bioroebe 0.10.80

Sign up to get free protection for your applications and to get access to all the features.
Files changed (802) hide show
  1. checksums.yaml +7 -0
  2. data/LICENSE.md +428 -0
  3. data/README.md +9280 -0
  4. data/bin/advanced_dotplot +7 -0
  5. data/bin/align_open_reading_frames +12 -0
  6. data/bin/all_positions_of_this_nucleotide +7 -0
  7. data/bin/aminoacid_composition +7 -0
  8. data/bin/aminoacid_frequencies +12 -0
  9. data/bin/aminoacid_substitution +7 -0
  10. data/bin/automatically_rename_this_fasta_file +7 -0
  11. data/bin/base_composition +7 -0
  12. data/bin/batch_create_windows_executables +7 -0
  13. data/bin/biomart_console +11 -0
  14. data/bin/bioroebe +27 -0
  15. data/bin/bioroebe_controller +10 -0
  16. data/bin/bioshell +26 -0
  17. data/bin/blosum_2D_table +12 -0
  18. data/bin/calculate_n50_value +12 -0
  19. data/bin/chunked_display +12 -0
  20. data/bin/codon_frequency +9 -0
  21. data/bin/codon_to_aminoacid +30 -0
  22. data/bin/colourize_this_fasta_sequence +14 -0
  23. data/bin/compact_fasta_file +7 -0
  24. data/bin/complement +7 -0
  25. data/bin/complementary_dna_strand +12 -0
  26. data/bin/complementary_rna_strand +12 -0
  27. data/bin/compseq +7 -0
  28. data/bin/consensus_sequence +17 -0
  29. data/bin/count_AT +12 -0
  30. data/bin/count_GC +12 -0
  31. data/bin/create_random_aminoacids +7 -0
  32. data/bin/decode_this_aminoacid_sequence +20 -0
  33. data/bin/deduce_aminoacid_sequence +13 -0
  34. data/bin/deduce_most_likely_aminoacid_sequence +7 -0
  35. data/bin/display_aminoacid_table +12 -0
  36. data/bin/display_open_reading_frames +7 -0
  37. data/bin/dna_to_aminoacid_sequence +7 -0
  38. data/bin/dna_to_rna +7 -0
  39. data/bin/downcase_chunked_display +12 -0
  40. data/bin/download_this_pdb +7 -0
  41. data/bin/fasta_index +7 -0
  42. data/bin/fetch_data_from_uniprot +12 -0
  43. data/bin/filter_away_invalid_nucleotides +12 -0
  44. data/bin/find_substring +19 -0
  45. data/bin/genbank_to_fasta +7 -0
  46. data/bin/hamming_distance +12 -0
  47. data/bin/input_as_dna +12 -0
  48. data/bin/is_palindrome +13 -0
  49. data/bin/leading_five_prime +7 -0
  50. data/bin/levensthein +7 -0
  51. data/bin/longest_ORF +14 -0
  52. data/bin/longest_substring +12 -0
  53. data/bin/n_stop_codons_in_this_sequence +15 -0
  54. data/bin/open_reading_frames +14 -0
  55. data/bin/overwrite_fasta_header +7 -0
  56. data/bin/palindrome_2D_structure +7 -0
  57. data/bin/palindrome_generator +7 -0
  58. data/bin/parse_fasta +7 -0
  59. data/bin/partner_nucleotide +9 -0
  60. data/bin/possible_codons_for_this_aminoacid +12 -0
  61. data/bin/random_dna_sequence +12 -0
  62. data/bin/random_sequence +12 -0
  63. data/bin/raw_hamming_distance +12 -0
  64. data/bin/return_longest_substring_via_LCS_algorithm +7 -0
  65. data/bin/reverse_complement +7 -0
  66. data/bin/reverse_sequence +7 -0
  67. data/bin/ruler +12 -0
  68. data/bin/scan_this_input_for_startcodons +12 -0
  69. data/bin/short_aminoacid_letter_from_long_aminoacid_name +7 -0
  70. data/bin/show_atomic_composition +7 -0
  71. data/bin/show_codon_usage +12 -0
  72. data/bin/show_fasta_header +7 -0
  73. data/bin/show_nucleotide_sequence +7 -0
  74. data/bin/show_this_codon_table +7 -0
  75. data/bin/show_this_dna_sequence +7 -0
  76. data/bin/showorf +14 -0
  77. data/bin/simplify_fasta +7 -0
  78. data/bin/sort_aminoacid_based_on_its_hydrophobicity +7 -0
  79. data/bin/split_this_fasta_file_into_chromosomes +7 -0
  80. data/bin/strict_filter_away_invalid_aminoacids +7 -0
  81. data/bin/taxonomy +63 -0
  82. data/bin/three_to_one +7 -0
  83. data/bin/to_rna +7 -0
  84. data/bin/trailing_three_prime +7 -0
  85. data/bin/trypsin_digest +7 -0
  86. data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +7 -0
  87. data/bioroebe.gemspec +97 -0
  88. data/doc/IUPAC_aminoacids_code.md +36 -0
  89. data/doc/IUPAC_nucleotide_code.md +19 -0
  90. data/doc/README.gen +9237 -0
  91. data/doc/blosum.md +5 -0
  92. data/doc/compatibility/BIO_PHP.md +37 -0
  93. data/doc/compatibility/README.md +3 -0
  94. data/doc/compatibility/emboss.md +56 -0
  95. data/doc/extensive_usage_example.md +35 -0
  96. data/doc/german_names_for_the_aminoacids.md +27 -0
  97. data/doc/instructions_for_the_taxonomy_subproject.md +504 -0
  98. data/doc/legacy_paths.md +9 -0
  99. data/doc/pdb_ATOM_entry.md +33 -0
  100. data/doc/quality_control/README.md +2 -0
  101. data/doc/quality_control/commandline_applications.md +13 -0
  102. data/doc/resources.md +23 -0
  103. data/doc/setup.rb +1655 -0
  104. data/doc/statistics/statistics.md +41 -0
  105. data/doc/todo/README.md +5 -0
  106. data/doc/todo/bioroebe_GUI_todo.md +15 -0
  107. data/doc/todo/bioroebe_todo.md +2823 -0
  108. data/doc/using_biomart.md +258 -0
  109. data/html/test.html +144 -0
  110. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +118 -0
  111. data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +118 -0
  112. data/lib/bioroebe/aminoacids/codon_percentage.rb +189 -0
  113. data/lib/bioroebe/aminoacids/colourize_hydrophilic_and_hydrophobic_aminoacids.rb +110 -0
  114. data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +221 -0
  115. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +460 -0
  116. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +231 -0
  117. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +184 -0
  118. data/lib/bioroebe/annotations/README.md +2 -0
  119. data/lib/bioroebe/annotations/create_annotation_format.rb +208 -0
  120. data/lib/bioroebe/autoinclude.rb +7 -0
  121. data/lib/bioroebe/base/base.rb +35 -0
  122. data/lib/bioroebe/base/colours.rb +14 -0
  123. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +275 -0
  124. data/lib/bioroebe/base/commandline_application/README.md +7 -0
  125. data/lib/bioroebe/base/commandline_application/aminoacids.rb +33 -0
  126. data/lib/bioroebe/base/commandline_application/commandline_application.rb +37 -0
  127. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +144 -0
  128. data/lib/bioroebe/base/commandline_application/directory.rb +33 -0
  129. data/lib/bioroebe/base/commandline_application/extract.rb +22 -0
  130. data/lib/bioroebe/base/commandline_application/misc.rb +485 -0
  131. data/lib/bioroebe/base/commandline_application/opn.rb +47 -0
  132. data/lib/bioroebe/base/commandline_application/reset.rb +40 -0
  133. data/lib/bioroebe/base/commandline_application/warnings.rb +36 -0
  134. data/lib/bioroebe/base/commandline_application/write_what_into.rb +29 -0
  135. data/lib/bioroebe/base/initialize.rb +18 -0
  136. data/lib/bioroebe/base/misc.rb +94 -0
  137. data/lib/bioroebe/base/namespace.rb +16 -0
  138. data/lib/bioroebe/base/prototype/README.md +12 -0
  139. data/lib/bioroebe/base/prototype/e_and_ee.rb +24 -0
  140. data/lib/bioroebe/base/prototype/misc.rb +108 -0
  141. data/lib/bioroebe/base/prototype/mkdir.rb +20 -0
  142. data/lib/bioroebe/base/prototype/prototype.rb +21 -0
  143. data/lib/bioroebe/base/prototype/reset.rb +26 -0
  144. data/lib/bioroebe/base/reset.rb +11 -0
  145. data/lib/bioroebe/biomart/LICENSE.md +27 -0
  146. data/lib/bioroebe/biomart/attribute.rb +77 -0
  147. data/lib/bioroebe/biomart/biomart.rb +227 -0
  148. data/lib/bioroebe/biomart/database.rb +128 -0
  149. data/lib/bioroebe/biomart/dataset.rb +572 -0
  150. data/lib/bioroebe/biomart/filter.rb +97 -0
  151. data/lib/bioroebe/biomart/server.rb +152 -0
  152. data/lib/bioroebe/blosum/blosum.rb +88 -0
  153. data/lib/bioroebe/calculate/calculate_blosum_score.rb +145 -0
  154. data/lib/bioroebe/calculate/calculate_gc_content.rb +301 -0
  155. data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +100 -0
  156. data/lib/bioroebe/calculate/calculate_melting_temperature.rb +398 -0
  157. data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +304 -0
  158. data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +166 -0
  159. data/lib/bioroebe/cell/README.md +1 -0
  160. data/lib/bioroebe/cell/cell.rb +63 -0
  161. data/lib/bioroebe/cleave_and_digest/README.md +2 -0
  162. data/lib/bioroebe/cleave_and_digest/cleave.rb +80 -0
  163. data/lib/bioroebe/cleave_and_digest/digestion.rb +75 -0
  164. data/lib/bioroebe/cleave_and_digest/trypsin.rb +192 -0
  165. data/lib/bioroebe/codon_tables/README.md +9 -0
