/bin/codon_to_aminoacid +6 -4
  6. data/bin/compacter +7 -0
  7. data/bin/plain_palindrome +7 -0
  8. data/bioroebe.gemspec +3 -3
  9. data/doc/README.gen +3918 -2793
  10. data/doc/quality_control/commandline_applications.md +3 -3
  11. data/doc/statistics/statistics.md +7 -7
  12. data/doc/todo/bioroebe_GUI_todo.md +19 -14
  13. data/doc/todo/bioroebe_java_todo.md +22 -0
  14. data/doc/todo/bioroebe_todo.md +2075 -2620
  15. data/lib/bioroebe/C++/DNA.cpp +69 -0
  16. data/lib/bioroebe/C++/RNA.cpp +58 -0
  17. data/lib/bioroebe/C++/sequence.cpp +35 -0
  18. data/lib/bioroebe/abstract/README.md +1 -0
  19. data/lib/bioroebe/abstract/features.rb +29 -0
  20. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -9
  21. data/lib/bioroebe/aminoacids/codon_percentage.rb +1 -9
  22. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +1 -9
  23. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -0
  24. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +1 -6
  25. data/lib/bioroebe/base/base_module/base_module.rb +36 -0
  26. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +18 -8
  27. data/lib/bioroebe/base/commandline_application/commandline_application.rb +13 -9
  28. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +24 -19
  29. data/lib/bioroebe/base/commandline_application/misc.rb +66 -49
  30. data/lib/bioroebe/base/commandline_application/opn.rb +8 -8
  31. data/lib/bioroebe/base/commandline_application/reset.rb +5 -3
  32. data/lib/bioroebe/base/internal_hash_module/internal_hash_module.rb +42 -0
  33. data/lib/bioroebe/base/misc.rb +35 -0
  34. data/lib/bioroebe/base/prototype/misc.rb +15 -9
  35. data/lib/bioroebe/base/prototype/reset.rb +10 -0
  36. data/lib/bioroebe/cleave_and_digest/digestion.rb +10 -2
  37. data/lib/bioroebe/cleave_and_digest/trypsin.rb +104 -50
  38. data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +2 -10
  39. data/lib/bioroebe/codons/codons.rb +1 -1
  40. data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +208 -59
  41. data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +1 -9
  42. data/lib/bioroebe/codons/show_codon_tables.rb +8 -3
  43. data/lib/bioroebe/codons/show_codon_usage.rb +15 -4
  44. data/lib/bioroebe/colours/rev.rb +4 -1
  45. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +1 -0
  46. data/lib/bioroebe/constants/database_constants.rb +1 -1
  47. data/lib/bioroebe/constants/files_and_directories.rb +31 -4
  48. data/lib/bioroebe/constants/misc.rb +20 -0
  49. data/lib/bioroebe/constants/nucleotides.rb +7 -0
  50. data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +109 -39
  51. data/lib/bioroebe/count/count_amount_of_aminoacids.rb +3 -2
  52. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +3 -0
  53. data/lib/bioroebe/cpp +1 -0
  54. data/lib/bioroebe/crystal/README.md +2 -0
  55. data/lib/bioroebe/crystal/to_rna.cr +19 -0
  56. data/lib/bioroebe/data/README.md +11 -8
  57. data/lib/bioroebe/data/electron_microscopy/pos_example.pos +396 -0
  58. data/lib/bioroebe/data/electron_microscopy/test_particles.star +36 -0
  59. data/lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_alpha_HBB_mRNA.fasta +9 -0
  60. data/lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_beta_HBB_mRNA.fasta +8 -0
  61. data/lib/bioroebe/data/fasta/human/README.md +2 -0
  62. data/lib/bioroebe/dotplots/advanced_dotplot.rb +1 -1
  63. data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +15 -18
  64. data/lib/bioroebe/{fasta_and_fastq/parse_fasta/run.rb → electron_microscopy/electron_microscopy_module.rb} +16 -8
  65. data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +1 -9
  66. data/lib/bioroebe/electron_microscopy/flipy.rb +83 -0
  67. data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +2 -10
  68. data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +1 -9
  69. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +4 -9
  70. data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +10 -3
  71. data/lib/bioroebe/enzymes/restriction_enzyme.rb +23 -1
  72. data/lib/bioroebe/enzymes/restriction_enzymes/statistics.rb +65 -0
  73. data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +1 -9
  74. data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +7 -9
  75. data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +1 -5
  76. data/lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb +81 -0
  77. data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +1518 -7
  78. data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +11 -2
  79. data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +27 -12
  80. data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +1 -5
  81. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb +0 -5
  82. data/lib/bioroebe/genome/README.md +4 -0
  83. data/lib/bioroebe/genome/genome.rb +130 -0
  84. data/lib/bioroebe/genomes/genome_pattern.rb +3 -9
  85. data/lib/bioroebe/gui/gtk +1 -0
  86. data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +106 -137
  87. data/lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb +27 -61
  88. data/lib/bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb +1 -1
  89. data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +1 -2
  90. data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +1 -2
  91. data/lib/bioroebe/gui/gtk3/controller/controller.rb +46 -29
  92. data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +77 -52
  93. data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +1 -2
  94. data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +100 -23
  95. data/lib/bioroebe/gui/gtk3/format_converter/format_converter.rb +1 -2
  96. data/lib/bioroebe/gui/gtk3/gene/gene.rb +1 -2
  97. data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +43 -30
  98. data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +1 -2
  99. data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +120 -73
  100. data/lib/bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb +1 -2
  101. data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +19 -20
  102. data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +20 -13
  103. data/lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb +1 -2
  104. data/lib/bioroebe/gui/gtk3/show_codon_table/misc.rb +97 -22
  105. data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +3 -73
  106. data/lib/bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb +1 -2
  107. data/lib/bioroebe/gui/gtk3/sizeseq/sizeseq.rb +1 -2
  108. data/lib/bioroebe/gui/gtk3/three_to_one/three_to_one.rb +1 -2
  109. data/lib/bioroebe/gui/gtk3/www_finder/www_finder.rb +1 -2
