bioroebe 0.10.80

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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
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  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
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  585. data/lib/bioroebe/taxonomy/help/helpline.rb +53 -0
  586. data/lib/bioroebe/taxonomy/info/check_available.rb +143 -0
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  591. data/lib/bioroebe/taxonomy/node.rb +118 -0
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  596. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +715 -0
  597. data/lib/bioroebe/toplevel_methods/atomic_composition.rb +198 -0
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  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
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  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
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  628. data/lib/bioroebe/toplevel_methods/nucleotides.rb +715 -0
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  633. data/lib/bioroebe/toplevel_methods/palindromes.rb +127 -0
  634. data/lib/bioroebe/toplevel_methods/parse.rb +59 -0
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  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
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  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
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  650. data/lib/bioroebe/toplevel_methods/truncate.rb +48 -0
  651. data/lib/bioroebe/toplevel_methods/url.rb +36 -0
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  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
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  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
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  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
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  680. data/lib/bioroebe/utility_scripts/showorf/help.rb +33 -0
  681. data/lib/bioroebe/utility_scripts/showorf/initialize.rb +52 -0
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  684. data/lib/bioroebe/utility_scripts/showorf/run.rb +152 -0
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  686. data/lib/bioroebe/utility_scripts/showorf/showorf.rb +488 -0
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  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
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  697. data/lib/bioroebe/yaml/aminoacids/amino_acids_average_mass_table.yml +33 -0
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  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
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  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
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  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
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  717. data/lib/bioroebe/yaml/blosum/blosum_matrix.yml +200 -0
  718. data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +30 -0
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  755. data/lib/bioroebe/yaml/default_dna_input.yml +3 -0
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  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
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  767. data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +10 -0
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  772. data/lib/bioroebe/yaml/pathways/glycolysis.yml +20 -0
  773. data/lib/bioroebe/yaml/pathways/shikimate_pathway.yml +23 -0
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  776. data/lib/bioroebe/yaml/primers/primers.yml +3 -0
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  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
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  785. data/lib/bioroebe/yaml/sequences/README.md +2 -0
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  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
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  795. data/test/testing_codons.rb +45 -0
  796. data/test/testing_dna_to_rna_conversion.rb +15 -0
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  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
@@ -0,0 +1,491 @@
1
+ #!/usr/bin/ruby -w
2
+ # Encoding: UTF-8
3
+ # frozen_string_literal: true
4
+ # =========================================================================== #
5
+ # === Bioroebe::CountAmountOfNucleotides
6
+ #
7
+ # This class will simply count how many A, T, C and G are in a
8
+ # given Nucleotide string. The main idea behind this class is
9
+ # to visually present this information to the user - typically
10
+ # on the commandline.
11
+ #
12
+ # Usage example:
13
+ #
14
+ # cnuc ATTACCCCCCATCGAAAAAAATAAATAAAACAAATATATA
15
+ #
16
+ # =========================================================================== #
17
+ # require 'bioroebe/count/count_amount_of_nucleotides.rb
18
+ # =========================================================================== #
19
+ require 'bioroebe/base/commandline_application/commandline_application.rb'
20
+
21
+ module Bioroebe
22
+
23
+ class CountAmountOfNucleotides < ::Bioroebe::CommandlineApplication # === Bioroebe::CountAmountOfNucleotides
24
+
25
+ # ========================================================================= #
26
+ # === USE_THIS_START_CODON
27
+ # ========================================================================= #
28
+ USE_THIS_START_CODON = 'ATG'
29
+
30
+ # ========================================================================= #
31
+ # === DEFAULT_DNA_STRING_TO_USE
32
+ # ========================================================================= #
33
+ DEFAULT_DNA_STRING_TO_USE =
34
+ 'ATCGAAAAAAATAAATAAAACAAATATATA' # ← Our test string.