  166. data/lib/bioroebe/codon_tables/frequencies/287_Pseudomonas_aeruginosa.yml +101 -0
  167. data/lib/bioroebe/codon_tables/frequencies/3702_Arabidopsis_thaliana.yml +77 -0
  168. data/lib/bioroebe/codon_tables/frequencies/4932_Saccharomyces_cerevisiae.yml +103 -0
  169. data/lib/bioroebe/codon_tables/frequencies/7227_Drosophila_melanogaster.yml +71 -0
  170. data/lib/bioroebe/codon_tables/frequencies/83333_Escherichia_coli_K12.yml +103 -0
  171. data/lib/bioroebe/codon_tables/frequencies/9606_Homo_sapiens.yml +123 -0
  172. data/lib/bioroebe/codon_tables/frequencies/9685_Felis_catus.yml +78 -0
  173. data/lib/bioroebe/codon_tables/frequencies/README.md +10 -0
  174. data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +337 -0
  175. data/lib/bioroebe/codons/README.md +28 -0
  176. data/lib/bioroebe/codons/codon_table.rb +416 -0
  177. data/lib/bioroebe/codons/codon_tables.rb +123 -0
  178. data/lib/bioroebe/codons/codons.rb +517 -0
  179. data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +102 -0
  180. data/lib/bioroebe/codons/detect_minimal_codon.rb +180 -0
  181. data/lib/bioroebe/codons/determine_optimal_codons.rb +74 -0
  182. data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +380 -0
  183. data/lib/bioroebe/codons/sanitize_codon_frequency.rb +144 -0
  184. data/lib/bioroebe/codons/show_codon_tables.rb +130 -0
  185. data/lib/bioroebe/codons/show_codon_usage.rb +197 -0
  186. data/lib/bioroebe/codons/show_this_codon_table.rb +573 -0
  187. data/lib/bioroebe/codons/start_codons.rb +105 -0
  188. data/lib/bioroebe/colours/colour_schemes/README.md +10 -0
  189. data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +38 -0
  190. data/lib/bioroebe/colours/colour_schemes/buried.rb +70 -0
  191. data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +101 -0
  192. data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +262 -0
  193. data/lib/bioroebe/colours/colour_schemes/helix.rb +65 -0
  194. data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +70 -0
  195. data/lib/bioroebe/colours/colour_schemes/nucleotide.rb +47 -0
  196. data/lib/bioroebe/colours/colour_schemes/score.rb +112 -0
  197. data/lib/bioroebe/colours/colour_schemes/simple.rb +42 -0
  198. data/lib/bioroebe/colours/colour_schemes/strand.rb +65 -0
  199. data/lib/bioroebe/colours/colour_schemes/taylor.rb +58 -0
  200. data/lib/bioroebe/colours/colour_schemes/turn.rb +65 -0
  201. data/lib/bioroebe/colours/colour_schemes/zappo.rb +59 -0
  202. data/lib/bioroebe/colours/colourize_sequence.rb +262 -0
  203. data/lib/bioroebe/colours/colours.rb +119 -0
  204. data/lib/bioroebe/colours/misc_colours.rb +80 -0
  205. data/lib/bioroebe/colours/rev.rb +41 -0
  206. data/lib/bioroebe/colours/sdir.rb +21 -0
  207. data/lib/bioroebe/colours/sfancy.rb +21 -0
  208. data/lib/bioroebe/colours/sfile.rb +21 -0
  209. data/lib/bioroebe/colours/simp.rb +21 -0
  210. data/lib/bioroebe/colours/swarn.rb +29 -0
  211. data/lib/bioroebe/colours/use_colours.rb +27 -0
  212. data/lib/bioroebe/configuration/configuration.rb +114 -0
  213. data/lib/bioroebe/configuration/constants.rb +35 -0
  214. data/lib/bioroebe/constants/GUIs.rb +79 -0
  215. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +146 -0
  216. data/lib/bioroebe/constants/base_directory.rb +120 -0
  217. data/lib/bioroebe/constants/carriage_return.rb +14 -0
  218. data/lib/bioroebe/constants/codon_tables.rb +77 -0
  219. data/lib/bioroebe/constants/database_constants.rb +107 -0
  220. data/lib/bioroebe/constants/files_and_directories.rb +579 -0
  221. data/lib/bioroebe/constants/misc.rb +189 -0
  222. data/lib/bioroebe/constants/newline.rb +14 -0
  223. data/lib/bioroebe/constants/nucleotides.rb +114 -0
  224. data/lib/bioroebe/constants/regex.rb +28 -0
  225. data/lib/bioroebe/constants/roebe.rb +38 -0
  226. data/lib/bioroebe/constants/row_terminator.rb +16 -0
  227. data/lib/bioroebe/constants/tabulator.rb +14 -0
  228. data/lib/bioroebe/constants/unicode.rb +12 -0
  229. data/lib/bioroebe/constants/urls.rb +50 -0
  230. data/lib/bioroebe/conversions/README.md +3 -0
  231. data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +298 -0
  232. data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +569 -0
  233. data/lib/bioroebe/count/README.md +1 -0
  234. data/lib/bioroebe/count/count_amount_of_aminoacids.rb +352 -0
  235. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +491 -0
  236. data/lib/bioroebe/count/count_at.rb +39 -0
  237. data/lib/bioroebe/count/count_gc.rb +43 -0
  238. data/lib/bioroebe/css/README.md +5 -0
  239. data/lib/bioroebe/css/project.css +121 -0
  240. data/lib/bioroebe/data/README.md +10 -0
  241. data/lib/bioroebe/data/bam/README.md +1 -0
  242. data/lib/bioroebe/data/data.txt +192 -0
  243. data/lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta +12 -0
  244. data/lib/bioroebe/data/fasta/alu_elements.fasta +42 -0
  245. data/lib/bioroebe/data/fasta/lady_slippers_orchid.fasta +1197 -0
  246. data/lib/bioroebe/data/fasta/loxP.fasta +2 -0
  247. data/lib/bioroebe/data/fasta/ls_orchid.fasta +1197 -0
  248. data/lib/bioroebe/data/fasta/pax6_in_mouse.fasta +1 -0
  249. data/lib/bioroebe/data/fasta/test.fasta +7 -0
  250. data/lib/bioroebe/data/fasta/test_DNA.fasta +1 -0
  251. data/lib/bioroebe/data/fastq/fastq_example_file.fastq +32 -0
  252. data/lib/bioroebe/data/fastq/fastq_example_file_SP1.fastq +1000 -0
  253. data/lib/bioroebe/data/fastq/one_random_fastq_entry.fastq +4 -0
  254. data/lib/bioroebe/data/genbank/sample_file.genbank +15 -0
  255. data/lib/bioroebe/data/genbank/standard.fasta +3 -0
  256. data/lib/bioroebe/data/gff/Escherichia_coli_K12_plasmid_F_DNA_NC_002483.1.gff3 +345 -0
  257. data/lib/bioroebe/data/gff/sample.gff +2 -0
  258. data/lib/bioroebe/data/gff/test_gene.gff +4 -0
  259. data/lib/bioroebe/data/gff/transcripts.gff +16 -0
  260. data/lib/bioroebe/data/gtf/README.md +1 -0
  261. data/lib/bioroebe/data/json/example_config.json +48 -0
  262. data/lib/bioroebe/data/pdb/1VII.pdb +754 -0
  263. data/lib/bioroebe/data/pdb/ala_phe_ala.pdb +228 -0
  264. data/lib/bioroebe/data/pdb/rcsb_pdb_1VII.fasta +2 -0
  265. data/lib/bioroebe/data/phylip/README.md +11 -0
  266. data/lib/bioroebe/data/phylip/example.phylip +7 -0
  267. data/lib/bioroebe/data/svg/example.svg +301 -0
  268. data/lib/bioroebe/databases/README.md +1 -0
  269. data/lib/bioroebe/databases/download_taxonomy_database.rb +102 -0
  270. data/lib/bioroebe/dotplots/README.md +5 -0
  271. data/lib/bioroebe/dotplots/advanced_dotplot.rb +256 -0
  272. data/lib/bioroebe/dotplots/dotplot.rb +184 -0
  273. data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +191 -0
  274. data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +102 -0
  275. data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +122 -0
  276. data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +197 -0
  277. data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +282 -0
  278. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +131 -0
  279. data/lib/bioroebe/encoding/README.md +2 -0
  280. data/lib/bioroebe/encoding/encoding.rb +45 -0
  281. data/lib/bioroebe/enzymes/README.md +2 -0
  282. data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +46 -0
  283. data/lib/bioroebe/enzymes/restriction_enzyme.rb +200 -0
  284. data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +72 -0
  285. data/lib/bioroebe/enzymes/return_restriction_enzyme_sequence_and_cut_position.rb +80 -0
  286. data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +65 -0
  287. data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +119 -0
  288. data/lib/bioroebe/exceptions/README.md +2 -0
  289. data/lib/bioroebe/exceptions/exceptions.rb +17 -0
  290. data/lib/bioroebe/ext/LICENCE.md +5 -0
  291. data/lib/bioroebe/ext/README.md +7 -0
  292. data/lib/bioroebe/ext/main.cpp +45 -0
  293. data/lib/bioroebe/ext/nucleotide.cpp +24 -0
  294. data/lib/bioroebe/ext/nussinov_algorithm.cpp +348 -0
  295. data/lib/bioroebe/ext/sequence +0 -0
  296. data/lib/bioroebe/ext/sequence.cpp +162 -0
  297. data/lib/bioroebe/fasta_and_fastq/README.md +6 -0
  298. data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +88 -0
  299. data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +151 -0