  110. data/lib/bioroebe/gui/javafx/bioroebe/Bioroebe.class +0 -0
  111. data/lib/bioroebe/gui/javafx/bioroebe/Bioroebe.java +104 -0
  112. data/lib/bioroebe/gui/javafx/bioroebe.jar +0 -0
  113. data/lib/bioroebe/gui/javafx/bioroebe.mf +1 -0
  114. data/lib/bioroebe/gui/javafx/module-info.class +0 -0
  115. data/lib/bioroebe/gui/javafx/module-info.java +5 -0
  116. data/lib/bioroebe/gui/jruby/alignment/alignment.rb +165 -0
  117. data/lib/bioroebe/gui/jruby/aminoacid_composition/aminoacid_composition.rb +166 -0
  118. data/lib/bioroebe/gui/libui/alignment/alignment.rb +3 -1
  119. data/lib/bioroebe/gui/libui/controller/controller.rb +116 -0
  120. data/lib/bioroebe/gui/libui/random_sequence/random_sequence.rb +18 -2
  121. data/lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb +2 -0
  122. data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +8 -6
  123. data/lib/bioroebe/gui/shared_code/alignment/alignment_module.rb +102 -0
  124. data/lib/bioroebe/gui/shared_code/aminoacid_composition/aminoacid_composition_module.rb +94 -0
  125. data/lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb +18 -16
  126. data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +14 -14
  127. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$1.class +0 -0
  128. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$CloseListener.class +0 -0
  129. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.class +0 -0
  130. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.java +141 -0
  131. data/lib/bioroebe/images/FORWARD_PRIMER.png +0 -0
  132. data/lib/bioroebe/images/REVERSE_PRIMER.png +0 -0
  133. data/lib/bioroebe/images/images.html +29845 -0
  134. data/lib/bioroebe/java/README.md +5 -0
  135. data/lib/bioroebe/java/bioroebe/AllInOne.java +1 -0
  136. data/lib/bioroebe/java/bioroebe/Base.class +0 -0
  137. data/lib/bioroebe/java/bioroebe/Base.java +39 -5
  138. data/lib/bioroebe/java/bioroebe/IsPalindrome.java +23 -5
  139. data/lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.java +0 -0
  140. data/lib/bioroebe/java/bioroebe/Sequence.java +28 -3
  141. data/lib/bioroebe/java/bioroebe/ToCamelcase.class +0 -0
  142. data/lib/bioroebe/java/bioroebe/ToCamelcase.java +16 -4
  143. data/lib/bioroebe/java/bioroebe/ToRNA.java +43 -0
  144. data/lib/bioroebe/java/bioroebe/ToplevelMethods.java +6 -0
  145. data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.class → src/BisulfiteTreatment.class} +0 -0
  146. data/lib/bioroebe/java/bioroebe/{Codons.class → src/Codons.class} +0 -0
  147. data/lib/bioroebe/java/bioroebe/src/Codons.java +35 -0
  148. data/lib/bioroebe/java/bioroebe/src/Commandline.class +0 -0
  149. data/lib/bioroebe/java/bioroebe/src/Commandline.java +101 -0
  150. data/lib/bioroebe/java/bioroebe/{Esystem.class → src/Esystem.class} +0 -0
  151. data/lib/bioroebe/java/bioroebe/{Esystem.java → src/Esystem.java} +6 -1
  152. data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.class → src/GenerateRandomDnaSequence.class} +0 -0
  153. data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.java → src/GenerateRandomDnaSequence.java} +8 -2
  154. data/lib/bioroebe/java/bioroebe/src/PartnerNucleotide.class +0 -0
  155. data/lib/bioroebe/java/bioroebe/src/PartnerNucleotide.java +56 -0
  156. data/lib/bioroebe/java/bioroebe/{RemoveFile.java → src/RemoveFile.java} +10 -4
  157. data/lib/bioroebe/java/bioroebe/{RemoveNumbers.class → src/RemoveNumbers.class} +0 -0
  158. data/lib/bioroebe/java/bioroebe/{RemoveNumbers.java → src/RemoveNumbers.java} +1 -0
  159. data/lib/bioroebe/java/bioroebe/src/toplevel_methods/BaseComposition.class +0 -0
  160. data/lib/bioroebe/java/bioroebe/src/toplevel_methods/BaseComposition.java +75 -0
  161. data/lib/bioroebe/misc/ruler.rb +11 -2
  162. data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +1 -9
  163. data/lib/bioroebe/nucleotides/sanitize_nucleotide_sequence.rb +59 -18
  164. data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +7 -7
  165. data/lib/bioroebe/parsers/genbank_parser.rb +347 -26
  166. data/lib/bioroebe/parsers/gff.rb +1 -9
  167. data/lib/bioroebe/patterns/scan_for_repeat.rb +1 -5
  168. data/lib/bioroebe/pdb/fetch_fasta_sequence_from_pdb.rb +1 -9
  169. data/lib/bioroebe/pdb/parse_mmCIF_file.rb +1 -9
  170. data/lib/bioroebe/pdb/parse_pdb_file.rb +4 -10
  171. data/lib/bioroebe/project/project.rb +1 -1
  172. data/lib/bioroebe/python/README.md +1 -0
  173. data/lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc +0 -0
  174. data/lib/bioroebe/python/gui/gtk3/all_in_one.css +4 -0
  175. data/lib/bioroebe/python/gui/gtk3/all_in_one.py +59 -0
  176. data/lib/bioroebe/python/gui/gtk3/widget1.py +20 -0
  177. data/lib/bioroebe/python/gui/tkinter/all_in_one.py +91 -0
  178. data/lib/bioroebe/python/mymodule.py +8 -0
  179. data/lib/bioroebe/python/protein_to_dna.py +33 -0
  180. data/lib/bioroebe/python/shell/shell.py +19 -0
  181. data/lib/bioroebe/python/to_rna.py +14 -0
  182. data/lib/bioroebe/python/toplevel_methods/convert_dna_to_aminoacid_sequence.py +137 -0
  183. data/lib/bioroebe/python/toplevel_methods/esystem.py +12 -0
  184. data/lib/bioroebe/python/toplevel_methods/open_in_browser.py +20 -0
  185. data/lib/bioroebe/python/toplevel_methods/palindromes.py +52 -0
  186. data/lib/bioroebe/python/toplevel_methods/rds.py +13 -0
  187. data/lib/bioroebe/python/toplevel_methods/shuffleseq.py +23 -0
  188. data/lib/bioroebe/python/toplevel_methods/three_delimiter.py +37 -0
  189. data/lib/bioroebe/python/toplevel_methods/time_and_date.py +43 -0
  190. data/lib/bioroebe/python/toplevel_methods/to_camelcase.py +21 -0
  191. data/lib/bioroebe/requires/require_cleave_and_digest.rb +3 -1
  192. data/lib/bioroebe/requires/require_the_bioroebe_project.rb +3 -1
  193. data/lib/bioroebe/sequence/alignment.rb +14 -4
  194. data/lib/bioroebe/sequence/dna.rb +1 -0
  195. data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +28 -25
  196. data/lib/bioroebe/sequence/protein.rb +105 -3
  197. data/lib/bioroebe/sequence/rna.rb +220 -0
  198. data/lib/bioroebe/sequence/sequence.rb +128 -40
  199. data/lib/bioroebe/shell/menu.rb +3815 -3696
  200. data/lib/bioroebe/shell/misc.rb +9019 -3133
  201. data/lib/bioroebe/shell/readline/readline.rb +1 -1
  202. data/lib/bioroebe/shell/shell.rb +1137 -28
  203. data/lib/bioroebe/siRNA/siRNA.rb +81 -1
  204. data/lib/bioroebe/string_matching/find_longest_substring.rb +3 -2
  205. data/lib/bioroebe/string_matching/hamming_distance.rb +1 -9
  206. data/lib/bioroebe/taxonomy/class_methods.rb +3 -8
  207. data/lib/bioroebe/taxonomy/constants.rb +4 -3