35
+
36
+ # ========================================================================= #
37
+ # === FORMAT_STRING1
38
+ # ========================================================================= #
39
+ FORMAT_STRING1 = '%-12s'
40
+
41
+ # ========================================================================= #
42
+ # === FORMAT_STRING2
43
+ # ========================================================================= #
44
+ FORMAT_STRING2 = '%4s'
45
+
46
+ # ========================================================================= #
47
+ # === intitialize
48
+ # ========================================================================= #
49
+ def initialize(
50
+ this_dna_string = DEFAULT_DNA_STRING_TO_USE,
51
+ run_already = true
52
+ )
53
+ super()
54
+ reset
55
+ this_dna_string = parse_commandline_arguments(this_dna_string)
56
+ set_dna_string(
57
+ this_dna_string
58
+ )
59
+ # ======================================================================= #
60
+ # === Handle blocks given to this method next:
61
+ # ======================================================================= #
62
+ if block_given?
63
+ yielded = yield
64
+ case yielded
65
+ when :display_short_form
66
+ @display_short_form = true
67
+ else
68
+ if yielded.is_a? Hash
69
+ # ================================================================= #
70
+ # === :use_colours
71
+ # ================================================================= #
72
+ if yielded.has_key? :use_colours
73
+ set_use_colours(yielded.delete(:use_colours))
74
+ end
75
+ end
76
+ end
77
+ end
78
+ case run_already
79
+ # ======================================================================= #
80
+ # === :do_not_run_yet
81
+ # ======================================================================= #
82
+ when :do_not_run_yet
83
+ run_already = false
84
+ # ======================================================================= #
85
+ # === :use_cliner
86
+ # ======================================================================= #
87
+ when :use_cliner
88
+ @use_cliner = true
89
+ run_already = true
90
+ end
91
+ run if run_already
92
+ end
93
+
94
+ # ========================================================================= #
95
+ # === reset
96
+ # ========================================================================= #
97
+ def reset
98
+ super()
99
+ # ======================================================================= #
100
+ # === @format_string1
101
+ # ======================================================================= #
102
+ @format_string1 = FORMAT_STRING1
103
+ # ======================================================================= #
104
+ # === @format_string2
105
+ # ======================================================================= #
106
+ @format_string2 = FORMAT_STRING2
107
+ # ======================================================================= #
108
+ # === @use_cliner
109
+ # ======================================================================= #
110
+ @use_cliner = false
111
+ # ======================================================================= #
112
+ # === @display_short_form
113
+ # ======================================================================= #
114
+ @display_short_form = false # If this is true, we will only report the numbers.
115
+ # ======================================================================= #
116
+ # === @hash_percentages
117
+ # ======================================================================= #
118
+ @hash_percentages = {}
119
+ # ======================================================================= #
120
+ # === @l_padding
121
+ #
122
+ # l_padding means left_padding. We must make this more dynamic,
123
+ # in that it must depend on the amount of nucleotides given.
124
+ # ======================================================================= #
125
+ @l_padding = ' '
126
+ # ======================================================================= #
127
+ # === @dna_string
128
+ # ======================================================================= #
129
+ @dna_string = ''.dup
130
+ end
131
+
132
+ # ========================================================================= #
133
+ # === parse_commandline_arguments
134
+ # ========================================================================= #
135
+ def parse_commandline_arguments(i)
136
+ if i.is_a? Array
137
+ if i.any? {|entry| entry.start_with? '--' }
138
+ # =================================================================== #
139
+ # All entries leading with two '-' will be passed into menu()
140
+ # and also be removed from the given input. We let code in
141
+ # base.rb deal with this, though.