  300. data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +111 -0
  301. data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +248 -0
  302. data/lib/bioroebe/fasta_and_fastq/fasta_defline/README.md +2 -0
  303. data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +113 -0
  304. data/lib/bioroebe/fasta_and_fastq/fasta_parser.rb +167 -0
  305. data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +131 -0
  306. data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +87 -0
  307. data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +50 -0
  308. data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +86 -0
  309. data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +117 -0
  310. data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +981 -0
  311. data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +27 -0
  312. data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +156 -0
  313. data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +128 -0
  314. data/lib/bioroebe/fasta_and_fastq/parse_fasta/run.rb +20 -0
  315. data/lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb +83 -0
  316. data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +112 -0
  317. data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +135 -0
  318. data/lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb +188 -0
  319. data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +111 -0
  320. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb +26 -0
  321. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/menu.rb +41 -0
  322. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/misc.rb +23 -0
  323. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/reset.rb +68 -0
  324. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb +290 -0
  325. data/lib/bioroebe/genbank/README.md +1 -0
  326. data/lib/bioroebe/genbank/genbank_flat_file_format_generator.rb +275 -0
  327. data/lib/bioroebe/genbank/genbank_parser.rb +291 -0
  328. data/lib/bioroebe/gene/gene.rb +64 -0
  329. data/lib/bioroebe/genomes/genome_pattern.rb +165 -0
  330. data/lib/bioroebe/genomes/genome_retriever.rb +79 -0
  331. data/lib/bioroebe/gui/experimental/README.md +1 -0
  332. data/lib/bioroebe/gui/experimental/snapgene/snapgene.rb +147 -0
  333. data/lib/bioroebe/gui/gtk3/README.md +2 -0
  334. data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +337 -0
  335. data/lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb +510 -0
  336. data/lib/bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb +55 -0
  337. data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.config +6 -0
  338. data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb +29 -0
  339. data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +196 -0
  340. data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.config +6 -0
  341. data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +106 -0
  342. data/lib/bioroebe/gui/gtk3/controller/controller.rb +406 -0
  343. data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +609 -0
  344. data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.config +6 -0
  345. data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +189 -0
  346. data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +245 -0
  347. data/lib/bioroebe/gui/gtk3/format_converter/format_converter.rb +346 -0
  348. data/lib/bioroebe/gui/gtk3/gene/gene.rb +182 -0
  349. data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.config +6 -0
  350. data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +370 -0
  351. data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.config +6 -0
  352. data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +175 -0
  353. data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +428 -0
  354. data/lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb +342 -0
  355. data/lib/bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb +580 -0
  356. data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.config +6 -0
  357. data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +182 -0
  358. data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +566 -0
  359. data/lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.config +6 -0
  360. data/lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb +329 -0
  361. data/lib/bioroebe/gui/gtk3/show_codon_table/misc.rb +556 -0
  362. data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +171 -0
  363. data/lib/bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb +146 -0
  364. data/lib/bioroebe/gui/gtk3/sizeseq/sizeseq.rb +207 -0
  365. data/lib/bioroebe/gui/gtk3/three_to_one/three_to_one.rb +279 -0
  366. data/lib/bioroebe/gui/gtk3/three_to_one/title.rb +23 -0
  367. data/lib/bioroebe/gui/gtk3/www_finder/www_finder.config +6 -0
  368. data/lib/bioroebe/gui/gtk3/www_finder/www_finder.rb +368 -0
  369. data/lib/bioroebe/gui/jruby/blosum_matrix_viewer/blosum_matrix_viewer.rb +82 -0
  370. data/lib/bioroebe/gui/libui/README.md +4 -0
  371. data/lib/bioroebe/gui/libui/alignment/alignment.rb +114 -0
  372. data/lib/bioroebe/gui/libui/blosum_matrix_viewer/blosum_matrix_viewer.rb +112 -0
  373. data/lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +60 -0
  374. data/lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +161 -0
  375. data/lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +76 -0
  376. data/lib/bioroebe/gui/libui/hamming_distance/hamming_distance.rb +135 -0
  377. data/lib/bioroebe/gui/libui/levensthein_distance/levensthein_distance.rb +118 -0
  378. data/lib/bioroebe/gui/libui/protein_to_DNA/protein_to_DNA.rb +115 -0
  379. data/lib/bioroebe/gui/libui/random_sequence/random_sequence.rb +174 -0
  380. data/lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb +132 -0
  381. data/lib/bioroebe/gui/libui/show_codon_usage/show_codon_usage.rb +89 -0
  382. data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +111 -0
  383. data/lib/bioroebe/gui/shared_code/blosum_matrix_viewer/blosum_matrix_viewer_module.rb +42 -0
  384. data/lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb +216 -0
  385. data/lib/bioroebe/gui/shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb +284 -0
  386. data/lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb +402 -0
  387. data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +192 -0
  388. data/lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb +72 -0
  389. data/lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb +213 -0
  390. data/lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb +206 -0
  391. data/lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb +140 -0
  392. data/lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb +262 -0
  393. data/lib/bioroebe/gui/tk/levensthein_distance/levensthein_distance.rb +243 -0
  394. data/lib/bioroebe/gui/tk/three_to_one/three_to_one.rb +199 -0
  395. data/lib/bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb +519 -0
  396. data/lib/bioroebe/images/BIOROEBE.png +0 -0
  397. data/lib/bioroebe/images/BIOROEBE_NEW_LOGO.png +0 -0
  398. data/lib/bioroebe/images/BlosumMatrixViewer.png +0 -0
  399. data/lib/bioroebe/images/DnaToAminoacidWidget.png +0 -0
  400. data/lib/bioroebe/images/PRINTED_AMINOACID_TABLE.png +0 -0
  401. data/lib/bioroebe/images/class_ConvertAminoacidToDNA.png +0 -0
  402. data/lib/bioroebe/images/class_SimpleStringComparer.png +0 -0
  403. data/lib/bioroebe/images/example_of_FASTA_coloured_output.png +0 -0
  404. data/lib/bioroebe/images/libui_hamming_distance_widget.png +0 -0
  405. data/lib/bioroebe/images/pretty_DNA_picture.png +0 -0
  406. data/lib/bioroebe/images/primer_design_widget.png +0 -0
  407. data/lib/bioroebe/images/restriction_enzyme_commandline_result.png +0 -0
  408. data/lib/bioroebe/images/ruby-gtk_three_to_one_widget.png +0 -0
  409. data/lib/bioroebe/images/small_DNA_logo.png +0 -0
  410. data/lib/bioroebe/images/small_drosophila_image.png +0 -0
  411. data/lib/bioroebe/java/README.md +6 -0
  412. data/lib/bioroebe/java/bioroebe/AllInOne.class +0 -0
  413. data/lib/bioroebe/java/bioroebe/AllInOne.java +214 -0
  414. data/lib/bioroebe/java/bioroebe/Base.class +0 -0
  415. data/lib/bioroebe/java/bioroebe/Base.java +102 -0
