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
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