  208. data/lib/bioroebe/taxonomy/edit.rb +2 -1
  209. data/lib/bioroebe/taxonomy/help/help.rb +10 -10
  210. data/lib/bioroebe/taxonomy/help/helpline.rb +2 -2
  211. data/lib/bioroebe/taxonomy/info/check_available.rb +15 -9
  212. data/lib/bioroebe/taxonomy/info/info.rb +18 -11
  213. data/lib/bioroebe/taxonomy/info/is_dna.rb +46 -36
  214. data/lib/bioroebe/taxonomy/interactive.rb +140 -104
  215. data/lib/bioroebe/taxonomy/menu.rb +27 -18
  216. data/lib/bioroebe/taxonomy/parse_fasta.rb +3 -1
  217. data/lib/bioroebe/taxonomy/shared.rb +1 -0
  218. data/lib/bioroebe/taxonomy/taxonomy.rb +1 -0
  219. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +31 -24
  220. data/lib/bioroebe/toplevel_methods/colourize_related_methods.rb +164 -0
  221. data/lib/bioroebe/toplevel_methods/databases.rb +1 -1
  222. data/lib/bioroebe/toplevel_methods/digest.rb +18 -8
  223. data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +107 -63
  224. data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +14 -2
  225. data/lib/bioroebe/toplevel_methods/frequencies.rb +8 -1
  226. data/lib/bioroebe/toplevel_methods/misc.rb +175 -11
  227. data/lib/bioroebe/toplevel_methods/nucleotides.rb +118 -46
  228. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +2 -0
  229. data/lib/bioroebe/toplevel_methods/palindromes.rb +75 -47
  230. data/lib/bioroebe/toplevel_methods/taxonomy.rb +3 -3
  231. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +5 -0
  232. data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +1 -9
  233. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +1 -9
  234. data/lib/bioroebe/utility_scripts/compacter/compacter.rb +251 -0
  235. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +1 -9
  236. data/lib/bioroebe/utility_scripts/consensus_sequence.rb +6 -6
  237. data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +1 -9
  238. data/lib/bioroebe/utility_scripts/dot_alignment.rb +1 -9
  239. data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +1 -4
  240. data/lib/bioroebe/utility_scripts/parse_taxonomy.rb +2 -2
  241. data/lib/bioroebe/utility_scripts/permutations.rb +36 -9
  242. data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -5
  243. data/lib/bioroebe/utility_scripts/showorf/reset.rb +1 -4
  244. data/lib/bioroebe/version/version.rb +2 -2
  245. data/lib/bioroebe/www/embeddable_interface.rb +121 -58
  246. data/lib/bioroebe/www/sinatra/sinatra.rb +186 -71
  247. data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +2 -2
  248. data/lib/bioroebe/yaml/aminoacids/weight_of_common_proteins.yml +17 -17
  249. data/lib/bioroebe/yaml/configuration/browser.yml +1 -1
  250. data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -1
  251. data/lib/bioroebe/yaml/consensus_sequences/consensus_sequences.yml +1 -0
  252. data/lib/bioroebe/yaml/genomes/README.md +3 -4
  253. data/lib/bioroebe/yaml/nucleotides/nucleotides.yml +5 -0
  254. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +57 -57
  255. data/spec/README.md +6 -0
  256. data/spec/project_wide_specification/classes.md +5 -0
  257. metadata +107 -70
  258. data/doc/setup.rb +0 -1655
  259. data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +0 -50
  260. data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +0 -86
  261. data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +0 -117
  262. data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +0 -981
  263. data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +0 -156
  264. data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +0 -128
  265. data/lib/bioroebe/genbank/genbank_parser.rb +0 -291
  266. data/lib/bioroebe/java/bioroebe/AllInOne.class +0 -0
  267. data/lib/bioroebe/java/bioroebe/Cat.class +0 -0
  268. data/lib/bioroebe/java/bioroebe/Codons.java +0 -22
  269. data/lib/bioroebe/java/bioroebe/IsPalindrome.class +0 -0
  270. data/lib/bioroebe/java/bioroebe/PartnerNucleotide.class +0 -0
  271. data/lib/bioroebe/java/bioroebe/PartnerNucleotide.java +0 -19
  272. data/lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.class +0 -0
  273. data/lib/bioroebe/java/bioroebe/ToplevelMethods.class +0 -0
  274. data/lib/bioroebe/java/bioroebe.jar +0 -0
  275. data/lib/bioroebe/shell/add.rb +0 -108
  276. data/lib/bioroebe/shell/assign.rb +0 -360
  277. data/lib/bioroebe/shell/chop_and_cut.rb +0 -281
  278. data/lib/bioroebe/shell/constants.rb +0 -166
  279. data/lib/bioroebe/shell/download.rb +0 -335
  280. data/lib/bioroebe/shell/enable_and_disable.rb +0 -158
  281. data/lib/bioroebe/shell/enzymes.rb +0 -310
  282. data/lib/bioroebe/shell/fasta.rb +0 -345
  283. data/lib/bioroebe/shell/gtk.rb +0 -76
  284. data/lib/bioroebe/shell/history.rb +0 -132
  285. data/lib/bioroebe/shell/initialize.rb +0 -217
  286. data/lib/bioroebe/shell/loop.rb +0 -74
  287. data/lib/bioroebe/shell/prompt.rb +0 -107
  288. data/lib/bioroebe/shell/random.rb +0 -289
  289. data/lib/bioroebe/shell/reset.rb +0 -335
  290. data/lib/bioroebe/shell/scan_and_parse.rb +0 -135
  291. data/lib/bioroebe/shell/search.rb +0 -337
  292. data/lib/bioroebe/shell/sequences.rb +0 -200
  293. data/lib/bioroebe/shell/show_report_and_display.rb +0 -2901
  294. data/lib/bioroebe/shell/startup.rb +0 -127
  295. data/lib/bioroebe/shell/taxonomy.rb +0 -14
  296. data/lib/bioroebe/shell/tk.rb +0 -23
  297. data/lib/bioroebe/shell/user_input.rb +0 -88
  298. data/lib/bioroebe/shell/xorg.rb +0 -45
  299. data/lib/bioroebe/utility_scripts/compacter.rb +0 -131
  300. /data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.java → src/BisulfiteTreatment.java} +0 -0
  301. /data/lib/bioroebe/java/bioroebe/{RemoveFile.class → src/RemoveFile.class} +0 -0
data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml CHANGED
@@ -49,7 +49,7 @@ AccII: CGCG 2
49
49
  AccIII: TCCGGA 1
50
50
  Acc16I: TGCGCA 3
51
51
  Acc65I: GGTACC 1
52
- Acc113I: AGTACT 3
52
+ Acc113I: AGTACT 3 # blunt end
53
53
  AccB1I: GGYRCC 1
54
54
  AccB7I: CCANNNNNTGG 7
55
55
  AclI: AACGTT 2
@@ -104,15 +104,15 @@ AxyI: CCTNAGG 2
104
104
  # === b tig
105
105
  # =========================================================================== #
106
106
  BsaI: GGTCTC(1/5) # URL: https://www.neb.com/tools-and-resources/selection-charts/enzymes-with-nonpalindromic-sequences
107
- BalI: TGGCCA 3
108
- BamHI: GGATCC 1
109
- BanI: GGYRCC 1
110
- BanII: GRGCYC 5
111
- BanIII: ATCGAT 2
112
- BbeI: GGCGCC 5
113
- BbrPI: CACGTG 3
114
- BbuI: GCATGC 5
115
- Bbv12I: GWGCWC 5
107
+ BalI: TGGCCA 3
108
+ BamHI: GGATCC 1
109
+ BanI: GGYRCC 1
110
+ BanII: GRGCYC 5
111
+ BanIII: ATCGAT 2 # At CG.