  416. data/lib/bioroebe/java/bioroebe/BisulfiteTreatment.class +0 -0
  417. data/lib/bioroebe/java/bioroebe/BisulfiteTreatment.java +23 -0
  418. data/lib/bioroebe/java/bioroebe/Cat.class +0 -0
  419. data/lib/bioroebe/java/bioroebe/Codons.class +0 -0
  420. data/lib/bioroebe/java/bioroebe/Codons.java +22 -0
  421. data/lib/bioroebe/java/bioroebe/Esystem.class +0 -0
  422. data/lib/bioroebe/java/bioroebe/Esystem.java +47 -0
  423. data/lib/bioroebe/java/bioroebe/GUI/BaseFrame.class +0 -0
  424. data/lib/bioroebe/java/bioroebe/GUI/BaseFrame.java +65 -0
  425. data/lib/bioroebe/java/bioroebe/GenerateRandomDnaSequence.class +0 -0
  426. data/lib/bioroebe/java/bioroebe/GenerateRandomDnaSequence.java +32 -0
  427. data/lib/bioroebe/java/bioroebe/IsPalindrome.class +0 -0
  428. data/lib/bioroebe/java/bioroebe/IsPalindrome.java +18 -0
  429. data/lib/bioroebe/java/bioroebe/PartnerNucleotide.class +0 -0
  430. data/lib/bioroebe/java/bioroebe/PartnerNucleotide.java +19 -0
  431. data/lib/bioroebe/java/bioroebe/README.md +4 -0
  432. data/lib/bioroebe/java/bioroebe/RemoveFile.class +0 -0
  433. data/lib/bioroebe/java/bioroebe/RemoveFile.java +24 -0
  434. data/lib/bioroebe/java/bioroebe/RemoveNumbers.class +0 -0
  435. data/lib/bioroebe/java/bioroebe/RemoveNumbers.java +14 -0
  436. data/lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.class +0 -0
  437. data/lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.java +20 -0
  438. data/lib/bioroebe/java/bioroebe/SaveFile.java +44 -0
  439. data/lib/bioroebe/java/bioroebe/Sequence.java +28 -0
  440. data/lib/bioroebe/java/bioroebe/ToCamelcase.class +0 -0
  441. data/lib/bioroebe/java/bioroebe/ToCamelcase.java +32 -0
  442. data/lib/bioroebe/java/bioroebe/ToplevelMethods.class +0 -0
  443. data/lib/bioroebe/java/bioroebe/ToplevelMethods.java +15 -0
  444. data/lib/bioroebe/java/bioroebe/enums/DNA.java +6 -0
  445. data/lib/bioroebe/java/bioroebe.jar +0 -0
  446. data/lib/bioroebe/matplotlib/matplotlib_generator.rb +104 -0
  447. data/lib/bioroebe/misc/quiz/README.md +6 -0
  448. data/lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb +163 -0
  449. data/lib/bioroebe/misc/ruler.rb +244 -0
  450. data/lib/bioroebe/misc/useful_formulas.rb +129 -0
  451. data/lib/bioroebe/ncbi/efetch.rb +253 -0
  452. data/lib/bioroebe/ncbi/ncbi.rb +93 -0
  453. data/lib/bioroebe/ngs/README.md +2 -0
  454. data/lib/bioroebe/ngs/phred_quality_score_table.rb +123 -0
  455. data/lib/bioroebe/nucleotides/complementary_dna_strand.rb +166 -0
  456. data/lib/bioroebe/nucleotides/molecular_weight_of_nucleotides.rb +135 -0
  457. data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +198 -0
  458. data/lib/bioroebe/nucleotides/sanitize_nucleotide_sequence.rb +133 -0
  459. data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +556 -0
  460. data/lib/bioroebe/palindromes/palindrome_2D_structure.rb +139 -0
  461. data/lib/bioroebe/palindromes/palindrome_finder.rb +208 -0
  462. data/lib/bioroebe/palindromes/palindrome_generator.rb +272 -0
  463. data/lib/bioroebe/parsers/biolang_parser.rb +156 -0
  464. data/lib/bioroebe/parsers/blosum_parser.rb +222 -0
  465. data/lib/bioroebe/parsers/genbank_parser.rb +78 -0
  466. data/lib/bioroebe/parsers/gff.rb +346 -0
  467. data/lib/bioroebe/parsers/parse_embl.rb +76 -0
  468. data/lib/bioroebe/parsers/stride_parser.rb +117 -0
  469. data/lib/bioroebe/patterns/README.md +5 -0
  470. data/lib/bioroebe/patterns/analyse_glycosylation_pattern.rb +149 -0
  471. data/lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb +66 -0
  472. data/lib/bioroebe/patterns/profile_pattern.rb +182 -0
  473. data/lib/bioroebe/patterns/rgg_scanner.rb +160 -0
  474. data/lib/bioroebe/patterns/scan_for_repeat.rb +157 -0
  475. data/lib/bioroebe/pdb/download_this_pdb.rb +67 -0
  476. data/lib/bioroebe/pdb/fetch_fasta_sequence_from_pdb.rb +164 -0
  477. data/lib/bioroebe/pdb/parse_mmCIF_file.rb +63 -0
  478. data/lib/bioroebe/pdb/parse_pdb_file.rb +1086 -0
  479. data/lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb +225 -0
  480. data/lib/bioroebe/perl/README.md +7 -0
  481. data/lib/bioroebe/perl/local_to_global.pl +694 -0
  482. data/lib/bioroebe/project/project.rb +264 -0
  483. data/lib/bioroebe/protein_structure/alpha_helix.rb +96 -0
  484. data/lib/bioroebe/protein_structure/helical_wheel.rb +205 -0
  485. data/lib/bioroebe/raw_sequence/README.md +17 -0
  486. data/lib/bioroebe/raw_sequence/raw_sequence.rb +557 -0
  487. data/lib/bioroebe/readline/README.md +2 -0
  488. data/lib/bioroebe/readline/readline.rb +31 -0
  489. data/lib/bioroebe/regexes/README.md +2 -0
  490. data/lib/bioroebe/regexes/regexes.rb +34 -0
  491. data/lib/bioroebe/requires/commandline_application.rb +5 -0
  492. data/lib/bioroebe/requires/require_all_aminoacids_files.rb +28 -0
  493. data/lib/bioroebe/requires/require_all_calculate_files.rb +26 -0
  494. data/lib/bioroebe/requires/require_all_codon_files.rb +26 -0
  495. data/lib/bioroebe/requires/require_all_colour_scheme_files.rb +26 -0
  496. data/lib/bioroebe/requires/require_all_count_files.rb +26 -0
  497. data/lib/bioroebe/requires/require_all_dotplot_files.rb +28 -0
  498. data/lib/bioroebe/requires/require_all_electron_microscopy_files.rb +26 -0
  499. data/lib/bioroebe/requires/require_all_enzymes_files.rb +28 -0
  500. data/lib/bioroebe/requires/require_all_fasta_and_fastq_files.rb +32 -0
  501. data/lib/bioroebe/requires/require_all_nucleotides_files.rb +28 -0
  502. data/lib/bioroebe/requires/require_all_palindromes_files.rb +29 -0
  503. data/lib/bioroebe/requires/require_all_parser_files.rb +28 -0
  504. data/lib/bioroebe/requires/require_all_pattern_files.rb +29 -0
  505. data/lib/bioroebe/requires/require_all_pdb_files.rb +26 -0
  506. data/lib/bioroebe/requires/require_all_sequence_files.rb +26 -0
  507. data/lib/bioroebe/requires/require_all_string_matching_files.rb +28 -0
  508. data/lib/bioroebe/requires/require_all_svg_files.rb +12 -0
  509. data/lib/bioroebe/requires/require_all_taxonomy_files.rb +35 -0
  510. data/lib/bioroebe/requires/require_all_utility_scripts_files.rb +32 -0
  511. data/lib/bioroebe/requires/require_cleave_and_digest.rb +24 -0
  512. data/lib/bioroebe/requires/require_colours.rb +20 -0
  513. data/lib/bioroebe/requires/require_encoding.rb +7 -0
  514. data/lib/bioroebe/requires/require_sequence.rb +7 -0
  515. data/lib/bioroebe/requires/require_the_bioroebe_project.rb +162 -0
  516. data/lib/bioroebe/requires/require_the_bioroebe_shell.rb +7 -0
  517. data/lib/bioroebe/requires/require_the_bioroebe_sinatra_components.rb +7 -0
  518. data/lib/bioroebe/requires/require_the_constants.rb +23 -0
  519. data/lib/bioroebe/requires/require_the_toplevel_methods.rb +29 -0
  520. data/lib/bioroebe/requires/require_yaml.rb +94 -0
  521. data/lib/bioroebe/sequence/alignment.rb +214 -0
  522. data/lib/bioroebe/sequence/dna.rb +211 -0
  523. data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +404 -0
  524. data/lib/bioroebe/sequence/protein.rb +281 -0
  525. data/lib/bioroebe/sequence/reverse_complement.rb +148 -0
  526. data/lib/bioroebe/sequence/sequence.rb +706 -0
  527. data/lib/bioroebe/shell/add.rb +108 -0
  528. data/lib/bioroebe/shell/assign.rb +360 -0
  529. data/lib/bioroebe/shell/chop_and_cut.rb +281 -0
  530. data/lib/bioroebe/shell/colours/colours.rb +235 -0
  531. data/lib/bioroebe/shell/configuration/additionally_set_xorg_buffer.yml +1 -0
  532. data/lib/bioroebe/shell/configuration/may_we_show_the_startup_information.yml +1 -0
  533. data/lib/bioroebe/shell/configuration/upcase_nucleotides.yml +1 -0
  534. data/lib/bioroebe/shell/configuration/use_silent_startup.yml +1 -0
  535. data/lib/bioroebe/shell/constants.rb +166 -0
  536. data/lib/bioroebe/shell/download.rb +335 -0
  537. data/lib/bioroebe/shell/enable_and_disable.rb +158 -0
  538. data/lib/bioroebe/shell/enzymes.rb +310 -0
  539. data/lib/bioroebe/shell/fasta.rb +345 -0
  540. data/lib/bioroebe/shell/gtk.rb +76 -0
  541. data/lib/bioroebe/shell/help/class.rb +443 -0
  542. data/lib/bioroebe/shell/help/help.rb +25 -0
  543. data/lib/bioroebe/shell/history.rb +132 -0
  544. data/lib/bioroebe/shell/initialize.rb +217 -0
  545. data/lib/bioroebe/shell/loop.rb +74 -0
  546. data/lib/bioroebe/shell/menu.rb +5320 -0