142
+ # =================================================================== #
143
+ menu(
144
+ select_entries_starting_with_two_hyphens(i)
145
+ )
146
+ i.reject! {|entry| entry.start_with? '--' }
147
+ end
148
+ end
149
+ i
150
+ end
151
+
152
+ # ========================================================================= #
153
+ # === menu (menu tag)
154
+ # ========================================================================= #
155
+ def menu(i)
156
+ if i.is_a? Array
157
+ i.each {|entry| menu(entry) }
158
+ else
159
+ case i # case tag
160
+ # ===================================================================== #
161
+ # === --short-form
162
+ # ===================================================================== #
163
+ when /^-?-?short(-|_)?form$/i,
164
+ /^-?-?short$/
165
+ @display_short_form = true
166
+ end
167
+ end
168
+ end
169
+
170
+ # ========================================================================= #
171
+ # === set_percentage_of
172
+ # ========================================================================= #
173
+ def set_percentage_of(i)
174
+ case i
175
+ when :adenine,
176
+ :guanine,
177
+ :cytosine,
178
+ :thymine
179
+ i = i.to_s[0,1].capitalize
180
+ end
181
+ n_times = @dna_string.count(i.to_s)
182
+ @hash_percentages[i] = n_times
183
+ n_times = n_times.to_f * 100
184
+ total_size = @dna_string.size.to_f
185
+ percentage = n_times / total_size
186
+ percentage = '%.2f' % percentage
187
+ percentage.prepend ' ' if percentage.size == 4 # Prepend ' '.
188
+ @percentage = rev+' | '+percentage.to_s+' '+
189
+ swarn('%')
190
+ end
191
+
192
+ # ========================================================================= #
193
+ # === report_GC_content
194
+ # ========================================================================= #
195
+ def report_GC_content
196
+ n_percent = ((
197
+ @hash_percentages['G']+@hash_percentages['C']
198
+ ) * 100.0) / @dna_string.size
199
+ erev "The GC content (G+C) is: #{sfancy(n_percent.round(2).to_s)}#{rev} %"
200
+ end; alias report_gc_content report_GC_content # === report_gc_content
201
+
202
+ # ========================================================================= #
203
+ # === report_AT_content
204
+ #
205
+ # This method is, for now, a dependent method - the method
206
+ # report_GC_content does the calculation.
207
+ # ========================================================================= #
208
+ def report_AT_content(n_percent = :calculate_anew)
209
+ case n_percent
210
+ when :calculate_anew
211
+ n_percent = ((
212
+ @hash_percentages['A']+@hash_percentages['T']
213
+ ) * 100.0) / @dna_string.size
214
+ end
215
+ erev 'The AT content (A+T) is: '+
216
+ sfancy(n_percent.round(2).to_s)+rev+' %'
217
+ end
218
+
219
+ # ========================================================================= #
220
+ # === report_total_amount
221
+ # ========================================================================= #
222
+ def report_total_amount
223
+ report_how_many_nucleotides_we_have_found
224
+ report_AT_content
225
+ report_GC_content
226
+ end
227
+
228
+ # ========================================================================= #
229
+ # === n_a
230
+ # ========================================================================= #
231
+ def n_a(i = @dna_string)
232
+ i.count('A')
233
+ end
234
+
235
+ # ========================================================================= #
236
+ # === n_g
237
+ # ========================================================================= #
238
+ def n_g(i = @dna_string)
239
+ i.count('G')
240
+ end
241
+
242
+ # ========================================================================= #
243
+ # === n_c
244
+ # ========================================================================= #
245
+ def n_c(i = @dna_string)
246
+ i.count('C')
247
+ end
248
+
249
+ # ========================================================================= #
250
+ # === n_t
251
+ # ========================================================================= #
252
+ def n_t(i = @dna_string)
253
+ i.count('T')
254
+ end
255
+
256
+ # ========================================================================= #
257
+ # === dna_string?
258
+ # ========================================================================= #
259
+ def dna_string?
260
+ @dna_string
261
+ end
262
+
263
+ # ========================================================================= #
264
+ # === string?
265
+ # ========================================================================= #
266
+ def string?