112
+ BbeI: GGCGCC 5
113
+ BbrPI: CACGTG 3
114
+ BbuI: GCATGC 5
115
+ Bbv12I: GWGCWC 5
116
116
  BclI: TGATCA 1
117
117
  BcnI: CCSGG 2
118
118
  BcoI: CYCGRG 1
@@ -129,21 +129,21 @@ BlnI: CCTAGG 1
129
129
  BloHII: CTGCAG 5
130
130
  BlpI: GCTNAGC 2
131
131
  Bme18I: GGWCC 1
132
- Bme1390I: CCNGG 2
133
- Bme1580I: GKGCMC 5
134
- BmtI: GCTAGC 5
135
- BmyI: GDGCHC 5
136
- BoxI: GACNNNNGTC 5
137
- Bpu14I: TTCGAA 2
138
- Bpu1102I: GCTNAGC 2
139
- Bsa29I: ATCGAT 2
140
- BsaAI: YACGTR 3
141
- BsaBI: GATNNNNATC 5
142
- BsaHI: GRCGYC 2
143
- BsaJI: CCNNGG 1
144
- BsaOI: CGRYCG 4
145
- BsaWI: WCCGGW 1
146
- BscI: ATCGAT 2
132
+ Bme1390I: CCNGG 2
133
+ Bme1580I: GKGCMC 5
134
+ BmtI: GCTAGC 5
135
+ BmyI: GDGCHC 5
136
+ BoxI: GACNNNNGTC 5
137
+ Bpu14I: TTCGAA 2
138
+ Bpu1102I: GCTNAGC 2
139
+ Bsa29I: ATCGAT 2
140
+ BsaAI: YACGTR 3
141
+ BsaBI: GATNNNNATC 5
142
+ BsaHI: GRCGYC 2
143
+ BsaJI: CCNNGG 1
144
+ BsaOI: CGRYCG 4
145
+ BsaWI: WCCGGW 1
146
+ BscI: ATCGAT 2
147
147
  Bsc4I: CCNNNNNNNGG 7
148
148
  BscBI: GGNNCC 3
149
149
  BscFI: GATC 0
@@ -337,14 +337,14 @@ EspI: GCTNAGC 2
337
337
  # =========================================================================== #
338
338
  # === f tig
339
339
  # =========================================================================== #
340
- FatI: CATG 0
341
- FauNDI: CATATG 2
342
- FbaI: TGATCA 1
343
- FblI: GTMKAC 2
344
- FmuI: GGNCC 4
345
- FnuDII: CGCG 2
346
- Fnu4HI: GCNGC 2
347
- FriOI: GRGCYC 5
340
+ FatI: CATG 0
341
+ FauNDI: CATATG 2
342
+ FbaI: TGATCA 1
343
+ FblI: GTMKAC 2
344
+ FmuI: GGNCC 4
345
+ FnuDII: CGCG 2
346
+ Fnu4HI: GCNGC 2
347
+ FriOI: GRGCYC 5
348
348
  FseI: GGCCGGCC 6
349
349
  FspI: TGCGCA 3
350
350
  FspAI: RTGCGCAY 4
@@ -495,31 +495,31 @@ Ppu10I: ATGCAT 1
495
495
  PpuMI: RGGWCCY 2
496
496
  PpuXI: RGGWCCY 2
497
497
  PshAI: GACNNNNGTC 5
498
- PshBI: ATTAAT 2
499
- PsiI: TTATAA 3
500
- Psp03I: GGWCC 4
501
- Psp5II: RGGWCCY 2
502
- Psp6I: CCWGG 0
503
- Psp1406I: AACGTT 2
504
- PspAI: CCCGGG 1
505
- Psp124BI: GAGCTC 5
506
- PspEI: GGTNACC 1
507
- PspGI: CCWGG 0
508
- PspLI: CGTACG 1
509
- PspN4I: GGNNCC 3
510
- PspOMI: GGGCCC 1
511
- PspPI: GGNCC 1
512
- PspPPI: RGGWCCY 2
513
- PssI: RGGNCCY 5
514
- PstI: CTGCAG 5
515
- PsuI: RGATCY 1
498
+ PshBI: ATTAAT 2
499
+ PsiI: TTATAA 3
500
+ Psp03I: GGWCC 4
501
+ Psp5II: RGGWCCY 2
502
+ Psp6I: CCWGG 0
503
+ Psp1406I: AACGTT 2
504
+ PspAI: CCCGGG 1
505
+ Psp124BI: GAGCTC 5
506
+ PspEI: GGTNACC 1
507
+ PspGI: CCWGG 0
508
+ PspLI: CGTACG 1
509
+ PspN4I: GGNNCC 3
510
+ PspOMI: GGGCCC 1
511
+ PspPI: GGNCC 1
512
+ PspPPI: RGGWCCY 2
513
+ PssI: RGGNCCY 5
514
+ PstI: CTGCAG 5
515
+ PsuI: RGATCY 1
516
516
  PsyI: GACNNNGTC 4
517
- PvuI: CGATCG 4
518
- PvuII: CAGCTG 3
519
- RcaI: TCATGA 1
520
- RsaI: GTAC 2
521
- RsrII: CGGWCCG 2
522
- Rsr2I: CGGWCCG 2
517
+ PvuI: CGATCG 4
518
+ PvuII: CAGCTG 3 # will cleave at 5'-CAG/CTG-3', and generate blunt termini.
519
+ RcaI: TCATGA 1
520
+ RsaI: GTAC 2
521
+ RsrII: CGGWCCG 2
522
+ Rsr2I: CGGWCCG 2
523
523
 
524
524
  # =========================================================================== #
525
525
  # === s tig
data/spec/README.md ADDED
@@ -0,0 +1,6 @@
1
+ This directory may contain some tests for the specification of
2
+ the bioroebe project.
3
+
4
+ Since as of April 2023, it may also include some high-level
5
+ specifications that can be used to implement the same set of
6
+ software for different programming languages.
data/spec/project_wide_specification/classes.md ADDED
@@ -0,0 +1,5 @@
1
+ - class Sequence represents a class.