  547. data/lib/bioroebe/shell/misc.rb +4341 -0
  548. data/lib/bioroebe/shell/prompt.rb +107 -0
  549. data/lib/bioroebe/shell/random.rb +289 -0
  550. data/lib/bioroebe/shell/readline/readline.rb +91 -0
  551. data/lib/bioroebe/shell/reset.rb +335 -0
  552. data/lib/bioroebe/shell/scan_and_parse.rb +135 -0
  553. data/lib/bioroebe/shell/search.rb +337 -0
  554. data/lib/bioroebe/shell/sequences.rb +200 -0
  555. data/lib/bioroebe/shell/shell.rb +41 -0
  556. data/lib/bioroebe/shell/show_report_and_display.rb +2901 -0
  557. data/lib/bioroebe/shell/startup.rb +127 -0
  558. data/lib/bioroebe/shell/taxonomy.rb +14 -0
  559. data/lib/bioroebe/shell/tk.rb +23 -0
  560. data/lib/bioroebe/shell/user_input.rb +88 -0
  561. data/lib/bioroebe/shell/xorg.rb +45 -0
  562. data/lib/bioroebe/siRNA/README.md +2 -0
  563. data/lib/bioroebe/siRNA/siRNA.rb +93 -0
  564. data/lib/bioroebe/string_matching/README.md +13 -0
  565. data/lib/bioroebe/string_matching/find_longest_substring.rb +162 -0
  566. data/lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb +175 -0
  567. data/lib/bioroebe/string_matching/hamming_distance.rb +313 -0
  568. data/lib/bioroebe/string_matching/levensthein.rb +698 -0
  569. data/lib/bioroebe/string_matching/simple_string_comparer.rb +294 -0
  570. data/lib/bioroebe/string_matching/smith_waterman.rb +276 -0
  571. data/lib/bioroebe/svg/README.md +1 -0
  572. data/lib/bioroebe/svg/glyph.rb +719 -0
  573. data/lib/bioroebe/svg/mini_feature.rb +111 -0
  574. data/lib/bioroebe/svg/page.rb +570 -0
  575. data/lib/bioroebe/svg/primitive.rb +70 -0
  576. data/lib/bioroebe/svg/svgee.rb +326 -0
  577. data/lib/bioroebe/svg/track.rb +263 -0
  578. data/lib/bioroebe/taxonomy/README.md +1 -0
  579. data/lib/bioroebe/taxonomy/chart.rb +95 -0
  580. data/lib/bioroebe/taxonomy/class_methods.rb +181 -0
  581. data/lib/bioroebe/taxonomy/colours.rb +26 -0
  582. data/lib/bioroebe/taxonomy/constants.rb +218 -0
  583. data/lib/bioroebe/taxonomy/edit.rb +97 -0
  584. data/lib/bioroebe/taxonomy/help/help.rb +65 -0
  585. data/lib/bioroebe/taxonomy/help/helpline.rb +53 -0
  586. data/lib/bioroebe/taxonomy/info/check_available.rb +143 -0
  587. data/lib/bioroebe/taxonomy/info/info.rb +337 -0
  588. data/lib/bioroebe/taxonomy/info/is_dna.rb +150 -0
  589. data/lib/bioroebe/taxonomy/interactive.rb +1933 -0
  590. data/lib/bioroebe/taxonomy/menu.rb +905 -0
  591. data/lib/bioroebe/taxonomy/node.rb +118 -0
  592. data/lib/bioroebe/taxonomy/parse_fasta.rb +383 -0
  593. data/lib/bioroebe/taxonomy/shared.rb +287 -0
  594. data/lib/bioroebe/taxonomy/taxonomy.rb +521 -0
  595. data/lib/bioroebe/toplevel_methods/ad_hoc_task.rb +56 -0
  596. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +715 -0
  597. data/lib/bioroebe/toplevel_methods/atomic_composition.rb +198 -0
  598. data/lib/bioroebe/toplevel_methods/base_composition.rb +121 -0
  599. data/lib/bioroebe/toplevel_methods/blast.rb +153 -0
  600. data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +57 -0
  601. data/lib/bioroebe/toplevel_methods/cat.rb +71 -0
  602. data/lib/bioroebe/toplevel_methods/chunked_display.rb +92 -0
  603. data/lib/bioroebe/toplevel_methods/cliner.rb +81 -0
  604. data/lib/bioroebe/toplevel_methods/complement.rb +58 -0
  605. data/lib/bioroebe/toplevel_methods/convert_global_env.rb +39 -0
  606. data/lib/bioroebe/toplevel_methods/databases.rb +73 -0
  607. data/lib/bioroebe/toplevel_methods/delimiter.rb +19 -0
  608. data/lib/bioroebe/toplevel_methods/digest.rb +71 -0
  609. data/lib/bioroebe/toplevel_methods/download_and_fetch_data.rb +146 -0
  610. data/lib/bioroebe/toplevel_methods/e.rb +20 -0
  611. data/lib/bioroebe/toplevel_methods/editor.rb +21 -0
  612. data/lib/bioroebe/toplevel_methods/esystem.rb +22 -0
  613. data/lib/bioroebe/toplevel_methods/exponential_growth.rb +74 -0
  614. data/lib/bioroebe/toplevel_methods/extract.rb +56 -0
  615. data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +353 -0
  616. data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +257 -0
  617. data/lib/bioroebe/toplevel_methods/frequencies.rb +92 -0
  618. data/lib/bioroebe/toplevel_methods/hamming_distance.rb +60 -0
  619. data/lib/bioroebe/toplevel_methods/infer.rb +66 -0
  620. data/lib/bioroebe/toplevel_methods/is_on_roebe.rb +39 -0
  621. data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb +101 -0
  622. data/lib/bioroebe/toplevel_methods/levensthein.rb +63 -0
  623. data/lib/bioroebe/toplevel_methods/log_directory.rb +109 -0
  624. data/lib/bioroebe/toplevel_methods/longest_common_substring.rb +55 -0
  625. data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb +88 -0
  626. data/lib/bioroebe/toplevel_methods/matches.rb +259 -0
  627. data/lib/bioroebe/toplevel_methods/misc.rb +432 -0
  628. data/lib/bioroebe/toplevel_methods/nucleotides.rb +715 -0
  629. data/lib/bioroebe/toplevel_methods/number_of_clones.rb +63 -0
  630. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +77 -0
  631. data/lib/bioroebe/toplevel_methods/open_reading_frames.rb +236 -0
  632. data/lib/bioroebe/toplevel_methods/opn.rb +34 -0
  633. data/lib/bioroebe/toplevel_methods/palindromes.rb +127 -0
  634. data/lib/bioroebe/toplevel_methods/parse.rb +59 -0
  635. data/lib/bioroebe/toplevel_methods/phred_error_probability.rb +68 -0
  636. data/lib/bioroebe/toplevel_methods/rds.rb +24 -0
  637. data/lib/bioroebe/toplevel_methods/remove.rb +86 -0
  638. data/lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb +35 -0
  639. data/lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb +68 -0
  640. data/lib/bioroebe/toplevel_methods/rna_splicing.rb +73 -0
  641. data/lib/bioroebe/toplevel_methods/rnalfold.rb +69 -0
  642. data/lib/bioroebe/toplevel_methods/searching_and_finding.rb +116 -0
  643. data/lib/bioroebe/toplevel_methods/shuffleseq.rb +37 -0
  644. data/lib/bioroebe/toplevel_methods/statistics.rb +53 -0
  645. data/lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb +62 -0
  646. data/lib/bioroebe/toplevel_methods/taxonomy.rb +187 -0
  647. data/lib/bioroebe/toplevel_methods/three_delimiter.rb +34 -0
  648. data/lib/bioroebe/toplevel_methods/time_and_date.rb +53 -0
  649. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +26 -0
  650. data/lib/bioroebe/toplevel_methods/truncate.rb +48 -0
  651. data/lib/bioroebe/toplevel_methods/url.rb +36 -0
  652. data/lib/bioroebe/toplevel_methods/verbose.rb +59 -0
  653. data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +191 -0
  654. data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb +119 -0
  655. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +230 -0
  656. data/lib/bioroebe/utility_scripts/compacter.rb +131 -0
  657. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +529 -0
  658. data/lib/bioroebe/utility_scripts/consensus_sequence.rb +374 -0
  659. data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +130 -0
  660. data/lib/bioroebe/utility_scripts/determine_antigenic_areas.rb +115 -0
  661. data/lib/bioroebe/utility_scripts/determine_missing_nucleotides_percentage.rb +137 -0
  662. data/lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb +73 -0
  663. data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +31 -0
  664. data/lib/bioroebe/utility_scripts/display_open_reading_frames/initialize.rb +37 -0
  665. data/lib/bioroebe/utility_scripts/display_open_reading_frames/menu.rb +49 -0
  666. data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb +471 -0
  667. data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb +113 -0
  668. data/lib/bioroebe/utility_scripts/display_open_reading_frames/reset.rb +56 -0
  669. data/lib/bioroebe/utility_scripts/dot_alignment.rb +177 -0
  670. data/lib/bioroebe/utility_scripts/download_files_from_rebase.rb +72 -0
  671. data/lib/bioroebe/utility_scripts/find_gene.rb +202 -0
  672. data/lib/bioroebe/utility_scripts/mirror_repeat.rb +235 -0
  673. data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +151 -0
  674. data/lib/bioroebe/utility_scripts/parse_taxonomy.rb +168 -0
  675. data/lib/bioroebe/utility_scripts/pathways.rb +152 -0
  676. data/lib/bioroebe/utility_scripts/permutations.rb +145 -0
  677. data/lib/bioroebe/utility_scripts/punnet/punnet.rb +126 -0
  678. data/lib/bioroebe/utility_scripts/show_this_dna_sequence.rb +148 -0