267
+ @string
268
+ end; alias string string? # === string
269
+
270
+ # ========================================================================= #
271
+ # === return_colourized_start_codon
272
+ # ========================================================================= #
273
+ def return_colourized_start_codon
274
+ swarn(USE_THIS_START_CODON)
275
+ end; alias colourized_start_codon return_colourized_start_codon # === colourized_start_codon
276
+
277
+ # ========================================================================= #
278
+ # === report_the_amount_of_nucleotides_in_short_form_on_a_single_line
279
+ # ========================================================================= #
280
+ def report_the_amount_of_nucleotides_in_short_form_on_a_single_line
281
+ # ======================================================================= #
282
+ # Output will be:
283
+ #
284
+ # A G C T
285
+ #
286
+ # ======================================================================= #
287
+ e return_the_amount_of_nucleotides_in_short_form_on_a_single_line
288
+ end
289
+
290
+ # ========================================================================= #
291
+ # === return_the_amount_of_nucleotides_in_short_form_on_a_single_line
292
+ #
293
+ # The order of nucleotides that is to be favoured here, is:
294
+ #
295
+ # A C G T
296
+ #
297
+ # ========================================================================= #
298
+ def return_the_amount_of_nucleotides_in_short_form_on_a_single_line
299
+ n_a.to_s+' '+ # A
300
+ n_c.to_s+' '+ # C
301
+ n_g.to_s+' '+ # G
302
+ n_t.to_s # T
303
+ end
304
+
305
+ # ========================================================================= #
306
+ # === report_how_many_nucleotides_we_have_found
307
+ # ========================================================================= #
308
+ def report_how_many_nucleotides_we_have_found
309
+ erev "#{N}In total "\
310
+ "#{simportant(@dna_string.size.to_s)}#{rev} nucleotides were found."
311
+ end
312
+
313
+ # ========================================================================= #
314
+ # === report_how_many_start_codons_exist
315
+ # ========================================================================= #
316
+ def report_how_many_start_codons_exist
317
+ n_start_codons = dna_string?.scan(/#{USE_THIS_START_CODON}/).size
318
+ erev "In the given DNA string "\
319
+ "#{simp(n_start_codons)}#{rev} start codons ("\
320
+ "#{return_colourized_start_codon}#{rev}) were found.#{N}"
321
+ end
322
+
323
+ # ========================================================================= #
324
+ # === return_colourized_truncated_at_message
325
+ # ========================================================================= #
326
+ def return_colourized_truncated_at_message
327
+ " [#{swarn('TRUNCATED at 80')}#{rev}]"
328
+ end
329
+
330
+ # ========================================================================= #
331
+ # === report_everything
332
+ # ========================================================================= #
333
+ def report_everything(
334
+ i = @dna_string
335
+ )
336
+ if i.empty?
337
+ erev '@dna_string is empty, this means that you have not yet assigned a '
338
+ erev 'string. Please assign a DNA string to this class first.'
339
+ else
340
+ # ===================================================================== #
341
+ # This else clause can output too much / too long strings.
342
+ #
343
+ # Since this can become quite spammy, we will report a truncated
344
+ # version.
345
+ # ===================================================================== #
346
+ erev "Analyzing the DNA string `"+
347
+ colourize_dna(
348
+ remove_escape_sequences(
349
+ return_truncated_dna_string(:default, false)
350
+ ),
351
+ use_colours?
352
+ )+
353
+ "#{rev}"+
354
+ return_colourized_truncated_at_message+
355
+ "`.#{N}#{N}"
356
+ n_nucleotides = i.size.to_i
357
+ erev "These #{simp(n_nucleotides.to_s)}#{rev} Nucleotides "\
358
+ "were found:#{rev}#{N}#{N}"
359
+ cliner if @use_cliner
360
+ set_percentage_of(:adenine)
361
+ e
362
+ erev @l_padding+slateblue(@format_string1 % 'Adenines: ')+simp(
363
+ (@format_string2 % n_a)
364
+ )+@percentage
365
+ set_percentage_of(:guanine)
366
+ erev @l_padding+slateblue(@format_string1 % 'Guanines: ')+simp(
367
+ (@format_string2 % n_g)
368
+ )+@percentage
369
+ set_percentage_of(:cytosine)
370
+ erev @l_padding+slateblue(@format_string1 % 'Cytosines: ')+simp(
371
+ (@format_string2 % n_c)
372
+ )+@percentage
373
+ set_percentage_of(:thymine)
374
+ erev @l_padding+slateblue(@format_string1 % 'Thymine: ')+simp(
375
+ (@format_string2 % n_t)
376
+ )+@percentage+N+rev # Append extra newline.