2
+
3
+ - DNA must subclass from Sequence.
4
+
5
+ - RNA must subclass from Sequence.
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bioroebe
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.10.80
4
+ version: 0.12.24
5
5
  platform: ruby
6
6
  authors:
7
7
  - Robert A. Heiler
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2022-06-24 00:00:00.000000000 Z
11
+ date: 2023-09-12 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: chemistry_paradise
@@ -94,8 +94,8 @@ dependencies:
94
94
  - - ">="
95
95
  - !ruby/object:Gem::Version
96
96
  version: '0'
97
- description: "\nWelcome to the bioroebe-0.10.x release series! It is recommended to\nuse
98
- ruby 3.x for this series, as it is the most tested version of \nruby in regards
97
+ description: "\nThis is the bioroebe-0.12.x release series. It is recommended\nto
98
+ use ruby 3.x for this series, as it is the most tested \nversion of ruby in regards
99
99
  to this project.\n\nThe bioroebe-project is a software suite focusing on bio-related\nlife
100
100
  sciences in general - in particular molecular biology, molecular\ngenetics, bioinformatics,
101
101
  biotechnology, system biology, synthetic\nbiology and related topics close to the
@@ -119,6 +119,7 @@ executables:
119
119
  - biomart_console
120
120
  - bioroebe
121
121
  - bioroebe_controller
122
+ - bioroebe_hash
122
123
  - bioshell
123
124
  - blosum_2D_table
124
125
  - calculate_n50_value
@@ -127,6 +128,7 @@ executables:
127
128
  - codon_to_aminoacid
128
129
  - colourize_this_fasta_sequence
129
130
  - compact_fasta_file
131
+ - compacter
130
132
  - complement
131
133
  - complementary_dna_strand
132
134
  - complementary_rna_strand
@@ -163,6 +165,7 @@ executables:
163
165
  - palindrome_generator
164
166
  - parse_fasta
165
167
  - partner_nucleotide
168
+ - plain_palindrome
166
169
  - possible_codons_for_this_aminoacid
167
170
  - random_dna_sequence
168
171
  - random_sequence
@@ -207,6 +210,7 @@ files:
207
210
  - bin/biomart_console
208
211
  - bin/bioroebe
209
212
  - bin/bioroebe_controller
213
+ - bin/bioroebe_hash
210
214
  - bin/bioshell
211
215
  - bin/blosum_2D_table
212
216
  - bin/calculate_n50_value
@@ -215,6 +219,7 @@ files:
215
219
  - bin/codon_to_aminoacid
216
220
  - bin/colourize_this_fasta_sequence
217
221
  - bin/compact_fasta_file
222
+ - bin/compacter
218
223
  - bin/complement
219
224
  - bin/complementary_dna_strand
220
225
  - bin/complementary_rna_strand
@@ -251,6 +256,7 @@ files:
251
256
  - bin/palindrome_generator
252
257
  - bin/parse_fasta
253
258
  - bin/partner_nucleotide
259
+ - bin/plain_palindrome
254
260
  - bin/possible_codons_for_this_aminoacid
255
261
  - bin/random_dna_sequence
256
262
  - bin/random_sequence
@@ -294,14 +300,19 @@ files:
294
300
  - doc/quality_control/README.md
295
301
  - doc/quality_control/commandline_applications.md
296
302
  - doc/resources.md
297
- - doc/setup.rb
298
303
  - doc/statistics/statistics.md
299
304
  - doc/todo/README.md
300
305
  - doc/todo/bioroebe_GUI_todo.md
306
+ - doc/todo/bioroebe_java_todo.md
301
307
  - doc/todo/bioroebe_todo.md
302
308
  - doc/using_biomart.md
303
309
  - html/test.html
304
310
  - lib/bioroebe.rb
311
+ - lib/bioroebe/C++/DNA.cpp
312
+ - lib/bioroebe/C++/RNA.cpp
313
+ - lib/bioroebe/C++/sequence.cpp
314
+ - lib/bioroebe/abstract/README.md
315
+ - lib/bioroebe/abstract/features.rb
305
316
  - lib/bioroebe/aminoacids/aminoacid_substitution.rb
306
317
  - lib/bioroebe/aminoacids/aminoacids_mass_table.rb
307
318
  - lib/bioroebe/aminoacids/codon_percentage.rb
@@ -314,6 +325,7 @@ files:
314
325
  - lib/bioroebe/annotations/create_annotation_format.rb
315
326
  - lib/bioroebe/autoinclude.rb
316
327
  - lib/bioroebe/base/base.rb
328
+ - lib/bioroebe/base/base_module/base_module.rb
317
329
  - lib/bioroebe/base/colours.rb
318
330
  - lib/bioroebe/base/colours_for_base/colours_for_base.rb
319
331
  - lib/bioroebe/base/commandline_application/README.md
@@ -328,6 +340,7 @@ files:
328
340
  - lib/bioroebe/base/commandline_application/warnings.rb
329
341
  - lib/bioroebe/base/commandline_application/write_what_into.rb
330
342
  - lib/bioroebe/base/initialize.rb
343
+ - lib/bioroebe/base/internal_hash_module/internal_hash_module.rb
331
344
  - lib/bioroebe/base/misc.rb
332
345
  - lib/bioroebe/base/namespace.rb
333
346
  - lib/bioroebe/base/prototype/README.md
@@ -430,13 +443,21 @@ files:
430
443
  - lib/bioroebe/count/count_amount_of_nucleotides.rb
431
444
  - lib/bioroebe/count/count_at.rb
432
445
  - lib/bioroebe/count/count_gc.rb
446
+ - lib/bioroebe/cpp
447
+ - lib/bioroebe/crystal/README.md
448
+ - lib/bioroebe/crystal/to_rna.cr
433
449
  - lib/bioroebe/css/README.md
434
450
  - lib/bioroebe/css/project.css
435
451
  - lib/bioroebe/data/README.md
436
452
  - lib/bioroebe/data/bam/README.md
437
453
  - lib/bioroebe/data/data.txt
454
+ - lib/bioroebe/data/electron_microscopy/pos_example.pos
455
+ - lib/bioroebe/data/electron_microscopy/test_particles.star
438
456
  - lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta
439
457
  - lib/bioroebe/data/fasta/alu_elements.fasta
458
+ - lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_alpha_HBB_mRNA.fasta
459
+ - lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_beta_HBB_mRNA.fasta
460
+ - lib/bioroebe/data/fasta/human/README.md
440
461
  - lib/bioroebe/data/fasta/lady_slippers_orchid.fasta
441
462
  - lib/bioroebe/data/fasta/loxP.fasta
442
463
  - lib/bioroebe/data/fasta/ls_orchid.fasta
@@ -466,7 +487,9 @@ files:
466
487
  - lib/bioroebe/dotplots/advanced_dotplot.rb
467
488
  - lib/bioroebe/dotplots/dotplot.rb
468
489
  - lib/bioroebe/electron_microscopy/coordinate_analyzer.rb
490
+ - lib/bioroebe/electron_microscopy/electron_microscopy_module.rb