  679. data/lib/bioroebe/utility_scripts/showorf/constants.rb +36 -0
  680. data/lib/bioroebe/utility_scripts/showorf/help.rb +33 -0
  681. data/lib/bioroebe/utility_scripts/showorf/initialize.rb +52 -0
  682. data/lib/bioroebe/utility_scripts/showorf/menu.rb +68 -0
  683. data/lib/bioroebe/utility_scripts/showorf/reset.rb +39 -0
  684. data/lib/bioroebe/utility_scripts/showorf/run.rb +152 -0
  685. data/lib/bioroebe/utility_scripts/showorf/show.rb +97 -0
  686. data/lib/bioroebe/utility_scripts/showorf/showorf.rb +488 -0
  687. data/lib/bioroebe/version/version.rb +44 -0
  688. data/lib/bioroebe/viennarna/README.md +3 -0
  689. data/lib/bioroebe/viennarna/rnafold_wrapper.rb +196 -0
  690. data/lib/bioroebe/with_gui.rb +18 -0
  691. data/lib/bioroebe/www/bioroebe.cgi +44 -0
  692. data/lib/bioroebe/www/embeddable_interface.rb +686 -0
  693. data/lib/bioroebe/www/sinatra/sinatra.rb +1013 -0
  694. data/lib/bioroebe/yaml/agarose/agarose_concentrations.yml +21 -0
  695. data/lib/bioroebe/yaml/aminoacids/amino_acids.yml +92 -0
  696. data/lib/bioroebe/yaml/aminoacids/amino_acids_abbreviations.yml +31 -0
  697. data/lib/bioroebe/yaml/aminoacids/amino_acids_average_mass_table.yml +33 -0
  698. data/lib/bioroebe/yaml/aminoacids/amino_acids_classification.yml +18 -0
  699. data/lib/bioroebe/yaml/aminoacids/amino_acids_english.yml +26 -0
  700. data/lib/bioroebe/yaml/aminoacids/amino_acids_frequency.yml +44 -0
  701. data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +61 -0
  702. data/lib/bioroebe/yaml/aminoacids/amino_acids_molecular_formula.yml +32 -0
  703. data/lib/bioroebe/yaml/aminoacids/amino_acids_monoisotopic_mass_table.yml +38 -0
  704. data/lib/bioroebe/yaml/aminoacids/amino_acids_reste.yml +35 -0
  705. data/lib/bioroebe/yaml/aminoacids/amino_acids_three_to_one.yml +34 -0
  706. data/lib/bioroebe/yaml/aminoacids/hydropathy_table.yml +44 -0
  707. data/lib/bioroebe/yaml/aminoacids/molecular_weight.yml +29 -0
  708. data/lib/bioroebe/yaml/aminoacids/simple_aminoacids.yml +66 -0
  709. data/lib/bioroebe/yaml/aminoacids/weight_of_common_proteins.yml +33 -0
  710. data/lib/bioroebe/yaml/antisense/antisense.yml +9 -0
  711. data/lib/bioroebe/yaml/base_composition_of_dna.yml +37 -0
  712. data/lib/bioroebe/yaml/blosum/blosum45.yml +36 -0
  713. data/lib/bioroebe/yaml/blosum/blosum50.yml +34 -0
  714. data/lib/bioroebe/yaml/blosum/blosum62.yml +35 -0
  715. data/lib/bioroebe/yaml/blosum/blosum80.yml +37 -0
  716. data/lib/bioroebe/yaml/blosum/blosum90.yml +36 -0
  717. data/lib/bioroebe/yaml/blosum/blosum_matrix.yml +200 -0
  718. data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +30 -0
  719. data/lib/bioroebe/yaml/codon_tables/1.yml +113 -0
  720. data/lib/bioroebe/yaml/codon_tables/10.yml +89 -0
  721. data/lib/bioroebe/yaml/codon_tables/11.yml +91 -0
  722. data/lib/bioroebe/yaml/codon_tables/12.yml +89 -0
  723. data/lib/bioroebe/yaml/codon_tables/13.yml +89 -0
  724. data/lib/bioroebe/yaml/codon_tables/14.yml +89 -0
  725. data/lib/bioroebe/yaml/codon_tables/15.yml +94 -0
  726. data/lib/bioroebe/yaml/codon_tables/16.yml +89 -0
  727. data/lib/bioroebe/yaml/codon_tables/2.yml +86 -0
  728. data/lib/bioroebe/yaml/codon_tables/21.yml +89 -0
  729. data/lib/bioroebe/yaml/codon_tables/22.yml +89 -0
  730. data/lib/bioroebe/yaml/codon_tables/23.yml +91 -0
  731. data/lib/bioroebe/yaml/codon_tables/24.yml +89 -0
  732. data/lib/bioroebe/yaml/codon_tables/25.yml +89 -0
  733. data/lib/bioroebe/yaml/codon_tables/26.yml +96 -0
  734. data/lib/bioroebe/yaml/codon_tables/27.yml +104 -0
  735. data/lib/bioroebe/yaml/codon_tables/28.yml +97 -0
  736. data/lib/bioroebe/yaml/codon_tables/29.yml +93 -0
  737. data/lib/bioroebe/yaml/codon_tables/3.yml +98 -0
  738. data/lib/bioroebe/yaml/codon_tables/30.yml +91 -0
  739. data/lib/bioroebe/yaml/codon_tables/31.yml +94 -0
  740. data/lib/bioroebe/yaml/codon_tables/33.yml +101 -0
  741. data/lib/bioroebe/yaml/codon_tables/4.yml +96 -0
  742. data/lib/bioroebe/yaml/codon_tables/5.yml +100 -0
  743. data/lib/bioroebe/yaml/codon_tables/6.yml +96 -0
  744. data/lib/bioroebe/yaml/codon_tables/9.yml +97 -0
  745. data/lib/bioroebe/yaml/codon_tables/overview.yml +42 -0
  746. data/lib/bioroebe/yaml/configuration/README.md +12 -0
  747. data/lib/bioroebe/yaml/configuration/browser.yml +1 -0
  748. data/lib/bioroebe/yaml/configuration/colourize_fasta_sequences.yml +14 -0
  749. data/lib/bioroebe/yaml/configuration/default_colours_for_the_aminoacids.yml +28 -0
  750. data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -0
  751. data/lib/bioroebe/yaml/configuration/try_to_use_matplotlib.yml +1 -0
  752. data/lib/bioroebe/yaml/configuration/use_opn.yml +1 -0
  753. data/lib/bioroebe/yaml/configuration/use_this_database.yml +1 -0
  754. data/lib/bioroebe/yaml/create_these_directories_on_startup/create_these_directories_on_startup.yml +9 -0
  755. data/lib/bioroebe/yaml/default_dna_input.yml +3 -0
  756. data/lib/bioroebe/yaml/enzymes/enzyme_classes.yml +15 -0
  757. data/lib/bioroebe/yaml/enzymes/pH-Optima.yml +11 -0
  758. data/lib/bioroebe/yaml/fasta_and_fastq/fastq_quality_schemes.yml +44 -0
  759. data/lib/bioroebe/yaml/genomes/README.md +16 -0
  760. data/lib/bioroebe/yaml/humans/README.md +2 -0
  761. data/lib/bioroebe/yaml/humans/human_chromosomes.yml +53 -0
  762. data/lib/bioroebe/yaml/laboratory/README.md +1 -0
  763. data/lib/bioroebe/yaml/laboratory/pipettes.yml +8 -0
  764. data/lib/bioroebe/yaml/mRNA/mRNA.yml +16 -0
  765. data/lib/bioroebe/yaml/nuclear_localization_sequences.yml +15 -0
  766. data/lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml +29 -0
  767. data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +10 -0
  768. data/lib/bioroebe/yaml/nucleotides/nucleotides.yml +34 -0
  769. data/lib/bioroebe/yaml/nucleotides/nucleotides_weight.yml +12 -0
  770. data/lib/bioroebe/yaml/pathways/README.md +2 -0
  771. data/lib/bioroebe/yaml/pathways/citric_acid_cycle.yml +16 -0
  772. data/lib/bioroebe/yaml/pathways/glycolysis.yml +20 -0
  773. data/lib/bioroebe/yaml/pathways/shikimate_pathway.yml +23 -0
  774. data/lib/bioroebe/yaml/pathways/urea_cycle.yml +11 -0
  775. data/lib/bioroebe/yaml/primers/README.md +4 -0
  776. data/lib/bioroebe/yaml/primers/primers.yml +3 -0
  777. data/lib/bioroebe/yaml/promoters/35S.yml +15 -0
  778. data/lib/bioroebe/yaml/promoters/strong_promoters.yml +24 -0
  779. data/lib/bioroebe/yaml/proteases/proteases.yml +3 -0
  780. data/lib/bioroebe/yaml/proteins/ubiquitin.yml +4 -0
  781. data/lib/bioroebe/yaml/remote_urls/README.md +4 -0
  782. data/lib/bioroebe/yaml/remote_urls/remote_urls.yml +3 -0
  783. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +630 -0
  784. data/lib/bioroebe/yaml/sequences/JX472995_Green_fluorescent_protein_from_Aequorea_victoria.fasta +14 -0
  785. data/lib/bioroebe/yaml/sequences/README.md +2 -0
  786. data/lib/bioroebe/yaml/talens.yml +22 -0
  787. data/lib/bioroebe/yaml/viruses/ecoli_phages.yml +63 -0
  788. data/lib/bioroebe/yaml/viruses/viruses.yml +6 -0
  789. data/lib/bioroebe.rb +5 -0
  790. data/spec/testing_toplevel_method_editor.rb +20 -0
  791. data/spec/testing_toplevel_method_url.rb +15 -0
  792. data/spec/testing_toplevel_method_verbose.rb +13 -0
  793. data/test/advanced_svg_example.rb +307 -0
  794. data/test/testing_bioroebe.rb +25 -0
  795. data/test/testing_codons.rb +45 -0
  796. data/test/testing_dna_to_rna_conversion.rb +15 -0
  797. data/test/testing_parse_pdb_file.rb +23 -0
  798. data/test/testing_reverse_complement.rb +32 -0
  799. data/test/testing_svg_component_of_bioroebe.rb +311 -0
  800. data/test/testing_svg_component_of_bioroebe_from_json_dataset.rb +34 -0
  801. data/test/testing_taxonomy.rb +22 -0
  802. metadata +1059 -0
data/lib/bioroebe/codon_tables/frequencies/3702_Arabidopsis_thaliana.yml ADDED
@@ -0,0 +1,77 @@
1
+ # =========================================================================== #
2
+ # Filename:
3
+ #
4
+ # 3702_Arabidopsis_thaliana.yml
5
+ #
6
+ # This is Arabidopsis thaliana:
7
+ #
8
+ # https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=3702
9
+ #
10
+ # =========================================================================== #
11
+ UUU: 21.8
12
+ UCU: 25.2
13
+ UAU: 14.6
14
+ UGU: 10.5
15
+ UUC: 20.7