377
+ cliner if @use_cliner
378
+ report_total_amount
379
+ report_how_many_start_codons_exist
380
+ end
381
+ end
382
+
383
+ # ========================================================================= #
384
+ # === return_truncated_dna_string
385
+ #
386
+ # We can toggle whether we truncate or whether we will not.
387
+ #
388
+ # Since as of December 2020, the truncate-notification will
389
+ # only be shown if the input-sequence length exceeds the
390
+ # threshold value.
391
+ # ========================================================================= #
392
+ def return_truncated_dna_string(
393
+ do_truncate = :default,
394
+ add_the_truncated_at_notice = true
395
+ )
396
+ case do_truncate
397
+ # ======================================================================= #
398
+ # === :default
399
+ # ======================================================================= #
400
+ when :default
401
+ do_truncate = Bioroebe.do_truncate?
402
+ end
403
+ dna_string = @dna_string
404
+ if dna_string.size > 100
405
+ _ = ''.dup
406
+ _ << rev if add_the_truncated_at_notice
407
+ _ << dna_string[0..79]
408
+ _ << return_colourized_truncated_at_message if add_the_truncated_at_notice
409
+ dna_string = _
410
+ end if do_truncate
411
+ return dna_string
412
+ end
413
+
414
+ # ========================================================================= #
415
+ # === set_dna_string
416
+ #
417
+ # This method also supports loading the content of a file - if the given
418
+ # input is a locally existing file, then the content of said file
419
+ # will be used.
420
+ # ========================================================================= #
421
+ def set_dna_string(
422
+ i = DEFAULT_DNA_STRING_TO_USE
423
+ )
424
+ i = DEFAULT_DNA_STRING_TO_USE if i.nil?
425
+ if File.exist? i.to_s
426
+ i = File.read(i.to_s).strip.delete(N)
427
+ end
428
+ i = i.to_s.dup if i.frozen?
429
+ i.upcase! # Want to keep it upcased.
430
+ @dna_string = i
431
+ end
432
+
433
+ # ========================================================================= #
434
+ # === run (run tag)
435
+ # ========================================================================= #
436
+ def run
437
+ if @display_short_form
438
+ report_the_amount_of_nucleotides_in_short_form_on_a_single_line
439
+ else
440
+ report_everything
441
+ end
442
+ end
443
+
444
+ # ========================================================================= #
445
+ # === CountAmountOfNucleotides.show_composition
446
+ #
447
+ # This class method will return a Hash with the proper A,T,C,G count.
448
+ #
449
+ # Specific Usage Example:
450
+ #
451
+ # CountAmountOfNucleotides.show_composition "ATATTTGCCCTATTTTTCC" # => {"a"=>3, "t"=>10, "g"=>1, "c"=>5}
452
+ #
453
+ # ========================================================================= #
454
+ def self.show_composition(i)
455
+ _ = CountAmountOfNucleotides.new(i, false)
456
+ hash = {}
457
+ hash['A'] = _.n_a # n Adenines
458
+ hash['T'] = _.n_t # n Thymines
459
+ hash['G'] = _.n_g # n Guanosines
460
+ hash['C'] = _.n_c # n Cytosines
461
+ return hash
462
+ end
463
+
464
+ end
465
+
466
+ # =========================================================================== #
467
+ # === Bioroebe.count_amount_of_nucleotides
468
+ #
469
+ # This method will always return the result in the form of a single line.
470
+ # The order is: A C G T
471
+ #
472
+ # This can also be used to solve a problem listed at Rosalind.