469
491
  - lib/bioroebe/electron_microscopy/fix_pos_file.rb
492
+ - lib/bioroebe/electron_microscopy/flipy.rb
470
493
  - lib/bioroebe/electron_microscopy/generate_em2em_file.rb
471
494
  - lib/bioroebe/electron_microscopy/parse_coordinates.rb
472
495
  - lib/bioroebe/electron_microscopy/read_file_xmd.rb
@@ -476,6 +499,7 @@ files:
476
499
  - lib/bioroebe/enzymes/README.md
477
500
  - lib/bioroebe/enzymes/has_this_restriction_enzyme.rb
478
501
  - lib/bioroebe/enzymes/restriction_enzyme.rb
502
+ - lib/bioroebe/enzymes/restriction_enzymes/statistics.rb
479
503
  - lib/bioroebe/enzymes/restriction_enzymes_file.rb
480
504
  - lib/bioroebe/enzymes/return_restriction_enzyme_sequence_and_cut_position.rb
481
505
  - lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb
@@ -497,16 +521,10 @@ files:
497
521
  - lib/bioroebe/fasta_and_fastq/fasta_defline/README.md
498
522
  - lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb
499
523
  - lib/bioroebe/fasta_and_fastq/fasta_parser.rb
524
+ - lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb
500
525
  - lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb
501
526
  - lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb
502
- - lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb
503
- - lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb
504
- - lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb
505
- - lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb
506
527
  - lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb
507
- - lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb
508
- - lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb
509
- - lib/bioroebe/fasta_and_fastq/parse_fasta/run.rb
510
528
  - lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb
511
529
  - lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb
512
530
  - lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb
@@ -519,12 +537,14 @@ files:
519
537
  - lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb
520
538
  - lib/bioroebe/genbank/README.md
521
539
  - lib/bioroebe/genbank/genbank_flat_file_format_generator.rb
522
- - lib/bioroebe/genbank/genbank_parser.rb
523
540
  - lib/bioroebe/gene/gene.rb
541
+ - lib/bioroebe/genome/README.md
542
+ - lib/bioroebe/genome/genome.rb
524
543
  - lib/bioroebe/genomes/genome_pattern.rb
525
544
  - lib/bioroebe/genomes/genome_retriever.rb
526
545
  - lib/bioroebe/gui/experimental/README.md
527
546
  - lib/bioroebe/gui/experimental/snapgene/snapgene.rb
547
+ - lib/bioroebe/gui/gtk
528
548
  - lib/bioroebe/gui/gtk3/README.md
529
549
  - lib/bioroebe/gui/gtk3/alignment/alignment.rb
530
550
  - lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb
@@ -561,11 +581,20 @@ files:
561
581
  - lib/bioroebe/gui/gtk3/three_to_one/title.rb
562
582
  - lib/bioroebe/gui/gtk3/www_finder/www_finder.config
563
583
  - lib/bioroebe/gui/gtk3/www_finder/www_finder.rb
584
+ - lib/bioroebe/gui/javafx/bioroebe.jar
585
+ - lib/bioroebe/gui/javafx/bioroebe.mf
586
+ - lib/bioroebe/gui/javafx/bioroebe/Bioroebe.class
587
+ - lib/bioroebe/gui/javafx/bioroebe/Bioroebe.java
588
+ - lib/bioroebe/gui/javafx/module-info.class
589
+ - lib/bioroebe/gui/javafx/module-info.java
590
+ - lib/bioroebe/gui/jruby/alignment/alignment.rb
591
+ - lib/bioroebe/gui/jruby/aminoacid_composition/aminoacid_composition.rb
564
592
  - lib/bioroebe/gui/jruby/blosum_matrix_viewer/blosum_matrix_viewer.rb
565
593
  - lib/bioroebe/gui/libui/README.md
566
594
  - lib/bioroebe/gui/libui/alignment/alignment.rb
567
595
  - lib/bioroebe/gui/libui/blosum_matrix_viewer/blosum_matrix_viewer.rb
568
596
  - lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb
597
+ - lib/bioroebe/gui/libui/controller/controller.rb
569
598
  - lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb
570
599
  - lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb
571
600
  - lib/bioroebe/gui/libui/hamming_distance/hamming_distance.rb
@@ -575,6 +604,8 @@ files:
575
604
  - lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb
576
605
  - lib/bioroebe/gui/libui/show_codon_usage/show_codon_usage.rb
577
606
  - lib/bioroebe/gui/libui/three_to_one/three_to_one.rb
607
+ - lib/bioroebe/gui/shared_code/alignment/alignment_module.rb
608
+ - lib/bioroebe/gui/shared_code/aminoacid_composition/aminoacid_composition_module.rb
578
609
  - lib/bioroebe/gui/shared_code/blosum_matrix_viewer/blosum_matrix_viewer_module.rb
579
610
  - lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb
580
611
  - lib/bioroebe/gui/shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb
@@ -582,6 +613,10 @@ files:
582
613
  - lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb
583
614
  - lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb
584
615
  - lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb
616
+ - lib/bioroebe/gui/swing/three_to_one/ThreeToOne$1.class
617
+ - lib/bioroebe/gui/swing/three_to_one/ThreeToOne$CloseListener.class
618
+ - lib/bioroebe/gui/swing/three_to_one/ThreeToOne.class
619
+ - lib/bioroebe/gui/swing/three_to_one/ThreeToOne.java
585
620
  - lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb
586
621
  - lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb
587
622
  - lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb
@@ -592,10 +627,13 @@ files:
592
627
  - lib/bioroebe/images/BIOROEBE_NEW_LOGO.png
593
628
  - lib/bioroebe/images/BlosumMatrixViewer.png
594
629
  - lib/bioroebe/images/DnaToAminoacidWidget.png
630
+ - lib/bioroebe/images/FORWARD_PRIMER.png
595
631
  - lib/bioroebe/images/PRINTED_AMINOACID_TABLE.png
632
+ - lib/bioroebe/images/REVERSE_PRIMER.png
596
633
  - lib/bioroebe/images/class_ConvertAminoacidToDNA.png
597
634