16
+ UCC: 11.2
17
+ UAC: 13.7
18
+ UGC: 7.2
19
+ UUA: 12.7
20
+ UCA: 18.3
21
+ UAA: 0.9
22
+ UGA: 1.2
23
+ UUG: 20.9
24
+ UCG: 9.3
25
+ UAG: 0.5
26
+ UGG: 12.5
27
+
28
+ CUU: 24.1
29
+ CCU: 18.7
30
+ CAU: 13.8
31
+ CGU: 9.0
32
+ CUC: 16.1
33
+ CCC: 5.3
34
+ CAC: 8.7
35
+ CGC: 3.8
36
+ CUA: 9.9
37
+ CCA: 16.1
38
+ CAA: 19.4
39
+ CGA: 6.3
40
+ CUG: 9.8
41
+ CCG: 8.6
42
+ CAG: 15.2
43
+ CGG: 4.9
44
+
45
+ AUU: 21.5
46
+ ACU: 17.5
47
+ AAU: 22.3
48
+ AGU: 14.0
49
+ AUC: 18.5
50
+ ACC: 10.3
51
+ AAC: 20.9
52
+ AGC: 11.3
53
+ AUA: 12.6
54
+ ACA: 15.7
55
+ AAA: 30.8
56
+ AGA: 19.0
57
+ AUG: 24.5
58
+ ACG: 7.7
59
+ AAG: 32.7
60
+ AGG: 11.0
61
+
62
+ GUU: 27.2
63
+ GCU: 28.3
64
+ GAU: 36.6
65
+ GGU: 22.2
66
+ GUC: 12.8
67
+ GCC: 10.3
68
+ GAC: 17.2
69
+ GGC: 9.2
70
+ GUA: 9.9
71
+ GCA: 17.5
72
+ GAA: 34.3
73
+ GGA: 24.2
74
+ GUG: 17.4
75
+ GCG: 9.0
76
+ GAG: 32.2
77
+ GGG: 10.2
data/lib/bioroebe/codon_tables/frequencies/4932_Saccharomyces_cerevisiae.yml ADDED
@@ -0,0 +1,103 @@
1
+ # =========================================================================== #
2
+ # Filename:
3
+ #
4
+ # 4932_Saccharomyces_cerevisiae.yml
5
+ #
6
+ # Saccharomyces cerevisiae [gbpln]: 14411 CDS's (6534504 codons)
7
+ # fields: [triplet] [frequency: per thousand] ([number])
8
+ #
9
+ # URL: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=4932
10
+ # URL: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=4932
11
+ #
12
+ # Last update to this file:
13
+ #
14
+ # 17.09.2019
15
+ #
16
+ # =========================================================================== #
17
+ # UUU 26.1(170666) UCU 23.5(153557) UAU 18.8(122728) UGU 8.1( 52903)
18
+ # UUC 18.4(120510) UCC 14.2( 92923) UAC 14.8( 96596) UGC 4.8( 31095)
19
+ # UUA 26.2(170884) UCA 18.7(122028) UAA 1.1( 6913) UGA 0.7( 4447)
20
+ # UUG 27.2(177573) UCG 8.6( 55951) UAG 0.5( 3312) UGG 10.4( 67789)
21
+ #
22
+ # CUU 12.3( 80076) CCU 13.5( 88263) CAU 13.6( 89007) CGU 6.4( 41791)
23
+ # CUC 5.4( 35545) CCC 6.8( 44309) CAC 7.8( 50785) CGC 2.6( 16993)
24
+ # CUA 13.4( 87619) CCA 18.3(119641) CAA 27.3(178251) CGA 3.0( 19562)
25
+ # CUG 10.5( 68494) CCG 5.3( 34597) CAG 12.1( 79121) CGG 1.7( 11351)
26
+ #
27
+ # AUU 30.1(196893) ACU 20.3(132522) AAU 35.7(233124) AGU 14.2( 92466)
28
+ # AUC 17.2(112176) ACC 12.7( 83207) AAC 24.8(162199) AGC 9.8( 63726)
29
+ # AUA 17.8(116254) ACA 17.8(116084) AAA 41.9(273618) AGA 21.3(139081)
30
+ # AUG 20.9(136805) ACG 8.0( 52045) AAG 30.8(201361) AGG 9.2( 60289)
31
+ #
32
+ # GUU 22.1(144243) GCU 21.2(138358) GAU 37.6(245641) GGU 23.9(156109)
33
+ # GUC 11.8( 76947) GCC 12.6( 82357) GAC 20.2(132048) GGC 9.8( 63903)
34
+ # GUA 11.8( 76927) GCA 16.2(105910) GAA 45.6(297944) GGA 10.9( 71216)
35
+ # GUG 10.8( 70337) GCG 6.2( 40358) GAG 19.2(125717) GGG 6.0( 39359)
36
+ # =========================================================================== #
37
+ UUU: 26.1
38
+ UCU: 23.5
39
+ UAU: 18.8
40
+ UGU: 8.1
41
+ UUC: 18.4
42
+ UCC: 14.2
43
+ UAC: 14.8
44
+ UGC: 4.8
45
+ UUA: 26.2
46
+ UCA: 18.7
47
+ UAA: 1.1
48
+ UGA: 0.7
49
+ UUG: 27.2
50
+ UCG: 8.6
51
+ UAG: 0.5
52
+ UGG: 10.4
53
+
54
+ CUU: 12.3
55
+ CCU: 13.5
56
+ CAU: 13.6
57
+ CGU: 6.4
58
+ CUC: 5.4
59
+ CCC: 6.8
60
+ CAC: 7.8
61
+ CGC: 2.6
62
+ CUA: 13.4
63
+ CCA: 18.3
64
+ CAA: 27.3
65
+ CGA: 3.0
66
+ CUG: 10.5
67
+ CCG: 5.3
68
+ CAG: 12.1
69
+ CGG: 1.7
70
+
71
+ AUU: 30.1
72
+ ACU: 20.3
73
+ AAU: 35.7
74
+ AGU: 14.2
75
+ AUC: 17.2
76
+ ACC: 12.7
77
+ AAC: 24.8
78
+ AGC: 9.8
79
+ AUA: 17.8
80
+ ACA: 17.8
81
+ AAA: 41.9
82
+ AGA: 21.3
83
+ AUG: 20.9
84
+ ACG: 8.0
85
+ AAG: 30.8
86
+ AGG: 9.2
87
+
88
+ GUU: 22.1
89
+ GCU: 21.2
90
+ GAU: 37.6
91
+ GGU: 23.9
92
+ GUC: 11.8
93
+ GCC: 12.6
94
+ GAC: 20.2
95
+ GGC: 9.8
96
+ GUA: 11.8
97
+ GCA: 16.2
98
+ GAA: 45.6
99
+ GGA: 10.9
100
+ GUG: 10.8
101
+ GCG: 6.2
102
+ GAG: 19.2
103
+ GGG: 6.0
data/lib/bioroebe/codon_tables/frequencies/7227_Drosophila_melanogaster.yml ADDED
@@ -0,0 +1,71 @@
1
+ # Filename: 7227_Drosophila_melanogaster.yml
2
+ #
3
+ # The following dataset was obtained from:
4
+ #
5
+ # https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=7227
6
+ #
7
+ #
8
+ UUU: 13.2
9
+ UCU: 7.0
10
+ UAU: 10.8
11
+ UGU: 5.4
12
+ UUC: 21.8
13
+ UCC: 19.6
14
+ UAC: 18.4
15
+ UGC: 13.2
16
+ UUA: 4.5
17
+ UCA: 7.8
18
+ UAA: 0.8
19
+ UGA: 0.5
20
+ UUG: 16.1
21
+ UCG: 16.6
22
+ UAG: 0.7
23
+ UGG: 9.9
24
+ CUU: 9.0
25
+ CCU: 6.9
26
+ CAU: 10.8
27
+ CGU: 8.8
28
+ CUC: 13.8
29
+ CCC: 18.1
30
+ CAC: 16.2
31
+ CGC: 18.0
32
+ CUA: 8.2
33
+ CCA: 13.5
34
+ CAA: 15.6
35
+ CGA: 8.4
36
+ CUG: 38.2
37
+ CCG: 15.8
38
+ CAG: 36.1
39
+ CGG: 8.2
40
+ AUU: 16.6
41
+ ACU: 9.5
42
+ AAU: 21.0
43
+ AGU: 11.5
44
+ AUC: 22.9
45
+ ACC: 21.3
46
+ AAC: 26.2
47
+ AGC: 20.4
48
+ AUA: 9.5
49
+ ACA: 11.0
50
+ AAA: 17.0
51
+ AGA: 5.1
52
+ AUG: 23.6
53
+ ACG: 14.4
54
+ AAG: 39.5
55
+ AGG: 6.3
56
+ GUU: 11.0
57
+ GCU: 14.4
58
+ GAU: 27.6
59
+ GGU: 13.3
60
+ GUC: 13.9
61
+ GCC: 33.6
62
+ GAC: 24.6
63
+ GGC: 26.7
64
+ GUA: 6.4
65
+ GCA: 12.8
66
+ GAA: 21.1
67
+ GGA: 18.0
68
+ GUG: 27.8
69
+ GCG: 14.0
70
+ GAG: 42.5
71
+ GGG: 4.7
data/lib/bioroebe/codon_tables/frequencies/83333_Escherichia_coli_K12.yml ADDED
@@ -0,0 +1,103 @@
1
+ # =========================================================================== #
2
+ # === E. coli K12, Taxonomy ID 83333
3
+ #
4
+ # Filename:
5
+ #
6
+ # 83333_Escherichia_coli_K12.yml
7
+ #
8
+ # 14 CDS's (5122 codons) fields: [triplet] [frequency: per thousand] ([number])
9
+ #
10
+ # Last update to this file:
11
+ #
12
+ # 17.09.2019
13
+ #
14
+ # URL: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=83333
15
+ # URL: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=83333
16
+ # =========================================================================== #
17
+ # UUU 19.7( 101) UCU 5.7( 29) UAU 16.8( 86) UGU 5.9( 30)
18
+ # UUC 15.0( 77) UCC 5.5( 28) UAC 14.6( 75) UGC 8.0( 41)
19
+ # UUA 15.2( 78) UCA 7.8( 40) UAA 1.8( 9) UGA 1.0( 5)
20
+ # UUG 11.9( 61) UCG 8.0( 41) UAG 0.0( 0) UGG 10.7( 55)
21
+ #
22
+ # CUU 11.9( 61) CCU 8.4( 43) CAU 15.8( 81) CGU 21.1( 108)
23
+ # CUC 10.5( 54) CCC 6.4( 33) CAC 13.1( 67) CGC 26.0( 133)
24
+ # CUA 5.3( 27) CCA 6.6( 34) CAA 12.1( 62) CGA 4.3( 22)
25
+ # CUG 46.9( 240) CCG 26.7( 137) CAG 27.7( 142) CGG 4.1( 21)
26
+ #
27
+ # AUU 30.5( 156) ACU 8.0( 41) AAU 21.9( 112) AGU 7.2( 37)
28
+ # AUC 18.2( 93) ACC 22.8( 117) AAC 24.4( 125) AGC 16.6( 85)
29
+ # AUA 3.7( 19) ACA 6.4( 33) AAA 33.2( 170) AGA 1.4( 7)
30
+ # AUG 24.8( 127) ACG 11.5( 59) AAG 12.1( 62) AGG 1.6( 8)
31
+ #
32
+ # GUU 16.8( 86) GCU 10.7( 55) GAU 37.9( 194) GGU 21.3( 109)
33
+ # GUC 11.7( 60) GCC 31.6( 162) GAC 20.5( 105) GGC 33.4( 171)
34
+ # GUA 11.5( 59) GCA 21.1( 108) GAA 43.7( 224) GGA 9.2( 47)
35
+ # GUG 26.4( 135) GCG 38.5( 197) GAG 18.4( 94) GGG 8.6( 44)
36
+ # =========================================================================== #
37
+ UUU: 19.7
38
+ UCU: 5.7
39
+ UAU: 16.8
40
+ UGU: 5.9
41
+ UUC: 15.0
42
+ UCC: 5.5
43
+ UAC: 14.6
44
+ UGC: 8.0
45
+ UUA: 15.2
46
+ UCA: 7.8
47
+ UAA: 1.8
48
+ UGA: 1.0
49
+ UUG: 11.9
50
+ UCG: 8.0
51
+ UAG: 0.0
52
+ UGG: 10.7
53
+
54
+ CUU: 11.9
55
+ CCU: 8.4
56
+ CAU: 15.8
57
+ CGU: 21.1
58
+ CUC: 10.5
59
+ CCC: 6.4
60
+ CAC: 13.1
61
+ CGC: 26.0
62
+ CUA: 5.3
63
+ CCA: 6.6
64
+ CAA: 12.1
65
+ CGA: 4.3
66
+ CUG: 46.9
67
+ CCG: 26.7
68
+ CAG: 27.7
69
+ CGG: 4.1
70
+
71
+ AUU: 30.5
72
+ ACU: 8.0
73
+ AAU: 21.9
74
+ AGU: 7.2
75
+ AUC: 18.2
76
+ ACC: 22.8
77
+ AAC: 24.4
78
+ AGC: 16.6
79
+ AUA: 3.7
80
+ ACA: 6.4
81
+ AAA: 33.2
82
+ AGA: 1.4
83
+ AUG: 24.8
84
+ ACG: 11.5
85
+ AAG: 12.1
86
+ AGG: 1.6
87
+
88
+ GUU: 16.8
89
+ GCU: 10.7
90
+ GAU: 37.9
91
+ GGU: 21.3
92
+ GUC: 11.7
93
+ GCC: 31.6
94
+ GAC: 20.5
95
+ GGC: 33.4
96
+ GUA: 11.5
97
+ GCA: 21.1
98
+ GAA: 43.7
99
+ GGA: 9.2
100
+ GUG: 26.4
101
+ GCG: 38.5
102
+ GAG: 18.4
103
+ GGG: 8.6
data/lib/bioroebe/codon_tables/frequencies/9606_Homo_sapiens.yml ADDED
@@ -0,0 +1,123 @@
1
+ # =========================================================================== #
2
+ # === 9606_Homo_sapiens.yml
3
+ #
4
+ # Path:
5
+ #
6
+ # $RUBY_BIOROEBE/codon_tables/frequencies/9606_Homo_sapiens.yml
7
+ #
8
+ # Homo sapiens [gbpri]: 93487 CDS's (40662582 codons) fields:
9
+ # [triplet] [frequency: per thousand] ([number])
10
+ #
11
+ # So 17.6 would mean 17.6 out of 1000.