473
+ #
474
+ # Invocation examples:
475
+ #
476
+ # Bioroebe.count_amount_of_nucleotides 'AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC' => "20 17 12 21"
477
+ # Bioroebe.count_amount_of_nucleotides File.read('/rosalind_dna.txt').strip
478
+ #
479
+ # =========================================================================== #
480
+ def self.count_amount_of_nucleotides(i)
481
+ _ = ::Bioroebe::CountAmountOfNucleotides.new(i, :do_not_run_yet) { :display_short_form }
482
+ _.return_the_amount_of_nucleotides_in_short_form_on_a_single_line
483
+ end
484
+
485
+ end
486
+
487
+ if __FILE__ == $PROGRAM_NAME
488
+ _ = Bioroebe::CountAmountOfNucleotides.new(ARGV.first)
489
+ # puts _.string
490
+ Bioroebe::CountAmountOfNucleotides.show_composition(ARGV.first)
491
+ end # cnuc ATATTTGCCCTATTTTTCCTATTTTTCCATGGATG
@@ -0,0 +1,39 @@
1
+ #!/usr/bin/ruby -w
2
+ # Encoding: UTF-8
3
+ # frozen_string_literal: true
4
+ # =========================================================================== #
5
+ # require 'bioroebe/count/count_at.rb'
6
+ # Bioroebe.count_AT(ARGV)
7
+ # =========================================================================== #
8
+ module Bioroebe
9
+
10
+ # ========================================================================= #
11
+ # === Bioroebe.count_AT
12
+ #
13
+ # This method will count how characters in a given String are "A" or
14
+ # "T", in total. The method will assume that an Array passed to it
15
+ # is meant to be a String.
16
+ #
17
+ # So, every time this method encounters a "A" or a "T" in that string,
18
+ # we will "add" +1 to the number that will be returned by that method.
19
+ #
20
+ # Usage example:
21
+ #
22
+ # Bioroebe.count_AT 'ATTATATACCGCGCCCATATAAA' # => 15
23
+ #
24
+ # ========================================================================= #
25
+ def self.count_AT(i = ARGV)
26
+ i = i.join(' ').strip if i.is_a? Array
27
+ i.upcase.count('A')+
28
+ i.upcase.count('T')
29
+ end
30
+
31
+ end
32
+
33
+ if __FILE__ == $PROGRAM_NAME
34
+ if ARGV.empty?
35
+ p Bioroebe.count_AT 'ATTATATACCGCGCCCATATAAA' # => 15
36
+ else
37
+ p Bioroebe.count_AT(ARGV)
38
+ end
39
+ end # countAT ATTA
@@ -0,0 +1,43 @@
1
+ #!/usr/bin/ruby -w
2
+ # Encoding: UTF-8
3
+ # frozen_string_literal: true
4
+ # =========================================================================== #
5
+ # require 'bioroebe/count/count_gc.rb'
6
+ # Bioroebe.count_GC(ARGV)
7
+ # Bioroebe.count_GC 'ATG' # => 1
8
+ # =========================================================================== #
9
+ module Bioroebe
10
+
11
+ # ========================================================================= #
12
+ # === Bioroebe.count_GC
13
+ #
14
+ # This method will count how characters in a given String are "G" or
15
+ # "C", in total. The method will assume that an Array passed to it
16
+ # is meant to be a String.
17
+ #
18
+ # So, every time this method encounters a "G" or a "C" in that string,
19
+ # we will "add" +1 to the number that will be returned by that method.
20
+ #
21
+ # Specific usage examples:
22
+ #
23
+ # Bioroebe.count_GC 'ATTATTATGGCCAATATA' # => 4
24
+ # Bioroebe.count_GC 'ATG' # => 1
25
+ #
26
+ # ========================================================================= #
27
+ def self.count_GC(i = ARGV)
28
+ i = i.join(' ').strip if i.is_a? Array
29
+ i.upcase.count('G')+
30
+ i.upcase.count('C')
31
+ end
32
+
33
+ end
34
+
35
+ if __FILE__ == $PROGRAM_NAME
36
+ if ARGV.empty?