  - lib/bioroebe/images/class_SimpleStringComparer.png
598
635
  - lib/bioroebe/images/example_of_FASTA_coloured_output.png
636
+ - lib/bioroebe/images/images.html
599
637
  - lib/bioroebe/images/libui_hamming_distance_widget.png
600
638
  - lib/bioroebe/images/pretty_DNA_picture.png
601
639
  - lib/bioroebe/images/primer_design_widget.png
@@ -604,40 +642,39 @@ files:
604
642
  - lib/bioroebe/images/small_DNA_logo.png
605
643
  - lib/bioroebe/images/small_drosophila_image.png
606
644
  - lib/bioroebe/java/README.md
607
- - lib/bioroebe/java/bioroebe.jar
608
- - lib/bioroebe/java/bioroebe/AllInOne.class
609
645
  - lib/bioroebe/java/bioroebe/AllInOne.java
610
646
  - lib/bioroebe/java/bioroebe/Base.class
611
647
  - lib/bioroebe/java/bioroebe/Base.java
612
- - lib/bioroebe/java/bioroebe/BisulfiteTreatment.class
613
- - lib/bioroebe/java/bioroebe/BisulfiteTreatment.java
614
- - lib/bioroebe/java/bioroebe/Cat.class
615
- - lib/bioroebe/java/bioroebe/Codons.class
616
- - lib/bioroebe/java/bioroebe/Codons.java
617
- - lib/bioroebe/java/bioroebe/Esystem.class
618
- - lib/bioroebe/java/bioroebe/Esystem.java
619
648
  - lib/bioroebe/java/bioroebe/GUI/BaseFrame.class
620
649
  - lib/bioroebe/java/bioroebe/GUI/BaseFrame.java
621
- - lib/bioroebe/java/bioroebe/GenerateRandomDnaSequence.class
622
- - lib/bioroebe/java/bioroebe/GenerateRandomDnaSequence.java
623
- - lib/bioroebe/java/bioroebe/IsPalindrome.class
624
650
  - lib/bioroebe/java/bioroebe/IsPalindrome.java
625
- - lib/bioroebe/java/bioroebe/PartnerNucleotide.class
626
- - lib/bioroebe/java/bioroebe/PartnerNucleotide.java
627
651
  - lib/bioroebe/java/bioroebe/README.md
628
- - lib/bioroebe/java/bioroebe/RemoveFile.class
629
- - lib/bioroebe/java/bioroebe/RemoveFile.java
630
- - lib/bioroebe/java/bioroebe/RemoveNumbers.class
631
- - lib/bioroebe/java/bioroebe/RemoveNumbers.java
632
- - lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.class
633
652
  - lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.java
634
653
  - lib/bioroebe/java/bioroebe/SaveFile.java
635
654
  - lib/bioroebe/java/bioroebe/Sequence.java
636
655
  - lib/bioroebe/java/bioroebe/ToCamelcase.class
637
656
  - lib/bioroebe/java/bioroebe/ToCamelcase.java
638
- - lib/bioroebe/java/bioroebe/ToplevelMethods.class
657
+ - lib/bioroebe/java/bioroebe/ToRNA.java
639
658
  - lib/bioroebe/java/bioroebe/ToplevelMethods.java
640
659
  - lib/bioroebe/java/bioroebe/enums/DNA.java
660
+ - lib/bioroebe/java/bioroebe/src/BisulfiteTreatment.class
661
+ - lib/bioroebe/java/bioroebe/src/BisulfiteTreatment.java
662
+ - lib/bioroebe/java/bioroebe/src/Codons.class
663
+ - lib/bioroebe/java/bioroebe/src/Codons.java
664
+ - lib/bioroebe/java/bioroebe/src/Commandline.class
665
+ - lib/bioroebe/java/bioroebe/src/Commandline.java
666
+ - lib/bioroebe/java/bioroebe/src/Esystem.class
667
+ - lib/bioroebe/java/bioroebe/src/Esystem.java
668
+ - lib/bioroebe/java/bioroebe/src/GenerateRandomDnaSequence.class
669
+ - lib/bioroebe/java/bioroebe/src/GenerateRandomDnaSequence.java
670
+ - lib/bioroebe/java/bioroebe/src/PartnerNucleotide.class
671
+ - lib/bioroebe/java/bioroebe/src/PartnerNucleotide.java
672
+ - lib/bioroebe/java/bioroebe/src/RemoveFile.class
673
+ - lib/bioroebe/java/bioroebe/src/RemoveFile.java
674
+ - lib/bioroebe/java/bioroebe/src/RemoveNumbers.class
675
+ - lib/bioroebe/java/bioroebe/src/RemoveNumbers.java
676
+ - lib/bioroebe/java/bioroebe/src/toplevel_methods/BaseComposition.class
677
+ - lib/bioroebe/java/bioroebe/src/toplevel_methods/BaseComposition.java
641
678
  - lib/bioroebe/matplotlib/matplotlib_generator.rb
642
679
  - lib/bioroebe/misc/quiz/README.md
643
680
  - lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb
@@ -677,6 +714,25 @@ files:
677
714
  - lib/bioroebe/project/project.rb
678
715
  - lib/bioroebe/protein_structure/alpha_helix.rb
679
716
  - lib/bioroebe/protein_structure/helical_wheel.rb
717
+ - lib/bioroebe/python/README.md
718
+ - lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc
719
+ - lib/bioroebe/python/gui/gtk3/all_in_one.css
720
+ - lib/bioroebe/python/gui/gtk3/all_in_one.py
721
+ - lib/bioroebe/python/gui/gtk3/widget1.py
722
+ - lib/bioroebe/python/gui/tkinter/all_in_one.py
723
+ - lib/bioroebe/python/mymodule.py
724
+ - lib/bioroebe/python/protein_to_dna.py
725
+ - lib/bioroebe/python/shell/shell.py
726
+ - lib/bioroebe/python/to_rna.py
727
+ - lib/bioroebe/python/toplevel_methods/convert_dna_to_aminoacid_sequence.py
728
+ - lib/bioroebe/python/toplevel_methods/esystem.py
729
+ - lib/bioroebe/python/toplevel_methods/open_in_browser.py
730
+ - lib/bioroebe/python/toplevel_methods/palindromes.py
731
+ - lib/bioroebe/python/toplevel_methods/rds.py
732
+ - lib/bioroebe/python/toplevel_methods/shuffleseq.py
733
+ - lib/bioroebe/python/toplevel_methods/three_delimiter.py
734
+ - lib/bioroebe/python/toplevel_methods/time_and_date.py
735
+ - lib/bioroebe/python/toplevel_methods/to_camelcase.py
680
736
  - lib/bioroebe/raw_sequence/README.md
681
737
  - lib/bioroebe/raw_sequence/raw_sequence.rb
682
738
  - lib/bioroebe/readline/README.md
@@ -718,42 +774,19 @@ files:
718
774
  - lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb
719
775
  - lib/bioroebe/sequence/protein.rb
720
776
  - lib/bioroebe/sequence/reverse_complement.rb
777
+ - lib/bioroebe/sequence/rna.rb
721
778
  - lib/bioroebe/sequence/sequence.rb
722
- - lib/bioroebe/shell/add.rb
723
- - lib/bioroebe/shell/assign.rb
724
- - lib/bioroebe/shell/chop_and_cut.rb
725
779
  - lib/bioroebe/shell/colours/colours.rb
726
780
  - lib/bioroebe/shell/configuration/additionally_set_xorg_buffer.yml
727
781
  - lib/bioroebe/shell/configuration/may_we_show_the_startup_information.yml
728
782
  - lib/bioroebe/shell/configuration/upcase_nucleotides.yml
729