12
+ #
13
+ # The dataset was obtained from:
14
+ #
15
+ # https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9606&aa=1&style=N
16
+ #
17
+ # Last update to this .yml file:
18
+ #
19
+ # 17.09.2019
20
+ #
21
+ # =========================================================================== #
22
+ # x = YAML.load_file(ENV['RUBY_SRC'].to_s+'/bioroebe/lib/bioroebe/codon_tables/frequencies/9606_Homo_sapiens.yml')
23
+ # =========================================================================== #
24
+ # UUU 17.6(714298) UCU 15.2(618711) UAU 12.2(495699) UGU 10.6(430311)
25
+ # UUC 20.3(824692) UCC 17.7(718892) UAC 15.3(622407) UGC 12.6(513028)
26
+ # UUA 7.7(311881) UCA 12.2(496448) UAA 1.0( 40285) UGA 1.6( 63237)
27
+ # UUG 12.9(525688) UCG 4.4(179419) UAG 0.8( 32109) UGG 13.2(535595)
28
+ #
29
+ # CUU 13.2(536515) CCU 17.5(713233) CAU 10.9(441711) CGU 4.5(184609)
30
+ # CUC 19.6(796638) CCC 19.8(804620) CAC 15.1(613713) CGC 10.4(423516)
31
+ # CUA 7.2(290751) CCA 16.9(688038) CAA 12.3(501911) CGA 6.2(250760)
32
+ # CUG 39.6(1611801) CCG 6.9(281570) CAG 34.2(1391973) CGG 11.4(464485)
33
+ #
34
+ # AUU 16.0(650473) ACU 13.1(533609) AAU 17.0(689701) AGU 12.1(493429)
35
+ # AUC 20.8(846466) ACC 18.9(768147) AAC 19.1(776603) AGC 19.5(791383)
36
+ # AUA 7.5(304565) ACA 15.1(614523) AAA 24.4(993621) AGA 12.2(494682)
37
+ # AUG 22.0(896005) ACG 6.1(246105) AAG 31.9(1295568) AGG 12.0(486463)
38
+ #
39
+ # GUU 11.0(448607) GCU 18.4(750096) GAU 21.8(885429) GGU 10.8(437126)
40
+ # GUC 14.5(588138) GCC 27.7(1127679) GAC 25.1(1020595) GGC 22.2(903565)
41
+ # GUA 7.1(287712) GCA 15.8(643471) GAA 29.0(1177632) GGA 16.5(669873)
42
+ # GUG 28.1(1143534) GCG 7.4(299495) GAG 39.6(1609975) GGG 16.5(669768)
43
+ # =========================================================================== #
44
+
45
+ # =========================================================================== #
46
+ # === U tag
47
+ # =========================================================================== #
48
+ UUU: 17.6 # F
49
+ UCU: 15.2 # S
50
+ UAU: 12.2 # Y
51
+ UGU: 10.6 # C
52
+ UUC: 20.3
53
+ UCC: 17.7
54
+ UAC: 15.3
55
+ UGC: 12.6
56
+ UUA: 7.7
57
+ UCA: 12.2
58
+ UAA: 1.0
59
+ UGA: 1.6
60
+ UUG: 12.9
61
+ UCG: 4.4
62
+ UAG: 0.8
63
+ UGG: 13.2 # W
64
+
65
+ # =========================================================================== #
66
+ # === C tag
67
+ # =========================================================================== #
68
+ CUU: 13.2
69
+ CCU: 17.5
70
+ CAU: 10.9
71
+ CGU: 4.5
72
+ CUC: 19.6
73
+ CCC: 19.8
74
+ CAC: 15.1
75
+ CGC: 10.4
76
+ CUA: 7.2
77
+ CCA: 16.9
78
+ CAA: 12.3
79
+ CGA: 6.2
80
+ CUG: 39.6
81
+ CCG: 6.9
82
+ CAG: 34.2
83
+ CGG: 11.4
84
+
85
+ # =========================================================================== #
86
+ # === A tag
87
+ # =========================================================================== #
88
+ AUU: 16.0
89
+ ACU: 13.1
90
+ AAU: 17.0
91
+ AGU: 12.1
92
+ AUC: 20.8
93
+ ACC: 18.9
94
+ AAC: 19.1
95
+ AGC: 19.5
96
+ AUA: 7.5
97
+ ACA: 15.1
98
+ AAA: 24.4
99
+ AGA: 12.2
100
+ AUG: 22.0
101
+ ACG: 6.1
102
+ AAG: 31.9
103
+ AGG: 12.0
104
+
105
+ # =========================================================================== #
106
+ # === G tag
107
+ # =========================================================================== #
108
+ GUU: 11.0
109
+ GCU: 18.4
110
+ GAU: 21.8
111
+ GGU: 10.8
112
+ GUC: 14.5
113
+ GCC: 27.7
114
+ GAC: 25.1
115
+ GGC: 22.2
116
+ GUA: 7.1
117
+ GCA: 15.8
118
+ GAA: 29.0
119
+ GGA: 16.5
120
+ GUG: 28.1
121
+ GCG: 7.4
122
+ GAG: 39.6
123
+ GGG: 16.5
data/lib/bioroebe/codon_tables/frequencies/9685_Felis_catus.yml ADDED
@@ -0,0 +1,78 @@
1
+ # =========================================================================== #
2
+ # Filename:
3
+ #
4
+ # 9685_Felis_catus.yml
5
+ #
6
+ # This is the cat:
7
+ #
8
+ # https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9685
9
+ #
10
+ # =========================================================================== #
11
+
12
+ UUU: 17.7
13
+ UCU: 14.2
14
+ UAU: 12.1
15
+ UGU: 10.5
16
+ UUC: 25.9
17
+ UCC: 18.9
18
+ UAC: 18.9
19
+ UGC: 13.8
20
+ UUA: 6.3
21
+ UCA: 9.5
22
+ UAA: 0.7
23
+ UGA: 1.5
24
+ UUG: 13.5
25
+ UCG: 4.9
26
+ UAG: 0.5
27
+ UGG: 15.3
28
+
29
+ CUU: 11.9
30
+ CCU: 13.9
31
+ CAU: 8.7
32
+ CGU: 3.7
33
+ CUC: 22.9
34
+ CCC: 20.4
35
+ CAC: 14.8
36
+ CGC: 9.8
37
+ CUA: 6.4
38
+ CCA: 13.1
39
+ CAA: 11.6
40
+ CGA: 5.0
41
+ CUG: 45.8
42
+ CCG: 6.8
43
+ CAG: 30.1
44
+ CGG: 10.7
45
+
46
+ AUU: 14.9
47
+ ACU: 11.4
48
+ AAU: 17.0
49
+ AGU: 10.2
50
+ AUC: 24.9
51
+ ACC: 21.6
52
+ AAC: 24.2
53
+ AGC: 18.8
54
+ AUA: 7.4
55
+ ACA: 12.7
56
+ AAA: 23.3
57
+ AGA: 12.0
58
+ AUG: 22.4
59
+ ACG: 8.5
60
+ AAG: 30.7
61
+ AGG: 12.7
62
+
63
+ GUU: 10.2
64
+ GCU: 16.5
65
+ GAU: 19.5
66
+ GGU: 9.2
67
+ GUC: 18.3
68
+ GCC: 31.4
69
+ GAC: 26.8
70
+ GGC: 22.5
71
+ GUA: 6.2
72
+ GCA: 13.1
73
+ GAA: 27.1
74
+ GGA: 16.0
75
+ GUG: 30.5
76
+ GCG: 8.6
77
+ GAG: 35.8
78
+ GGG: 15.6
data/lib/bioroebe/codon_tables/frequencies/README.md ADDED
@@ -0,0 +1,10 @@
1
+ This directory will store the frequencies of how likely it is
2
+ to have certain aminoacids.
3
+
4
+ The format will be:
5
+
6
+ TAXONOMICID_NAME
7
+
8
+ For instance, humans will have this file:
9
+
10
+ 9606_Homo_sapiens.yml