37
+ p Bioroebe.count_GC 'ATTATTATGGCCAATATA' # => 4
38
+ else
39
+ p Bioroebe.count_GC(ARGV)
40
+ end
41
+ end # countGC
42
+ # countGC ATACGACGATCCACAACAACAC
43
+ # countGC ATGC
@@ -0,0 +1,5 @@
1
+ This directory can be used to specify CSS for the whole
2
+ bioroebe project. Presently (since as of 2021) it is
3
+ used primarily to style ruby-gtk3 applications, but
4
+ in the future we may extend it for .cgi files and
5
+ sinatra (for the www) as well.
@@ -0,0 +1,121 @@
1
+ /*
2
+ * This contains CSS rules for the whole Bioroebe-project.
3
+ */
4
+
5
+ .BG_light_yellow { background-color: rgb(255, 255, 204); }
6
+ .BG_lightskyblue { background-color: lightblue; }
7
+ .clear_background { background-image: none; }
8
+
9
+ .darkblue { color: darkblue; }
10
+ .darkgreen { color: darkgreen; }
11
+ .tomato { color: tomato; }
12
+
13
+ .pad0px { padding: 0px}
14
+ .pad1px { padding: 1px}
15
+ .pad2px { padding: 2px}
16
+ .pad3px { padding: 3px}
17
+ .pad4px { padding: 4px}
18
+ .pad5px { padding: 5px}
19
+
20
+ tooltip {
21
+ padding: 4px;
22
+ border-width: 2px;
23
+ border-style: solid;
24
+ border-color: orange;
25
+ font-size: 25px;
26
+ }
27
+
28
+ #BG_yellow {
29
+ background: yellow;
30
+ }
31
+
32
+ #BG_lightgreen {
33
+ background: lightgreen;
34
+ }
35
+
36
+ #h1 {
37
+ font-size: 1.2em;
38
+ font-weight: bold;
39
+ color: royalblue;
40
+ }
41
+
42
+ #bold_royalblue {
43
+ color: royalblue;
44
+ font-weight: 800;
45
+ }
46
+
47
+ #table_bblack1 {
48
+ border: 1px solid black;
49
+ }
50
+
51
+ #red {
52
+ color: red;
53
+ }
54
+
55
+ #black {
56
+ color: black;
57
+ }
58
+
59
+ #forestgreen {
60
+ color: forestgreen;
61
+ }
62
+
63
+ .bblack1 { border: 1px solid black; }
64
+ .bblack2 { border: 2px solid black; }
65
+ .bblack3 { border: 3px solid black; }
66
+
67
+ .tomato { color: tomato; }
68
+
69
+ #differently_coloured_selection selection {
70
+ background-color: navajowhite;
71
+ color: steelblue;
72
+ }
73
+
74
+ #button1 {
75
+ color: black;
76
+ padding: 4px;
77
+ border: 4px solid steelblue;
78
+ }
79
+
80
+ #BG_black_and_white {
81
+ background: black;
82
+ color: white;
83
+ }
84
+
85
+ .window-frame {
86
+ box-shadow: none;
87
+ margin: 220px;
88
+ }
89
+
90
+ #BG_yellow {
91
+ background: yellow;
92
+ }
93
+
94
+ #BG_white {
95
+ background: crimson;
96
+ }
97
+
98
+ #BG_mintcream {
99
+ background: mintcream;
100
+ }
101
+
102
+ #lightgreen_background {
103
+ background: lightgreen;
104
+ }
105
+
106
+ #BG_floralwhite {
107
+ background: floralwhite;
108
+ }
109
+
110
+ #BG_lightblue {
111
+ background: lightblue;
112
+ }
113
+
114
+ /*
115
+ * This can be used for buttons to appear wider while
116
+ * using a double-border style.
117
+ */
118
+ #border_double_and_wider {
119
+ border-style: double;
120
+ border-width: 3px;
121
+ }