783
  - lib/bioroebe/shell/configuration/use_silent_startup.yml
730
- - lib/bioroebe/shell/constants.rb
731
- - lib/bioroebe/shell/download.rb
732
- - lib/bioroebe/shell/enable_and_disable.rb
733
- - lib/bioroebe/shell/enzymes.rb
734
- - lib/bioroebe/shell/fasta.rb
735
- - lib/bioroebe/shell/gtk.rb
736
784
  - lib/bioroebe/shell/help/class.rb
737
785
  - lib/bioroebe/shell/help/help.rb
738
- - lib/bioroebe/shell/history.rb
739
- - lib/bioroebe/shell/initialize.rb
740
- - lib/bioroebe/shell/loop.rb
741
786
  - lib/bioroebe/shell/menu.rb
742
787
  - lib/bioroebe/shell/misc.rb
743
- - lib/bioroebe/shell/prompt.rb
744
- - lib/bioroebe/shell/random.rb
745
788
  - lib/bioroebe/shell/readline/readline.rb
746
- - lib/bioroebe/shell/reset.rb
747
- - lib/bioroebe/shell/scan_and_parse.rb
748
- - lib/bioroebe/shell/search.rb
749
- - lib/bioroebe/shell/sequences.rb
750
789
  - lib/bioroebe/shell/shell.rb
751
- - lib/bioroebe/shell/show_report_and_display.rb
752
- - lib/bioroebe/shell/startup.rb
753
- - lib/bioroebe/shell/taxonomy.rb
754
- - lib/bioroebe/shell/tk.rb
755
- - lib/bioroebe/shell/user_input.rb
756
- - lib/bioroebe/shell/xorg.rb
757
790
  - lib/bioroebe/siRNA/README.md
758
791
  - lib/bioroebe/siRNA/siRNA.rb
759
792
  - lib/bioroebe/string_matching/README.md
@@ -796,6 +829,7 @@ files:
796
829
  - lib/bioroebe/toplevel_methods/cat.rb
797
830
  - lib/bioroebe/toplevel_methods/chunked_display.rb
798
831
  - lib/bioroebe/toplevel_methods/cliner.rb
832
+ - lib/bioroebe/toplevel_methods/colourize_related_methods.rb
799
833
  - lib/bioroebe/toplevel_methods/complement.rb
800
834
  - lib/bioroebe/toplevel_methods/convert_global_env.rb
801
835
  - lib/bioroebe/toplevel_methods/databases.rb
@@ -848,7 +882,7 @@ files:
848
882
  - lib/bioroebe/utility_scripts/align_open_reading_frames.rb
849
883
  - lib/bioroebe/utility_scripts/analyse_local_dataset.rb
850
884
  - lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb
851
- - lib/bioroebe/utility_scripts/compacter.rb
885
+ - lib/bioroebe/utility_scripts/compacter/compacter.rb
852
886
  - lib/bioroebe/utility_scripts/compseq/compseq.rb
853
887
  - lib/bioroebe/utility_scripts/consensus_sequence.rb
854
888
  - lib/bioroebe/utility_scripts/create_batch_entrez_file.rb
@@ -946,6 +980,7 @@ files:
946
980
  - lib/bioroebe/yaml/configuration/try_to_use_matplotlib.yml
947
981
  - lib/bioroebe/yaml/configuration/use_opn.yml
948
982
  - lib/bioroebe/yaml/configuration/use_this_database.yml
983
+ - lib/bioroebe/yaml/consensus_sequences/consensus_sequences.yml
949
984
  - lib/bioroebe/yaml/create_these_directories_on_startup/create_these_directories_on_startup.yml
950
985
  - lib/bioroebe/yaml/default_dna_input.yml
951
986
  - lib/bioroebe/yaml/enzymes/enzyme_classes.yml
@@ -981,6 +1016,8 @@ files:
981
1016
  - lib/bioroebe/yaml/talens.yml
982
1017
  - lib/bioroebe/yaml/viruses/ecoli_phages.yml
983
1018
  - lib/bioroebe/yaml/viruses/viruses.yml
1019
+ - spec/README.md
1020
+ - spec/project_wide_specification/classes.md
984
1021
  - spec/testing_toplevel_method_editor.rb
985
1022
  - spec/testing_toplevel_method_url.rb
986
1023
  - spec/testing_toplevel_method_verbose.rb
@@ -1025,7 +1062,7 @@ post_install_message: |2+
1025
1062
 
1026
1063
  For more documentation, have a look at:
1027
1064
 
1028
- https://www.rubydoc.info/gems/bioroebe/0.10.80
1065
+ https://www.rubydoc.info/gems/bioroebe/0.12.24
1029
1066
 
1030
1067
  rdoc_options: []
1031
1068
  require_paths:
@@ -1034,24 +1071,24 @@ required_ruby_version: !ruby/object:Gem::Requirement
1034
1071
  requirements:
1035
1072
  - - ">="
1036
1073
  - !ruby/object:Gem::Version
1037
- version: 2.5.8
1074
+ version: 2.7.6
1038
1075
  required_rubygems_version: !ruby/object:Gem::Requirement
1039
1076
  requirements:
1040
1077
  - - ">="
1041
1078
  - !ruby/object:Gem::Version
1042
- version: 3.3.16
1079
+ version: 3.4.18
1043
1080
  requirements: []
1044
- rubygems_version: 3.3.16
1081
+ rubygems_version: 3.4.18
1045
1082
  signing_key:
1046
1083
  specification_version: 4
1047
- summary: 'Welcome to the bioroebe-0.10.x release series! It is recommended to use
1048
- ruby 3.x for this series, as it is the most tested version of ruby in regards to
1049
- this project. The bioroebe-project is a software suite focusing on bio-related
1050
- life sciences in general - in particular molecular biology, molecular genetics,
1051
- bioinformatics, biotechnology, system biology, synthetic biology and related topics
1052
- close to the life sciences in general. The primary objective for the bioroebe project
1053
- is to provide a "practical glue" between these different topics while also focusing
1054
- on "getting real work done", as a toolset-project, trying to efficiently solve existing
1084
+ summary: 'This is the bioroebe-0.12.x release series. It is recommended to use ruby
1085
+ 3.x for this series, as it is the most tested version of ruby in regards to this
1086
+ project. The bioroebe-project is a software suite focusing on bio-related life
1087
+ sciences in general - in particular molecular biology, molecular genetics, bioinformatics,
1088
+ biotechnology, system biology, synthetic biology and related topics close to the
1089
+ life sciences in general. The primary objective for the bioroebe project is to
1090
+ provide a "practical glue" between these different topics while also focusing on
1091
+ "getting real work done", as a toolset-project, trying to efficiently solve existing
1055
1092
  problems. For additional information about this project, have a look at the link
1056
1093
  called "documentation" on the rubygems webpage of this gem, on the very bottom right
1057
1094
  side (The direct URL is: https://www.rubydoc.info/gems/bioroebe/ ).'